Merge branch 'master' into staging.

With conflicts resolved in:
	gnu/packages/version-control.scm

.dir-locals.el

@@ -61,7 +61,7 @@
    (eval . (put 'eval-when 'scheme-indent-function 1))
    (eval . (put 'call-with-prompt 'scheme-indent-function 1))
    (eval . (put 'test-assert 'scheme-indent-function 1))
-   (eval . (put 'test-assertm 'scheme-indent-function 1))
+   (eval . (put 'test-assertm 'scheme-indent-function 2))
    (eval . (put 'test-equalm 'scheme-indent-function 1))
    (eval . (put 'test-equal 'scheme-indent-function 1))
    (eval . (put 'test-eq 'scheme-indent-function 1))
@@ -94,6 +94,7 @@
    (eval . (put 'origin 'scheme-indent-function 0))
    (eval . (put 'build-system 'scheme-indent-function 0))
    (eval . (put 'bag 'scheme-indent-function 0))
+   (eval . (put 'computed-file 'scheme-indent-function 1))
    (eval . (put 'gexp->derivation 'scheme-indent-function 1))
    (eval . (put 'graft 'scheme-indent-function 0))
    (eval . (put 'operating-system 'scheme-indent-function 0))

Makefile.am

@@ -405,10 +405,6 @@ AUX_FILES =						\
   gnu/packages/aux-files/linux-libre/6.1-arm64.conf	\
   gnu/packages/aux-files/linux-libre/6.1-i686.conf	\
   gnu/packages/aux-files/linux-libre/6.1-x86_64.conf	\
-  gnu/packages/aux-files/linux-libre/6.0-arm.conf	\
-  gnu/packages/aux-files/linux-libre/6.0-arm64.conf	\
-  gnu/packages/aux-files/linux-libre/6.0-i686.conf	\
-  gnu/packages/aux-files/linux-libre/6.0-x86_64.conf	\
   gnu/packages/aux-files/linux-libre/5.15-arm.conf	\
   gnu/packages/aux-files/linux-libre/5.15-arm64.conf	\
   gnu/packages/aux-files/linux-libre/5.15-i686.conf	\

doc/contributing.texi

@@ -1467,10 +1467,16 @@ address and the @option{-v} flag with @command{git send-email}.
 
 @example
 $ git commit -a
-$ git send-email -1 -a --base=auto -v @var{REVISION} \
+$ git send-email -1 -a --base=auto -v@var{REVISION} \
       --to=@var{ISSUE_NUMBER}@@debbugs.gnu.org
 @end example
 
+@quotation Note
+Due to an apparent bug in @command{git send-email},
+@option{-v @var{REVISION}} (with the space) will not work; you
+@emph{must} use @option{-v@var{REVISION}}.
+@end quotation
+
 You can find out @var{ISSUE_NUMBER} either by searching on the mumi
 interface at @url{issues.guix.gnu.org} for the name of your patch or
 reading the acknowledgement email sent automatically by Debbugs in
@@ -1824,23 +1830,27 @@ It additionally calls @code{make check-channel-news} to be sure
 
 @subsection Commit Policy
 
-If you get commit access, please make sure to follow
+If you get commit access, please make sure to follow the policy below
-the policy below (discussions of the policy can take place on
+(discussions of the policy can take place on
 @email{guix-devel@@gnu.org}).
 
-Non-trivial patches should always be posted to
+Changes should be posted to @email{guix-patches@@gnu.org}.  This mailing
-@email{guix-patches@@gnu.org} (trivial patches include fixing typos,
+list fills the patch-tracking database (@pxref{Tracking Bugs and
-etc.).  This mailing list fills the patch-tracking database
+Patches}).  It also allows patches to be picked up and tested by the
-(@pxref{Tracking Bugs and Patches}).
+quality assurance tooling; the result of that testing eventually shows
+up on the dashboard at
+@indicateurl{https://qa.guix.gnu.org/issue/@var{ISSUE_NUMBER}}, where
+@var{ISSUE_NUMBER} is the number assigned by the issue tracker.  Leave
+time for a review, without committing anything (@pxref{Submitting
+Patches}).  If you didn’t receive any reply after one week (two weeks
+for more significant changes), and if you're confident, it's OK to
+commit.
 
-For patches that just add a new package, and a simple one, it's OK to
+As an exception, some changes considered ``trivial'' or ``obvious'' may
-commit, if you're confident (which means you successfully built it in a
+be pushed directly.  This includes changes to fix typos and reverting
-chroot setup, and have done a reasonable copyright and license
+commits that caused immediate problems.  This is subject to being
-auditing).  Likewise for package upgrades, except upgrades that trigger
+adjusted, allowing individuals to commit directly on non-controversial
-a lot of rebuilds (for example, upgrading GnuTLS or GLib).  We have a
+changes on parts they’re familiar with.
-mailing list for commit notifications (@email{guix-commits@@gnu.org}),
-so people can notice.  Before pushing your changes, make sure to run
-@code{git pull --rebase}.
 
 When pushing a commit on behalf of somebody else, please add a
 @code{Signed-off-by} line at the end of the commit log message---e.g.,
@@ -1855,14 +1865,6 @@ right before pushing:
 make check-channel-news
 @end example
 
-For anything else, please post to @email{guix-patches@@gnu.org} and
-leave time for a review, without committing anything (@pxref{Submitting
-Patches}).  If you didn’t receive any reply after two weeks, and if
-you're confident, it's OK to commit.
-
-That last part is subject to being adjusted, allowing individuals to commit
-directly on non-controversial changes on parts they’re familiar with.
-
 @subsection Addressing Issues
 
 Peer review (@pxref{Submitting Patches}) and tools such as

etc/news.scm

@@ -1,6 +1,6 @@
 ;; GNU Guix news, for use by 'guix pull'.
 ;;
-;; Copyright © 2019-2022 Ludovic Courtès <ludo@gnu.org>
+;; Copyright © 2019-2023 Ludovic Courtès <ludo@gnu.org>
 ;; Copyright © 2019–2021 Tobias Geerinckx-Rice <me@tobias.gr>
 ;; Copyright © 2019, 2020 Miguel Ángel Arruga Vivas <rosen644835@gmail.com>
 ;; Copyright © 2019, 2020 Konrad Hinsen <konrad.hinsen@fastmail.net>
@@ -26,6 +26,85 @@
 (channel-news
  (version 0)
 
+ (entry (commit "137b91f03bbb7f1df71cf10c4f79ae57fbcea400")
+        (title
+         (en "New @option{--with-version} package transformation option")
+         (de "Neue Paketumwandlungsoption @option{--with-version}")
+         (fr "Nouvelle option de transformation @option{--with-version}"))
+        (body
+         (en "The new @option{--with-version} package transformation option
+generalizes @option{--with-latest}: it gets the specified upstream release of
+a package and uses it instead of the currently-packaged version.
+
+For example, the command below would spawn GNOME Clocks built against GTK
+4.7.0, skipping its test suite:
+
+@example
+guix shell gnome-clocks --with-version=gtk=4.7.0 \\
+  --without-tests=gtk -- gnome-clocks
+@end example
+
+Run @command{info \"(guix) Package Transformation Options\"} for more info.")
+         (de "Die neue Paketumwandlungsoption @option{--with-version}
+verallgemeinert @option{--with-latest}: Mit ihr kann man angeben, welche
+vom Anbieter veröffentlichte Version man anstelle der derzeit im Paket
+vorgegebenen haben möchte.
+
+Zum Beispiel kann mit folgendem Befehl ein für die GTK-Version 4.7.0
+erstelltes GNOME Clocks aufgerufen werden, wobei der Testkatalog dafür
+übersprungen wird.
+
+@example
+guix shell gnome-clocks --with-version=gtk=4.7.0 \\
+  --without-tests=gtk -- gnome-clocks
+@end example
+
+Führen Sie für mehr Informationen @command{info \"(guix.de)
+Paketumwandlungsoptionen\"} aus.")
+         (fr "La nouvelle option de transformation de paquets
+@option{--with-version} généralise @option{--with-latest} : elle permet de
+spécifier quelle version amont d'un logiciel utiliser à la place de celle
+actuellement fournie.
+
+Par exemple, la commande ci-dessous démarre GNOME Clocks construit avec GTK
+4.7.0, sans lancer sa suite de tests :
+
+@example
+guix shell gnome-clocks --with-version=gtk=4.7.0 \\
+  --without-tests=gtk -- gnome-clocks
+@end example
+
+Voir @command{info \"(guix.fr) Options de transformation de paquets\"} pour
+plus de détails.")))
+
+ (entry (commit "9ea37eb9f5329c213757bbfe5d9241cde8433858")
+        (title
+          (en "Linux-libre 6.0 removed due to end of upstream support")
+          (de "Linux-libre 6.0 wurde entfernt"))
+        (body
+          (en "The linux-libre 6.0 kernel series has reached the end of
+             its life, and no longer supported upstream.  For this
+             reason, it has been removed from GNU Guix.")
+          (de "Vom Kernel @code{linux-libre} wird die 6.0-Versionsreihe keine
+Unterstützung von dessen Anbieter mehr erfahren („end of life“).  Daher ist es
+aus GNU Guix entfernt worden.")))
+
+ (entry (commit "ce8a34bc9ab89f31f107383ba791954864aed372")
+        (title
+         (en "Linux-libre kernel updated to 6.1")
+         (de "Linux-libre-Kernel wird auf 6.1 aktualisiert")
+         (fr "Le noyau linux-libre est mis à jour vers la 6.1")
+         (pt "Kernel linux-libre atualizado para 6.1"))
+        (body
+         (en "The default version of the linux-libre kernel has been updated to
+              the 6.1 release series.")
+         (de "Der standardmäßig verwendete @code{linux-libre}-Kernel basiert
+              jetzt auf der 6.1-Versionsreihe.")
+         (fr "La version par défaut du noyau linux-libre est mise à jour
+              vers la série des 6.1.")
+         (pt "A versão padrão do kernel linux-libre foi atualizada para a
+              série do kernel 6.1.")))
+
  (entry (commit "064c5b7e450f9f6d55cfcd0ec2bc9e96ee0b2958")
         (title
           (en "Linux-libre 4.9 removed due to end of upstream support")

etc/release-manifest.scm

@@ -82,7 +82,7 @@ TARGET."
   ;; Packages that must be cross-buildable from x86_64-linux.
   ;; FIXME: Add (@ (gnu packages gcc) gcc) when <https://bugs.gnu.org/40463>
   ;; is fixed.
-  (append (list (@ (gnu packages guile) guile-3.0/fixed))
+  (append (list (@ (gnu packages guile) guile-3.0/pinned))
           (map specification->package
                '("coreutils" "grep" "sed" "findutils" "diffutils" "patch"
                  "gawk" "gettext" "gzip" "xz"

etc/teams.scm.in

@@ -416,11 +416,14 @@ importer."
         #:scope (list "gnu/packages/chez.scm"
                       "gnu/packages/racket.scm")))
 
-
+(define-team reproduciblebuilds
-(define-member (person "Thiago Jung Bauermann"
+  (team 'reproduciblebuilds
-                       "bauermann@kolabnow.com")
+        #:name "Reproducible Builds team"
-  embedded-bootstrap translations)
+        #:description
+        "Reproducible Builds tooling and issues that affect any guix packages."
+        #:scope (list "gnu/packages/diffoscope.scm")))
 
+
 (define-member (person "Eric Bavier"
                        "bavier@posteo.net")
   science)
@@ -521,6 +524,10 @@ importer."
                        "iyzsong@envs.net")
   games localization)
 
+(define-member (person "Vagrant Cascadian"
+                       "vagrant@reproducible-builds.org")
+  reproduciblebuilds)
+
 
 (define (find-team name)
   (or (hash-ref %teams (string->symbol name))

gnu/bootloader/u-boot.scm

@@ -3,6 +3,7 @@
 ;;; Copyright © 2017, 2019 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2020 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
+;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -42,6 +43,7 @@
             u-boot-puma-rk3399-bootloader
             u-boot-rock64-rk3328-bootloader
             u-boot-rockpro64-rk3399-bootloader
+            u-boot-ts7970-q-2g-1000mhz-c-bootloader
             u-boot-wandboard-bootloader))
 
 (define install-u-boot
@@ -127,6 +129,12 @@
 
 (define install-pinebook-pro-rk3399-u-boot install-rockpro64-rk3399-u-boot)
 
+(define install-u-boot-ts7970-q-2g-1000mhz-c-u-boot
+  #~(lambda (bootloader device mount-point)
+      (let ((u-boot.imx (string-append bootloader "/libexec/u-boot.imx"))
+            (install-dir (string-append mount-point "/boot")))
+        (install-file u-boot.imx install-dir))))
+
 
 
 ;;;
@@ -255,3 +263,13 @@
    (inherit u-boot-bootloader)
    (package u-boot-pinebook-pro-rk3399)
    (disk-image-installer install-pinebook-pro-rk3399-u-boot)))
+
+(define u-boot-ts7970-q-2g-1000mhz-c-bootloader
+  ;; This bootloader doesn't really need to be installed, as it is read from
+  ;; an SPI memory chip, not the SD card.  It is copied to /boot/u-boot.imx
+  ;; for convenience and should be manually flashed at the U-Boot prompt.
+  (bootloader
+   (inherit u-boot-bootloader)
+   (package u-boot-ts7970-q-2g-1000mhz-c)
+   (installer install-u-boot-ts7970-q-2g-1000mhz-c-u-boot)
+   (disk-image-installer #f)))

gnu/build/linux-container.scm

@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015 David Thompson <davet@gnu.org>
-;;; Copyright © 2017-2019, 2022 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2017-2019, 2022, 2023 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -404,7 +404,7 @@ load path must be adjusted as needed."
 
 (define (container-excursion pid thunk)
   "Run THUNK as a child process within the namespaces of process PID and
-return the exit status."
+return the exit status, an integer as returned by 'waitpid'."
   (define (namespace-file pid namespace)
     (string-append "/proc/" (number->string pid) "/ns/" namespace))
 
@@ -432,11 +432,20 @@ return the exit status."
                   '("user" "ipc" "uts" "net" "pid" "mnt"))
         (purify-environment)
         (chdir "/")
-        (thunk))))
+
+        ;; Per setns(2), changing the PID namespace only applies to child
+        ;; processes, not to the process itself.  Thus fork so that THUNK runs
+        ;; in the right PID namespace, which also gives it access to /proc.
+        (match (primitive-fork)
+          (0 (call-with-clean-exit thunk))
+          (pid (primitive-exit
+                (match (waitpid pid)
+                  ((_ . status)
+                   (or (status:exit-val status) 127)))))))))
     (pid
      (match (waitpid pid)
        ((_ . status)
-        (status:exit-val status))))))
+        status)))))
 
 (define (container-excursion* pid thunk)
   "Like 'container-excursion', but return the return value of THUNK."

gnu/home/services/fontutils.scm

@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2021 Andrew Tropin <andrew@trop.in>
 ;;; Copyright © 2021 Xinglu Chen <public@yoctocell.xyz>
+;;; Copyright © 2023 Giacomo Leidi <goodoldpaul@autistici.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -21,6 +22,7 @@
   #:use-module (gnu home services)
   #:use-module (gnu packages fontutils)
   #:use-module (guix gexp)
+  #:use-module (srfi srfi-1)
 
   #:export (home-fontconfig-service-type))
 
@@ -33,15 +35,17 @@
 ;;;
 ;;; Code:
 
-(define (add-fontconfig-config-file he-symlink-path)
+(define (add-fontconfig-config-file directories)
   `(("fontconfig/fonts.conf"
      ,(mixed-text-file
        "fonts.conf"
-       "<?xml version='1.0'?>
+       (apply string-append
+              `("<?xml version='1.0'?>
 <!DOCTYPE fontconfig SYSTEM 'fonts.dtd'>
-<fontconfig>
+<fontconfig>\n" ,@(map (lambda (directory)
-  <dir>~/.guix-home/profile/share/fonts</dir>
+                         (string-append "  <dir>" directory "</dir>\n"))
-</fontconfig>"))))
+                       directories)
+                "</fontconfig>\n"))))))
 
 (define (regenerate-font-cache-gexp _)
   `(("profile/share/fonts"
@@ -59,7 +63,9 @@
                        (service-extension
                         home-profile-service-type
                         (const (list fontconfig)))))
-                (default-value #f)
+                (compose concatenate)
+                (extend append)
+                (default-value '("~/.guix-home/profile/share/fonts"))
                 (description
                  "Provides configuration file for fontconfig and make
 fc-* utilities aware of font packages installed in Guix Home's profile.")))

gnu/local.mk

@@ -362,7 +362,6 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/kde-systemtools.scm		\
   %D%/packages/kde-utils.scm			\
   %D%/packages/kerberos.scm			\
-  %D%/packages/key-mon.scm			\
   %D%/packages/kodi.scm				\
   %D%/packages/language.scm			\
   %D%/packages/lean.scm				\
@@ -918,6 +917,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/awesome-4.3-fno-common.patch		\
   %D%/packages/patches/aws-c-auth-install-private-headers.patch	\
   %D%/packages/patches/azr3.patch				\
+  %D%/packages/patches/azr3-remove-lash.patch			\
   %D%/packages/patches/barony-fix-textures.patch		\
   %D%/packages/patches/bash-completion-directories.patch	\
   %D%/packages/patches/bash-linux-pgrp-pipe.patch		\
@@ -939,6 +939,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/bsd-games-prevent-name-collisions.patch	\
   %D%/packages/patches/bsd-games-stdio.h.patch			\
   %D%/packages/patches/beancount-disable-googleapis-fonts.patch	\
+  %D%/packages/patches/bees-beesd-honor-destdir-on-installation.patch	\
   %D%/packages/patches/beignet-correct-file-names.patch		\
   %D%/packages/patches/bidiv-update-fribidi.patch		\
   %D%/packages/patches/binutils-2.37-file-descriptor-leak.patch	\
@@ -1037,7 +1038,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/desmume-gcc6-fixes.patch			\
   %D%/packages/patches/desmume-gcc7-fixes.patch			\
   %D%/packages/patches/dfu-programmer-fix-libusb.patch		\
-  %D%/packages/patches/diffoscope-fix-llvm-test.patch		\
   %D%/packages/patches/diffutils-fix-signal-processing.patch	\
   %D%/packages/patches/dkimproxy-add-ipv6-support.patch		\
   %D%/packages/patches/docbook-xsl-nonrecursive-string-subst.patch	\
@@ -1066,7 +1066,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/emacs-json-reformat-fix-tests.patch	\
   %D%/packages/patches/emacs-helpful-fix-docstring-test.patch	\
   %D%/packages/patches/emacs-highlight-stages-add-gexp.patch	\
-  %D%/packages/patches/emacs-libgit-use-system-libgit2.patch    \
   %D%/packages/patches/emacs-lispy-fix-thread-last-test.patch   \
   %D%/packages/patches/emacs-native-comp-driver-options.patch   \
   %D%/packages/patches/emacs-polymode-fix-lexical-variable-error.patch  \
@@ -1280,8 +1279,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/guile-linux-syscalls.patch		\
   %D%/packages/patches/guile-3.0-linux-syscalls.patch		\
   %D%/packages/patches/guile-ac-d-bus-fix-tests.patch		\
-  %D%/packages/patches/guile-continuation-stack-leak.patch	\
-  %D%/packages/patches/guile-cross-compilation.patch		\
   %D%/packages/patches/guile-fibers-destroy-peer-schedulers.patch \
   %D%/packages/patches/guile-fibers-epoll-instance-is-dead.patch \
   %D%/packages/patches/guile-fibers-fd-finalizer-leak.patch	\
@@ -1628,6 +1625,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/password-store-tree-compat.patch		\
   %D%/packages/patches/pciutils-hurd-configure.patch		\
   %D%/packages/patches/pciutils-hurd-fix.patch			\
+  %D%/packages/patches/petri-foo-0.1.87-fix-recent-file-not-exist.patch			\
   %D%/packages/patches/plasma-framework-fix-KF5PlasmaMacros.cmake.patch \
   %D%/packages/patches/pocketfft-cpp-prefer-preprocessor-if.patch			\
   %D%/packages/patches/pokerth-boost.patch			\
@@ -1637,6 +1635,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-louvain-fix-test.patch		\
   %D%/packages/patches/python-random2-getrandbits-test.patch		\
   %D%/packages/patches/python-poppler-qt5-fix-build.patch	\
+  %D%/packages/patches/python-pypdf-annotate-tests-appropriately.patch	\
   %D%/packages/patches/python-telingo-fix-comparison.patch	\
   %D%/packages/patches/python-w3lib-fix-test-failure.patch	\
   %D%/packages/patches/sdcc-disable-non-free-code.patch		\
@@ -1774,6 +1773,8 @@ dist_patch_DATA =						\
   %D%/packages/patches/quagga-reproducible-build.patch          \
   %D%/packages/patches/quickswitch-fix-dmenu-check.patch	\
   %D%/packages/patches/qtwayland-gcc-11.patch			\
+  %D%/packages/patches/qtwayland-dont-recreate-callbacks.patch	\
+  %D%/packages/patches/qtwayland-cleanup-callbacks.patch	\
   %D%/packages/patches/qtwebkit-pbutils-include.patch		\
   %D%/packages/patches/qtwebkit-fix-building-with-bison-3.7.patch \
   %D%/packages/patches/qtwebkit-fix-building-with-python-3.9.patch	\
@@ -1827,6 +1828,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/rust-nettle-sys-disable-vendor.patch	 \
   %D%/packages/patches/rust-openssl-sys-no-vendor.patch	\
   %D%/packages/patches/rust-wl-clipboard-rs-newer-wl.patch      \
+  %D%/packages/patches/rw-igraph-0.10.patch			\
   %D%/packages/patches/sbc-fix-build-non-x86.patch		\
   %D%/packages/patches/sbcl-aserve-add-HTML-5-elements.patch	\
   %D%/packages/patches/sbcl-aserve-fix-rfe12668.patch	\
@@ -1895,6 +1897,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/texlive-hyph-utf8-no-byebug.patch	\
   %D%/packages/patches/thefuck-test-environ.patch		\
   %D%/packages/patches/tidy-CVE-2015-5522+5523.patch		\
+  %D%/packages/patches/timewarrior-time-sensitive-tests.patch	\
   %D%/packages/patches/tinyxml-use-stl.patch			\
   %D%/packages/patches/tipp10-disable-downloader.patch		\
   %D%/packages/patches/tipp10-fix-compiling.patch		\
@@ -1918,9 +1921,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/twinkle-bcg729.patch			\
   %D%/packages/patches/u-boot-allow-disabling-openssl.patch	\
   %D%/packages/patches/u-boot-infodocs-target.patch		\
-  %D%/packages/patches/u-boot-patman-fix-help.patch		\
+  %D%/packages/patches/u-boot-patman-guix-integration.patch	\
-  %D%/packages/patches/u-boot-patman-get-maintainer.patch	\
-  %D%/packages/patches/u-boot-patman-local-conf.patch		\
   %D%/packages/patches/u-boot-nintendo-nes-serial.patch		\
   %D%/packages/patches/u-boot-rockchip-inno-usb.patch		\
   %D%/packages/patches/u-boot-sifive-prevent-reloc-initrd-fdt.patch	\
@@ -2006,11 +2007,9 @@ dist_patch_DATA =						\
   %D%/packages/patches/xdg-desktop-portal-wlr-harcoded-length.patch\
   %D%/packages/patches/xf86-video-ark-remove-mibstore.patch	\
   %D%/packages/patches/xf86-video-nouveau-fixup-ABI.patch	\
-  %D%/packages/patches/xf86-video-qxl-fix-build.patch	\
   %D%/packages/patches/xf86-video-savage-xorg-compat.patch 	\
   %D%/packages/patches/xf86-video-siliconmotion-fix-ftbfs.patch \
   %D%/packages/patches/xf86-video-tga-remove-mibstore.patch	\
-  %D%/packages/patches/xf86-video-voodoo-pcitag.patch		\
   %D%/packages/patches/xfce4-panel-plugins.patch		\
   %D%/packages/patches/xfce4-settings-defaults.patch		\
   %D%/packages/patches/xgboost-use-system-dmlc-core.patch       \

gnu/packages.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012-2020, 2022 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2012-2020, 2022-2023 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2016, 2017 Alex Kost <alezost@gmail.com>
@@ -38,6 +38,7 @@
   #:use-module (ice-9 vlist)
   #:use-module (ice-9 match)
   #:use-module (ice-9 binary-ports)
+  #:autoload   (rnrs bytevectors) (bytevector?)
   #:autoload   (system base compile) (compile)
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-26)
@@ -442,10 +443,15 @@ reducing the memory footprint."
     (lambda (port)
       ;; Store the cache as a '.go' file.  This makes loading fast and reduces
       ;; heap usage since some of the static data is directly mmapped.
-      (put-bytevector port
+      (match (compile `'(,@exp)
-                      (compile `'(,@exp)
+                      #:to 'bytecode
-                               #:to 'bytecode
+                      #:opts '(#:to-file? #t))
-                               #:opts '(#:to-file? #t)))))
+        ((? bytevector? bv)
+         (put-bytevector port bv))
+        (proc
+         ;; In Guile 3.0.9, the linker can return a procedure instead of a
+         ;; bytevector.  Adjust to that.
+         (proc port)))))
   cache-file)
 
 

gnu/packages/accessibility.scm

@@ -348,4 +348,4 @@ CONFIG_SPEAKUP=m
 @item
 CONFIG_SPEAKUP_SOFT=m
 @end itemize")
-    (home-page "ttps://github.com/linux-speakup/espeakup")))
+    (home-page "https://github.com/linux-speakup/espeakup")))

gnu/packages/admin.scm

@@ -55,6 +55,7 @@
 ;;; Copyright © 2022 ( <paren@disroot.org>
 ;;; Copyright © 2022 Matthew James Kraai <kraai@ftbfs.org>
 ;;; Copyright © 2022 jgart <jgart@dismail.de>
+;;; Copyright © 2023 Juliana Sims <jtsims@protonmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1968,7 +1969,7 @@ system administrator.")
 (define-public sudo
   (package
     (name "sudo")
-    (version "1.9.12p1")
+    (version "1.9.12p2")
     (source (origin
               (method url-fetch)
               (uri
@@ -1978,7 +1979,7 @@ system administrator.")
                                     version ".tar.gz")))
               (sha256
                (base32
-                "1n5ppabp9ark1qz7xi63528s07pmpak67c7agj8v5a1xxfl1hnj7"))
+                "0fc55axh2hfd8hn66dpmyrrgb0gf0nz71zpaygkrpp8x1ypb385r"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -3944,6 +3945,48 @@ be used in screenshots to show other users what operating system or distribution
 you are running, what theme or icon set you are using, etc.")
     (license license:expat)))
 
+(define-public uwufetch
+  (package
+    (name "uwufetch")
+    (version "2.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/TheDarkBug/uwufetch")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0s4pzaqmlq6rn54kgmlpcrc0sy3q5zn6lxh4448k9iimshljsjfs"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:tests? #f ;no tests
+      #:make-flags
+      #~(list (string-append "DESTDIR=" #$output)
+              (string-append "ETC_DIR=" #$output "/etc")
+              (string-append "CC=" #$(cc-for-target)))
+      #:phases
+      #~(modify-phases %standard-phases
+          (delete 'configure)
+          (add-before 'build 'path-source-paths
+            (lambda _
+              (substitute* "uwufetch.c"
+                (("(/usr(/local)?)(.*;)" all _ _ rest)
+                 (string-append #$output rest))))))))
+    (inputs (list lshw
+                  ;; viu XXX not yet packaged in Guix
+                  xwininfo))
+    (home-page "https://github.com/TheDarkBug/uwufetch")
+    (synopsis "Meme system info tool based on Nyan/UwU trend")
+    (description
+     "UwUFetch is a system information tool in the lineage of NeoFetch,
+PFetch, HyFetch, and the like.  It prints ASCII art of your system's logo as
+well as a summary of system information.  UwUFetch's unique contribution is the
+uwu-ification of various words used in the description.  For example, Guix
+becomes gUwUix.")
+    (license license:gpl3+)))
+
 (define-public screenfetch
   (package
     (name "screenfetch")
@@ -4122,7 +4165,7 @@ hard-coded.")
 (define-public thermald
   (package
     (name "thermald")
-    (version "2.4.7")
+    (version "2.5.1")
     (source
      (origin
       (method git-fetch)
@@ -4131,7 +4174,7 @@ hard-coded.")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-       (base32 "1n0ih86bkm09bzhjl7hllxkl4gzcxvzsznbwi8dx87ragsjlix6n"))))
+       (base32 "06p1154w3n4lm0nq8fdsr6ksxl8shrc9z8yz0sbviss9afpawxcg"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags

gnu/packages/algebra.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2022 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2013, 2015, 2017, 2018, 2021 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2016-2022 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2016-2023 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2014, 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2016, 2018, 2019, 2021 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017, 2020-2022 Efraim Flashner <efraim@flashner.co.il>
@@ -224,7 +224,7 @@ the real span of the lattice.")
 (define-public pari-gp
   (package
     (name "pari-gp")
-    (version "2.15.1")
+    (version "2.15.2")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -232,7 +232,7 @@ the real span of the lattice.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "0gcyj0p0z5s1i9y67z5awwmmdvqrisvyrq22gvkbx1b6gjvrsha5"))))
+                "1pg0przhb3cgyn0rwkx2mx7a7fpy6bxxl72bk98pca723q8jhimh"))))
     (build-system gnu-build-system)
     (native-inputs (list (texlive-updmap.cfg
                           (list texlive-amsfonts))))
@@ -327,7 +327,7 @@ precision.")
 (define-public giac
   (package
     (name "giac")
-    (version "1.9.0-33")
+    (version "1.9.0-37")
     (source
      (origin
        (method url-fetch)
@@ -339,7 +339,7 @@ precision.")
                            "~parisse/debian/dists/stable/main/source/"
                            "giac_" version ".tar.gz"))
        (sha256
-        (base32 "00hdfakys4xpvmf2v851dr4hf3j6483pwwkfy5i63s5hs10mjsq5"))))
+        (base32 "0ch18wp6b3nr0zg31961rxng2mbw5mj76s00jf5qz7jdxl65s27n"))))
     (build-system gnu-build-system)
     (arguments
      (list
@@ -464,7 +464,9 @@ GCDs, factoring, solving linear systems, and evaluating special
 functions.  In addition, FLINT provides various low-level routines for
 fast arithmetic.")
    (license license:lgpl2.1+)
-   (home-page "http://flintlib.org/")))
+   (home-page "http://flintlib.org/")
+   (properties
+    '((release-monitoring-url . "http://flintlib.org/downloads.html")))))
 
 (define-public arb
   (package

gnu/packages/animation.scm

@@ -290,7 +290,7 @@ audio or video backends, ensuring good performance.")
 (define-public lightspark
   (package
     (name "lightspark")
-    (version "0.8.6")
+    (version "0.8.6.1")
     (source
      (origin
        (method git-fetch)
@@ -299,7 +299,7 @@ audio or video backends, ensuring good performance.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0v7d7vwb0xqkk3v8dyks0wyk52ga57v5lg93y74v1d2wh7spmmzw"))))
+        (base32 "1a78l9na01pd7a77r9n8lqih893s54rllpjvrx72sh0yyal1q3gz"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f ;requires Adobe Flex SDK, see README.tests

gnu/packages/astronomy.scm

@@ -67,6 +67,7 @@
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages qt)
   #:use-module (gnu packages readline)
+  #:use-module (gnu packages sphinx)
   #:use-module (gnu packages textutils)
   #:use-module (gnu packages time)
   #:use-module (gnu packages version-control)
@@ -983,13 +984,13 @@ accurately in real time at any rate desired.")
 (define-public python-astropy
   (package
     (name "python-astropy")
-    (version "5.1.1")
+    (version "5.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astropy" version))
        (sha256
-        (base32 "10dxjim60ch4qznqa5s63q936mkvy95p0k26kcwzv43hmybdcjxs"))
+        (base32 "08xc6brs7xwiqchhsjq8l10p6qc5p68cfxps7s889spqfyh2gbpn"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -1308,13 +1309,13 @@ the easy construction of interactive matplotlib widget based animations.")
 (define-public python-photutils
   (package
     (name "python-photutils")
-    (version "1.5.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "photutils" version))
        (sha256
-        (base32 "129n268wnziprrv09f7y6f98cj1vh1bzp7ygsna10h3ilnjplkq1"))))
+        (base32 "0w4kxl6aqjp2wv396krw30kwg6cmmska8gvgpihm2i2zxyzz39vd"))))
     (build-system python-build-system)
     (arguments
      `(#:test-target "pytest"
@@ -1339,6 +1340,50 @@ the easy construction of interactive matplotlib widget based animations.")
 of astronomical sources.")
     (license license:bsd-3)))
 
+(define-public python-poppy
+  (package
+    (name "python-poppy")
+    (version "1.0.3")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "poppy" version))
+              (sha256
+               (base32
+                "050cn6aabd1dxbi7zihbqnkl79hz6q6d5n6g25zmrpvc4sii171m"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs
+     ;; XXX: With python-synphot (marked as optional) package added to the list
+     ;; it tries to download from remote host during tests and fails. Overall
+     ;; tests take up to 5-8min to pass.
+     (list python-astropy
+           python-matplotlib
+           python-numpy
+           python-scipy))
+    (native-inputs
+     (list python-docutils
+           python-h5py
+           python-pandas
+           python-pytest
+           python-pytest-astropy
+           python-sphinx
+           python-setuptools-scm))
+    (home-page "https://poppy-optics.readthedocs.io/")
+    (synopsis "Physical Optics Propagation in Python")
+    (description
+     "@acronym{POPPY, Physical Optics Propagation in Python} is a Python package that
+simulates physical optical propagation including diffraction.  It implements a
+flexible framework for modeling Fraunhofer and Fresnel diffraction and point
+spread function formation, particularly in the context of astronomical
+telescopes.
+
+POPPY was developed as part of a simulation package for the James Webb Space
+Telescope, but is more broadly applicable to many kinds of imaging simulations.
+It is not, however, a substitute for high fidelity optical design software such
+as Zemax or Code V, but rather is intended as a lightweight alternative for
+cases for which diffractive rather than geometric optics is the topic of
+interest, and which require portability between platforms or ease of scripting.")
+    (license license:bsd-3)))
+
 (define-public python-pyvo
   (package
     (name "python-pyvo")
@@ -1375,13 +1420,13 @@ Virtual observatory (VO) using Python.")
 (define-public python-regions
   (package
     (name "python-regions")
-    (version "0.6")
+    (version "0.7")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "regions" version))
        (sha256
-        (base32 "0p95bxxw4dgd16rh1yj7zvfbijk52dqvqj20nj6q8kr5ms08acl0"))))
+        (base32 "08wsg9kxnki5pz8gdp81bq06jdmsip382fl02rvnr96cvzr7wf3m"))))
     (build-system python-build-system)
     (arguments
      `(#:test-target "pytest"
@@ -1499,13 +1544,13 @@ orbits described in TLE files.")
 (define-public python-sunpy
   (package
     (name "python-sunpy")
-    (version "4.0.6")
+    (version "4.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "sunpy" version))
        (sha256
-        (base32 "0aiirb6l8zshdrpsvh6d5ki759ah9zfm9gbl0in985hprwwxyrq1"))))
+        (base32 "1h8dnsic96bxm5l278vk6jj5h4bh1b143fghsvv5rhigk137vysp"))))
     (build-system pyproject-build-system)
     (arguments
      (list

gnu/packages/audio.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015-2023 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2015 Alex Kost <alezost@gmail.com>
@@ -8,7 +8,7 @@
 ;;; Copyright © 2016, 2017 Alex Griffin <a@ajgrf.com>
 ;;; Copyright © 2016 Nikita <nikita@n0.is>
 ;;; Copyright © 2016 Lukas Gradl <lgradl@openmailbox.org>
-;;; Copyright © 2016–2022 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2016–2023 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018, 2020 Oleg Pykhalov <go.wigust@gmail.com>
 ;;; Copyright © 2018 okapi <okapi@firemail.cc>
 ;;; Copyright © 2018, 2020, 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
@@ -40,6 +40,8 @@
 ;;; Copyright © 2022 Juliana Sims <jtsims@protonmail.com>
 ;;; Copyright © 2022 Simon Streit <simon@netpanic.org>
 ;;; Copyright © 2022 Andy Tai <atai@atai.org>
+;;; Copyright © 2023 Sergiu Ivanov <sivanov@colimite.fr>
+;;; Copyright © 2023 David Thompson <dthompson2@worcester.edu>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -854,7 +856,7 @@ engineers, musicians, soundtrack editors and composers.")
 (define-public audacity
   (package
     (name "audacity")
-    (version "3.2.2")
+    (version "3.2.3")
     (source
      (origin
        (method git-fetch)
@@ -863,7 +865,7 @@ engineers, musicians, soundtrack editors and composers.")
              (commit (string-append "Audacity-" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1akp9marc4y2g9mwwgfnl43q0gbb2dv7vhsnybh8wdn8ql30hfdw"))
+        (base32 "0wg75fblxlnrn5kqvg0w1fi2pwdkn1nd6vgya3sad84l3ki7wpyh"))
        (patches (search-patches "audacity-ffmpeg-fallback.patch"))
        (modules '((guix build utils)))
        (snippet
@@ -1089,45 +1091,56 @@ formant warp.")
     (license license:gpl2+)))
 
 (define-public azr3
-  (package
+  (let ((commit "3391a0a509e7fa3fb46c7627fd5979b67e468038")
-    (name "azr3")
+        (revision "1"))
-    (version "1.2.3")
+    (package
-    (source (origin
+      (name "azr3")
-              (method url-fetch)
+      (version (git-version "1.2.3" revision commit))
-              (uri (string-append "mirror://savannah/ll-plugins/azr3-jack-"
+      (source (origin
-                                  version
+                (method git-fetch)
-                                  ".tar.bz2"))
+                (uri (git-reference
-              (sha256
+                      (url "https://git.savannah.gnu.org/git/ll-plugins/azr3-jack.git")
-               (base32
+                      (commit commit)))
-                "18mdw6nc0vgj6k9rsy0x8w64wvzld0frqshrxxbxfj9qi9843vlc"))
+                (file-name (git-file-name name version))
-              (patches (search-patches "azr3.patch"))))
+                (sha256
-    (build-system gnu-build-system)
+                 (base32
-    (arguments
+                  "09wy0z4kiid7mwf5b5j8rzzgxafi4mg88xs550n7864p0n351chx"))
-     `(#:tests? #f ; no check target
+                (patches (search-patches "azr3.patch"
-       #:make-flags
+                                         "azr3-remove-lash.patch"))))
-       (list "LV2PEG=ttl2c"
+      (build-system gnu-build-system)
-             (string-append "prefix=" %output)
+      (arguments
-             (string-append "pkgdatadir=" %output "/share/azr3-jack"))
+       (list
-       #:phases
+        #:tests? #f                       ; no check target
-       (modify-phases %standard-phases
+        #:make-flags
-         (add-before 'install 'fix-timestamp
+        #~(list "LV2PEG=ttl2c"
-           (lambda _
+                (string-append "prefix=" #$output)
-             (let ((early-1980 315619200)) ; 1980-01-02 UTC
+                (string-append "pkgdatadir=" #$output "/share/azr3-jack"))
-               (utime "azr3.1" early-1980 early-1980))
+        #:phases
-             #t)))))
+        #~(modify-phases %standard-phases
-    (inputs
+            (replace 'bootstrap
-     (list gtkmm-2 lvtk jack-1 lash))
+              (lambda _
-    (native-inputs
+                (call-with-output-file "Makefile.config"
-     (list pkg-config))
+                  (lambda (port) (display "" port)))
-    (home-page "http://ll-plugins.nongnu.org/azr3/")
+                (substitute* "Makefile"
-    (synopsis "Tonewheel organ synthesizer")
+                  (("^PACKAGE_VERSION =.*")
-    (description
+                   (string-append "PACKAGE_VERSION = \"" #$version "\"\n")))))
-     "AZR-3 is a port of the free VST plugin AZR-3.  It is a tonewheel organ
+            (add-before 'install 'fix-timestamp
+              (lambda _
+                (let ((early-1980 315619200)) ; 1980-01-02 UTC
+                  (utime "azr3.1" early-1980 early-1980)))))))
+      (inputs
+       (list gtkmm-2 jack-2 lvtk))
+      (native-inputs
+       (list pkg-config))
+      (home-page "http://ll-plugins.nongnu.org/azr3/")
+      (synopsis "Tonewheel organ synthesizer")
+      (description
+       "AZR-3 is a port of the free VST plugin AZR-3.  It is a tonewheel organ
 with drawbars, distortion and rotating speakers.  The organ has three
 sections, two polyphonic sections with nine drawbars each and one monophonic
 bass section with five drawbars.  A standalone JACK application and LV2
 plugins are provided.")
-    (license license:gpl2)))
+      (license license:gpl2))))
 
 (define-public calf
   (package
@@ -1147,7 +1160,6 @@ plugins are provided.")
            glib
            gtk+-2
            cairo
-           lash
            jack-1
            lv2
            ladspa
@@ -1211,7 +1223,7 @@ generators of mostly elementary and occasionally exotic nature.")
 (define-public iir
   (package
     (name "iir")
-    (version "1.9.3")
+    (version "1.9.4")
     (source
      (origin
        (method git-fetch)
@@ -1220,7 +1232,7 @@ generators of mostly elementary and occasionally exotic nature.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0wbh804as740kjvmyaqx4rwvwwrbwh0fnj979dvv1ljlx1p50bk0"))))
+        (base32 "1fqxn0qlvykpk9hiliivmkjjcz3g1bp83yd0zfm82r14abkjbj2g"))))
     (build-system cmake-build-system)
     (arguments
      (list
@@ -2364,6 +2376,8 @@ especially for creating reverb effects.  It supports impulse responses with 1,
 2 or 4 channels, in any soundfile format supported by libsndfile.")
     (license license:gpl2+)))
 
+;; Packages depending on JACK should always prefer jack-2.
+;; JACK1 is provided for legacy applications
 (define-public jack-1
   (package
     (name "jack")
@@ -2409,9 +2423,8 @@ synchronous execution of all clients, and low latency operation.")
     ;; licensed under the LGPL in order to allow for proprietary usage.
     (license (list license:gpl2+ license:lgpl2.1+))))
 
-;; Packages depending on JACK should always prefer jack-1.  Both jack-1 and
+;; Packages depending on JACK should always prefer jack-2.  Both jack-1 and
-;; jack-2 implement the same API.  JACK2 is provided primarily as a client
+;; jack-2 implement the same API.
-;; program for users who might benefit from the D-BUS features.
 (define-public jack-2
   (package
     (inherit jack-1)
@@ -2463,6 +2476,36 @@ synchronous execution of all clients, and low latency operation.")
     ;; Most files are under GPLv2+, but some headers are under LGPLv2.1+
     (license (list license:gpl2+ license:lgpl2.1+))))
 
+(define-public jack-example-tools
+  (package
+    (name "jack-example-tools")
+    (version "3")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/jackaudio/jack-example-tools")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0x684clxqib1bq3zvvrqlh7hb3arb1bf672xyx1jbwv76dcmm5mh"))))
+    (build-system meson-build-system)
+    (inputs
+     (list alsa-lib
+           jack-2
+           libsndfile
+           opus
+           readline))
+    (native-inputs
+     (list pkg-config))
+    (home-page "https://github.com/jackaudio/jack-example-tools")
+    (synopsis "Tools for JACK connections")
+    (description "This package provides tools for managing JACK connections
+and testing or configuring the JACK session.  Tools include @code{jack_lsp},
+@code{jack_connect}, and @code{jack_transport}.")
+    ;; Most files are under GPLv2+, but zalsa is GPLv3+.
+    (license (list license:gpl2+ license:gpl3+))))
+
 (define-public jacktrip
   (package
     (name "jacktrip")
@@ -2509,17 +2552,26 @@ audio signal streaming.")
 (define-public jalv
   (package
     (name "jalv")
-    (version "1.6.6")
+    (version "1.6.8")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://download.drobilla.net/jalv-"
-                                  version ".tar.bz2"))
+                                  version ".tar.xz"))
               (sha256
                (base32
-                "05lycfq0f06zjp5xqvzjz9hx9kmqx72yng1lghh76hv63dw43lcj"))))
+                "1q8mzjv577vdi64s47gd4pg0ydzxvs32cwrb1d64v90f52qpgbpd"))))
-    (build-system waf-build-system)
+    (build-system meson-build-system)
     (arguments
-     `(#:tests? #f))                    ; no check target
+     `(#:tests? #f                      ; no check target
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'build-PIC
+           ;; The default -fPIE #errors when combined with our Qt packages.
+           ;; Work around the broken meson.build script clobbering c_args.
+           (lambda _
+             (substitute* "meson.build"
+               (("'-DZIX_STATIC'" match)
+                (string-append match ", '-fPIC'"))))))))
     (inputs
      (list lv2
            lilv
@@ -2724,6 +2776,38 @@ compensation, (de)interleaving, and byte-swapping
 cross-platform audio input/output stream library.")
     (license license:expat)))
 
+(define-public python-pulsectl
+  (package
+    (name "python-pulsectl")
+    (version "22.3.2")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "pulsectl" version))
+              (sha256
+               (base32
+                "115ha1cwpd2r84ssnxdbr59hgs0jbx0lz3xpqli64kmxxqf4w5yc"))))
+    (build-system python-build-system)
+    (inputs (list pulseaudio))
+    (arguments
+     `(#:tests? #f                      ; tests try to communicate with PulseAudio
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-path
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "pulsectl/_pulsectl.py"
+               (("libpulse.so.0")
+                (string-append (search-input-file inputs "/lib/libpulse.so.0")))))))))
+    (home-page "https://github.com/mk-fg/python-pulse-control")
+    (synopsis
+     "Python bindings for mixer-like controls in PulseAudio")
+    (description
+     "This package provides a Python high-level interface and ctypes-based
+bindings for PulseAudio (libpulse), to use in simple synchronous code.
+This wrapper is mostly for mixer-like controls and introspection-related
+operations, as opposed to e.g. submitting sound samples to play and
+player-like clients.")
+    (license license:expat)))
+
 (define-public python-pyliblo
   (package
     (name "python-pyliblo")
@@ -3464,7 +3548,7 @@ tempo and pitch of an audio recording independently of one another.")
                 "1ff2yfq3k4l209fr71v3w98fpjjv1chs09vkbmxj03lcikahxns8"))))
     (build-system gnu-build-system)
     (inputs
-     (list jack-1 alsa-lib))
+     (list alsa-lib jack-2))
     (native-inputs
      (list autoconf automake libtool pkg-config))
     (home-page "https://www.music.mcgill.ca/~gary/rtmidi")
@@ -5979,7 +6063,7 @@ and DSD streams.")
 (define-public qpwgraph
   (package
     (name "qpwgraph")
-    (version "0.3.7")
+    (version "0.3.9")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -5988,7 +6072,7 @@ and DSD streams.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "05zbwikixxp5524ps7bd0i4xialgnp1m201rfvlz284sm40wk1vv"))))
+                "1zdqgn2a139bazazbccpb65zn7qdynndwm9mafq54nkpa7n7lri8"))))
     (build-system cmake-build-system)
     (arguments (list #:tests? #f)) ;; no tests
     (inputs (list alsa-lib
@@ -6031,3 +6115,39 @@ streams.  For shoutcast style streams it finds the “meta data” or track
 separation data, and uses that as a marker for where the track should
 be separated.")
     (license license:gpl2+)))
+
+(define-public cubeb
+  (let ((commit "9e29d728b0025c674904f83f5a13a88d1a6a5edc")
+        (revision "1"))
+    (package
+      (name "cubeb")
+      (version (git-version "0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/mozilla/cubeb")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1sxkr3h8a4hd3c3a3cjydrszz6npxk3vh6ra3y67lds3zgc69c7n"))))
+      (build-system cmake-build-system)
+      (arguments
+       '(#:configure-flags
+         ;; Sanitizers-cmake requires a git submodule.
+         '("-DUSE_SANITIZERS=0"
+           ;; Tests require a git submodule for googletest.
+           "-DBUILD_TESTS=0"
+           ;; Use our speex, not a bundled one.
+           "-DBUNDLE_SPEEX=0"
+           ;; A static library would be built by default.
+           "-DBUILD_SHARED_LIBS=1"
+           ;; Explicitly link against audio libraries so they are on the
+           ;; runpath.  Otherwise cubeb tries to dlopen them at runtime.
+           "-DCMAKE_SHARED_LINKER_FLAGS=-lasound -lpulse -lspeex")
+         #:tests? #f))
+      (inputs (list alsa-lib pulseaudio speex))
+      (synopsis "Cross-platform audio library")
+      (description "Cubeb is Mozilla's cross-platform audio library.")
+      (home-page "https://github.com/mozilla/cubeb")
+      (license license:isc))))

gnu/packages/autotools.scm

@@ -209,7 +209,7 @@ files with a system-specific shebang."
     (inputs `(("guile"
                ;; XXX: Kludge to hide the circular dependency.
                ,(module-ref (resolve-interface '(gnu packages guile))
-                            'guile-3.0/fixed))
+                            'guile-3.0/pinned))
               ("autoconf" ,autoconf)
               ("bash" ,bash-minimal)))
     (arguments

gnu/packages/backup.scm

@@ -333,7 +333,8 @@ reading and writing archives compressed using various compression filters such
 as gzip and bzip2.  The library is inherently stream-oriented; readers
 serially iterate through the archive, writers serially add things to the
 archive.  In particular, note that there is currently no built-in support for
-random access nor for in-place modification.")
+random access nor for in-place modification.  This package provides the
+@command{bsdcat}, @command{bsdcpio} and @command{bsdtar} commands.")
     (license license:bsd-2)))
 
 (define-public rdup
@@ -523,7 +524,7 @@ rdiff-backup is easy to use and settings have sensible defaults.")
 (define-public rsnapshot
   (package
     (name "rsnapshot")
-    (version "1.4.4")
+    (version "1.4.5")
     (source
      (origin
        (method url-fetch)
@@ -531,7 +532,7 @@ rdiff-backup is easy to use and settings have sensible defaults.")
              "https://github.com/rsnapshot/rsnapshot/releases/download/"
              version "/rsnapshot-" version ".tar.gz"))
        (sha256
-        (base32 "0yc5k2fhm54ypxgm1fsaf8vrg5b7qbvbsqk371n6baf592vprjy1"))))
+        (base32 "0hl2ncld0xkwlnv1cqjmmnld2nlp65alkkdacs11wl95r80mxdqh"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases

gnu/packages/bioconductor.scm

@@ -5,13 +5,14 @@
 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2017, 2022 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2019, 2020, 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
+;;; Copyright © 2019, 2020, 2021, 2022, 2023 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
-;;; Copyright © 2020, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2020-2023 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
 ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
 ;;; Copyright © 2021 Nicolas Vallet <nls.vallet@gmail.com>
+;;; Copyright © 2023 Navid Afkhami <Navid.Afkhami@mdc-berlin.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -114,6 +115,33 @@ analysis.")
 based on mapping using Entrez Gene identifiers.")
     (license license:artistic2.0)))
 
+(define-public r-pd-mapping50k-xba240
+  (package
+    (name "r-pd-mapping50k-xba240")
+    (version "3.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "pd.mapping50k.xba240" version
+                              'annotation))
+       (sha256
+        (base32 "1a1f3lh5ywhyjawdbj2fzban85c8jz70lfcv3pagd5piincjwxq8"))))
+    (properties `((upstream-name . "pd.mapping50k.xba240")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biostrings
+           r-dbi
+           r-iranges
+           r-oligo
+           r-oligoclasses
+           r-rsqlite
+           r-s4vectors))
+    (home-page "https://bioconductor.org/packages/pd.mapping50k.xba240")
+    (synopsis "Platform design info for Affymetrix Mapping50K_Xba240")
+    (description "This package provides platform design info for Affymetrix
+Mapping50K_Xba240 (pd.mapping50k.xba240).")
+    (license license:artistic2.0)))
+
 (define-public r-reactome-db
   (package
     (name "r-reactome-db")
@@ -1247,6 +1275,29 @@ demonstration purposes in the @code{AneuFinder} package.")
 from Illumina 450k methylation arrays.")
     (license license:artistic2.0)))
 
+(define-public r-bcellviper
+  (package
+    (name "r-bcellviper")
+    (version "1.34.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "bcellViper" version
+                                     'experiment))
+              (sha256
+               (base32
+                "1fpgh70x2r68v0ximgcdphnyzq2hgiwbamyhbac3yka8flhrd1fm"))))
+    (properties `((upstream-name . "bcellViper")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biobase))
+    (home-page "https://bioconductor.org/packages/bcellViper")
+    (synopsis
+     "Transcriptional interactome and normal human B-cell expression data")
+    (description
+     "This is a tool for human B-cell context-specific transcriptional
+regulatory network.  In addition, this package provides a human normal B-cells
+dataset for the examples in package viper.")
+    (license license:gpl2+)))
+
 (define-public r-bladderbatch
   (package
     (name "r-bladderbatch")
@@ -1291,6 +1342,26 @@ from Illumina 450k methylation arrays.")
 biscuiteer.")
     (license license:gpl3)))
 
+(define-public r-breakpointrdata
+  (package
+    (name "r-breakpointrdata")
+    (version "1.16.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "breakpointRdata" version 'experiment))
+              (sha256
+               (base32
+                "0f23i4ynb4vgn22c3d2l64z92rzv3qnwd4j8qyvalklrxkwilhfn"))))
+    (properties `((upstream-name . "breakpointRdata")))
+    (build-system r-build-system)
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/daewoooo/breakpointRdata")
+    (synopsis "Strand-seq data for demonstration purposes")
+    (description
+     "This package is a collection of Strand-seq data.  The main purpose is to
+demonstrate functionalities of the @code{breakpointR} package.")
+    (license license:expat)))
+
 (define-public r-celldex
   (package
     (name "r-celldex")
@@ -1410,6 +1481,25 @@ genomation package.  Included are Chip Seq, Methylation and Cage data,
 downloaded from Encode.")
     (license license:gpl3+)))
 
+(define-public r-italicsdata
+  (package
+    (name "r-italicsdata")
+    (version "2.36.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ITALICSData" version 'experiment))
+       (sha256
+        (base32 "09d2igic3b5p7wpq98hb2lffxm1nfq9mwmnqlbdn3jv49pgz3hmw"))))
+    (properties `((upstream-name . "ITALICSData")))
+    (build-system r-build-system)
+    (home-page "http://bioinfo.curie.fr")
+    (synopsis "ITALICS data")
+    (description "This package provides data needed to use the ITALICS
+package.")
+    ;; Expanded from GPL
+    (license (list license:gpl2+ license:gpl3+))))
+
 (define-public r-macrophage
   (package
     (name "r-macrophage")
@@ -1736,6 +1826,48 @@ expression level and gene-specific dispersion, that might facilitate the gene
 ranking by fold-change and visualization.")
     (license license:gpl3+)))
 
+(define-public r-adacgh2
+  (package
+    (name "r-adacgh2")
+    (version "2.38.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ADaCGH2" version))
+       (sha256
+        (base32 "0g9x3lnr56035wq9ijdcri4sz5pwj8184yxm415gmsxrii9xvpfd"))))
+    (properties `((upstream-name . "ADaCGH2")))
+    (build-system r-build-system)
+    (arguments
+     (list
+      #:phases
+      '(modify-phases %standard-phases
+         (add-after 'unpack 'python3-compatibility
+           (lambda _
+             (substitute* "inst/imagemap-example/toMap.py"
+               (("print nameMap") "print(nameMap)")))))))
+    (inputs (list python-wrapper))
+    (propagated-inputs
+     (list r-acgh
+           r-bit
+           r-cluster
+           r-dnacopy
+           r-ff
+           r-glad
+           r-snapcgh
+           r-tilingarray
+           r-waveslim))
+    (home-page "https://github.com/rdiaz02/adacgh2")
+    (synopsis "Big data analysis from aCGH experiments")
+    (description
+     "This package analyzes and creates plots of array @acronym{CGH,
+comparative genomic hybridization} data.  Also, it allows usage of
+@acronym{CBS, Circular Binary Segementation}, wavelet-based smoothing, HMM,
+BioHMM, GLAD, CGHseg.  Most computations are parallelized (either via forking
+or with clusters, including MPI and sockets clusters) and use @code{ff} for
+storing data.")
+    (license license:gpl3+)))
+
 (define-public r-adam
   (package
     (name "r-adam")
@@ -2443,6 +2575,47 @@ Powerful interactive and dynamic figures generated by animalcules enable users
 to understand their data better and discover new insights.")
     (license license:artistic2.0)))
 
+(define-public r-anvil
+  (package
+    (name "r-anvil")
+    (version "1.10.1")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "AnVIL" version))
+              (sha256
+               (base32
+                "0iqsffkrxv28g9cddx2w05f2dbscwxhh6bpizwa8xaxhvn5bcpsv"))))
+    (properties `((upstream-name . "AnVIL")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocmanager
+           r-dplyr
+           r-dt
+           r-futile-logger
+           r-htmltools
+           r-httr
+           r-jsonlite
+           r-miniui
+           r-rapiclient
+           r-rlang
+           r-shiny
+           r-tibble
+           r-tidyr
+           r-tidyselect))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/AnVIL")
+    (synopsis "Provides access to AnVIL, Terra, Leonardo and other projects")
+    (description
+     "The AnVIL is a cloud computing resource developed in part by the
+National Human Genome Research Institute.  The AnVIL package provides end-user
+and developer functionality.  AnVIL provides fast binary package installation,
+utilities for working with Terra/AnVIL table and data resources, and
+convenient functions for file movement to and from Google cloud storage.  For
+developers, AnVIL provides programatic access to the Terra, Leonardo, Rawls,
+Dockstore, and Gen3 RESTful programming interface, including helper functions
+to transform JSON responses to formats more amenable to manipulation in R.")
+    (license license:artistic2.0)))
+
 (define-public r-aldex2
   (package
     (name "r-aldex2")
@@ -2598,6 +2771,59 @@ mapped reads).  It is currently designed for un-stranded paired-end RNA-seq
 data.")
     (license license:gpl2+)))
 
+(define-public r-alpsnmr
+  (package
+    (name "r-alpsnmr")
+    (version "4.0.2")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "AlpsNMR" version))
+              (sha256
+               (base32
+                "1y4qqc6l8flv5ns4qwzjwmcykm6zcm4jg097mn8xyp7mnxymy7pl"))))
+    (properties `((upstream-name . "AlpsNMR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-baseline
+           r-biocparallel
+           r-dplyr
+           r-fs
+           r-future
+           r-generics
+           r-ggplot2
+           r-glue
+           r-htmltools
+           r-magrittr
+           r-matrixstats
+           r-mixomics
+           r-pcapp
+           r-purrr
+           r-readxl
+           r-reshape2
+           r-rlang
+           r-rmarkdown
+           r-scales
+           r-signal
+           r-speaq
+           r-stringr
+           r-tibble
+           r-tidyr
+           r-tidyselect
+           r-vctrs))
+    (native-inputs (list r-knitr))
+    (home-page "https://sipss.github.io/AlpsNMR/")
+    (synopsis "Automated spectral processing system for NMR")
+    (description
+     "This package reads Bruker @acronym{NMR, Nuclear Magnetic Resonance} data
+directories both zipped and unzipped.  It provides automated and efficient
+signal processing for untargeted NMR metabolomics.  It is able to interpolate
+the samples, detect outliers, exclude regions, normalize, detect peaks, align
+the spectra, integrate peaks, manage metadata and visualize the spectra.
+After spectra processing, it can apply multivariate analysis on extracted
+data.  Efficient plotting with 1-D data is also available.  Basic reading of
+1D ACD/Labs exported JDX samples is also available.")
+    (license license:expat)))
+
 (define-public r-altcdfenvs
   (package
     (name "r-altcdfenvs")
@@ -3480,6 +3706,40 @@ of Bioconductor.")
 packages.")
     (license license:artistic2.0)))
 
+(define-public r-breakpointr
+  (package
+    (name "r-breakpointr")
+    (version "1.16.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "breakpointR" version))
+              (sha256
+               (base32
+                "0j1f43lhgkapjyxlil9fflqh9nf3andhmvirdcv45y60wvljn4gx"))))
+    (properties `((upstream-name . "breakpointR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocgenerics
+           r-breakpointrdata
+           r-cowplot
+           r-doparallel
+           r-foreach
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicranges
+           r-ggplot2
+           r-gtools
+           r-iranges
+           r-rsamtools
+           r-s4vectors))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/daewoooo/BreakPointR")
+    (synopsis "Find breakpoints in Strand-seq data")
+    (description
+     "This package implements functions for finding breakpoints, plotting and
+export of Strand-seq data.")
+    (license license:expat)))
+
 (define-public r-cardelino
   (package
     (name "r-cardelino")
@@ -4318,6 +4578,37 @@ domains etc.) from quantification of all types of RNASeq by tools such as
 Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.")
     (license license:gpl2+)))
 
+(define-public r-italics
+  (package
+    (name "r-italics")
+    (version "2.58.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ITALICS" version))
+       (sha256
+        (base32 "0g937h9zxkxnm424wh58b46mfasdd7pqy5c04r0a46mx9lxibgbs"))))
+    (properties `((upstream-name . "ITALICS")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-affxparser
+           r-dbi
+           r-glad
+           r-italicsdata
+           r-oligo
+           r-oligoclasses
+           r-pd-mapping50k-xba240))
+    (home-page "http://bioinfo.curie.fr")
+    (synopsis "Normalizing of the Affymetrix GeneChip human mapping")
+    (description
+     "This package provides tools for normalizing and analyzing of GeneChip
+Mapping 100K and 500K Set.  Affymetrix GeneChip Human Mapping 100K and 500K
+Set allows the DNA copy number mea- surement of respectively 2× 50K and 2×
+250K SNPs along the genome.  Their high density allows a precise localization
+of genomic alterations and makes them a powerful tool for cancer and copy
+number polymorphism study.")
+    (license license:gpl2)))
+
 ;; This is a CRAN package, but it depends on r-biobase and r-limma from Bioconductor.
 (define-public r-absfiltergsea
   (package
@@ -5973,6 +6264,30 @@ GenomicRanges package defines general purpose containers for storing and
 manipulating genomic intervals and variables defined along a genome.")
     (license license:artistic2.0)))
 
+(define-public r-glad
+  (package
+    (name "r-glad")
+    (version "2.62.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "GLAD" version))
+              (sha256
+               (base32
+                "0gb52ic5r6nkgm2ynm174vcvbmkbhhjgv71lsmxpxzcsb6rr7qj6"))))
+    (properties `((upstream-name . "GLAD")))
+    (build-system r-build-system)
+    (inputs (list gsl))
+    (propagated-inputs (list r-aws))
+    (native-inputs (list pkg-config))
+    (home-page "http://bioinfo.curie.fr")
+    (synopsis "Gain and loss analysis of DNA")
+    (description
+     "This package helps with the analysis of array @acronym{CGH, comparative
+genomic hybridization} data by detecting of the breakpoints in the genomic
+profiles and assignment of a status (gain, normal or loss) to each chromosomal
+regions identified.")
+    (license license:gpl2)))
+
 (define-public r-gostats
   (package
     (name "r-gostats")
@@ -6274,6 +6589,61 @@ containing the location/probe set membership mapping.  The other one creates a
 package that automatically loads that environment.")
     (license license:gpl2+)))
 
+(define-public r-manor
+  (package
+    (name "r-manor")
+    (version "1.70.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "MANOR" version))
+       (sha256
+        (base32 "16b30bmyzml97cjdbh6h9ky5c4h5ws2a3g2xkxnd55sd3jg64jgx"))))
+    (properties `((upstream-name . "MANOR")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-glad))
+    (native-inputs (list r-knitr))
+    (home-page "http://bioinfo.curie.fr/projects/manor/index.html")
+    (synopsis "CGH micro-array normalization")
+    (description
+     "This package ofers functions for importation, normalization,
+visualization, and quality control to correct identified sources of
+variability in array of @acronym{CGH, comparative genomic hybridization}
+experiments.")
+    (license license:gpl2)))
+
+(define-public r-maser
+  (package
+    (name "r-maser")
+    (version "1.16.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "maser" version))
+              (sha256
+               (base32
+                "1zycx8s046g4d3w5qrn950bmi0nrnq1g7fvqji48mr6hmsyzplvv"))))
+    (properties `((upstream-name . "maser")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocgenerics
+           r-data-table
+           r-dplyr
+           r-dt
+           r-genomeinfodb
+           r-genomicranges
+           r-ggplot2
+           r-gviz
+           r-iranges
+           r-reshape2
+           r-rtracklayer))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/DiogoVeiga/maser")
+    (synopsis "Mapping alternative splicing events to proteins")
+    (description
+     "This package provides functionalities for downstream analysis, annotation
+and visualizaton of alternative splicing events generated by rMATS.")
+    (license license:expat)))
+
 (define-public r-metaneighbor
   (package
     (name "r-metaneighbor")
@@ -6664,6 +7034,73 @@ proteowizard library for mzML and mzIdentML.  The netCDF reading code has
 previously been used in XCMS.")
     (license license:artistic2.0)))
 
+;; This is a CRAN package, but it depends on a Bioconductor package.
+(define-public r-numbat
+  (package
+    (name "r-numbat")
+    (version "1.2.1")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "numbat" version))
+              (sha256
+               (base32
+                "1jkz24j99cd333mvisp8x5swwr0iyix1kc962d2yx3mv5cn28xdb"))))
+    (properties `((upstream-name . "numbat")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-ape
+                             r-catools
+                             r-data-table
+                             r-dendextend
+                             r-dplyr
+                             r-genomicranges
+                             r-ggplot2
+                             r-ggraph
+                             r-ggtree
+                             r-glue
+                             r-igraph
+                             r-iranges
+                             r-logger
+                             r-magrittr
+                             r-matrix
+                             r-optparse
+                             r-paralleldist
+                             r-patchwork
+                             r-pryr
+                             r-purrr
+                             r-r-utils
+                             r-rcpp
+                             r-rcpparmadillo
+                             r-rhpcblasctl
+                             r-roptim
+                             r-scales
+                             r-scistreer
+                             r-stringr
+                             r-tibble
+                             r-tidygraph
+                             r-tidyr
+                             r-vcfr
+                             r-zoo))
+    (home-page "https://github.com/kharchenkolab/numbat")
+    (synopsis "Haplotype-aware CNV analysis from scRNA-Seq")
+    (description
+     "This package provides a computational method that infers copy number
+variations (CNV) in cancer scRNA-seq data and reconstructs the tumor
+phylogeny.  It integrates signals from gene expression, allelic ratio, and
+population haplotype structures to accurately infer allele-specific CNVs in
+single cells and reconstruct their lineage relationship.  It does not require
+tumor/normal-paired DNA or genotype data, but operates solely on the donor
+scRNA-data data (for example, 10x Cell Ranger output).  It can be used to:
+
+@enumerate
+@item detect allele-specific copy number variations from single-cells
+@item differentiate tumor versus normal cells in the tumor microenvironment
+@item infer the clonal architecture and evolutionary history of profiled tumors
+@end enumerate
+
+For details on the method see @url{https://doi.org/10.1038/s41587-022-01468-y,
+Gao et al in Nature Biotechnology 2022}.")
+    (license license:expat)))
+
 (define-public r-organism-dplyr
   (package
     (name "r-organism-dplyr")
@@ -7311,6 +7748,43 @@ includes methods formerly found in the scran package, and the new fast and
 comprehensive scDblFinder method.")
     (license license:gpl3)))
 
+;; This is a CRAN package, but it depends on packages from Bioconductor.
+(define-public r-scistreer
+  (package
+    (name "r-scistreer")
+    (version "1.1.0")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "scistreer" version))
+              (sha256
+               (base32
+                "0cdp26ngfp5rxa21nqnj6j2098f6996368g4msb3shh7n75np4s9"))))
+    (properties `((upstream-name . "scistreer")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-ape
+                             r-dplyr
+                             r-ggplot2
+                             r-ggtree
+                             r-igraph
+                             r-paralleldist
+                             r-patchwork
+                             r-phangorn
+                             r-rcpp
+                             r-rcpparmadillo
+                             r-rcppparallel
+                             r-reshape2
+                             r-rhpcblasctl
+                             r-stringr
+                             r-tidygraph))
+    (home-page "https://github.com/kharchenkolab/scistreer")
+    (synopsis "Maximum-likelihood perfect phylogeny Inference at scale")
+    (description
+     "This package provides fast maximum-likelihood phylogeny inference from
+noisy single-cell data using the ScisTree algorithm proposed by
+@code{doi.org/10.1093/bioinformatics/btz676, Yufeng Wu (2019)}.  It makes the
+method applicable to massive single-cell datasets (>10,000 cells).")
+    (license license:gpl3)))
+
 (define-public r-scmap
   (package
     (name "r-scmap")
@@ -7592,6 +8066,34 @@ includes a function to create a cluster-level minimum spanning tree and data
 structures to hold pseudotime inference results.")
     (license license:gpl3)))
 
+(define-public r-scds
+  (package
+    (name "r-scds")
+    (version "1.14.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "scds" version))
+              (sha256
+               (base32
+                "0zdf9yf5s0l8ma7d8yhi7bjd964yj84f5h6aq2p0sypjlnc515hd"))))
+    (properties `((upstream-name . "scds")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-dplyr
+                             r-matrix
+                             r-proc
+                             r-s4vectors
+                             r-singlecellexperiment
+                             r-summarizedexperiment
+                             r-xgboost))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/scds")
+    (synopsis "In-silico doublet annotation for single cell RNA sequencing data")
+    (description
+     "This is an R package for doublet annotation of single cell RNA
+sequencing data.  @code{scds} provides methods to annotate doublets in
+scRNA-seq data computationally.")
+    (license license:expat)))
+
 (define-public r-slingshot
   (package
    (name "r-slingshot")
@@ -7624,6 +8126,46 @@ events and allows for the incorporation of prior knowledge through supervised
 graph construction.")
    (license license:artistic2.0)))
 
+;; This is a CRAN package but it depends on a bioconductor package.
+(define-public r-speaq
+  (package
+    (name "r-speaq")
+    (version "2.7.0")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "speaq" version))
+              (sha256
+               (base32
+                "0z9a3nbfazphp090c6hg892vjq7jp4g4cij3s5wbs1q567inbmlk"))))
+    (properties `((upstream-name . "speaq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-cluster
+           r-data-table
+           r-dosnow
+           r-foreach
+           r-ggplot2
+           r-gridextra
+           r-impute
+           r-massspecwavelet
+           r-missforest
+           r-reshape2
+           r-rfast
+           r-rvest
+           r-xml2))
+    (native-inputs (list r-knitr))
+    (home-page "https://cran.r-project.org/package=speaq")
+    (synopsis "Tools for nuclear magnetic resonance spectra alignment")
+    (description
+     "This package aims to make @acronym{NMR, Nuclear Magnetic Resonance}
+spectroscopy data analysis as easy as possible.  It only requires a small set
+of functions to perform an entire analysis.  Speaq offers the possibility of
+raw spectra alignment and quantitation but also an analysis based on features
+whereby the spectra are converted to peaks which are then grouped and turned
+into features.  These features can be processed with any number of statistical
+tools either included in speaq or available elsewhere on CRAN.")
+    (license license:asl2.0)))
+
 (define-public r-stager
   (package
     (name "r-stager")
@@ -8267,6 +8809,33 @@ arrays (expression/SNP/tiling/exon) at probe-level.  It currently supports
 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
     (license license:lgpl2.0+)))
 
+(define-public r-quantsmooth
+  (package
+    (name "r-quantsmooth")
+    (version "1.64.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "quantsmooth" version))
+       (sha256
+        (base32 "1adwws3brb01d4g6yidipnd8akkiyc3gpdr876hy57qnmcq8xipp"))))
+    (properties `((upstream-name . "quantsmooth")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-quantreg))
+    (home-page "https://bioconductor.org/packages/quantsmooth")
+    (synopsis "Quantile smoothing and genomic visualization of array data")
+    (description
+     "This package implements quantile smoothing.  It contains a dataset used
+to produce human chromosomal ideograms for plotting purposes and a collection
+of arrays that contains data of chromosome 14 of 3 colorectal tumors.  The
+package provides functions for painting chromosomal icons, chromosome or
+chromosomal idiogram and other types of plots.  Quantsmooth offers options
+like converting chromosomal ids to their numeric form, retrieving the human
+chromosomal length from NCBI data, retrieving regions of interest in a vector
+of intensities using quantile smoothing, determining cytoband position based
+on the location of the probe, and other useful tools.")
+    (license license:gpl2)))
+
 (define-public r-qvalue
   (package
     (name "r-qvalue")
@@ -14489,6 +15058,47 @@ be applied to the analysis of other NGS data obtained from experimental
 procedures that induce nucleotide substitutions (e.g. BisSeq).")
     (license license:gpl2)))
 
+(define-public r-tilingarray
+  (package
+    (name "r-tilingarray")
+    (version "1.76.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "tilingArray" version))
+              (sha256
+               (base32
+                "19bkgblpkcp3w3sdyn82c37gkz1sv3r4d546zpbnh36q2pi3l4zd"))))
+    (properties `((upstream-name . "tilingArray")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-affy
+           r-biobase
+           r-genefilter
+           r-pixmap
+           r-rcolorbrewer
+           r-strucchange
+           r-vsn))
+    (home-page "https://bioconductor.org/packages/tilingArray")
+    (synopsis "Transcript mapping with high-density oligonucleotide tiling arrays")
+    (description
+     "The package provides functionality that can be useful for the analysis
+of the high-density tiling microarray data (such as from Affymetrix genechips)
+or for measuring the transcript abundance and the architecture.  The main
+functionalities of the package are:
+
+@enumerate
+@item the class segmentation for representing partitionings of a linear series
+  of data;
+@item the function segment for fitting piecewise constant models using a
+  dynamic programming algorithm that is both fast and exact;
+@item the function @code{confint} for calculating confidence intervals using
+  the @code{strucchange} package;
+@item the function @code{plotAlongChrom} for generating pretty plots;
+@item the function @code{normalizeByReference} for probe-sequence dependent
+  response adjustment from a (set of) reference hybridizations.
+@end enumerate")
+    (license license:artistic2.0)))
+
 (define-public r-timeseriesexperiment
   (package
     (name "r-timeseriesexperiment")
@@ -16543,6 +17153,26 @@ variety of commonly used matrix types, including sparse and HDF5-backed
 matrices.")
     (license license:gpl3)))
 
+(define-public r-beadarraysnp
+  (package
+    (name "r-beadarraysnp")
+    (version "1.64.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "beadarraySNP" version))
+       (sha256
+        (base32 "06hy89pclbyxjw5yf5i9bc3wr789b9pmhd9sdchgljlijs9vcj6g"))))
+    (properties `((upstream-name . "beadarraySNP")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biobase r-quantsmooth))
+    (home-page "https://bioconductor.org/packages/beadarraySNP")
+    (synopsis "Normalization and reporting of Illumina SNP bead arrays")
+    (description
+     "This package is importing data from Illumina SNP experiments and it
+performs copy number calculations and reports.")
+    (license license:gpl2)))
+
 ;; This package includes files that have been taken from kentutils.  Some
 ;; parts of kentutils are not released under a free license, but this package
 ;; only uses files that are also found in the free parts of kentutils.
@@ -17674,6 +18304,34 @@ integrates with pathway and gene set (enrichment) analysis tools for
 large-scale and fully automated analysis.")
     (license license:gpl3+)))
 
+(define-public r-snapcgh
+  (package
+    (name "r-snapcgh")
+    (version "1.68.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "snapCGH" version))
+              (sha256
+               (base32
+                "1zxvl8mkby7yb5kppddag6k9w78d1fm6adx52h4cgrfckn28w64q"))))
+    (properties `((upstream-name . "snapCGH")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-acgh
+           r-cluster
+           r-dnacopy
+           r-glad
+           r-limma
+           r-tilingarray))
+    (home-page "https://bioconductor.org/packages/snapCGH")
+    (synopsis "Segmentation, normalisation and processing of the aCGH data")
+    (description
+     "This package provides methods for segmenting, normalising and processing
+aCGH data.  snapCGH also includes plotting functions for visualising raw and
+segmented data for individual and multiple arrays.")
+    ;; Expanded from GPL
+    (license (list license:gpl2+ license:gpl3+))))
+
 (define-public r-snpstats
   (package
     (name "r-snpstats")

gnu/packages/bioinformatics.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2014-2023 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2015, 2016, 2018, 2019, 2020 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
@@ -11,7 +11,7 @@
 ;;; Copyright © 2017, 2021, 2022 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
-;;; Copyright © 2018, 2019, 2020, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2018-2023 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;; Copyright © 2019, 2020, 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com>
 ;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
@@ -21,9 +21,9 @@
 ;;; Copyright © 2020 Bonface Munyoki Kilyungi <bonfacemunyoki@gmail.com>
 ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
 ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
-;;; Copyright © 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
+;;; Copyright © 2021, 2022, 2023 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2021 Felix Gruber <felgru@posteo.net>
-;;; Copyright © 2022 Navid Afkhami <navid.afkhami@mdc-berlin.de>
+;;; Copyright © 2022, 2023 Navid Afkhami <navid.afkhami@mdc-berlin.de>
 ;;; Copyright © 2022 Antero Mejr <antero@mailbox.org>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -512,6 +512,106 @@ BED, GFF/GTF, VCF.")
     (inputs
      (list samtools zlib))))
 
+(define-public bitmapperbs
+  (package
+    (name "bitmapperbs")
+    (version "1.0.2.3")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/chhylp123/BitMapperBS/")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "02ksssfnvmpskld0a2016smfz5nrzm3d90v8974f3cpzywckvp8v"))
+              (modules '((guix build utils)))
+              ;; This package bundles a modified copy of htslib, so we cannot
+              ;; unbundle it.
+              (snippet
+               '(begin
+                  (delete-file-recursively "libdivsufsort-2.0.1")
+                  (delete-file-recursively "pSAscan-0.1.0")))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:tests? #false
+      #:make-flags '(list "bitmapperBS")
+      ;; The build system checks for CPU features.  For this reason, we want
+      ;; users to build it locally instead of using substitutes.
+      #:substitutable? #false
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'fix-build-system
+            (lambda _
+              (substitute* "Makefile"
+                (("make prefix=../htslib_aim install")
+                 (string-append "make prefix=" #$output " install-so"))
+                (("htslib_aim/include") "htslib")
+                (("htslib_aim/lib")
+                 (string-append #$output "/lib")))))
+          (add-after 'unpack 'patch-references-to-psascan
+            (lambda* (#:key inputs #:allow-other-keys)
+              (substitute* "Makefile"
+                (("\"(./)?psascan" pre all)
+                 (string-append "\"" pre (search-input-file inputs "/bin/psascan"))))))
+          (delete 'configure)
+          (replace 'install
+            (lambda _
+              (install-file "bitmapperBS"
+                            (string-append #$output "/bin/")))))))
+    (inputs
+     (list libdivsufsort psascan zlib))
+    (home-page "https://github.com/chhylp123/BitMapperBS/")
+    (synopsis "Read aligner for whole-genome bisulfite sequencing")
+    (description
+     "BitMapperBS is memory-efficient aligner that is designed for
+whole-genome bisulfite sequencing (WGBS) reads from directional protocol.")
+    (license license:asl2.0)))
+
+(define-public cellsnp-lite
+  ;; Last release is from November 2021 and does not contain fixes.
+  (let ((commit "0885d746b0b1ea65c8ef92f8943ca7669ca9734a")
+        (revision "0"))
+    (package
+      (name "cellsnp-lite")
+      (version (git-version "1.2.2" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/single-cell-genetics/cellsnp-lite")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1qrvqgbvw6mbhpyqvqbmvv8dmyc67bsk1041cn7ib6zmd47qm444"))))
+      (build-system gnu-build-system)
+      (arguments
+       (list
+        #:configure-flags
+        #~(list (string-append "--with-htslib="
+                               #$(this-package-input "htslib")))))
+      (inputs
+       (list curl
+             htslib
+             openssl
+             zlib))
+      (native-inputs
+       (list autoconf))
+      (home-page "https://cellsnp-lite.readthedocs.io")
+      (synopsis "Pileup expresses alleles in single-cell or bulk RNA-seq data")
+      (description
+       "This package is designed to pileup the expressed alleles in
+single-cell or bulk RNA-seq data, which can be directly used for donor
+deconvolution in multiplexed single-cell RNA-seq data, particularly with other
+packages, which assigns cells to donors and detects doublets as vireo, even
+without genotyping reference.
+
+This package is the C version of the deprecated cellSNP implemented in Python.
+Compared to cellSNP, this package is more efficient with higher speed and less
+memory usage.")
+      (license license:asl2.0))))
+
 (define-public pbcopper
   (package
     (name "pbcopper")
@@ -647,6 +747,41 @@ high-throughput sequence analysis.  The package is primarily useful to
 developers of other R packages who wish to make use of HTSlib.")
       (license license:lgpl2.0+))))
 
+(define-public r-streamgraph
+  (let ((commit "76f7173ec89d456ace5943a512e20b1f6810bbcb")
+        (revision "1"))
+    (package
+      (name "r-streamgraph")
+      (version (git-version "0.9.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/hrbrmstr/streamgraph")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "010rhnby5a9dg08jvlkr65b3p9iipdxi2f5m1k6j53s80p25yvig"))))
+      (properties `((upstream-name . "streamgraph")))
+      (build-system r-build-system)
+      (propagated-inputs
+       (list r-dplyr
+             r-htmltools
+             r-htmlwidgets
+             r-magrittr
+             r-tidyr
+             r-xts))
+      (native-inputs (list r-knitr))
+      (home-page "https://github.com/hrbrmstr/streamgraph")
+      (synopsis "Htmlwidget for building streamgraph visualizations")
+      (description
+       "A streamgraph is a type of stacked area chart.  It represents the
+evolution of a numeric variable for several groups.  Areas are usually
+displayed around a central axis, and edges are rounded to give a flowing
+shape.  This package provides an @code{htmlwidget} for building streamgraph
+visualizations.")
+      (license license:expat))))
+
 (define-public pbbam
   (package
     (name "pbbam")
@@ -933,6 +1068,13 @@ intended to behave exactly the same as the original BWK awk.")
 Format (GFF) with Biopython integration.")
     (license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE"))))
 
+(define-public python-bcbio-gff/biopython-1.73
+  (package
+    (inherit python-bcbio-gff)
+    (propagated-inputs
+     (modify-inputs (package-propagated-inputs python-bcbio-gff)
+       (replace "python-biopython" python-biopython-1.73)))))
+
 (define-public python-cellbender
   (package
     (name "python-cellbender")
@@ -946,7 +1088,7 @@ Format (GFF) with Biopython integration.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "12q22va7rbc3sx9ygc6p6hh6xw9wbqjmhba5h5gb836p5xplj5fa"))))
+         "0h9d9pznffdbya631hkk7b7jwjrgx5saqssar1d42qbyvdji3hgy"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:tests? #false)) ;there are none
@@ -971,6 +1113,95 @@ Format (GFF) with Biopython integration.")
 from high-throughput single-cell RNA sequencing (scRNA-seq) data.")
     (license license:bsd-3)))
 
+(define-public python-cmseq
+  (package
+    (name "python-cmseq")
+    (version "1.0.4")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "CMSeq" version))
+              (sha256
+               (base32
+                "0p6a99c299m5wi2z57dgqz52m1z3nfr8mv7kdnk2jvl2p9nql0wk"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:tests? #false ;there are no tests
+      #:phases
+      '(modify-phases %standard-phases
+         (add-after 'unpack 'patch-samtools-reference
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "cmseq/cmseq.py"
+               (("'samtools'")
+                (string-append "'" (search-input-file inputs "/bin/samtools") "'"))))))))
+    (inputs (list samtools))
+    (propagated-inputs
+     (list python-bcbio-gff/biopython-1.73
+           python-biopython-1.73
+           python-numpy
+           python-pandas
+           python-pysam
+           python-scipy))
+    (home-page "https://github.com/SegataLab/cmseq/")
+    (synopsis "Set of utilities on sequences and BAM files")
+    (description
+     "CMSeq is a set of commands to provide an interface to .bam files for coverage
+and sequence consensus.")
+    (license license:expat)))
+
+(define-public python-demuxem
+  (package
+    (name "python-demuxem")
+    (version "0.1.7")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "demuxEM" version))
+              (sha256
+               (base32
+                "1bhyxqjk44bmyd26m1smapf68wyf7252kk65i27k50dd3kswgnd6"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs
+     (list python-docopt
+           python-importlib-metadata
+           python-numpy
+           python-pandas
+           python-pegasusio
+           python-scikit-learn
+           python-scipy
+           python-seaborn))
+    (native-inputs (list python-cython python-setuptools-scm))
+    (home-page "https://github.com/lilab-bcb/demuxEM")
+    (synopsis "Analyze cell-hashing/nucleus-hashing data")
+    (description
+     "This is a Python module for analyzing cell-hashing/nucleus-hashing data.
+It is the demultiplexing module of Pegasus, which is used by Cumulus in the
+demultiplexing step.")
+    (license license:bsd-3)))
+
+(define-public python-hclust2
+  (package
+    (name "python-hclust2")
+    (version "1.0.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "hclust2" version))
+              (sha256
+               (base32
+                "0v89n2g42d7jhgfs8glf06apgxx6aswp3mfisgnhm518cv8z2rwn"))))
+    (build-system pyproject-build-system)
+    (arguments (list #:tests? #f))      ;there are no tests
+    (propagated-inputs
+     (list python-matplotlib
+           python-numpy
+           python-pandas
+           python-scipy))
+    (home-page "https://github.com/SegataLab/hclust2/")
+    (synopsis "Plotting heat-maps for publications")
+    (description
+     "Hclust2 is a handy tool for plotting heat-maps with several useful options
+to produce high quality figures that can be used in publications.")
+    (license license:expat)))
+
 (define-public python-htsget
   (package
    (name "python-htsget")
@@ -993,6 +1224,74 @@ protocol.  It provides a simple and reliable way to retrieve genomic data from
 servers supporting the protocol.")
    (license license:asl2.0)))
 
+(define-public python-pegasusio
+  (package
+    (name "python-pegasusio")
+    (version "0.7.1")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "pegasusio" version))
+              (sha256
+               (base32
+                "0gqygspdy398vjymdy6756jmk99s7fhwav9rivdx59kpqjcdxaz9"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs
+     (list python-anndata
+           python-docopt
+           python-h5py
+           python-importlib-metadata
+           python-loompy
+           python-natsort
+           python-numpy
+           python-pandas
+           python-pillow
+           python-scipy
+           python-zarr))
+    (native-inputs (list python-cython python-setuptools-scm))
+    (home-page "https://github.com/lilab-bcb/pegasusio")
+    (synopsis "Read or write single-cell genomics data")
+    (description
+     "Pegasusio is a Python package for reading or writing single-cell
+genomics data.")
+    (license license:bsd-3)))
+
+(define-public python-phylophlan
+  (package
+    (name "python-phylophlan")
+    (version "3.0.3")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/biobakery/phylophlan")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1wz70xzxqx2sf5flmf45m15jq027dqijfaj1r51pl50w5x6dkawx"))))
+    (build-system pyproject-build-system)
+    (arguments (list #:tests? #f))      ;there are no tests
+    (propagated-inputs
+     (list python-biopython
+           python-dendropy
+           python-matplotlib
+           python-numpy
+           python-pandas
+           python-seaborn))
+    (home-page "https://github.com/biobakery/phylophlan")
+    (synopsis
+     "Phylogenetic analysis of microbial isolates and genomes from metagenomes")
+    (description
+     "This package is an integrated pipeline for large-scale phylogenetic
+profiling of genomes and metagenomes.  PhyloPhlAn is an accurate, rapid, and
+easy-to-use method for large-scale microbial genome characterization and
+phylogenetic analysis at multiple levels of resolution.  This software package
+can assign both genomes and @acronym{MAGs, metagenome-assembled genomes} to
+@acronym{SGBs, species-level genome bins}.  PhyloPhlAn can reconstruct
+strain-level phylogenies using clade- specific maximally informative
+phylogenetic markers, and can also scale to very large phylogenies comprising
+>17,000 microbial species.")
+    (license license:expat)))
+
 (define-public python-pybedtools
   (package
     (name "python-pybedtools")
@@ -6865,6 +7164,38 @@ Values such as sequence name, sequence description, sequence quality and the
 sequence itself can be retrieved from these databases.")
     (license license:bsd-3)))
 
+(define-public python-slamdunk
+  (package
+    (name "python-slamdunk")
+    (version "0.4.3")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/t-neumann/slamdunk")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0lv3h5k2pn1pz35kz0wk5xmricxzy8qscs2y7nwh0k6x4pn0m0s5"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     (list python-biopython
+           python-intervaltree
+           python-joblib
+           python-pandas
+           python-pybedtools
+           python-pysam))
+    (native-inputs
+     (list python-cython python-pytest))
+    (home-page "https://t-neumann.github.io/slamdunk/")
+    (synopsis "Streamline SLAM-seq analysis with high sensitivity")
+    (description "SlamDunk is a fully automated tool for automated, robust,
+scalable and reproducible SLAMseq data analysis.  Diagnostic plotting features
+and a MultiQC plugin will make your SLAMseq data ready for immediate QA and
+interpretation.")
+    (license license:agpl3+)))
+
 (define-public python-taggd
   (package
     (name "python-taggd")
@@ -7721,6 +8052,36 @@ sequence.")
 3D perspective axes, 3D perspective annotations, and wireframe plots.")
       (license license:gpl3+))))
 
+(define-public r-ggsankey
+  (let ((commit "be08dd0f86eaee9f9ff9e7ff95d47930660a3c36")
+        (revision "1"))
+    (package
+      (name "r-ggsankey")
+      (version (git-version "0.0.99999" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/davidsjoberg/ggsankey")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0acpmydqqc91pq5p9wpkpmgqp3nhiljabd7d3i00kwhjxgm2bvba"))))
+      (properties `((upstream-name . "ggsankey")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-dplyr
+                               r-ggplot2
+                               r-magrittr
+                               r-purrr
+                               r-stringr
+                               r-tidyr))
+      (home-page "https://github.com/davidsjoberg/ggsankey")
+      (synopsis "Sankey, Alluvial and Sankey bump plots")
+      (description
+       "This package provides a package that makes it easy to implement
+sankey, alluvial and sankey bump plots in @code{ggplot2}.")
+      (license license:expat))))
+
 (define-public r-gutils
   (let ((commit "10e36c7b580aacb2d952140a3fdd82418aaddea6")
         (revision "1"))
@@ -7943,6 +8304,93 @@ tasks.")
 Pore-C concatemers.")
       (license license:gpl3))))
 
+(define-public r-doubletcollection
+  (let ((commit "c0d62f1853942ee6a087eaf7b000d9e4261e2dfd")
+        (revision "1"))
+    (package
+      (name "r-doubletcollection")
+      (version (git-version "1.1.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/xnnba1984/DoubletCollection")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "02cvibyc2nwc4037ramm5cskjwyrb9ib9hkrfhmvhbslkn5ixz1v"))))
+      (properties `((upstream-name . "DoubletCollection")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-biocgenerics
+                               r-doubletfinder
+                               r-gam
+                               r-ggplot2
+                               r-ggthemes
+                               r-mast
+                               r-mclust
+                               r-prroc
+                               r-reticulate
+                               r-scales
+                               r-scdblfinder
+                               r-scds
+                               r-seurat
+                               r-singlecellexperiment
+                               r-slingshot
+                               r-summarizedexperiment))
+      (home-page "https://github.com/xnnba1984/DoubletCollection")
+      (synopsis "Tool for finding doublets in scRNA-seq data")
+      (description
+       "This is an R package that integrates the installation of
+doublet-detection methods.  In addition, this tool is used for execution and
+benchmark of those eight mentioned methods.")
+      (license license:gpl3+))))
+
+(define-public r-psupertime
+  (let ((commit "73825a28d3bd9bc881c15ee0c4c218eec1c9c207")
+        (revision "1"))
+    (package
+      (name "r-psupertime")
+      (version (git-version "0.2.6" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/wmacnair/psupertime")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "00h1r3ffz6m9dwcgkvyki8405b059qn6mnjsd8d76a1rabaf2vfh"))))
+      (properties `((upstream-name . "psupertime")))
+      (build-system r-build-system)
+      (propagated-inputs
+       (list r-cowplot
+             r-data-table
+             r-fastcluster
+             r-forcats
+             r-ggplot2
+             r-glmnet
+             r-knitr
+             r-matrix
+             r-rcolorbrewer
+             r-scales
+             r-scran
+             r-singlecellexperiment
+             r-stringr
+             r-summarizedexperiment
+             r-topgo))
+      (native-inputs (list r-knitr))
+      (home-page "https://github.com/wmacnair/psupertime")
+      (synopsis
+       "Psupertime is supervised pseudotime for single cell RNAseq data")
+      (description
+       "Psupertime is supervised pseudotime for single cell RNAseq data.  It
+uses single cell RNAseq data, where the cells have a known ordering.  This
+ordering helps to identify a small number of genes which place cells in that
+known order.  It can be used for discovery of relevant genes, for
+identification of subpopulations, and characterization of further unknown or
+differently labelled data.")
+      (license license:gpl3))))
+
 (define-public r-pando
   (package
     (name "r-pando")
@@ -8132,6 +8580,38 @@ clustering analysis, differential analysis, motif inference and exploration of
 single cell ATAC-seq sequencing data.")
     (license license:gpl3)))
 
+(define-public r-tsis
+  (let ((commit "24460298fbe1d26e4da390f6e4f3d4d9d62334dc")
+        (revision "1"))
+    (package
+      (name "r-tsis")
+      (version (git-version "0.2.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/wyguo/TSIS")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "17c8i25iwhldvs3c51m0wny40iffm8szzijalpwrxhzbv0xa94rb"))))
+      (properties `((upstream-name . "TSIS")))
+      (build-system r-build-system)
+      (native-inputs (list r-knitr))
+      (home-page "https://github.com/wyguo/TSIS")
+      (synopsis "Time-series isoform switch of alternative splicing")
+      (description
+       "TSIS is used for detecting transcript isoform switches in time-series
+data.  Transcript isoform switches occur when a pair of alternatively spliced
+isoforms reverse the order of their relative expression levels.  TSIS
+characterizes the transcript switch by defining the isoform switch time-points
+for any pair of transcript isoforms within a gene.  In addition, this tool
+describes the switch using five different features or metrics.  Also it
+filters the results with user’s specifications and visualizes the results
+using different plots for the user to examine further details of the
+switches.")
+      (license license:gpl3))))
+
 (define-public r-umi4cpackage
   (let ((commit "88b07d896a137418ba6c31c2474b9dbe1d86fc20")
         (revision "1"))
@@ -16689,20 +17169,20 @@ translates between different variant encodings.")
       (license license:asl2.0))))
 
 (define-public r-signac
-  (let ((commit "458e647b503c3472b0b98c0aeca934f452e039ee")
+  (let ((commit "af4142724b72574d957f7fe3d422ed5828ec3ad0")
-        (revision "2"))
+        (revision "1"))
     (package
       (name "r-signac")
-      (version (git-version "1.6.0" revision commit))
+      (version (git-version "1.9.0" revision commit))
-      (source
+      (source (origin
-       (origin
+                (method git-fetch)
-         (method git-fetch)
+                (uri (git-reference
-         (uri (git-reference
+                      (url "https://github.com/timoast/signac/")
-               (url "https://github.com/timoast/signac/")
+                      (commit commit)))
-               (commit commit)))
+                (file-name (git-file-name name version))
-         (file-name (git-file-name name version))
+                (sha256
-         (sha256
+                 (base32
-          (base32 "1hgwpgighkvfkai80n4d2252s4sdpa4faag4ncdiylicl5wa7lbj"))))
+                  "0ps0lp1dcy20r6lakil6ih81m04r0s6fnirvfjf01sfs0gsyddww"))))
       (properties `((upstream-name . "Signac")))
       (build-system r-build-system)
       (inputs (list zlib))
@@ -16715,27 +17195,22 @@ translates between different variant encodings.")
              r-future-apply
              r-genomeinfodb
              r-genomicranges
-             r-ggforce
              r-ggplot2
-             r-ggrepel
-             r-ggseqlogo
              r-iranges
              r-irlba
-             r-lsa
              r-matrix
              r-patchwork
              r-pbapply
-             r-qlcmatrix
              r-rcpp
              r-rcpproll
              r-rsamtools
              r-s4vectors
              r-scales
-             r-seurat
              r-seuratobject
              r-stringi
              r-tidyr
-             r-tidyselect))
+             r-tidyselect
+             r-vctrs))
       (home-page "https://github.com/timoast/signac/")
       (synopsis "Analysis of single-cell chromatin data")
       (description
@@ -17503,21 +17978,20 @@ Genomics with R\".")
       (license license:gpl3))))
 
 (define-public r-cytonorm
-  (let ((commit "e4b9d343ee65db3c422800f1db3e77c25abde987")
+  (let ((commit "166f9ff3d692278241018c2846cb4f86ab16065b")
         (revision "1"))
     (package
       (name "r-cytonorm")
-      (version (git-version "0.0.7" revision commit))
+      (version (git-version "0.0.10" revision commit))
-      (source
+      (source (origin
-       (origin
+                (method git-fetch)
-         (method git-fetch)
+                (uri (git-reference
-         (uri (git-reference
+                      (url "https://github.com/saeyslab/CytoNorm")
-               (url "https://github.com/saeyslab/CytoNorm")
+                      (commit commit)))
-               (commit commit)))
+                (file-name (git-file-name name version))
-         (file-name (git-file-name name version))
+                (sha256
-         (sha256
+                 (base32
-          (base32
+                  "0vbqy3b26j1zqmwgqx59kkn9pm2m0qwlcppskvahrxcwrj6m1s5y"))))
-           "0h2rdy15i4zymd4dv60n5w0frbsdbmzpv99dgm0l2dn041qv7fah"))))
       (properties `((upstream-name . "CytoNorm")))
       (build-system r-build-system)
       (propagated-inputs
@@ -17567,6 +18041,28 @@ interest.")
       ;; Any version of the GPL
       (license license:gpl3+))))
 
+(define-public python-vireosnp
+  (package
+    (name "python-vireosnp")
+    (version "0.5.7")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "vireoSNP" version))
+              (sha256
+               (base32
+                "02ybhzivsxwnb1axlgbs63wni1j27xajnkl4jw1ps5vmsz2l4b0d"))))
+    (build-system python-build-system)
+    (propagated-inputs (list python-matplotlib python-numpy python-scipy))
+    (home-page "https://github.com/huangyh09/vireoSNP")
+    (synopsis "Deconvolution based on SNP for multiplexed scRNA-seq data")
+    (description
+     "This package provides a deconvolution based on Single Nucleotide
+Position (SNP) for multiplexed scRNA-seq data.  The name vireo stand for
+Variational Inference for Reconstructing Ensemble Origin by expressed SNPs in
+multiplexed scRNA-seq data and follows the clone identification from
+single-cell data named @url{https://github.com/PMBio/cardelino, cardelino}.")
+    (license license:asl2.0)))
+
 (define-public ccwl
   (package
     (name "ccwl")
@@ -17804,7 +18300,7 @@ module capable of computing base-level alignments for very large sequences.")
 (define-public gdcm
   (package
     (name "gdcm")
-    (version "2.8.9")
+    (version "3.0.20")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -17814,19 +18310,36 @@ module capable of computing base-level alignments for very large sequences.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1j8mjnxcwn2xvzhf25lv4dbawxbgc4im1crh8081li7i4mbwswaj"))))
+                "1rf0p7dnakjry0fa6ax1h762bn0l5n6ibfdxn077mjvwgpqan51l"))))
     (build-system cmake-build-system)
+    (outputs '("out" "doc"))
     (arguments
      (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'build 'set-HOME
+            ;; The build spams ‘Fontconfig error: No writable cache
+            ;; directories’ in a seemingly endless loop otherwise.
+            (lambda _
+              (setenv "HOME" "/tmp"))))
       #:configure-flags
       #~(list "-DGDCM_BUILD_TESTING=true"
               (string-append "-DCMAKE_CTEST_ARGUMENTS=-E;"
                              "'TestFileMetaInformation"
                              "|TestElement2"
                              "|TestSCUValidation"
+                             "|TestWriter"
+                             "|TestAnonymizer4"
+                             "|TestPrinter1"
                              "|TestEcho"
-                             "|TestFind'"))))
+                             "|TestFind'")
-    (home-page "http://gdcm.sourceforge.net/wiki/index.php/Main_Page")
+              "-DGDCM_DOCUMENTATION:BOOL=ON"
+              "-DGDCM_PDF_DOCUMENTATION:BOOL=OFF"
+              (string-append "-DGDCM_INSTALL_DOC_DIR="
+                             #$output:doc "/share/doc/" #$name)
+              "-DGDCM_BUILD_DOCBOOK_MANPAGES:BOOL=OFF"))) ; TODO: need ‘xsl-ns’
+    (native-inputs (list doxygen graphviz))
+    (home-page "https://gdcm.sourceforge.net/wiki/index.php/Main_Page")
     (synopsis "Grassroots DICOM library")
     (description
      "Grassroots DICOM (GDCM) is an implementation of the DICOM standard
@@ -17835,7 +18348,7 @@ directly.  GDCM includes a file format definition and a network communications
 protocol, both of which should be extended to provide a full set of tools for
 a researcher or small medical imaging vendor to interface with an existing
 medical database.")
-    (license license:bsd-2)))
+    (license license:bsd-3)))
 
 (define-public wiggletools
   (package

gnu/packages/bootloaders.scm

@@ -652,9 +652,7 @@ tree binary files.  These are board description files used by Linux and BSD.")
                      %u-boot-sifive-prevent-relocating-initrd-fdt
                      %u-boot-rk3399-enable-emmc-phy-patch
                      (search-patch "u-boot-infodocs-target.patch")
-                     (search-patch "u-boot-patman-fix-help.patch")
+                     (search-patch "u-boot-patman-guix-integration.patch")))
-                     (search-patch "u-boot-patman-local-conf.patch")
-                     (search-patch "u-boot-patman-get-maintainer.patch")))
               (method url-fetch)
               (uri (string-append
                     "https://ftp.denx.de/pub/u-boot/"
@@ -664,8 +662,7 @@ tree binary files.  These are board description files used by Linux and BSD.")
                 "1y5x8vxdgsqdqlsvq01mn8lmw53fqairkhvhhjx83hjva0m4id2h"))))
     (build-system  gnu-build-system)
     (native-inputs
-     (list bc
+     (list bison
-           bison
            dtc
            gnutls
            flex
@@ -674,9 +671,6 @@ tree binary files.  These are board description files used by Linux and BSD.")
            perl
            pkg-config                   ;for 'make menuconfig'
            python
-           python-coverage
-           python-pycryptodomex
-           python-pytest
            swig
            (list util-linux "lib")))
     (home-page "https://www.denx.de/wiki/U-Boot/")
@@ -727,7 +721,7 @@ Info manual.")))
     (name "u-boot-tools")
     (native-inputs
      (modify-inputs (package-native-inputs u-boot)
-       (prepend sdl2)))
+       (prepend python-coverage python-pycryptodomex python-pytest sdl2)))
     (arguments
      `(#:make-flags '("HOSTCC=gcc")
        #:test-target "tcheck"
@@ -862,14 +856,18 @@ def test_ctrl_c"))
                                      defconfig
                                      configs
                                      name-suffix
-                                     append-description)
+                                     append-description
+                                     (u-boot u-boot))
   "Return a U-Boot package for BOARD cross-compiled for TRIPLET with the
 optional DEFCONFIG file and optional configuration changes from CONFIGS.
-NAME-SUFFIX is appended to the package name, while APPEND-DESCRIPTION is
+TRIPLET may also be set to #f to disable cross-compilation.  NAME-SUFFIX is
-appended to the package description."
+appended to the package name, while APPEND-DESCRIPTION is appended to the
-  (let ((same-arch? (lambda ()
+package description.  U-BOOT can be used when a fork or a different version of
-                      (string=? (%current-system)
+U-Boot must be used."
-                                (gnu-triplet->nix-system triplet)))))
+  (let ((native-build? (lambda ()
+                         (or (not triplet) ;disable cross-compilation
+                             (string=? (%current-system)
+                                       (gnu-triplet->nix-system triplet))))))
     (package
       (inherit u-boot)
       (name (string-append "u-boot-"
@@ -880,95 +878,98 @@ appended to the package description."
                        (string-append (package-description u-boot)
                                       "\n\n" append-description)
                        (package-description u-boot)))
-      (native-inputs
+      (build-system gnu-build-system)
-       `(,@(if (not (same-arch?))
-               `(("cross-gcc" ,(cross-gcc triplet))
-                 ("cross-binutils" ,(cross-binutils triplet)))
-               `())
-         ,@(package-native-inputs u-boot)))
       (arguments
-       `(#:modules ((ice-9 ftw)
+       (substitute-keyword-arguments (package-arguments u-boot)
-                    (srfi srfi-1)
+         ((#:target _ #f)
-                    (guix build gnu-build-system)
+          (and (not (native-build?)) triplet))
-                    (guix build kconfig)
+         ((#:modules modules '())
-                    (guix build utils))
+          `((ice-9 ftw)
-         #:imported-modules (,@%gnu-build-system-modules
+            (srfi srfi-1)
-                             (guix build kconfig))
+            (guix build gnu-build-system)
-         #:test-target "test"
+            (guix build kconfig)
-         #:make-flags
+            (guix build utils)
-         (list "HOSTCC=gcc"
+            ,@modules))
-               "KBUILD_VERBOSE=1"
+         ((#:imported-modules imported-modules '())
-               ,@(if (not (same-arch?))
+          `((guix build kconfig)
-                     `((string-append "CROSS_COMPILE=" ,triplet "-"))
+            ,@%gnu-build-system-modules
-                     '()))
+            ,@imported-modules))
-         #:phases
+         ((#:test-target _ "test")
-         (modify-phases %standard-phases
+          "test")
-           (replace 'configure
+         ((#:make-flags make-flags '())
-             (lambda* (#:key outputs make-flags #:allow-other-keys)
+          #~(list "HOSTCC=gcc"
-               (let* ((config-name (string-append ,board "_defconfig"))
+                  "KBUILD_VERBOSE=1"
-                      (config-file (string-append "configs/" config-name))
+                  #$@(if (not (native-build?))
-                      (defconfig ,defconfig)
+                         (list (string-append "CROSS_COMPILE=" triplet "-"))
-                      (configs ',configs))
+                         '())
-                 (when defconfig
+                  #$@make-flags))
-                   ;; Replace the board-specific defconfig with the given one.
+         ((#:phases phases '%standard-phases)
-                   (copy-file defconfig config-file))
+          #~(modify-phases #$phases
-                 (if (file-exists? config-file)
+              (replace 'configure
-                     (begin
+                (lambda* (#:key make-flags #:allow-other-keys)
-                       (when configs
+                  (let* ((config-name (string-append #$board "_defconfig"))
-                         (modify-defconfig config-file configs))
+                         (config-file (string-append "configs/" config-name))
-                       (apply invoke "make" `(,@make-flags ,config-name))
+                         (defconfig #$defconfig)
-                       (verify-config ".config" config-file))
+                         (configs '#$configs))
-                     (begin
+                    (when defconfig
-                       (display "invalid board name; valid board names are:"
+                      ;; Replace the board-specific defconfig with the given
-                                (current-error-port))
+                      ;; one.
-                       (let ((suffix-len (string-length "_defconfig"))
+                      (copy-file defconfig config-file))
-                             (entries (scandir "configs")))
+                    (if (file-exists? config-file)
-                         (for-each (lambda (file-name)
+                        (begin
-                                     (when (string-suffix? "_defconfig" file-name)
+                          (when configs
-                                       (format (current-error-port)
+                            (modify-defconfig config-file configs))
-                                               "- ~A\n"
+                          (apply invoke "make" `(,@make-flags ,config-name))
-                                               (string-drop-right file-name
+                          (verify-config ".config" config-file))
-                                                                  suffix-len))))
+                        (begin
-                                   (sort entries string-ci<)))
+                          (display "invalid board name; valid board names are:"
-                       (error "invalid boardname ~s" ,board))))))
+                                   (current-error-port))
-           (add-after 'configure 'disable-tools-libcrypto
+                          (let ((suffix-len (string-length "_defconfig"))
-             ;; Disable libcrypto due to GPL and OpenSSL license
+                                (entries (scandir "configs")))
-             ;; incompatibilities
+                            (for-each (lambda (file-name)
-             (lambda _
+                                        (when (string-suffix? "_defconfig"
-               (substitute* ".config"
+                                                              file-name)
-                 (("CONFIG_TOOLS_LIBCRYPTO=.*$") "CONFIG_TOOLS_LIBCRYPTO=n"))))
+                                          (format (current-error-port)
-           (replace 'install
+                                                  "- ~A\n"
-             (lambda* (#:key outputs #:allow-other-keys)
+                                                  (string-drop-right
-               (let* ((out (assoc-ref outputs "out"))
+                                                   file-name suffix-len))))
-                      (libexec (string-append out "/libexec"))
+                                      (sort entries string-ci<)))
-                      (uboot-files (append
+                          (error "invalid boardname ~s" #$board))))))
-                                    (remove
+              (add-after 'configure 'disable-tools-libcrypto
-                                     ;; Those would not be reproducible
+                ;; Disable libcrypto due to GPL and OpenSSL license
-                                     ;; because of the randomness used
+                ;; incompatibilities
-                                     ;; to produce them.
+                (lambda _
-                                     ;; It's expected that the user will
+                  (substitute* ".config"
-                                     ;; use u-boot-tools to generate them
+                    (("CONFIG_TOOLS_LIBCRYPTO=.*$")
-                                     ;; instead.
+                     "CONFIG_TOOLS_LIBCRYPTO=n"))))
-                                     (lambda (name)
+              (replace 'install
-                                       (string-suffix?
+                (lambda _
-                                        "sunxi-spl-with-ecc.bin"
+                  (let ((libexec (string-append #$output "/libexec"))
-                                        name))
+                        (uboot-files
-                                     (find-files "." ".*\\.(bin|efi|img|spl|itb|dtb|rksd)$"))
+                         (append
-                                    (find-files "." "^(MLO|SPL)$"))))
+                          (remove
-                 (mkdir-p libexec)
+                           ;; Those would not be reproducible
-                 (install-file ".config" libexec)
+                           ;; because of the randomness used to
-                 ;; Useful for "qemu -kernel".
+                           ;; produce them.  It's expected that the
-                 (install-file "u-boot" libexec)
+                           ;; user will use u-boot-tools to generate
-                 (for-each
+                           ;; them instead.
-                  (lambda (file)
+                           (lambda (name)
-                    (let ((target-file (string-append libexec "/" file)))
+                             (string-suffix?
-                      (mkdir-p (dirname target-file))
+                              "sunxi-spl-with-ecc.bin"
-                      (copy-file file target-file)))
+                              name))
-                  uboot-files)
+                           (find-files "."
-                 #t)))))))))
+                                       ".*\\.(bin|efi|img|imx|spl|itb|dtb|rksd)$"))
-
+                          (find-files "." "^(MLO|SPL)$"))))
-(define-public u-boot-malta
+                    (mkdir-p libexec)
-  (make-u-boot-package "malta" "mips64el-linux-gnuabi64"))
+                    (install-file ".config" libexec)
+                    ;; Useful for "qemu -kernel".
+                    (install-file "u-boot" libexec)
+                    (for-each
+                     (lambda (file)
+                       (let ((target-file (string-append libexec "/" file)))
+                         (mkdir-p (dirname target-file))
+                         (copy-file file target-file)))
+                     uboot-files)))))))))))
 
 (define-public u-boot-am335x-boneblack
   (let ((base (make-u-boot-package
@@ -1000,17 +1001,13 @@ removed so that it fits within common partitioning schemes.")))
       (arguments
        (substitute-keyword-arguments (package-arguments base)
          ((#:phases phases)
-          `(modify-phases ,phases
+          #~(modify-phases #$phases
-             (add-after 'unpack 'set-environment
+              (add-after 'unpack 'set-environment
-               (lambda* (#:key native-inputs inputs #:allow-other-keys)
+                (lambda* (#:key native-inputs inputs #:allow-other-keys)
-                 (let ((bl31
+                  (setenv "BL31" (search-input-file inputs "bl31.bin"))))))))
-                        (string-append
+      (inputs
-                         (assoc-ref (or native-inputs inputs) "firmware")
+       (modify-inputs (package-inputs base)
-                         "/bl31.bin")))
+         (append arm-trusted-firmware-sun50i-a64))))))
-                   (setenv "BL31" bl31))))))))
-      (native-inputs
-       `(("firmware" ,arm-trusted-firmware-sun50i-a64)
-         ,@(package-native-inputs base))))))
 
 (define-public u-boot-pine64-plus
   (make-u-boot-sunxi64-package "pine64_plus" "aarch64-linux-gnu"))
@@ -1094,17 +1091,16 @@ partition."))
       (arguments
        (substitute-keyword-arguments (package-arguments base)
          ((#:phases phases)
-          `(modify-phases ,phases
+          #~(modify-phases #$phases
-             (add-after 'unpack 'set-environment
+              (add-after 'unpack 'set-environment
-               (lambda* (#:key inputs #:allow-other-keys)
+                (lambda* (#:key inputs #:allow-other-keys)
-                 (setenv "BL31"
+                  (setenv "BL31" (search-input-file inputs "/bl31.elf"))))
-                         (search-input-file inputs "/bl31.elf"))))
+              ;; Phases do not succeed on the bl31 ELF.
-             ;; Phases do not succeed on the bl31 ELF.
+              (delete 'strip)
-             (delete 'strip)
+              (delete 'validate-runpath)))))
-             (delete 'validate-runpath)))))
+      (inputs
-      (native-inputs
+       (modify-inputs (package-native-inputs base)
-       `(("firmware" ,arm-trusted-firmware-rk3399)
+         (append arm-trusted-firmware-rk3399))))))
-         ,@(package-native-inputs base))))))
 
 (define-public u-boot-qemu-riscv64
   (make-u-boot-package "qemu-riscv64" "riscv64-linux-gnu"))
@@ -1112,6 +1108,46 @@ partition."))
 (define-public u-boot-qemu-riscv64-smode
   (make-u-boot-package "qemu-riscv64_smode" "riscv64-linux-gnu"))
 
+(define-public u-boot-sandbox
+  (let ((base (make-u-boot-package
+               "sandbox" #f             ;build for the native system
+               ;; Disable CONFIG_TOOLS_LIBCRYPTO, CONFIG_FIT_SIGNATURE and
+               ;; CONFIG_FIT_CIPHER and their selectors as these features
+               ;; require OpenSSL, which is incompatible with the GPLv2-only
+               ;; parts of U-boot.  The options below replicate the changes
+               ;; that disabling the above features in 'make menuconfig' then
+               ;; refreshing the defconfig with 'make savedefconfig' would do.
+               #:configs (list "# CONFIG_FIT_RSASSA_PSS is not set"
+                               "# CONFIG_FIT_CIPHER is not set"
+                               "# CONFIG_LEGACY_IMAGE_FORMAT is not set"
+                               "# CONFIG_IMAGE_PRE_LOAD is not set"
+                               "# CONFIG_IMAGE_PRE_LOAD_SIG is not set"
+                               "# CONFIG_CMD_BOOTM_PRE_LOAD is not set"
+                               "CONFIG_RSA=y"
+                               "# CONFIG_EFI_SECURE_BOOT is not set"
+                               "# CONFIG_TOOLS_LIBCRYPTO is not set")
+               #:append-description
+               "The sandbox configuration of U-Boot provides a
+@command{u-boot} command that runs as a normal user space application.  It can
+be used to test the functionality of U-Boot interactively without having to
+deploy to an actual target device.  @xref{Sandbox<6>,,,u-boot, The U-Boot
+Documentation} for more information (for example by running @samp{info
+\"(u-boot) Sandbox<6>\"}).")))
+    (package
+      (inherit base)
+      (arguments
+       (substitute-keyword-arguments (package-arguments base)
+         ((#:phases phases '%standard-phases)
+          #~(modify-phases #$phases
+              (add-after 'install 'symlink-u-boot-command
+                (lambda* (#:key outputs #:allow-other-keys)
+                  ;; For ease of discovery.
+                  (mkdir (string-append #$output "/bin"))
+                  (symlink (search-input-file outputs "libexec/u-boot")
+                           (string-append #$output "/bin/u-boot"))))))))
+      (inputs (modify-inputs (package-inputs base)
+                (append sdl2))))))
+
 (define-public u-boot-sifive-unleashed
   (make-u-boot-package "sifive_unleashed" "riscv64-linux-gnu"))
 
@@ -1122,15 +1158,14 @@ partition."))
       (arguments
        (substitute-keyword-arguments (package-arguments base)
          ((#:phases phases)
-          `(modify-phases ,phases
+          #~(modify-phases #$phases
-             (add-after 'unpack 'set-environment
+              (add-after 'unpack 'set-environment
-               (lambda* (#:key inputs #:allow-other-keys)
+                (lambda* (#:key inputs #:allow-other-keys)
-                 (let ((opensbi (string-append (assoc-ref inputs "firmware")
+                  (setenv "OPENSBI" (search-input-file inputs
-                                               "/fw_dynamic.bin")))
+                                                       "fw_dynamic.bin"))))))))
-                   (setenv "OPENSBI" opensbi))))))))
       (inputs
-       `(("firmware" ,opensbi-generic)
+       (modify-inputs (package-inputs base)
-         ,@(package-inputs base))))))
+         (append opensbi-generic))))))
 
 (define-public u-boot-rock64-rk3328
   (let ((base (make-u-boot-package "rock64-rk3328" "aarch64-linux-gnu")))
@@ -1139,14 +1174,13 @@ partition."))
       (arguments
        (substitute-keyword-arguments (package-arguments base)
          ((#:phases phases)
-          `(modify-phases ,phases
+          #~(modify-phases #$phases
-             (add-after 'unpack 'set-environment
+              (add-after 'unpack 'set-environment
-               (lambda* (#:key inputs #:allow-other-keys)
+                (lambda* (#:key native-inputs inputs #:allow-other-keys)
-                 (let ((bl31 (search-input-file inputs "/bl31.elf")))
+                  (setenv "BL31 "(search-input-file inputs "bl31.elf"))))))))
-                   (setenv "BL31" bl31))))))))
+      (inputs
-      (native-inputs
+       (modify-inputs (package-inputs base)
-       `(("firmware" ,arm-trusted-firmware-rk3328)
+         (append arm-trusted-firmware-rk3328))))))
-         ,@(package-native-inputs base))))))
 
 (define-public u-boot-firefly-rk3399
   (let ((base (make-u-boot-package "firefly-rk3399" "aarch64-linux-gnu")))
@@ -1155,16 +1189,16 @@ partition."))
       (arguments
        (substitute-keyword-arguments (package-arguments base)
          ((#:phases phases)
-          `(modify-phases ,phases
+          #~(modify-phases #$phases
-             (add-after 'unpack 'set-environment
+              (add-after 'unpack 'set-environment
-               (lambda* (#:key inputs #:allow-other-keys)
+                (lambda* (#:key native-inputs inputs #:allow-other-keys)
-                 (setenv "BL31" (search-input-file inputs "/bl31.elf"))))
+                  (setenv "BL31" (search-input-file inputs "bl31.elf"))))
-             ;; Phases do not succeed on the bl31 ELF.
+              ;; Phases do not succeed on the bl31 ELF.
-             (delete 'strip)
+              (delete 'strip)
-             (delete 'validate-runpath)))))
+              (delete 'validate-runpath)))))
-      (native-inputs
+      (inputs
-       `(("firmware" ,arm-trusted-firmware-rk3399)
+       (modify-inputs (package-inputs base)
-         ,@(package-native-inputs base))))))
+         (append arm-trusted-firmware-rk3399))))))
 
 (define-public u-boot-rockpro64-rk3399
   (let ((base (make-u-boot-package "rockpro64-rk3399" "aarch64-linux-gnu"
@@ -1181,37 +1215,36 @@ partition."))
       (arguments
        (substitute-keyword-arguments (package-arguments base)
          ((#:phases phases)
-          `(modify-phases ,phases
+          #~(modify-phases #$phases
-             (add-after 'unpack 'set-environment
+              (add-after 'unpack 'set-environment
-               (lambda* (#:key inputs #:allow-other-keys)
+                (lambda* (#:key inputs #:allow-other-keys)
-                 (setenv "BL31"
+                  (setenv "BL31" (search-input-file inputs "/bl31.elf"))))
-                         (search-input-file inputs "/bl31.elf"))))
+              (add-after 'unpack 'patch-header
-             (add-after 'unpack 'patch-header
+                (lambda _
-               (lambda _
+                  (substitute* "include/config_distro_bootcmd.h"
-                 (substitute* "include/config_distro_bootcmd.h"
+                    (("\"scsi_need_init=false")
-                   (("\"scsi_need_init=false")
+                     "\"setenv scsi_need_init false")
-                    "\"setenv scsi_need_init false")
+                    (("#define BOOTENV_SET_SCSI_NEED_INIT \"scsi_need_init=;")
-                   (("#define BOOTENV_SET_SCSI_NEED_INIT \"scsi_need_init=;")
+                     "#define BOOTENV_SET_SCSI_NEED_INIT \"setenv scsi_need_init;"))
-                    "#define BOOTENV_SET_SCSI_NEED_INIT \"setenv scsi_need_init;"))
+                  (substitute* "include/configs/rockchip-common.h"
-                 (substitute* "include/configs/rockchip-common.h"
+                    (("#define BOOT_TARGET_DEVICES\\(func\\)")
-                   (("#define BOOT_TARGET_DEVICES\\(func\\)")
+                     "
-                    "
 #if CONFIG_IS_ENABLED(CMD_SCSI)
        #define BOOT_TARGET_SCSI(func) func(SCSI, scsi, 0)
 #else
        #define BOOT_TARGET_SCSI(func)
 #endif
 #define BOOT_TARGET_DEVICES(func)")
-                   (("BOOT_TARGET_NVME\\(func\\) \\\\")
+                    (("BOOT_TARGET_NVME\\(func\\) \\\\")
-                    "\
+                     "\
 BOOT_TARGET_NVME(func) \\
        BOOT_TARGET_SCSI(func) \\"))))
-             ;; Phases do not succeed on the bl31 ELF.
+              ;; Phases do not succeed on the bl31 ELF.
-             (delete 'strip)
+              (delete 'strip)
-             (delete 'validate-runpath)))))
+              (delete 'validate-runpath)))))
-      (native-inputs
+      (inputs
-       `(("firmware" ,arm-trusted-firmware-rk3399)
+       (modify-inputs (package-inputs base)
-         ,@(package-native-inputs base))))))
+         (append arm-trusted-firmware-rk3399))))))
 
 (define-public u-boot-pinebook-pro-rk3399
   (let ((base (make-u-boot-package "pinebook-pro-rk3399" "aarch64-linux-gnu")))
@@ -1220,17 +1253,16 @@ BOOT_TARGET_NVME(func) \\
       (arguments
        (substitute-keyword-arguments (package-arguments base)
          ((#:phases phases)
-          `(modify-phases ,phases
+          #~(modify-phases #$phases
-             (add-after 'unpack 'set-environment
+              (add-after 'unpack 'set-environment
-               (lambda* (#:key inputs #:allow-other-keys)
+                (lambda* (#:key native-inputs inputs #:allow-other-keys)
-                 (setenv "BL31"
+                  (setenv "BL31" (search-input-file inputs "bl31.elf"))))
-                         (search-input-file inputs "/bl31.elf"))))
+              ;; Phases do not succeed on the bl31 ELF.
-             ;; Phases do not succeed on the bl31 ELF.
+              (delete 'strip)
-             (delete 'strip)
+              (delete 'validate-runpath)))))
-             (delete 'validate-runpath)))))
+      (inputs
-      (native-inputs
+       (modify-inputs (package-inputs base)
-       `(("firmware" ,arm-trusted-firmware-rk3399)
+         (append arm-trusted-firmware-rk3399))))))
-         ,@(package-native-inputs base))))))
 
 (define*-public (make-u-boot-bin-package u-boot-package
                                          #:key
@@ -1344,6 +1376,158 @@ grub-efi-netboot-removable-bootloader.")
 (define-public u-boot-rpi-arm64-efi-bin
   (make-u-boot-bin-package u-boot-rpi-arm64-efi))
 
+(define u-boot-ts-mx6
+  ;; There is no release; use the latest commit of the
+  ;; 'imx_v2015.04_3.14.52_1.1.0_ga' branch.
+  (let ((revision "0")
+        (commit "08809160fbc60d6e949fa9d37d9a41aab8fef742"))
+    (package
+      (inherit u-boot)
+      (name "u-boot-ts-mx6")
+      (version (git-version "2015.04_3" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/embeddedTS/u-boot-imx")
+                      (commit commit)))
+                (file-name (git-file-name "u-boot-imx-ts" version))
+                (sha256
+                 (base32
+                  "01mja33351hkcs59rmfvppqlxqw4rh9gng7a7hx2cfspqwh2y6kr"))))
+      (arguments
+       (substitute-keyword-arguments (package-arguments u-boot)
+         ((#:phases phases '%standard-phases)
+          #~(modify-phases #$phases
+              (add-after 'unpack 'patch-u-boot
+                (lambda _
+                  (substitute* (find-files "include/configs" "^ts[0-9]{4}\\.h$")
+                    ;; Default to boot a standard zImage instead of a uImage.
+                    (("/boot/uImage")
+                     "/boot/zImage")
+                    (("uimage")
+                     "zimage")
+                    (("bootm \\$\\{loadaddr}")
+                     "bootz ${loadaddr}")
+                    ;; This reference DTB is not available in mainline.
+                    (("ts7970-revf.dtb")
+                     "ts7970.dtb")
+                    ;; Enable support for DISTRO_DEFAULTS, which enables to
+                    ;; use 'sysboot' to boot Guix System.  Also enable
+                    ;; "standard" boot commands for dealing with discovery and
+                    ;; booting of syslinux configurations (extlinux.conf).
+
+                    ;; Disable the stock CONFIG_BOOTCOMMAND to avoid a
+                    ;; redefinition error.
+                    (("CONFIG_BOOTCOMMAND")
+                     "CONFIG_BOOTCOMMAND_DISABLED")
+                    (("CONFIG_BOOTDELAY")
+                     "CONFIG_BOOTDELAY_DISABLED")
+                    ;; Inspired by include/configs/embestmx6boards.h
+                    (("#define CONFIG_EXTRA_ENV_SETTINGS.*" anchor)
+                     (string-append "\
+#include <config_distro_defaults.h>
+
+#define MEM_LAYOUT_ENV_SETTINGS    \\
+\t\"bootm_size=0x10000000\\0\"     \\
+\t\"kernel_addr_r=0x10800000\\0\"  \\
+\t\"fdt_addr_r=0x18000000\\0\"     \\
+\t\"scriptaddr=0x18100000\\0\"     \\
+\t\"pxefile_addr_r=0x18200000\\0\" \\
+\t\"ramdisk_addr_r=0x18300000\\0\"
+
+#define BOOT_TARGET_DEVICES(func)  \\
+\tfunc(MMC, mmc, 0)                \\
+\tfunc(MMC, mmc, 1)                \\
+\tfunc(SATA, sata, 0)              \\
+\tfunc(USB, usb, 0)                \\
+\tfunc(PXE, pxe, na)               \\
+\tfunc(DHCP, dhcp, na)
+
+#include <config_distro_bootcmd.h>
+
+" anchor
+
+;; Sadly, the user config CONFIG_DEFAULT_FDT_FILE did not exist in that older
+;; U-Boot.  A placeholder is added here, to be substituted in each TS U-Boot
+;; board package.
+"\
+\t\"fdtfile=DEFAULT_FDT_FILE\\0\" \\
+\tMEM_LAYOUT_ENV_SETTINGS \\
+\tBOOTENV \\\n")))))
+              (add-after 'unpack 'patch-for-reproducibility
+                (lambda _
+                  ;; Substitute dynamically computed timestamps with static
+                  ;; ones.
+                  (substitute* "Makefile"
+                    (("U_BOOT_DATE \"%b %d %C%y\"")
+                     "U_BOOT_DATE \"Jan 01 1969\"")
+                    (("U_BOOT_TIME \"%T\"")
+                     "U_BOOT_TIME \"00:00:00\""))))
+              (add-before 'build 'adjust-for-gcc10
+                (lambda _
+                  (copy-file "include/linux/compiler-gcc6.h"
+                             "include/linux/compiler-gcc10.h")
+                  (substitute* "arch/arm/Makefile"
+                    (("march=armv5")
+                     "march=armv5te"))))
+              (add-after 'install 'build+install-tools
+                (lambda* (#:key make-flags #:allow-other-keys)
+                  (apply invoke "make" "tools-all" make-flags)
+                  (install-file "tools/env/fw_printenv"
+                                (string-append #$output "/bin"))
+                  (symlink (string-append #$output "/bin/fw_printenv")
+                           (string-append #$output "/bin/fw_setenv"))))))))
+      (native-inputs
+       (modify-inputs (package-native-inputs u-boot)
+         (delete "dtc"))))))            ;otherwise the build fails
+
+;;; Note: the default cross-build of this package is currently broken on
+;;; master; the fix exists as commit 6454208222d6e7760daa964b590f35ea75ffe0e5
+;;; ("build: gnu-build-system: Remove source from native inputs.") on
+;;; core-updates.
+(define-public u-boot-ts7970-q-2g-1000mhz-c
+  (let ((base
+         (make-u-boot-package "ts7970-q-2g-1000mhz-c" "arm-linux-gnueabihf"
+                              #:u-boot u-boot-ts-mx6
+                              #:append-description
+                              "This U-Boot variant is for the Technologic
+Systems TS-7970 revision C board, which includes a quad core Freescale i.MX6
+CPU and 2 GiB of RAM clocked at 1000MHz.  The binary U-Boot image to flash is
+the @file{libexec/u-boot.imx} file.  It can be used with the @file{zImage} and
+the @file{imx6q-ts7970.dtb} files provided by the
+@code{linux-libre-arm-generic} image.
+
+To flash this bootloader, write it to an SD card, then using the U-Boot serial
+console:
+@example
+mmc dev 0
+load mmc 0:1 ${loadaddr} /u-boot.imx
+sf probe
+sf erase 0 0x80000
+sf write ${loadaddr} 0x400 $filesize
+@end example
+
+The factory values of U-Boot must also be reset so that it boots using a
+zImage instead of the default uImage:
+@example
+run clearenv
+reset
+@end example
+
+For more information, refer to
+@url{https://docs.embeddedts.com/TS-7970#Update_U-Boot}.")))
+    (package
+      (inherit base)
+      (arguments
+       (substitute-keyword-arguments (package-arguments base)
+         ((#:phases phases '%standard-phases)
+          #~(modify-phases #$phases
+              (add-after 'patch-u-boot 'set-default-fdt-file
+                (lambda _
+                  (substitute* "include/configs/ts7970.h"
+                    (("DEFAULT_FDT_FILE")
+                     "imx6q-ts7970.dtb")))))))))))
+
 (define-public vboot-utils
   (package
     (name "vboot-utils")

gnu/packages/bootstrap.scm

@@ -315,7 +315,8 @@ or false to signal an error."
                                  (%current-system))))
   "Return the name of Glibc's dynamic linker for SYSTEM."
   ;; See the 'SYSDEP_KNOWN_INTERPRETER_NAMES' cpp macro in libc.
-  (let ((platform (lookup-platform-by-system system)))
+  (let ((platform (false-if-platform-not-found
+                   (lookup-platform-by-system system))))
     (cond
      ((platform? platform)
       (platform-glibc-dynamic-linker platform))

gnu/packages/build-tools.scm

@@ -32,6 +32,7 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages build-tools)
+  #:use-module (ice-9 optargs)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix utils)
   #:use-module (guix packages)
@@ -39,20 +40,28 @@
   #:use-module (guix download)
   #:use-module (guix git-download)
   #:use-module (guix build-system cmake)
+  #:use-module (guix build-system copy)
+  #:use-module (guix modules)
   #:use-module (gnu packages)
   #:use-module (gnu packages adns)
+  #:use-module (gnu packages autotools)
   #:use-module (gnu packages base)
   #:use-module (gnu packages bash)
   #:use-module (gnu packages check)
+  #:use-module (gnu packages code)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cpp)
+  #:use-module (gnu packages cppi)
   #:use-module (gnu packages elf)
+  #:use-module (gnu packages gcc)
   #:use-module (gnu packages linux)
+  #:use-module (gnu packages lisp)
   #:use-module (gnu packages logging)
   #:use-module (gnu packages lua)
   #:use-module (gnu packages ninja)
   #:use-module (gnu packages package-management)
   #:use-module (gnu packages pcre)
+  #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages pretty-print)
   #:use-module (gnu packages protobuf)
@@ -65,6 +74,7 @@
   #:use-module (gnu packages rpc)
   #:use-module (gnu packages sqlite)
   #:use-module (gnu packages tls)
+  #:use-module (gnu packages unicode)
   #:use-module (gnu packages version-control)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system python))
@@ -803,3 +813,195 @@ Build has features such as:
 same settings to multiple projects.  It supports generating projects using GNU
 Makefiles, JSON Compilation Database, and experimentally Ninja.")
       (license license:bsd-3))))
+
+(define*-public (gnulib-checkout #:key
+                                 version
+                                 (revision "1")
+                                 commit
+                                 hash)
+  "Return as a package the exact gnulib checkout."
+  (package
+    (name "gnulib")
+    (version (git-version version revision commit))
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://git.savannah.gnu.org/git/gnulib.git/")
+             (commit commit)))
+       (file-name (git-file-name name version))
+       (sha256 hash)
+       (snippet
+        (with-imported-modules (source-module-closure '((guix build utils)))
+          #~(begin
+              (use-modules (guix build utils)
+                           (ice-9 ftw)
+                           (ice-9 rdelim))
+              ;; .c, .h and .gperf files whose first line is /* DO NOT EDIT!
+              ;; GENERATED AUTOMATICALLY! */ are generated automatically based
+              ;; on the unicode database. Since we replace the unicode
+              ;; database with our own, we need to regenerate them. So, they
+              ;; are removed from the source. They are sprinkled all over the
+              ;; place unfortunately, so we can’t exclude whole directories.
+              (let ((generated-automatically?
+                     (lambda (filename . unused)
+                       (and (or (string-suffix? ".c" filename)
+                                (string-suffix? ".h" filename)
+                                (string-suffix? ".gperf" filename))
+                            (call-with-input-file filename
+                              (lambda (port)
+                                (let ((first-line (read-line port)))
+                                  (equal?
+                                   first-line
+                                   "/* DO NOT EDIT! GENERATED AUTOMATICALLY! */"))))))))
+                (for-each delete-file (find-files (getcwd) generated-automatically?)))
+              ;; Other files are copied from UCD.
+              (for-each delete-file
+                        '("tests/unigbrk/GraphemeBreakTest.txt"
+                          "tests/uninorm/NormalizationTest.txt"
+                          "tests/uniname/UnicodeData.txt"
+                          "tests/uniname/NameAliases.txt"
+                          ;; FIXME: tests/uniname/HangulSyllableNames.txt
+                          ;; seems like a UCD file but it is not distributed
+                          ;; with UCD.
+                          "tests/uniwbrk/WordBreakTest.txt")))))))
+    (build-system copy-build-system)
+    (arguments
+     (list
+      #:install-plan
+      #~'(("./gnulib-tool" "bin/")
+          ("." "src/gnulib" #:exclude-regexp ("\\.git.*")))
+      #:modules '((ice-9 match)
+                  (guix build utils)
+                  (guix build copy-build-system)
+                  ((guix build gnu-build-system) #:prefix gnu:))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'install 'check
+            (assoc-ref gnu:%standard-phases 'check))
+          (add-before 'check 'fix-tests
+            (lambda _
+              (substitute* "Makefile"
+                (("-f maint.mk syntax-check")
+                 "_gl-Makefile=yes -f maint.mk syntax-check"))
+              (invoke "git" "init")
+              (invoke "git" "config" "user.name" "Guix")
+              (invoke "git" "config" "user.email" "guix@localhost")
+              (invoke "git" "add" ".")
+              ;; Syntax checks are only run against committed files.
+              (invoke "git" "commit" "-m" "Prepare for tests.")))
+          (add-before 'check 'disable-failing-tests
+            (lambda _
+              (substitute* "cfg.mk"
+                (("local-checks-to-skip =")
+                 ;; sc_copyright_check fails because the fake commit date may
+                 ;; be later than the copyright year.
+                 "local-checks-to-skip = \\
+  sc_Wundef_boolean \\
+  sc_copyright_check \\
+  sc_file_system \\
+  sc_indent \\
+  sc_keep_gnulib_texi_files_mostly_ascii \\
+  sc_prohibit_assert_without_use \\
+  sc_prohibit_close_stream_without_use \\
+  sc_prohibit_defined_have_decl_tests \\
+  sc_prohibit_doubled_word \\
+  sc_prohibit_empty_lines_at_EOF \\
+  sc_prohibit_intprops_without_use \\
+  sc_prohibit_openat_without_use \\
+  sc_prohibit_test_minus_ao \\
+  sc_unportable_grep_q"))
+              (substitute* "Makefile"
+                (("sc_check_(sym_list|copyright)" rule)
+                 (string-append "disabled_check_" rule))
+                (("sc_cpp_indent_check")
+                 "disabled_cpp_indent_check")
+                (("sc_prefer_ac_check_funcs_once")
+                 "disabled_prefer_ac_check_funcs_once")
+                (("sc_prohibit_(AC_LIBOBJ_in_m4|leading_TABs)" rule)
+                 (string-append "disabled_prohibit_" rule)))))
+          (add-before 'check 'regenerate-unicode
+            (lambda* (#:key inputs #:allow-other-keys)
+              (define (find-ucd-file name)
+                (search-input-file inputs (string-append "share/ucd/" name)))
+              (define (find-ucd-files . names)
+                (map find-ucd-file names))
+              (with-directory-excursion "lib"
+                ;; See the compile-command buffer-local variable in
+                ;; lib/gen-uni-tables.c
+                (invoke "gcc" "-O" "-Wall" "gen-uni-tables.c"
+                        "-Iunictype" "-o" "gen-uni-tables")
+                (apply invoke
+                       "./gen-uni-tables"
+                       (append
+                        (find-ucd-files "UnicodeData.txt"
+                                        "PropList.txt"
+                                        "DerivedCoreProperties.txt"
+                                        "emoji/emoji-data.txt"
+                                        "ArabicShaping.txt"
+                                        "Scripts.txt"
+                                        "Blocks.txt")
+                        (list
+                         #$(origin
+                             (method url-fetch)
+                             (uri (string-append
+                                   "https://www.unicode.org/Public/"
+                                   "3.0-Update1/PropList-3.0.1.txt"))
+                             (sha256
+                              (base32
+                               "0k6wyijyzdl5g3nibcwfm898kfydx1pqaz28v7fdvnzdvd5fz7lh"))))
+                        (find-ucd-files "EastAsianWidth.txt"
+                                        "LineBreak.txt"
+                                        "auxiliary/WordBreakProperty.txt"
+                                        "auxiliary/GraphemeBreakProperty.txt"
+                                        "CompositionExclusions.txt"
+                                        "SpecialCasing.txt"
+                                        "CaseFolding.txt")
+                         (list #$(package-version (this-package-native-input "ucd")))))
+                (invoke "clisp" "-C" "uniname/gen-uninames.lisp"
+                        (find-ucd-file "UnicodeData.txt")
+                        "uniname/uninames.h"
+                        (find-ucd-file "NameAliases.txt"))
+                (for-each
+                 (match-lambda
+                  ((ucd-file . directory)
+                   (copy-file (find-ucd-file ucd-file)
+                              (string-append "../tests/" directory "/"
+                                             (basename ucd-file)))))
+                 '(("NameAliases.txt" . "uniname")
+                   ("UnicodeData.txt" . "uniname")
+                   ("NormalizationTest.txt" . "uninorm")
+                   ("auxiliary/GraphemeBreakTest.txt" . "unigbrk")
+                   ("auxiliary/WordBreakTest.txt" . "uniwbrk")))
+                (delete-file "gen-uni-tables")))))))
+    (inputs ;; Shebangs for some auxiliary build files.
+     (list python perl clisp))
+    (native-inputs
+     (list
+      python perl clisp
+      ;; Unicode data:
+      ucd-next
+      ;; Programs for the tests:
+      cppi indent git autoconf))
+    (home-page "https://www.gnu.org/software/gnulib/")
+    (synopsis "Source files to share among distributions")
+    (description
+     "Gnulib is a central location for common infrastructure needed by GNU
+packages.  It provides a wide variety of functionality, e.g., portability
+across many systems, working with Unicode strings, cryptographic computation,
+and much more.  The code is intended to be shared at the level of source
+files, rather than being a standalone library that is distributed, built, and
+installed.  The included @command{gnulib-tool} script helps with using Gnulib
+code in other packages.  Gnulib also includes copies of licensing and
+maintenance-related files, for convenience.")
+    (native-search-paths
+     (list (search-path-specification
+            (variable "GNULIB_SRCDIR")
+            (files (list "src/gnulib")))))
+    (license (list license:lgpl2.0+ license:gpl3+))))
+
+(define-public gnulib
+  (gnulib-checkout
+   #:version "2022-12-31"
+   #:commit "875461ffdf58ac04677957b4ae4160465b83b940"
+   #:hash (base32 "0bf7a6wdns9c5wwv60qfcn9llg0j6jz5ryd2qgsqqx2i6xkmp77c")))

gnu/packages/busybox.scm

@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014 John Darrington <jmd@gnu.org>
-;;; Copyright © 2016, 2017, 2018, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016-2020, 2023 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018–2022 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2022 LuHui <luhux76@gmail.com>
 ;;;
@@ -35,7 +35,7 @@
 (define-public busybox
   (package
     (name "busybox")
-    (version "1.35.0")
+    (version "1.36.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -43,7 +43,7 @@
                     version ".tar.bz2"))
               (sha256
                (base32
-                "1556hfgw32xf226dd138gfq0z1zf4r3f8naa9wrqld2sqd2b5vps"))))
+                "19b1mzkc2hc2qsg4fnshdyqfxk1xkzwv900p40767ckwmz4509sl"))))
     (build-system gnu-build-system)
     (arguments
      (list #:phases

gnu/packages/c.scm

@@ -70,8 +70,8 @@
   #:use-module (gnu packages xml))
 
 (define-public c-intro-and-ref
-  (let ((revision "0")
+  (let ((revision "1")
-        (commit "f88559678feeb1391a0e9c7cf060c4429ef22ffc"))
+        (commit "47e5a234a7c036392e0f9e1e8e48ff3e6855840d"))
     (package
       (name "c-intro-and-ref")
       (version (git-version "0.0.0" revision commit))
@@ -83,7 +83,7 @@
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "0c08h8k7wkn5lw0jqnnaayx55d3vf1q11pgsixfw31i58rnwa5y2"))))
+                  "0aza4vvlg2w0ss6n5xp741ycvg16d041c1x87yh5hpnzcb6y0ii3"))))
       (build-system copy-build-system)
       (arguments
        (list #:phases #~(modify-phases %standard-phases
@@ -425,14 +425,14 @@ whose behaviour is inconsistent across *NIX flavours.")
 (define-public libhx
   (package
     (name "libhx")
-    (version "4.8")
+    (version "4.9")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://inai.de/files/libhx/"
                            "libHX-" version ".tar.xz"))
        (sha256
-        (base32 "1mj6n4p0fs1jzj1dvk2xkyiyc1s7s5fxv27iciwn0xkwhasjmhxa"))))
+        (base32 "16rwp8b2j8l0m27rffvb7ma350r79l611sa135hzfywkdli2bqh2"))))
     (build-system gnu-build-system)
     (home-page "https://inai.de/projects/libhx/")
     (synopsis "C library with common data structures and functions")
@@ -1128,7 +1128,7 @@ Telemetry Transport (MQTT) publish-subscribe messaging protocol.")
 (define-public mimalloc
   (package
     (name "mimalloc")
-    (version "2.0.7")
+    (version "2.0.9")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1137,7 +1137,7 @@ Telemetry Transport (MQTT) publish-subscribe messaging protocol.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0g54z9c4w7zjp3m1s70cgrjhxa5hr43pkhdbj61a2rb54z09lzw7"))))
+                "19w0i28p6knjd192rrcw1ayc3x0qp6rcm48cwkls4kwn8fng81fj"))))
     (build-system cmake-build-system)
     (arguments
      `(#:build-type "Release"))

gnu/packages/check.scm

@@ -2672,6 +2672,24 @@ pragmas to control it from within your code.  Additionally, it is
 possible to write plugins to add your own checks.")
     (license license:gpl2+)))
 
+(define-public python-setuptools-lint
+  (package
+    (name "python-setuptools-lint")
+    (version "0.6.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "setuptools-lint" version))
+              (sha256
+               (base32
+                "16a1ac5n7k7sx15cnk03gw3fmslab3a7m74dc45rgpldgiff3577"))))
+    (build-system python-build-system)
+    (propagated-inputs (list python-pylint))
+    (home-page "https://github.com/johnnoone/setuptools-pylint")
+    (synopsis "Run pylint with @command{python setup.py lint}")
+    (description "This package expose pylint as a lint command into
+setup.py.")
+    (license license:bsd-3)))
+
 (define-public python-paramunittest
   (package
     (name "python-paramunittest")

gnu/packages/chemistry.scm

@@ -357,68 +357,66 @@ stored with user-specified precision.")
 (define-public gromacs
   (package
     (name "gromacs")
-    (version "2020.2")
+    (version "2022.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1wyjgcdl30wy4hy6jvi9lkq53bqs9fgfq6fri52dhnb3c76y8rbl"))
+                "15vjwasxjq0h18dmzacjkdim51zrvr0ni42hbc30557j5xhbw4f5"))
               ;; Our version of tinyxml2 is far newer than the bundled one and
               ;; require fixing `testutils' code. See patch header for more info
               (patches (search-patches "gromacs-tinyxml2.patch"))))
     (build-system cmake-build-system)
     (arguments
-     `(#:configure-flags
+     (list #:configure-flags
-       (list "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests
+           #~(list "-DGMX_DEVELOPER_BUILD=on"     ; Needed to run tests
-             ;; Unbundling
+                   ;; Unbundling
-             "-DGMX_USE_LMFIT=EXTERNAL"
+                   "-DGMX_USE_LMFIT=EXTERNAL"
-             "-DGMX_BUILD_OWN_FFTW=off"
+                   "-DGMX_BUILD_OWN_FFTW=off"
-             "-DGMX_EXTERNAL_BLAS=on"
+                   "-DGMX_EXTERNAL_BLAS=on"
-             "-DGMX_EXTERNAL_LAPACK=on"
+                   "-DGMX_EXTERNAL_LAPACK=on"
-             "-DGMX_EXTERNAL_TNG=on"
+                   "-DGMX_EXTERNAL_TNG=on"
-             "-DGMX_EXTERNAL_ZLIB=on"
+                   "-DGMX_EXTERNAL_ZLIB=on"
-             "-DGMX_EXTERNAL_TINYXML2=on"
+                   "-DGMX_EXTERNAL_TINYXML2=on"
-             (string-append "-DTinyXML2_DIR="
+                   (string-append "-DTinyXML2_DIR="
-                            (assoc-ref %build-inputs "tinyxml2"))
+                                  #$(this-package-input "tinyxml2"))
-             ;; Workaround for cmake/FindSphinx.cmake version parsing that does
+                   ;; Workaround for cmake/FindSphinx.cmake version parsing that does
-             ;; not understand the guix-wrapped `sphinx-build --version' answer
+                   ;; not understand the guix-wrapped `sphinx-build --version' answer
-             (string-append "-DSPHINX_EXECUTABLE_VERSION="
+                   (string-append "-DSPHINX_EXECUTABLE_VERSION="
-                            ,(package-version python-sphinx)))
+                                  #$(package-version python-sphinx)))
-       #:phases
+           #:phases
-       (modify-phases %standard-phases
+           #~(modify-phases %standard-phases
-         (add-after 'unpack 'fixes
+               (add-after 'unpack 'fixes
-           (lambda* (#:key inputs #:allow-other-keys)
+                 (lambda* (#:key inputs #:allow-other-keys)
-             ;; Still bundled: part of gromacs, source behind registration
+                   ;; Still bundled: part of gromacs, source behind registration
-             ;; but free software anyways
+                   ;; but free software anyways
-             ;;(delete-file-recursively "src/external/vmd_molfile")
+                   ;;(delete-file-recursively "src/external/vmd_molfile")
-             ;; Still bundled: threads-based OpenMPI-compatible fallback
+                   ;; Still bundled: threads-based OpenMPI-compatible fallback
-             ;; designed to be bundled like that
+                   ;; designed to be bundled like that
-             ;;(delete-file-recursively "src/external/thread_mpi")
+                   ;;(delete-file-recursively "src/external/thread_mpi")
-             ;; Unbundling
+                   ;; Unbundling
-             (delete-file-recursively "src/external/lmfit")
+                   (delete-file-recursively "src/external/lmfit")
-             (delete-file-recursively "src/external/clFFT")
+                   (delete-file-recursively "src/external/clFFT")
-             (delete-file-recursively "src/external/fftpack")
+                   (delete-file-recursively "src/external/fftpack")
-             (delete-file-recursively "src/external/build-fftw")
+                   (delete-file-recursively "src/external/build-fftw")
-             (delete-file-recursively "src/external/tng_io")
+                   (delete-file-recursively "src/external/tng_io")
-             (delete-file-recursively "src/external/tinyxml2")
+                   (delete-file-recursively "src/external/tinyxml2")
-             (delete-file-recursively "src/external/googletest")
+                   (delete-file-recursively "src/external/googletest")
-             (copy-recursively (assoc-ref inputs "googletest-source")
+                   (copy-recursively #$(package-source googletest)
-                               "src/external/googletest")
+                                     "src/external/googletest")
-             ;; This test warns about the build host hardware, disable
+                   ;; This test warns about the build host hardware, disable
-             (substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp"
+                   (substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp"
-               (("TEST\\(HardwareTopologyTest, HwlocExecute\\)")
+                     (("TEST\\(HardwareTopologyTest, HwlocExecute\\)")
-                "void __guix_disabled()"))
+                      "void __guix_disabled()")))))))
-             #t)))))
     (native-inputs
-     `(("doxygen" ,doxygen)
+     (list doxygen
-       ("googletest-source" ,(package-source googletest))
+           graphviz
-       ("graphviz" ,graphviz)
+           pkg-config
-       ("pkg-config" ,pkg-config)
+           python
-       ("python" ,python)
+           python-pygments
-       ("python-pygments" ,python-pygments)
+           python-sphinx))
-       ("python-sphinx" ,python-sphinx)))
     (inputs
      (list fftwf
            `(,hwloc-2 "lib")
@@ -437,7 +435,8 @@ interactions, but since GROMACS is extremely fast at calculating the nonbonded
 interactions (that usually dominate simulations) many groups are also using it
 for research on non-biological systems, e.g. polymers.  GROMACS supports all the
 usual algorithms you expect from a modern molecular dynamics implementation.")
-    (license license:lgpl2.1+)))
+    (license license:lgpl2.1+)
+    (properties '((tunable? . #t)))))
 
 (define-public openbabel
   (package

gnu/packages/chromium.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2019, 2020, 2021, 2022 Marius Bakke <marius@gnu.org>
+;;; Copyright © 2019-2023 Marius Bakke <marius@gnu.org>
 ;;; Copyright © 2019 Alex Griffin <a@ajgrf.com>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -27,7 +27,6 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages)
-  #:use-module (gnu packages assembly)
   #:use-module (gnu packages base)
   #:use-module (gnu packages bash)
   #:use-module (gnu packages bison)
@@ -56,7 +55,6 @@
   #:use-module (gnu packages nss)
   #:use-module (gnu packages pciutils)
   #:use-module (gnu packages pkg-config)
-  #:use-module (gnu packages protobuf)
   #:use-module (gnu packages pulseaudio)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-web)
@@ -70,10 +68,8 @@
   #:use-module (gnu packages video)
   #:use-module (gnu packages xiph)
   #:use-module (gnu packages xml)
-  #:use-module (gnu packages xdisorg)
   #:use-module (gnu packages xorg)
-  #:use-module (ice-9 match)
+  #:use-module (ice-9 match))
-  #:use-module (srfi srfi-1))
 
 (define %preserved-third-party-files
   '("base/third_party/cityhash" ;Expat
@@ -152,6 +148,8 @@
     "third_party/devtools-frontend/src/front_end/third_party/lodash-isequal" ;Expat
     "third_party/devtools-frontend/src/front_end/third_party/marked" ;Expat, BSD-3
     "third_party/devtools-frontend/src/front_end/third_party/puppeteer" ;ASL2.0
+    "third_party/devtools-frontend/src/front_end/third_party/puppeteer\
+/package/lib/esm/third_party/mitt" ;Expat
     "third_party/devtools-frontend/src/front_end/third_party/wasmparser" ;ASL2.0
     "third_party/devtools-frontend/src/third_party/pyjson5" ;ASL2.0
     "third_party/devtools-frontend/src/third_party/typescript" ;ASL2.0
@@ -245,6 +243,7 @@
     "third_party/ruy" ;ASL2.0
     "third_party/s2cellid" ;ASL2.0
     "third_party/securemessage" ;ASL2.0
+    "third_party/selenium-atoms" ;ASL2.0
     "third_party/shell-encryption" ;ASL2.0
     "third_party/skia" ;BSD-3
     "third_party/skia/third_party/vulkanmemoryallocator" ;BSD-3, Expat
@@ -317,10 +316,10 @@
   ;; run the Blink performance tests, just remove everything to save ~70MiB.
   '("third_party/blink/perf_tests"))
 
-(define %chromium-version "108.0.5359.124")
+(define %chromium-version "109.0.5414.119")
 (define %ungoogled-revision (string-append %chromium-version "-1"))
 (define %debian-revision "debian/102.0.5005.61-1")
-(define %arch-revision "4de5019014aeb77187a517c5ca6db8723d622a40")
+(define %arch-revision "a0b214b3bdfbc7ee3d9004a70494a2b9e3da2c80")
 
 (define %ungoogled-origin
   (origin
@@ -330,7 +329,7 @@
     (file-name (git-file-name "ungoogled-chromium" %ungoogled-revision))
     (sha256
      (base32
-      "18sz2ksawyb08h4kbxzkf1zhxs832z8mwvndm43nykz01wxk20bp"))))
+      "1nb0099gwkhxv3zc184jyvpl5jrrq194pv6yq95nbc27vw6zz7qv"))))
 
 (define %debian-origin
   (origin
@@ -378,7 +377,9 @@
 (define %arch-patches
   (list
    (arch-patch %arch-revision "disable-GlobalMediaControlsCastStartStop.patch"
-               "00m361ka38d60zpbss7qnfw80vcwnip2pjcz3wf46wd2sqi1nfvz")))
+               "00m361ka38d60zpbss7qnfw80vcwnip2pjcz3wf46wd2sqi1nfvz")
+   (arch-patch %arch-revision "fix-the-way-to-handle-codecs-in-the-system-icu.patch"
+               "1qy7ldw7lnfbg0dl49m7myrflw0ps80adaisq5dqjndhn0rcbmd5")))
 
 (define %guix-patches
   (list (local-file
@@ -491,7 +492,7 @@
                                   %chromium-version ".tar.xz"))
               (sha256
                (base32
-                "0x9ac6m4xdccjdrk2bmq4y7bhfpgf2dv0q7lsbbsa50vlv1gm3fl"))
+                "0bdyb14v12izxkldq27jx532p0bid3wdwfpd1mwm7jqswxgfzkfb"))
               (modules '((guix build utils)))
               (snippet (force ungoogled-chromium-snippet))))
     (build-system gnu-build-system)
@@ -589,7 +590,7 @@
               "ffmpeg_branding=\"Chrome\""
 
               ;; WebRTC stuff.
-              "rtc_use_h264=true"
+              "rtc_use_h264=false"      ;XXX needs bundled openh264
               "rtc_use_pipewire=true"
               "rtc_link_pipewire=true"
               ;; Don't use bundled sources.
@@ -619,9 +620,6 @@
                 ;; Adjust minizip header inclusions.
                 (substitute* (find-files "third_party/tflite_support\
 /src/tensorflow_lite_support/metadata/cc")
-                  (("#include \"contrib/minizip/ioapi\\.h\"")
-                   ;; This one can be removed for M108 or so.
-                   "#include \"minizip/ioapi.h\"")
                   (("third_party/zlib/contrib/minizip/")
                    "minizip/"))
 
@@ -670,6 +668,11 @@
                   (("include \"third_party/lcms/include/lcms2\\.h\"")
                    "include \"lcms2.h\""))
 
+                ;; The unbundling script leaves behind an empty pyyaml directory
+                ;; which prevents the code that tries to use it from falling
+                ;; back to the pyyaml provided by Guix.
+                (delete-file-recursively "third_party/pyyaml")
+
                 (substitute*
                     "third_party/breakpad/breakpad/src/common/linux/libcurl_wrapper.h"
                   (("include \"third_party/curl")
@@ -747,9 +750,7 @@
                    (string-append mesa-lib "/libGLESv2.so.2"))))))
           (add-before 'configure 'prepare-build-environment
             (lambda* (#:key native-inputs inputs #:allow-other-keys)
-              (let ((c++ (search-input-directory (or native-inputs inputs)
+              (let ((node (search-input-file (or native-inputs inputs)
-                                                 "include/c++"))
-                    (node (search-input-file (or native-inputs inputs)
                                              "/bin/node")))
                 ;; Define the GN toolchain.
                 (setenv "AR" "llvm-ar") (setenv "NM" "llvm-nm")
@@ -888,6 +889,7 @@
            which
            python-beautifulsoup4
            python-html5lib
+           python-pyyaml
            python-wrapper
            wayland))
     (inputs

gnu/packages/ci.scm

@@ -166,13 +166,7 @@
              ;; the inputs to add it to GUILE_LOAD_PATH.
              guile-bytestructures
 
-             ;; FIXME: The 'cuirass evaluate' command is multithreaded, but it
+             guix))
-             ;; uses 'open-inferior', which calls 'primitive-fork', thus
-             ;; potentially creating child processes that deadlock.  To work
-             ;; around that, use the last revision of Guix where
-             ;; 'open-inferior' was using 'open-pipe*' rather than
-             ;; 'primitive-fork'.  See <https://issues.guix.gnu.org/55441>.
-             guix-for-cuirass))
       (native-inputs
        (list autoconf automake pkg-config texinfo ephemeralpg))
       (native-search-paths

gnu/packages/cinnamon.scm

@@ -23,9 +23,12 @@
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix git-download)
+  #:use-module (guix gexp)
   #:use-module (guix utils)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system meson)
   #:use-module (gnu packages)
+  #:use-module (gnu packages admin)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gettext)
@@ -37,6 +40,84 @@
   #:use-module (gnu packages python)
   #:use-module (gnu packages xorg))
 
+(define-public libxapp
+  (package
+    (name "libxapp")
+    (version "2.4.2")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/linuxmint/xapp/")
+                    (commit version)))
+              (sha256
+               (base32
+                "0cy9g0zqcbx9zscc9qavqmghfyfb8244cg299llv1ha8n6mpxl3s"))))
+    (build-system meson-build-system)
+    (arguments
+     (list
+      #:modules
+      `((guix build meson-build-system)
+        (guix build utils)
+        ((guix build python-build-system) #:prefix python:))
+      #:imported-modules
+      `(,@%meson-build-system-modules
+        (guix build python-build-system))
+      #:configure-flags
+      #~(list (string-append
+               "-Dpy-overrides-dir="
+               (python:site-packages %build-inputs %outputs) "/gi/overrides"))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'configure 'set-gtk-module-path
+            (lambda* (#:key inputs outputs #:allow-other-keys)
+              (substitute* "libxapp/meson.build"
+                (("gtk3_dep\\.get_pkgconfig_variable[(]'libdir'[)]")
+                 (string-append "'" (assoc-ref outputs "out") "/lib'")))
+
+              (substitute* "scripts/pastebin"
+                (("'nc'")
+                 (string-append "'"
+                                (search-input-file inputs "/bin/nc")
+                                "'")))
+
+              (substitute* "scripts/upload-system-info"
+                (("'inxi'")
+                 (string-append "'"
+                                (search-input-file inputs "/bin/inxi")
+                                "'"))
+                (("'/usr/bin/pastebin'")
+                 (string-append "'"
+                                (assoc-ref outputs "out")
+                                "/bin/pastebin'"))
+                (("'xdg-open'")
+                 (string-append "'"
+                                (search-input-file inputs "/bin/xdg-open")
+                                "'"))))))))
+    (inputs
+     (list dbus
+           glib                         ; for gio
+           gtk+
+           inxi-minimal                 ; used by upload-system-info
+           libdbusmenu
+           libgnomekbd
+           netcat                       ; used by pastebin
+           xdg-utils))                  ; used by upload-system-info
+    (native-inputs
+     (list gettext-minimal
+           `(,glib "bin")               ; for glib-mkenums
+           gobject-introspection
+           pkg-config
+           python
+           python-pygobject
+           vala))
+    (home-page "https://github.com/linuxmint/xapp")
+    (synopsis "Library for traditional GTK applications")
+    (description
+     "The libxapp package contains the components which are common to multiple
+GTK desktop environments (Cinnamon, MATE and Xfce) and required to implement
+cross-DE solutions.")
+    (license license:lgpl3+)))
+
 (define-public cinnamon-desktop
   (package
     (name "cinnamon-desktop")

gnu/packages/cmake.scm

@@ -333,7 +333,7 @@ and workspaces that can be used in the compiler environment of your choice.")
   (package
     (inherit cmake-minimal)
     (name "cmake")
-    (version "3.24.2")
+    (version "3.25.1")
     (source (origin
               (inherit (package-source cmake-minimal))
               (method url-fetch)
@@ -348,7 +348,7 @@ and workspaces that can be used in the compiler environment of your choice.")
                                   ,@rest))))
               (sha256
                (base32
-                "1ny8y2dzc6fww9gzb1ml0vjpx4kclphjihkxagxigprxdzq2140d"))
+                "1n4inb3fvk70sni5gmkljqw3cyllalyg3fnr9rlr7x3aa44isl8w"))
               (patches (search-patches "cmake-curl-certificates-3.24.patch"))))
     (outputs '("out" "doc"))
     (arguments

gnu/packages/code.scm

@@ -430,7 +430,7 @@ features that are not supported by the standard @code{stdio} implementation.")
 (define-public universal-ctags
   (package
     (name "universal-ctags")
-    (version "5.9.20221127.0")
+    (version "6.0.20230122.0")
     (source
      (origin
        (method git-fetch)
@@ -440,7 +440,7 @@ features that are not supported by the standard @code{stdio} implementation.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0nvkx5j2vyzjf935a2s5w56gamlr6f12jy1x38bkqz78p5l0d3ja"))
+         "121d1dyc3wd4bzv4wky3x66j1va3d6ywbw71abp3l88fv7sc0f73"))
        (modules '((guix build utils)))
        (snippet
         '(begin

gnu/packages/commencement.scm

@@ -3623,7 +3623,7 @@ exec ~a/bin/~a-~a -B~a/lib -Wl,-dynamic-linker -Wl,~a/~a \"$@\"~%"
   ;; This package must be public because other modules refer to it.  However,
   ;; mark it as hidden so that 'fold-packages' ignores it.
   (with-boot4 (hidden-package
-               (package-with-bootstrap-guile guile-3.0/fixed))))
+               (package-with-bootstrap-guile guile-3.0/pinned))))
 
 (define-public glibc-utf8-locales-final
   ;; Now that we have GUILE-FINAL, build the UTF-8 locales.  They are needed

gnu/packages/compression.scm

@@ -36,6 +36,7 @@
 ;;; Copyright © 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2021 Ahmad Jarara <git@ajarara.io>
 ;;; Copyright © 2022 Zhu Zihao <all_but_last@163.com>
+;;; Copyright © 2021 Foo Chuan Wei <chuanwei.foo@hotmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -2325,7 +2326,7 @@ decompression is a little bit slower.")
 (define-public upx
   (package
     (name "upx")
-    (version "4.0.0")
+    (version "4.0.1")
     (source
      (origin
        (method url-fetch)
@@ -2333,7 +2334,7 @@ decompression is a little bit slower.")
                            version "/upx-" version "-src.tar.xz"))
        (sha256
         (base32
-         "1sinky0rq40q2qqzly99c5hdd6ilz2bxlbqla9lg0rafhbw3iyga"))))
+         "1471nxzrbv8sw2pmxn817q5l40sr0l7v7bpvw829iai95s73q03p"))))
     (build-system cmake-build-system)
     (home-page "https://upx.github.io/")
     (synopsis "Compression tool for executables")
@@ -2384,7 +2385,7 @@ reading from and writing to ZIP archives.")
   (package
     (inherit quazip-0)
     (name "quazip")
-    (version "1.3")
+    (version "1.4")
     (source
      (origin
        (method git-fetch)
@@ -2393,7 +2394,7 @@ reading from and writing to ZIP archives.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0njgbdm3dm5p7xic5mhppbqsl36zn83zz0xfsfh624hlk0ff7n0a"))))))
+        (base32 "1jsw4xm5wyaqcj1pma5zzd8f5xbgd5lcjh18ah3kg36xz5i69yi4"))))))
 
 (define-public zchunk
   (package
@@ -2833,3 +2834,33 @@ serializations such as ASN.1 and MessagePack.")
     (synopsis "Zip password cracker")
     (description "Fcrackzip is a Zip file password cracker.")
     (license license:gpl2+)))
+
+(define-public unrar-free
+  (package
+    (name "unrar-free")
+    (version "0.1.3")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://gitlab.com/bgermann/unrar-free")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "12idmr5rjmw7dg2mi6250q599nywrirgc8553353a4swf5n1pmx4"))))
+    (build-system gnu-build-system)
+    (inputs
+     `(("libarchive" ,libarchive)))
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("pkg-config" ,pkg-config)))
+    (home-page "https://gitlab.com/bgermann/unrar-free")
+    (synopsis "Extract files from RAR archives")
+    (description
+     "@code{unrar-free} is a free software version of the non-free @code{unrar}
+utility.  This program is a simple command-line front-end to libarchive, and can
+list and extract not only RAR archives but also other formats supported by
+libarchive.  It does not rival the non-free @code{unrar} in terms of features,
+but special care has been taken to ensure it meets most user's needs.")
+    (license license:gpl2+)))

gnu/packages/compton.scm

@@ -4,6 +4,7 @@
 ;;; Copyright © 2019 Alexandru-Sergiu Marton <brown121407@member.fsf.org>
 ;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
 ;;; Copyright © 2022 Jai Vetrivelan <jaivetrivelan@gmail.com>
+;;; Copyright © 2023 John Kehayias <john.kehayias@protonmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -23,6 +24,7 @@
 (define-module (gnu packages compton)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
+  #:use-module (guix gexp)
   #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
@@ -111,7 +113,7 @@ performance).
 (define-public picom
   (package
     (name "picom")
-    (version "9.1")
+    (version "10.2")
     (source
      (origin
        (method git-fetch)
@@ -120,7 +122,7 @@ performance).
              (commit (string-append "v" version))))
        (sha256
         (base32
-         "0q7j6kh9k7i201cwhnfc3bmp0hqrx7ngk3v4qsp8k0qfy1n3ma8n"))
+         "1vd4nhvfykwdhpyhb0jmcj333zxhm6dyikafd76fa4z4fhjrrs0b"))
        (file-name (string-append "picom-" version))))
     (build-system meson-build-system)
     (inputs
@@ -140,8 +142,20 @@ performance).
     (native-inputs
      (list asciidoc pkg-config xorgproto))
     (arguments
-     `(#:build-type "release"
+     (list #:build-type "release"
-       #:configure-flags '("-Dwith_docs=true")))
+           #:configure-flags #~'("-Dwith_docs=true")
+           #:phases
+           #~(modify-phases %standard-phases
+               ;; This file would be patched by 'patch-dot-desktop-files but
+               ;; only in share/applications and not etc/xdg/autostart, so
+               ;; manually patch it before it is installed in either location.
+               ;; The 'patch-dot-desktop-files phase is still needed for other
+               ;; .desktop files.
+               (add-after 'unpack 'patch-autostart-files
+                 (lambda _
+                   (substitute* "picom.desktop"
+                     (("Exec=")
+                      (string-append "Exec=" #$output "/bin/"))))))))
     (home-page "https://github.com/yshui/picom")
     (synopsis "Compositor for X11, forked from Compton")
     (description

gnu/packages/configuration-management.scm

@@ -97,7 +97,7 @@
            go-golang-org-x-net
            go-golang-org-x-oauth2
            go-github-com-rogpeppe-go-internal
-           gopkg-in-errgo-fmt-errors))
+           go-gopkg-in-errgo-fmt-errors))
     (home-page "https://www.chezmoi.io/")
     (synopsis "Personal configuration files manager")
     (description "This package helps to manage personal configuration files

gnu/packages/containers.scm

@@ -26,6 +26,7 @@
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix git-download)
+  #:use-module (guix build-system copy)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
   #:use-module (guix build-system meson)
@@ -46,7 +47,8 @@
   #:use-module (gnu packages selinux)
   #:use-module (gnu packages version-control)
   #:use-module (gnu packages virtualization)
-  #:use-module (gnu packages web))
+  #:use-module (gnu packages web)
+  #:use-module (gnu packages wget))
 
 (define-public crun
   (let ((commit "c381048530aa750495cf502ddb7181f2ded5b400"))
@@ -153,6 +155,41 @@ manager (like Podman or CRI-O) and an Open Container Initiative (OCI)
 runtime (like runc or crun) for a single container.")
     (license license:asl2.0)))
 
+(define-public distrobox
+  (package
+    (name "distrobox")
+    (version "1.4.2.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/89luca89/distrobox")
+             (commit version)))
+       (sha256
+        (base32 "0gs81m1bvlyq6ad22zsdsw1q6s3agy79vx94kdf6zjzngbanlydk"))
+       (file-name (git-file-name name version))))
+    (build-system copy-build-system)
+    (inputs
+     (list podman wget))
+    (arguments
+     (list #:phases
+           #~(modify-phases %standard-phases
+               (add-before 'install 'refer-to-inputs
+                 (lambda* (#:key inputs #:allow-other-keys)
+                   (substitute* (find-files "." "^distrobox.*")
+                     (("podman") (search-input-file inputs "/bin/podman"))
+                     (("wget") (search-input-file inputs "/bin/wget"))
+                     (("command -v") "test -x"))))
+               (replace 'install
+                 (lambda _
+                   (invoke "./install" "--prefix" #$output))))))
+    (home-page "https://distrobox.privatedns.org/")
+    (synopsis "Create and start containers highly integrated with the hosts")
+    (description
+     "Distrobox is a fancy wrapper around Podman or Docker to create and start
+containers highly integrated with the hosts.")
+    (license license:gpl3)))
+
 (define-public libslirp
   (package
     (name "libslirp")
@@ -281,6 +318,10 @@ configure network interfaces in Linux containers.")
        (uri (git-reference
              (url "https://github.com/containers/podman")
              (commit (string-append "v" version))))
+       (modules '((guix build utils)))
+       ;; FIXME: Btrfs libraries not detected by these scripts.
+       (snippet '(substitute* "Makefile"
+                   ((".*hack/btrfs.*") "")))
        (sha256
         (base32 "05hv4xdf06n728lmsx793zygypc9i404bgcgpy0fyrg8c2s11q2h"))
        (file-name (git-file-name name version))))

gnu/packages/cpp.scm

@@ -33,6 +33,7 @@
 ;;; Copyright © 2022 Zheng Junjie <873216071@qq.com>
 ;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2023 Sughosha <Sughosha@proton.me>
+;;; Copyright © 2023 Artyom V. Poptsov <poptsov.artyom@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -293,7 +294,7 @@ various formats, including @code{json}.")
 (define-public libzen
   (package
     (name "libzen")
-    (version "0.4.39")
+    (version "0.4.40")
     (source (origin
               (method url-fetch)
               ;; Warning: This source has proved unreliable 1 time at least.
@@ -304,7 +305,7 @@ various formats, including @code{json}.")
                                   "libzen_" version ".tar.bz2"))
               (sha256
                (base32
-                "1rwaxmid9iv65n0y6xlcyxxydsvihjni9ldxpg6pbqz43amp49xx"))))
+                "17pnp5i1ppcxhxnfs9qlkzzy35h23pkdwhsgpbqdkf8lab2f4hsm"))))
     (native-inputs
      (list autoconf automake libtool))
     (build-system gnu-build-system)
@@ -447,7 +448,7 @@ operating on batches.")
 (define-public google-highway
   (package
     (name "google-highway")
-    (version "1.0.2")
+    (version "1.0.3")
     (source
      (origin
        (method git-fetch)
@@ -456,7 +457,7 @@ operating on batches.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1dxv61ag0pl5nl6ql4k83k4i95937nhl98img8gz9fx76cpw6z08"))))
+        (base32 "1828rz9w9sr3zlyg25b6nm7j5j5m0xnic7hy36gpsbxvq358ibpf"))))
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags (list "-DHWY_SYSTEM_GTEST=on")))
@@ -1817,7 +1818,7 @@ syntax with variables, conditions, functions and more.")
 (define-public simdjson
   (package
     (name "simdjson")
-    (version "1.0.2")
+    (version "3.1.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1826,7 +1827,7 @@ syntax with variables, conditions, functions and more.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "05i5jnqd7ngps79cws16ls48gnx08ykkkib3n2hbrdhr1wwrnv7a"))))
+                "0q784bm8xbz3p782dw02cdds6m71wk3acy94vva8krc9g88142ws"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f                      ; tests require downloading dependencies
@@ -2377,3 +2378,52 @@ queues, resource pools, strings, etc.
 @item And more.
 @end itemize")
       (license license:zlib))))
+
+(define-public ftxui
+  (package
+    (name "ftxui")
+    (version "3.0.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/ArthurSonzogni/FTXUI")
+                    (commit (string-append "v" version))))
+              (sha256
+               (base32
+                "10a4yw2h29kixxyhll6cvrwyscsvz9asxry857a9l8nqvbhs946s"))
+              (file-name (git-file-name name version))))
+    (build-system cmake-build-system)
+    (native-inputs (list googletest))
+    (arguments
+     (list #:configure-flags
+           #~(list "-DFTXUI_BUILD_TESTS:BOOL=ON"
+                   "-DFTXUI_BUILD_TESTS_FUZZER:BOOL=OFF")
+           #:phases
+           #~(modify-phases %standard-phases
+               (add-after 'unpack 'patch-cmake-tests
+                 (lambda _
+                   (substitute* "cmake/ftxui_test.cmake"
+                     (("NOT googletest_POPULATED")
+                      "FALSE"))
+                   ;; Disable benchmarks for a while as they require bundled Google
+                   ;; benchmark and when the 'googlebenchmark' is unbundled, there's
+                   ;; a CMake configuration error.
+                   (substitute* "cmake/ftxui_benchmark.cmake"
+                     (("NOT WIN32")
+                      "FALSE")))) )))
+    (home-page "https://github.com/ArthurSonzogni/FTXUI")
+    (synopsis "C++ Functional Terminal User Interface")
+    (description
+     "Functional Terminal (X) User interface (FTXUI) is a simple C++ library for
+terminal based user interfaces.
+
+Main features:
+@itemize
+@item Functional style.
+@item Keyboard & mouse navigation.
+@item Support for UTF8 and fullwidth chars.
+@item Support for animations.
+@item Support for drawing.
+@item No dependencies.
+@end itemize")
+    (license license:expat)))

gnu/packages/cran.scm

@@ -11,7 +11,7 @@
 ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
 ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
-;;; Copyright © 2018, 2020, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2018, 2020-2023 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com>
 ;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
@@ -31,11 +31,11 @@
 ;;; Copyright © 2020 Antoine Côté <antoine.cote@posteo.net>
 ;;; Copyright © 2020 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2020 Magali Lemes <magalilemes00@gmail.com>
-;;; Copyright © 2020, 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
+;;; Copyright © 2020, 2021, 2022, 2023 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2020 Aniket Patil <aniket112.patil@gmail.com>
 ;;; Copyright © 2021 Marcel Schilling <marcel.schilling@uni-luebeck.de>
 ;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net>
-;;; Copyright © 2022 Navid Afkhami <navid.afkhami@mdc-berlin.de>
+;;; Copyright © 2022, 2023 Navid Afkhami <navid.afkhami@mdc-berlin.de>
 ;;; Copyright © 2022 Greg Hogan <code@greghogan.com>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -256,6 +256,33 @@ can limit either their total size or the age of the oldest object (or both),
 automatically pruning objects to maintain the constraints.")
     (license license:expat)))
 
+(define-public r-castor
+  (package
+    (name "r-castor")
+    (version "1.7.6")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "castor" version))
+              (sha256
+               (base32
+                "1qbndwmzzpkzgiah0hgid9z5f9iv2j53d515bjcci1591gx1fk36"))))
+    (properties `((upstream-name . "castor")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-matrix r-naturalsort r-rcpp r-rspectra))
+    (home-page "https://cran.r-project.org/package=castor")
+    (synopsis "Efficient phylogenetics on large trees")
+    (description
+     "This tool supports analyses on massive phylogenies comprising up to
+millions of tips.  Functions include pruning, rerooting, calculation of
+most-recent common ancestors, calculating distances from the tree root and
+calculating pairwise distances.  In addition, this tool takes care of
+calculation of phylogenetic signal and mean trait depth (trait conservatism),
+ancestral state reconstruction and hidden character prediction of discrete
+characters, simulating and fitting models of trait evolution, fitting and
+simulating diversification models, dating trees, comparing trees, and
+reading/writing trees in Newick format.")
+    (license license:gpl2+)))
+
 (define-public r-collections
   (package
     (name "r-collections")
@@ -717,6 +744,57 @@ differential abundance analysis of zero-inflated high-dimensional
 compositional data.")
     (license license:gpl3)))
 
+(define-public r-gwidgets2
+  (package
+    (name "r-gwidgets2")
+    (version "1.0-9")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "gWidgets2" version))
+              (sha256
+               (base32
+                "1ifljpdazzmwf3mgkg9g76365n2cmw8dd3da161fpvw84xxyznfl"))))
+    (properties `((upstream-name . "gWidgets2")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-digest))
+    (home-page "https://github.com/gWidgets3/gWidgets2")
+    (synopsis "Rewrite of gWidgets API for simplified GUI construction")
+    (description
+     "This package provides a re-implementation of the @code{gWidgets} API.
+The API is defined in this package.  A second, toolkit-specific package is
+required to use it.")
+    (license license:gpl3+)))
+
+(define-public r-gwidgets2tcltk
+  (package
+    (name "r-gwidgets2tcltk")
+    (version "1.0-8")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "gWidgets2tcltk" version))
+              (sha256
+               (base32
+                "02ic4avpa33dnqsnm1mzg7ci1psngk1p169pqf259szf6v39qf8h"))))
+    (properties `((upstream-name . "gWidgets2tcltk")))
+    (build-system r-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'install 'start-x-server
+            (lambda _
+              ;; Tests require a running X server.
+              (system "Xvfb :1 +extension GLX &")
+              (setenv "DISPLAY" ":1"))))))
+    (propagated-inputs (list r-digest r-gwidgets2 r-memoise))
+    (native-inputs
+     (list xorg-server-for-tests))
+    (home-page "https://github.com/jverzani/gWidgets2tcltk")
+    (synopsis "Toolkit implementation of gWidgets2 for tcltk")
+    (description "This package is a port of the @code{gWidgets2} API for the
+@code{tcltk} package.")
+    (license license:gpl2+)))
+
 (define-public r-ids
   (package
     (name "r-ids")
@@ -3202,6 +3280,30 @@ rmarkdown, etc.) depend on this package to avoid bundling redundant copies of
 jQuery.")
     (license license:expat)))
 
+(define-public r-jqr
+  (package
+    (name "r-jqr")
+    (version "1.2.3")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "jqr" version))
+              (sha256
+               (base32
+                "1a91zcjxdilhqdyr2lipnwc35f90h0wyqlbg0vw9ay7sq6llxgs9"))))
+    (properties `((upstream-name . "jqr")))
+    (build-system r-build-system)
+    (inputs (list jq))
+    (propagated-inputs (list r-lazyeval r-magrittr))
+    (native-inputs (list pkg-config))
+    (home-page "https://docs.ropensci.org/jqr/")
+    (synopsis "R client for jq, a JSON Processor")
+    (description
+     "This package provides an R client for @command{jq}, a JSON processor.
+@command{jq} allows the following with JSON data: index into, parse, do
+calculations, cut up and filter, change key names and values, perform
+conditionals and comparisons, and more.")
+    (license license:expat)))
+
 (define-public r-sass
   (package
     (name "r-sass")
@@ -9190,6 +9292,27 @@ facilitate data exploration.")
 experimental designs and random samples for common sampling designs.")
     (license license:expat)))
 
+(define-public r-roptim
+  (package
+    (name "r-roptim")
+    (version "0.1.6")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "roptim" version))
+              (sha256
+               (base32
+                "11h6qdi0rsv0bpps6nxkzzapan284q0gldzkmgx3ww5kvnic5w3y"))))
+    (properties `((upstream-name . "roptim")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-rcpp r-rcpparmadillo))
+    (home-page "https://github.com/ypan1988/roptim/")
+    (synopsis "General purpose optimization in R using C++")
+    (description
+     "This package performs optimization in R using C++.  A unified wrapper
+interface is provided to call C functions of the five optimization algorithms
+(Nelder-Mead, BFGS, CG, L-BFGS-B and SANN) underlying @code{optim()}.")
+    (license license:gpl2+)))
+
 (define-public r-base64url
   (package
     (name "r-base64url")
@@ -9217,6 +9340,34 @@ with a simple base32 encoder/decoder suited for case insensitive file
 systems.")
     (license license:gpl3)))
 
+(define-public r-baseline
+  (package
+    (name "r-baseline")
+    (version "1.3-4")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "baseline" version))
+              (sha256
+               (base32
+                "1kl68zvyi2zd73jy3axrvrymwn4y6l4pd62nz0fciwbgkjhz3yyx"))))
+    (properties `((upstream-name . "baseline")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-gwidgets2tcltk ;for GUI
+           r-limsolve
+           r-sparsem))
+    (home-page "https://github.com/khliland/baseline/")
+    (synopsis "Baseline correction of spectra")
+    (description
+     "This package is a collection of baseline correction algorithms.  Beside
+those it provides a framework and a Tcl/Tk enabled GUI for optimizing baseline
+algorithm parameters.  Typical use is the removal of the background effects from
+spectra, which are originating from various types of spectroscopy and spectrometry.
+Also, there is a possibility of optimizing this with regard to regression or
+classification results.  Correction methods include polynomial fitting, weighted
+local smoothers and many more.")
+    (license license:gpl2)))
+
 (define-public r-radiant-data
   (package
     (name "r-radiant-data")
@@ -10228,6 +10379,28 @@ Tooltips and color gradients can be mapped to nodes using a numeric column in
 the source data frame.")
     (license license:gpl3+)))
 
+(define-public r-rapiclient
+  (package
+    (name "r-rapiclient")
+    (version "0.1.3")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "rapiclient" version))
+              (sha256
+               (base32
+                "1pm4kdga2nz1cpmchdb0ad8gr3bqfm84b1kl32cyc0x3x5rr2syz"))))
+    (properties `((upstream-name . "rapiclient")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-httr r-jsonlite r-yaml))
+    (home-page "https://github.com/bergant/rapiclient")
+    (synopsis "Dynamic OpenAPI/Swagger client")
+    (description
+     "This package lets you access services specified in OpenAPI (formerly
+Swagger) format.  It is not a code generator.  The client is generated
+dynamically as a list of R functions.")
+    (license license:expat)))
+
 (define-public r-rappdirs
   (package
     (name "r-rappdirs")
@@ -15178,6 +15351,36 @@ isosurfaces.")
     ;; Any version of the GPL.
     (license (list license:gpl2+ license:gpl3+))))
 
+(define-public r-missforest
+  (package
+    (name "r-missforest")
+    (version "1.5")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "missForest" version))
+              (sha256
+               (base32
+                "13c38hpl60ca1kwyv61cxsla6ccmsj4qzp0vrxcq7b827fh5aw21"))))
+    (properties `((upstream-name . "missForest")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-dorng
+           r-foreach
+           r-iterators
+           r-itertools
+           r-randomforest))
+    (home-page "https://github.com/stekhoven/missForest")
+    (synopsis "Nonparametric missing value imputation using Random Forest")
+    (description
+     "The function @code{missForest} in this package is used to impute missing
+values, particularly in the case of mixed-type data.  It uses a random forest
+trained on the observed values of a data matrix to predict the missing values.
+It can be used to impute continuous and/or categorical data, including complex
+interactions and non-linear relations.  It yields an @acronym{OOB, out-of-bag}
+imputation error estimate without the need of a test set or elaborate cross-
+validation.  It can be run in parallel to save computation time.")
+    (license license:gpl2+)))
+
 (define-public r-ks
   (package
     (name "r-ks")

gnu/packages/crates-io.scm

@@ -66318,7 +66318,11 @@ hardware registers.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1kz8svnqnxclllsgh0ck20rplw3qzp46b5v30yscnzrgw8vgahjg"))))
+         "1kz8svnqnxclllsgh0ck20rplw3qzp46b5v30yscnzrgw8vgahjg"))
+       (snippet
+        '(begin
+           (delete-file "vim10m_match")
+           (delete-file "vim10m_table")))))
     (arguments
      `(#:tests? #f      ; tests not included in release
        #:cargo-inputs

gnu/packages/crypto.scm

@@ -1264,7 +1264,7 @@ quickly by using all your CPU cores and hardware acceleration.")
 (define-public minisign
   (package
     (name "minisign")
-    (version "0.10")
+    (version "0.11")
     (source
      (origin
        (method git-fetch)
@@ -1273,7 +1273,7 @@ quickly by using all your CPU cores and hardware acceleration.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0gi5z03w9sg72vyjs94y0mhkzz7bbhyzcg92mgmd9r2ydpi5gads"))))
+        (base32 "1vv2bhhsyhlpnjclfa7gkqgd9xi3jfcdrss7abbdxvvflyrwdk5i"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f))                    ; no test suite
@@ -1670,7 +1670,7 @@ checksum tool based on the BLAKE3 cryptographic hash function.")
 (define-public libxcrypt
   (package
     (name "libxcrypt")
-    (version "4.4.28")
+    (version "4.4.33")
     (source
      (origin
        (method git-fetch)
@@ -1679,8 +1679,7 @@ checksum tool based on the BLAKE3 cryptographic hash function.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32
+        (base32 "174k5cj95617akg6pplv371mpd35j9q8il245f2zcpq76yz4qydl"))))
-         "0pacj0s1hlv22iz0k2bkysjslc6rbrgmvmsr02qq17lp4d2gw5rs"))))
     (build-system gnu-build-system)
     (native-inputs
      (list autoconf

gnu/packages/databases.scm

@@ -488,14 +488,14 @@ mapping from string keys to string values.")
 (define-public memcached
   (package
     (name "memcached")
-    (version "1.6.17")
+    (version "1.6.18")
     (source
      (origin
        (method url-fetch)
        (uri (string-append
              "https://memcached.org/files/memcached-" version ".tar.gz"))
        (sha256
-        (base32 "090jpprdjhbr1v9ph15s077bj8ryrsnz1ydg54aw53rxc5ry6m90"))))
+        (base32 "0n21svnjw8j7bdbwrn0apnfql7ckraqgrl7wj9fsqj86h6w6mpfb"))))
     (build-system gnu-build-system)
     (inputs
      (list libevent cyrus-sasl))
@@ -1154,7 +1154,7 @@ developed in C/C++ to MariaDB and MySQL databases.")
 (define-public galera
   (package
     (name "galera")
-    (version "26.4.12")
+    (version "26.4.13")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1163,7 +1163,7 @@ developed in C/C++ to MariaDB and MySQL databases.")
                     (recursive? #t)))
               (file-name (git-file-name name version))
               (sha256
-               (base32 "0n4272mvr8a6h5prbhvl376asdp89ipix5yx5n6i1iiw9bs3v76l"))))
+               (base32 "06kf6w0bjkgcmddjd3k1q4cjpg8i78l0c7hcf368h09i1hqd23i6"))))
     (build-system cmake-build-system)
     (inputs
      (list check boost openssl))

gnu/packages/debug.scm

@@ -834,7 +834,7 @@ engineering.")
 (define-public seer-gdb
   (package
     (name "seer-gdb")
-    (version "1.11")
+    (version "1.14")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -843,7 +843,7 @@ engineering.")
               (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "0778573rixhdanmzp4slghpwgv7pm08n7cpa24rm3wrvs77ic3kb"))))
+                "16mz1c58jf1zrgjpxmp58bx8viyidhs1qg0y8ql2f07wgyy6zx33"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f ; Those are strangely manual

gnu/packages/dezyne.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2022 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
+;;; Copyright © 2022, 2023 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -31,14 +31,14 @@
 (define-public dezyne
   (package
     (name "dezyne")
-    (version "2.16.2")
+    (version "2.17.1")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://dezyne.org/download/dezyne/"
                            name "-" version ".tar.gz"))
        (sha256
-        (base32 "0dnh8wji9npaxg3qjivc45dwxwrzz9fbs77000g8s2192sf4ms7k"))))
+        (base32 "008svf32sy80c98nax3xkvxb0b93xgh9xjvw5ygzkq8zflr3ihm8"))))
     (inputs (list bash-minimal
                   guile-3.0-latest
                   guile-json-4

gnu/packages/diffoscope.scm

@@ -5,7 +5,7 @@
 ;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2018, 2019 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2019 Vagrant Cascadian <vagrant@reproducible-builds.org>
-;;; Copyright © 2022 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2022, 2023 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -75,7 +75,7 @@
 (define-public diffoscope
   (package
     (name "diffoscope")
-    (version "224")
+    (version "233")
     (source
      (origin
        (method git-fetch)
@@ -84,9 +84,7 @@
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1qdivsf4yygg2az5018pw0q4169zas3hfqjydd0q3bhdrfpl0q4q"))
+        (base32 "1m6fc7k8cd7ahra05vqccw1fdbjj6d20vr3q8v67ynnyih5nmbnb"))))
-       (patches
-        (search-patches "diffoscope-fix-llvm-test.patch"))))
     (build-system python-build-system)
     (arguments
      `(#:phases (modify-phases %standard-phases
@@ -113,8 +111,8 @@
                         (("\\[\"getfacl\",")
                          (string-append "[\"" (which "getfacl") "\",")))))
                   (add-after 'build 'build-man-page
-                    (lambda* (#:key (make-flags '()) #:allow-other-keys)
+                    (lambda _
-                      (apply invoke "make" "-C" "doc" make-flags)))
+                      (invoke "make" "-C" "doc")))
                   (add-before 'check 'writable-test-data
                     (lambda _
                       ;; Tests may need write access to tests directory.
@@ -142,93 +140,94 @@
                       (let* ((out (assoc-ref outputs "out"))
                              (man (string-append out "/share/man/man1")))
                         (install-file "doc/diffoscope.1" man)))))))
-    (inputs (list rpm ;for rpm-python
+    (inputs (list rpm                   ;for rpm-python
                   python-debian
                   python-libarchive-c
                   python-magic
                   python-tlsh
-                  acl ;for getfacl
+                  acl                   ;for getfacl
-                  coreutils ;for stat
+                  coreutils             ;for stat
-                  diffutils ;for diff
+                  diffutils             ;for diff
                   xxd))
     (native-inputs
      (append
-       (list help2man
+      (list help2man
 
-             ;; Below are packages used for tests.
+            ;; Below are packages used for tests.
-             binwalk
+            binwalk
-             python-pytest
+            python-pytest
-             python-chardet
+            python-chardet
-             python-h5py
+            python-h5py
-             python-pypdf2
+            python-pypdf
-             python-progressbar33
+            python-progressbar33
 
-             abootimg
+            abootimg
-             bdb
+            bdb
-             binutils
+            binutils
-             bzip2
+            bzip2
-             cdrtools
+            cdrkit-libre
-             colord
+            colord
-             cpio
+            cpio
-             docx2txt
+            docx2txt
-             dtc
+            dtc
-             e2fsprogs
+            e2fsprogs
-             ffmpeg
+            ffmpeg
 
-             ;; XXX: Must be the same version as python-magic uses;
+            ;; XXX: Must be the same version as python-magic uses;
-             ;; remove when 'file' is updated.
+            ;; remove when 'file' is updated.
-             file-next)
+            file-next)
 
-       (match (%current-system)
+      (match (%current-system)
-              ;; fpc is only available on x86 currently.
+        ;; fpc is only available on x86 currently.
-              ((or "x86_64-linux" "i686-linux")
+        ((or "x86_64-linux" "i686-linux")
-               (list fpc))
+         (list fpc))
-              (_ '()))
+        (_ '()))
 
-       (list gettext-minimal
+      (list gettext-minimal
-             ghostscript
+            ghostscript
-             `(,giflib "bin")
+            `(,giflib "bin")
-             gnumeric
+            gnumeric
-             gnupg
+            gnupg
-             hdf5
+            hdf5
-             imagemagick
+            imagemagick
-             libarchive
+            libarchive
-             llvm-9
+            llvm
-             lz4
+            lz4
-             ocaml
+            lzip
-             odt2txt
+            ocaml
-             openssh
+            odt2txt
-             openssl
+            openssh
-             pgpdump
+            openssl
-             poppler
+            pgpdump
-             python-jsbeautifier
+            poppler
-             r-minimal
+            python-jsbeautifier
-             rpm
+            r-minimal
-             sng
+            rpm
-             sqlite
+            sng
-             squashfs-tools
+            sqlite
-             tcpdump
+            squashfs-tools
-             unzip
+            tcpdump
-             wabt
+            unzip
-             xxd
+            wabt
-             xz
+            xxd
-             zip
+            xz
-             zstd)
+            zip
+            zstd)
 
-       ;; Also for tests.  The test suite skips tests when these are missing.
+      ;; Also for tests.  The test suite skips tests when these are missing.
-       (match (%current-system)
+      (match (%current-system)
-         ;; ghc is only available on x86 currently.
+        ;; ghc is only available on x86 currently.
-         ((or "x86_64-linux" "i686-linux")
+        ((or "x86_64-linux" "i686-linux")
-          (list ghc))
+         (list ghc))
-         (_ '()))
+        (_ '()))
-       (match (%current-system)
+      (match (%current-system)
-         ;; openjdk and dependent packages are only
+        ;; openjdk and dependent packages are only
-         ;; available on x86_64 currently.
+        ;; available on x86_64 currently.
-         ((or "x86_64-linux")
+        ((or "x86_64-linux")
-          (list enjarify)
+         (list enjarify)
-          ;; No unversioned openjdk available.
+         ;; No unversioned openjdk available.
-          (list `(,openjdk12 "jdk")))
+         (list `(,openjdk12 "jdk")))
-         (_ '()))))
+        (_ '()))))
     (home-page "https://diffoscope.org/")
     (synopsis "Compare files, archives, and directories in depth")
     (description

gnu/packages/disk.scm

@@ -431,14 +431,14 @@ scheme.")
 (define-public ddrescue
   (package
     (name "ddrescue")
-    (version "1.26")
+    (version "1.27")
     (source
      (origin
       (method url-fetch)
       (uri (string-append "mirror://gnu/ddrescue/ddrescue-"
                           version ".tar.lz"))
       (sha256
-       (base32 "07smgh9f2p90zgyyrddzjwaz0v8glh5d95qiv7yhv0frj0xcs4z5"))))
+       (base32 "1srj68c7q0r5m7rzv3km43ndcs7xjw053r336vjiakx4qnc0rj1q"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags (list (string-append "CXX=" ,(cxx-for-target)))))
@@ -917,7 +917,7 @@ passphrases.")
 (define-public ndctl
   (package
     (name "ndctl")
-    (version "73")
+    (version "75")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -926,14 +926,19 @@ passphrases.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "19kp1ly74bj7gavs03q7caci0lqr0rsi5y45zx5m8in4h19xk1kb"))))
+                "0i3fmda285qnwnmkxzwji5ffz123yrq9dpcwzg922qpysir7zq40"))))
     (build-system meson-build-system)
     (arguments
+     ;; The test suite runs but SKIPs all tests: do not consider this tested!
      (list #:configure-flags
            #~(list (string-append "-Drootprefix=" #$output)
+                   (string-append "-Dlibdir=" #$output "/lib")
                    (string-append "-Dbashcompletiondir=" #$output
                                   "/share/bash-completion/completions")
                    (string-append "-Dsysconfdir=" #$output "/etc")
+                   (string-append "-Diniparserdir="
+                                  #$(this-package-input "iniparser")
+                                  "/include")
                    "-Dasciidoctor=disabled" ; use docbook-xsl instead
                    "-Dsystemd=disabled")
            #:phases

gnu/packages/dns.scm

@@ -333,14 +333,14 @@ and BOOTP/TFTP for network booting of diskless machines.")
     ;; When updating, check whether isc-dhcp's bundled copy should be as well.
     ;; The BIND release notes are available here:
     ;; https://www.isc.org/bind/
-    (version "9.16.35")
+    (version "9.16.37")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://ftp.isc.org/isc/bind9/" version
                            "/bind-" version ".tar.xz"))
        (sha256
-        (base32 "0gkvilfhqwalcv69240v6j1p3hwj0j4fyzli18q5qil2y4brc59y"))
+        (base32 "1az2y8zdpn6vfmx4xqnsh5znagcrsvkqa1hz3h8izzm24ban2ihf"))
        (patches
         (search-patches "bind-re-add-attr-constructor-priority.patch"))))
     (build-system gnu-build-system)

gnu/packages/documentation.scm

@@ -66,7 +66,7 @@
 (define-public latex2html
   (package
     (name "latex2html")
-    (version "2020.2")
+    (version "2022.2")
     (source
      (origin
        (method git-fetch)
@@ -76,29 +76,26 @@
          (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1icyl6kl60wh7cavprgbd8q6lpjwr7wn24m34kpiif7ahknhcbcm"))))
+        (base32 "1z71anjzxy5jsdlaqba4w9spncc6iycldarnr2z1dq8xmk6yhpjn"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:phases
+     (list #:phases
-       (modify-phases %standard-phases
+           #~(modify-phases %standard-phases
-         (add-after 'unpack 'patch-configure
+               (add-after 'unpack 'patch-configure
-           (lambda* (#:key outputs #:allow-other-keys)
+                 (lambda* (#:key outputs #:allow-other-keys)
-             (substitute* "configure"
+                   (substitute* "configure"
-               (("/usr/local")
+                     (("/usr/local")
-                (assoc-ref outputs "out"))
+                      #$output)
-               (("\\$\\{CONFIG_SHELL-/bin/sh\\}")
+                     (("\\$\\{CONFIG_SHELL-/bin/sh\\}")
-                (which "bash")))
+                      (which "bash")))))
-             #t))
+               (replace 'configure
-         (replace 'configure
+                 (lambda _
-           (lambda _
+                   (invoke "./configure")))
-             (invoke "./configure")
+               (add-after 'configure 'patch-cfgcache
-             #t))
+                 (lambda* (#:key outputs #:allow-other-keys)
-         (add-after 'configure 'patch-cfgcache
+                   (substitute* "cfgcache.pm"
-           (lambda* (#:key outputs #:allow-other-keys)
+                     (("/usr/local")
-             (substitute* "cfgcache.pm"
+                      #$output)))))))
-               (("/usr/local")
-                (assoc-ref outputs "out")))
-             #t)))))
     (inputs
      (list perl))
     (synopsis "LaTeX documents to HTML")
@@ -254,7 +251,7 @@ and to some extent D.")
     (build-system gnu-build-system)
     (native-inputs
      (list flex gettext-minimal))
-    (home-page "http://docpp.sourceforge.net/")
+    (home-page "https://docpp.sourceforge.net")
     (synopsis "Documentation system for C, C++, IDL, and Java")
     (description
      "DOC++ is a documentation system for C, C++, IDL, and Java.  It can

gnu/packages/education.scm

@@ -4,7 +4,7 @@
 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2017, 2018, 2019, 2020, 2021, 2022 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018–2021 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2018-2022 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2018-2023 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2020 Robert Smith <robertsmith@posteo.net>
 ;;; Copyright © 2020 Guy Fleury Iteriteka <gfleury@disroot.org>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
@@ -582,7 +582,7 @@ a pen-tablet display and a beamer.")
 (define-public fet
   (package
     (name "fet")
-    (version "6.7.7")
+    (version "6.8.2")
     (source
      (origin
        (method url-fetch)
@@ -591,7 +591,7 @@ a pen-tablet display and a beamer.")
               (list (string-append directory base)
                     (string-append directory "old/" base))))
        (sha256
-        (base32 "08rm3yka3swr6wf3lcmzh2jlq5ajxi8c6nd2likqzvbg6plrjx6b"))))
+        (base32 "1wv7qwfmpmmfyr2kklp2q047rl38ps55cizjrm6v8np2cjl0ah3g"))))
     (build-system gnu-build-system)
     (arguments
      (list
@@ -623,14 +623,14 @@ hours.")
 (define-public klavaro
   (package
     (name "klavaro")
-    (version "3.13")
+    (version "3.14")
     (source
       (origin
         (method url-fetch)
         (uri (string-append "mirror://sourceforge/klavaro/klavaro-"
                             version ".tar.bz2"))
         (sha256
-         (base32 "0z6c3lqikk50mkz3ipm93l48qj7b98lxyip8y6ndg9y9k0z0n878"))))
+         (base32 "1avdwpmd7jmdkrwzsxd8s8qg0sqj2avcv620jvk11i81sd4pw647"))))
     (build-system gnu-build-system)
     (native-inputs
      (list intltool pkg-config))

gnu/packages/elf.scm

@@ -30,8 +30,9 @@
   #:use-module (guix utils)
   #:use-module (guix packages)
   #:use-module (guix download)
+  #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
-  #:use-module ((guix licenses) #:select (gpl3+ lgpl3+ lgpl2.0+))
+  #:use-module ((guix licenses) #:select (gpl3+ lgpl3+ lgpl2.0+ lgpl2.1 gpl2 bsd-2))
   #:use-module (gnu packages)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages compression)
@@ -282,3 +283,31 @@ changed.")
     (properties
      '((release-monitoring-url . "https://github.com/NixOS/patchelf/releases")))
     (license gpl3+)))
+
+(define-public libdwarf
+  (package
+    (name "libdwarf")
+    (version "0.5.0")
+    (source (origin
+              (method git-fetch)
+              ;; The archive at
+              ;; https://www.prevanders.net/libdwarf-0.5.0.tar.xz
+              ;; has a bad date header (3600).
+              (uri (git-reference
+                    (url "https://github.com/davea42/libdwarf-code")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "17sgjxx666nxvxn3g1xc8fj0b89jazq9v8ddp3j3ck0r257ki8n2"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:configure-flags '("--enable-shared")))
+    (native-inputs (list autoconf automake libtool pkg-config python))
+    (inputs (list elfutils))
+    (home-page "https://www.prevanders.net/dwarf.html")
+    (synopsis "Handle DWARF debugging information")
+    (description "@code{libdwarf} is a library that handles the DWARF
+debugging information format.")
+    ;; See https://www.prevanders.net/dwarflicense.html:
+    (license (list lgpl2.1 gpl2 bsd-2))))

gnu/packages/emacs.scm

@@ -23,6 +23,7 @@
 ;;; Copyright © 2020 Jack Hill <jackhill@jackhill.us>
 ;;; Copyright © 2020 Morgan Smith <Morgan.J.Smith@outlook.com>
 ;;; Copyright © 2022 Zhu Zihao <all_but_last@163.com>
+;;; Copyright © 2023 Declan Tsien <declantsien@riseup.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -75,6 +76,7 @@
   #:use-module (gnu packages sqlite)
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages tls)
+  #:use-module (gnu packages text-editors) ; for tree-sitter
   #:use-module (gnu packages web)       ; for jansson
   #:use-module (gnu packages webkit)
   #:use-module (gnu packages xml)
@@ -381,12 +383,12 @@ languages.")
     (license license:gpl3+)))
 
 (define-public emacs-next
-  (let ((commit "22e8a775838ef12bd43102315f13d202e2f215bd")
+  (let ((commit "ac7ec87a7a0db887e4ae7fe9005aea517958b778")
-        (revision "3"))
+        (revision "0"))
     (package
       (inherit emacs)
       (name "emacs-next")
-      (version (git-version "29.0.50" revision commit))
+      (version (git-version "29.0.60" revision commit))
       (source
        (origin
          (inherit (package-source emacs))
@@ -401,10 +403,10 @@ languages.")
                                   "emacs-native-comp-driver-options.patch"))
          (sha256
           (base32
-           "1byp8m13d03swifmc6s9f1jq4py4xm6bqpzzgsbnari7v70zayyg"))))
+           "1akq6dbllwwqwx21wnwnv6aax1nsi2ypbd7j3i79sw62s3gf399z"))))
       (inputs
        (modify-inputs (package-inputs emacs)
-         (prepend sqlite)))
+         (prepend sqlite tree-sitter)))
       (native-inputs
        (modify-inputs (package-native-inputs emacs)
          (prepend autoconf))))))
@@ -448,6 +450,7 @@ GTK and also enables xwidgets.")))
        ((#:phases phases)
         #~(modify-phases #$phases
             (delete 'set-libgccjit-path)
+            (delete 'patch-compilation-driver)
             (delete 'restore-emacs-pdmp)
             (delete 'strip-double-wrap)))))
     (inputs (list ncurses coreutils gzip))

gnu/packages/emulators.scm

@@ -3,10 +3,10 @@
 ;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
 ;;; Copyright © 2015, 2016, 2021 Sou Bunnbu <iyzsong@member.fsf.org>
 ;;; Copyright © 2015, 2016 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
-;;; Copyright © 2015, 2018 David Thompson <dthompson2@worcester.edu>
+;;; Copyright © 2015, 2018, 2023 David Thompson <dthompson2@worcester.edu>
 ;;; Copyright © 2016 Manolis Fragkiskos Ragkousis <manolis837@gmail.com>
 ;;; Copyright © 2016, 2017, 2018, 2020 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2017-2022 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2017-2023 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2017, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017, 2018, 2019 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2019 Pierre Neidhardt <mail@ambrevar.xyz>
@@ -74,6 +74,7 @@
   #:use-module (gnu packages gl)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
+  #:use-module (gnu packages graphics)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages image)
   #:use-module (gnu packages libedit)
@@ -722,7 +723,7 @@ The following systems are supported:
 (define-public mgba
   (package
     (name "mgba")
-    (version "0.10.0")
+    (version "0.10.1")
     (source
      (origin
        (method git-fetch)
@@ -731,7 +732,7 @@ The following systems are supported:
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "14miy6fgg4dy2pp0w17pnqzizrj6yf468i5l7rswn3yszpd5rn6s"))
+        (base32 "0pqfjsr9q61a3mgmvqxxkalxb838k46q9ilz31frpcvvndif0sm1"))
        (modules '((guix build utils)))
        (snippet
         ;; Make sure we don't use the bundled software.
@@ -1506,6 +1507,57 @@ reference frontend for the libretro API, currently used by most as a modular
 multi-system game/emulator system.")
     (license license:gpl3+)))
 
+(define-public wasm4
+  (package
+    (name "wasm4")
+    (version "2.5.4")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/aduros/wasm4")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0ycnznwy4i4fw6l507y5xm986rxqvnpl971725q8xinsnq2swpnl"))))
+    (build-system cmake-build-system)
+    (arguments
+     (list
+      #:tests? #f ; no check target
+      #:configure-flags
+      #~(list (string-append "-DCMAKE_C_FLAGS="
+                             "-I" #$minifb "/include "
+                             "-I" #$wasm3 "/include"))
+      #:phases
+      '(modify-phases %standard-phases
+         ;; WASM4's source is a combination of multiple runtimes.  We want to
+         ;; build the native one.
+         (add-after 'unpack 'chdir-to-native-runtime
+           (lambda _
+             (chdir "runtimes/native")))
+         ;; WASM4 uses git submodules to bundle several dependencies, which we
+         ;; have instead made dedicated packages for.  This phase hacks the
+         ;; build system to use our own stuff.
+         (add-after 'chdir-to-native-runtime 'unbundle
+           (lambda _
+             (substitute* "CMakeLists.txt"
+               ;; These directories do not exist because we aren't pulling in
+               ;; submodules.
+               (("add_subdirectory\\(vendor/minifb\\)") "")
+               (("add_subdirectory\\(vendor/cubeb\\)") "")
+               ;; Add additional libraries needed to successfully link the
+               ;; wasm4 executable using the unbundled dependencies.
+               (("target_link_libraries\\(wasm4 minifb cubeb\\)")
+                "target_link_libraries(wasm4 m GL X11 xkbcommon minifb cubeb m3)")))))))
+    (inputs (list cubeb minifb wasm3))
+    (synopsis "WebAssembly fantasy console")
+    (description "WASM-4 is a low-level fantasy game console for building
+small games with WebAssembly.  Game cartridges (ROMs) are small,
+self-contained .wasm files that can be built with any programming language
+that compiles to WebAssembly.")
+    (home-page "https://wasm4.org")
+    (license license:isc)))
+
 (define-public scummvm
   (package
     (name "scummvm")
@@ -1716,7 +1768,7 @@ This is a part of the TiLP project.")
 (define-public mame
   (package
     (name "mame")
-    (version "0.249")
+    (version "0.251")
     (source
      (origin
        (method git-fetch)
@@ -1725,7 +1777,7 @@ This is a part of the TiLP project.")
              (commit (apply string-append "mame" (string-split version #\.)))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1akws4l3b7z5mkf09mdaz640rj41sbg3sh1xlv1sp0yhdjqjpi90"))
+        (base32 "102p6kz4ph9m0sxsyavqhjzg00gmnq8m5mnd5sf14c61d2jc0vzk"))
        (modules '((guix build utils)))
        (snippet
         ;; Remove bundled libraries.

gnu/packages/engineering.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
-;;; Copyright © 2016, 2018, 2020, 2021, 2022 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2018, 2020-2023 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 David Thompson <davet@gnu.org>
 ;;; Copyright © 2016, 2017, 2018, 2019, 2021 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016, 2017, 2018 Theodoros Foradis <theodoros@foradis.org>
@@ -19,7 +19,7 @@
 ;;; Copyright © 2020, 2023 Marius Bakke <marius@gnu.org>
 ;;; Copyright © 2020, 2021 Ekaitz Zarraga <ekaitz@elenq.tech>
 ;;; Copyright © 2020 B. Wilson <elaexuotee@wilsonb.com>
-;;; Copyright © 2020, 2021, 2022 Vinicius Monego <monego@posteo.net>
+;;; Copyright © 2020, 2021, 2022, 2023 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2020, 2021 Morgan Smith <Morgan.J.Smith@outlook.com>
 ;;; Copyright © 2021 qblade <qblade@protonmail.com>
 ;;; Copyright © 2021 Gerd Heber <gerd.heber@gmail.com>
@@ -68,6 +68,7 @@
   #:use-module (guix build-system emacs)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
+  #:use-module (guix build-system pyproject)
   #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (gnu packages)
@@ -944,7 +945,7 @@ Emacs).")
 (define-public kicad
   (package
     (name "kicad")
-    (version "6.0.10")
+    (version "6.0.11")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -952,7 +953,7 @@ Emacs).")
                     (commit version)))
               (sha256
                (base32
-                "0pz8d96imc0q3nh7npr5zf0jkzi94wchvw57spcrgqfac9yrld3q"))
+                "1bhzmgs921wv1pc0mpyigmpp630086kmpifc3a91cbkv4xf0akkq"))
               (file-name (git-file-name name version))))
     (build-system cmake-build-system)
     (arguments
@@ -1051,7 +1052,7 @@ electrical diagrams), gerbview (viewing Gerber files) and others.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "06aw8f1pnh63dscv2bkii0cpr2m5yc4baka3avszsxnv8mqn0hwx"))))
+                "0f191ifzgl2k196ph7ljip97s17gq8bsfkn1s3aza1qaafhg7acd"))))
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags (list "-DBUILD_FORMATS=html")
@@ -2351,6 +2352,74 @@ specification can be downloaded at @url{http://3mf.io/specification/}.")
     (home-page "https://3mf.io/")
     (license license:bsd-2)))
 
+(define-public python-pyvisa
+  (package
+    (name "python-pyvisa")
+    (version "1.13.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "PyVISA" version))
+              (sha256
+               (base32
+                "1iprr3h6d4w6v8ksgqpkgg545sai7i8hi5a5an394p26b25h1yl9"))
+              (modules '((guix build utils)))
+              (snippet '(begin
+                          ;; Delete bundled python-prettytable.
+                          (delete-file-recursively "pyvisa/thirdparty")))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list #:phases #~(modify-phases %standard-phases
+                        (add-after 'unpack 'use-system-prettytable
+                          (lambda _
+                            (substitute* "pyvisa/shell.py"
+                              (("from .thirdparty import prettytable")
+                               "import prettytable")))))))
+    (native-inputs (list python-pytest-7.1))
+    (propagated-inputs (list python-dataclasses python-prettytable
+                             python-typing-extensions))
+    (home-page "https://pyvisa.readthedocs.io/en/latest/")
+    (synopsis "Python binding for the VISA library")
+    (description "PyVISA is a Python package for support of the
+@acronym{VISA, Virtual Instrument Software Architecture}, in order to control
+measurement devices and test equipment via GPIB, RS232, Ethernet or USB.")
+    (license license:expat)))
+
+(define-public python-scikit-rf
+  (package
+    (name "python-scikit-rf")
+    (version "0.24.1")
+    (source (origin
+              (method git-fetch) ;PyPI misses some files required for tests
+              (uri (git-reference
+                    (url "https://github.com/scikit-rf/scikit-rf")
+                    (commit (string-append "v" version))))
+              (sha256
+               (base32
+                "1shp8q8324dkwf448mv9zzi7krx882p122ma4fk015qz91sg4wff"))
+              (file-name (git-file-name name version))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-matplotlib
+                             python-networkx
+                             python-numpy
+                             python-openpyxl
+                             python-pandas
+                             python-pyqt
+                             python-pyqtgraph
+                             python-qtpy
+                             python-scipy))
+    (native-inputs (list python-coverage
+                         python-flake8
+                         python-nbval
+                         python-networkx
+                         python-pytest-7.1
+                         python-pytest-cov
+                         python-pyvisa))
+    (home-page "https://scikit-rf.org/")
+    (synopsis "Radio frequency and Microwave Engineering Scikit")
+    (description "Scikit-rf, or @code{skrf}, is a Python package for RF and
+Microwave engineering.")
+    (license license:bsd-3)))
+
 (define-public openscad
   (package
     (name "openscad")
@@ -2844,13 +2913,13 @@ program that can perform mesh processing tasks in batch mode, without a GUI.")
 (define-public poke
   (package
     (name "poke")
-    (version "2.4")
+    (version "3.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnu/poke/poke-" version
                                   ".tar.gz"))
               (sha256
-               (base32 "0ivfzslpdy0n9wcdjyascnqczppaxcq0x4x6hblqqwy62xcjh7l4"))
+               (base32 "1pbs6587wcbgdhn4v4l896nzdv7ymgpdmyls95y3534z7krv5abr"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -2901,7 +2970,11 @@ program that can perform mesh processing tasks in batch mode, without a GUI.")
     (arguments
      ;; To build the GUI, add the `--enable-gui' configure flag.
      ;; To enable the "hyperlink server", add the `--enable-hserver' flag.
-     `(#:configure-flags '("--enable-mi")))
+     `(#:configure-flags
+       '("--enable-mi"
+         "--disable-static"
+         ;; The emacs files are provided in emacs-poke.
+         "--with-lispdir=/tmp/share/emacs")))
     (home-page "https://www.gnu.org/software/poke/#documentation")
     (synopsis "Editing of arbitrary binary data")
     (description "GNU poke is an interactive, extensible editor for binary data.
@@ -2910,6 +2983,24 @@ full-fledged procedural, interactive programming language designed to describe
 data structures and to operate on them.")
     (license license:gpl3+)))
 
+(define-public emacs-poke
+  (package
+    (inherit poke)
+    (name "emacs-poke")
+    (build-system emacs-build-system)
+    (arguments
+     (list
+       #:phases
+       #~(modify-phases %standard-phases
+           (add-before 'expand-load-path 'change-working-directory
+             (lambda _ (chdir "etc"))))))
+    (inputs '())
+    (native-inputs '())
+    (synopsis "GNU Poke major modes for Emacs")
+    (description
+     "This package provides two Emacs major modes for working with GNU Poke:
+@code{Poke Ras mode} and @code{Poke Map mode}.")))
+
 (define-public pcb2gcode
   ;; Take some additional commits after v2.4.0 to fix build against
   ;; geos 3.10.1.

gnu/packages/enlightenment.scm

@@ -5,6 +5,7 @@
 ;;; Copyright © 2017 Nikita <nikita@n0.is>
 ;;; Copyright © 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Timo Eisenmann <eisenmann@fn.de>
+;;; Copyright © 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -82,63 +83,63 @@
                 "05bxc58hj0z6pkp6yy5cmy1lc575q0nrbr5lxr6z8d4kznh3my6r"))))
     (build-system meson-build-system)
     (native-inputs
-     `(("check" ,check)
+     (list check
-       ("gettext" ,gettext-minimal)
+           gettext-minimal
-       ("pkg-config" ,pkg-config)
+           pkg-config
-       ("python" ,python)))
+           python))
     (inputs
-     `(("curl" ,curl)
+     (list curl
-       ("giflib" ,giflib)
+           giflib
-       ("gstreamer" ,gstreamer)
+           gstreamer
-       ("gst-plugins-base" ,gst-plugins-base)
+           gst-plugins-base
-       ("ibus" ,ibus)
+           ibus-minimal
-       ("mesa" ,mesa)
+           mesa
-       ("libraw" ,libraw)
+           libraw
-       ("librsvg" ,(librsvg-for-system))
+           (librsvg-for-system)
-       ("libspectre" ,libspectre)
+           libspectre
-       ("libtiff" ,libtiff)
+           libtiff
-       ("libxau" ,libxau)
+           libxau
-       ("libxcomposite" ,libxcomposite)
+           libxcomposite
-       ("libxcursor" ,libxcursor)
+           libxcursor
-       ("libxdamage" ,libxdamage)
+           libxdamage
-       ("libxdmcp" ,libxdmcp)
+           libxdmcp
-       ("libxext" ,libxext)
+           libxext
-       ("libxi" ,libxi)
+           libxi
-       ("libxfixes" ,libxfixes)
+           libxfixes
-       ("libxinerama" ,libxinerama)
+           libxinerama
-       ("libxrandr" ,libxrandr)
+           libxrandr
-       ("libxrender" ,libxrender)
+           libxrender
-       ("libxss" ,libxscrnsaver)
+           libxscrnsaver
-       ("libxtst" ,libxtst)
+           libxtst
-       ("libwebp" ,libwebp)
+           libwebp
-       ("openjpeg" ,openjpeg)
+           openjpeg
-       ("poppler" ,poppler)
+           poppler
-       ("util-linux" ,util-linux "lib")
+           `(,util-linux "lib")
-       ("wayland-protocols" ,wayland-protocols)))
+           wayland-protocols))
     (propagated-inputs
      ;; All these inputs are in package config files in section
      ;; Requires.private.
-     `(("dbus" ,dbus)
+     (list dbus
-       ("elogind" ,elogind)
+           elogind
-       ("eudev" ,eudev)
+           eudev
-       ("fontconfig" ,fontconfig)
+           fontconfig
-       ("freetype" ,freetype)
+           freetype
-       ("fribidi" ,fribidi)
+           fribidi
-       ("glib" ,glib)
+           glib
-       ("harfbuzz" ,harfbuzz)
+           harfbuzz
-       ("libinput" ,libinput-minimal)
+           libinput-minimal
-       ("libjpeg" ,libjpeg-turbo)
+           libjpeg-turbo
-       ("libsndfile" ,libsndfile)
+           libsndfile
-       ("libpng" ,libpng)
+           libpng
-       ("libunwind" ,libunwind)
+           libunwind
-       ("libx11" ,libx11)
+           libx11
-       ("libxkbcommon" ,libxkbcommon)
+           libxkbcommon
-       ("luajit" ,luajit)
+           luajit
-       ("lz4" ,lz4)
+           lz4
-       ("openssl" ,openssl)
+           openssl
-       ("pulseaudio" ,pulseaudio)
+           pulseaudio
-       ("wayland" ,wayland)
+           wayland
-       ("zlib" ,zlib)))
+           zlib))
     (arguments
      `(#:configure-flags
        `("-Dembedded-lz4=false"
@@ -158,22 +159,17 @@
          ;; have to wrap the outputs of efl's dependencies in those libraries.
          (add-after 'unpack 'hardcode-dynamic-libraries
            (lambda* (#:key inputs #:allow-other-keys)
-             (let ((curl    (assoc-ref inputs "curl"))
+             (substitute* "src/lib/ecore_con/ecore_con_url_curl.c"
-                   (pulse   (assoc-ref inputs "pulseaudio"))
+               (("libcurl.so.4")
-                   (sndfile (assoc-ref inputs "libsndfile"))
+                (search-input-file inputs "lib/libcurl.so.4")))
-                   (elogind (assoc-ref inputs "elogind"))
+             (substitute* "src/lib/ecore_audio/ecore_audio.c"
-                   (lib     "/lib/"))
+               (("libpulse.so.0")
-               (substitute* "src/lib/ecore_con/ecore_con_url_curl.c"
+                (search-input-file inputs "lib/libpulse.so.0"))
-                 (("libcurl.so.?" libcurl) ; libcurl.so.[45]
+               (("libsndfile.so.1")
-                  (string-append curl lib libcurl)))
+                (search-input-file inputs "lib/libsndfile.so.1")))
-               (substitute* "src/lib/ecore_audio/ecore_audio.c"
+             (substitute* "src/lib/elput/elput_logind.c"
-                 (("libpulse.so.0" libpulse)
+               (("libelogind.so.0")
-                  (string-append pulse lib libpulse))
+                (search-input-file inputs "lib/libelogind.so.0")))))
-                 (("libsndfile.so.1" libsnd)
-                  (string-append sndfile lib libsnd)))
-               (substitute* "src/lib/elput/elput_logind.c"
-                 (("libelogind.so.0" libelogind)
-                  (string-append elogind "/lib/" libelogind))))))
          (add-after 'unpack 'fix-install-paths
            (lambda _
              (substitute* "dbus-services/meson.build"

gnu/packages/erlang.scm

@@ -376,7 +376,7 @@ Markdown.")
     (propagated-inputs
      (list erlang-cf))
     (native-inputs
-     (list git-minimal/fixed))  ;; Required for tests
+     (list git-minimal/pinned))  ;; Required for tests
     (arguments
      `(#:phases
        (modify-phases %standard-phases
@@ -701,7 +701,7 @@ applications as a dependent libraries.")
           (base32 "1dfz56034pa25axly9vqdzv3phkn8ll0qwrkws96pbgcprhky1hx"))))
     (build-system rebar-build-system)
     (inputs
-     (list git-minimal/fixed))
+     (list git-minimal/pinned))
     (arguments
      `(;; Running the tests require binary artifact (tar-file containing
        ;; samples git repos)  TODO: remove these from the source

gnu/packages/fcitx5.scm

@@ -56,7 +56,7 @@
 (define-public xcb-imdkit
   (package
     (name "xcb-imdkit")
-    (version "1.0.3")
+    (version "1.0.4")
     (source
      (origin
        (method url-fetch)
@@ -64,7 +64,7 @@
              "https://download.fcitx-im.org/fcitx5/xcb-imdkit/xcb-imdkit-"
              version ".tar.xz"))
        (sha256
-        (base32 "1s58vjkdrgr8h183jz4b4mjn7pbvdc9cli01cn66mgczl9p65hh9"))
+        (base32 "1jfhrqq89grrkwmp4lbn1pxi7935jhhz9xr8yqa07aarqb86skw2"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -87,7 +87,7 @@ client.")
 (define-public fcitx5
   (package
     (name "fcitx5")
-    (version "5.0.19")
+    (version "5.0.21")
     (source
      (origin
        (method url-fetch)
@@ -95,7 +95,7 @@ client.")
              "https://download.fcitx-im.org/fcitx5/fcitx5/fcitx5-"
              version "_dict.tar.xz"))
        (sha256
-        (base32 "13zp6f8z590m34yjfzkw1jckvw1k0p8gzbkwm9lfzbrz9pzgdl1p"))))
+        (base32 "10hchay93ld3fs2p17gmq50gsv96q908hzjinn0nh0qcnpz8sx60"))))
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags
@@ -172,14 +172,14 @@ client.")
 (define-public libime
   (package
     (name "libime")
-    (version "1.0.14")
+    (version "1.0.16")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://download.fcitx-im.org/fcitx5/libime/libime-"
                            version "_dict.tar.xz"))
        (sha256
-        (base32 "0qvi9wpm4hx42h05bd4ngwzr4sv4x7i18m3ppzwc8n6q3sz5cfbh"))))
+        (base32 "1ydja6bpb9q7j2dj87yni1jlw9nj7256g3dqvz1hl4dl8zill0rz"))))
     (build-system cmake-build-system)
     (inputs
      (list fcitx5 boost))
@@ -194,7 +194,7 @@ editors.")
 (define-public fcitx5-gtk
   (package
     (name "fcitx5-gtk")
-    (version "5.0.19")
+    (version "5.0.21")
     (source
      (origin
        (method url-fetch)
@@ -202,7 +202,7 @@ editors.")
                            "/fcitx5-gtk/fcitx5-gtk-"
                            version ".tar.xz"))
        (sha256
-        (base32 "007ls91jfbs3anvcfbza1pjbbsi7q5nrw7f3nzdbyngsl3nj6k37"))))
+        (base32 "04909s99nng835qaycsbhwkmml4prhvpg3r3b39ranqyjy4m4dqj"))))
     (build-system cmake-build-system)
     (arguments
      (list
@@ -312,7 +312,7 @@ IM module for GTK+3 applications.
 (define-public fcitx5-qt
   (package
     (name "fcitx5-qt")
-    (version "5.0.15")
+    (version "5.0.16")
     (source
      (origin
        (method url-fetch)
@@ -320,7 +320,7 @@ IM module for GTK+3 applications.
                            "/fcitx5-qt/fcitx5-qt-"
                            version ".tar.xz"))
        (sha256
-        (base32 "1a21fgfsdpxxchpd5bjb7f2aj3fk7i4iawgs491974y7ad1kqx11"))))
+        (base32 "1wsal20629iwcjdqs8mj4ksg62al2aw05da11ak35fjbbw2w2fjq"))))
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags
@@ -347,7 +347,7 @@ for Qt based application.")
 (define-public fcitx5-anthy
   (package
     (name "fcitx5-anthy")
-    (version "5.0.12")
+    (version "5.0.13")
     (source
      (origin
        (method url-fetch)
@@ -355,7 +355,7 @@ for Qt based application.")
                            "/fcitx5-anthy/fcitx5-anthy-"
                            version ".tar.xz"))
        (sha256
-        (base32 "090wdxsd0clynw5k3l522mcrywqv5p194kjl79g8jbwa637642w0"))))
+        (base32 "1qj8kylskjyxcvrc0mg46s3cn8rrfblgp6kkkw26x5js4di74shh"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f)) ;; no tests
@@ -371,7 +371,7 @@ the Anthy input method.")
 (define-public fcitx5-chinese-addons
   (package
     (name "fcitx5-chinese-addons")
-    (version "5.0.15")
+    (version "5.0.16")
     (source
      (origin
        (method url-fetch)
@@ -379,7 +379,7 @@ the Anthy input method.")
                            "/fcitx5-chinese-addons/fcitx5-chinese-addons-"
                            version "_dict.tar.xz"))
        (sha256
-        (base32 "0l3qa958ngb19ydm4jsm44yvw2gn3p6gfjvknm4iv4fdazcr4plp"))))
+        (base32 "06s7d3n4h5b0msw0b48pmy3xcz7268b7r00p3wfr83wb1m9rv0xw"))))
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags
@@ -435,7 +435,7 @@ including input methods previous bundled inside Fcitx 4:
 (define-public fcitx5-configtool
   (package
     (name "fcitx5-configtool")
-    (version "5.0.15")
+    (version "5.0.16")
     (source
      (origin
        (method url-fetch)
@@ -443,7 +443,7 @@ including input methods previous bundled inside Fcitx 4:
              "https://download.fcitx-im.org/fcitx5"
              "/fcitx5-configtool/fcitx5-configtool-" version ".tar.xz"))
        (sha256
-        (base32 "1k5qmwp2v8k2r1lvagdy6ffsafcqkx4k803j9a0fm5pp5yz0ibk8"))))
+        (base32 "06n8yhmkammr04nhv0zaw14da3i0dg02wszbr15812shcmdcwazf"))))
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags
@@ -545,7 +545,7 @@ for Fcitx 5 with following color variants:
 (define-public fcitx5-rime
   (package
     (name "fcitx5-rime")
-    (version "5.0.14")
+    (version "5.0.15")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://download.fcitx-im.org/fcitx5"
@@ -553,7 +553,7 @@ for Fcitx 5 with following color variants:
                                   ".tar.xz"))
               (sha256
                (base32
-                "1i8wb7pbjifz48j4c18lp07ms1a2wc3p9d9g13dgimgf9yi64brm"))))
+                "0qq2khc1816sbc3lw2djhpadbhlcp8g7j8wjzb2rzw9yl6n10lkh"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f ;no tests

gnu/packages/file-systems.scm

@@ -46,26 +46,36 @@
   #:use-module (gnu packages admin)
   #:use-module (gnu packages attr)
   #:use-module (gnu packages autotools)
+  #:use-module (gnu packages backup)
   #:use-module (gnu packages base)
   #:use-module (gnu packages bash)
   #:use-module (gnu packages bison)
+  #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages cpp)
   #:use-module (gnu packages crypto)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages cyrus-sasl)
   #:use-module (gnu packages datastructures)
+  #:use-module (gnu packages digest)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages docbook)
+  #:use-module (gnu packages elf)
   #:use-module (gnu packages flex)
   #:use-module (gnu packages gawk)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages golang)
   #:use-module (gnu packages guile)
+  #:use-module (gnu packages jemalloc)
   #:use-module (gnu packages kerberos)
+  #:use-module (gnu packages libevent)
   #:use-module (gnu packages libffi)
+  #:use-module (gnu packages libunwind)
   #:use-module (gnu packages linux)
+  #:use-module (gnu packages maths)
+  #:use-module (gnu packages man)
   #:use-module (gnu packages nfs)
   #:use-module (gnu packages onc-rpc)
   #:use-module (gnu packages openldap)
@@ -73,6 +83,8 @@
   #:use-module (gnu packages perl)
   #:use-module (gnu packages photo)
   #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages popt)
+  #:use-module (gnu packages pretty-print)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-crypto)
   #:use-module (gnu packages python-web)
@@ -81,6 +93,7 @@
   #:use-module (gnu packages rsync)
   #:use-module (gnu packages sssd)
   #:use-module (gnu packages sqlite)
+  #:use-module (gnu packages textutils)
   #:use-module (gnu packages time)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages valgrind)
@@ -922,14 +935,14 @@ All of this is accomplished without a centralized metadata server.")
 (define-public libeatmydata
   (package
     (name "libeatmydata")
-    (version "130")
+    (version "131")        ; also update the "debian-files" input if available
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://www.flamingspork.com/projects/libeatmydata/"
                            "libeatmydata-" version ".tar.gz"))
        (sha256
-        (base32 "1h212l2s0g3pv6q96d94dk7kpp9qzyxqydrrcgyp7zqjwvbiqws8"))))
+        (base32 "1i5bp9a2vmljci3ihzlxf8482106di2ayy1lpr0qb8rq472sh66g"))))
     (build-system gnu-build-system)
     (arguments
      ;; All tests pass---but only if the host kernel allows PTRACE_TRACEME.
@@ -968,10 +981,12 @@ All of this is accomplished without a centralized metadata server.")
     (native-inputs
      `(("debian-files"                  ; for the man page
         ,(origin
+           ;; Debian being what it is, its version can lag behind a bit.  This
+           ;; is tolerable as the man page is general and the command stable.
            (method url-fetch)
            (uri (string-append "https://deb.debian.org/debian/pool/main/"
-                               "libe/libeatmydata/libeatmydata_" version
+                               "libe/libeatmydata/libeatmydata_130-2"
-                               "-2.debian.tar.xz"))
+                               ".debian.tar.xz"))
            (sha256
             (base32 "1sg9g1nv3wl9ymzz33ig4ns563npkbxj67a64m7p34cc813jl95w"))))
        ;; For the test suite.
@@ -1790,3 +1805,162 @@ and rewritable media that wears out (DVD/CD-RW).")
     (description "This package provides an implementation of overlay+shiftfs
 in FUSE for rootless containers.")
     (license license:gpl3)))
+
+(define-public bees
+  (package
+    (name "bees")
+    (version "0.8")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/Zygo/bees")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (modules '((guix build utils)))
+              (snippet
+               ;; Unbundle cityhash.
+               #~(begin
+                   (for-each delete-file
+                             '("lib/city.cc" "include/crucible/city.h"))
+                   (substitute* "lib/Makefile"
+                     (("city.o.*") ""))
+                   (substitute* "src/bees-hash.cc"
+                     (("#include .crucible/city.h.") "#include <city.h>"))))
+              (patches
+               (search-patches
+                ;; XXX: Cherry-picked from upstream, remove the patch when
+                ;; bumping version.
+                "bees-beesd-honor-destdir-on-installation.patch"))
+              (sha256
+               (base32
+                "1kxpz1p9k5ir385kpvmfjawki5vg22hlx768k7835w6n5z5a65y4"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list #:test-target "test"
+           #:make-flags
+           #~(list (string-append "CC=" #$(cc-for-target))
+                   (string-append "DESTDIR=" #$output)
+                   (string-append "BEES_VERSION=" #$version)
+                   "PREFIX=''")
+           #:phases
+           #~(modify-phases %standard-phases
+               (delete 'configure)
+               (add-after 'unpack 'fixpath
+                 (lambda* (#:key inputs #:allow-other-keys)
+                   (substitute* "scripts/beesd.in"
+                     (((string-append "\\<(" (string-join (list "realpath"
+                                                                "uuidparse"
+                                                                "grep"
+                                                                "false"
+                                                                "sed"
+                                                                "true"
+                                                                "head"
+                                                                "mkdir"
+                                                                "mount"
+                                                                "touch"
+                                                                "du"
+                                                                "cut"
+                                                                "rm"
+                                                                "truncate"
+                                                                "chmod")
+                                                          "|") ")\\>") command)
+                      (search-input-file inputs (string-append "/bin/" command)))
+
+                     (("btrfs sub")
+                      (string-append (search-input-file inputs "/bin/btrfs") " sub"))))))))
+    (inputs (list btrfs-progs cityhash util-linux))
+    (home-page "https://github.com/Zygo/bees")
+    (synopsis "Best-Effort Extent-Same, a btrfs dedupe agent")
+    (description
+     "@code{bees} is a block-oriented userspace deduplication agent designed
+for large btrfs filesystems.  It is an offline dedupe combined with an
+incremental data scan capability to minimize time data spends on disk from
+write to dedupe.")
+    (license license:gpl3+)))
+
+(define-public dwarfs
+  (package
+    (name "dwarfs")
+    (version "0.6.2")
+    (source (origin
+              (method url-fetch)
+              ;; The release archive is needed so that version.h is included.
+              (uri (string-append "https://github.com/mhx/dwarfs/releases/download/v"
+                                  version "/dwarfs-" version ".tar.xz"))
+              (sha256
+               (base32
+                "1kncxf85gsj3anck8ccjmxn2azp5ifqbgkiky2kharmvphkbmfcv"))
+              (snippet
+               #~(begin
+                   (use-modules (guix build utils))
+                   ;; Prefer system libraries instead of submodules.
+                   ;; TODO: Package fbthrift.
+                   ;; TODO: Can we use Guix own folly?  There is no CMake option for it.
+                   ;; TODO: Package parallel-hashmap.
+                   (for-each delete-file-recursively
+                             '(;; "fbthrift"
+                               ;; "folly"
+                               ;; "parallel-hashmap"
+                               "xxHash"
+                               "zstd"))))))
+    (build-system cmake-build-system)
+    (arguments
+     '(#:tests? #f ; TODO: 1 test fails because 'modprobe fuse' needs privileged access.
+       #:configure-flags
+       (list "-DPREFER_SYSTEM_ZSTD=ON"
+             "-DPREFER_SYSTEM_XXHASH=ON"
+             "-DPREFER_SYSTEM_GTEST=ON"
+             "-DWITH_TESTS=ON"
+             ;; Disable man pages since ronn fails to run without hpricot.
+             "-DWITH_MAN_PAGES=OFF")))
+    (native-inputs
+     (list
+      ;; FIXME: Building with ronn fails because hpricot is missing from Guix.
+      folly googletest libdwarf libevent pkg-config))
+    (inputs
+     (list
+      boost
+      double-conversion
+      fmt
+      fuse-3
+      gflags
+      jemalloc
+      libarchive
+      libunwind
+      lz4
+      openssl
+      xxhash
+      xz
+      `(,zstd "lib")))
+    (home-page "https://github.com/mhx/dwarfs")
+    (synopsis "Fast high compression read-only file system")
+    (description "DwarFS is a read-only file system with a focus on achieving
+very high compression ratios in particular for very redundant data.
+
+DwarFS also doesn't compromise on speed and for some cases it is on par with
+or performs better than SquashFS.  For the primary use case, DwarFS
+compression is an order of magnitude better than SquashFS compression, it's 6
+times faster to build the file system, it's typically faster to access files
+on DwarFS and it uses less CPU resources.
+
+Distinct features of DwarFS are:
+
+@itemize
+
+@item Clustering of files by similarity using a similarity hash function.  This
+makes it easier to exploit the redundancy across file boundaries.
+
+@item Segmentation analysis across file system blocks in order to reduce the
+size of the uncompressed file system.  This saves memory when using the
+compressed file system and thus potentially allows for higher cache hit rates
+as more data can be kept in the cache.
+
+@item Highly multi-threaded implementation.  Both the file system creation tool
+as well as the FUSE driver are able to make good use of the many cores of your
+system.
+
+@item Optional experimental Python scripting support to provide custom
+filtering and ordering functionality.
+
+@end itemize\n")
+    (license license:gpl3)))

gnu/packages/finance.scm

@@ -11,7 +11,7 @@
 ;;; Copyright © 2018 Adriano Peluso <catonano@gmail.com>
 ;;; Copyright © 2018-2022 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
-;;; Copyright © 2019, 2020, 2021, 2022 Guillaume Le Vaillant <glv@posteo.net>
+;;; Copyright © 2019-2023 Guillaume Le Vaillant <glv@posteo.net>
 ;;; Copyright © 2019 Tanguy Le Carrour <tanguy@bioneland.org>
 ;;; Copyright © 2019, 2020 Martin Becze <mjbecze@riseup.net>
 ;;; Copyright © 2019 Sebastian Schott <sschott@mailbox.org>
@@ -32,6 +32,7 @@
 ;;; Copyright © 2022 Philip McGrath <philip@philipmcgrath.com>
 ;;; Copyright © 2022 Collin J. Doering <collin@rekahsoft.ca>
 ;;; Copyright © 2022 Justin Veilleux <terramorpha@cock.li>
+;;; Copyright © 2023 Frank Pursel <frank.pursel@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -227,6 +228,14 @@ line client and a client based on Qt.")
         (base32
          "07fcfkmv4cy92njnf2qc7jh0naz96q962hxldcd7hk4k7ddv0mss"))))
     (build-system haskell-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'install 'install-doc
+            (lambda _
+              (install-file "hledger.info" (string-append #$output "/share/info"))
+              (install-file "hledger.1" (string-append #$output "/man/man1")))))))
     (inputs
      (list ghc-ansi-terminal
            ghc-base-compat-batteries
@@ -271,14 +280,14 @@ Accounting.")
 (define-public homebank
   (package
     (name "homebank")
-    (version "5.6")
+    (version "5.6.1")
     (source (origin
               (method url-fetch)
-              (uri (string-append "http://homebank.free.fr/public/homebank-"
+              (uri (string-append "http://homebank.free.fr/public/sources/"
-                                  version ".tar.gz"))
+                                  "homebank-" version ".tar.gz"))
               (sha256
                (base32
-                "1ig00d3wby6lisz3vbyb5qm7h4a6npfwqyphdl8fjgibzpapq5a1"))))
+                "03wgyc777bzys32iv32yf7aj3z4hx87dskq1maw9l9jkqlqrqj1s"))))
     (build-system glib-or-gtk-build-system)
     (native-inputs
      (list pkg-config intltool))
@@ -342,7 +351,8 @@ and dynamically with report tools based on filtering and graphical charts.")
              (let ((examples (string-append (assoc-ref outputs "out")
                                             "/share/doc/ledger/examples")))
                (install-file "test/input/sample.dat" examples)
-               (install-file "test/input/demo.ledger" examples))
+               (install-file "test/input/demo.ledger" examples)
+               (install-file "contrib/report" examples))
              #t))
          (add-after 'build 'build-doc
            (lambda _ (invoke "make" "doc")))
@@ -873,9 +883,38 @@ the Monero command line client and daemon.")
                                      "\";")))))
                (replace 'install
                  (lambda _
-                   (let ((bin (string-append #$output "/bin")))
+                   ;; Binary
-                     (mkdir-p bin)
+                   (let ((dir (string-append #$output "/bin")))
-                     (install-file "../build/bin/monero-wallet-gui" bin))))
+                     (mkdir-p dir)
+                     (install-file "../build/bin/monero-wallet-gui" dir))
+                   ;; Icons
+                   (for-each
+                    (lambda (size)
+                      (let ((dir (string-append #$output
+                                                "/share/icons/hicolor/"
+                                                size
+                                                "/apps")))
+                        (mkdir-p dir)
+                        (copy-file (string-append "../source/images/appicons/"
+                                                  size ".png")
+                                   (string-append dir
+                                                  "/monero-gui.png"))))
+                    '("16x16" "24x24" "32x32" "48x48"
+                      "64x64" "96x96" "128x128" "256x256"))
+                   ;; Menu entry file
+                   (let ((dir (string-append #$output "/share/applications")))
+                     (mkdir-p dir)
+                     (call-with-output-file
+                         (string-append dir "/monero-gui.desktop")
+                       (lambda (port)
+                         (format port
+                                 "[Desktop Entry]~@
+                                  Type=Application~@
+                                  Name=Monero wallet~@
+                                  Exec=~a/bin/monero-wallet-gui~@
+                                  Icon=monero-gui~@
+                                  Categories=Office;Finance;~%"
+                                 #$output))))))
                (add-after 'qt-wrap 'install-monerod-link
                  ;; The monerod program must be available so that
                  ;; monero-wallet-gui can start a Monero daemon if necessary.

gnu/packages/firmware.scm

@@ -2,13 +2,13 @@
 ;;; Copyright © 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2017 David Craven <david@craven.ch>
-;;; Copyright © 2017, 2018, 2022 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2017, 2018, 2022, 2023 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Vagrant Cascadian <vagrant@debian.org>
 ;;; Copyright © 2019 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2020, 2021, 2022 Marius Bakke <marius@gnu.org>
 ;;; Copyright © 2021 Petr Hodina <phodina@protonmail.com>
-;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -414,6 +414,13 @@ provide OpenFirmware functionality on top of an already running system.")
       (inherit base)
       (arguments
        (substitute-keyword-arguments (package-arguments base)
+         ((#:system system (%current-system))
+          (if (string-prefix? "aarch64-linux" (or (%current-system)
+                                                  (%current-target-system)))
+            "armhf-linux"
+            system))
+         ;; No need to cross-compile, package produces reproducible firmware.
+         ((#:target _ #f) #f)
          ((#:phases phases)
           #~(modify-phases #$phases
               (add-after 'install 'rename-executable
@@ -527,6 +534,7 @@ executing in M-mode.")
     (arguments
      (list
       #:tests? #f                       ;no tests
+      #:target #f                       ; Package produces firmware.
       #:make-flags
       ;; If EXTRAVERSION is not set the build system will embed the current
       ;; date in binaries.  Use this opportunity to personalize as recommended
@@ -698,6 +706,7 @@ coreboot.")
                      "HOSTCC=gcc")
              #:parallel-build? #f
              #:tests? #f   ;no tests
+             #:target #f   ; Package produces firmware.
              #:phases
              #~(modify-phases %standard-phases
                  (add-after 'unpack 'build-reproducibly
@@ -894,11 +903,11 @@ Virtual Machines.  OVMF contains a sample UEFI firmware for QEMU and KVM.")
      (substitute-keyword-arguments (package-arguments ovmf)
        ((#:phases phases)
         #~(modify-phases #$phases
-            (add-before 'configure 'set-env
+            #$@(if (string-prefix? "aarch64" (%current-system))
-              (lambda _
+                   '()
-                #$@(if (not (string-prefix? "aarch64" (%current-system)))
+                   '((add-before 'configure 'set-env
-                       #~((setenv "GCC49_AARCH64_PREFIX" "aarch64-linux-gnu-"))
+                       (lambda _
-                       #~())))
+                         (setenv "GCC49_AARCH64_PREFIX" "aarch64-linux-gnu-")))))
             (replace 'build
               (lambda _
                 (invoke "build" "-a" "AARCH64" "-t" "GCC49"
@@ -926,11 +935,11 @@ Virtual Machines.  OVMF contains a sample UEFI firmware for QEMU and KVM.")
      (substitute-keyword-arguments (package-arguments ovmf)
        ((#:phases phases)
         #~(modify-phases #$phases
-            (add-before 'configure 'set-env
+            #$@(if (string-prefix? "armhf" (%current-system))
-              (lambda _
+                   '()
-                #$@(if (not (string-prefix? "armhf" (%current-system)))
+                   '((add-before 'configure 'set-env
-                       #~((setenv "GCC49_ARM_PREFIX" "arm-linux-gnueabihf-"))
+                       (lambda _
-                       #~())))
+                         (setenv "GCC49_ARM_PREFIX" "arm-linux-gnueabihf-")))))
             (replace 'build
               (lambda _
                 (invoke "build" "-a" "ARM" "-t" "GCC49"
@@ -944,70 +953,58 @@ Virtual Machines.  OVMF contains a sample UEFI firmware for QEMU and KVM.")
                              (string-append fmw "/ovmf_arm.bin")))))))))
     (supported-systems %supported-systems)))
 
-(define* (make-arm-trusted-firmware platform #:optional (arch "aarch64"))
+(define* (make-arm-trusted-firmware platform
-  (package
+                                    #:key (triplet "aarch64-linux-gnu"))
-    (name (string-append "arm-trusted-firmware-" platform))
+  (let ((native-build? (lambda ()
-    (version "2.8")
+                         ;; Note: %current-system is a *triplet*, unlike its
-    (source
+                         ;; name would suggest.
-      (origin
+                         (or (not triplet) ;disable cross-compilation
-        (method git-fetch)
+                             (string=? (%current-system)
-        (uri (git-reference
+                                       (gnu-triplet->nix-system triplet))))))
+    (package
+      (name (string-append "arm-trusted-firmware-" platform))
+      (version "2.8")
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
                ;; There are only GitHub generated release snapshots.
                (url "https://git.trustedfirmware.org/TF-A/trusted-firmware-a.git/")
                (commit (string-append "v" version))))
-        (file-name (git-file-name "arm-trusted-firmware" version))
+         (file-name (git-file-name "arm-trusted-firmware" version))
-       (sha256
+         (sha256
-        (base32
+          (base32
-         "0grq3fgxi9xhcljnhwlxjvdghyz15gaq50raw41xy4lm8rkmnzp3"))
+           "0grq3fgxi9xhcljnhwlxjvdghyz15gaq50raw41xy4lm8rkmnzp3"))
-       (snippet
+         (snippet
-        #~(begin
+          #~(begin
-            (use-modules (guix build utils))
+              (use-modules (guix build utils))
-            ;; Remove binary blobs which do not contain source or proper license.
+              ;; Remove binary blobs which do not contain source or proper
-            (for-each (lambda (file)
+              ;; license.
-                        (delete-file file))
+              (for-each (lambda (file)
-                      (find-files "." "\\.bin$"))))))
+                          (delete-file file))
-    (build-system gnu-build-system)
+                        (find-files "." "\\.bin$"))))))
-    (arguments
+      (build-system gnu-build-system)
-     `(#:phases
+      (arguments
-       (modify-phases %standard-phases
+       (list
-         (delete 'configure) ; no configure script
+        #:target (and (not (native-build?)) triplet)
-         (replace 'install
+        #:phases
-           (lambda* (#:key outputs #:allow-other-keys)
+        #~(modify-phases %standard-phases
-             (let ((out (assoc-ref outputs "out"))
+            (delete 'configure)         ;no configure script
-                   (bin (find-files "." "\\.(bin|elf)$")))
+            (replace 'install
-               (for-each
+              (lambda _
-                 (lambda (file)
+                (for-each (lambda (file)
-                   (install-file file out))
+                            (install-file file #$output))
-                 bin)))))
+                          (find-files "." "\\.(bin|elf)$")))))
-       #:make-flags (list (string-append "PLAT=" ,platform)
+        #:make-flags #~(list (string-append "PLAT=" #$platform)
-                          ,@(if (and (not (string-prefix? "aarch64"
+                             #$@(if (not (native-build?))
-                                                          (%current-system)))
+                                    (list (string-append "CROSS_COMPILE=" triplet "-"))
-                                     (string-prefix? "aarch64" arch))
+                                    '())
-                              `("CROSS_COMPILE=aarch64-linux-gnu-")
+                             "DEBUG=1")
-                              '())
+        #:tests? #f))                   ;no test suite
-                          ,@(if (and (not (string-prefix? "armhf"
+      (home-page "https://www.trustedfirmware.org/")
-                                                          (%current-system)))
+      (synopsis "Implementation of \"secure world software\"")
-                                     (string-prefix? "armhf" arch))
+      (description
-                              `("CROSS_COMPILE=arm-linux-gnueabihf-")
+       "ARM Trusted Firmware provides a reference implementation of secure world
-                              '())
-                          "DEBUG=1")
-       #:tests? #f)) ; no tests
-    (native-inputs
-     (let ((system (%current-system)))
-       (cond
-        ((and (not (string-prefix? "aarch64" system))
-              (string-prefix? "aarch64" arch))
-         (list (cross-gcc "aarch64-linux-gnu")
-               (cross-binutils "aarch64-linux-gnu")))
-        ((and (not (string-prefix? "armhf" system))
-              (string-prefix? "armhf" arch))
-         (list (cross-gcc "arm-linux-gnueabihf")
-               (cross-binutils "arm-linux-gnueabihf")))
-        (else '()))))
-    (home-page "https://www.trustedfirmware.org/")
-    (synopsis "Implementation of \"secure world software\"")
-    (description
-     "ARM Trusted Firmware provides a reference implementation of secure world
 software for ARMv7A and ARMv8-A, including a Secure Monitor executing at
 @dfn{Exception Level 3} (EL3).  It implements various ARM interface standards,
 such as:
@@ -1018,8 +1015,8 @@ such as:
 @item System Control and Management Interface
 @item Software Delegated Exception Interface (SDEI)
 @end enumerate\n")
-    (license (list license:bsd-3
+      (license (list license:bsd-3
-                   license:bsd-2)))) ; libfdt
+                     license:bsd-2))))) ; libfdt
 
 (define-public arm-trusted-firmware-sun50i-a64
   (let ((base (make-arm-trusted-firmware "sun50i_a64")))

gnu/packages/fonts.scm

@@ -286,6 +286,30 @@ The Lato 2.010 family supports more than 100 Latin-based languages, over
 50 Cyrillic-based languages as well as Greek and IPA phonetics.")
     (license license:silofl1.1)))
 
+(define-public font-carlito
+  (let ((commit "64cab86c9b602088697294736b86f2831f3f44be")
+        (revision "0"))
+    (package
+      (name "font-carlito")
+      (version (git-version "0.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/googlefonts/carlito")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "02wy8vs5m4whm5apl3p6cpz0qa9jwjj9qi219zjspiszha2ivssz"))))
+      (build-system font-build-system)
+      (home-page "https://github.com/googlefonts/carlito")
+      (synopsis "Free alternative to Calibri")
+      (description
+       "Carlito is a font designed by Łukasz Dziedzic derived from
+Lato (also designed by Łukasz Dziedzic) that is metric-compatible with
+Calibri.")
+      (license license:silofl1.1))))
+
 (define-public font-gfs-ambrosia
   ;; Based on
   ;; https://src.fedoraproject.org/rpms/gfs-ambrosia-fonts
@@ -939,6 +963,37 @@ all languages with a consistent look and aesthetic.  Its goal is to properly
 display all Unicode symbols.")
     (license license:silofl1.1)))
 
+(define-public font-google-noto-emoji
+  (package
+    (name "font-google-noto-emoji")
+    (version "2.038")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/googlefonts/noto-emoji")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "1rgmcc6nqq805iqr8kvxxlk5cf50q714xaxk3ld6rjrd69kb8ix9"))))
+    (build-system font-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'remove-unsupported
+            (lambda* _
+              (delete-file "fonts/NotoColorEmoji_WindowsCompatible.ttf")
+              (delete-file "fonts/Noto-COLRv1-noflags.ttf")
+              (delete-file "fonts/Noto-COLRv1.ttf"))))))
+    (home-page "https://fonts.google.com/noto/specimen/Noto+Color+Emoji")
+    (synopsis "Font for rendering color emoji characters")
+    (description
+     "This package provides the color emoji font from the Google Noto font
+family.")
+    (license license:silofl1.1)))
+
 (define-public font-google-noto-sans-cjk
   (package
     (name "font-google-noto-sans-cjk")
@@ -1666,7 +1721,7 @@ programming.  Iosevka is completely generated from its source code.")
 (define-public font-sarasa-gothic
   (package
     (name "font-sarasa-gothic")
-    (version "0.37.4")
+    (version "0.39.0")
     (source
      (origin
        (method url-fetch)
@@ -1674,7 +1729,7 @@ programming.  Iosevka is completely generated from its source code.")
                            "/releases/download/v" version
                            "/sarasa-gothic-ttc-" version ".7z"))
        (sha256
-        (base32 "12i8lccl4ysinhz40s2fz6249r9n35in4rqmk3a0fgcjfaby3kfm"))))
+        (base32 "19a4a9zsfzkg7xak2sys6jiia7qw1j69206qzn8r2vchrib5lvcz"))))
     (build-system font-build-system)
     (arguments
      `(#:phases (modify-phases %standard-phases
@@ -2823,7 +2878,7 @@ and readability.  This package bundles those icons into a font.")
 (define-public font-lxgw-wenkai
   (package
     (name "font-lxgw-wenkai")
-    (version "1.245.1")
+    (version "1.250")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2831,7 +2886,7 @@ and readability.  This package bundles those icons into a font.")
                     version "/lxgw-wenkai-v" version ".tar.gz"))
               (sha256
                (base32
-                "13hvr1jz9xpb0cgi4xk3zfbn6w5x258zja55hznbgny2sijnjn8a"))))
+                "04c1cszxhs2zw3qn7rs3ik2aaczvf8n28gq9ch6iv782fv2p8irn"))))
     (build-system font-build-system)
     (home-page "https://lxgw.github.io/2021/01/28/Klee-Simpchin/")
     (synopsis "Simplified Chinese Imitation Song typeface")
@@ -2845,7 +2900,7 @@ within GB 2312, standard glyphs for Mainland China is used.")
   (package
     (inherit font-lxgw-wenkai)
     (name "font-lxgw-wenkai-tc")
-    (version "0.922.1")
+    (version "0.932")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2853,7 +2908,7 @@ within GB 2312, standard glyphs for Mainland China is used.")
                     version "/lxgw-wenkai-tc-v" version ".tar.gz"))
               (sha256
                (base32
-                "0a1n0yfnh3sc3ldgjxxglw4xyg82i2pk432sk8hfdzrrl4zzjyz3"))))
+                "12yp3q3hhv847qj7a51cjxxqb2rqm4lvbm54wdr2j4awg3g8lflg"))))
     (home-page "https://github.com/lxgw/LxgwWenKaitc")
     (synopsis "Traditional Chinese Imitation Song typeface")
     (description

gnu/packages/fpga.scm

@@ -433,7 +433,7 @@ a hardware description and verification language.")
 (define-public nvc
   (package
     (name "nvc")
-    (version "1.7.2")
+    (version "1.8.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -442,7 +442,7 @@ a hardware description and verification language.")
               (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "01b0yhr0fw59nxwi4pz04mp9b71mg6s7zaysp0r8h0m2nd5pbpgc"))))
+                "03dnn77n50b5n06gd81hh36gh0h2nc266yzwl70qjlb00qs8cf7p"))))
     (build-system gnu-build-system)
     (arguments
      `(#:out-of-source? #t
@@ -464,7 +464,8 @@ a hardware description and verification language.")
            check)) ; for the tests
     (inputs
      (list elfutils
-           llvm-9))
+           llvm-9
+           libffi))
     (synopsis "VHDL compiler and simulator")
     (description "This package provides a VHDL compiler and simulator.")
     (home-page "https://www.nickg.me.uk/nvc/")

gnu/packages/freedesktop.scm

@@ -133,7 +133,7 @@
 (define-public appstream
   (package
     (name "appstream")
-    (version "0.15.5")
+    (version "0.15.6")
     (source
      (origin
        (method url-fetch)
@@ -142,7 +142,7 @@
                        "appstream/releases/"
                        "AppStream-" version ".tar.xz"))
        (sha256
-        (base32 "1hh41r82a2p7anyadfsp9lmylrrj1a6gknx2g4w6ha97riifs5fb"))))
+        (base32 "03pirmc5r4izl6mzff879g7pk1nxq03kgpr2yvnnqnlb6r0ckmi3"))))
     (build-system meson-build-system)
     (arguments
      (list
@@ -782,7 +782,7 @@ of a the system to know what users are logged in, and where.")
 (define-public basu
   (package
     (name "basu")
-    (version "0.2.0")
+    (version "0.2.1")
     (home-page "https://git.sr.ht/~emersion/basu")
     (source
      (origin
@@ -793,7 +793,7 @@ of a the system to know what users are logged in, and where.")
          (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0h23n7wg18xc7xwldca18wi00iajyliixwicqyvv38qx831d8q18"))))
+        (base32 "054mg6f9aqi0i3i3w8fc37qnns1vng3qq5b8nfd9g51wi8h891nc"))))
     (build-system meson-build-system)
     (native-inputs
      (list pkg-config python gperf))
@@ -2636,7 +2636,7 @@ compatible with the well-known scripts of the same name.")
 (define-public xdg-desktop-portal
   (package
     (name "xdg-desktop-portal")
-    (version "1.14.4")
+    (version "1.14.6")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2644,7 +2644,7 @@ compatible with the well-known scripts of the same name.")
                     version "/xdg-desktop-portal-" version ".tar.xz"))
               (sha256
                (base32
-                "0wqc9x3k7lf3mig53i4rjazi0xi8bcykwaaw7r7prvnscnd1k405"))))
+                "1q0djpnwlrqm0h0alyh1r6dlkqdrr7mj5hiam4mqzxqa5jbqkrgj"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)

gnu/packages/game-development.scm

@@ -27,6 +27,7 @@
 ;;; Copyright © 2021 Andy Tai <atai@atai.org>
 ;;; Copyright © 2022 Felix Gruber <felgru@posteo.net>
 ;;; Copyright © 2022 Jai Vetrivelan <jaivetrivelan@gmail.com>
+;;; Copyright © 2022 dan <i@dan.games>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1772,7 +1773,7 @@ of use.")
      (list boost doxygen pkg-config))
     (inputs
      (list bullet
-           ffmpeg
+           ffmpeg-4                     ; https://gitlab.com/OpenMW/openmw/-/issues/6631
            libxt
            lz4
            mygui-gl              ; OpenMW does not need Ogre.
@@ -2835,3 +2836,35 @@ systems where you stream new navigation data in and out as the player
 progresses the level, or you may regenerate tiles as the world changes.")
       (home-page "https://github.com/recastnavigation/recastnavigation")
       (license license:zlib))))
+
+(define-public raylib
+  (package
+    (name "raylib")
+    (version "4.2.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/raysan5/raylib/")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "14v5iwxh8grywiyw9agpd2sfpyriq1rwwkd9f2s4iihh0z5j7hk8"))))
+    (build-system cmake-build-system)
+    (arguments
+     (list #:tests? #f)) ;no test
+    (inputs (list alsa-lib
+                  libx11
+                  libxrandr
+                  libxi
+                  libxinerama
+                  libxcursor
+                  mesa))
+    (native-inputs (list pkg-config))
+    (synopsis "C library for videogame programming")
+    (description
+     "raylib is a high-level library for video game programming.  It aims to
+  abstract away platform and graphics details, allowing you to focus on
+  writing your game.")
+    (home-page "https://www.raylib.com/")
+    (license license:zlib)))

gnu/packages/games.scm

@@ -30,7 +30,7 @@
 ;;; Copyright © 2017, 2019, 2020 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2017-2022 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2017-2023 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2018 okapi <okapi@firemail.cc>
 ;;; Copyright © 2018 Tim Gesthuizen <tim.gesthuizen@yahoo.de>
 ;;; Copyright © 2018 Madalin Ionel-Patrascu <madalinionel.patrascu@mdc-berlin.de>
@@ -6578,7 +6578,7 @@ becoming difficult enough to tax even the brightest of minds.")
            (sha256
             (base32
              "169p0yqh2gxvhdilvjc2ld8aap7lv2nhkhkg4i1hlmgc6pxpkjgh"))))))
-    (home-page "http://fillets.sourceforge.net/")
+    (home-page "https://fillets.sourceforge.net")
     (synopsis "Puzzle game")
     (description "Fish Fillets NG is strictly a puzzle game.  The goal in
 every of the seventy levels is always the same: find a safe way out.  The fish
@@ -7931,7 +7931,7 @@ ncurses for text display.")
 (define-public naev
   (package
     (name "naev")
-    (version "0.10.1")
+    (version "0.10.3")
     (source
      (origin
        (method git-fetch)
@@ -7941,7 +7941,7 @@ ncurses for text display.")
              (recursive? #t))) ; for game data
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0kvfv2ra0jq1ggf4apsx1j1xhrhjz3fn1j8p4q3a9c4m19fq4qzr"))))
+        (base32 "0hqc2j7lf5ay461l164c63jncmjdvnkm2nf90246njimhz2in056"))))
     (build-system meson-build-system)
     (arguments
      ;; XXX: Do not add debugging symbols, which cause the build to fail.
@@ -8739,7 +8739,7 @@ where the player draws runes in real time to effect the desired spell.")
 (define-public edgar
   (package
     (name "edgar")
-    (version "1.35")
+    (version "1.36")
     (source
      (origin
        (method url-fetch)
@@ -8747,7 +8747,7 @@ where the player draws runes in real time to effect the desired spell.")
         (string-append "https://github.com/riksweeney/edgar/releases/download/"
                        version "/edgar-" version "-1.tar.gz"))
        (sha256
-        (base32 "0hwp73ili10kzx0aibhvgxfddqm94pimdaqhpnba6jzn119834q7"))))
+        (base32 "0fcsmwwfdwap5v6qdijw91kqnnc2i91yzgwfi7vpwvasw70qvna1"))))
     (build-system gnu-build-system)
     (arguments '(#:tests? #f            ; there are no tests
                  #:make-flags
@@ -10409,14 +10409,14 @@ ChessX.")
 (define-public barrage
   (package
     (name "barrage")
-    (version "1.0.5")
+    (version "1.0.6")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "mirror://sourceforge/lgames/barrage/"
                            "barrage-" version ".tar.gz"))
        (sha256
-        (base32 "0139wxyrir10cbkvkjn548xgmp84wax8mfwk80yxbxlcdamrg257"))))
+        (base32 "1bhx708s7viv01m6bmpjsdgr33wk5kqw4wf7bvgw73a07v6j8ncw"))))
     (build-system gnu-build-system)
     (inputs
      (list hicolor-icon-theme sdl sdl-mixer))

gnu/packages/geo.scm

@@ -7,7 +7,7 @@
 ;;; Copyright © 2018, 2019 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;; Copyright © 2018, 2019, 2020, 2021 Julien Lepiller <julien@lepiller.eu>
-;;; Copyright © 2019, 2020, 2021, 2022 Guillaume Le Vaillant <glv@posteo.net>
+;;; Copyright © 2019-2023 Guillaume Le Vaillant <glv@posteo.net>
 ;;; Copyright © 2019-2022 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2019, 2021 Wiktor Żelazny <wzelazny@vurv.cz>
 ;;; Copyright © 2019, 2020 Hartmut Goebel <h.goebel@crazy-compilers.com>
@@ -15,7 +15,7 @@
 ;;; Copyright © 2020 Christopher Baines <mail@cbaines.net>
 ;;; Copyright © 2020, 2021, 2022 Felix Gruber <felgru@posteo.net>
 ;;; Copyright © 2021 Sharlatan Hellseher <sharlatanus@gmail.com>
-;;; Copyright © 2021 Vinicius Monego <monego@posteo.net>
+;;; Copyright © 2021, 2023 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2021 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2021, 2022 Nikolay Korotkiy <sikmir@disroot.org>
 ;;; Copyright © 2022 Roman Scherer <roman.scherer@burningswell.com>
@@ -1167,13 +1167,13 @@ utilities for data translation and processing.")
   (package
     (name "python-cartopy")
     ;; This is a post-release fix that adds build_ext to setup.py.
-    (version "0.21.0")
+    (version "0.21.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "Cartopy" version))
        (sha256
-        (base32 "0hnfs75dcnz12ximah5xn9566r8zz189lxikmj4lrs9jl4l3l7ff"))))
+        (base32 "02i5rjhvrsi3vgj8kfsdx77g1xl59jh2a671qqqj4n682abn9mc9"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -1281,7 +1281,7 @@ extension.")
 (define-public tegola
   (package
     (name "tegola")
-    (version "0.7.0")
+    (version "0.16.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1290,20 +1290,13 @@ extension.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0agqj1b7l41m0imvxjriw44jcpa99mhq1z1vbsfzjhcr94zhwmfr"))))
+                "1mjfn0izf1lj402845mx0cv9fald8s5443q35y16d9crqf3i6mav"))))
     (build-system go-build-system)
     (arguments
      `(#:import-path "github.com/go-spatial/tegola/cmd/tegola"
        #:unpack-path "github.com/go-spatial/tegola"
-       #:phases
+       #:build-flags '(,(string-append "-ldflags=-X github.com/go-spatial/tegola/internal/build.Version=" version))
-       (modify-phases %standard-phases
+       #:install-source? #f))
-         (add-before 'build 'set-version
-           (lambda _
-             (with-directory-excursion "src/github.com/go-spatial/tegola"
-               (substitute* '("cmd/tegola/cmd/root.go"
-                              "cmd/tegola_lambda/main.go")
-                 (("version not set") ,version)))
-             #t)))))
     (home-page "https://tegola.io")
     (synopsis "Vector tile server for maps")
     (description "Tegola is a free vector tile server written in Go.  Tegola
@@ -2739,6 +2732,51 @@ architecture.")
       license:public-domain
       license:qwt1.0))))
 
+(define-public splat
+  (package
+    (name "splat")
+    (version "1.5.0b3")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/hoche/splat")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "10djwjwb1pvznr0fjwnxdm5d961f3yngispb4zj9hyzdgq1xh217"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           ;; Delete pre-compiled libraries.
+           (delete-file-recursively "vstudio")))))
+    (build-system gnu-build-system)
+    (inputs
+     (list bzip2 libjpeg-turbo libpng zlib))
+    (arguments
+     (list #:tests? #f ; No test suite.
+           #:phases
+           #~(modify-phases %standard-phases
+               (add-after 'unpack 'fix-installation-scripts
+                 (lambda _
+                   (substitute* (list "install" "utils/install")
+                     (("/usr/local")
+                      #$output)
+                     (("whoami=`whoami`")
+                      "whoami=root"))))
+               (delete 'configure)
+               (add-before 'install 'create-bin-directory
+                 (lambda _
+                   (mkdir-p (string-append #$output "/bin")))))))
+    (synopsis "Signal propagation and coverage analysis tool")
+    (description
+     "The SPLAT (Signal Propagation, Loss, And Terrain) program can use the
+Longley-Rice path loss and coverage prediction using the Irregular Terrain
+Model to predict the behaviour and reliability of radio links, and to predict
+path loss.")
+    (home-page "https://www.qsl.net/kd2bd/splat.html")
+    (license license:gpl2+)))
+
 (define-public python-geographiclib
   (package
     (name "python-geographiclib")
@@ -2788,6 +2826,36 @@ coordinates of addresses, cities, countries, and landmarks across the globe
 using third-party geocoders and other data sources.")
     (license license:expat)))
 
+(define-public python-haversine
+  (package
+    (name "python-haversine")
+    (version "2.7.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    ;; There are no tests in the PyPi archive.
+                    (url "https://github.com/mapado/haversine")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0inxyj5n4jzgg5xiadqx9sk83gdx5ff989l9s04smdzbd3b8c0c8"))))
+    (build-system python-build-system)
+    (native-inputs (list python-pytest python-numpy))
+    (arguments
+      (list #:phases
+            #~(modify-phases %standard-phases
+                (replace 'check
+                  (lambda* (#:key tests? inputs #:allow-other-keys)
+                    (when tests?
+                      (invoke "pytest")))))))
+    (home-page "https://github.com/mapado/haversine")
+    (synopsis "Calculate the distance between 2 points on Earth")
+    (description "This package provides functions to calculate the
+distance in various units between two points on Earth using their
+latitude and longitude.")
+    (license license:expat)))
+
 (define-public gplates
   (package
     (name "gplates")

gnu/packages/gnome-xyz.scm

@@ -6,7 +6,7 @@
 ;;; Copyright © 2020 Jack Hill <jackhill@jackhill.us>
 ;;; Copyright © 2020 Kei Kebreau <kkebreau@posteo.net>
 ;;; Copyright © 2020 Ekaitz Zarraga <ekaitz@elenq.tech>
-;;; Copyright © 2020 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2020, 2023 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2020 Ryan Prior <rprior@protonmail.com>
 ;;; Copyright © 2020 Ellis Kenyo <me@elken.dev>
 ;;; Copyright © 2020 Stefan Reichör <stefan@xsteve.at>
@@ -198,7 +198,7 @@ simple and consistent.")
 (define-public papirus-icon-theme
   (package
     (name "papirus-icon-theme")
-    (version "20220508")
+    (version "20230104")
     (source
      (origin
        (method git-fetch)
@@ -206,7 +206,7 @@ simple and consistent.")
              (url "https://github.com/PapirusDevelopmentTeam/papirus-icon-theme")
              (commit version)))
        (sha256
-        (base32 "0rpcniaw8xbn23q67m26vgx3fynn4v056azrfp63lxdh46gfsvmc"))
+        (base32 "1x40gdqyw0gj389by6904g5a64r72by544k3nlyiamjhg2zmpx97"))
        (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (arguments
@@ -216,7 +216,23 @@ simple and consistent.")
        (modify-phases %standard-phases
          (delete 'bootstrap)
          (delete 'configure)
-         (delete 'build))))
+         (delete 'build)
+         (add-after 'install 'halve-inode-consumption
+           ;; This package uses over 100K inodes, which is a lot.  We can easily
+           ;; halve that number by using (hard) links, to no ill effect.
+           ;; See <https://logs.guix.gnu.org/guix/2023-01-31.log#171227>.
+           ;; However, the source checkout will still use the full amount!
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out"))
+                   (symlink? (lambda (_ stat)
+                               (eq? 'symlink (stat:type stat)))))
+               (for-each (lambda (file)
+                           (with-directory-excursion (dirname file)
+                             (let ((target (readlink file)))
+                               (when (eq? 'regular (stat:type (stat target)))
+                                 (delete-file file)
+                                 (link target file)))))
+                         (find-files out symlink?))))))))
     (native-inputs
      (list `(,gtk+ "bin")))
     (home-page "https://git.io/papirus-icon-theme")
@@ -1093,7 +1109,7 @@ GNOME Shell, including the top panel, dash and overview.")
 (define-public gnome-shell-extension-radio
   (package
     (name "gnome-shell-extension-radio")
-    (version "19")
+    (version "20")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1103,7 +1119,7 @@ GNOME Shell, including the top panel, dash and overview.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1qsi6c57hxh4jqdw18knm06601lhag6jdbvzg0r79aa9572zy8a0"))))
+                "01dmziad9g7bs3hr59aaz3mivkc6rqfyb9bz2v202zk22vcr5a2y"))))
     (build-system copy-build-system)
     (arguments
      (list
@@ -1189,7 +1205,7 @@ of windows.")
 (define-public arc-theme
   (package
     (name "arc-theme")
-    (version "20220405")
+    (version "20221218")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1198,11 +1214,11 @@ of windows.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1gjwf75sg4xyfypb08qiy2cmqyr2mamjc4i46ifrq7snj15gy608"))))
+                "0yznqjz1a1mcwks8z7pybgzrjiwg978bfpdmkaq926wy82qslngd"))))
     (build-system meson-build-system)
     (arguments
      '(#:configure-flags
-       '("-Dthemes=gnome-shell,gtk2,gtk3,metacity,plank,unity,xfwm")
+       '("-Dthemes=gnome-shell,gtk2,gtk3,gtk4,metacity,plank,unity,xfwm")
        #:phases
        (modify-phases %standard-phases
          (add-before 'build 'set-home   ;placate Inkscape
@@ -1217,6 +1233,7 @@ of windows.")
            pkg-config
            python
            sassc/libsass-3.5))
+    (inputs (list gtk-engines)) ;for gtk+-2 to work properly
     (synopsis "Flat GTK+ theme with transparent elements")
     (description "Arc is a flat theme with transparent elements for GTK 3, GTK
 2, and GNOME Shell which supports GTK 3 and GTK 2 based desktop environments
@@ -1301,7 +1318,7 @@ like Gnome, Unity, Budgie, Pantheon, XFCE, Mate and others.")
 (define-public materia-theme
   (package
     (name "materia-theme")
-    (version "20200916")
+    (version "20210322")
     (source
       (origin
         (method git-fetch)
@@ -1312,7 +1329,7 @@ like Gnome, Unity, Budgie, Pantheon, XFCE, Mate and others.")
         (file-name (git-file-name name version))
         (sha256
           (base32
-            "0qaxxafsn5zd2ysgr0jyv5j73360mfdmxyd55askswlsfphssn74"))))
+            "1fsicmcni70jkl4jb3fvh7yv0v9jhb8nwjzdq8vfwn256qyk0xvl"))))
     (build-system meson-build-system)
     (native-inputs
      (list gtk+ sassc))

gnu/packages/gnome.scm

@@ -909,7 +909,7 @@ tomorrow, the rest of the week and for special occasions.")
      (list dbus
            desktop-file-utils
            gettext-minimal
-           git-minimal/fixed
+           git-minimal/pinned
            `(,glib "bin")
            gobject-introspection
            gsettings-desktop-schemas
@@ -1048,7 +1048,7 @@ between different kinds of computer systems.")
 (define-public tepl
   (package
     (name "tepl")
-    (version "6.1.2")
+    (version "6.4.0")
     (source
      (origin
        (method url-fetch)
@@ -1058,7 +1058,7 @@ between different kinds of computer systems.")
                        name "-" version ".tar.xz"))
        (sha256
         (base32
-         "16x14j3nvsjj7jb2qmxpzygnlcy7sd7p6skv0sqshkwdlp4jxzha"))))
+         "08bkp3wrvmcks0082lfw4a0ian9c6j68rdb43px0bkyhd43b4mjy"))))
     (build-system meson-build-system)
     (arguments
      `(#:glib-or-gtk? #t
@@ -4599,7 +4599,7 @@ targeting the GNOME stack simple.")
 (define-public vte
   (package
     (name "vte")
-    (version "0.69.99")
+    (version "0.70.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/vte/"
@@ -4607,7 +4607,7 @@ targeting the GNOME stack simple.")
                                   "vte-" version ".tar.xz"))
               (sha256
                (base32
-                "1v3i38yrjhc48nvs1g333s3q709mq824qq0k2fnsmrrwv15c3cg9"))))
+                "102d6cd9f96czlq01ixhymfp0z20khw0dl5bgvan9xg31lwb85ad"))))
     (build-system meson-build-system)
     (arguments
      (list #:configure-flags #~(list "-Dvapi=true"
@@ -4634,6 +4634,15 @@ gnome-terminal, but can also be used to embed a console/terminal in games,
 editors, IDEs, etc.")
     (license license:lgpl2.1+)))
 
+(define-public vte-with-gtk-4
+  (package/inherit vte
+    (name "vte-with-gtk4")
+    (arguments (substitute-keyword-arguments (package-arguments vte)
+                 ((#:configure-flags flags #~'())
+                  #~(cons* "-Dgtk4=true" "-Dgtk3=false" #$flags))))
+    (propagated-inputs (modify-inputs (package-propagated-inputs vte)
+                         (replace "gtk+" gtk)))))
+
 (define-public vte-ng
   (package
     (inherit vte)
@@ -5190,7 +5199,7 @@ as OpenStreetMap, OpenCycleMap, OpenAerialMap and Maps.")
            sqlite
            zlib))
     (inputs
-     (list mit-krb5 samba/fixed))     ; For ntlm_auth support
+     (list mit-krb5 samba/pinned))     ; For ntlm_auth support
     (home-page "https://wiki.gnome.org/Projects/libsoup")
     (synopsis "GLib-based HTTP Library")
     (description
@@ -6216,7 +6225,7 @@ which are easy to play with the aid of a mouse.")
 (define-public amtk
   (package
     (name "amtk")
-    (version "5.5.1")
+    (version "5.6.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/amtk/"
@@ -6224,7 +6233,7 @@ which are easy to play with the aid of a mouse.")
                                   "amtk-" version ".tar.xz"))
               (sha256
                (base32
-                "176vplk3inf0pp0prma8478hp0yhziq0krp5a9l47hg22z86v2gc"))))
+                "0a1j2ynsa2nx1rzd55mdyp35d89zd9rfxd9ld4lsqal7bjw1a0fm"))))
     (build-system meson-build-system)
     (native-inputs
      (list gobject-introspection
@@ -6243,7 +6252,7 @@ both a traditional UI or a modern UI with a GtkHeaderBar.")
 (define-public devhelp
   (package
     (name "devhelp")
-    (version "41.3")
+    (version "43.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/" name "/"
@@ -6251,7 +6260,7 @@ both a traditional UI or a modern UI with a GtkHeaderBar.")
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "1rxn6kciyfdhnjrcjyf02cn3rki2xgwb4wrg5plbzjvpqasq66ml"))))
+                "016xhpz16b9b13y7wnvkllymb4s2fb6ixvw190204bir0pyyxkk3"))))
     (build-system meson-build-system)
     (arguments
      `(#:glib-or-gtk? #t
@@ -6260,8 +6269,9 @@ both a traditional UI or a modern UI with a GtkHeaderBar.")
          (add-after 'unpack 'skip-gtk-update-icon-cache
            ;; Don't create 'icon-theme.cache'.
            (lambda _
-             (substitute* "build-aux/meson/meson_post_install.py"
+             (substitute* "meson.build"
-               (("gtk-update-icon-cache") "true")))))))
+               (("gtk_update_icon_cache: true")
+                "gtk_update_icon_cache: false")))))))
     (propagated-inputs
      (list gsettings-desktop-schemas))
     (native-inputs
@@ -7074,7 +7084,7 @@ part of udev-extras, then udev, then systemd.  It's now a project on its own.")
 (define-public gvfs
   (package
     (name "gvfs")
-    (version "1.50.2")
+    (version "1.50.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/gvfs/"
@@ -7082,7 +7092,7 @@ part of udev-extras, then udev, then systemd.  It's now a project on its own.")
                                   "gvfs-" version ".tar.xz"))
               (sha256
                (base32
-                "0pmc0vda1ksm9l7v64h4bm8qnv16amb7nifgy0882hzg2n62pmq3"))))
+                "1z8332qg4kpa3lm3lbwb3xir4rba9ajsbqbq4yfh45mvjyg135v8"))))
     (build-system meson-build-system)
     (arguments
      (list #:glib-or-gtk? #t
@@ -7754,7 +7764,7 @@ share them with others via social networking and more.")
     (description "File Roller is an archive manager for the GNOME desktop
 environment that allows users to view, unpack, and create compressed archives
 such as gzip tarballs.")
-    (home-page "http://fileroller.sourceforge.net/")
+    (home-page "https://fileroller.sourceforge.net")
     (license license:gpl2+)))
 
 (define-public gnome-session
@@ -7872,7 +7882,7 @@ javascript engine and the GObject introspection framework.")
 (define-public gedit
   (package
     (name "gedit")
-    (version "42.2")
+    (version "44.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/" name "/"
@@ -7880,7 +7890,7 @@ javascript engine and the GObject introspection framework.")
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "1jlgzihi4ywvlr4xj2vbnnxzar8j3mwj0jcn8jp6dh0a3w8jjqiw"))))
+                "1nlgbnagahymb8l41kgz3nwc4p9cj3zx39428z6zik44fa6kfqh4"))))
     (build-system meson-build-system)
     (arguments
      (list
@@ -7916,6 +7926,7 @@ javascript engine and the GObject introspection framework.")
      (list desktop-file-utils           ;for update-desktop-database
            `(,glib "bin")               ;for glib-mkenums, etc.
            gobject-introspection
+           gtk-doc
            intltool
            itstool
            libxml2
@@ -7924,6 +7935,7 @@ javascript engine and the GObject introspection framework.")
            vala))
     (inputs
      (list adwaita-icon-theme
+           amtk
            bash-minimal
            glib
            gsettings-desktop-schemas
@@ -7933,7 +7945,8 @@ javascript engine and the GObject introspection framework.")
            libpeas
            libsoup
            python
-           python-pygobject))
+           python-pygobject
+           tepl))
     (home-page "https://wiki.gnome.org/Apps/Gedit")
     (synopsis "GNOME text editor")
     (description "While aiming at simplicity and ease of use, gedit is a
@@ -11441,7 +11454,7 @@ photo-booth-like software, such as Cheese.")
 (define-public cheese
   (package
     (name "cheese")
-    (version "41.1")
+    (version "43.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/" name "/"
@@ -11449,25 +11462,29 @@ photo-booth-like software, such as Cheese.")
                                   version ".tar.xz"))
               (sha256
                (base32
-                "0iz5cwndl65j13z5pmv0ansln2lyii0h82q775jgc3vk53560aaj"))))
+                "02vzcvk2s6cwvdw6v6qmlq3znamy6zwv7l6nlbqjfwrj7i54qmvl"))))
     (arguments
-     `(#:glib-or-gtk? #t
+     (list #:glib-or-gtk? #t
-       #:phases
+           #:phases
-       (modify-phases %standard-phases
+           #~(modify-phases %standard-phases
-         (add-after 'unpack 'skip-gtk-update-icon-cache
+               (add-after 'unpack 'skip-gtk-update-icon-cache
-           (lambda _
+                 (lambda _
-             ;; Don't create 'icon-theme.cache'
+                   ;; Don't create 'icon-theme.cache'.
-             (substitute* "meson_post_install.py"
+                   (substitute* "meson_post_install.py"
-               (("gtk-update-icon-cache") (which "true")))))
+                     (("gtk-update-icon-cache") (which "true")))))
-         (add-after 'install 'wrap-cheese
+               (add-after 'install 'wrap-cheese
-           (lambda* (#:key inputs outputs #:allow-other-keys)
+                 (lambda* (#:key inputs outputs #:allow-other-keys)
-             (wrap-program (search-input-file outputs "bin/cheese")
+                   (wrap-program (search-input-file outputs "bin/cheese")
-               `("GST_PLUGIN_SYSTEM_PATH" ":" prefix
+                     `("GST_PLUGIN_SYSTEM_PATH" prefix
-                 (,(getenv "GST_PLUGIN_SYSTEM_PATH")))))))))
+                       (,(getenv "GST_PLUGIN_SYSTEM_PATH")))
+                     `("GST_PRESET_PATH" prefix
+                       (,(dirname (search-input-file inputs
+                                                     "share/gstreamer-1.0\
+/presets/GstVP8Enc.prs"))))))))))
     (build-system meson-build-system)
     (native-inputs
-     (list docbook-xsl
+     (list docbook-xml-4.3
-           docbook-xml-4.3
+           docbook-xsl
            gettext-minimal
            `(,glib "bin")
            gobject-introspection
@@ -11478,20 +11495,20 @@ photo-booth-like software, such as Cheese.")
            pkg-config
            vala))
     (propagated-inputs
-     (list bash-minimal
+     (list clutter
-           gnome-video-effects
-           clutter
            clutter-gst
            clutter-gtk
-           libcanberra
            gdk-pixbuf
            glib
-           gstreamer))
+           gnome-video-effects
+           gstreamer
+           libcanberra))
     (inputs
-     (list gnome-desktop
+     (list bash-minimal
+           gnome-desktop
+           gst-plugins-bad
            gst-plugins-base
            gst-plugins-good
-           gst-plugins-bad
            gtk+
            libx11
            libxtst))
@@ -11924,7 +11941,7 @@ advanced image management tool")
 (define-public terminator
   (package
     (name "terminator")
-    (version "2.1.1")
+    (version "2.1.2")
     (source
      (origin
        (method url-fetch)
@@ -11932,7 +11949,7 @@ advanced image management tool")
                            "releases/download/v" version "/"
                            name "-" version ".tar.gz"))
        (sha256
-        (base32 "0xdgmam7ghnxw6g38a4gjw3kk3rhga8c66lns18k928jlr9fmddw"))))
+        (base32 "10shpn8id7z43d4dpx16x76mgxnk4mr976j5cg28icjiiaidyfc2"))))
     (build-system python-build-system)
     (native-inputs
      `(("gettext" ,gettext-minimal)
@@ -12638,7 +12655,7 @@ card sheets that you’ll find at most office supply stores.")
 (define-public gnome-latex
   (package
     (name "gnome-latex")
-    (version "3.41.2")
+    (version "3.44.0")
     (source
      (origin
        (method url-fetch)
@@ -12646,7 +12663,7 @@ card sheets that you’ll find at most office supply stores.")
                            (version-major+minor version)  "/"
                            "gnome-latex-" version ".tar.xz"))
        (sha256
-        (base32 "0cynhmrn99f4f3kddczsc58ak4b9sv2zkfbcyz7z16848nhz047k"))))
+        (base32 "0i77m431ilbaprcwcnnzfckr1g9bfc03lslnqw0yvir8pm057gc8"))))
     (build-system glib-or-gtk-build-system)
     (native-inputs
      (list gettext-minimal
@@ -13204,7 +13221,7 @@ profiler via Sysprof, debugging support, and more.")
 (define-public komikku
   (package
     (name "komikku")
-    (version "1.7.0")
+    (version "1.10.1")
     (source
      (origin
        (method git-fetch)
@@ -13214,7 +13231,7 @@ profiler via Sysprof, debugging support, and more.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0pgls9lfmgx1wgk7navvr44hdp6ziac19979lkqw2a09jn8y6xxa"))))
+         "17nyfpg15i87204017as2dq491bq3dy261flwx71b2z4f4k6q83b"))))
     (build-system meson-build-system)
     (arguments
      (list

gnu/packages/gnuzilla.scm

@@ -477,8 +477,8 @@ in C/C++.")
 ;; XXXX: Workaround 'snippet' limitations.
 (define computed-origin-method (@@ (guix packages) computed-origin-method))
 
-(define %icecat-version "102.6.0-guix0-preview1")
+(define %icecat-version "102.7.0-guix0-preview1")
-(define %icecat-build-id "20221213000000") ;must be of the form YYYYMMDDhhmmss
+(define %icecat-build-id "20230117000000") ;must be of the form YYYYMMDDhhmmss
 
 ;; 'icecat-source' is a "computed" origin that generates an IceCat tarball
 ;; from the corresponding upstream Firefox ESR tarball, using the 'makeicecat'
@@ -500,11 +500,11 @@ in C/C++.")
                   "firefox-" upstream-firefox-version ".source.tar.xz"))
             (sha256
              (base32
-              "1zhggzrk7lgip8jm37idh22qks76kmjy4yqy2qi63mvnv2j58cfj"))))
+              "1ahl66x8chnsz80capqa5ivyrqhc50s91zrcgz1jxd7w2ws61957"))))
 
-         (upstream-icecat-base-version "102.6.0") ; maybe older than base-version
+         (upstream-icecat-base-version "102.7.0") ; maybe older than base-version
          ;;(gnuzilla-commit (string-append "v" upstream-icecat-base-version))
-         (gnuzilla-commit "b6260130b9808f550bdb35061af2d7962109a181")
+         (gnuzilla-commit "7f76da3cfd5d04fa38d894f6ea6ac5f2fd0ea837")
          (gnuzilla-source
           (origin
             (method git-fetch)
@@ -516,7 +516,7 @@ in C/C++.")
                                       (string-take gnuzilla-commit 8)))
             (sha256
              (base32
-              "19v443w43jbcl9m5kl52nfai7hs4j07nf2ad9ggca7b2b0cz89b4"))))
+              "19i66qvwzgllgnlw270bxphymybjj1qb5hdznqi4i2dcgpcrq77l"))))
 
          ;; 'search-patch' returns either a valid file name or #f, so wrap it
          ;; in 'assume-valid-file-name' to avoid 'local-file' warnings.
@@ -1097,8 +1097,8 @@ standards of the IceCat project.")
        (cpe-name . "firefox_esr")
        (cpe-version . ,(first (string-split version #\-)))))))
 
-(define %icedove-build-id "20221213000000") ;must be of the form YYYYMMDDhhmmss
+(define %icedove-build-id "20230119000000") ;must be of the form YYYYMMDDhhmmss
-(define %icedove-version "102.6.0")
+(define %icedove-version "102.7.0")
 
 ;; Provides the "comm" folder which is inserted into the icecat source.
 ;; Avoids the duplication of Icecat's source tarball.
@@ -1107,11 +1107,11 @@ standards of the IceCat project.")
     (method hg-fetch)
     (uri (hg-reference
           (url "https://hg.mozilla.org/releases/comm-esr102")
-          (changeset "d46a947ae837300f19cc45c75d473c7b1cf4ebb3")))
+          (changeset "a786f143946e93a3059e6fe290bb954840ab9778")))
     (file-name (string-append "thunderbird-" %icedove-version "-checkout"))
     (sha256
      (base32
-      "0klr6i2sbaiv2gc8q1cxrz87zd5cskdwa9qacp3dhfb8x17qwb41"))))
+      "02pz9yhpp3lswjmvj30vbx05mbi31bnzzfwyw5v996zg5wz2fpyv"))))
 
 (define-public icedove
   (package

gnu/packages/golang.scm

@@ -12,7 +12,7 @@
 ;;; Copyright © 2018 Tomáš Čech <sleep_walker@gnu.org>
 ;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr>
 ;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
-;;; Copyright © 2018, 2019, 2020 Katherine Cox-Buday <cox.katherine.e@gmail.com>
+;;; Copyright © 2018, 2019, 2020, 2023 Katherine Cox-Buday <cox.katherine.e@gmail.com>
 ;;; Copyright © 2019 Giovanni Biscuolo <g@xelera.eu>
 ;;; Copyright © 2019, 2020 Alex Griffin <a@ajgrf.com>
 ;;; Copyright © 2019, 2020, 2021 Arun Isaac <arunisaac@systemreboot.net>
@@ -626,9 +626,7 @@ in the style of communicating sequential processes (@dfn{CSP}).")
                  (("^#!.*") "#!/usr/bin/env perl\n"))))))))
     (native-inputs
      `(("go-fix-script-tests.patch" ,(search-patch "go-fix-script-tests.patch"))
-       ,@(if (not (member (%current-system) (package-supported-systems go-1.4)))
+       ,@(package-native-inputs go-1.14)))))
-             (alist-replace "go" (list gccgo-10) (package-native-inputs go-1.14))
-             (package-native-inputs go-1.14))))))
 
 (define-public go-1.17
   (package
@@ -850,7 +848,7 @@ in the style of communicating sequential processes (@dfn{CSP}).")
   (package
     (inherit go-1.17)
     (name "go")
-    (version "1.18.6")
+    (version "1.18.10")
     (source
      (origin
        (method git-fetch)
@@ -860,13 +858,13 @@ in the style of communicating sequential processes (@dfn{CSP}).")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1s2xwgd3mfbjdf7ls9gyj7n1lbqc4276qkr3znyq9694isj1ak20"))))))
+         "0ph3ajfq5q8j3nd91pfb25pm21aiphc58zf7fwis0h3a6nqbdyq9"))))))
 
 (define-public go-1.19
   (package
     (inherit go-1.18)
     (name "go")
-    (version "1.19.1")
+    (version "1.19.5")
     (source
      (origin
        (method git-fetch)
@@ -876,7 +874,7 @@ in the style of communicating sequential processes (@dfn{CSP}).")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1gah4zhbkgbwrrryfmzdv2qwi1rgxk10q2r3hnlcb1dybf9c1i1w"))))
+         "0ah4l01h8qj0vj9668bdgr5m69fq16dz1fjlj332vhysxc6bkc27"))))
     (arguments
      (substitute-keyword-arguments (package-arguments go-1.18)
        ((#:phases phases)
@@ -2855,36 +2853,73 @@ expressing configuration which is easy for both humans and machines to read.")
     (home-page "https://github.com/hashicorp/hcl")
     (license license:mpl2.0)))
 
+(define-public go-golang-org-x-exp
+  (package
+    (name "go-golang-org-x-exp")
+    (version "0.0.0-20221004215720-b9f4876ce741")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://go.googlesource.com/exp")
+                    (commit (go-version->git-ref version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "030b929xyg8dpp6f4qbyg63msi6zgzj9sqmvnyphfcrjkqf7nr41"))))
+    (build-system go-build-system)
+    (arguments
+     '(#:import-path "golang.org/x/exp"
+       ;; Source-only package
+       #:tests? #f
+       #:phases (modify-phases %standard-phases
+                  (delete 'build))))
+    (home-page "https://golang.org/x/exp")
+    (synopsis "Experimental and deprecated Go packages")
+    (description
+     "This subrepository holds experimental and deprecated (in the @code{old}
+directory) packages.")
+    (license license:bsd-3)))
+
 (define-public go-golang-org-x-tools
-  (let ((commit "8b927904ee0dec805c89aaf9172f4459296ed6e8")
+  (package
-        (revision "0"))
+    (name "go-golang-org-x-tools")
-    (package
+    (version "0.5.0")
-      (name "go-golang-org-x-tools")
+    (source
-      (version (git-version "0.1.3" revision commit))
+     (origin
-      (source (origin
+       (method git-fetch)
-                (method git-fetch)
+       (uri (git-reference
-                (uri (git-reference
+             (url "https://go.googlesource.com/tools")
-                      (url "https://go.googlesource.com/tools")
+             (commit (string-append "v" version))))
-                      (commit commit)))
+       (file-name (git-file-name name version))
-                (file-name (string-append "go.googlesource.com-tools-"
+       (sha256
-                                          version "-checkout"))
+        (base32
-                (sha256
+         "08kx2nndq3sr6xai7403mbsqvz5shxmp2icylfr2fmwagr59cb2n"))
-                 (base32
+       (modules '((guix build utils)))
-                  "0iinb70xhcjsddgi42ia1n745lx2ibnjdm6m2v666qrk3876vpck"))))
+       (snippet
-      (build-system go-build-system)
+        '(begin
-      (arguments
+           ;; gopls versions are tagged separately, and it is a
-       `(#:import-path "golang.org/x/tools"
+           ;; separate Guix package.
+           (delete-file-recursively "gopls")))))
+    (build-system go-build-system)
+    (arguments
+     `(#:import-path "golang.org/x/tools"
+       ;; Source-only package
+       #:tests? #f
+       #:phases
+       (modify-phases %standard-phases
          ;; Source-only package
-         #:tests? #f
+         (delete 'build))))
-         #:phases
+    (propagated-inputs
-         (modify-phases %standard-phases
+     (list
-           ;; Source-only package
+      go-github-com-yuin-goldmark
-           (delete 'build))))
+      go-golang-org-x-mod
-      (synopsis "Tools that support the Go programming language")
+      go-golang-org-x-net
-      (description "This package provides miscellaneous tools that support the
+      go-golang-org-x-sys))
+    (synopsis "Tools that support the Go programming language")
+    (description "This package provides miscellaneous tools that support the
 Go programming language.")
-      (home-page "https://go.googlesource.com/tools/")
+    (home-page "https://go.googlesource.com/tools/")
-      (license license:bsd-3))))
+    (license license:bsd-3)))
 
 (define-public go-golang-org-x-crypto
   (let ((commit "2aa609cf4a9d7d1126360de73b55b6002f9e052a")
@@ -2919,6 +2954,116 @@ for the Go language.")
       (home-page "https://go.googlesource.com/crypto/")
       (license license:bsd-3))))
 
+(define-public govulncheck
+  (package
+    (name "govulncheck")
+    (version "0.0.0-20221229164908-ebf31f7dc3ef")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://go.googlesource.com/vuln")
+                    (commit (go-version->git-ref version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1w055g90k7anrrcvfrsqklxzl9pl0vqdiwpayj9f0brwys9xhj7d"))))
+    (build-system go-build-system)
+    (arguments
+     `(#:import-path "golang.org/x/vuln"
+       #:go ,go-1.19
+       #:install-source? #f
+       #:phases ,#~(modify-phases %standard-phases
+                     (add-after 'unpack 'remove-go-mod-tidy
+                       (lambda _
+                         (substitute* "src/golang.org/x/vuln/checks.bash"
+                           (("go mod tidy")
+                            #$(file-append coreutils-minimal "/bin/true")))))
+                     (replace 'build
+                       (lambda arguments
+                         (apply (assoc-ref %standard-phases
+                                           'build)
+                                `(,@arguments #:import-path
+                                  "golang.org/x/vuln/cmd/govulncheck")))))))
+    (native-inputs (list coreutils-minimal))
+    (inputs (list go-golang-org-x-sys
+                  go-github-com-google-renameio
+                  go-github-com-burntsushi-toml
+                  go-mvdan-cc-unparam
+                  go-honnef-co-go-tools
+                  go-golang-org-x-tools
+                  go-golang-org-x-sync
+                  go-golang-org-x-mod
+                  go-golang-org-x-exp
+                  go-github-com-google-go-cmp-cmp
+                  go-github-com-google-go-cmdtest
+                  go-github-com-client9-misspell))
+    (home-page "https://golang.org/x/vuln")
+    (synopsis "Go Vulnerability Management")
+    (description
+     "This repository contains packages for accessing and analyzing data from
+the @url{https://vuln.go.dev,Go Vulnerability Database}.")
+    (license license:bsd-3)))
+
+(define-public go-golang-org-x-vuln
+  (package
+    (inherit govulncheck)
+    (name "go-golang-org-x-vuln")
+    (arguments
+     `(#:import-path "golang.org/x/vuln"
+       #:tests? #f
+       #:install-source? #t
+       #:phases (modify-phases %standard-phases
+                  (delete 'build))))
+    (propagated-inputs (package-inputs govulncheck))
+    (native-inputs '())
+    (inputs '())))
+
+(define-public gopls
+  (package
+    (name "gopls")
+    (version "0.11.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://go.googlesource.com/tools")
+                    (commit (string-append "gopls/v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1l9y1rp7x51s6dnjn227fhdlnz4z1h41jn3x1aq49qki241w7m73"))))
+    (build-system go-build-system)
+    (arguments
+     `(#:import-path "golang.org/x/tools/gopls"
+       #:unpack-path "golang.org/x/tools"
+       #:install-source? #f
+       #:phases (modify-phases %standard-phases
+                  (add-before 'unpack 'override-tools
+                    (lambda _
+                      (delete-file-recursively "src/golang.org/x/tools"))))))
+    (propagated-inputs (list go-github-com-google-go-cmp-cmp
+                             go-github-com-jba-printsrc
+                             go-github-com-jba-templatecheck
+                             go-github-com-sergi-go-diff
+                             go-golang-org-x-mod
+                             go-golang-org-x-sync
+                             go-golang-org-x-sys
+                             go-golang-org-x-text
+                             go-gopkg-in-yaml-v3
+                             go-honnef-co-go-tools
+                             go-github-com-burntsushi-toml
+                             go-github-com-google-safehtml
+                             go-golang-org-x-exp
+                             go-mvdan-cc-gofumpt
+                             go-golang-org-x-vuln
+                             go-mvdan-cc-xurls))
+    (home-page "https://golang.org/x/tools/gopls")
+    (synopsis "Official language server for the Go language")
+    (description
+     "Pronounced ``Go please'', this is the official Go language server
+developed by the Go team.  It provides IDE features to any LSP-compatible
+editor.")
+    (license license:bsd-3)))
+
 (define-public go-github-com-protonmail-go-crypto
   (package
     (name "go-github-com-protonmail-go-crypto")
@@ -3021,11 +3166,11 @@ processing.")
       (license license:bsd-3))))
 
 (define-public go-golang-org-x-sync
-  (let ((commit "6e8e738ad208923de99951fe0b48239bfd864f28")
+  (let ((commit "8fcdb60fdcc0539c5e357b2308249e4e752147f1")
         (revision "1"))
     (package
       (name "go-golang-org-x-sync")
-      (version (git-version "0.0.0" revision commit))
+      (version (git-version "0.1.0" revision commit))
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
@@ -3034,17 +3179,17 @@ processing.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "1avk27pszd5l5df6ff7j78wgla46ir1hhy2jwfl9a3c0ys602yx9"))))
+                  "07qrhni6f5hh5p95k1yk6s4wsj341q663irvx6rllrxfsymj6a0z"))))
       (build-system go-build-system)
       (arguments
        `(#:import-path "golang.org/x/sync"
          #:tests? #f
          ;; Source-only package
-         #:phases
+         #:phases (modify-phases %standard-phases
-         (modify-phases %standard-phases
+                    (delete 'build))))
-           (delete 'build))))
       (synopsis "Additional Go concurrency primitives")
-      (description "This package provides Go concurrency primitives in addition
+      (description
+       "This package provides Go concurrency primitives in addition
 to the ones provided by the language and “sync” and “sync/atomic”
 packages.")
       (home-page "https://go.googlesource.com/sync/")
@@ -3190,28 +3335,27 @@ time.")
       (license license:bsd-3))))
 
 (define-public go-golang-org-x-mod
-  (let ((commit "0f08993efd8a8ec67e75bcccf86b0e1569b0ab0a")
+  (let ((commit "7c05a442b7c1d1a107879b4a090bb5a38d3774a1")
         (revision "0"))
     (package
       (name "go-golang-org-x-mod")
-      (version (git-version "0.5.0" revision commit))
+      (version (git-version "0.7.0" revision commit))
-      (source
+      (source (origin
-       (origin
+                (method git-fetch)
-         (method git-fetch)
+                (uri (git-reference
-         (uri (git-reference
+                      (url "https://github.com/golang/mod")
-               (url "https://github.com/golang/mod")
+                      (commit commit)))
-               (commit commit)))
+                (file-name (git-file-name name version))
-         (file-name (git-file-name name version))
+                (sha256
-         (sha256
+                 (base32
-          (base32 "0pl0jc5jvg7hxj4z66zg6kglnq5g7li09f3k9klwvyr4jx5dw88k"))))
+                  "14r24fq3kn84k2y2jvvg8hwpy52a3q429pimrdwl5zwknbr2awmh"))))
       (build-system go-build-system)
       (arguments
        '(#:import-path "golang.org/x/mod/"
          #:tests? #f
-         #:phases
+         #:phases (modify-phases %standard-phases
-         (modify-phases %standard-phases
+                    ;; Source-only package
-           ;; Source-only package
+                    (delete 'build))))
-           (delete 'build))))
       (home-page "https://golang.org/x/mod")
       (synopsis "Tools to work directly with Go module mechanics")
       (description
@@ -3227,23 +3371,23 @@ loading algorithms.")
 (define-public go-github-com-burntsushi-toml
   (package
     (name "go-github-com-burntsushi-toml")
-    (version "0.3.1")
+    (version "1.2.1")
-    (source
+    (source (origin
-     (origin
+              (method git-fetch)
-       (method git-fetch)
+              (uri (git-reference
-       (uri (git-reference
+                    (url "https://github.com/BurntSushi/toml")
-             (url "https://github.com/BurntSushi/toml")
+                    (commit (string-append "v" version))))
-             (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
-       (file-name (git-file-name name version))
+              (sha256
-       (sha256
+               (base32
-        (base32
+                "1v9czq4hsyvdz7yx70y6sgq77wmrgfmn09r9cj4w85z38jqnamv7"))))
-         "1fjdwwfzyzllgiwydknf1pwjvy49qxfsczqx5gz3y0izs7as99j6"))))
     (build-system go-build-system)
     (arguments
      '(#:import-path "github.com/BurntSushi/toml"))
     (home-page "https://github.com/BurntSushi/toml")
     (synopsis "Toml parser and encoder for Go")
-    (description "This package is toml parser and encoder for Go.  The interface
+    (description
+     "This package is toml parser and encoder for Go.  The interface
 is similar to Go's standard library @code{json} and @code{xml} package.")
     (license license:expat)))
 
@@ -4785,6 +4929,51 @@ Looks for an identical word on a list of words, if none is found, look for a
 similar word.")
       (license license:expat))))
 
+(define-public misspell
+  (package
+    (name "misspell")
+    (version "0.3.4")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/client9/misspell")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1vwf33wsc4la25zk9nylpbp9px3svlmldkm0bha4hp56jws4q9cs"))))
+    (build-system go-build-system)
+    (arguments
+     '(#:import-path "github.com/client9/misspell"
+       #:phases (modify-phases %standard-phases
+                  (replace 'build
+                    (lambda arguments
+                      (apply (assoc-ref %standard-phases
+                                        'build)
+                             `(,@arguments #:import-path
+                               "github.com/client9/misspell/cmd/misspell")))))))
+    (home-page "https://github.com/client9/misspell")
+    (synopsis "Correct commonly misspelled English words in source files")
+    (description
+     "misspell assists with correcting commonly misspelled English words in
+source files.  A neutral variety of English is used by default, but a US or UK
+locale can be selected.")
+    (license license:expat)))
+
+(define-public go-github-com-client9-misspell
+  (package
+    (inherit misspell)
+    (name "go-github-com-client9-misspell")
+    (arguments
+     `(#:import-path "github.com/client9/misspell"
+       #:tests? #f
+       #:install-source? #t
+       #:phases (modify-phases %standard-phases
+                  (delete 'build))))
+    (propagated-inputs (package-inputs misspell))
+    (native-inputs '())
+    (inputs '())))
+
 (define-public go-github-com-stevedonovan-luar
   (let ((commit "22d247e5366095f491cd83edf779ee99a78f5ead")
         (revision "0"))
@@ -6998,28 +7187,27 @@ colorized or SGR defined output to the standard output.")
 (define-public go-github-com-google-go-cmp-cmp
   (package
     (name "go-github-com-google-go-cmp-cmp")
-    (version "0.5.2")
+    (version "0.5.9")
     (source (origin
               (method git-fetch)
               (uri (git-reference
-                     (url "https://github.com/google/go-cmp")
+                    (url "https://github.com/google/go-cmp")
-                     (commit (string-append "v" version))))
+                    (commit (string-append "v" version))))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0qchy411jm9q2l9mf7x3ry2ycaqp9xdhf2nx14qrpzcxfigv2705"))))
+                "0a13m7l1jrysa7mrlmra8y7n83zcnb23yjyg3a609p8i9lxkh1wm"))))
     (build-system go-build-system)
     (arguments
      '(#:import-path "github.com/google/go-cmp/cmp"
        #:unpack-path "github.com/google/go-cmp"))
-    (propagated-inputs
-     (list go-golang-org-x-xerrors))
     (synopsis "Determine equality of values in Go")
-    (description "This package provides a more powerful and safer
+    (description
-alternative to @code{reflect.DeepEqual} for comparing whether two values
+     "This package is intended to be a more powerful and safer
-are semantically equal in Go (for writing tests).")
+alternative to @@code{reflect.DeepEqual} for comparing whether two values are
-    (home-page "https://godoc.org/github.com/google/go-cmp/cmp")
+semantically equal.")
-    (license license:asl2.0)))
+    (home-page "https://github.com/google/go-cmp")
+    (license license:bsd-3)))
 
 (define-public go-github-com-google-uuid
   (package
@@ -7043,6 +7231,28 @@ are semantically equal in Go (for writing tests).")
 4122 and DCE 1.1: Authentication and Security Services.")
     (license license:bsd-3)))
 
+(define-public go-github-com-google-gopacket
+  (package
+    (name "go-github-com-google-gopacket")
+    (version "1.1.19")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/google/gopacket")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "048qwm2n0wrpql4qqgd7jyynn3gk069yvqbxnshlayzmbhf87ls4"))))
+    (build-system go-build-system)
+    (arguments
+     '(#:import-path "github.com/google/gopacket"))
+    (home-page "https://github.com/google/gopacket")
+    (synopsis "Packet processing capabilities library")
+    (description
+     "This package provides packet processing capabilities for Go.")
+    (license license:bsd-3)))
+
 (define-public go-github-com-google-goterm
   (let ((commit "fc88cf888a3fa99ecc23d1efc1a44284268457d3")
         (revision "1"))
@@ -7335,6 +7545,29 @@ This package is a successor to @code{go-github-com-golang-protobuf} with an
 improved and cleaner API.")
     (license license:bsd-3)))
 
+(define-public go-github-com-macronut-go-tproxy
+  (package
+    (name "go-github-com-macronut-go-tproxy")
+    (version "0.0.0-20190726054950-ef7efd7f24ed")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/FutureProtocolLab/go-tproxy")
+                    (commit (go-version->git-ref version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0jibsg0xhsn0h1jq4g9qd4nr58w43y8majlwfri9ffk2cbfrwqdr"))))
+    (build-system go-build-system)
+    (arguments
+     '(#:import-path "github.com/macronut/go-tproxy"))
+    (home-page "https://github.com/FutureProtocolLab/go-tproxy")
+    (synopsis "Linux Transparent Proxy library")
+    (description
+     "Golang TProxy provides an easy to use wrapper for the Linux Transparent
+Proxy functionality.")
+    (license license:expat)))
+
 (define-public go-github-com-mattn-go-zglob
   (package
     (name "go-github-com-mattn-go-zglob")
@@ -8002,7 +8235,7 @@ converts it into syntax highlighted HTML, ANSI-coloured text, etc.")
 (define-public go-github-com-andybalholm-cascadia
   (package
     (name "go-github-com-andybalholm-cascadia")
-    (version "1.0.0")
+    (version "1.3.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -8011,7 +8244,7 @@ converts it into syntax highlighted HTML, ANSI-coloured text, etc.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "09j8cavbhqqdxjqrkwbc40g8p0i49zf3184rpjm5p2rjbprcghcc"))))
+                "0zgc9fjkn7d66cnmgnmalr9lrq4ii1spap95pf2x1hln4pflib5s"))))
     (build-system go-build-system)
     (arguments
      `(#:import-path "github.com/andybalholm/cascadia"))
@@ -8489,6 +8722,57 @@ This makes it virtually free to implement mocks and testing over
 file system operations.")
     (license license:asl2.0)))
 
+(define-public go-github-com-jba-printsrc
+  (package
+    (name "go-github-com-jba-printsrc")
+    (version "0.2.2")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/jba/printsrc")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1gyy3kmb5a5i710wkv3b7ah7i7sz5sdc7v3sab5m4rxch1sd2fpj"))))
+    (build-system go-build-system)
+    (arguments
+     '(#:import-path "github.com/jba/printsrc"
+       ;; TODO: Open bug; expecting time.Local, but when local=UTC, we get time.UTC
+       #:tests? #f))
+    (home-page "https://github.com/jba/printsrc")
+    (synopsis "Prints Go values as sourcecode")
+    (description
+     "Package printsrc prints Go values as Go source.  It strives to render
+legal Go source code, and returns an error when detects that it cannot.")
+    (license license:expat)))
+
+(define-public go-github-com-jba-templatecheck
+  (package
+    (name "go-github-com-jba-templatecheck")
+    (version "0.6.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/jba/templatecheck")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "12iwkidz4p6wdl65jfddqxls80mv879k2rpb42dj7y4dja5advlc"))))
+    (build-system go-build-system)
+    (arguments
+     '(#:import-path "github.com/jba/templatecheck"))
+    (propagated-inputs (list go-github-com-google-safehtml))
+    (home-page "https://github.com/jba/templatecheck")
+    (synopsis "Checks Go templates for problems")
+    (description
+     "Package templatecheck checks Go templates for problems.  It can detect
+many errors that are normally caught only during execution.  Use templatecheck
+in tests to find template errors early, and along template execution paths
+that might only rarely be reached.")
+    (license license:expat)))
+
 (define-public go-github-com-jbenet-go-context
   (let ((commit "d14ea06fba99483203c19d92cfcd13ebe73135f4")
         (revision "1"))
@@ -8658,30 +8942,26 @@ temporal directories.")
     (license license:asl2.0)))
 
 (define-public go-github-com-pkg-diff
-  (let ((commit "531926345625d489a6b56f860a569e68245ace36")
+  (package
-        (revision "1"))
+    (name "go-github-com-pkg-diff")
-    (package
+    (version "0.0.0-20210226163009-20ebb0f2a09e")
-      (name "go-github-com-pkg-diff")
+    (source (origin
-      (version (git-version "0.0.1" revision commit))
+              (method git-fetch)
-      (source (origin
+              (uri (git-reference
-                (method git-fetch)
+                    (url "https://github.com/pkg/diff")
-                (uri (git-reference
+                    (commit "20ebb0f2a09e612109b224b32f79370409108bcc")))
-                      (url "https://github.com/pkg/diff")
+              (file-name (git-file-name name version))
-                      (commit commit)))
+              (sha256
-                (file-name (git-file-name name version))
+               (base32
-                (sha256
+                "1g3dzgwhz4fx3ddpsv7fsa4r1v5clsp2lbw2qrkdk9y1vc5gi8yi"))))
-                 (base32
+    (build-system go-build-system)
-                  "1770m7qhww6lm0wj1v3mhv6hwa2v92p4w2fqxj1xyrg5dd58d944"))))
+    (arguments
-      (build-system go-build-system)
+     `(#:import-path "github.com/pkg/diff"))
-      (arguments
+    (home-page "https://github.com/pkg/diff/")
-       `(#:import-path "github.com/pkg/diff"))
+    (synopsis "Create and print diffs")
-      (native-inputs
+    (description
-       (list go-github-com-sergi-go-diff))
+     "This package provides a Go library to create and print diffs.")
-      (home-page "https://github.com/pkg/diff/")
+    (license license:bsd-3)))
-      (synopsis "Create and print diffs")
-      (description
-       "This package provides a Go library to create and print diffs.")
-      (license license:bsd-3))))
 
 (define-public go-github-com-twpayne-go-shell
   (package
@@ -9030,7 +9310,7 @@ the necessary APIs to build a wide array of higher-level primitives.")
 (define-public go-github-com-rogpeppe-go-internal
   (package
     (name "go-github-com-rogpeppe-go-internal")
-    (version "1.6.1")
+    (version "1.9.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -9039,7 +9319,7 @@ the necessary APIs to build a wide array of higher-level primitives.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "00j2vpp1bsggdvw1winkz23mg0q6drjiir5q0k49pmqx1sh7106l"))))
+                "0bh08k8fy1qcc0vzyv0xkg0sx5kjx348zd1dpjmp3rbrr6xrpaaw"))))
     (build-system go-build-system)
     (arguments
      `(#:import-path "github.com/rogpeppe/go-internal"
@@ -9048,6 +9328,8 @@ the necessary APIs to build a wide array of higher-level primitives.")
        #:phases
        (modify-phases %standard-phases
          (delete 'build))))
+    (propagated-inputs
+     (list go-github-com-pkg-diff))
     (home-page "https://github.com/rogpeppe/go-internal/")
     (synopsis "Internal packages from the Go standard library")
     (description "This repository factors out an opinionated selection of
@@ -9071,9 +9353,9 @@ Included are the following:
 @end itemize\n")
     (license license:bsd-3)))
 
-(define-public gopkg-in-errgo-fmt-errors
+(define-public go-gopkg-in-errgo-fmt-errors
   (package
-    (name "gopkg-in-errgo-fmt-errors")
+    (name "go-gopkg-in-errgo-fmt-errors")
     (version "2.1.0")
     (source (origin
               (method git-fetch)
@@ -9086,7 +9368,7 @@ Included are the following:
                 "065mbihiy7q67wnql0bzl9y1kkvck5ivra68254zbih52jxwrgr2"))))
     (build-system go-build-system)
     (arguments
-     `(#:import-path "gopkg.in/errgo.v2/fmt/errors"
+     `(#:import-path "gopkg.in/errgo.v2"
        #:tests? #f
        ;; Source-only package
        #:phases
@@ -9674,6 +9956,173 @@ atomic access.")
      "@code{multierr} allows combining one or more Go errors together.")
     (license license:expat)))
 
+(define-public gofumpt
+  (package
+    (name "gofumpt")
+    (version "0.4.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/mvdan/gofumpt")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "13ahi8q1a9h4dj6a7xp95c79d5svz5p37b6z91aswbq043qd417k"))
+              (modules '((guix build utils)))
+              (snippet `(let ((fixed-version (string-append ,version
+                                                            " (GNU Guix)")))
+                          ;; Gofumpt formats Go files, and therefore modifies
+                          ;; them. To help the developers diagnose issues, it
+                          ;; replaces any occurrence of a `//gofumpt:diagnose`
+                          ;; comment with some debugging information which
+                          ;; includes the module version. In the event gofumpt
+                          ;; was built without module support, it falls back
+                          ;; to a string "(devel)". Since our build system
+                          ;; does not yet support modules, we'll inject our
+                          ;; version string instead, since this is more
+                          ;; helpful.
+                          (substitute* "internal/version/version.go"
+                            (("^const fallbackVersion.+")
+                             (format #f "const fallbackVersion = \"~a\"~%"
+                                     fixed-version)))
+                          ;; These tests rely on `//gofumpt:diagnose` comments
+                          ;; being replaced with fixed information injected
+                          ;; from the test scripts, but this requires a binary
+                          ;; compiled as a Go module. Since we can't do this
+                          ;; yet, modify the test scripts with the version
+                          ;; string we're injecting.
+                          (delete-file "testdata/script/diagnose.txtar")
+                          (substitute* (find-files "testdata/script/"
+                                                   "\\.txtar$")
+                            (("v0.0.0-20220727155840-8dda8068d9f3")
+                             fixed-version)
+                            (("(devel)")
+                             fixed-version)
+                            (("v0.3.2-0.20220627183521-8dda8068d9f3")
+                             fixed-version))))))
+    (build-system go-build-system)
+    (arguments
+     `(#:import-path "mvdan.cc/gofumpt"
+       #:go ,go-1.19))
+    (native-inputs (list go-gopkg-in-errgo-fmt-errors))
+    (propagated-inputs (list go-github-com-pkg-diff
+                             go-github-com-kr-text
+                             go-github-com-kr-pretty
+                             go-golang-org-x-tools
+                             go-golang-org-x-sys
+                             go-golang-org-x-sync
+                             go-golang-org-x-mod
+                             go-github-com-rogpeppe-go-internal
+                             go-github-com-google-go-cmp-cmp
+                             go-github-com-frankban-quicktest))
+    (home-page "https://mvdan.cc/gofumpt/")
+    (synopsis "Formats Go files with a stricter ruleset than gofmt")
+    (description
+     "Enforce a stricter format than @code{gofmt}, while being backwards compatible.
+That is, @code{gofumpt} is happy with a subset of the formats that
+@code{gofmt} is happy with.")
+    (license license:bsd-3)))
+
+(define-public go-mvdan-cc-gofumpt
+  (package
+    (inherit gofumpt)
+    (name "go-mvdan-cc-gofumpt")
+    (arguments
+     `(#:import-path "mvdan.cc/gofumpt"
+       #:tests? #f
+       #:install-source? #t
+       #:phases (modify-phases %standard-phases
+                  (delete 'build))))
+    (propagated-inputs (package-inputs gofumpt))
+    (native-inputs '())
+    (inputs '())))
+
+(define-public unparam
+  (package
+    (name "unparam")
+    (version "0.0.0-20221223090309-7455f1af531d")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/mvdan/unparam")
+                    (commit (go-version->git-ref version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0wynf0b32azxljncw5fh9bwkxpdflvf9q1z16wyj432566yjh12c"))))
+    (build-system go-build-system)
+    (arguments
+     `(#:import-path "mvdan.cc/unparam"
+       #:go ,go-1.19))
+    (inputs (list go-golang-org-x-sys go-golang-org-x-mod
+                  go-github-com-pkg-diff go-golang-org-x-tools
+                  go-github-com-rogpeppe-go-internal))
+    (home-page "https://mvdan.cc/unparam/")
+    (synopsis "Find unused parameters in Go")
+    (description "Reports unused function parameters and results in Go code.")
+    (license license:bsd-3)))
+
+(define-public go-mvdan-cc-unparam
+  (package
+    (inherit unparam)
+    (name "go-mvdan-cc-unparam")
+    (arguments
+     `(#:import-path "github.com/mvdan/unparam"
+       #:tests? #f
+       #:install-source? #t
+       #:phases (modify-phases %standard-phases
+                  (delete 'build))))
+    (propagated-inputs (package-inputs unparam))
+    (native-inputs '())
+    (inputs '())))
+
+(define-public xurls
+  (package
+    (name "xurls")
+    (version "2.4.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/mvdan/xurls")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0b040nbk1vwlk1qljavh8w8fn2r243q700n6gr8j2asmnz0xq84p"))))
+    (build-system go-build-system)
+    (arguments
+     `(#:import-path "mvdan.cc/xurls/v2"
+       #:unpack-path "mvdan.cc/xurls/v2"
+       #:phases (modify-phases %standard-phases
+                  (replace 'build
+                    (lambda arguments
+                      (apply (assoc-ref %standard-phases
+                                        'build)
+                             `(,@arguments #:import-path
+                               "mvdan.cc/xurls/v2/cmd/xurls")))))))
+    (inputs (list go-golang-org-x-sync go-github-com-rogpeppe-go-internal))
+    (home-page "https://mvdan.cc/xurls/v2/")
+    (synopsis "Extracts URLs from text")
+    (description
+     "Xurls extracts urls from plain text using regular expressions.  It can
+be used as both a binary and a library.")
+    (license license:bsd-3)))
+
+(define-public go-mvdan-cc-xurls
+  (package
+    (inherit xurls)
+    (name "go-mvdan-cc-xurls")
+    (arguments
+     `(#:import-path "mvdan.cc/xurls"
+       #:tests? #f
+       #:install-source? #t
+       #:phases (modify-phases %standard-phases
+                  (delete 'build))))
+    (propagated-inputs (package-inputs xurls))
+    (native-inputs '())
+    (inputs '())))
+
 (define-public go-golang-org-x-lint
   (let ((commit "83fdc39ff7b56453e3793356bcff3070b9b96445")
         (revision "0"))
@@ -9729,27 +10178,26 @@ tools with similar semantics.")
 (define-public go-honnef-co-go-tools
   (package
     (name "go-honnef-co-go-tools")
-    (version "0.1.3")
+    (version "0.3.3")
-    (source
+    (source (origin
-     (origin
+              (method git-fetch)
-       (method git-fetch)
+              (uri (git-reference
-       (uri (git-reference
+                    (url "https://github.com/dominikh/go-tools")
-             (url "https://github.com/dominikh/go-tools")
+                    (commit (string-append "v" version))))
-             (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
-       (file-name (git-file-name name version))
+              (sha256
-       (sha256
+               (base32
-        (base32 "17li8jbw3cpn59kpcl3j3r2an4wkx3fc81xn0j4xgbjpkxh9493n"))))
+                "099z04v7vvwwglnps315s9fmal68xvzlc1g8m26iqi980grbwn32"))))
     (build-system go-build-system)
     (arguments
      `(#:import-path "honnef.co/go/tools"
        #:tests? #f
        ;; Source-only package
-       #:phases
+       #:phases (modify-phases %standard-phases
-       (modify-phases %standard-phases
+                  (delete 'build))))
-         (delete 'build))))
+    (propagated-inputs (list go-golang-org-x-exp go-golang-org-x-tools
-    (propagated-inputs
+                             go-golang-org-x-mod go-github-com-kisielk-gotool
-     (list go-golang-org-x-tools go-github-com-kisielk-gotool
+                             go-github-com-burntsushi-toml))
-           go-github-com-burntsushi-toml))
     (home-page "https://honnef.co/go/tools")
     (synopsis "Staticcheck advanced Go linter")
     (description
@@ -10869,6 +11317,60 @@ production-ready implementation, compatible with the original Jsonnet C++
 implementation.")
     (license license:asl2.0)))
 
+(define-public go-github-com-google-go-cmdtest
+  (let ((commit "55ab3332a786118933ddf71544aae14951ba9bc5")
+        (revision "0"))
+    (package
+      (name "go-github-com-google-go-cmdtest")
+      (version (git-version "0.4.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/google/go-cmdtest")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "10kswvbdwissjb5mr0ys4b3ppxkxlpklqg7cr2z7rv21g2vwczbl"))))
+      (build-system go-build-system)
+      (arguments
+       '(#:import-path "github.com/google/go-cmdtest"))
+      (propagated-inputs (list go-github-com-google-renameio
+                               go-github-com-google-go-cmp-cmp))
+      (home-page "https://github.com/google/go-cmdtest")
+      (synopsis "Testing for your CLI")
+      (description
+       "The cmdtest package simplifies testing of command-line interfaces.  It
+provides a simple, cross-platform, shell-like language to express command
+execution.  It can compare actual output with the expected output, and can
+also update a file with new \"golden\" output that is deemed correct.")
+      (license license:asl2.0))))
+
+(define-public go-github-com-google-safehtml
+  (package
+    (name "go-github-com-google-safehtml")
+    (version "0.1.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/google/safehtml")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0j2xjy8xrk9y9k6bqpvimj84i6hg1wwsyvwsb0axhmp49cmnrp86"))))
+    (build-system go-build-system)
+    (arguments
+     '(#:import-path "github.com/google/safehtml"))
+    (propagated-inputs `(("go-golang-org-x-text" ,go-golang-org-x-text)))
+    (home-page "https://github.com/google/safehtml")
+    (synopsis "Safe HTML for Go")
+    (description
+     "Package safehtml provides immutable string-like types which represent values
+that are guaranteed to be safe, by construction or by escaping or sanitization,
+to use in various HTML contexts and with various DOM APIs.")
+    (license license:bsd-3)))
+
 (define-public go-github-com-google-shlex
   (package
     (name "go-github-com-google-shlex")

gnu/packages/graph.scm

@@ -8,7 +8,7 @@
 ;;; Copyright © 2020 Pierre Langlois <pierre.langlos@gmx.com>
 ;;; Copyright © 2021 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2021 Alexandre Hannud Abdo <abdo@member.fsf.org>
-;;; Copyright © 2021, 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2021, 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2022 Marius Bakke <marius@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -34,6 +34,7 @@
   #:use-module (guix utils)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system pyproject)
   #:use-module (guix build-system python)
   #:use-module (guix build-system r)
   #:use-module ((guix licenses) #:prefix license:)
@@ -91,35 +92,40 @@ distributions in empirical data.  SIAM Review 51, 661-703 (2009)}).")
 (define-public igraph
   (package
     (name "igraph")
-    (version "0.9.8")
+    (version "0.10.4")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://github.com/igraph/igraph/releases/"
                            "download/" version "/igraph-" version ".tar.gz"))
-       (modules '((guix build utils)))
+       (modules '((guix build utils)
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
        (snippet '(begin
-                   ;; Fully unbundle igraph (see:
+                   ;; igraph insists on building its own copy of CxSparse
-                   ;; https://github.com/igraph/igraph/issues/1897).
+                   ;; (see: https://github.com/igraph/igraph/commit/\
-                   (delete-file-recursively "vendor")
+                   ;; 334318b7dfe46501236272ca336580f4748114b0) and the build
-                   (substitute* "CMakeLists.txt"
+                   ;; has no support to use a system provided 'pcg'.
-                     (("add_subdirectory\\(vendor\\).*")
+                   (define keep-libraries '("cs" "pcg"))
-                      ""))
+                   (define keep (append '("." ".." "CMakeLists.txt")
-                   ;; Help CMake to find our plfit headers.
+                                        keep-libraries))
-                   (substitute* "etc/cmake/FindPLFIT.cmake"
+                   (define keep? (cut member <> keep))
-                     (("^  NAMES plfit.h.*" all)
+                   (with-directory-excursion "vendor"
-                      (string-append all
+                     (for-each delete-file-recursively
-                                     "  PATH_SUFFIXES plfit")))
+                               (scandir "." (negate keep?))))
+                   (call-with-output-file "vendor/CMakeLists.txt"
+                     (cut format <> "~{add_subdirectory(~a)~%~}"
+                          keep-libraries))
                    (substitute* '("src/CMakeLists.txt"
                                   "etc/cmake/benchmark_helpers.cmake")
-                     ;; Remove bundling related variables.
+                     ;; Remove extraneous bundling related variables.
                      ((".*_IS_VENDORED.*")
                       ""))))
        (sha256
-        (base32 "15v3ydq95gahnas37cip637hvc2nwrmk76xp0nv3gq53rrrk9a7r"))))
+        (base32 "1z1ay3l1h64jc2igbl2ibvi20sswy56v2yk3ykhis7jzijsh0mxa"))))
     (build-system cmake-build-system)
-    (arguments
+    (arguments (list #:configure-flags #~(list "-DBUILD_SHARED_LIBS=ON")
-     '(#:configure-flags (list "-DBUILD_SHARED_LIBS=ON")))
+                     #:test-target "check"))
     (native-inputs (list pkg-config))
     (inputs
      (list arpack-ng
@@ -128,8 +134,9 @@ distributions in empirical data.  SIAM Review 51, 661-703 (2009)}).")
            libxml2
            lapack
            openblas
-           plfit
+           plfit))
-           suitesparse))
+    ;; libxml2 is in the 'Requires.private' of igraph.pc.
+    (propagated-inputs (list libxml2))
     (home-page "https://igraph.org")
     (synopsis "Network analysis and visualization")
     (description
@@ -140,48 +147,47 @@ more.")
     (license license:gpl2+)))
 
 (define-public python-igraph
-  (package
+  ;; Temporarily use a precise commit, as there was a mistake in the last
-    (inherit igraph)
+  ;; release that was fixed by it (see:
-    (name "python-igraph")
+  ;; https://github.com/igraph/python-igraph/issues/632).
-    (version "0.9.11")
+  (let ((revision "0")
-    (source (origin
+        (commit "b6ebd8eb277fc1d0e33340a6624629a10c638992"))
-              (method git-fetch)
+    (package
-              ;; The PyPI archive lacks tests.
+      (inherit igraph)
-              (uri (git-reference
+      (name "python-igraph")
-                    (url "https://github.com/igraph/python-igraph")
+      (version (git-version "0.10.4" revision commit))
-                    (commit version)))
+      (source (origin
-              (file-name (git-file-name name version))
+                (method git-fetch)
-              (sha256
+                ;; The PyPI archive lacks tests.
-               (base32
+                (uri (git-reference
-                "1xlr0cnf3a1vs9n2psvgrmjhld4n1xr79kkjqzby4pxxyzk1bydn"))))
+                      (url "https://github.com/igraph/python-igraph")
-    (build-system python-build-system)
+                      (commit commit)))
-    (arguments
+                (file-name (git-file-name name version))
-     (list
+                (sha256
-      #:phases
+                 (base32
-      #~(modify-phases %standard-phases
+                  "0dhrz5a6pi6vs94fm8q4nmkh6v1nmpw1sk482xls213zcbbh67hd"))))
-          (add-after 'unpack 'specify-libigraph-location
+      (build-system pyproject-build-system)
-            (lambda _
+      (arguments
-              (let ((igraph #$(this-package-input "igraph")))
+       (list
-                (substitute* "setup.py"
+        #:phases
-                  (("(LIBIGRAPH_FALLBACK_INCLUDE_DIRS = ).*" _ var)
+        #~(modify-phases %standard-phases
-                   (string-append
+            (add-after 'unpack 'specify-libigraph-location
-                    var (format #f "[~s]~%" (string-append igraph
+              (lambda _
-                                                           "/include/igraph"))))
+                (let ((igraph #$(this-package-input "igraph")))
-                  (("(LIBIGRAPH_FALLBACK_LIBRARY_DIRS = ).*" _ var)
+                  (substitute* "setup.py"
-                   (string-append
+                    (("(LIBIGRAPH_FALLBACK_INCLUDE_DIRS = ).*" _ var)
-                    var (format #f "[~s]~%" (string-append igraph "/lib"))))))))
+                     (string-append
-          (replace 'check
+                      var (format #f "[~s]~%"
-            (lambda* (#:key tests? #:allow-other-keys)
+                                  (string-append igraph "/include/igraph"))))
-              (when tests?
+                    (("(LIBIGRAPH_FALLBACK_LIBRARY_DIRS = ).*" _ var)
-                (invoke "pytest" "-v")))))))
+                     (string-append
-    (inputs
+                      var (format #f "[~s]~%"
-     (list igraph))
+                                  (string-append igraph "/lib")))))))))))
-    (propagated-inputs
+      (inputs (list igraph))
-     (list python-texttable))
+      (propagated-inputs (list python-texttable))
-    (native-inputs
+      (native-inputs (list python-pytest))
-     (list python-pytest))
+      (home-page "https://igraph.org/python/")
-    (home-page "https://igraph.org/python/")
+      (synopsis "Python bindings for the igraph network analysis library"))))
-    (synopsis "Python bindings for the igraph network analysis library")))
 
 (define-public r-rbiofabric
   (let ((commit "666c2ae8b0a537c006592d067fac6285f71890ac")
@@ -305,58 +311,6 @@ subplots, multiple-axes, polar charts, and bubble charts.")
 algorithm for community detection in large networks.")
     (license license:bsd-3)))
 
-(define-public python-louvain-0.7
-  (package
-    (name "python-louvain")
-    (version "0.7.1")
-    ;; The tarball on Pypi does not include the tests.
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/vtraag/louvain-igraph")
-                    (commit version)))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "1g6b5c2jgwagnhnqh859g61h7x6a81d8hm3g6mkin6kzwafww3g2"))))
-    (build-system python-build-system)
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-before 'build 'pretend-version
-            ;; The version string is usually derived via setuptools-scm, but
-            ;; without the git metadata available this fails.
-            (lambda _
-              (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)))
-          (add-before 'build 'find-igraph
-            (lambda* (#:key inputs #:allow-other-keys)
-              (setenv "IGRAPH_EXTRA_INCLUDE_PATH"
-                      (string-append (assoc-ref inputs "igraph")
-                                     "/include/igraph:"
-                                     (getenv "C_INCLUDE_PATH")))
-              (setenv "IGRAPH_EXTRA_LIBRARY_PATH"
-                      (getenv "LIBRARY_PATH")))))))
-    (propagated-inputs
-     (list python-ddt python-igraph))
-    (inputs
-     (list igraph))
-    (native-inputs
-     (list pkg-config
-           python-pytest
-           python-setuptools-scm
-           python-wheel))
-    (home-page "https://github.com/vtraag/louvain-igraph")
-    (synopsis "Algorithm for methods of community detection in large networks")
-    (description
-     "This package provides an implementation of the Louvain algorithm for use
-with igraph.  Louvain is a general algorithm for methods of community
-detection in large networks.
-
-This package has been superseded by the @code{leidenalg} package and should
-not be used for new projects.")
-    (license license:gpl3+)))
-
 (define-public faiss
   (package
     (name "faiss")
@@ -496,14 +450,14 @@ Faiss library.")))
 (define-public python-leidenalg
   (package
     (name "python-leidenalg")
-    (version "0.8.10")
+    (version "0.9.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "leidenalg" version))
        (sha256
         (base32
-         "1hbvagp1yyazvl7cid7mii5263qi48lpkq543n5w71qysgz1f0v7"))))
+         "1wvmi6ca9kf8pbxg6b18n64h82wr9a6wcdazyn82pww0dwxzwp3y"))))
     (build-system python-build-system)
     (arguments
      '(#:tests? #f                      ;tests are not included
@@ -566,19 +520,18 @@ isolating planarity obstructions.")
     (name "rw")
     ;; There is a version 0.8, but the tarball is broken with symlinks
     ;; to /usr/share.
-    (version "0.7")
+    (version "0.9")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/rankwidth/"
                                   "rw-" version ".tar.gz"))
-       (sha256
+              (sha256
-        (base32
+               (base32
-         "1rv2v42x2506x7f10349m1wpmmfxrv9l032bkminni2gbip9cjg0"))))
+                "0hdlxxmlccb6fp7g58zv0rdzpbyjn9bgqlf052sgrk95zq33bq61"))
+              (patches (search-patches "rw-igraph-0.10.patch"))))
     (build-system gnu-build-system)
-    (native-inputs
+    (native-inputs (list pkg-config))
-     (list pkg-config))
+    (inputs (list igraph))
-    (inputs
-     (list igraph))
     (home-page "https://sourceforge.net/projects/rankwidth/")
     (synopsis "Rank-width and rank-decomposition of graphs")
     (description "rw computes rank-width and rank-decompositions

gnu/packages/graphics.scm

@@ -33,6 +33,8 @@
 ;;; Copyright © 2022 Tobias Kortkamp <tobias.kortkamp@gmail.com>
 ;;; Copyright © 2022 Paul A. Patience <paul@apatience.com>
 ;;; Copyright © 2022 dan <i@dan.games>
+;;; Copyright © 2023 Sharlatan Hellseher <sharlatanus@gmail.com>
+;;; Copyright © 2023 David Thompson <dthompson2@worcester.edu>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -233,6 +235,52 @@ minimum of resource usage and overhead.")
     (home-page "https://github.com/deniskropp/DirectFB")
     (license license:lgpl2.1+)))
 
+(define-public minifb
+  (let ((commit "43f8c1309341f4709a471b592d04434326042483")
+        (revision "1"))
+    (package
+      (name "minifb")
+      (version (git-version "0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri
+                 (git-reference
+                  (url "https://github.com/emoon/minifb")
+                  (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32 "1z0720azsgi83yg4ysmfvpvsg0566s2cq59xx52w8w5rpkla4cjh"))))
+      (build-system cmake-build-system)
+      (arguments
+       ;; Don't build examples.
+       '(#:configure-flags '("-DMINIFB_BUILD_EXAMPLES=0")
+         #:phases
+         ;; There is no install target, so we have to copy the static library
+         ;; and headers to the output directory ourselves.
+         (modify-phases %standard-phases
+           (replace 'install
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let* ((out (assoc-ref outputs "out"))
+                      (includedir (string-append out "/include"))
+                      (libdir (string-append out "/lib")))
+                 (mkdir-p includedir)
+                 (mkdir-p libdir)
+                 (for-each (lambda (header)
+                             (copy-file header
+                                        (string-append includedir "/"
+                                                       (basename header))))
+                           (find-files "../source/include" "\\.h$"))
+                 (copy-file "libminifb.a" (string-append libdir "/libminifb.a"))))))
+         ;; No check target.
+         #:tests? #f))
+      ;; libminifb.a won't work without these libraries, so propagate them.
+      (propagated-inputs (list libx11 libxkbcommon mesa))
+      (synopsis "Small library for rendering pixels to a framebuffer")
+      (description "MiniFB (Mini FrameBuffer) is a small, cross-platform
+library that makes it easy to render (32-bit) pixels in a window.")
+      (home-page "https://github.com/emoon/minifb")
+      (license license:expat))))
+
 (define-public flux
   (package
     (name "flux")
@@ -594,6 +642,20 @@ vertices, sorting by primitive type, merging of redundant materials and many
 more.")
     (license license:bsd-3)))
 
+(define-public assimp-5.0
+  (package
+    (inherit assimp)
+    (version "5.0.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/assimp/assimp")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name "assimp" version))
+              (sha256
+               (base32
+                "1w2484lg823bql7lpfq84vnsfsnag5v65qrbphslj866z9ia68l7"))))))
+
 (define-public mikktspace
   ;; The latest commit is used as there is no release.
   (let ((commit   "3e895b49d05ea07e4c2133156cfa94369e19e409")
@@ -2121,7 +2183,7 @@ a complete and conforming implementation of the OpenXR API made by Khronos.")
 (define-public azpainter
   (package
     (name "azpainter")
-    (version "3.0.5")
+    (version "3.0.6")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -2130,7 +2192,7 @@ a complete and conforming implementation of the OpenXR API made by Khronos.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1iplp3p8pw9q44kb43hrk89sv2aff6bdy9fk58j2v6k5lqbk6kvf"))))
+                "0lk74drrksk340fzyzvrq0ixwj498adshbp505cj163qsqnndj7y"))))
     (build-system gnu-build-system) ;actually a home grown build system
     (arguments
      (list #:tests? #f
@@ -2443,3 +2505,39 @@ on the command line.  It supports a range of file formats (including animated
 glTF, STL, STEP, PLY, OBJ, FBX), and provides numerous rendering and texturing
 options.")
     (license license:bsd-3)))
+
+(define-public gpaint
+  (package
+    (name "gpaint")
+    (version "0.3.3")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://alpha.gnu.org/gnu/"
+                                  name "/"
+                                  name "-2-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1syh5l5fnzk7cw77iykafn73fvmnc83kg815fa8vvj0h0r30c5sl"))))
+    (build-system gnu-build-system)
+    (inputs (list gtk+-2 libglade))
+    (native-inputs
+     (list gettext-minimal `(,glib "bin") pkg-config))
+    (arguments
+     (list #:phases #~(modify-phases %standard-phases
+                        (add-after 'unpack 'remove-undefined-references
+                          (lambda _
+                            (substitute* "src/drawing.c"
+                              (("GTK_STOCK_DISCARD,GTK_RESPONSE_DISCARD")
+                               "GTK_STOCK_DISCARD,GTK_RESPONSE_NO"))
+                            (substitute* "src/menu.c"
+                              (("\\#include \"menu.h\"")
+                               "")))))))
+
+    (synopsis "Simple paint program for GNOME")
+    (description
+     "GNU Paint is a simple, easy-to-use paint program for the GNOME
+environment.  It supports drawing freehand as well as basic shapes and text.
+It features cut-and-paste for irregular regions or polygons.")
+    (home-page "https://www.gnu.org/software/gpaint/")
+    (license license:gpl3+)))
+

gnu/packages/gstreamer.scm

@@ -357,8 +357,7 @@ playback by a single audio device.  You can also pre-load samples, and play them
 back without having to send all the data for the sound.  Network transparency is
 also built in, so you can play sounds on one machine, and listen to them on
 another.")
-    (home-page "https://web.archive.org/web/20160528230227/
+    (home-page "https://web.archive.org/web/20160528230227/http://www.tux.org/~ricdude/overview.html")
-http://www.tux.org/~ricdude/overview.html")
     (license
      (list
       ;; Libraries.

gnu/packages/gtk.scm

@@ -33,6 +33,7 @@
 ;;; Copyright © 2022 Benjamin Slade <slade@lambda-y.net>
 ;;; Copyright © 2022 Denis 'GNUtoo' Carikli <GNUtoo@cyberdimension.org>
 ;;; Copyright © 2022 Petr Hodina <phodina@protonmail.com>
+;;; Copyright © 2023 Sergiu Ivanov <sivanov@colimite.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -67,6 +68,7 @@
   #:use-module (guix build-system waf)
   #:use-module (gnu packages)
   #:use-module (gnu packages algebra)
+  #:use-module (gnu packages audio)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages base)
   #:use-module (gnu packages bash)
@@ -2517,7 +2519,7 @@ Parcellite and adds bugfixes and features.")
               '("-Dintrospection=false")
               '()))))
     (native-inputs
-     `(("git" ,git-minimal/fixed)
+     `(("git" ,git-minimal/pinned)
        ("gobject-introspection" ,gobject-introspection)
        ("mutest" ,mutest)
        ("pkg-config" ,pkg-config)))
@@ -2949,7 +2951,7 @@ user interaction (e.g.  measuring distances).")
 (define-public volctl
   (package
     (name "volctl")
-    (version "0.8.2")
+    (version "0.9.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference (url "https://github.com/buzz/volctl")
@@ -2957,28 +2959,28 @@ user interaction (e.g.  measuring distances).")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1cx27j83pz2qffnzb85fbl1x6pp3irv1kbw7g1hri7kaw6ky4xiz"))))
+                "0fz80w3ywq54jn4v31frfdj01s5g9lz6v9cd7hpg3kirca0zisln"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'patch-path
            (lambda* (#:key inputs #:allow-other-keys)
-             (let ((pulse (assoc-ref inputs "pulseaudio"))
+             (substitute* "volctl/xwrappers.py"
-                   (xfixes (assoc-ref inputs "libxfixes")))
+               (("libXfixes.so")
-               (substitute* "volctl/lib/xwrappers.py"
+                (string-append (search-input-file inputs
-                 (("libXfixes.so")
+                                                  "/lib/libXfixes.so")))))))))
-                  (string-append xfixes "/lib/libXfixes.so")))
-               (substitute* "volctl/lib/pulseaudio.py"
-                 (("libpulse.so.0")
-                  (string-append pulse "/lib/libpulse.so.0")))
-               #t))))))
     (inputs
-     (list gtk+ libxfixes pulseaudio))
+     (list libxfixes))
     (propagated-inputs
-     (list python-click python-pycairo python-pygobject python-pyyaml))
+     (list python-click
+           python-pycairo
+           python-pygobject
+           python-pyyaml
+           python-pulsectl
+           gtk+))
     (home-page "https://buzz.github.io/volctl/")
-    (synopsis "Per-application volume control and on-screen display for graphical desktops")
+    (synopsis "Per-application volume control and on-screen display")
     (description "Volctl is a PulseAudio-enabled tray icon volume control and
 OSD applet for graphical desktops.  It's not meant to be an replacement for a
 full-featured mixer application.  If you're looking for that check out the

gnu/packages/guile-xyz.scm

@@ -1020,6 +1020,38 @@ It has a nice, simple s-expression based syntax.")
     (name "guile2.2-sjson")
     (inputs (list guile-2.2))))
 
+(define-public guile-scheme-json-rpc
+  (let ((commit "45ae6890f6619286f5679f88c094c88127b54c4a")
+        (revision "0")
+        (version "0.2.11"))
+    (package
+      (name "guile-scheme-json-rpc")
+      (version (git-version version revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://codeberg.org/rgherdt/scheme-json-rpc.git")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0w4m8xx8yyj0rv0q57mjr8ja87l7yikscj33i3ck26wg7230ppa5"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:phases (modify-phases %standard-phases
+                    (add-after 'unpack 'change-to-guile-dir
+                      (lambda _
+                        (chdir "guile"))))))
+      (inputs (list guile-3.0 guile-json-3))
+      (native-inputs (list pkg-config))
+      (synopsis "Library providing JSON-RPC capability in Scheme")
+      (description
+       "This library implements parts of the
+@uref{https://www.jsonrpc.org/specification,JSON-RPC specification}, allowing
+for calling methods on remote servers by exchanging JSON objects.")
+      (home-page "https://codeberg.org/rgherdt/scheme-json-rpc/")
+      (license license:expat))))
+
 (define-public guile-squee
   (let ((commit "a151fd006fa819945ca1d4749b173854269b9f70")
         (revision "3"))
@@ -1261,7 +1293,23 @@ types are supported.")
                (base32
                 "0044c105r3q9vpl17pv3phl1b79kjm1llhkakqgiasixyav01blh"))))
     (build-system guile-build-system)
-    (native-inputs (list guile-2.2))
+    (inputs (list guile-3.0))
+    (arguments
+     (list
+      #:scheme-file-regexp "^aa-tree\\.scm"
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'install-documentation 'check
+            (lambda* (#:key inputs #:allow-other-keys)
+              (let* ((guile      #$(this-package-input "guile"))
+                     (effective  (target-guile-effective-version guile))
+                     (go-dir     (string-append #$output "/lib/guile/"
+                                                effective "/site-ccache/")))
+                (invoke (search-input-file inputs "/bin/guile")
+                        "--no-auto-compile"
+                        "-C" go-dir
+                        "-c" (string-append
+                              "(load \"" (getcwd) "/test-aa-tree.scm\")"))))))))
     ;; https://savannah.nongnu.org/projects/guile-aa-tree
     (home-page "https://qlfiles.net/guile-aa-tree/")
     (synopsis "AA tree data structure for Guile")
@@ -1503,27 +1551,6 @@ Extensions) compliant email messages and reading emails from the mbox
 format.")
     (license license:agpl3+)))
 
-(define-public guile-email-latest
-  (let ((commit "ea60bb902d3677d5c653851c7aa6afbbf710140e")
-        (revision "2"))
-    (package
-      (inherit guile-email)
-      (name "guile-email-latest")
-      (version (git-version "0.2.2" revision commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://git.systemreboot.net/guile-email")
-               (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32
-           "1g4rn7ai3nfxmpppc8qbpv8b18wnsld29y5xa58cv9b8pf3pbwnj"))))
-      (arguments '())
-      (native-inputs
-       (list pkg-config autoconf automake texinfo)))))
-
 (define-public guile2.2-email
   (package
     (inherit guile-email)
@@ -2208,91 +2235,90 @@ capabilities.")
     (license license:gpl3+)))
 
 (define-public guile-g-golf
-  (let ((commit   "1824633d37da3794f349d6829e9dac2cf89adaa8")
+  (package
-        (revision "1010"))
+    (name "guile-g-golf")
-    (package
+    (version "0.8.0-a.1")
-      (name "guile-g-golf")
+    (source
-      (version (git-version "0.1.0" revision commit))
+     (origin
-      (source
+       (method git-fetch)
-       (origin
+       (uri (git-reference
-         (method git-fetch)
+             (url "https://git.savannah.gnu.org/git/g-golf.git")
-         (uri (git-reference
+             (commit (string-append "v" version))))
-               (url "https://git.savannah.gnu.org/git/g-golf.git")
+       (file-name (git-file-name name version))
-               (commit commit)))
+       (sha256
-         (file-name (git-file-name name version))
+        (base32 "1lszlssa6k8dhhya5px271gfzas7fyy1iwjqmlxibz5vdirzi565"))))
-         (sha256
+    (build-system gnu-build-system)
-          (base32 "0ncpqv6pbsx9fjmdzvzbjljnhqgw9pynqy9vr9aq35nb7rzrhfdf"))))
+    (arguments
-      (build-system gnu-build-system)
+     (list
-      (arguments
+      #:configure-flags
-       (list
+      #~(list "--with-guile-site=no")
-        #:configure-flags
+      #:parallel-build? #f
-        #~(list "--with-guile-site=no")
+      #:phases
-        #:phases
+      #~(modify-phases %standard-phases
-        #~(modify-phases %standard-phases
+          (add-after 'unpack 'fix-guile-site-directory
-            (add-after 'unpack 'fix-guile-site-directory
+            (lambda _
-              (lambda _
+              (substitute* "configure.ac"
-                (substitute* "configure.ac"
+                (("SITEDIR=.*$")
-                  (("SITEDIR=.*$")
+                 "SITEDIR=\"$datadir/guile/site/$GUILE_EFFECTIVE_VERSION\";\n")
-                   "SITEDIR=\"$datadir/guile/site/$GUILE_EFFECTIVE_VERSION\";\n")
+                (("SITECCACHEDIR=\"\\$libdir/g-golf/")
-                  (("SITECCACHEDIR=\"\\$libdir/g-golf/")
+                 "SITECCACHEDIR=\"$libdir/"))))
-                   "SITECCACHEDIR=\"$libdir/"))))
+          (add-before 'configure 'tests-work-arounds
-            (add-before 'configure 'tests-work-arounds
+            (lambda* (#:key inputs #:allow-other-keys)
-              (lambda* (#:key inputs #:allow-other-keys)
+              ;; In build environment, There is no /dev/tty
-                ;; In build environment, There is no /dev/tty
+              (substitute* "test-suite/tests/gobject.scm"
-                (substitute* "test-suite/tests/gobject.scm"
+                (("/dev/tty") "/dev/null"))))
-                  (("/dev/tty") "/dev/null"))))
+          (add-before 'configure 'substitute-libs
-            (add-before 'configure 'substitute-libs
+            (lambda* (#:key inputs outputs #:allow-other-keys)
-              (lambda* (#:key inputs outputs #:allow-other-keys)
+              (define (get lib)
-                (define (get lib)
+                (search-input-file inputs (string-append "lib/" lib ".so")))
-                  (search-input-file inputs (string-append "lib/" lib ".so")))
 
-                (let* ((libgi      (get "libgirepository-1.0"))
+              (let* ((libgi      (get "libgirepository-1.0"))
-                       (libglib    (get "libglib-2.0"))
+                     (libglib    (get "libglib-2.0"))
-                       (libgobject (get "libgobject-2.0"))
+                     (libgobject (get "libgobject-2.0"))
-                       (libg-golf (string-append #$output "/lib/libg-golf")))
+                     (libg-golf (string-append #$output "/lib/libg-golf")))
-                  (substitute* "g-golf/init.scm"
+                (substitute* "g-golf/init.scm"
-                    (("libgirepository-1.0") libgi)
+                  (("libgirepository-1.0") libgi)
-                    (("libglib-2.0") libglib)
+                  (("libglib-2.0") libglib)
-                    (("libgobject-2.0") libgobject)
+                  (("libgobject-2.0") libgobject)
-                    (("\\(dynamic-link \"libg-golf\"\\)")
+                  (("\\(dynamic-link \"libg-golf\"\\)")
-                     (format #f "~s"
+                   (format #f "~s"
-                             `(catch #t
+                           `(catch #t
-                                (lambda ()
+                              (lambda ()
-                                  (dynamic-link "libg-golf"))
+                                (dynamic-link "libg-golf"))
-                                (lambda _
+                              (lambda _
-                                  (dynamic-link ,libg-golf))))))
+                                (dynamic-link ,libg-golf))))))
-                  (setenv "GUILE_AUTO_COMPILE" "0")
+                (setenv "GUILE_AUTO_COMPILE" "0")
-                  #t)))
+                #t)))
-            (add-before 'check 'start-xorg-server
+          (add-before 'check 'start-xorg-server
-              (lambda* (#:key inputs #:allow-other-keys)
+            (lambda* (#:key inputs #:allow-other-keys)
-                ;; The test suite requires a running X server.
+              ;; The test suite requires a running X server.
-                (system "Xvfb :1 &")
+              (system "Xvfb :1 &")
-                (setenv "DISPLAY" ":1")
+              (setenv "DISPLAY" ":1")
-                #t)))))
+              #t)))))
-      (inputs
+    (inputs
-       (list guile-3.0 guile-lib glib))
+     (list guile-3.0 guile-lib glib-next))
-      (native-inputs
+    (native-inputs
-       (list autoconf
+     (list autoconf
-             automake
+           automake
-             texinfo
+           texinfo
-             gettext-minimal
+           gettext-minimal
-             libtool
+           libtool
-             pkg-config
+           pkg-config
-             ;; required for tests
+           ;; required for tests
-             gtk+
+           gtk+
-             clutter
+           clutter
-             xorg-server-for-tests))
+           xorg-server-for-tests))
-      (propagated-inputs
+    (propagated-inputs
-       (list gobject-introspection))
+     (list gobject-introspection-next))
-      (home-page "https://www.gnu.org/software/g-golf/")
+    (home-page "https://www.gnu.org/software/g-golf/")
-      (synopsis "Guile bindings for GObject Introspection")
+    (synopsis "Guile bindings for GObject Introspection")
-      (description
+    (description
-       "G-Golf (Gnome: (Guile Object Library for)) is a library for developing
+     "G-Golf (Gnome: (Guile Object Library for)) is a library for developing
 modern applications in Guile Scheme.  It comprises a direct binding to the
 GObject Introspection API and higher-level functionality for importing Gnome
 libraries and making GObject classes (and methods) available in Guile's
 object-oriented programming system, GOOPS.")
-      (license license:lgpl3+))))
+    (license license:lgpl3+)))
 
 (define-public g-golf
   (deprecated-package "g-golf" guile-g-golf))
@@ -2574,6 +2600,41 @@ for Guile\".  It provides the following modules:
     ;; details.
     (license license:gpl3+)))
 
+(define-public guile-simple-iterators
+  (let ((commit "50f16a2b2aa57e657e52e19fb3c35bdc182cfa36")
+        (revision "0"))
+    (package
+      (name "guile-simple-iterators")
+      (version (git-version "0.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://gitlab.com/dustyweb/guile-simple-iterators")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "1m1wirlnfwmp5a4rpszd5qsbwabz4ji033w6p2714p1r524ylah8"))))
+      (build-system guile-build-system)
+      (native-inputs (list guile-3.0))
+      (home-page "https://gitlab.com/dustyweb/guile-simple-iterators")
+      (synopsis "Simple iterators for Guile")
+      (description
+       "This is a collection of iteration macros for Guile. They are inspired by
+@code{racket}'s family of iterators. Specifically, the following iterators are
+available:
+@itemize
+@item @code{for}
+@item @code{for/map}
+@item @code{for/c}
+@item @code{for/fold}
+@item @code{for/fold-right}
+@item @code{for/folder}
+@item @code{folder}
+@end itemize")
+      (license license:asl2.0))))
+
 (define-public guile2.0-lib
   (package
     (inherit guile-lib)
@@ -4374,7 +4435,10 @@ models and also supports a rich set of boolean query operators.")
     (name "guile2.2-xapian")
     (inputs
      (modify-inputs (package-inputs guile-xapian)
-       (replace "guile" guile-2.2)))))
+       (replace "guile" guile-2.2)))
+    (propagated-inputs
+     (modify-inputs (package-propagated-inputs guile-xapian)
+       (replace "guile-lib" guile2.2-lib)))))
 
 (define-public guile-torrent
   (package
@@ -4667,60 +4731,31 @@ errors.")
     (license license:expat)))
 
 (define-public guile-avahi
-  (let ((commit "6d43caf64f672a9694bf6c98bbf7a734f17a51e8")
+  (package
-        (revision "1"))
+    (name "guile-avahi")
-    (package
+    (version "0.4.1")
-      (name "guile-avahi")
+    (source (origin
-      (version (git-version "0.4.0" revision commit))
+              (method git-fetch)
-      (source (origin
+              (uri (git-reference
-                (method git-fetch)
+                    (url "https://git.sv.gnu.org/git/guile-avahi.git/")
-                (uri (git-reference
+                    (commit (string-append "v" version))))
-                      (url "git://git.sv.gnu.org/guile-avahi.git")
+              (file-name (git-file-name name version))
-                      (commit commit)))
+              (sha256
-                (file-name (git-file-name name version))
+               (base32
-                (sha256
+                "0pxdi13kr4ylpms0xyf3xwwbhg025k7a2liwnbha1gw6ls58xgv2"))))
-                 (base32
+    (build-system gnu-build-system)
-                  "0fvrf8x22yvc71180hd3xkhspg9yvadi0pbv8shzlsaxqncwy1m9"))
+    (inputs
-                (modules '((guix build utils)))))
+     (list guile-3.0 avahi))
-      (build-system gnu-build-system)
+    (native-inputs
-      (arguments
+     (list autoconf automake libtool pkg-config texinfo guile-3.0))
-       `(#:modules (((guix build guile-build-system)
+    (synopsis "Guile bindings to Avahi")
-                     #:select (target-guile-effective-version))
+    (description
-                    ,@%gnu-build-system-modules)
+     "This package provides bindings for Avahi.  It allows programmers to
-         #:imported-modules ((guix build guile-build-system)
-                             ,@%gnu-build-system-modules)
-         #:make-flags
-         '("GUILE_AUTO_COMPILE=0")    ;to prevent guild warnings
-         ;; Parallel builds fail on powerpc64le-linux.
-         ;; See https://lists.nongnu.org/archive/html/guile-avahi-bugs/2021-01/msg00000.html
-         #:parallel-build? #f
-         #:phases
-         (modify-phases %standard-phases
-           (add-before 'check 'fix-guile-avahi-file-name
-           (lambda* (#:key outputs #:allow-other-keys)
-             (with-directory-excursion "src"
-               (invoke "make" "install"
-                       "-j" (number->string
-                             (parallel-job-count))))
-             (let* ((out   (assoc-ref outputs "out"))
-                    (files (find-files "modules" ".scm")))
-               (substitute* files
-                 (("\"guile-avahi-v-0\"")
-                  (format #f "\"~a/lib/guile/~a/extensions/guile-avahi-v-0\""
-                          out (target-guile-effective-version))))
-               #t))))))
-      (inputs
-       (list guile-3.0 avahi))
-      (native-inputs
-       (list autoconf automake libtool pkg-config texinfo guile-3.0))
-      (synopsis "Guile bindings to Avahi")
-      (description
-       "This package provides bindings for Avahi.  It allows programmers to
 use functionalities of the Avahi client library from Guile Scheme programs.
 Avahi itself is an implementation of multicast DNS (mDNS) and DNS Service
 Discovery (DNS-SD).")
-      (home-page "https://www.nongnu.org/guile-avahi/")
+    (home-page "https://www.nongnu.org/guile-avahi/")
-      (license license:lgpl3+))))
+    (license license:lgpl3+)))
 
 (define-public guile-dns
   (package
@@ -5493,44 +5528,37 @@ This module implements this interface by use of Guile's dynamic FFI.")
 (define-public guile-goblins
   (package
     (name "guile-goblins")
-    (version "0.8")
+    (version "0.10")
     (source
      (origin
-       (method git-fetch)
+       (method url-fetch)
-       (uri (git-reference
+       (uri (string-append "https://spritely.institute/files/releases"
-             (url "https://gitlab.com/spritely/guile-goblins/")
+                           "/guile-goblins/guile-goblins-"
-             (commit (string-append "v" version))))
+                           version ".tar.gz"))
-       (file-name (string-append name "-" version))
        (sha256
         (base32
-         "1mmyykh79jwhrfgnhhw94aw7a8m6qw249kj7k60ynj16mcfm5iyy"))))
+         "13nzmwi4m0j27rmn2ks0p3k620npnhx736q25n8llj2ivkn2vxd2"))))
     (build-system gnu-build-system)
     (arguments
      (list #:make-flags
            #~(list "GUILE_AUTO_COMPILE=0")))
     (native-inputs
-     (list autoconf automake pkg-config texinfo))
+     (list pkg-config texinfo))
     (inputs (list guile-3.0))
     (propagated-inputs
      (list guile-fibers guile-gcrypt))
     (home-page "https://spritely.institute/goblins")
     (synopsis "Distributed programming environment for Guile")
-    ;; In guile-goblins 0.9, OCapN support will be added (it already
-    ;; exists in racket-goblins).  At that point we should add the
-    ;; following to this description:
-    ;;
-    ;;   Goblins allows for cooperation between networked programs
-    ;;   in a mutually suspicious network through OCapN, the Object
-    ;;   Capability Network.  This includes collaboration across
-    ;;   runtimes; for instance, programs written in the Guile and Racket
-    ;;   versions of Goblins are able to speak to each other.
     (description
      "@code{guile-goblins} is the Guile version of
-@url{https://spritely.institute/goblins, Spritely Goblins},
+@url{https://spritely.institute/goblins, Spritely Goblins}, a transactional,
-a transactional, distributed programming environment following object
+distributed programming environment following object capability security
-capability security designs.  Goblins is a general toolkit, and also
+designs.  Goblins is a general toolkit, and also the core layer of Spritely's
-the core layer of Spritely's work to support healthy distributed
+work to support healthy distributed networked communities.  Goblins allows for
-networked communities.")
+cooperation between networked programs in a mutually suspicious network
+through OCapN, the Object Capability Network.  This includes collaboration
+across runtimes; for instance, programs written in the Guile and Racket
+versions of Goblins are able to speak to each other.")
     (license license:asl2.0)))
 
 ;;;

gnu/packages/guile.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012-2022 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2012-2023 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014 Cyril Roelandt <tipecaml@gmail.com>
 ;;; Copyright © 2014, 2016, 2018 David Thompson <davet@gnu.org>
 ;;; Copyright © 2014, 2017, 2018 Mark H Weaver <mhw@netris.org>
@@ -391,19 +391,17 @@ without requiring the source code to be rewritten.")
 (define-public guile-3.0-latest
   (package
     (inherit guile-3.0)
-    (version "3.0.8")
+    (version "3.0.9")
     (source (origin
               (inherit (package-source guile-3.0))
               (uri (string-append "mirror://gnu/guile/guile-"
                                   version ".tar.xz"))
               (sha256
                (base32
-                "04wagg0zr0sib0w9ly5jm91jplgfigzfgmy8fjdlx07jaq50d9ys"))
+                "03bm1mnfc9kkg2ls942a0js7bxrdzmcffgrgg6anwdmjfan2a9hs"))))
-              (patches (search-patches "guile-cross-compilation.patch"
-                                       "guile-continuation-stack-leak.patch"))))
     (arguments
      (substitute-keyword-arguments (package-arguments guile-3.0)
-       ;; Guile 3.0.8 is bit-reproducible when built in parallel, thanks to
+       ;; Guile 3.0.9 is bit-reproducible when built in parallel, thanks to
        ;; its multi-stage build process for cross-module inlining, except when
        ;; cross-compiling.
        ((#:parallel-build? _ #f)
@@ -421,7 +419,11 @@ without requiring the source code to be rewritten.")
                         "GUILE_OPTIMIZATIONS = -O1 -Oresolve-primitives -Ocps\n")))))
                '())))))))
 
-(define-public guile-3.0/fixed
+;;; The symbol guile-3.0/fixed should be used when guile-3.0 needs fixes
+;;; (security or else) and this deprecation could be removed.
+(define-deprecated/public-alias guile-3.0/fixed guile-3.0/pinned)
+
+(define-public guile-3.0/pinned
   ;; A package of Guile that's rarely changed.  It is the one used in the
   ;; `base' module, and thus changing it entails a full rebuild.
   (package
@@ -453,6 +455,16 @@ without requiring the source code to be rewritten.")
        (substitute-keyword-arguments (package-arguments guile-3.0)
          ((#:phases phases '%standard-phases)
           `(modify-phases ,phases
+             (add-before 'bootstrap 'set-version
+               (lambda _
+                 ;; Tell 'git-version-gen' what version this is, or it will
+                 ;; just pick "UNKNOWN", making it unusable as a replacement
+                 ;; for 'guile-3.0'.  XXX: This is inaccurate when using
+                 ;; '--with-branch' but using (package-version this-package)
+                 ;; wouldn't give us a valid version string.
+                 (call-with-output-file ".tarball-version"
+                   (lambda (port)
+                     (display ,version port)))))
              (add-before 'check 'skip-failing-tests
                (lambda _
                  (substitute* "test-suite/standalone/test-out-of-memory"
@@ -467,7 +479,8 @@ without requiring the source code to be rewritten.")
                   flex
                   gnu-gettext
                   texinfo
-                  gperf)))
+                  gperf)
+         (replace "self" this-package)))
       (synopsis "Development version of GNU Guile"))))
 
 (define* (make-guile-readline guile #:optional (name "guile-readline"))

gnu/packages/hardware.scm

@@ -325,7 +325,7 @@ operability and find drivers.")
 (define-public hwinfo
   (package
     (name "hwinfo")
-    (version "21.82")
+    (version "22.2")
     (home-page "https://github.com/openSUSE/hwinfo")
     (source
      (origin
@@ -336,7 +336,7 @@ operability and find drivers.")
          (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1ih6vrgh64408cijywy9by2snynkw91p3h0ry5pzk3lyqsl0wnlh"))
+        (base32 "1lfzcyiipxwi8rh0aw5sy7n8x986b9f9pa9g048rxn6k7anfpxk7"))
        (modules
         '((guix build utils)))
        (snippet
@@ -824,7 +824,7 @@ specific SMBIOS tables.")
 (define-public memtest86+
   (package
     (name "memtest86+")
-    (version "6.00")
+    (version "6.01")
     (source
      (origin
        (method git-fetch)
@@ -833,7 +833,7 @@ specific SMBIOS tables.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0fv605blaf4z0jyl1wp37x5x014dkp0z0a0fh114ws62fhnhdnlv"))
+        (base32 "1axf8y3nppyskcysypqpkjl0sxz39f1x0v4syplx35qj3y2kq1h4"))
        (patches
         (search-patches "memtest86+-build-reproducibly.patch"))))
     (build-system gnu-build-system)
@@ -897,15 +897,22 @@ can scan as much of your RAM as possible for hardware defects.")
 (define-public memtester
   (package
     (name "memtester")
-    (version "4.5.1")
+    (version "4.6.0")
     (source
      (origin
        (method url-fetch)
        ;; Even the latest release is available under 'old-versions/'.
-       (uri (string-append "http://pyropus.ca/software/memtester/old-versions/"
+       (uri (list
-                           "memtester-" version ".tar.gz"))
+             (string-append "https://pyropus.ca/software/memtester/old-versions/"
+                            "memtester-" version ".tar.gz")
+             ;; XXX ‘pyropus.ca’ redirects to ‘pyropus.ca.’.  Valid, but wreaks
+             ;; havoc with Guile's Web stack & TLS verification.
+             ;; Remove this random mirror when that changes.
+             (string-append "https://ftp.dimensiondata.com/mirrors/"
+                            "ftp.gentoo.org/distfiles/3e/"
+                            "memtester-" version ".tar.gz")))
        (sha256
-        (base32 "0issrasdihav8jgsqb49cfyj0v564z8k9lyg2jrq9h3n4lwc4pqw"))))
+        (base32 "0bmv7n7gj02pda8mwif08xk63xc20r65q1pr099fz30cx2vlxzn9"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags

gnu/packages/haskell-apps.scm

@@ -50,6 +50,7 @@
   #:use-module (gnu packages haskell-crypto)
   #:use-module (gnu packages haskell-web)
   #:use-module (gnu packages haskell-xyz)
+  #:use-module (gnu packages lsof)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
@@ -335,7 +336,11 @@ to @code{cabal repl}).")
              ;; webapp' runs without making the user also install xdg-utils.
              (substitute* '("Assistant/WebApp/DashBoard.hs"
                             "Utility/WebApp.hs")
-               (("xdg-open") (which "xdg-open")))))
+               (("xdg-open") (which "xdg-open")))
+             ;; Also replace loose references to lsof.
+             (substitute* "Assistant/Threads/Watcher.hs"
+               (("\"lsof\"")
+                (string-append "\"" (which "lsof") "\"")))))
          (add-before 'configure 'factor-setup
            (lambda _
              ;; Factor out necessary build logic from the provided
@@ -480,6 +485,7 @@ to @code{cabal repl}).")
            ghc-yesod-core
            ghc-yesod-form
            ghc-yesod-static
+           lsof
            rsync
            xdg-utils))
     (propagated-inputs
@@ -836,7 +842,7 @@ too slow and you'll get wound up in the scroll and crushed.")
 (define-public shellcheck
   (package
     (name "shellcheck")
-    (version "0.8.0")
+    (version "0.9.0")
     (source
      (origin
        (method url-fetch)
@@ -844,7 +850,7 @@ too slow and you'll get wound up in the scroll and crushed.")
              "https://hackage.haskell.org/package/ShellCheck/ShellCheck-"
              version ".tar.gz"))
        (sha256
-        (base32 "05jlapp4m997w36h2wszdxz9gvczdczaylypsbn14jqpb650w232"))
+        (base32 "071k2gc8rzpg9lwq9g10c9xx0zm1wcgsf8v4n1csj9fm56vy7gmb"))
        (file-name (string-append name "-" version ".tar.gz"))))
     (build-system haskell-build-system)
     (arguments
@@ -862,7 +868,7 @@ too slow and you'll get wound up in the scroll and crushed.")
     (native-inputs
      (list pandoc))
     (inputs
-     (list ghc-aeson ghc-diff ghc-quickcheck ghc-regex-tdfa))
+     (list ghc-aeson ghc-diff ghc-fgl ghc-quickcheck ghc-regex-tdfa))
     (home-page "https://www.shellcheck.net/")
     (synopsis "Static analysis for shell scripts")
     (description "@code{shellcheck} provides static analysis for

gnu/packages/haskell-xyz.scm

@@ -9215,6 +9215,30 @@ building up, manipulating and serialising @code{Pandoc} structures.")
      "This package provides a library for parallel programming.")
     (license license:bsd-3)))
 
+(define-public ghc-parsec
+  (package
+    (name "ghc-parsec")
+    (version "3.1.14.0")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "parsec" version))
+              (sha256
+               (base32
+                "132waj2cpn892midbhpkfmb74qq83v0zv29v885frlp1gvh94b67"))))
+    (build-system haskell-build-system)
+    (native-inputs (list ghc-hunit ghc-test-framework ghc-test-framework-hunit))
+    (arguments
+     `(#:cabal-revision
+       ("4" "0p65q054iaz2117a5qk1428dic4sb41acclys9k00zna24ks7iq3")))
+    (home-page "https://github.com/haskell/parsec")
+    (synopsis "Monadic parser combinators")
+    (description "Parsec is designed from scratch as an industrial-strength
+parser library.  It is simple, safe, well documented (on the package
+homepage), has extensive libraries, good error messages, and is fast.  It is
+defined as a monad transformer that can be stacked on arbitrary monads, and it
+is also parametric in the input stream type.")
+    (license license:bsd-3)))
+
 (define-public ghc-parsec-numbers
   (package
     (name "ghc-parsec-numbers")

gnu/packages/haskell.scm

@@ -1143,7 +1143,7 @@ interactive environment for the functional language Haskell.")
            (sha256
             (base32
              "0c55pj2820q26rikhpf636sn4mjgqsxjrl94vsywrh79dxp3k14z"))))
-       ("git" ,git-minimal/fixed)                 ; invoked during tests
+       ("git" ,git-minimal/pinned)                 ; invoked during tests
        ,@(filter (match-lambda
                    (("ghc-bootstrap" . _) #f)
                    (("ghc-testsuite" . _) #f)
@@ -1195,7 +1195,7 @@ interactive environment for the functional language Haskell.")
            (sha256
             (base32
              "1zl25gg6bpx5601k8h3cqnns1xfc0nqgwnh8jvn2s65ra3f2g1nz"))))
-       ("git" ,git-minimal/fixed)                 ; invoked during tests
+       ("git" ,git-minimal/pinned)                 ; invoked during tests
        ,@(filter (match-lambda
                    (("ghc-bootstrap" . _) #f)
                    (("ghc-testsuite" . _) #f)

gnu/packages/image-viewers.scm

@@ -750,7 +750,7 @@ displayed in a terminal.")
 (define-public imv
   (package
     (name "imv")
-    (version "4.3.1")
+    (version "4.4.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -758,21 +758,21 @@ displayed in a terminal.")
                     (commit (string-append "v" version))))
               (sha256
                (base32
-                "01x6qg7nhikqh68gnzrdvq0rxma5v9z19il89y8bvdrcr7r1vh40"))
+                "1zlds43z17jrnsrfz3rf3sb3pa5gkmxaibq87509ikc7p1p09c9c"))
               (file-name (git-file-name name version))))
     (build-system meson-build-system)
     (arguments
-     `(#:phases
+     (list #:phases
-       (modify-phases %standard-phases
+           #~(modify-phases %standard-phases
-         (add-after 'install 'record-absolute-file-names
+               (add-after 'install 'record-absolute-file-names
-           (lambda* (#:key outputs #:allow-other-keys)
+                 (lambda _
-             ;; 'imv' is a script that execs 'imv-x11' or 'imv-wayland'.
+                   ;; 'imv' is a script that execs 'imv-x11' or 'imv-wayland'.
-             ;; Record their absolute file name.
+                   ;; 'imv-dir' execs 'imv'. Record their absolute file names.
-             (let* ((out (assoc-ref outputs "out"))
+                   (let ((bin (string-append #$output "/bin")))
-                    (bin (string-append out "/bin")))
+                     (substitute* (string-append bin "/imv")
-               (substitute* (string-append bin "/imv")
+                       (("imv-") (string-append bin "/imv-")))
-                 (("imv-")
+                     (substitute* (string-append bin "/imv-dir")
-                  (string-append bin "/imv-")))))))))
+                       (("imv") (string-append bin "/imv")))))))))
     (native-inputs
      (list asciidoc
            pkg-config))

gnu/packages/image.scm

@@ -178,12 +178,11 @@ library.  It supports almost all PNG features and is extensible.")
    (license license:zlib)
    (home-page "http://www.libpng.org/pub/png/libpng.html")))
 
-;; libpng-apng should be updated when the APNG patch is released:
-;; <https://bugs.gnu.org/27556>
 (define-public libpng-apng
+  ;; The APNG patch is maintained separately and may lag behind upstream libpng.
   (package
     (name "libpng-apng")
-    (version "1.6.37")
+    (version "1.6.39")
     (source
      (origin
        (method url-fetch)
@@ -196,8 +195,7 @@ library.  It supports almost all PNG features and is extensible.")
                    "ftp://ftp.simplesystems.org/pub/libpng/png/src/history"
                    "/libpng16/libpng-" version ".tar.xz")))
        (sha256
-        (base32
+        (base32 "0dv90dxvmqpk7mbywyjbz8lh08cv4b0ksqp1y62mzvmlf379cihz"))))
-         "1jl8in381z0128vgxnvn33nln6hzckl7l7j9nqvkaf1m9n1p0pjh"))))
     (build-system gnu-build-system)
     (arguments
      `(#:modules ((guix build gnu-build-system)
@@ -215,14 +213,12 @@ library.  It supports almost all PNG features and is extensible.")
                        apng.gz)
                (invoke "sh" "-c"
                        (string-append "gunzip < " apng.gz " > the-patch"))
-               (apply-patch "the-patch")
+               (apply-patch "the-patch"))))
-               #t)))
          (add-before 'configure 'no-checks
            (lambda _
              (substitute* "Makefile.in"
                (("^scripts/symbols.chk") "")
-               (("check: scripts/symbols.chk") ""))
+               (("check: scripts/symbols.chk") "")))))))
-             #t)))))
     (inputs
      `(("apng" ,(origin
                   (method url-fetch)
@@ -231,7 +227,7 @@ library.  It supports almost all PNG features and is extensible.")
                                   version "/libpng-" version "-apng.patch.gz"))
                   (sha256
                    (base32
-                    "1dh0250mw9b2hx7cdmnb2blk7ddl49n6vx8zz7jdmiwxy38v4fw2"))))))
+                    "1z8cx011a2c7vagwgi92rbmky1wi8awmrdldqh9f5k80pbmbdi2a"))))))
     (native-inputs
      (list libtool))
     ;; libpng.la says "-lz", so propagate it.
@@ -2407,7 +2403,7 @@ Wacom-style graphics tablets.")
 (define-public phockup
   (package
     (name "phockup")
-    (version "1.9.0")
+    (version "1.9.2")
     (source
      (origin
        (method git-fetch)
@@ -2416,8 +2412,7 @@ Wacom-style graphics tablets.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32
+        (base32 "0j4mnsy12bhsmd80vgqknv004xbqd165y8gpalw87gp8i8xv172r"))))
-         "1xs2h3nj19wsfffl87akinx14drk5nn2svjwyj0csv10apk0q4pp"))))
     (build-system copy-build-system)
     (arguments
      `(#:install-plan '(("src" "share/phockup/")
@@ -2426,12 +2421,18 @@ Wacom-style graphics tablets.")
        (modify-phases %standard-phases
          (add-after 'unpack 'configure
            (lambda* (#:key inputs #:allow-other-keys)
-             (substitute* (list "src/dependency.py" "src/exif.py")
+             (substitute* (list "src/dependency.py"
-               (("'exiftool'")
+                                "src/exif.py")
-                (string-append "'" (search-input-file inputs "/bin/exiftool") "'")))))
+               (("'exiftool")
+                (string-append "'" (search-input-file inputs "bin/exiftool"))))))
          (add-before 'install 'check
            (lambda _
-             (invoke "pytest")))
+             ;; Test without PATH to make sure ‘exiftool’ is properly found.
+             (let ((path (getenv "PATH"))
+                   (pytest (which "pytest")))
+               (setenv "PATH" "")
+               (invoke pytest)
+               (setenv "PATH" path))))
          (add-after 'install 'install-bin
            (lambda* (#:key outputs #:allow-other-keys)
              (let ((out (assoc-ref outputs "out")))

gnu/packages/inkscape.scm

@@ -46,6 +46,7 @@
   #:use-module (gnu packages pdf)
   #:use-module (gnu packages popt)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages ghostscript)
@@ -273,5 +274,6 @@ as the native format.")
     (inputs (modify-inputs (package-inputs inkscape/stable)
               (replace "lib2geom" lib2geom-1.2)
               (append bash-minimal
-                      librsvg)))        ;for the pixbuf loader
+                      librsvg           ;for the pixbuf loader
+                      python-cssselect)))        ;to render qrcode
     (properties (alist-delete 'hidden? (package-properties inkscape/stable)))))

gnu/packages/irc.scm

@@ -195,14 +195,14 @@ Conferencing} and @acronym{ICB, Internet Citizen's Band}.")
 (define-public weechat
   (package
     (name "weechat")
-    (version "3.6")
+    (version "3.8")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://weechat.org/files/src/weechat-"
                                   version ".tar.xz"))
               (sha256
                (base32
-                "1ppj676gwh67krq92xnfkmh3qnwbz8d51djsscxw013x7cdxg1cx"))))
+                "0a5zfkqqdkya111rl2gpwlbfala0305qry9cdz2r1h7q0316bjzp"))))
     (build-system cmake-build-system)
     (outputs '("out" "doc"))
     (native-inputs
@@ -210,9 +210,7 @@ Conferencing} and @acronym{ICB, Internet Citizen's Band}.")
        ("pkg-config" ,pkg-config)
        ,@(if (target-x86?)
            `(("ruby-asciidoctor" ,ruby-asciidoctor))
-           '())
+           '())))
-       ;; For tests.
-       ("cpputest" ,cpputest)))
     (inputs
      (list aspell
            curl
@@ -234,8 +232,7 @@ Conferencing} and @acronym{ICB, Internet Citizen's Band}.")
              ,@(if (target-x86?)
                  '("-DENABLE_MAN=ON"
                    "-DENABLE_DOC=ON")
-                '())
+                '()))
-             "-DENABLE_TESTS=ON")       ; ‘make test’ fails otherwise
        #:phases
        (modify-phases %standard-phases
          ,@(if (target-x86?)
@@ -346,14 +343,14 @@ for the IRCv3 protocol.")
 (define-public catgirl
   (package
     (name "catgirl")
-    (version "1.9a")
+    (version "2.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://git.causal.agency/catgirl/snapshot/"
                                   name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0pci8crcgm33zb58y7ky2aydzyqsirj8ri8ik1zdlz6npadbjj9h"))))
+                "13pfphcfkdzqfb4x7w21xp6rnmg3ix9f39mpqmxxzg15ys1gp2x6"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; no tests
@@ -438,7 +435,7 @@ highlighted.
 (define-public kirc
   (package
     (name "kirc")
-    (version "0.2.9")
+    (version "0.3.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -446,7 +443,7 @@ highlighted.
                      (commit version)))
               (file-name (git-file-name name version))
               (sha256
-               (base32 "0ahmfxhgcvnlgmxxbv9vga5x6krab1n7qq55ygj7hj3x7s7ra419"))))
+               (base32 "1ighpinss3k6xyqk05wrs76wvp2ahhh0jkkg8h7bhg66b14fsws9"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; no tests
@@ -590,14 +587,14 @@ interface for those who are accustomed to the ircII way of doing things.")
 (define-public litterbox
   (package
     (name "litterbox")
-    (version "1.8")
+    (version "1.9")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://git.causal.agency/litterbox/snapshot/litterbox-"
                            version ".tar.gz"))
        (sha256
-        (base32 "0ll5d18slngdg2qhaxkvrcq2p1admh0h7sr06wx8347ka0vvrgjl"))))
+        (base32 "1ag5x7h71pxjaaf4b561rwdqr05zzywkc0p3jf2yhg3lbjkjrc7z"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; There are no tests.

gnu/packages/jami.scm

@@ -2,7 +2,7 @@
 ;;; Copyright © 2019 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
 ;;; Copyright © 2019, 2020 Jan Wielkiewicz <tona_kosmicznego_smiecia@interia.pl>
-;;; Copyright © 2020, 2021, 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2020, 2021, 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -69,31 +69,24 @@
   #:use-module (guix packages)
   #:use-module (guix utils))
 
-(define %jami-version "20221220.0956.79e1207")
+(define %jami-version "20230206.0")
 
 (define %jami-sources
   ;; Return an origin object of the tarball release sources archive of the
   ;; Jami project.
   (origin
     (method url-fetch)
-    (uri (string-append "https://dl.jami.net/release/tarballs/jami_"
+    (uri (string-append "https://dl.jami.net/release/tarballs/jami-"
-                        %jami-version
+                        %jami-version ".tar.gz"))
-                        ".tar.gz"))
     (modules '((guix build utils)))
     (snippet
-     `(begin
+     ;; Delete multiple MiBs of bundled tarballs.  The daemon/contrib
-        ;; Delete multiple MiBs of bundled tarballs.  The contrib directory
+     ;; directory contains the custom patches for pjproject and other
-        ;; contains the custom patches for pjproject and other libraries used
+     ;; libraries used by Jami.
-        ;; by Jami.
+     '(delete-file-recursively "daemon/contrib/tarballs"))
-        (delete-file-recursively "daemon/contrib/tarballs")
-        ;; Remove the git submodule directories of unused Jami clients.
-        (for-each delete-file-recursively '("client-android"
-                                            "client-ios"
-                                            "client-macosx"
-                                            "plugins"))))
     (sha256
      (base32
-      "0g5709rmb9944s0ij9g4pm1b871f5z0s5nawvm10z14wx3y1np8m"))
+      "1fx7c6q8j0x3q8cgzzd4kpsw3npqggsi1n493cv1jg7v5d01d3jz"))
     (patches (search-patches "jami-disable-integration-tests.patch"
                              "jami-libjami-headers-search.patch"))))
 
@@ -107,14 +100,12 @@
         (invoke "tar" "-xvf" #$%jami-sources
                 "-C" patches-directory
                 "--strip-components=5"
-                (string-append "jami-project/daemon/contrib/src/"
+                "--wildcards"
-                               dep-name))
+                (string-append "jami-*/daemon/contrib/src/" dep-name))
-        (for-each
+        (for-each (lambda (f)
-         (lambda (file)
+                    (invoke "patch" "--force" "--ignore-whitespace" "-p1" "-i"
-           (invoke "patch" "--force" "--ignore-whitespace" "-p1" "-i"
+                            (string-append patches-directory "/" f ".patch")))
-                   (string-append patches-directory "/"
+                  patches))))
-                                  file ".patch")))
-         patches))))
 
 (define-public pjproject-jami
   (let ((commit "513a3f14c44b2c2652f9219ec20dea64b236b713")
@@ -153,10 +144,12 @@
                    '("0009-add-config-site")))))))))))
 
 ;; The following variables are configure flags used by ffmpeg-jami.  They're
-;; from the jami-project/daemon/contrib/src/ffmpeg/rules.mak file.  We try to
+;; from the jami/daemon/contrib/src/ffmpeg/rules.mak file.  We try to keep it
-;; keep it as close to the official Jami package as possible, to provide all
+;; as close to the official Jami package as possible, to provide all the
-;; the codecs and extra features that are expected (see:
+;; codecs and extra features that are expected (see:
-;; https://review.jami.net/plugins/gitiles/ring-daemon/+/refs/heads/master/contrib/src/ffmpeg/rules.mak)
+;; https://review.jami.net/plugins/gitiles/jami-daemon/+/refs/heads/master/contrib/src/ffmpeg/rules.mak).
+;; An exception are the ffnvcodec-related switches, which is not packaged in
+;; Guix and would not work with Mesa.
 (define %ffmpeg-default-configure-flags
   '("--disable-everything"
     "--enable-zlib"
@@ -348,34 +341,12 @@
     "--enable-encoder=mjpeg_vaapi"
     "--enable-encoder=hevc_vaapi"))
 
-;; ffnvcodec is not supported on ARM; enable it only for the i386 and x86_64
-;; architectures.
-(define %ffmpeg-linux-x86-configure-flags
-  '("--arch=x86"
-    "--enable-cuvid"
-    "--enable-ffnvcodec"
-    "--enable-nvdec"
-    "--enable-nvenc"
-    "--enable-hwaccel=h264_nvdec"
-    "--enable-hwaccel=hevc_nvdec"
-    "--enable-hwaccel=vp8_nvdec"
-    "--enable-hwaccel=mjpeg_nvdec"
-    "--enable-encoder=h264_nvenc"
-    "--enable-encoder=hevc_nvenc"))
-
-;; This procedure composes the configure flags list for ffmpeg-jami.
 (define (ffmpeg-compose-configure-flags)
-  (define (system=? s)
+  "Compose the configure flag lists of ffmpeg-jami."
-    (string-prefix? s (%current-system)))
+  #~(append '#$%ffmpeg-default-configure-flags
-
+            (if (string-contains #$(%current-system) "linux")
-  `(,@%ffmpeg-default-configure-flags
+                '#$%ffmpeg-linux-configure-flags
-    ,@(if (string-contains (%current-system) "linux")
+                '())))
-          (if (or (system=? "i686")
-                  (system=? "x86_64"))
-              (append %ffmpeg-linux-configure-flags
-                      %ffmpeg-linux-x86-configure-flags)
-              %ffmpeg-linux-configure-flags)
-          '())))
 
 (define-public ffmpeg-jami
   (package
@@ -391,10 +362,14 @@
               (sha256
                (base32
                 "0yq0jcdc4qm5znrzylj3dsicrkk2n3n8bv28vr0a506fb7iglbpg"))))
+    (outputs '("out" "debug"))
     (arguments
      (substitute-keyword-arguments (package-arguments ffmpeg-5)
-       ((#:configure-flags '())
+       ((#:configure-flags _ '())
-        (ffmpeg-compose-configure-flags))
+        #~(cons* "--disable-static"
+                 "--enable-shared"
+                 "--disable-stripping"
+                 #$(ffmpeg-compose-configure-flags)))
        ((#:phases phases)
         #~(modify-phases #$phases
             (add-after 'unpack 'apply-patches
@@ -424,7 +399,7 @@
     (name "libjami")
     (version %jami-version)
     (source %jami-sources)
-    (outputs '("out" "debug"))
+    (outputs '("out" "bin" "debug"))    ;"bin' contains jamid
     (build-system gnu-build-system)
     (arguments
      (list
@@ -447,7 +422,20 @@
             (lambda _
               (for-each delete-file
                         (find-files (string-append #$output "/lib")
-                                    "\\.a$")))))))
+                                    "\\.a$"))))
+          (add-after 'install 'move-jamid
+            ;; This nearly halves the size of the main output (from 1566.2 MiB
+            ;; to 833.6 MiB), due to not depending on dbus-c++ and its large
+            ;; dependencies.
+            (lambda* (#:key outputs #:allow-other-keys)
+              (let ((libexec (string-append #$output:bin "/libexec"))
+                    (share (string-append #$output:bin "/share")))
+                (mkdir-p libexec)
+                (rename-file (search-input-file outputs "libexec/jamid")
+                             (string-append libexec "/jamid"))
+                (mkdir-p share)
+                (rename-file (search-input-directory outputs "share/dbus-1")
+                             (string-append share "/dbus-1"))))))))
     (inputs
      (list alsa-lib
            asio
@@ -483,7 +471,9 @@
 Jami core functionality.  Jami is a secure and distributed voice, video and
 chat communication platform that requires no centralized server and leaves the
 power of privacy in the hands of the user.  It supports the SIP and IAX
-protocols, as well as decentralized calling using P2P-DHT.")
+protocols, as well as decentralized calling using P2P-DHT.  The @samp{\"bin\"}
+output contains the D-Bus daemon (@command{jamid}) as well as the Jami D-Bus
+service definitions.")
     (home-page "https://jami.net/")
     (license license:gpl3+)))
 
@@ -550,9 +540,6 @@ protocols, as well as decentralized calling using P2P-DHT.")
            pkg-config
            python
            qttools
-           doxygen
-           graphviz
-           gsettings-desktop-schemas    ;for tests
            vulkan-headers))
     (inputs
      (list ffmpeg-jami

gnu/packages/java.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2023 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016, 2017 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2017, 2019, 2021 Carlo Zancanaro <carlo@zancanaro.id.au>
@@ -1493,8 +1493,25 @@ blacklisted.certs.pem"
   (make-openjdk openjdk17 "18.0.2"
                 "1yimfdkwpinhg5cf1mcrzk9xvjwnray3cx762kypb9jcwbranjwx"))
 
+(define-public openjdk19
+  (make-openjdk openjdk18 "19.0.1"
+                "0kyalb391znw6idmfn3dsx6c2mal1hl63f0bwa4mlnsxfl380bi1"
+   (arguments
+    (substitute-keyword-arguments (package-arguments openjdk18)
+      ((#:phases phases)
+       #~(modify-phases #$phases
+           (replace 'fix-java-shebangs
+             (lambda _
+               ;; Update file path.
+               (substitute* "src/java.base/share/data/blockedcertsconverter/blocked.certs.pem"
+                 (("^#!.*") "#! java BlockedCertsConverter SHA-256\n"))))
+           (add-before 'configure 'define-java-environment-variables
+             (lambda* (#:key inputs #:allow-other-keys)
+               ;; Fix for "valid range 1980-01-01T00:00:02Z to 2099-12-31T23:59:59Z".
+               (setenv "SOURCE_DATE_EPOCH" "1234567890")))))))))
+
 ;;; Convenience alias to point to the latest version of OpenJDK.
-(define-public openjdk openjdk18)
+(define-public openjdk openjdk19)
 
 
 (define-public ant/java8
@@ -12914,18 +12931,17 @@ static code analysis or code manipulation.")))
     (name "java-logback-core")
     (version "1.2.3")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (string-append "https://github.com/qos-ch/logback/archive/v_"
+              (uri (git-reference
-                                  version ".tar.gz"))
+                    (url "https://github.com/qos-ch/logback/")
-              (file-name (string-append name "-" version ".tar.gz"))
+                    (commit (string-append "v_" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1x6ga74yfgm94cfx98gybakbrlilx8i2gn6dx13l40kasmys06mi"))
+                "055jbfpg3l5qw7pw2snkdag0gjkb4vcxfg9110cqqyc40k2nd17z"))
               (modules '((guix build utils)))
               (snippet
-               '(begin
+               '(delete-file-recursively "logback-access/lib"))))
-                  (delete-file-recursively "logback-access/lib")
-                  #t))))
     (build-system ant-build-system)
     (arguments
      `(#:jar-name "logback.jar"
@@ -12943,22 +12959,20 @@ static code analysis or code manipulation.")))
        #:phases
        (modify-phases %standard-phases
          (add-before 'configure 'chdir
-           (lambda _
+           (lambda _ (chdir "logback-core"))))))
-             (chdir "logback-core")
-             #t)))))
     (inputs
-     `(("java-javax-mail" ,java-javax-mail)
+     (list java-javax-mail
-       ("servlet" ,java-javaee-servletapi)
+           java-javaee-servletapi
-       ("java-commons-compiler" ,java-commons-compiler)
+           java-commons-compiler
-       ("java-janino" ,java-janino)))
+           java-janino))
     (native-inputs
-     `(("java-junit" ,java-junit)
+     (list java-junit
-       ("java-hamcrest-core" ,java-hamcrest-core)
+           java-hamcrest-core
-       ("java-mockito-1" ,java-mockito-1)
+           java-mockito-1
-       ("java-cglib" ,java-cglib)
+           java-cglib
-       ("java-asm" ,java-asm)
+           java-asm
-       ("java-objenesis" ,java-objenesis)
+           java-objenesis
-       ("java-joda-time" ,java-joda-time)))
+           java-joda-time))
     (home-page "https://logback.qos.ch")
     (synopsis "Logging for java")
     (description "Logback is intended as a successor to the popular log4j project.
@@ -12992,7 +13006,7 @@ This module lays the groundwork for the other two modules.")
                                             (find-files (assoc-ref inputs input)
                                                         ".*.jar"))
                                           '("java-logback-core" "java-slf4j-api"
-                                            "java-commons-compiler" "servlet"
+                                            "java-commons-compiler" "java-javaee-servletapi"
                                             "groovy")))
                        ":"))
              (apply invoke "groovyc" "-d" "build/classes" "-j"

gnu/packages/julia-jll.scm

@@ -3,6 +3,7 @@
 ;;; Copyright © 2021 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2021 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2021 Jean-Baptiste Volatier <jbv@pm.me>
+;;; Copyright © 2023 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -26,6 +27,7 @@
   #:use-module (guix utils)
   #:use-module (guix build-system julia)
   #:use-module (gnu packages)
+  #:use-module (gnu packages astronomy)
   #:use-module (gnu packages audio)
   #:use-module (gnu packages base)
   #:use-module (gnu packages compression)
@@ -146,6 +148,48 @@ compression program.")
     (description "This package provides a wrapper for the cairo library.")
     (license license:expat)))
 
+(define-public julia-cfitsio-jll
+  (package
+    (name "julia-cfitsio-jll")
+    (version "4.0.0+0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaBinaryWrappers/CFITSIO_jll.jl")
+             (commit (string-append "CFITSIO-v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1k0mqmpyfjr3ibcmda08llw8m166zw0n3lh5y5aj81q37lrxw990"))))
+    (build-system julia-build-system)
+    (arguments
+     '(#:tests? #f  ; no runtests
+      #:phases
+      (modify-phases %standard-phases
+          (add-after 'link-depot 'override-binary-path
+            (lambda* (#:key inputs #:allow-other-keys)
+              (map
+               (lambda (wrapper)
+                 (substitute* wrapper
+                   ;; We're not downloading and unpacking cfitsio.
+                   (("using LibCURL_jll") "")
+                   (("using Zlib_jll") "")
+                   (("generate_init_header.*") "generate_init_header()\n" )
+                   (("generate_wrapper_header.*")
+                    (string-append
+                     "generate_wrapper_header(\"CFITSIO\", \""
+                     (assoc-ref inputs "cfitsio") "\")\n"))))
+               ;; There's a Julia file for each platform, override them all
+               (find-files "src/wrappers/" "\\.jl$")))))))
+    (inputs
+     (list cfitsio))
+    (propagated-inputs
+     (list julia-jllwrappers))
+    (home-page "https://github.com/JuliaBinaryWrappers/CFITSIO_jll.jl")
+    (synopsis "CFITSIO library wrappers")
+    (description "This package provides a wrapper for the cfitsio library.")
+    (license license:expat)))
+
 (define-public julia-compilersupportlibraries-jll
   (package
     (name "julia-compilersupportlibraries-jll")

gnu/packages/julia-xyz.scm

@@ -1,9 +1,10 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2020, 2021 Nicolò Balzarotti <nicolo@nixo.xyz>
 ;;; Copyright © 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
-;;; Copyright © 2021, 2022 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2021-2023 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2021 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2021 jgart <jgart@dismail.de>
+;;; Copyright © 2023 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -746,6 +747,36 @@ variables, both with unordered (nominal variables) and ordered categories
     (description "This package provides a C-compatible enum for Julia.")
     (license license:expat)))
 
+(define-public julia-cfitsio
+  (package
+    (name "julia-cfitsio")
+    (version "1.4.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaAstro/CFITSIO.jl")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "05bxzzjcc021p3hi092h06r2q7qnvql0xz1alggi83i0pp1mxp6d"))))
+    (build-system julia-build-system)
+    (native-inputs (list julia-aqua))
+    (propagated-inputs (list julia-cfitsio-jll))
+    (home-page "https://github.com/JuliaAstro/CFITSIO.jl")
+    (synopsis "C-style interface to the libcfitsio library")
+    (description "This package provides Julia implementation of C-style
+interface to CFITSIO functions with following features:
+@itemize
+@item Function names closely mirror the C interface (e.g.,
+@code{fits_open_file()}).
+@item Functions operate on @code{FITSFile}, a thin wrapper for fitsfile C
+struct (@code{FITSFile} has concept of \"current HDU\", as in CFITSIO).
+@item Wrapper functions do check the return status from CFITSIO and throw an
+error with the appropriate message.
+@end itemize")
+    (license license:expat)))
+
 (define-public julia-chainrules
   (package
     (name "julia-chainrules")
@@ -1202,7 +1233,7 @@ as SLAM (simultaneous localization and mapping).")
 (define-public julia-crayons
   (package
     (name "julia-crayons")
-    (version "4.0.4")
+    (version "4.1.1")
     (source
       (origin
         (method git-fetch)
@@ -1211,7 +1242,7 @@ as SLAM (simultaneous localization and mapping).")
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "0v3zhjlnb2914bxcj4myl8pgb7m31p77aj2k1bckmqs96jdph10z"))))
+         (base32 "0vfbb02pclwlbpcl7rhr98a495kga5wydf5wz1gp1xn1wxgpgxpd"))))
     (build-system julia-build-system)
     (home-page "https://github.com/KristofferC/Crayons.jl")
     (synopsis "Colored and styled strings for terminals")
@@ -1614,7 +1645,7 @@ valuable enough at this time.")
     (inputs
      (list python-wrapper))
     (native-inputs
-     (list git-minimal/fixed                  ;needed for the "Utilities" test
+     (list git-minimal/pinned                  ;needed for the "Utilities" test
            julia-documentermarkdown
            julia-documentertools))
     (home-page "https://juliadocs.github.io/Documenter.jl")
@@ -2097,6 +2128,31 @@ types and sparsity.")
 using finite difference.")
     (license license:expat)))
 
+(define-public julia-fitsio
+  (package
+    (name "julia-fitsio")
+    (version "0.17.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaAstro/FITSIO.jl")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "10w7cdb2cvcwpkcfdz2fwl4ji5rfdv8w9msc9gfd8d34k58bk8c5"))))
+    (build-system julia-build-system)
+    (native-inputs
+     (list julia-aqua julia-orderedcollections))
+    (propagated-inputs
+     (list julia-cfitsio julia-reexport julia-tables))
+    (home-page "https://github.com/JuliaAstro/CFITSIO.jl")
+    (synopsis "Astronomical FITS file support for Julia")
+    (description "This package provides Julia implementation for reading and
+writing @acronym{FITS, Flexible Image Transport System} files, based on the
+@code{cfitsio} library.")
+    (license license:expat)))
+
 (define-public julia-fixedpointnumbers
   (let ((commit "59ee94b93f2f1ee75544ef44187fc0e440cd8015")
         (revision "1"))
@@ -3439,7 +3495,7 @@ fixes.  The Julia IDE effort is pointed to extension for VSCode.")
 (define-public julia-latexstrings
   (package
     (name "julia-latexstrings")
-    (version "1.2.1")
+    (version "1.3.0")
     (source
       (origin
         (method git-fetch)
@@ -3448,7 +3504,7 @@ fixes.  The Julia IDE effort is pointed to extension for VSCode.")
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "117z27krcf8fydgp6mb0pgn75r4gng9qs7v90qb4bqzsry3faadp"))))
+         (base32 "0iijp96ca9mqg5skr6ps7q0lvqaa374lr2zkbbia5q6qgpq0j5ww"))))
     (build-system julia-build-system)
     (native-inputs
      (list julia-documenter))
@@ -3716,7 +3772,7 @@ TLS} and cryptography C library for Julia.")
 (define-public julia-measurements
   (package
     (name "julia-measurements")
-    (version "2.6.0")
+    (version "2.8.0")
     (source
       (origin
         (method git-fetch)
@@ -3725,14 +3781,15 @@ TLS} and cryptography C library for Julia.")
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "05p3f0gr4sv4maq8cix5fi8ldq0zagswqsd43xn6fhy046f936mz"))))
+         (base32 "1rn7qaf2s3l7awm8q5fjxlp1503g9mjgmsnvrbhjjvwyyn1k705r"))))
     (build-system julia-build-system)
     (propagated-inputs
      (list julia-calculus
            julia-recipesbase
            julia-requires))
     (native-inputs
-     (list julia-quadgk
+     (list julia-aqua
+           julia-quadgk
            julia-specialfunctions
            julia-unitful))
     (home-page "https://juliaphysics.github.io/Measurements.jl/stable/")
@@ -4077,7 +4134,7 @@ doesn't provide any other \"high-level\" functionality like layers or AD.")
 (define-public julia-optim
   (package
     (name "julia-optim")
-    (version "1.6.0")
+    (version "1.7.4")
     (source
       (origin
         (method git-fetch)
@@ -4086,7 +4143,7 @@ doesn't provide any other \"high-level\" functionality like layers or AD.")
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "0nvl3xp9c6r80y9n7fic4zyq2443apfmbcpnx0wvgkv4vsy08x5j"))))
+         (base32 "0pdwa2xm08c3g979qgsmcr343j4kkh4l6x5rdj1blhqh5gw8172b"))))
     (build-system julia-build-system)
     (arguments
      (list
@@ -4094,9 +4151,14 @@ doesn't provide any other \"high-level\" functionality like layers or AD.")
        #~(modify-phases %standard-phases
            (add-after 'unpack 'adjust-tests
              (lambda _
-               ;; TODO: Figure out why this test fails.
                (substitute* "test/runtests.jl"
-                 ((".*l_bfgs.*") "")))))))
+                 ;; Distributions.jl isn't packaged yet.
+                 ((".*newton_trust_region.*") ""))
+               (substitute*
+                 "test/multivariate/solvers/constrained/ipnewton/constraints.jl"
+                 ;; TODO: Figure out why this test fails.
+                 (("@test Optim\\.converged") "@test_skip Optim.converged")
+                 (("@test Optim\\.minimum") "@test_skip Optim.minimum")))))))
     (propagated-inputs
      (list julia-compat
            julia-fillarrays
@@ -4591,7 +4653,7 @@ Julia with little or no overhead (arrays are passed without making a copy).")
 (define-public julia-quadgk
   (package
     (name "julia-quadgk")
-    (version "2.4.1")
+    (version "2.5.0")
     (source
       (origin
         (method git-fetch)
@@ -4600,7 +4662,7 @@ Julia with little or no overhead (arrays are passed without making a copy).")
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "1hy0629yai6xflgxaflk9764lzr1lzhlghimxk1aqi212q9c6n33"))))
+         (base32 "0f14dhn0f7ln2j96qvmnsyy9ffzqsngd16ikc136snlxv4k4whiv"))))
     (build-system julia-build-system)
     (propagated-inputs
      (list julia-datastructures))

gnu/packages/kde.scm

@@ -1323,6 +1323,7 @@ creating routes by drag and drop and more.")
            qca
            qtdeclarative-5
            qtsvg-5
+           qtwayland-5
            threadweaver
            kcrash
            kjs))

gnu/packages/key-mon.scm

@@ -1,28 +0,0 @@
-;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015 Ludovic Courtès <ludo@gnu.org>
-;;;
-;;; This file is part of GNU Guix.
-;;;
-;;; GNU Guix is free software; you can redistribute it and/or modify it
-;;; under the terms of the GNU General Public License as published by
-;;; the Free Software Foundation; either version 3 of the License, or (at
-;;; your option) any later version.
-;;;
-;;; GNU Guix is distributed in the hope that it will be useful, but
-;;; WITHOUT ANY WARRANTY; without even the implied warranty of
-;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-;;; GNU General Public License for more details.
-;;;
-;;; You should have received a copy of the GNU General Public License
-;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
-
-(define-module (gnu packages key-mon)
-  #:use-module (guix licenses)
-  #:use-module (guix packages)
-  #:use-module (guix download)
-  #:use-module (gnu packages)
-  #:use-module (gnu packages python)
-  #:use-module (gnu packages python-xyz)
-  #:use-module (gnu packages gtk)
-  #:use-module (gnu packages gnome)
-  #:use-module (guix build-system python))

gnu/packages/less.scm

@@ -63,7 +63,7 @@ text editors.")
 (define-public lesspipe
   (package
     (name "lesspipe")
-    (version "2.06")
+    (version "2.07")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -72,7 +72,7 @@ text editors.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0f67f45dznhnw99r4zxrzf1xvspzj2rpg2z8b905ixmzpnv86772"))))
+                "0xci0c575hklb5y6vybvb48938fslb9zw3mlisvspx1p3fplyzrg"))))
     (build-system gnu-build-system)
     (arguments
      (list

gnu/packages/libusb.scm

@@ -85,7 +85,7 @@ devices on various operating systems.")
 (define-public libusb-compat
   (package
     (name "libusb-compat")
-    (version "0.1.5")
+    (version "0.1.8")
     (source
      (origin
       (method url-fetch)
@@ -94,11 +94,13 @@ devices on various operating systems.")
                           "libusb-compat-" version "/"
                           "libusb-compat-" version ".tar.bz2"))
       (sha256
-       (base32
+       (base32 "09q8w00djrkaxbiklcgjwya1w0n3aqavsz06fl0ixv1x9x47d339"))))
-        "0nn5icrfm9lkhzw1xjvaks9bq3w6mjg86ggv3fn7kgi4nfvg8kj0"))))
     (build-system gnu-build-system)
+    (arguments
+     (list #:configure-flags
+           #~(list "--disable-static")))
     (native-inputs
-     (list pkg-config))
+     (list autoconf automake libtool pkg-config))
     (inputs
      (list libusb))
     (home-page "https://libusb.info")

gnu/packages/linux.scm

@@ -127,6 +127,7 @@
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages haskell-apps)
   #:use-module (gnu packages haskell-xyz)
+  #:use-module (gnu packages image)
   #:use-module (gnu packages libunwind)
   #:use-module (gnu packages libusb)
   #:use-module (gnu packages llvm)
@@ -480,70 +481,55 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
 ;; The current "stable" kernels. That is, the most recently released major
 ;; versions that are still supported upstream.
 
-(define-public linux-libre-6.1-version "6.1.4")
+(define-public linux-libre-6.1-version "6.1.9")
 (define-public linux-libre-6.1-gnu-revision "gnu")
 (define deblob-scripts-6.1
   (linux-libre-deblob-scripts
    linux-libre-6.1-version
    linux-libre-6.1-gnu-revision
    (base32 "0p1cg5khpp8xkfaqy0cnp1m273z3xiz0m97rkrkggz9gr2klrjym")
-   (base32 "0va28vs359r0rfmzh8pw58055kgd8sb62gi78vrg9p8wmj4s87v6")))
+   (base32 "1g9xqc8ajs0g2yq9xizlgr7k47x75rk3y99yicky01fm13rvfvv3")))
 (define-public linux-libre-6.1-pristine-source
   (let ((version linux-libre-6.1-version)
-        (hash (base32 "17jmli5ddc3i0ryjq2y4f0m5wmfhpppiz3b0m60k7c8blr7zda4a")))
+        (hash (base32 "0awjynyy049px0h7li59w3zgn3z39alv6glzrmx6wf1wd62z236n")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-6.1)))
 
-(define-public linux-libre-6.0-version "6.0.18")
-(define-public linux-libre-6.0-gnu-revision "gnu")
-(define deblob-scripts-6.0
-  (linux-libre-deblob-scripts
-   linux-libre-6.0-version
-   linux-libre-6.0-gnu-revision
-   (base32 "0iwbjrgiwch5v1xpnm9wk9zqw2v6lxja0k8yj2x0amxc9ma68176")
-   (base32 "16g2bin3xay30zfss1vlb7pwcss5giaxaksp4v1gk05wn51wjrqr")))
-(define-public linux-libre-6.0-pristine-source
-  (let ((version linux-libre-6.0-version)
-        (hash (base32 "0ncljhhc6frjb9l6zpr4nk2yhj854d3gdizn6a6qsl8ij9ln3dls")))
-   (make-linux-libre-source version
-                            (%upstream-linux-source version hash)
-                            deblob-scripts-6.0)))
-
 ;; The "longterm" kernels — the older releases with long-term upstream support.
 ;; Here are the support timelines:
 ;; <https://www.kernel.org/category/releases.html>
-(define-public linux-libre-5.15-version "5.15.86")
+(define-public linux-libre-5.15-version "5.15.91")
 (define-public linux-libre-5.15-gnu-revision "gnu")
 (define deblob-scripts-5.15
   (linux-libre-deblob-scripts
    linux-libre-5.15-version
    linux-libre-5.15-gnu-revision
    (base32 "0vj60bra81fmbx3lz924czbhxs4dmvd4d584g9mcs80b7c4q52kg")
-   (base32 "1m73pgx8v047xb2gck2g7j7khniis8c9akn9vhzgsdfglrf8p6fj")))
+   (base32 "1lwmax7078w5p6li1gf66m494xijy4bwa7nm5dlx0k09cfif9q2f")))
 (define-public linux-libre-5.15-pristine-source
   (let ((version linux-libre-5.15-version)
-        (hash (base32 "1vpjnmwqsx6akph2nvbsv2jl7pp8b7xns3vmwbljsl23lkpxkz40")))
+        (hash (base32 "107yw7mibibhfrggm8idzn5bayjvkxaq1kv3kkm1lpxipsqjng56")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.15)))
 
-(define-public linux-libre-5.10-version "5.10.162")
+(define-public linux-libre-5.10-version "5.10.166")
 (define-public linux-libre-5.10-gnu-revision "gnu1")
 (define deblob-scripts-5.10
   (linux-libre-deblob-scripts
    linux-libre-5.10-version
    linux-libre-5.10-gnu-revision
    (base32 "0mw7qn77y9c6wrnw4rjvf75cpm1w6n1aqqhf8cnghcb97p2yxxrf")
-   (base32 "0a96g4pjdgwvxn2wpz6rfc8nwdlkw138r9pp66kvfrrn08i313ii")))
+   (base32 "0fk954nniva8a7s423fnfn2wz9j9jdhscc4pqyvwn0wlxxbjgyap")))
 (define-public linux-libre-5.10-pristine-source
   (let ((version linux-libre-5.10-version)
-        (hash (base32 "05yjgp1la5flwqji9b6j7nbdgg5fwzv2ph536v4f9pzza3y01i1f")))
+        (hash (base32 "1bz1sgkqniwg84wv9vcg08mksa5q533vgynsd3y0xnjv1rwa2l80")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.10)))
 
-(define-public linux-libre-5.4-version "5.4.228")
+(define-public linux-libre-5.4-version "5.4.230")
 (define-public linux-libre-5.4-gnu-revision "gnu1")
 (define deblob-scripts-5.4
   (linux-libre-deblob-scripts
@@ -553,12 +539,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
    (base32 "1bgblfkcnrabnr9hpdl07qgps57h6bq4v5pjrxs798vq43db66va")))
 (define-public linux-libre-5.4-pristine-source
   (let ((version linux-libre-5.4-version)
-        (hash (base32 "0935dq7zbpf0fkppl3q96a2gh1zrmq01h1nivzgmdhjlmhn3n9c0")))
+        (hash (base32 "0bz6hfhsahymys2g9s4nzf862z0zfq4346577cpvf98hrhnd6kx7")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.4)))
 
-(define-public linux-libre-4.19-version "4.19.269")
+(define-public linux-libre-4.19-version "4.19.271")
 (define-public linux-libre-4.19-gnu-revision "gnu1")
 (define deblob-scripts-4.19
   (linux-libre-deblob-scripts
@@ -568,12 +554,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
    (base32 "0g1yhzxm3ixfll6n630v7lddcyvf888sg114nimh0lkvzd180s99")))
 (define-public linux-libre-4.19-pristine-source
   (let ((version linux-libre-4.19-version)
-        (hash (base32 "02mjb16xxfj984vibpxvhjl84y5yg0jgzjccjdxnn8db4k9aa2vf")))
+        (hash (base32 "06lxh9skp9213n29ynx7a9cinz7wggaxjsz52kghdbwfnjf3yvb3")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.19)))
 
-(define-public linux-libre-4.14-version "4.14.302")
+(define-public linux-libre-4.14-version "4.14.304")
 (define-public linux-libre-4.14-gnu-revision "gnu1")
 (define deblob-scripts-4.14
   (linux-libre-deblob-scripts
@@ -583,7 +569,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
    (base32 "00i91lx938nqlgy63hiricqd0fnbbf26vgya9c5lb7m1f4x324im")))
 (define-public linux-libre-4.14-pristine-source
   (let ((version linux-libre-4.14-version)
-        (hash (base32 "102c9h0byr9v4bxzkdh7mnw1grm47ji6lf6l1gjlwah7f46j6ap3")))
+        (hash (base32 "1ma9qpsx0nvi0szlivf8v5l3pjykqwrv4x6y5g0nn6bcwhsb5jv4")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.14)))
@@ -622,12 +608,6 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
                              %linux-libre-arm-export-__sync_icache_dcache-patch
                              (search-patch "linux-libre-infodocs-target.patch"))))
 
-(define-public linux-libre-6.0-source
-  (source-with-patches linux-libre-6.0-pristine-source
-                       (list %boot-logo-patch
-                             %linux-libre-arm-export-__sync_icache_dcache-patch
-                             (search-patch "linux-libre-infodocs-target.patch"))))
-
 (define-public linux-libre-5.15-source
   (source-with-patches linux-libre-5.15-pristine-source
                        (list %boot-logo-patch
@@ -738,11 +718,6 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
                              linux-libre-6.1-gnu-revision
                              linux-libre-6.1-source))
 
-(define-public linux-libre-headers-6.0
-  (make-linux-libre-headers* linux-libre-6.0-version
-                             linux-libre-6.0-gnu-revision
-                             linux-libre-6.0-source))
-
 (define-public linux-libre-headers-5.15
   (make-linux-libre-headers* linux-libre-5.15-version
                              linux-libre-5.15-gnu-revision
@@ -782,12 +757,13 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
 ;;;
 
 (define* (kernel-config arch #:key variant)
-  "Return the absolute file name of the Linux-Libre build configuration file
+  "Return a file-like object of the Linux-Libre build configuration file for
-for ARCH and optionally VARIANT, or #f if there is no such configuration."
+ARCH and optionally VARIANT, or #f if there is no such configuration."
   (let* ((name (string-append (if variant (string-append variant "-") "")
                               (if (string=? "i386" arch) "i686" arch) ".conf"))
-         (file (string-append "linux-libre/" name)))
+         (file (string-append "linux-libre/" name))
-    (search-auxiliary-file file)))
+         (config (search-auxiliary-file file)))
+    (and config (local-file config))))
 
 (define %default-extra-linux-options
   `(;; Make the kernel config available at /proc/config.gz
@@ -895,8 +871,9 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration."
 (define* (make-linux-libre version gnu-revision hash-string supported-systems
                            #:key
                            (extra-version #f)
-                           ;; A function that takes an arch and a variant.
+                           ;; A function that takes an arch and a variant, and
-                           ;; See kernel-config for an example.
+                           ;; return a file-like object.  See kernel-config
+                           ;; for an example.
                            (configuration-file #f)
                            (defconfig "defconfig")
                            (extra-options %default-extra-linux-options)
@@ -980,8 +957,20 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration."
                       #$(and extra-version
                              (string-append "-" extra-version)))))
           (replace 'configure
-            (lambda* (#:key inputs #:allow-other-keys)
+            (lambda _
-              (let ((config (assoc-ref inputs "kconfig")))
+              (let ((config
+                     #$(match (let ((arch (platform-linux-architecture
+                                           (lookup-platform-by-target-or-system
+                                            (or (%current-target-system)
+                                                (%current-system))))))
+                                (and configuration-file arch
+                                     (configuration-file
+                                      arch
+                                      #:variant (version-major+minor version))))
+                         (#f            ;no config for this platform
+                          #f)
+                         ((? file-like? config)
+                          config))))
                 ;; Use a custom kernel configuration file or a default
                 ;; configuration file.
                 (if config
@@ -989,15 +978,15 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration."
                       (copy-file config ".config")
                       (chmod ".config" #o666))
                     (invoke "make" #$defconfig))
-                ;; Appending works even when the option wasn't in the
+                ;; Appending works even when the option wasn't in the file.
-                ;; file.  The last one prevails if duplicated.
+                ;; The last one prevails if duplicated.
                 (let ((port (open-file ".config" "a"))
                       (extra-configuration #$(config->string extra-options)))
                   (display extra-configuration port)
                   (close-port port))
                 (invoke "make" "oldconfig"))))
           (replace 'install
-            (lambda* (#:key inputs #:allow-other-keys)
+            (lambda _
               (let ((moddir (string-append #$output "/lib/modules"))
                     (dtbdir (string-append #$output "/lib/dtbs")))
                 ;; Install kernel image, kernel configuration and link map.
@@ -1012,11 +1001,11 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration."
                 ;; Install kernel modules
                 (mkdir-p moddir)
                 (invoke "make"
-                        ;; Disable depmod because the Guix system's
+                        ;; Disable depmod because the Guix system's module
-                        ;; module directory is an union of potentially
+                        ;; directory is an union of potentially multiple
-                        ;; multiple packages.  It is not possible to use
+                        ;; packages.  It is not possible to use depmod to
-                        ;; depmod to usefully calculate a dependency
+                        ;; usefully calculate a dependency graph while
-                        ;; graph while building only one of them.
+                        ;; building only one of them.
                         "DEPMOD=true"
                         (string-append "MODULE_DIR=" moddir)
                         (string-append "INSTALL_PATH=" #$output)
@@ -1029,8 +1018,8 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration."
                        (version (match versions
                                   ((x) x))))
                   ;; There are symlinks to the build and source directory.
-                  ;; Both will point to target /tmp/guix-build* and thus
+                  ;; Both will point to target /tmp/guix-build* and thus not
-                  ;; not be useful in a profile.  Delete the symlinks.
+                  ;; be useful in a profile.  Delete the symlinks.
                   (false-if-file-not-found
                    (delete-file
                     (string-append moddir "/" version "/build")))
@@ -1038,35 +1027,22 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration."
                    (delete-file
                     (string-append moddir "/" version "/source"))))))))))
     (native-inputs
-     `(("perl" ,perl)
+     (list perl
-       ("bc" ,bc)
+           bc
-       ("openssl" ,openssl)
+           openssl
-       ("elfutils" ,elfutils)        ;needed to enable CONFIG_STACK_VALIDATION
+           elfutils                  ;needed to enable CONFIG_STACK_VALIDATION
-       ("flex" ,flex)
+           flex
-       ("bison" ,bison)
+           bison
-
+           ;; These are needed to compile the GCC plugins.
-       ;; These are needed to compile the GCC plugins.
+           gmp
-       ("gmp" ,gmp)
+           mpfr
-       ("mpfr" ,mpfr)
+           mpc))
-       ("mpc" ,mpc)
-       ,@(match (let ((arch (platform-linux-architecture
-                             (lookup-platform-by-target-or-system
-                              (or (%current-target-system)
-                                  (%current-system))))))
-                  (and configuration-file arch
-                       (configuration-file
-                        arch
-                        #:variant (version-major+minor version))))
-           (#f                          ;no config for this platform
-            '())
-           ((? string? config)
-            `(("kconfig" ,config))))))
     (home-page "https://www.gnu.org/software/linux-libre/")
     (synopsis "100% free redistribution of a cleaned Linux kernel")
     (description "GNU Linux-Libre is a free (as in freedom) variant of the
 Linux kernel.  It has been modified to remove all non-free binary blobs.")
     (license license:gpl2)
-    (properties '((max-silent-time . 3600))))) ;don't timeout on blob scan.
+    (properties '((max-silent-time . 10800))))) ;don't timeout on blob scan
 
 
 ;;;
@@ -1081,19 +1057,11 @@ Linux kernel.  It has been modified to remove all non-free binary blobs.")
                        "aarch64-linux" "powerpc64le-linux" "riscv64-linux")
                      #:configuration-file kernel-config))
 
-(define-public linux-libre-6.0
+(define-public linux-libre-version         linux-libre-6.1-version)
-  (make-linux-libre* linux-libre-6.0-version
+(define-public linux-libre-gnu-revision    linux-libre-6.1-gnu-revision)
-                     linux-libre-6.0-gnu-revision
+(define-public linux-libre-pristine-source linux-libre-6.1-pristine-source)
-                     linux-libre-6.0-source
+(define-public linux-libre-source          linux-libre-6.1-source)
-                     '("x86_64-linux" "i686-linux" "armhf-linux"
+(define-public linux-libre                 linux-libre-6.1)
-                       "aarch64-linux" "powerpc64le-linux" "riscv64-linux")
-                     #:configuration-file kernel-config))
-
-(define-public linux-libre-version         linux-libre-6.0-version)
-(define-public linux-libre-gnu-revision    linux-libre-6.0-gnu-revision)
-(define-public linux-libre-pristine-source linux-libre-6.0-pristine-source)
-(define-public linux-libre-source          linux-libre-6.0-source)
-(define-public linux-libre                 linux-libre-6.0)
 
 (define-public linux-libre-5.15
   (make-linux-libre* linux-libre-5.15-version
@@ -1316,9 +1284,9 @@ Linux kernel.  It has been modified to remove all non-free binary blobs.")
 (define-public linux-libre-with-bpf
   (let ((base-linux-libre
          (make-linux-libre*
-          linux-libre-6.0-version
+          linux-libre-6.1-version
-          linux-libre-6.0-gnu-revision
+          linux-libre-6.1-gnu-revision
-          linux-libre-6.0-source
+          linux-libre-6.1-source
           '("x86_64-linux" "i686-linux" "armhf-linux"
             "aarch64-linux" "powerpc64le-linux" "riscv64-linux")
           #:extra-version "bpf"
@@ -2201,6 +2169,30 @@ The Discordian calendar was made popular by the \"Illuminatus!\" trilogy
 by Robert Shea and Robert Anton Wilson.")
     (license license:public-domain)))
 
+(define-public dislocker
+  (package
+    (name "dislocker")
+    (version "0.7.3")
+    (home-page "https://github.com/Aorimn/dislocker")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url home-page)
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1ak68s1v5dwh8y2dy5zjybmrh0pnqralmyqzis67y21m87g47h2k"))))
+    (build-system cmake-build-system)
+    (arguments
+     '(#:tests? #f)) ;no test suite
+    (inputs (list fuse mbedtls-apache))
+    (synopsis "FUSE driver to read/write Windows BitLocker drives")
+    (description
+     "This package provides means to to read BitLocker encrypted
+partitions.  Write functionality is also provided but check the README.")
+    (license license:gpl2+)))
+
 (define-public fbset
   (package
     (name "fbset")
@@ -2856,7 +2848,7 @@ external rate conversion.")
     (native-inputs
      (list pkg-config flex bison))
     (inputs
-     (list libmnl libnftnl/fixed))
+     (list libmnl libnftnl/pinned))
     (arguments
      (list #:tests? #f             ; no test suite
            #:configure-flags       ; add $libdir to the RUNPATH of executables
@@ -2881,7 +2873,7 @@ Both commands are targeted at system administrators.")
 (define-public bolt
   (package
     (name "bolt")
-    (version "0.9.4")
+    (version "0.9.5")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -2890,7 +2882,7 @@ Both commands are targeted at system administrators.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0w66shv7ra8yrhr0byifahbq25wi8qfsm3rifz0j31l7cmnys3js"))))
+                "1b9z0sfrz6bj0mddng9s0dx59g9239zmrl03hxx2x88mb7r0wmcg"))))
     (build-system meson-build-system)
     (arguments
      (list #:configure-flags '(list "--localstatedir=/var")
@@ -5811,7 +5803,7 @@ and copy/paste text in the console and in xterm.")
 (define-public btrfs-progs
   (package
     (name "btrfs-progs")
-    (version "6.0.2")
+    (version "6.1.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://kernel.org/linux/kernel/"
@@ -5819,7 +5811,7 @@ and copy/paste text in the console and in xterm.")
                                   "btrfs-progs-v" version ".tar.xz"))
               (sha256
                (base32
-                "063hmqwqlmp0llgqnfqgcj7slrv762kmbk6srhrgqifr94q8crb6"))))
+                "0ylxszcsm0jqsa5glccd1pv3rcfk1f5wjcf3ayxc0r9xgzcngrkb"))))
     (build-system gnu-build-system)
     (outputs '("out"
                "static"))      ; static versions of the binaries in "out"
@@ -6486,7 +6478,7 @@ from the ntfs-3g package.  It is meant to be used in initrds.")
 (define-public rdma-core
   (package
     (name "rdma-core")
-    (version "33.1")
+    (version "44.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/linux-rdma/rdma-core"
@@ -6494,26 +6486,26 @@ from the ntfs-3g package.  It is meant to be used in initrds.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1rah0v9gq9rksqd2c17nmydsxcjz178n7m2y4ricwlf5pq1b2yfi"))))
+                "12w5v74wz1akac09frw7qk1yd06b00239zh7bvbvqyzjc0g61mi5"))))
     (build-system cmake-build-system)
     (arguments
-     `(#:tests? #f ; no tests
+     `(#:tests? #f                      ;no tests
+
        ;; Upstream uses the "ninja" build system and encourage distros
        ;; to do the same for consistency.
        #:configure-flags (list "-GNinja"
 
                                ,@(if (%current-target-system)
-                                   `((string-append
+                                     `((string-append
-                                       "-DPKG_CONFIG_EXECUTABLE="
+                                        "-DPKG_CONFIG_EXECUTABLE="
-                                       (search-input-file
+                                        (search-input-file
                                          %build-inputs
                                          (string-append "/bin/"
                                                         ,(pkg-config-for-target)))))
-                                   '())
+                                     '())
                                (string-append "-DRST2MAN_EXECUTABLE="
-                                              (assoc-ref %build-inputs
+                                              (search-input-file
-                                                         "python-docutils")
+                                               %build-inputs "/bin/rst2man.py")))
-                                              "/bin/rst2man.py"))
        #:phases
        (modify-phases %standard-phases
          (replace 'build
@@ -6524,13 +6516,9 @@ from the ntfs-3g package.  It is meant to be used in initrds.")
            (lambda _
              (invoke "ninja" "install"))))))
     (native-inputs
-     `(("ninja" ,ninja)
+     (list ninja pkg-config python-wrapper python-docutils)) ;for 'rst2man'
-       ("pkg-config" ,pkg-config)
-       ("python" ,python-wrapper)
-       ("python-docutils" ,python-docutils)))     ;for 'rst2man'
     (inputs
-     `(("libnl" ,libnl)
+     (list libnl eudev))
-       ("udev" ,eudev)))
     (home-page "https://github.com/linux-rdma/rdma-core")
     (synopsis "Utilities and libraries for working with RDMA devices")
     (description
@@ -6981,7 +6969,7 @@ the @code{mce-inject} module loaded if it exists.")
 (define-public mcelog
   (package
     (name "mcelog")
-    (version "190")
+    (version "191")
     (source
      (origin
        (method git-fetch)
@@ -6990,7 +6978,7 @@ the @code{mce-inject} module loaded if it exists.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1466zkbxgjg8ik0gd9vwsjiwg0yg7g8ra4bw3lg3ypla2kiydy4q"))
+        (base32 "0vx0lziw6g20vh42ngs66fiq2bm714llx5xx6f0m1hbjcihi1afy"))
        (modules '((guix build utils)))
        (snippet
         `(begin
@@ -7666,9 +7654,13 @@ libnftnl has been previously known as libnftables.  This library is currently
 used by nftables.")
     (license license:gpl2+)))
 
+;;; The symbol libnftl/fixed should be used when libnftnl needs fixes
+;;; (security or else) and this deprecation could be removed.
+(define-deprecated/public-alias libnftnl/fixed libnftnl/pinned)
+
 ;; This is used in iptables, which contributes to rust.  We're pinning this
 ;; variant to avoid accidental rebuilds of rust.
-(define-public libnftnl/fixed
+(define-public libnftnl/pinned
   (package (inherit libnftnl)
     (version "1.2.0")
     (source
@@ -7687,16 +7679,16 @@ used by nftables.")
 (define-public nftables
   (package
     (name "nftables")
-    (version "1.0.5")
+    (version "1.0.6")
     (source
      (origin
        (method url-fetch)
        (uri (list (string-append "mirror://netfilter.org/nftables/nftables-"
-                                 version ".tar.bz2")
+                                 version ".tar.xz")
                   (string-append "https://www.nftables.org/projects/nftables"
-                                 "/files/nftables-" version ".tar.bz2")))
+                                 "/files/nftables-" version ".tar.xz")))
        (sha256
-        (base32 "02p59m773l2xqcb7ib7cprlpjfdnp792bahbs6c3dx1s74c4n6wd"))))
+        (base32 "0k2y03dz77b0inqlmh5yg8qaifl0walzvhldwiq7d642vl6l61r4"))))
     (build-system gnu-build-system)
     (arguments `(#:configure-flags
                  '("--disable-static"
@@ -7837,7 +7829,7 @@ of a system that deprecates the old ip_queue/libipq mechanism.")
 (define-public conntrack-tools
   (package
     (name "conntrack-tools")
-    (version "1.4.6")
+    (version "1.4.7")
     (source
      (origin
        (method url-fetch)
@@ -7845,8 +7837,7 @@ of a system that deprecates the old ip_queue/libipq mechanism.")
                            "conntrack-tools/files/"
                            "conntrack-tools-" version ".tar.bz2"))
        (sha256
-        (base32
+        (base32 "0pabq97rpci3z1bdc54cyhc3b9w86m4nnlbzsp7905p8az7yp789"))))
-         "0psx41bclqrh4514yzq03rvs3cq3scfpd1v4kkyxnic2hk65j22r"))))
     (build-system gnu-build-system)
     (native-inputs (list bison flex pkg-config))
     (inputs (list libtirpc
@@ -8464,7 +8455,8 @@ relevant @file{/dev/vcs*} file(s).")
     (synopsis "Take a screenshot of the contents of the Linux framebuffer")
     (description
      "fbcat saves the contents of the Linux framebuffer (@file{/dev/fb*}), or
-a dump therof.  It supports a wide range of drivers and pixel formats.
+a dump thereof.  It supports a wide range of drivers and pixel formats.
+
 @command{fbcat} can take screenshots of virtually any application that can be
 made to write its output to the framebuffer, including (but not limited to)
 text-mode or graphical applications that don't use a display server.
@@ -8473,6 +8465,38 @@ Also included is @command{fbgrab}, a wrapper around @command{fbcat} that
 emulates the behaviour of Gunnar Monell's older fbgrab utility.")
     (license license:gpl2)))
 
+(define-public fbgrab
+  (package
+    (name "fbgrab")
+    (version "1.5")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/GunnarMonell/fbgrab")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1npn7l8jg0nhjraybjl38v8635zawzmn06ql3hs3vhci1vi1r90r"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list #:tests? #f                  ;no test suite
+           #:make-flags #~(list (string-append "CC=" #$(cc-for-target))
+                                (string-append "DESTDIR=" #$output))
+           #:phases #~(modify-phases %standard-phases
+                        (add-after 'unpack 'strip-/usr-prefix
+                          (lambda _
+                            (substitute* "Makefile"
+                              (("/usr") ""))))
+                        (delete 'configure))))
+    (inputs (list libpng zlib))
+    (home-page "https://github.com/GunnarMonell/fbgrab")
+    (synopsis "Linux framebuffer screenshot/conversion utility")
+    (description "FBGrab is a framebuffer screenshot program that captures the
+Linux framebuffer and converts it to a PNG image.  It can also convert a
+framebuffer dump file (copy) to a PNG image.")
+    (license license:gpl2)))   ;GPL 2.0 only (per SPDX identifier in fbgrab.c)
+
 (define-public libcgroup
   (package
     (name "libcgroup")
@@ -9407,14 +9431,14 @@ receiving.  It is dedicated to the PL011 UART of the Raspberry Pi.")
 (define-public ipset
   (package
     (name "ipset")
-    (version "7.16")
+    (version "7.17")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://ipset.netfilter.org/"
                            "ipset-" version ".tar.bz2"))
        (sha256
-        (base32 "1l4nybq17gr2ick7bbb5gq46bsqiw4rxmrvi0qfkvpm1yk6xkcc7"))))
+        (base32 "1n34mkrdha9rggd0fizjx6baqkiqqd1yfhb5ml663mlx93zwjjdy"))))
     (build-system gnu-build-system)
     (inputs
      (list libmnl))
@@ -9508,7 +9532,7 @@ provides user-space tools for creating EROFS file systems.")
 (define-public rasdaemon
   (package
     (name "rasdaemon")
-    (version "0.6.8")
+    (version "0.7.0")
     (source
      (origin
        (method git-fetch)
@@ -9517,7 +9541,7 @@ provides user-space tools for creating EROFS file systems.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0r0339mg4rc12p63iiq2kwdqn1zjakyiv014i2a2l9s8v5rjik41"))))
+        (base32 "1a3ycx1g2zyshlna9fg8c9329m8wia42vkmlh2awfab0ngwi3g50"))))
     (native-inputs (list autoconf automake libtool))
     (inputs (list perl perl-dbd-sqlite sqlite dmidecode kmod))
     (arguments
@@ -9818,7 +9842,7 @@ directly by @code{make localmodconfig} as described above.")
 (define-public kconfig-hardened-check
   (package
     (name "kconfig-hardened-check")
-    (version "0.5.17")
+    (version "0.6.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -9827,7 +9851,7 @@ directly by @code{make localmodconfig} as described above.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0p9pywfxwyk4yfgaf7bhqrf72ywc6w6k77dbi7lldynha886ih4a"))))
+                "0bpdy2a7l75y5cqzzc92nh4gapzgza8ml5i8ximr6brf6pr3681z"))))
     (build-system python-build-system)
     (home-page "https://github.com/a13xp0p0v/kconfig-hardened-check")
     (synopsis

gnu/packages/lirc.scm

@@ -38,14 +38,14 @@
 (define-public lirc
   (package
     (name "lirc")
-    (version "0.10.1")
+    (version "0.10.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/lirc/LIRC/" version
                                   "/lirc-" version ".tar.bz2"))
               (sha256
                (base32
-                "1whlyifvvc7w04ahq07nnk1h18wc8j7c6wnvlb6mszravxh3qxcb"))
+                "0ai27l6hxfgkwvkqa3fy1b1gqzw2y10md030y5ig4748fj1fqi1x"))
               (patches (search-patches "lirc-localstatedir.patch"
                                        "lirc-reproducible-build.patch"))))
     (build-system gnu-build-system)
@@ -63,16 +63,14 @@
              ;; Correct the faulty assumption that systemd support should be
              ;; hard-wired when a build host's /proc/version contains "Ubuntu".
              (substitute* "configure"
-               (("kernelversion=.*") "kernelversion=irrelevant\n"))
+               (("kernelversion=.*") "kernelversion=irrelevant\n"))))
-             #t))
          (add-after 'unpack 'patch-lirc-make-devinput
            (lambda* (#:key inputs #:allow-other-keys)
              ;; 'lirc-make-devinput' script assumes that linux headers
              ;; are placed in "/usr/...".
              (let ((headers (assoc-ref inputs "kernel-headers")))
                (substitute* "tools/lirc-make-devinput"
-                 (("/usr/include") (string-append headers "/include"))))
+                 (("/usr/include") (string-append headers "/include"))))))
-             #t))
          (add-after 'unpack 'patch-doc/Makefile.in
            (lambda _
              ;; Lirc wants to install several images and a useless html page
@@ -82,8 +80,18 @@
              ;; "share/doc/lirc/images/" anyway).
              (substitute* "doc/Makefile.in"
                (("^vardocs_DATA =.*") "vardocs_DATA =\n")
-               (("^varimage_DATA =.*") "varimage_DATA =\n"))
+               (("^varimage_DATA =.*") "varimage_DATA =\n"))))
-             #t)))))
+         (add-after 'unpack 'omit-pip-sourceball
+           ;; ‘make install’ invokes ’setup.py sdist’, which has no known (to
+           ;; nckx) way to enforce mtimes.  The utility of this is questionable,
+           ;; IMO: let's disable it entirely & listen for complaints, if any.
+           (lambda _
+             (substitute* "Makefile.in"
+               (("(PYTHON_TARBALL.*=).*" _ tarball=)
+                (string-append tarball= "\n")))))
+         (add-before 'configure 'build-reproducibly
+           (lambda _
+             (setenv "LIRC_IRDB_CACHE_ID" "build time"))))))
     (native-inputs
      (list pkg-config libxslt))
     (inputs