Merge branch 'master' into gnome-team

doc/guix.texi

@@ -1297,6 +1297,11 @@ environment variable is set to the non-existent
 @file{/homeless-shelter}.  This helps to highlight inappropriate uses of
 @env{HOME} in the build scripts of packages.
 
+All this usually enough to ensure details of the environment do not
+influence build processes.  In some exceptional cases where more control
+is needed---typically over the date, kernel, or CPU---you can resort to
+a virtual build machine (@pxref{build-vm, virtual build machines}).
+
 You can influence the directory where the daemon stores build trees
 @i{via} the @env{TMPDIR} environment variable.  However, the build tree
 within the chroot is always called @file{/tmp/guix-build-@var{name}.drv-0},
@@ -9850,7 +9855,7 @@ MbedTLS package:
                   (("generate_wrapper_header.*")
                    (string-append
                     "generate_wrapper_header(\"MbedTLS\", \""
-                    (assoc-ref inputs "mbedtls-apache") "\")\n"))))
+                    (assoc-ref inputs "mbedtls") "\")\n"))))
               ;; There's a Julia file for each platform, override them all.
               (find-files "src/wrappers/" "\\.jl$"))))
 @end lisp
@@ -36369,6 +36374,138 @@ host.  If empty, QEMU uses a default file name.
 @end deftp
 
 
+@anchor{build-vm}
+@subsubheading Virtual Build Machines
+
+@cindex virtual build machines
+@cindex build VMs
+@cindex VMs, for offloading
+@dfn{Virtual build machines} or ``build VMs'' let you offload builds to
+a fully controlled environment.  ``How can it be more controlled than
+regular builds?  And why would it be useful?'', you ask.  Good
+questions.
+
+Builds spawned by @code{guix-daemon} indeed run in a controlled
+environment; specifically the daemon spawns build processes in separate
+namespaces and in a chroot, such as that build processes only see their
+declared dependencies and a well-defined subset of the file system tree
+(@pxref{Build Environment Setup}, for details).  A few aspects of the
+environments are not controlled though: the operating system kernel, the
+CPU model, and the date.  Most of the time, these aspects have no impact
+on the build process: the level of isolation @code{guix-daemon} provides
+is ``good enough''.
+
+@cindex time traps
+However, there are occasionally cases where those aspects @emph{do}
+influence the build process.  A typical example is @dfn{time traps}:
+build processes that stop working after a certain date@footnote{The most
+widespread example of time traps is test suites that involve checking
+the expiration date of a certificate.  Such tests exists in TLS
+implementations such as OpenSSL and GnuTLS, but also in high-level
+software such as Python.}.  Another one is software that optimizes for
+the CPU microarchitecture it is built on or, worse, bugs that manifest
+only on specific CPUs.
+
+To address that, @code{virtual-build-machine-service-type} lets you add
+a virtual build machine on your system, as in this example:
+
+@lisp
+(use-modules (gnu services virtualization))
+
+(operating-system
+  ;; @dots{}
+  (services (append (list (service virtual-build-machine-service-type))
+                    %base-services)))
+@end lisp
+
+By default, you have to explicitly start the build machine when you need
+it, at which point builds may be offloaded to it (@pxref{Daemon Offload
+Setup}):
+
+@example
+herd start build-vm
+@end example
+
+With the default setting shown above, the build VM runs with its clock
+set to a date several years in the past, and on a CPU model that
+corresponds to that date---a model possibly older than that of your
+machine.  This lets you rebuild today software from the past that would
+otherwise fail to build due to a time trap or other issues in its build
+process.
+
+You can configure the build VM, as in this example:
+
+@lisp
+(service virtual-build-machine-service-type
+         (virtual-build-machine
+          (cpu "Westmere")
+          (cpu-count 8)
+          (memory-size (* 1 1024))
+          (auto-start? #t)))
+@end lisp
+
+The available options are shown below.
+
+@defvar virtual-build-machine-service-type
+This is the service type to run @dfn{virtual build machines}.  Virtual
+build machines are configured so that builds are offloaded to them when
+they are running.
+@end defvar
+
+@deftp {Data Type} virtual-build-machine
+This is the data type specifying the configuration of a build machine.
+It contains the fields below:
+
+@table @asis
+@item @code{name} (default: @code{'build-vm})
+The name of this build VM.  It is used to construct the name of its
+Shepherd service.
+
+@item @code{image}
+The image of the virtual machine (@pxref{System Images}).  This notably
+specifies the virtual disk size and the operating system running into it
+(@pxref{operating-system Reference}).  The default value is a minimal
+operating system image.
+
+@item @code{qemu} (default: @code{qemu-minimal})
+The QEMU package to run the image.
+
+@item @code{cpu}
+The CPU model being emulated as a string denoting a model known to QEMU.
+
+The default value is a model that matches @code{date} (see below).  To
+see what CPU models are available, run, for example:
+
+@example
+qemu-system-x86_64 -cpu help
+@end example
+
+@item @code{cpu-count} (default: @code{4})
+The number of CPUs emulated by the virtual machine.
+
+@item @code{memory-size} (default: @code{2048})
+Size in mebibytes (MiB) of the virtual machine's main memory (RAM).
+
+@item @code{date} (default: a few years ago)
+Date inside the virtual machine when it starts; this must be a SRFI-19
+date object (@pxref{SRFI-19 Date,,, guile, GNU Guile Reference Manual}).
+
+@item @code{port-forwardings} (default: 11022 and 11004)
+TCP ports of the virtual machine forwarded to the host.  By default, the
+SSH and secrets ports are forwarded into the host.
+
+@item @code{systems} (default: @code{(list (%current-system))})
+List of system types supported by the build VM---e.g.,
+@code{"x86_64-linux"}.
+
+@item @code{auto-start?} (default: @code{#f})
+Whether to start the virtual machine when the system boots.
+@end table
+@end deftp
+
+In the next section, you'll find a variant on this theme: GNU/Hurd
+virtual machines!
+
 @anchor{hurd-vm}
 @subsubheading The Hurd in a Virtual Machine
 

etc/disarchive-manifest.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2021-2023 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2021-2024 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -35,6 +35,8 @@
      (and (origin-hash origin)
           (or (string-suffix? ".tar.gz" file)
               (string-suffix? ".tgz" file)
+              (string-suffix? ".tar.bz2" file)
+              (string-suffix? ".tbz2" file)
               (string-suffix? ".tar.xz" file)
               (string-suffix? ".tar" file))))))
 

etc/teams.scm

@@ -300,11 +300,7 @@ asdf-build-system."
   (team 'go
         #:name "Go team"
         #:scope (list "gnu/packages/configuration-management.scm"
-                      "gnu/packages/golang-check.scm"
+                      "gnu/packages/golang(-.+|)\\.scm$"
-                      "gnu/packages/golang-crypto.scm"
-                      "gnu/packages/golang-web.scm"
-                      "gnu/packages/golang-xyz.scm"
-                      "gnu/packages/golang.scm"
                       "gnu/packages/syncthing.scm"
                       "gnu/packages/terraform.scm"
                       "guix/build-system/go.scm"
@@ -501,7 +497,8 @@ asdf-build-system."
 and Thunderbird."
         #:scope (list "gnu/build/icecat-extension.scm"
                       "gnu/packages/browser-extensions.scm"
-                      "gnu/packages/gnuzilla.scm")))
+                      "gnu/packages/gnuzilla.scm"
+                      "gnu/packages/tor-browsers.scm")))
 
 (define-team racket
   (team 'racket
@@ -716,6 +713,10 @@ GLib/GIO, GTK, GStreamer and Webkit."
                        "w@wmeyer.eu")
   kernel)
 
+(define-member (person "Mark H Weaver"
+                       "mhw@netris.org")
+  mozilla)
+
 
 (define (find-team name)
   (or (hash-ref %teams (string->symbol name))

gnu/build/marionette.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2016-2022 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016-2022, 2024 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2018 Chris Marusich <cmmarusich@gmail.com>
 ;;; Copyright © 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2023 Bruno Victal <mirai@makinata.eu>
@@ -223,29 +223,49 @@ FILE has not shown up after TIMEOUT seconds, raise an error."
 (define* (wait-for-tcp-port port marionette
                             #:key
                             (timeout 20)
+                            (peek? #f)
                             (address `(make-socket-address AF_INET
                                                            INADDR_LOOPBACK
                                                            ,port)))
   "Wait for up to TIMEOUT seconds for PORT to accept connections in
 MARIONETTE.  ADDRESS must be an expression that returns a socket address,
-typically a call to 'make-socket-address'.  Raise an error on failure."
+typically a call to 'make-socket-address'.  When PEEK? is true, attempt to
+read a byte from the socket upon connection; retry if that gives the
+end-of-file object.
+
+Raise an error on failure."
   ;; Note: The 'connect' loop has to run within the guest because, when we
   ;; forward ports to the host, connecting to the host never raises
   ;; ECONNREFUSED.
   (match (marionette-eval
-          `(let* ((address ,address)
+          `(let* ((address ,address))
-                  (sock (socket (sockaddr:fam address) SOCK_STREAM 0)))
+             (define (open-socket)
-             (let loop ((i 0))
+               (socket (sockaddr:fam address) SOCK_STREAM 0))
+
+             (let loop ((sock (open-socket))
+                        (i 0))
                (catch 'system-error
                  (lambda ()
                    (connect sock address)
+                   (when ,peek?
+                     (let ((byte ((@ (ice-9 binary-ports) lookahead-u8)
+                                  sock)))
+                       (when (eof-object? byte)
+                         (close-port sock)
+                         (throw 'system-error
+                                "wait-for-tcp-port" "~A"
+                                (list (strerror ECONNRESET))
+                                (list ECONNRESET)))))
                    (close-port sock)
                    'success)
                  (lambda args
                    (if (< i ,timeout)
                        (begin
                          (sleep 1)
-                         (loop (+ 1 i)))
+                         (loop (if (port-closed? sock)
+                                   (open-socket)
+                                   sock)
+                               (+ 1 i)))
                        (list 'failure address))))))
           marionette)
     ('success #t)

gnu/build/secret-service.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2020-2022 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2020-2023 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -93,13 +93,28 @@ Return #t in the former case and #f in the latter case."
            ('readable #t)
            ('timeout  #f)))))))
 
-(define* (secret-service-send-secrets port secret-root
+(define (socket-address->string address)
+  "Return a human-readable representation of ADDRESS, an object as returned by
+'make-socket-address'."
+  (let ((family (sockaddr:fam address)))
+    (cond ((= AF_INET family)
+           (string-append (inet-ntop AF_INET (sockaddr:addr address))
+                          ":" (number->string (sockaddr:port address))))
+          ((= AF_INET6 family)
+           (string-append "[" (inet-ntop AF_INET6 (sockaddr:addr address)) "]"
+                          ":" (number->string (sockaddr:port address))))
+          ((= AF_UNIX family)
+           (sockaddr:path address))
+          (else
+           (object->string address)))))
+
+(define* (secret-service-send-secrets address secret-root
                                       #:key (retry 60)
                                       (handshake-timeout 180))
-  "Copy all files under SECRET-ROOT using TCP to secret-service listening at
+  "Copy all files under SECRET-ROOT by connecting to secret-service listening
-local PORT.  If connect fails, sleep 1s and retry RETRY times; once connected,
+at ADDRESS, an address as returned by 'make-socket-address'.  If connection
-wait for at most HANDSHAKE-TIMEOUT seconds for handshake to complete.  Return
+fails, sleep 1s and retry RETRY times; once connected, wait for at most
-#f on failure."
+HANDSHAKE-TIMEOUT seconds for handshake to complete.  Return #f on failure."
   (define (file->file+size+mode file-name)
     (let ((stat (stat file-name))
           (target (substring file-name (string-length secret-root))))
@@ -118,9 +133,9 @@ wait for at most HANDSHAKE-TIMEOUT seconds for handshake to complete.  Return
                       (dump-port input sock))))
                 files)))
 
-  (log "sending secrets to ~a~%" port)
+  (log "sending secrets to ~a~%" (socket-address->string address))
+
   (let ((sock (socket AF_INET (logior SOCK_CLOEXEC SOCK_STREAM) 0))
-        (addr (make-socket-address AF_INET INADDR_LOOPBACK port))
         (sleep (if (resolve-module '(fibers) #f)
                    (module-ref (resolve-interface '(fibers)) 'sleep)
                    sleep)))
@@ -129,7 +144,7 @@ wait for at most HANDSHAKE-TIMEOUT seconds for handshake to complete.  Return
     ;; forward port inside the guest.
     (let loop ((retry retry))
       (catch 'system-error
-        (cute connect sock addr)
+        (cute connect sock address)
         (lambda (key . args)
           (when (zero? retry)
             (apply throw key args))
@@ -147,7 +162,8 @@ wait for at most HANDSHAKE-TIMEOUT seconds for handshake to complete.  Return
           (('secret-service-server ('version version ...))
            (log "sending files from ~s...~%" secret-root)
            (send-files sock)
-           (log "done sending files to port ~a~%" port)
+           (log "done sending files to ~a~%"
+                (socket-address->string address))
            (close-port sock)
            secret-root)
           (x
@@ -155,7 +171,8 @@ wait for at most HANDSHAKE-TIMEOUT seconds for handshake to complete.  Return
            (close-port sock)
            #f))
         (begin                                    ;timeout
-         (log "timeout while sending files to ~a~%" port)
+         (log "timeout while sending files to ~a~%"
+              (socket-address->string address))
          (close-port sock)
          #f))))
 
@@ -168,19 +185,20 @@ wait for at most HANDSHAKE-TIMEOUT seconds for handshake to complete.  Return
       (unless (= ENOENT (system-error-errno args))
         (apply throw args)))))
 
-(define (secret-service-receive-secrets port)
+(define (secret-service-receive-secrets address)
-  "Listen to local PORT and wait for a secret service client to send secrets.
+  "Listen to ADDRESS, an address returned by 'make-socket-address', and wait
-Write them to the file system.  Return the list of files installed on success,
+for a secret service client to send secrets.  Write them to the file system.
-and #f otherwise."
+Return the list of files installed on success, and #f otherwise."
 
-  (define (wait-for-client port)
+  (define (wait-for-client address)
-    ;; Wait for a TCP connection on PORT.  Note: We cannot use the
+    ;; Wait for a connection on ADDRESS.  Note: virtio-serial ports are safer
-    ;; virtio-serial ports, which would be safer, because they are
+    ;; than TCP connections but they are (presumably) unsupported on GNU/Hurd.
-    ;; (presumably) unsupported on GNU/Hurd.
     (let ((sock (socket AF_INET (logior SOCK_CLOEXEC SOCK_STREAM) 0)))
-      (bind sock AF_INET INADDR_ANY port)
+      (bind sock address)
       (listen sock 1)
-      (log "waiting for secrets on port ~a...~%" port)
+      (log "waiting for secrets on ~a...~%"
+           (socket-address->string address))
+
       (match (select (list sock) '() '() 60)
         (((_) () ())
          (match (accept sock)
@@ -244,7 +262,7 @@ and #f otherwise."
        (log "invalid secrets received~%")
        #f)))
 
-  (let* ((port   (wait-for-client port))
+  (let* ((port   (wait-for-client address))
          (result (and=> port read-secrets)))
     (when port
       (close-port port))

gnu/local.mk

@@ -64,6 +64,7 @@
 # Copyright © 2023 gemmaro <gemmaro.dev@gmail.com>
 # Copyright © 2023 Herman Rimm <herman@rimm.ee>
 # Copyright © 2023 Troy Figiel <troy@troyfigiel.com>
+# Copyright © 2024 David Elsing <david.elsing@posteo.net>
 #
 # This file is part of GNU Guix.
 #
@@ -308,7 +309,9 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/gnu-pw-mgr.scm			\
   %D%/packages/gobby.scm			\
   %D%/packages/golang.scm			\
+  %D%/packages/golang-build.scm		\
   %D%/packages/golang-check.scm		\
+  %D%/packages/golang-compression.scm		\
   %D%/packages/golang-crypto.scm	      	\
   %D%/packages/golang-web.scm	        	\
   %D%/packages/golang-xyz.scm	        	\
@@ -959,6 +962,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/audiofile-function-signature.patch	\
   %D%/packages/patches/automake-skip-amhello-tests.patch	\
   %D%/packages/patches/avahi-localstatedir.patch		\
+  %D%/packages/patches/avalon-toolkit-rdkit-fixes.patch		\
   %D%/packages/patches/avidemux-install-to-lib.patch		\
   %D%/packages/patches/awesome-reproducible-png.patch		\
   %D%/packages/patches/awesome-4.3-fno-common.patch		\
@@ -1061,7 +1065,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/converseen-hide-non-free-pointers.patch	\
   %D%/packages/patches/cool-retro-term-wctype.patch		\
   %D%/packages/patches/coreutils-gnulib-tests.patch		\
-  %D%/packages/patches/coq-fix-envvars.patch			\
   %D%/packages/patches/cppcheck-disable-char-signedness-test.patch	\
   %D%/packages/patches/cpuinfo-system-libraries.patch		\
   %D%/packages/patches/cpulimit-with-glib-2.32.patch		\
@@ -1516,6 +1519,9 @@ dist_patch_DATA =						\
   %D%/packages/patches/libcall-ui-make-it-installable.patch	\
   %D%/packages/patches/libftdi-fix-paths-when-FTDIPP-set.patch	\
   %D%/packages/patches/libgeotiff-fix-tests-with-proj-9.1.1.patch	\
+  %D%/packages/patches/libgeotiff-fix-tests-with-proj-9.3.0.patch	\
+  %D%/packages/patches/libgeotiff-fix-tests-with-proj-9.3.1.patch	\
+  %D%/packages/patches/libgeotiff-fix-tests-on-i386.patch	\
   %D%/packages/patches/libobjc2-unbundle-robin-map.patch	\
   %D%/packages/patches/librime-fix-build-with-gcc10.patch	\
   %D%/packages/patches/libvirt-add-install-prefix.patch	\
@@ -1734,10 +1740,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/nvi-db4.patch				\
   %D%/packages/patches/nyacc-binary-literals.patch		\
   %D%/packages/patches/obs-modules-location.patch		\
-  %D%/packages/patches/ocaml-dose3-add-unix-dependency.patch	\
-  %D%/packages/patches/ocaml-dose3-Fix-for-ocaml-4.06.patch	\
-  %D%/packages/patches/ocaml-dose3-dont-make-printconf.patch	\
-  %D%/packages/patches/ocaml-dose3-Install-mli-cmx-etc.patch	\
   %D%/packages/patches/ocaml-multiple-definitions.patch		\
   %D%/packages/patches/ocaml-4.07-dynamically-allocate-signal-stack.patch	\
   %D%/packages/patches/ocaml-4.09-dynamically-allocate-signal-stack.patch	\
@@ -2017,6 +2019,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/rw-igraph-0.10.patch			\
   %D%/packages/patches/rxvt-unicode-fix-cursor-position.patch	\
   %D%/packages/patches/s7-flint-3.patch                      	\
+  %D%/packages/patches/sajson-for-gemmi-numbers-as-strings.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	\
@@ -2053,7 +2056,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/source-highlight-gcc-compat.patch	\
   %D%/packages/patches/softhsm-fix-openssl3-tests.patch		\
   %D%/packages/patches/spectre-meltdown-checker-externalize-fwdb.patch \
-  %D%/packages/patches/spdlog-fix-tests.patch			\
   %D%/packages/patches/sphinxbase-fix-doxygen.patch		\
   %D%/packages/patches/sssd-system-directories.patch		\
   %D%/packages/patches/steghide-fixes.patch			\

gnu/packages/admin.scm

@@ -130,6 +130,8 @@
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
+  #:use-module (gnu packages golang-compression)
   #:use-module (gnu packages groff)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages guile)
@@ -4907,6 +4909,33 @@ It can mount all local file systems supported by @command{mount}, as well as
 LUKS volumes encrypted with the user's log-in password.")
     (license (list license:gpl2+ license:lgpl2.1+))))
 
+(define-public pam-uaccess
+  (let ((commit "54fbf043c63cc500b4850b0b4a12ea14078f2b53")
+        (revision "0"))
+    (package
+      (name "pam-uaccess")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://git.sr.ht/~kennylevinsen/pam_uaccess")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "08068cw4nvcanym8b5dyccnnb3qc3f09pbvi6fcfiz227yx73npc"))))
+      (build-system meson-build-system)
+      (native-inputs (list pkg-config))
+      (inputs (list acl eudev linux-pam))
+      (home-page "https://git.sr.ht/~kennylevinsen/pam_uaccess")
+      (synopsis
+       "PAM module that grants access to devices tagged @code{uaccess} in udev")
+      (description
+       "@code{pam_uaccess} is a PAM module that grants access to devices tagged
+@code{uaccess} in udev for the duration of the users' session, replacing
+elogind's uaccess feature.")
+      (license license:expat))))
+
 (define-public jc
   (package
     (name "jc")

gnu/packages/antivirus.scm

@@ -45,14 +45,14 @@
 (define-public clamav
   (package
     (name "clamav")
-    (version "0.103.8")
+    (version "0.103.11")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.clamav.net/downloads/production/"
                                   "clamav-" version ".tar.gz"))
               (sha256
                (base32
-                "0gwcikzfdswrdh5vhh3x4lx8w92476fmb7im7phnv4r7x5pdljbg"))
+                "04by1g3p6awhi3j1y6zpwzmasdnvjgi6lwm34l2gadlwgkdfpmv1"))
               (modules '((guix build utils)))
               (snippet
                '(begin

gnu/packages/astronomy.scm

@@ -13,6 +13,7 @@
 ;;; Copyright © 2023 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2023 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2024 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2024 Andy Tai <lichengtai@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -949,7 +950,7 @@ different kinds of input files.")
 (define-public gnuastro
   (package
     (name "gnuastro")
-    (version "0.21")
+    (version "0.22")
     (source
      (origin
        (method url-fetch)
@@ -957,7 +958,7 @@ different kinds of input files.")
                            version ".tar.lz"))
        (sha256
         (base32
-         "1zyk764pmfrsfj45gnc3qp4z1zfmgrv7kcsji2bxfzvs9inzzq4c"))))
+         "15rljx1mx9dyvni17qpj7y9gv086cvmjf9f5j34m1pbiyn989fqz"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags '("--disable-static")))

gnu/packages/audio.scm

@@ -6311,7 +6311,7 @@ and DSD streams.")
 (define-public qpwgraph
   (package
     (name "qpwgraph")
-    (version "0.6.0")
+    (version "0.6.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -6320,7 +6320,7 @@ and DSD streams.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "17jl347rwagdyx6pgnp83l1ffhlyfl0s4jf7ii2i1j3s1m9sz7y0"))))
+                "0185hxbwqxhjiyym0s7bmrm50f3p4bnvx92qqmgvg3zd7r1x8m8s"))))
     (build-system cmake-build-system)
     (arguments
      (list #:tests? #f))                ; no tests

gnu/packages/backup.scm

@@ -71,6 +71,7 @@
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
   #:use-module (gnu packages golang-crypto)
   #:use-module (gnu packages golang-web)
   #:use-module (gnu packages gperf)
@@ -1278,27 +1279,28 @@ backup.")
 (define-public disarchive
   (package
     (name "disarchive")
-    (version "0.5.0")
+    (version "0.6.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://files.ngyro.com/disarchive/"
                                   "disarchive-" version ".tar.gz"))
               (sha256
                (base32
-                "16sjplkn9nr7zhfrqll7l1m2b2j4hg8k29p6bqjap9fkj6zpn2q2"))))
+                "1s4lyhhh1zsaxgn11hy2b1kdvnvpipii68wba0hwr471rd43m08k"))))
     (build-system gnu-build-system)
     (native-inputs
      (list autoconf
            automake
            pkg-config
            guile-3.0 ;for cross-compilation
+           guile-bzip2
            guile-gcrypt
            guile-lzma
            guile-quickcheck))
     (inputs
      (list guile-3.0 zlib))
     (propagated-inputs
-     (list guile-gcrypt guile-lzma))
+     (list guile-bzip2 guile-gcrypt guile-lzma))
     (home-page "https://ngyro.com/software/disarchive.html")
     (synopsis "Software archive disassembler")
     (description "Disarchive can disassemble software archives into data

gnu/packages/bioconductor.scm

@@ -2388,13 +2388,13 @@ yeast are also included.")
 (define-public r-curatedtcgadata
   (package
     (name "r-curatedtcgadata")
-    (version "1.24.0")
+    (version "1.24.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "curatedTCGAData" version 'experiment))
        (sha256
-        (base32 "0kfdzc5arzsrdaps7b3r718yawpv1x7wms5jp90j8cxpn0hz07az"))))
+        (base32 "0hr66p8l54nzfsizcxxd2njy44xnia607wvfhrgv46f3f8s95z02"))))
     (properties
      `((upstream-name . "curatedTCGAData")))
     (build-system r-build-system)
@@ -3356,13 +3356,13 @@ these biases and construct statistically consistent estimators.")
 (define-public r-animalcules
   (package
     (name "r-animalcules")
-    (version "1.18.2")
+    (version "1.18.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "animalcules" version))
               (sha256
                (base32
-                "1q0ca3pagqzj12kah79jg4py3ibz7qsdl975r2mxhphqwj76gnh8"))))
+                "0j8fa5cr6s20bgw7v62by61q7nk8iw64v4wshwbd2cc36gr7s3c8"))))
     (properties `((upstream-name . "animalcules")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6276,23 +6276,22 @@ Michailidis G (2016) <doi:10.1093/bioinformatics/btw410>.")
 (define-public r-nmf
   (package
     (name "r-nmf")
-    (version "0.26")
+    (version "0.27")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "NMF" version))
        (sha256
         (base32
-         "1h1fpjnj6vjvi9ygxpfxs8k5bhly0aflr54zj88khgzkylp5ci4d"))))
+         "1y9y7xpfd9y8j5b8s2x5g61455ilpgqpdhrirpz58xjarbph4hxg"))))
     (properties `((upstream-name . "NMF")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-cluster
+     (list r-biobase
-           r-codetools
-           r-biobase
            r-biocmanager
-           r-bigmemory ; suggested
+           r-bigmemory ;suggested
-           r-synchronicity ; suggested
+           r-cluster
+           r-codetools
            r-colorspace
            r-digest
            r-doparallel
@@ -6303,7 +6302,8 @@ Michailidis G (2016) <doi:10.1093/bioinformatics/btw410>.")
            r-registry
            r-reshape2
            r-rngtools
-           r-stringr))
+           r-stringr
+           r-synchronicity)) ;suggested
     (native-inputs
      (list r-knitr))
     (home-page "https://renozao.github.io/NMF")
@@ -6970,13 +6970,13 @@ effort and encourages consistency.")
 (define-public r-bsgenome
   (package
     (name "r-bsgenome")
-    (version "1.70.1")
+    (version "1.70.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BSgenome" version))
               (sha256
                (base32
-                "1bdrh1kp7ihnlyvgdvwdzly69l9zy5rr09gizm0l59zy4kh59nih"))))
+                "02qrqg7lfisj44gvlfn1gkhxxjqdh11q28inxggfpcda9b67j61d"))))
     (properties
      `((upstream-name . "BSgenome")))
     (build-system r-build-system)
@@ -7479,13 +7479,13 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
 (define-public r-dittoseq
   (package
     (name "r-dittoseq")
-    (version "1.14.0")
+    (version "1.14.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "dittoSeq" version))
               (sha256
                (base32
-                "17ks6bbhv8iw8grzlkibgqmwggrqp5hikg1p49m4a6b6bayillv2"))))
+                "0qyiq6azknjqim0hjy5xw5gvs5jyczx29vcs95dwsfk92sygdps0"))))
     (properties `((upstream-name . "dittoSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7881,13 +7881,13 @@ genomic intervals.  In addition, it can use BAM or BigWig files as input.")
 (define-public r-genomeinfodb
   (package
     (name "r-genomeinfodb")
-    (version "1.38.5")
+    (version "1.38.6")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomeInfoDb" version))
               (sha256
                (base32
-                "17w5zrvpk2x0sc55xfkbn9krphg4aszmvwmj1qfsf1bdrazfpwic"))))
+                "0z8wkv5jhx8wr6idnakm26lhhk4ssj6ivbb7hfbzhkajcbnnf7mq"))))
     (properties
      `((upstream-name . "GenomeInfoDb")))
     (build-system r-build-system)
@@ -10126,13 +10126,13 @@ the graph algorithms contained in the Boost library.")
 (define-public r-rcas
   (package
     (name "r-rcas")
-    (version "1.28.2")
+    (version "1.28.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "RCAS" version))
               (sha256
                (base32
-                "19ildsck3g8v4w0g2f473sb8hyhn4avprdi78fim0prva5f9nqnv"))))
+                "1d9icr17xwdmgm6b8ihrwxsg1fp342c2p9f8yqdjm2y52z88gmpd"))))
     (properties `((upstream-name . "RCAS")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10148,7 +10148,6 @@ the graph algorithms contained in the Boost library.")
            r-genomicfeatures
            r-genomicranges
            r-ggplot2
-           r-ggseqlogo
            r-gprofiler2
            r-iranges
            r-knitr
@@ -10162,7 +10161,7 @@ the graph algorithms contained in the Boost library.")
            r-rsqlite
            r-rtracklayer
            r-s4vectors
-           pandoc))
+           r-seqlogo))
     (native-inputs
      (list r-knitr))
     (synopsis "RNA-centric annotation system")
@@ -11475,14 +11474,14 @@ able to deal also with novel and case specific events.")
 (define-public r-trajectoryutils
   (package
     (name "r-trajectoryutils")
-    (version "1.10.0")
+    (version "1.10.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "TrajectoryUtils" version))
        (sha256
         (base32
-         "0pqdl0v16q90ffxla34rp07mq0if1q9izpbimfnq0rx7633mk95v"))))
+         "178v5r0nck9ils5k7hj92x7z1xk5zq6zyc78wqnz7s3shbnq9ld7"))))
     (properties
      `((upstream-name . "TrajectoryUtils")))
     (build-system r-build-system)
@@ -13533,13 +13532,13 @@ information.")
 (define-public r-glmgampoi
   (package
     (name "r-glmgampoi")
-    (version "1.14.0")
+    (version "1.14.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "glmGamPoi" version))
               (sha256
                (base32
-                "1qc3f1spzkcjk95b07jpxgrjiwmlamwwx6mlhml4lgzy5qby7dpw"))))
+                "1swbp560ss5sksf1m10c6md4b81yc9qwa6in64j4zzksmrn9jn2d"))))
     (properties `((upstream-name . "glmGamPoi")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16600,14 +16599,14 @@ footprints.")
 (define-public r-gofuncr
   (package
     (name "r-gofuncr")
-    (version "1.22.0")
+    (version "1.22.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOfuncR" version))
        (sha256
         (base32
-         "1baa3aabkhmwq66xkzf4jk5nz85kkx1ks0mqc91s2ra9916wj6cd"))))
+         "004483q584530mh5nb28ppa8wllkd639n9yyw309acs2s4rc7saa"))))
     (properties `((upstream-name . "GOfuncR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -19897,14 +19896,14 @@ gene expression.")
 (define-public r-bgx
   (package
     (name "r-bgx")
-    (version "1.68.0")
+    (version "1.68.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bgx" version))
        (sha256
         (base32
-         "0v85i0lwmxq5yq9ygfzljgy8fsflqq1p53rq8aasnndd6gsm8ld2"))))
+         "1a3hq2i1mxf6dpkk82b6y88q5fcjbqpdcxqplkfp5d2slzsqc3jp"))))
     (properties `((upstream-name . "bgx")))
     (build-system r-build-system)
     (arguments
@@ -20938,14 +20937,14 @@ analytics on packages.")
 (define-public r-biocset
   (package
     (name "r-biocset")
-    (version "1.16.0")
+    (version "1.16.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocSet" version))
        (sha256
         (base32
-         "0sk4kmvl86xm85dqaf8gvii0qavyycyn2qp0v6dmfcjqai528v2x"))))
+         "1qmi6b0hrfzj7ixcbxlsxyy3qg7d2qrq8jcjrjrgfyrgcfws46qd"))))
     (properties `((upstream-name . "BiocSet")))
     (build-system r-build-system)
     (propagated-inputs
@@ -21564,14 +21563,14 @@ block processing.")
 (define-public r-rhdf5lib
   (package
     (name "r-rhdf5lib")
-    (version "1.24.1")
+    (version "1.24.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhdf5lib" version))
        (sha256
         (base32
-         "0lb5dkzfnfvxwrk8s9vzfjp8ab1sbr7b22jnzg41hgmpysi7dswh"))
+         "0b2g57dxvzmnq6dig4dz7cy8lpy3q7fih5q643i5xjcds2cj6lk5"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -21632,11 +21631,10 @@ block processing.")
                  (("cp \"\\$\\{SZIP_LIB\\}.*") "")
                  (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))))))))
     (propagated-inputs
-     (list hdf5-1.10 r-biocstyle r-stringr zlib))
+     (list hdf5-1.10 zlib))
     (native-inputs
      `(("hdf5-source" ,(package-source hdf5-1.10))
-       ("r-knitr" ,r-knitr)
+       ("r-knitr" ,r-knitr)))
-       ("r-rmarkdown" ,r-rmarkdown)))
     (home-page "https://bioconductor.org/packages/Rhdf5lib")
     (synopsis "HDF5 library as an R package")
     (description "This package provides C and C++ HDF5 libraries for use in R
@@ -23974,14 +23972,14 @@ using aCGH or sequencing.")
 (define-public r-bionero
   (package
     (name "r-bionero")
-    (version "1.10.0")
+    (version "1.10.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioNERO" version))
        (sha256
         (base32
-         "0pq5fiacb2x8l5jk3p6bnha9bcwg91grpklgx2nirrlwwr80gf2h"))))
+         "0dxn4pijr6gsqybl8x3ix1xydizg7gzfp72risk37zc5i4xk2lca"))))
     (properties `((upstream-name . "BioNERO")))
     (build-system r-build-system)
     (propagated-inputs

gnu/packages/bioinformatics.scm

@@ -93,7 +93,9 @@
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gd)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
   #:use-module (gnu packages golang-check)
+  #:use-module (gnu packages golang-compression)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages graph)
   #:use-module (gnu packages graphics)
@@ -2244,6 +2246,38 @@ parallel.  It uses Python's native multiprocessing framework to apply a user
 defined rule on an input file.")
     (license license:gpl3)))
 
+(define-public python-pdbfixer
+  (package
+    (name "python-pdbfixer")
+    (version "1.9")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/openmm/pdbfixer")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1zjhb19q5dclkwvzh8n29p31n1vzkhlmmzwqllimi89jsis1cx35"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      '(list "-k"
+             ;; These tests fail because they require internet access.
+             (string-append "not test_build_and_simulate.py"
+                            " and not test_cli.py"
+                            " and not test_mutate.py"))))
+    (propagated-inputs (list openmm python-numpy))
+    (native-inputs (list python-pytest))
+    (home-page "https://github.com/openmm/pdbfixer")
+    (synopsis "Application for fixing problems in Protein Data Bank")
+    (description
+     "PDBFixer is designed to rectify issues in Protein Data Bank files.
+Its intuitive interface simplifies the process of resolving problems
+encountered in PDB files prior to simulation tasks.")
+    (license license:expat)))
+
 (define-public python-peaks2utr
   (package
     (name "python-peaks2utr")

gnu/packages/browser-extensions.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2020, 2021 Marius Bakke <marius@gnu.org>
 ;;; Copyright © 2023 Nicolas Graves <ngraves@ngraves.fr>
-;;; Copyright © 2023 Clément Lassieur <clement@lassieur.org>
+;;; Copyright © 2023, 2024 Clément Lassieur <clement@lassieur.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -58,7 +58,7 @@ supported content to the Kodi media center.")
   ;; Arbitrary commit of branch master,
   ;; Update when updating uBlockOrigin.
   (let* ((name "ublock-main-assets")
-         (commit "76bd7cb53036a36f7e7df5ee9173f588ba8aa966")
+         (commit "0cb71ec86524082c463d2fd2e18ecdea04fe335c")
          (revision "1")
          (version (git-version "0" revision commit)))
     (origin
@@ -68,13 +68,13 @@ supported content to the Kodi media center.")
             (commit commit)))
       (file-name (git-file-name name version))
       (sha256
-       (base32 "1kdzvflr1yxykyva5vsjqr0p2ik1200xbhxwpl3cx2jsiv8l95sk")))))
+       (base32 "1rsf7sznlnv12i7jx1b492whwqpkhkqy2ny3m04fbbv5x31gqp93")))))
 
 (define ublock-prod-assets
   ;; Arbitrary commit of branch gh-pages,
   ;; Update when updating uBlockOrigin.
   (let* ((name "ublock-prod-assets")
-         (commit "a379a168fc149ffbd6d10cd0700d4ab4801e57f2")
+         (commit "21c07155353d7ecca2ffdc9e786f252a8cf00935")
          (revision "1")
          (version (git-version "0" revision commit)))
     (origin
@@ -84,12 +84,12 @@ supported content to the Kodi media center.")
             (commit commit)))
       (file-name (git-file-name name version))
       (sha256
-       (base32 "0syf3kbhvsbn5xka5knpclxby2kp92my1w7ixvf5fs9n08ylcip1")))))
+       (base32 "0lwhvpvsf5p20c678qkmj5zy7hy33hl16sqpnp5gz00hbrdx1ddk")))))
 
 (define ublock-origin
   (package
     (name "ublock-origin")
-    (version "1.54.0")
+    (version "1.55.0")
     (home-page "https://github.com/gorhill/uBlock")
     (source (origin
               (method git-fetch)
@@ -99,7 +99,7 @@ supported content to the Kodi media center.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1yacqpf9z8lprwsj194bhlp2ba9ywzbagd6lwxj3h6g405s7zp2k"))))
+                "1cd03l78w0xzkyv5588kac1r5k741vdr3d7ircv50l349qp4sjnm"))))
     (build-system gnu-build-system)
     (outputs '("xpi" "firefox" "chromium"))
     (properties '((addon-id . "uBlock0@raymondhill.net")))

gnu/packages/c.scm

@@ -20,7 +20,7 @@
 ;;; Copyright © 2022 Antero Mejr <antero@mailbox.org>
 ;;; Copyright © 2023 zamfofex <zamfofex@twdb.moe>
 ;;; Copyright © 2023 Foundation Devices, Inc. <hello@foundationdevices.com>
-;;; Copyright © 2023 David Elsing <david.elsing@posteo.net>
+;;; Copyright © 2023, 2024 David Elsing <david.elsing@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1349,7 +1349,7 @@ performance concurrent systems developed in C99+.")
 (define-public tinydir
   (package
     (name "tinydir")
-    (version "1.2.5")
+    (version "1.2.6")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1358,7 +1358,7 @@ performance concurrent systems developed in C99+.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1nprgdfx4i8wzc1idw6chan4fjfa75b5ll8kghdc0q2278pny259"))
+                "143n6yabznxk032gv5g2k8glf0kzicarg9cx0714zsbfmzj8lr07"))
               (patches (search-patches "tinydir-fix-cbehave-test.patch"))
               (modules '((guix build utils)))
               (snippet '(delete-file-recursively "tests/cbehave"))))

gnu/packages/check.scm

@@ -77,6 +77,7 @@
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages guile-xyz)

gnu/packages/chemistry.scm

@@ -6,7 +6,7 @@
 ;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
 ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
 ;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2022, 2023 David Elsing <david.elsing@posteo.net>
+;;; Copyright © 2022, 2023, 2024 David Elsing <david.elsing@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -589,7 +589,7 @@ your colleagues, or to generate pre-rendered animations.")
 (define-public gemmi
   (package
     (name "gemmi")
-    (version "0.5.7")
+    (version "0.6.4")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -598,7 +598,7 @@ your colleagues, or to generate pre-rendered animations.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "00km5q726bslrw7xbfwb3f3mrsk19qbimfnl3hvr4wi1y3z8i18a"))
+                "0wciqqswc4p4v4kglfv36gnvyyimqn4lnywdzd0pgrjn443i860y"))
               (patches
                (search-patches "gemmi-fix-sajson-types.patch"
                                "gemmi-fix-pegtl-usage.patch"))
@@ -625,7 +625,7 @@ your colleagues, or to generate pre-rendered animations.")
       #~(modify-phases %standard-phases
           (add-after 'unpack 'patch-includes
             (lambda _
-              (substitute* (list "include/gemmi/sprintf.hpp"
+              (substitute* (list "src/sprintf.cpp"
                                  "include/gemmi/dirwalk.hpp"
                                  "include/gemmi/cif.hpp"
                                  "include/gemmi/json.hpp"
@@ -708,7 +708,12 @@ It can be used for working with
       #~(list "--enable-check"
               "--enable-parser-generator"
               "CXXFLAGS=-std=c++17"
-              "--enable-doxygen")
+              "--enable-doxygen"
+              ;; Some tests rely on replacing malloc with a wrapper which
+              ;; fails in a controlled way, but this does not work if the call
+              ;; is replaced. This was fixed upstream, remove once there is a
+              ;; new release.
+              "CFLAGS=-fno-builtin-malloc")
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'remove-libc++-linking
@@ -722,7 +727,7 @@ It can be used for working with
                 (("libfreesasa\\.a") "libfreesasa.la")
                 (("freesasa_LDADD \\+= libfreesasa\\.la" prev)
                  (string-append prev "\nlibfreesasa_la_LIBADD"
-                                " = -ljson-c ${libxml2_LIBS}\n"))
+                                " = -ljson-c -lgemmi_cpp ${libxml2_LIBS}\n"))
                 (("_a_SOURCES") "_la_SOURCES"))
               (substitute* "configure.ac"
                 (("AC_PROG_INSTALL" inst)
@@ -765,7 +770,7 @@ of the algorithms, the calculations give identical results.")
 (define-public maeparser
   (package
     (name "maeparser")
-    (version "1.3.0")
+    (version "1.3.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -774,7 +779,7 @@ of the algorithms, the calculations give identical results.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1yv4y5hn49fhylziigsg922bb244lb57p69r7vg9q899zd3l5b7l"))))
+                "0mr5glg4br04ql5grby8yqni9fqq1l1cc75wyc159a1b9lwr7q7r"))))
     (build-system cmake-build-system)
     (inputs (list boost zlib))
     (home-page "https://github.com/schrodinger/maeparser")
@@ -785,7 +790,7 @@ of the algorithms, the calculations give identical results.")
 (define-public coordgenlibs
   (package
     (name "coordgenlibs")
-    (version "3.0.1")
+    (version "3.0.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -794,7 +799,7 @@ of the algorithms, the calculations give identical results.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0d09x3v38i9y184bml020bq7xizdrdwng38qmdxlplzfhqkjdidv"))))
+                "1wjaxwaihjy9xm5ys23f5abl50zcar1h9pww5ajdkgygsqy0bavi"))))
     (build-system cmake-build-system)
     (arguments
      (list
@@ -812,7 +817,7 @@ emphasis on quality rather than speed.")
 (define-public yaehmop
   (package
     (name "yaehmop")
-    (version "2022.09.1")
+    (version "2023.03.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -821,7 +826,7 @@ emphasis on quality rather than speed.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1x0d75m1hgdb411fiv7c5bwq1n4y0swrll0gigh8v5c73kjxrja0"))
+                "18xnxqn8i7vswy3iffapfh9q2iimpnd23ps45hn4xxbs6dqgzprb"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -917,90 +922,67 @@ calculations and analyzing the results.")
 (define-public avalon-toolkit
   (package
     (name "avalon-toolkit")
-    (version "1.2.0")
+    (version "2.0.5a")
-    (source
+    (source (origin
-     (origin
+              (method git-fetch)
-       (method url-fetch)
+              (uri (git-reference
-       (uri (string-append
+                    (url "https://github.com/rohdebe1/ava-formake")
-             "mirror://sourceforge/avalontoolkit/"
+                    (commit (string-append "AvalonToolkit_" version))))
-             "AvalonToolkit_" (substring version 0 3) "/AvalonToolkit_"
+              (file-name (git-file-name name version))
-             version ".source.tar"))
+              (sha256
-       (sha256
+               (base32
-        (base32
+                "1mfg40y5xc17sm59zdfc5sk22n9zm5zk0z1aw47chvl6hp465szk"))
-         "0rnnyy6axs2da7aa4q6l30ldavbk49v6l22llj1adn74h1i67bpv"))
+              (patches
-       (modules '((guix build utils) (ice-9 ftw)))
+               (search-patches "avalon-toolkit-rdkit-fixes.patch"))
-       (snippet
+              (modules '((guix build utils) (ice-9 ftw)))
-        #~(begin
+              (snippet
-            (delete-file-recursively "../SourceDistribution/java")))))
+               #~(begin
+                   (delete-file-recursively "src/main/java")
+                   (delete-file-recursively "src/test/target")))))
     (build-system gnu-build-system)
     (arguments
      (list
-      ;; There are no intended tests
+      ;; There is only one test, which is missing a file
       #:tests? #f
       #:phases
-      #~(let ((programs '("canonizer" "matchtest" "sketch" "smi2mol" "struchk")))
+      #~(modify-phases %standard-phases
-          (modify-phases %standard-phases
+          (delete 'configure)
-            (add-after 'unpack 'chdir
+          (replace 'build
-              (lambda _ (chdir "common")))
+            (lambda* (#:key parallel-build? #:allow-other-keys)
-            (delete 'configure)
+              (mkdir "build")
-            (add-before 'build 'dont-free-static-memory
+              (mkdir-p "target/executables")
-              (lambda _
+              (mkdir-p "target/libraries")
-                (substitute* "reaccsio.c"
+              (invoke "make" "programs" "-j"
-                  (("MyFree\\(.*tempdir\\)" m)
+                      (if parallel-build?
-                   (string-append "/* freeing memory from getenv is bad */"
+                          (number->string (parallel-job-count))
-                                  "// " m)))))
+                          "1"))))
-            ;; The makefile has incorrect compiler flags and is missing some
+          (replace 'install
-            ;; object files, so we build it ourselves.
+            (lambda _
-            (replace 'build
+              ;; Executables
-              (lambda _
+              (let ((programs '("canonizer" "matchtest" "smi2mol" "struchk")))
-                (for-each
-                 (lambda (part)
-                   (format #t "Compiling ~a.c ~~> ~a.o~%" part part)
-                   (invoke #$(cc-for-target) "-c" "-fPIC" "-O2"
-                           (string-append part ".c")
-                           "-o" (string-append part ".o")))
-                 (list "aacheck" "casutils" "denormal" "depictutil"
-                       "didepict" "fixcharges" "forio" "geometry"
-                       "graph" "hashcode" "layout" "local" "pattern"
-                       "perceive" "reaccsio" "rtutils" "set" "shortcut"
-                       "sketch" "ssmatch" "stereo" "symbol_lists"
-                       "symboltable" "utilities"))
-                (display "Building libavalontoolkit.so\n")
-                (apply invoke "gcc" "-fPIC" "-shared" "-lm"
-                       "-o" "libavalontoolkit.so" "canonizer.c" "smi2mol.c"
-                       "struchk.c" "patclean.c" (find-files "." "\\.o$"))
-                ;; patclean is not built here as there is an undeclared
-                ;; variable in main().
                 (for-each
                  (lambda (program)
-                   (display (string-append "Building " program "\n"))
+                   (install-file (string-append "target/executables/" program)
-                   (invoke "gcc" "-L." "-lavalontoolkit" "-lm" "-O2"
+                                 (string-append #$output "/bin")))
-                           (string-append "-Wl,-rpath=" #$output "/lib")
+                 programs))
-                           "-DMAIN" (string-append program ".c") "-o" program))
+              (for-each
-                 programs)))
+               (lambda (name)
-            (replace 'install
+                 (symlink (string-append #$output "/bin/smi2mol")
-              (lambda _
+                          (string-append #$output "/bin/" name)))
-                ;; Executables
+               '("mol2smi" "rdf2smi" "mol2tbl" "mol2sma" "smi2rdf"))
-                (for-each
+              ;; Library
-                 (lambda (program)
+              (install-file "target/libraries/libavalon_tools.a"
-                   (install-file program (string-append #$output "/bin")))
+                            (string-append #$output "/lib"))
-                 programs)
+              (install-file "target/libraries/libavalon4rdkit.a"
-                (for-each
+                            (string-append #$output "/lib"))
-                 (lambda (name)
+              (for-each
-                   (symlink (string-append #$output "/bin/smi2mol")
+               (lambda (file)
-                            (string-append #$output "/bin/" name)))
+                 (install-file file (string-append #$output
-                 '("mol2smi" "rdf2smi" "mol2tbl" "mol2sma" "smi2rdf"))
+                                                   "/include/avalontoolkit")))
-                ;; Library
+               (find-files "src/main/C/include" "\\.h$"))
-                (install-file "libavalontoolkit.so"
+              (install-file "license.txt"
-                              (string-append #$output "/lib"))
+                            (string-append #$output "/share/doc/"
-                (for-each
+                                           #$name "-" #$version "/")))))))
-                 (lambda (file)
-                   (install-file file (string-append #$output
-                                                    "/include/avalontoolkit")))
-                 (find-files "." "\\.h$"))
-                (install-file "../license.txt"
-                              (string-append #$output "/share/doc/"
-                                             #$name "-" #$version "/"))))))))
     (home-page "https://sourceforge.net/projects/avalontoolkit/")
     (synopsis "Tools for SMILES and MOL files and for structure fingerprinting")
     (description "This package contains a library and programs for
@@ -1091,7 +1073,7 @@ other ring topology descriptions.")
 (define-public rdkit
   (package
     (name "rdkit")
-    (version "2022.03.5")
+    (version "2023.09.4")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1102,7 +1084,7 @@ other ring topology descriptions.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "19idgilabh04cbr1qj6zgrgsfjm248mmfz6fsr0smrd68d0xnml9"))
+                "1lgcgijlzzwpfxndsdlx13npdfk7hcii11zg25cvpmzhbpn6vyn8"))
               (patches
                (search-patches "rdkit-unbundle-external-dependencies.patch"))
               (modules '((guix build utils)))
@@ -1201,7 +1183,10 @@ other ring topology descriptions.")
                             "substructLibraryTest" "pyFeatures"
                             "pythonTestDirML" "pythonTestDirChem"
                             ;; Catching Python exception fails
-                            "pyRanker") "|")
+                            "pyRanker"
+                            ;; Flaky test depending on floating point rounding
+                            "testConrec"
+                            ) "|")
                          ")")))))))))
     (inputs
      (list avalon-toolkit
@@ -1218,7 +1203,7 @@ other ring topology descriptions.")
     (native-inputs
      (list bison
            boost
-           catch2
+           catch2-3
            eigen
            flex
            freesasa
@@ -1232,4 +1217,8 @@ other ring topology descriptions.")
     (description "RDKit is a C++ and Python library for cheminformatics, which
 includes (among other things) the analysis and modification of molecules in 2D
 and 3D and descriptor generation for machine learning.")
+    ;; For 32 bit systems, there is a bug in Boost.Python:
+    ;; https://github.com/boostorg/python/issues/312. Additionally, several
+    ;; other test fail.
+    (supported-systems %64bit-supported-systems)
     (license license:bsd-3)))

gnu/packages/clifm.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2023 Rodion Goritskov <rodion.goritskov@gmail.com>
+;;; Copyright © 2023, 2024 Rodion Goritskov <rodion.goritskov@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -30,7 +30,7 @@
 (define-public clifm
   (package
     (name "clifm")
-    (version "1.15")
+    (version "1.16")
     (source
      (origin
        (method git-fetch)
@@ -39,7 +39,7 @@
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1r9pxlyn8jg0wmzbmbc71l42098lz5k32k6yid09yz6d0gaax7g1"))))
+        (base32 "1ddg6d4y4kfjk34j0fb7nij5vi5m69vv48knv7j1plbhzqk6qg5n"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags (list (string-append "CC="

gnu/packages/clojure.scm

@@ -203,14 +203,14 @@ designs.")
 (define-public clojure-tools
   (package
     (name "clojure-tools")
-    (version "1.11.1.1165")
+    (version "1.11.1.1200")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://download.clojure.org/install/clojure-tools-"
                            version
                            ".tar.gz"))
-       (sha256 (base32 "1lg97waqfcgzr3dz5426fbc4kqcsavpbqil2iyjm1dw3zrfa8ysi"))
+       (sha256 (base32 "075naxfiddi6jqr6rqiywwy91r188n5m8yfqcxddmds2vm5rrpnv"))
        ;; Remove AOT compiled JAR.  The other JAR only contains uncompiled
        ;; Clojure source code.
        (snippet

gnu/packages/compression.scm

@@ -998,14 +998,14 @@ byte-for-byte identical output.")
 (define-public pigz
   (package
     (name "pigz")
-    (version "2.7")
+    (version "2.8")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://zlib.net/pigz/"
                                   name "-" version ".tar.gz"))
               (sha256
                (base32
-                "01y7n7lafp6maqnp4jrmasawnv67najh1bd7gjrmv3d08h1ydjdl"))))
+                "1l0g2zaz05pl3pijsjd8lqxqj122di88rggpr5cvw3hz1r7jp1zb"))))
     (build-system gnu-build-system)
     (arguments
      (list #:make-flags

gnu/packages/configuration-management.scm

@@ -21,6 +21,7 @@
   #:use-module (guix build-system go)
   #:use-module (guix git-download)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
   #:use-module (gnu packages golang-web)
   #:use-module (gnu packages version-control)
   #:use-module (gnu packages textutils)

gnu/packages/coq.scm

@@ -31,6 +31,7 @@
   #:use-module (gnu packages base)
   #:use-module (gnu packages bison)
   #:use-module (gnu packages boost)
+  #:use-module (gnu packages compression)
   #:use-module (gnu packages emacs)
   #:use-module (gnu packages flex)
   #:use-module (gnu packages gawk)
@@ -51,10 +52,10 @@
   #:use-module (guix utils)
   #:use-module ((srfi srfi-1) #:hide (zip)))
 
-(define-public coq-core
+(define-public coq
   (package
-    (name "coq-core")
+    (name "coq")
-    (version "8.16.1")
+    (version "8.17.1")
     (source
      (origin
        (method git-fetch)
@@ -64,28 +65,35 @@
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0ljpqhh5lfsim29fcfp2xfcvm3j84pf1mb0gnpdr8vcqqw7mqwpf"))
+         "0gg6hizq0i08lk741b579cbswhy6qvkh6inc3d3i5a2af98psq63"))))
-       (patches (search-patches "coq-fix-envvars.patch"))))
     (native-search-paths
      (list (search-path-specification
             (variable "COQPATH")
-            (files (list "lib/ocaml/site-lib/coq/user-contrib"
+            (files (list "lib/coq/user-contrib")))))
-                         "lib/coq/user-contrib")))
-           (search-path-specification
-            (variable "COQLIBPATH")
-            (files (list "lib/ocaml/site-lib/coq")))
-           (search-path-specification
-            (variable "COQCORELIB")
-            (files (list "lib/ocaml/site-lib/coq-core"))
-            (separator #f))))
     (build-system dune-build-system)
+    (arguments
+     (list
+      #:package "coq-core,coq-stdlib,coq"
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'build 'configure
+            (lambda* (#:key outputs #:allow-other-keys)
+              (let* ((out (assoc-ref outputs "out"))
+                     (coqlib (string-append out "/lib/ocaml/site-lib/coq/")))
+                (invoke "./configure" "-prefix" out
+                        "-libdir" coqlib))))
+          (add-before 'build 'make-dunestrap
+            (lambda _ (invoke "make" "dunestrap")))
+          (replace 'install
+            (lambda* (#:key outputs #:allow-other-keys)
+              (let* ((out (assoc-ref outputs "out"))
+                     (libdir (string-append out "/lib/ocaml/site-lib")))
+                (invoke "dune" "install" "--prefix" out
+                        "--libdir" libdir "coq" "coq-core" "coq-stdlib")))))))
     (inputs
      (list gmp ocaml-zarith))
     (native-inputs
      (list ocaml-ounit2 which))
-    (arguments
-     `(#:package "coq-core"
-       #:test-target "."))
     (properties '((upstream-name . "coq"))) ; also for inherited packages
     (home-page "https://coq.inria.fr")
     (synopsis "Proof assistant for higher-order logic")
@@ -97,39 +105,6 @@ It is developed using Objective Caml and Camlp5.")
     ;; Some of the documentation is distributed under opl1.0+.
     (license (list license:lgpl2.1 license:opl1.0+))))
 
-(define-public coq-stdlib
-  (package
-    (inherit coq-core)
-    (name "coq-stdlib")
-    (arguments
-     `(#:package "coq-stdlib"
-       #:test-target "."
-       #:phases
-       (modify-phases %standard-phases
-         (add-before 'build 'fix-dune
-           (lambda _
-             (substitute* "user-contrib/Ltac2/dune"
-               (("coq-core.plugins.ltac2")
-                (string-join
-                  (map (lambda (plugin) (string-append "coq-core.plugins." plugin))
-                       '("ltac2" "number_string_notation" "tauto" "cc"
-                         "firstorder"))
-                  " "))))))))
-    (inputs
-     (list coq-core gmp ocaml-zarith))
-    (native-inputs '())))
-
-(define-public coq
-  (package
-    (inherit coq-core)
-    (name "coq")
-    (arguments
-     `(#:package "coq"
-       #:test-target "."))
-    (propagated-inputs
-     (list coq-core coq-stdlib))
-    (native-inputs '())))
-
 (define-public coq-ide-server
   (package
     (inherit coq)
@@ -148,7 +123,7 @@ It is developed using Objective Caml and Camlp5.")
      `(#:tests? #f
        #:package "coqide"))
     (propagated-inputs
-     (list coq coq-ide-server))
+     (list coq coq-ide-server zlib))
     (inputs
      (list lablgtk3 ocaml-lablgtk3-sourceview3))))
 
@@ -242,7 +217,7 @@ provers.")
 (define-public coq-flocq
   (package
     (name "coq-flocq")
-    (version "4.1.0")
+    (version "4.1.1")
     (source
      (origin
        (method git-fetch)
@@ -252,7 +227,7 @@ provers.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1yscj1120wch6myakaia03j11qji416v78ylx842d23hrbaqwmw5"))))
+         "01x38w58j95ba9679vpb5wv4bvfnrapd5dzjqlyz8k7i8a9sfqn0"))))
     (build-system gnu-build-system)
     (native-inputs
      (list autoconf automake ocaml which coq))
@@ -315,7 +290,7 @@ inside Coq.")
 (define-public coq-gappa
   (package
     (name "coq-gappa")
-    (version "1.5.2")
+    (version "1.5.3")
     (source
      (origin
        (method git-fetch)
@@ -325,7 +300,7 @@ inside Coq.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0l65ah81yj9vabgkwqh47c02qvscvl8nl60gqn1qrs47dx1pi80q"))))
+         "1dzkb2sfglhik2ymw8p65khl163xxjsaqji9agnnkvlk5r6589v6"))))
     (build-system gnu-build-system)
     (native-inputs
      (list autoconf
@@ -375,7 +350,7 @@ assistant.")
 (define-public coq-mathcomp
   (package
     (name "coq-mathcomp")
-    (version "1.15.0")
+    (version "1.17.0")
     (source
      (origin
        (method git-fetch)
@@ -384,7 +359,7 @@ assistant.")
              (commit (string-append "mathcomp-" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "158zl36zbvi5qx2nqbfnrg00jpgp6hjr5hmls7d8d0421ar6b67i"))))
+        (base32 "06i6kw5p2024n6h9mf8bvwn54il1a4z2h4qrgc8y0iq8hkvx4fnd"))))
     (build-system gnu-build-system)
     (native-inputs
      (list ocaml which coq))
@@ -412,7 +387,7 @@ part of the distribution.")
 (define-public coq-coquelicot
   (package
     (name "coq-coquelicot")
-    (version "3.2.0")
+    (version "3.4.0")
     (source
      (origin
        (method git-fetch)
@@ -422,7 +397,7 @@ part of the distribution.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "146s5y2xsc7wb43m1pq1n4p14hw99gqbzx0ic3a4naxq16v7cv4w"))))
+         "1f6zim6hnm6zrij964vas6rfbxh5p147qsxxmmbxm7gyb85hhy45"))))
     (build-system gnu-build-system)
     (native-inputs
      (list autoconf automake ocaml which coq))
@@ -495,7 +470,7 @@ provides BigN, BigZ, BigQ that used to be part of Coq standard library.")
 (define-public coq-interval
   (package
     (name "coq-interval")
-    (version "4.5.2")
+    (version "4.8.0")
     (source
      (origin
        (method git-fetch)
@@ -505,7 +480,7 @@ provides BigN, BigZ, BigQ that used to be part of Coq standard library.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "138vgb0bq6wkygrhkahjgb9spwpzc6x6kkycj2qnf5naxx1z412w"))))
+         "0m3icx77p99ld9qfl3xjq62q572pyi4m77i1kc3whvipvg7834rh"))))
     (build-system gnu-build-system)
     (native-inputs
      (list autoconf automake ocaml which coq))
@@ -542,35 +517,31 @@ Coq proof assistant.")
     (license license:cecill-c)))
 
 (define-public coq-autosubst
-  ;; Latest commit on that branch, where work on supporting coq 8.6 and
+  (package
-  ;; more recent versions of coq happen.
+    (name "coq-autosubst")
-  (let ((branch "coq86-devel")
+    (version "1.8")
-        (commit "fa6ef30664511ffa659cbcf3c962715cbee03572"))
+    (source (origin
-    (package
+              (method git-fetch)
-      (name "coq-autosubst")
+              (uri (git-reference
-      (version (git-version "1" branch commit))
+                    (url "https://github.com/coq-community/autosubst")
-      (source (origin
+                    (commit (string-append "v" version))))
-                (method git-fetch)
+              (file-name (git-file-name name version))
-                (uri (git-reference
+              (sha256
-                      (url "git://github.com/uds-psl/autosubst")
+               (base32 "0qk72r6cqxwhqqkl2kmryhw365w3l2016qii1q1sk3md7zq46jcz"))))
-                      (commit commit)))
+    (build-system gnu-build-system)
-                (file-name (git-file-name name version))
+    (arguments
-                (sha256
+     `(#:tests? #f
-                 (base32 "1cl0bp96bk6lplbl7n5c703vd3gvbs5mvf2qrf8q333kkqd7jqq4"))))
-      (build-system gnu-build-system)
-      (arguments
-       `(#:tests? #f
        #:make-flags (list (string-append "COQLIBINSTALL="
                                          (assoc-ref %outputs "out")
                                          "/lib/coq/user-contrib"))
-         #:phases
+       #:phases
-         (modify-phases %standard-phases
+       (modify-phases %standard-phases
-           (delete 'configure))))
+         (delete 'configure))))
-      (native-inputs
+    (native-inputs
-       (list coq))
+     (list coq))
-      (home-page "https://www.ps.uni-saarland.de/autosubst/")
+    (home-page "https://www.ps.uni-saarland.de/autosubst/")
-      (synopsis "Coq library for parallel de Bruijn substitutions")
+    (synopsis "Coq library for parallel de Bruijn substitutions")
-      (description "Formalizing syntactic theories with variable binders is
+    (description "Formalizing syntactic theories with variable binders is
 not easy.  Autosubst is a library for the Coq proof assistant to
 automate this process.  Given an inductive definition of syntactic objects in
 de Bruijn representation augmented with binding annotations, Autosubst
@@ -581,21 +552,21 @@ usage of substitution lemmas unnecessary.  The tactic is based on our current
 work on a decision procedure for the equational theory of an extension of the
 sigma-calculus by Abadi et al.  The library is completely written in Coq and
 uses Ltac to synthesize the substitution operation.")
-      (license license:bsd-3))))
+    (license license:bsd-3)))
 
 (define-public coq-equations
   (package
     (name "coq-equations")
-    (version "1.3")
+    (version "1.3-8.17")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/mattam82/Coq-Equations")
-                    (commit (string-append "v" version "-8.16"))))
+                    (commit (string-append "v" version))))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "08f756vgdd1wklkarg0b93j4n5mhkqm5ixxrhyb23dcv2dwhc8yg"))))
+                "0g68h4c1ijpphixvl9wkd7sibds38v4236dpvvh194j5ii42vnn8"))))
     (build-system gnu-build-system)
     (native-inputs
      (list ocaml coq camlp5))
@@ -673,7 +644,7 @@ also provided in Coq, without associated proofs.")
 (define-public coq-stdpp
   (package
     (name "coq-stdpp")
-    (version "1.7.0")
+    (version "1.8.0")
     (synopsis "Alternative Coq standard library std++")
     (source (origin
               (method git-fetch)
@@ -683,7 +654,7 @@ also provided in Coq, without associated proofs.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0447wbzm23f9rl8byqf6vglasfn6c1wy6cxrrwagqjwsh3i5lx8y"))))
+                "0xawh3xkh76yhs689zw52k55cbzga2gyzl4g1a3pgg6yy420chjn"))))
     (build-system gnu-build-system)
     (inputs
      (list coq))
@@ -747,7 +718,7 @@ for goals involving set operations.
                                          "/lib/coq/user-contrib"))
        #:phases (modify-phases %standard-phases
                   (delete 'configure))))
-    (inputs (list coq coq-stdlib coq-mathcomp which))
+    (inputs (list coq coq coq-mathcomp which))
     (synopsis "Finite sets and finite types for coq-mathcomp")
     (description
      "This library is an extension of coq-mathcomp which supports finite sets
@@ -778,7 +749,7 @@ subsume notations for finite sets.")
        ;; by the packaged project in the future.
        #:tests? #f
        #:make-flags ,#~(list (string-append "COQBIN="
-                                            #$(this-package-input "coq-core")
+                                            #$(this-package-input "coq")
                                             "/bin/")
                              (string-append "COQMF_COQLIB="
                                             (assoc-ref %outputs "out")
@@ -788,7 +759,7 @@ subsume notations for finite sets.")
                                             "/lib/coq/user-contrib"))
        #:phases (modify-phases %standard-phases
                   (delete 'configure))))
-    (propagated-inputs (list coq coq-core coq-mathcomp which))
+    (propagated-inputs (list coq coq-mathcomp which))
     (home-page "https://math-comp.github.io/")
     (synopsis "Small library to do epsilon - N reasoning")
     (description

gnu/packages/cpp.scm

@@ -8,7 +8,7 @@
 ;;; Copyright © 2019 Jan Wielkiewicz <tona_kosmicznego_smiecia@interia.pl>
 ;;; Copyright © 2020, 2021 Nicolò Balzarotti <nicolo@nixo.xyz>
 ;;; Copyright © 2020 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2020, 2021, 2023 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2020, 2021, 2023, 2024 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2020 Brice Waegeneire <brice@waegenei.re>
 ;;; Copyright © 2020, 2021, 2022 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2020, 2022 Marius Bakke <marius@gnu.org>
@@ -29,7 +29,7 @@
 ;;; Copyright © 2022 muradm <mail@muradm.net>
 ;;; Copyright © 2022 Attila Lendvai <attila@lendvai.name>
 ;;; Copyright © 2022 Arun Isaac <arunisaac@systemreboot.net>
-;;; Copyright © 2022, 2023 David Elsing <david.elsing@posteo.net>
+;;; Copyright © 2022, 2023, 2024 David Elsing <david.elsing@posteo.net>
 ;;; Copyright © 2022, 2023 Zheng Junjie <873216071@qq.com>
 ;;; Copyright © 2022, 2023, 2024 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2022 Antero Mejr <antero@mailbox.org>
@@ -513,7 +513,17 @@ operating on batches.")
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags (list "-DHWY_SYSTEM_GTEST=on"
-                               "-DBUILD_SHARED_LIBS=ON")))
+                               "-DBUILD_SHARED_LIBS=ON")
+       ,@(if (string-prefix? "i686-linux" (or (%current-system)
+                                              (%current-target-system)))
+             '(#:phases
+               (modify-phases %standard-phases
+                 (add-after 'unpack 'really-skip-precision-tests
+                   (lambda _
+                     (substitute* "hwy/contrib/math/math_test.cc"
+                       (("Skipping math_test due to GCC issue with excess precision.*" m)
+                        (string-append m "return;\n")))))))
+             '())))
     (native-inputs
      (list googletest))
     (home-page "https://github.com/google/highway")
@@ -2442,7 +2452,7 @@ CRC32C algorithm, which is specified in RFC 3720, section 12.1.")
 (define-public fast-float
   (package
     (name "fast-float")
-    (version "3.5.1")
+    (version "6.0.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -2451,7 +2461,7 @@ CRC32C algorithm, which is specified in RFC 3720, section 12.1.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0z3rxxd0pwvw70dbnv63rm67biw829vdqf50y16isxm6g3sbrz8g"))))
+                "1xf4gbllha760cr0ri53zsja46dypj45lj070ijb5f78xavfd8f8"))))
     (build-system cmake-build-system)
     (arguments
      (list
@@ -2467,9 +2477,7 @@ CRC32C algorithm, which is specified in RFC 3720, section 12.1.")
                 (("if\\(NOT supplemental_test_files_POPULATED.*")
                  (string-append
                   "set(supplemental_test_files_BINARY_DIR "
-                  (search-input-directory (or native-inputs inputs)
+                  #$fast-float-test-files ")\nif(0)\n"))))))))
-                                          "data")
-                  ")\nif(0)\n"))))))))
     (native-inputs (list doctest fast-float-test-files))
     (home-page "https://github.com/fastfloat/fast_float")
     (synopsis "Floating point number parser for C++")

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, 2020-2023 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2018, 2020-2024 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>
@@ -119,13 +119,13 @@
 (define-public r-aer
   (package
     (name "r-aer")
-    (version "1.2-10")
+    (version "1.2-12")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "AER" version))
               (sha256
                (base32
-                "1p6vxr0220lim5i4gwsvphqrfd65zbs8h3qydz4gipca9asmy2k5"))))
+                "11pas7lglcw1h5649bgab13g8xlnx109pc2aqphwc3fdgvqv1ism"))))
     (properties `((upstream-name . "AER")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4418,13 +4418,13 @@ in systems and applications.")
 (define-public r-servr
   (package
     (name "r-servr")
-    (version "0.28")
+    (version "0.29")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "servr" version))
               (sha256
                (base32
-                "10nl6aal2kr0k1j7yfpggcxpjxby6z5hhc6wb4nkqhy2w5qi6g26"))))
+                "1zpwvqg9jpvrn8xl9yrlbd5mpxprdgw6v599d6f06rdgh2j537m3"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-httpuv r-jsonlite r-mime r-xfun))
@@ -6561,14 +6561,14 @@ functions and compiled functions callable by other packages.")
 (define-public r-rcppthread
   (package
     (name "r-rcppthread")
-    (version "2.1.6")
+    (version "2.1.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RcppThread" version))
        (sha256
         (base32
-         "1997ka0dd36d79fb4crqq0ar3bgzdv4mw5hd6v2pmq7555g0qiz9"))))
+         "1s5v4fa59gmjcd0cn7q7zy67ww9zwnly4apbgr87x9qkzgzbmpl8"))))
     (properties `((upstream-name . "RcppThread")))
     (build-system r-build-system)
     (native-inputs (list r-r-rsp))
@@ -6823,13 +6823,13 @@ graphics packages that comes with the base installation.")
 (define-public r-ctrdata
   (package
     (name "r-ctrdata")
-    (version "1.17.0")
+    (version "1.17.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "ctrdata" version))
               (sha256
                (base32
-                "0wx0922rlabjaiijh66sr940iawm38hcx1zpiyz9r8a2iscqxlwb"))))
+                "0vb6nxhms66p90lh8ky693k7hchi5fbxxf8lnjcj4vhc0c5ijxns"))))
     (properties `((upstream-name . "ctrdata")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7502,13 +7502,13 @@ provides an interactive R manager and worker environment.")
 (define-public r-rmumps
   (package
     (name "r-rmumps")
-    (version "5.2.1-26")
+    (version "5.2.1-27")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rmumps" version))
        (sha256
-        (base32 "16ii9yg20xkxhsqszay42s4cr29k74av5d9d1d28kmpw6cjh2r2c"))))
+        (base32 "08zvmbhjgcrlgdhfn8ssajy8vnwcyaw90zgc0v1ncn95z310gpl3"))))
     (properties `((upstream-name . "rmumps")))
     (build-system r-build-system)
     (inputs (list zlib))
@@ -7703,14 +7703,14 @@ software.")
 (define-public r-extremes
   (package
     (name "r-extremes")
-    (version "2.1-3")
+    (version "2.1-4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "extRemes" version))
        (sha256
         (base32
-         "0h1w177vz3z58vbqrfbiqapf9z2qsd7gcbv8fnbyn0i5akfz1k71"))))
+         "12mphdq9zi0r07x3gpj5dg4687hwnjx42d9a392rjbbsgvv2r96f"))))
     (properties `((upstream-name . "extRemes")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7951,14 +7951,14 @@ transportation problems.")
 (define-public r-limsolve
   (package
     (name "r-limsolve")
-    (version "1.5.7")
+    (version "1.5.7.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "limSolve" version))
        (sha256
         (base32
-         "1waqkkipks8h4h5lpn0xw0077hwpz963q42h7xv6f70p07zncxq4"))))
+         "14jvx0sjjdsm6fxvdck648h12sl4cmy8sgw8jx1744pmpcbm5555"))))
     (properties `((upstream-name . "limSolve")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8237,13 +8237,13 @@ contexts.")
 (define-public r-cvxr
   (package
     (name "r-cvxr")
-    (version "1.0-11")
+    (version "1.0-12")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "CVXR" version))
               (sha256
                (base32
-                "0alp1g4bszxqcrjbn54bz1zswg8y10372fwwlbi0jjazycw9cap9"))))
+                "1igzi231rkqi7pc5ak8b29a8x7fry0yqs8vg2m4i5ab9jdm8fsp7"))))
     (properties `((upstream-name . "CVXR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10306,13 +10306,13 @@ iVAT).")
 (define-public r-xfun
   (package
     (name "r-xfun")
-    (version "0.41")
+    (version "0.42")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "xfun" version))
        (sha256
-        (base32 "00ivgr557ja8l33lvawrivfhgj1xbjmdi4dj07zybwa1y6wc6x13"))))
+        (base32 "02kmlp5hzkcs35hwbvz06178i9rn96yfh93n6swzr89b47nzmfq7"))))
     (build-system r-build-system)
     (properties
      ;; knitr itself depends on xfun
@@ -11768,6 +11768,41 @@ point} (IP), @dfn{majorize and minimize} (MM), @dfn{coordinate descent} (CD),
 and @dfn{alternating direction method of multipliers algorithms} (ADMM).")
     (license license:gpl2+)))
 
+(define-public r-imifa
+  (package
+    (name "r-imifa")
+    (version "2.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "IMIFA" version))
+       (sha256
+        (base32 "08h53w1axvmvnd4z1nf5bsps5sr6g8a77q6pvg39ss7jcfqm800v"))))
+    (properties `((upstream-name . "IMIFA")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-matrixstats
+           r-mvnfast
+           r-mclust
+           r-rfast
+           r-slam
+           r-viridislite))
+    (native-inputs (list r-knitr))
+    (home-page "https://cran.r-project.org/package=IMIFA")
+    (synopsis
+     "Infinite mixtures of infinite factor analysers and related models")
+    (description
+     "This package provides flexible Bayesian estimation of @acronym{IMIFA,
+infinite mixtures of infinite factor analysers} and related models, for
+nonparametrically clustering high-dimensional data.  The IMIFA model conducts
+Bayesian nonparametric model-based clustering with factor analytic covariance
+structures without recourse to model selection criteria to choose the number of
+clusters or cluster-specific latent factors, mostly via efficient Gibbs updates.
+Model-specific diagnostic tools are also provided, as well as many options for
+plotting results, conducting posterior inference on parameters of interest,
+posterior predictive checking, and quantifying uncertainty.")
+    (license license:gpl3+)))
+
 (define-public r-import
   (package
     (name "r-import")
@@ -13477,16 +13512,17 @@ without rendering it again in shiny apps.")
 (define-public r-ggseqlogo
   (package
     (name "r-ggseqlogo")
-    (version "0.1")
+    (version "0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggseqlogo" version))
        (sha256
         (base32
-         "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
+         "1drncw73950dzjx3lyyfqrxm3rdbrp44n27sl4b17m9d0crdbgqw"))))
     (build-system r-build-system)
     (propagated-inputs (list r-ggplot2))
+    (native-inputs (list r-knitr))
     (home-page "https://github.com/omarwagih/ggseqlogo")
     (synopsis "ggplot2 extension for drawing genetic sequence logos")
     (description
@@ -14039,14 +14075,14 @@ references and Rd files.")
 (define-public r-officer
   (package
     (name "r-officer")
-    (version "0.6.3")
+    (version "0.6.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "officer" version))
        (sha256
         (base32
-         "0z3phawwxj4h1pwzw8lsl6pnypr77b329mg6r2qnzmj0j81585z5"))))
+         "1mhkb2k9l0fp7xxhx69h1cxyh8gnlpwr5rjiw25s7rp1czwmyjk5"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-openssl r-r6 r-ragg r-uuid r-xml2 r-zip))
@@ -14364,13 +14400,13 @@ tidyverse workflow.")
 (define-public r-nodbi
   (package
     (name "r-nodbi")
-    (version "0.10.0")
+    (version "0.10.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "nodbi" version))
               (sha256
                (base32
-                "11sq2avgc8607ibi4193iynjfr51l435zmvdj1izf2ci0ca04azw"))))
+                "180zydrq9wr53y0nd5v1z86f00v49m4xlam91ykc6jy4s7xvamz1"))))
     (properties `((upstream-name . "nodbi")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14478,14 +14514,14 @@ documents.")
 (define-public r-writexl
   (package
     (name "r-writexl")
-    (version "1.4.2")
+    (version "1.5.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "writexl" version))
        (sha256
         (base32
-         "09whcadnwqcshicbhv1vnvdai087yimmnz9lvc3rld5nn8z66xcg"))))
+         "1kkd17xw7giy1k2azw1xnagka7ihicp17bi7nzlm3gqay1cdqlz2"))))
     (build-system r-build-system)
     (inputs (list zlib))
     (home-page "https://github.com/ropensci/writexl")
@@ -16398,13 +16434,13 @@ handle data from simple random samples as well as complex surveys.")
 (define-public r-tarchetypes
   (package
     (name "r-tarchetypes")
-    (version "0.7.11")
+    (version "0.7.12")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "tarchetypes" version))
               (sha256
                (base32
-                "1iqrz27n8ndazx97ngqbz5yz5ppyimpbxam30zgdwnnzf963s5ym"))))
+                "0l5kk7a3p0pbqh9rrjz43aa4dgcfffcb3wwsl60bm9v48lzv7frv"))))
     (properties `((upstream-name . "tarchetypes")))
     (build-system r-build-system)
     (propagated-inputs (list r-digest
@@ -17170,14 +17206,14 @@ effects models and Bayesian models.")
 (define-public r-ggeffects
   (package
     (name "r-ggeffects")
-    (version "1.3.4")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggeffects" version))
        (sha256
         (base32
-         "0hxcal1rldi3295hy5n1nzad092gis1cxnjsbbhfrbj3z35aacbs"))))
+         "1r9mbfcanwh2f617fgxnz3gijgpcjxvwzvpd7z8dg30rcm3ajb5r"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-insight))
@@ -17911,6 +17947,30 @@ the interfaces between R and C++.")
 analysing multivariate abundance data in community ecology.")
     (license license:lgpl2.1+)))
 
+(define-public r-mvnfast
+  (package
+    (name "r-mvnfast")
+    (version "0.2.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "mvnfast" version))
+       (sha256
+        (base32 "1869xqq2wd7yw23q4ma5qawcnbdp7myafk6rdxazqymqak7f0wc8"))))
+    (properties `((upstream-name . "mvnfast")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-bh r-rcpp r-rcpparmadillo))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/mfasiolo/mvnfast/")
+    (synopsis "Fast multivariate normal and Student's t methods")
+    (description
+     "This package provides computationally efficient tools related to the
+multivariate normal and Student's t distributions.  The main functionalities
+are: simulating multivariate random vectors, evaluating multivariate normal or
+Student's t densities and Mahalanobis distances.  These tools are developed
+using C++ code and of the OpenMP API.")
+    (license license:gpl2+)))
+
 (define-public r-afex
   (package
     (name "r-afex")
@@ -18166,14 +18226,14 @@ This package provides an R interface.")
 (define-public r-rcpphnsw
   (package
     (name "r-rcpphnsw")
-    (version "0.5.0")
+    (version "0.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RcppHNSW" version))
        (sha256
         (base32
-         "0sb9g41lk2f7fj0hpg9qvyp6gbvwlcjpi9gxs3lh3xxfzrnap5w9"))))
+         "03sqzz1993jsjm5vpyd1n1fpsrdfrky6dpv7m9ialhs1m00fv9m5"))))
     (properties `((upstream-name . "RcppHNSW")))
     (build-system r-build-system)
     (propagated-inputs (list r-rcpp))
@@ -18355,14 +18415,14 @@ image formats, including PNG, Postscript, SVG, PGF.")
 (define-public r-multicool
   (package
     (name "r-multicool")
-    (version "1.0.0")
+    (version "1.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "multicool" version))
        (sha256
         (base32
-         "0gcic5w3z5yibq75j7jzjv3lmy04rfmxswmw60vxba4xsnbqxc2g"))))
+         "07vcyp7yd1rzlldxzpzrdgifnw88z0maq2dgsqc218vyplgxwwmx"))))
     (build-system r-build-system)
     (propagated-inputs (list r-rcpp))
     (home-page "https://cran.r-project.org/web/packages/multicool/")
@@ -19577,16 +19637,15 @@ Touzet and Varre (2007).")
 (define-public r-rnaturalearthdata
   (package
     (name "r-rnaturalearthdata")
-    (version "0.1.0")
+    (version "1.0.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "rnaturalearthdata" version))
               (sha256
                (base32
-                "1z32j5lz2lb8xgpkr73majw22k0b49iazj6jjc7j4w9k4zxxa102"))))
+                "0k8yzgpbf8d2jxxy9vzqfa3z3w4h3i9kp4rc811f4pspxbqzmzp1"))))
     (properties `((upstream-name . "rnaturalearthdata")))
     (build-system r-build-system)
-    (propagated-inputs (list r-sp))
     (home-page "https://github.com/ropenscilabs/rnaturalearthdata")
     (synopsis "World vector map data from Natural Earth")
     (description
@@ -21972,14 +22031,14 @@ numbers (e.g. concentrations).")
 (define-public r-cobs
   (package
     (name "r-cobs")
-    (version "1.3-5")
+    (version "1.3-7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "cobs" version))
        (sha256
         (base32
-         "04f6a6gp11p93j2k35mbrfqgjx5qsgi3dj1085a5v5s0z6l7vbkz"))))
+         "0gz6i8scvfkmg0z7rcqc422dm360xv5ygcxnj6yyvpcpdv7sdp9k"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-quantreg r-sparsem))
@@ -22607,13 +22666,13 @@ plotting functions are available for analyzing clustering results.")
 (define-public r-remacor
   (package
     (name "r-remacor")
-    (version "0.0.16")
+    (version "0.0.18")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "remaCor" version))
               (sha256
                (base32
-                "1xznj2y3qszw8s1fgbs8fiadg7c0gl3ml1blxmwixb32kr2cv5vq"))))
+                "0c8n2zj84m2z0vznx81qrspnyyj38imb73di4l2k0brr8jxgzr2p"))))
     (properties `((upstream-name . "remaCor")))
     (build-system r-build-system)
     (propagated-inputs
@@ -22709,14 +22768,14 @@ can be used with function approximation, eligibility traces (Singh & Sutton,
 (define-public r-lemon
   (package
     (name "r-lemon")
-    (version "0.4.7")
+    (version "0.4.9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lemon" version))
        (sha256
         (base32
-         "1r33n7bkfhjpyi23j7gsi387qvyazcy9b912dsd3vg2yqir8s26p"))))
+         "1yjam478s6sz1spggybb34akpmpgq8ybyrhzy3b1v9s1j81b6k87"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-ggplot2
@@ -23293,13 +23352,13 @@ or raster data cubes) are handled by package stars'.")
 (define-public r-spdep
   (package
     (name "r-spdep")
-    (version "1.3-1")
+    (version "1.3-3")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "spdep" version))
               (sha256
                (base32
-                "15jkx3f4c1255kidsqdq4gyi28r4jk3h46fm7jj114ag176jq1in"))
+                "06j26v0w33vyh5ilq1cn0rh8z0lrr3n0lxwxc7bsk2w524d3v6yw"))
               (snippet
                '(for-each delete-file '("inst/doc/CO69.html"
                                         "inst/doc/CO69.R"
@@ -23554,14 +23613,14 @@ include
 (define-public r-haplo-stats
   (package
     (name "r-haplo-stats")
-    (version "1.9.5")
+    (version "1.9.5.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "haplo.stats" version))
        (sha256
         (base32
-         "17h7nxpc5ggxwpc4j4cxf7n0qglc93vhwd4ljwa8ic33x3yab673"))))
+         "1fcnyglmz9ia6zpk0vvmjqiwxlpal58rksgb1yvrajqgylw3kbsy"))))
     (properties `((upstream-name . "haplo.stats")))
     (build-system r-build-system)
     (propagated-inputs
@@ -24683,14 +24742,14 @@ discriminant analysis for the purpose of classifying high dimensional data.")
 (define-public r-ggvis
   (package
     (name "r-ggvis")
-    (version "0.4.8")
+    (version "0.4.9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggvis" version))
        (sha256
         (base32
-         "0sm28s2zlr3rbp7qzpgin7d9axixn4kgi1apb5mw4mvsp6h80m1x"))
+         "0bx1bg19l8nfwzwhnn2jn0b0lwcb781l6v9k5zfsx44wg22d3fb9"))
        (snippet
         '(for-each delete-file
                    '("inst/www/lib/d3/d3.min.js"
@@ -25306,14 +25365,14 @@ matched.")
 (define-public r-ggnewscale
   (package
     (name "r-ggnewscale")
-    (version "0.4.9")
+    (version "0.4.10")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggnewscale" version))
        (sha256
         (base32
-         "1vy0i2gk57k06gzywy8hdhl2k9511c5mhy9dzvkzlagqihp5b8bh"))))
+         "1j8d512qhdlhfp3hb36d1dqlqlxs0i303mnn31xnq1adcwwibmlz"))))
     (properties `((upstream-name . "ggnewscale")))
     (build-system r-build-system)
     (propagated-inputs
@@ -26118,14 +26177,14 @@ annotated biological functions.")
 (define-public r-plot3d
   (package
     (name "r-plot3d")
-    (version "1.4")
+    (version "1.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "plot3D" version))
        (sha256
         (base32
-         "1h59zlsyzbjylaziwavppl9bjmnba4iiq34772y3dys6fqclajnh"))))
+         "1x6ian6hfkaih2aa11z92qlihqqf5wmpc9705dzigafx8i4gfvfv"))))
     (properties `((upstream-name . "plot3D")))
     (build-system r-build-system)
     (propagated-inputs (list r-misc3d))
@@ -27176,14 +27235,14 @@ in pipelines.")
 (define-public r-parameters
   (package
     (name "r-parameters")
-    (version "0.21.3")
+    (version "0.21.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "parameters" version))
        (sha256
         (base32
-         "091zpyq37v7xjicj4h4r4fqhrrc7d3hicgbdznsjn85sw4d7q595"))))
+         "0yxljycspmljj5s4i5knwyhxp29s616f7kg3xcwn0ip15kfg260v"))))
     (properties `((upstream-name . "parameters")))
     (build-system r-build-system)
     (propagated-inputs
@@ -28095,14 +28154,14 @@ Adibi et al. (2019) @url{doi:10.1101/651901}.")
 (define-public r-smpracticals
   (package
     (name "r-smpracticals")
-    (version "1.4-3")
+    (version "1.4-3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "SMPracticals" version))
        (sha256
         (base32
-         "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
+         "1xplp7ihy9ish7fqhc27bhvij9lk9w9mrs7lpdca38ppi4iiafi2"))))
     (properties `((upstream-name . "SMPracticals")))
     (build-system r-build-system)
     (propagated-inputs
@@ -30534,14 +30593,14 @@ these algorithms also detect anomalies (outliers).")
 (define-public r-idpmisc
   (package
     (name "r-idpmisc")
-    (version "1.1.20")
+    (version "1.1.21")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "IDPmisc" version))
        (sha256
         (base32
-         "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
+         "1308z4i2glr1260zjjymm19g3d7nk8djhdwdfbh7ipvkgsp9b2s7"))))
     (properties `((upstream-name . "IDPmisc")))
     (build-system r-build-system)
     (propagated-inputs
@@ -30736,14 +30795,14 @@ Francesca Mazzia (2012).")
 (define-public r-lim
   (package
     (name "r-lim")
-    (version "1.4.7")
+    (version "1.4.7.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "LIM" version))
        (sha256
         (base32
-         "0d9bgyd0mnag8wds993dsvlbpkhyakydlzwc3nghxzv2n8504hjj"))))
+         "1ygzj3mc01jfdn7y938gsnnbf358n0jpddkiyc1zmvjig37yz180"))))
     (properties `((upstream-name . "LIM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -31842,14 +31901,14 @@ fairly comprehensive overview.")
 (define-public r-lisreltor
   (package
     (name "r-lisreltor")
-    (version "0.1.5")
+    (version "0.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lisrelToR" version))
        (sha256
         (base32
-         "0i51v0x87277ly0kggdd594w6q4zq62b4n7xs9r25j08bzs82nfk"))))
+         "19xl85dkvjpdsmi6y8789zlyccwjf265alsd7985vbkqdzfvpgkb"))))
     (properties `((upstream-name . "lisrelToR")))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/package=lisrelToR")
@@ -33147,14 +33206,14 @@ is also implemented here.")
 (define-public r-aws
   (package
     (name "r-aws")
-    (version "2.5-3")
+    (version "2.5-5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "aws" version))
        (sha256
         (base32
-         "022igrvxlyi0ckl3c6chcm459kv213jxy5hrvc14m36yhn3xckhm"))))
+         "0nsc7fakwcppav2h2kys0j28ga2p2si4kbygfka955dmbiwv4z5j"))))
     (properties
      `((upstream-name . "aws")))
     (build-system r-build-system)
@@ -33474,27 +33533,19 @@ vignette for more information and examples.")
 (define-public r-distributional
   (package
     (name "r-distributional")
-    (version "0.3.2")
+    (version "0.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "distributional" version))
        (sha256
         (base32
-         "1y08s301mxz7c54lxa1j0zzbsrgphxv5hsyam3jswcw274rxd0y8"))))
+         "00p6427lw65py24qr9rlhj1wg4z5wgszgmbmbxbpjk7dkckz7d89"))))
     (properties
      `((upstream-name . "distributional")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-digest
+     (list r-generics r-lifecycle r-numderiv r-rlang r-vctrs))
-           r-farver
-           r-generics
-           r-ggplot2
-           r-lifecycle
-           r-numderiv
-           r-rlang
-           r-scales
-           r-vctrs))
     (home-page "https://pkg.mitchelloharawild.com/distributional/")
     (synopsis "Vectorized probability distributions")
     (description
@@ -33813,14 +33864,14 @@ counting and recursive k-means partitioning.")
 (define-public r-hardhat
   (package
     (name "r-hardhat")
-    (version "1.3.0")
+    (version "1.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "hardhat" version))
        (sha256
         (base32
-         "0bp83yw7j34iwir2f73ainic11cdz0q18m5v1kbx8vdsw84z17zy"))))
+         "0v0vvvyy075f0j9ppqkhys6w2k7zmfdg0v77l430582nhrvp99hf"))))
     (properties `((upstream-name . "hardhat")))
     (build-system r-build-system)
     (propagated-inputs
@@ -34329,13 +34380,13 @@ Kolmogorov-Smirnov, ANOVA) are also supported.")
 (define-public r-spatstat-model
   (package
     (name "r-spatstat-model")
-    (version "3.2-8")
+    (version "3.2-10")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "spatstat.model" version))
               (sha256
                (base32
-                "1x03fy921rq8dyr6jkpwnx7pf7fc5593mvnl8r1gz3sypnmp6p4d"))))
+                "0hl2pg5lhypqxlzrmf9sjp2m44g1yjbhnjff712x542vhwva889a"))))
     (properties `((upstream-name . "spatstat.model")))
     (build-system r-build-system)
     (propagated-inputs
@@ -34496,14 +34547,14 @@ user-level code from spatstat, except for the code for linear networks.")
 (define-public r-spatstat-linnet
   (package
     (name "r-spatstat-linnet")
-    (version "3.1-3")
+    (version "3.1-4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "spatstat.linnet" version))
        (sha256
         (base32
-         "1ybjl5ccp9r5ilbihwzk93zcm46pbpldn3nfbfpdw458xh894r3q"))))
+         "1inqirh58q19mvf4wvnhm31418xfzd1ysvcxwda3g11pv8jq2g3d"))))
     (properties
      `((upstream-name . "spatstat.linnet")))
     (build-system r-build-system)
@@ -36501,14 +36552,14 @@ designs.  Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
 (define-public r-seqminer
   (package
     (name "r-seqminer")
-    (version "9.3")
+    (version "9.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "seqminer" version))
        (sha256
         (base32
-         "07dig3ydybmi55qy1zpkxpw568midgc1bzdl3k36734yqnsp2sjs"))))
+         "0m9ysdq4ch4c2i3d86gd32rbi0v637djvr295wzzwgkflk66sz5c"))))
     (build-system r-build-system)
     (inputs
      (list zlib))

gnu/packages/crypto.scm

@@ -60,6 +60,7 @@
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages image)
   #:use-module (gnu packages kerberos)

gnu/packages/curl.scm

@@ -49,6 +49,7 @@
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages kerberos)
   #:use-module (gnu packages logging)

gnu/packages/databases.scm

@@ -107,6 +107,7 @@
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
   #:use-module (gnu packages golang-check)
   #:use-module (gnu packages golang-web)
   #:use-module (gnu packages gperf)

gnu/packages/debian.scm

@@ -2,6 +2,7 @@
 ;;; Copyright © 2018, 2020-2024 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2020 Marius Bakke <marius@gnu.org>
+;;; Copyright © 2023 Denis 'GNUtoo' Carikli <GNUtoo@cyberdimension.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -24,6 +25,7 @@
   #:use-module (guix git-download)
   #:use-module (guix gexp)
   #:use-module (guix packages)
+  #:use-module (guix build-system copy)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages autotools)
@@ -146,6 +148,29 @@ contains the archive keys used for that.")
     ;; "The keys in the keyrings don't fall under any copyright."
     (license license:public-domain)))
 
+(define-public trisquel-keyring
+  (package
+    (name "trisquel-keyring")
+    (version "2022.10.19")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "http://archive.trisquel.info/trisquel/"
+                    "pool/main/t/trisquel-keyring/trisquel-keyring_"
+                    version ".tar.gz"))
+              (sha256
+               (base32
+                "1qkqm3wb945i2izm47xni21hi3ad807bvl106r2mnwdxnjs4ij08"))))
+    (build-system copy-build-system)
+    (arguments
+     '(#:install-plan '(("keyrings/trisquel-archive-keyring.gpg"
+                         "share/keyrings/"))))
+    (home-page "http://archive.trisquel.info/trisquel/pool/main/t/trisquel-keyring")
+    (synopsis "GnuPG archive keys of the Trisquel archive")
+    (description "The Trisquel distribution signs its packages.  This package
+contains the archive keys used for that.")
+    (license license:gpl2+)))     ;; see debian/copyright
+
 (define-public ubuntu-keyring
   (package
     (name "ubuntu-keyring")
@@ -208,6 +233,7 @@ contains the archive keys used for that.")
            (add-after 'unpack 'patch-source
              (lambda* (#:key inputs outputs #:allow-other-keys)
                (let ((debian #$(this-package-input "debian-archive-keyring"))
+                     (trisquel #$(this-package-input "trisquel-keyring"))
                      (ubuntu #$(this-package-input "ubuntu-keyring")))
                  (substitute* "Makefile"
                    (("/usr") ""))
@@ -220,6 +246,11 @@ contains the archive keys used for that.")
                    (("/usr") debian))
                  (substitute* "scripts/gutsy"
                    (("/usr") ubuntu))
+                 (substitute* "scripts/robur"
+                   (("/usr/share/keyrings/trisquel-archive-keyring.gpg")
+                    (string-append
+                     trisquel
+                     "/share/keyrings/trisquel-archive-keyring.gpg")))
                  (substitute* "debootstrap"
                    (("=/usr") (string-append "=" #$output))
                    (("/usr/bin/dpkg") (search-input-file inputs "/bin/dpkg")))
@@ -227,6 +258,8 @@ contains the archive keys used for that.")
                  (substitute* (find-files "scripts")
                    (("keyring.*(debian-archive-keyring.gpg)"_ keyring)
                     (string-append "keyring " debian "/share/keyrings/" keyring))
+                   (("keyring.*(trisquel-archive-keyring.gpg)" _ keyring)
+                    (string-append "keyring " trisquel "/share/keyrings/" keyring))
                    (("keyring.*(ubuntu-archive-keyring.gpg)" _ keyring)
                     (string-append "keyring " ubuntu "/share/keyrings/" keyring)))
                  ;; Ensure PATH works both in guix and within the debian chroot
@@ -251,11 +284,14 @@ contains the archive keys used for that.")
          #:tests? #f))  ; no tests
     (inputs
      (list debian-archive-keyring
+           trisquel-keyring
            ubuntu-keyring
            bash-minimal
            dpkg
            tzdata
-
+           ;; Needed by dpkg-deb in extract_dpkg_deb_data for at least
+           ;; Trisquel 11 (aramo).
+           zstd
            ;; Called at run-time from various places, needs to be in PATH.
            gnupg
            wget))

gnu/packages/diffoscope.scm

@@ -74,7 +74,7 @@
 (define-public diffoscope
   (package
     (name "diffoscope")
-    (version "255")
+    (version "256")
     (source
      (origin
        (method git-fetch)
@@ -83,7 +83,7 @@
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "07mkmwp3ni2dh5w5q2vxkc588l5dabcly3jrd8ic62318si7d400"))))
+        (base32 "1sdg314a3hp2kv492130p8w7j8mlhymij7h2rndm4q7gqrshp6jf"))))
     (build-system python-build-system)
     (arguments
      (list

gnu/packages/disk.scm

@@ -69,6 +69,7 @@
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
   #:use-module (gnu packages graphics)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages guile)

gnu/packages/docker.scm

@@ -42,6 +42,7 @@
   #:use-module (gnu packages compression)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages networking)
   #:use-module (gnu packages pkg-config)

gnu/packages/education.scm

@@ -47,7 +47,9 @@
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
   #:use-module (gnu packages golang-check)
+  #:use-module (gnu packages golang-xyz)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages gstreamer)
   #:use-module (gnu packages image)

gnu/packages/elixir.scm

@@ -7,6 +7,8 @@
 ;;; Copyright © 2018 Nikita <nikita@n0.is>
 ;;; Copyright © 2021 Oskar Köök <oskar@maatriks.ee>
 ;;; Copyright © 2021 Cees de Groot <cg@evrl.com>
+;;; Copyright © 2024 Andrew Tropin <andrew@trop.in>
+;;; Copyright © 2024 Ivan Sokolov <ivan-p-sokolov@ya.ru>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -101,7 +103,18 @@
           (add-after 'install 'wrap-programs
             (lambda* (#:key inputs outputs #:allow-other-keys)
               (let* ((out (assoc-ref outputs "out"))
-                     (programs '("elixir" "elixirc" "iex" "mix")))
+                     (programs '("elixir" "elixirc" "iex")))
+                ;; mix can be sourced as an elixir script by other elixir
+                ;; program, for example `iex -S mix`, so we should not wrap
+                ;; mix into shell script.
+                (substitute* (string-append out "/bin/mix")
+                  (("Mix.start\\(\\)") "\
+~w[GUIX_ELIXIR_LIBS ERL_LIBS]
+|> Enum.map(&System.get_env/1)
+|> Enum.reject(&is_nil/1)
+|> Enum.join(\":\")
+|> case do \"\" -> :ok; erl_libs -> System.put_env(\"ERL_LIBS\", erl_libs) end
+Mix.start()"))
                 (for-each (lambda (program)
                             (wrap-program (string-append out "/bin/" program)
                               '("ERL_LIBS" prefix ("${GUIX_ELIXIR_LIBS}"))))

gnu/packages/emacs-xyz.scm

@@ -11018,8 +11018,8 @@ when the cursor enters a fragment and disappear when it leaves.")
 
 (define-public emacs-org-dailies
   ;; No tags or versions.
-  (let ((commit "64477d5c5cd92df72ba1375eeb149889d42371d7")
+  (let ((commit "58e58d4968ddb70312160def1c7c3c00382ef655")
-        (revision "0"))
+        (revision "1"))
     (package
       (name "emacs-org-dailies")
       (version (git-version "0" revision commit))
@@ -11031,9 +11031,8 @@ when the cursor enters a fragment and disappear when it leaves.")
                (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-          (base32 "1lxm2xr743c2a5wj82qpprcdfsspcw33ijyq5wfbhcv2kngm4yql"))))
+          (base32 "15xhpxkg2cn2fwaql99gnqcdl012g29lxn9fqb6s282mhr9yan7c"))))
       (build-system emacs-build-system)
-      (propagated-inputs (list emacs-dash))
       (home-page "https://git.sr.ht/~ngraves/org-dailies")
       (synopsis "Bare-bones daily journaling with Emacs")
       (description
@@ -26579,29 +26578,31 @@ autosuggestions with:
     (license license:gpl3+)))
 
 (define-public emacs-desktop-environment
-  (package
+  (let ((commit "bc1153aa619b12456304cca642424a0d8d2eb416")
-    (name "emacs-desktop-environment")
+        (revision "0"))
-    (version "0.5.0")
+    (package
-    (source
+      (name "emacs-desktop-environment")
-     (origin
+      (version (git-version "0.5.0" revision commit))
-       (method git-fetch)
+      (source
-       (uri (git-reference
+       (origin
-             (url "https://github.com/DamienCassou/desktop-environment")
+         (method git-fetch)
-             (commit (string-append "v" version))))
+         (uri (git-reference
-       (file-name (git-file-name name version))
+               (url "https://github.com/DamienCassou/desktop-environment")
-       (sha256
+               (commit commit)))
-        (base32
+         (file-name (git-file-name name version))
-         "03rl1z860jmirjrrg0xsjx0bqk73k043c8bz6049zhndh7pidri7"))))
+         (sha256
-    (build-system emacs-build-system)
+          (base32
-    (home-page "https://gitlab.petton.fr/DamienCassou/desktop-environment")
+           "0bslgm9rz7whk0ll21028dsl22wbd289cdc95qj8hhlk8m4hlp2h"))))
-    (synopsis "Control your GNU/Linux desktop environment from Emacs")
+      (build-system emacs-build-system)
-    (description
+      (home-page "https://gitlab.petton.fr/DamienCassou/desktop-environment")
-     "This package helps you control your GNU/Linux desktop from Emacs.
+      (synopsis "Control your GNU/Linux desktop environment from Emacs")
+      (description
+       "This package helps you control your GNU/Linux desktop from Emacs.
 With @code{desktop-environment}, you can control the brightness and volume as
 well as take screenshots and lock your screen.  The package depends on the
 availability of shell commands to do the hard work for us.  These commands can
 be changed by customizing the appropriate variables.")
-    (license license:gpl3+)))
+      (license license:gpl3+))))
 
 (define-public emacs-org-caldav
   (let ((commit "754989ae500b3f576bdb94fe2ef3059f12eaf7d7")) ;version bump
@@ -34530,11 +34531,11 @@ other @code{helm-type-file} sources such as @code{helm-locate}.")
     (license license:gpl3+)))
 
 (define-public emacs-telega-server
-  (let ((commit "304705fa007c3dae3c5d0c6dc66641ae783f0081")
+  (let ((commit "e8d9459ef725ed8fb60479b5fccadae1e4eac87a")
         (revision "0"))
     (package
       (name "emacs-telega-server")
-      (version (git-version "0.8.230" revision commit))
+      (version (git-version "0.8.240" revision commit))
       (source
        (origin
          (method git-fetch)
@@ -34542,7 +34543,7 @@ other @code{helm-type-file} sources such as @code{helm-locate}.")
                (url "https://github.com/zevlg/telega.el")
                (commit commit)))
          (sha256
-          (base32 "02yxjaxpf2f6pjg3ixw7jvx56x6lfh30mnsmiz1p2yi64kyllaan"))
+          (base32 "18f6i2w0iial2wi60vkqck30c0m4p2nj0bzd2x9p4il27dwv5hwq"))
          (file-name (git-file-name "emacs-telega" version))
          (patches
           (search-patches "emacs-telega-path-placeholder.patch"
@@ -39038,8 +39039,8 @@ latest Emacs.")
 
 (define-public emacs-flim-lb
   ;; No release since Nov 28, 2007.
-  (let ((commit "80b8121f05a5a0d7fcfe3e54085467a646dd2028")
+  (let ((commit "abdd2315006eb31476249223569808adb1c0f7b2")
-        (revision "137"))
+        (revision "142"))
     (package
       (name "emacs-flim-lb")
       (version (git-version "1.14.9" revision commit))
@@ -39051,7 +39052,7 @@ latest Emacs.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "02shd2mp9ywncn0wxgrijn0i8fa69kfx1y6nh5jjd64dyiczmskk"))))
+                  "1s21y0djlyiwmc1kz3dx19mdiq472ib07gdrw353imw5vmx3mp7d"))))
       (build-system emacs-build-system)
       (propagated-inputs (list emacs-apel-lb emacs-oauth2))
       (home-page "https://www.emacswiki.org/emacs/WanderLust")
@@ -39065,8 +39066,8 @@ Emacs.")
 
 (define-public emacs-semi-epg
   ;; No release since Dec 24, 2003.
-  (let ((commit "d15603b8eb791f2057b48071c262996ad7767505")
+  (let ((commit "9063a4485b148a767ea924f0e7cc78d3524ba256")
-        (revision "247"))
+        (revision "248"))
     (package
       (name "emacs-semi-epg")
       (version (git-version "1.14.6" revision commit))
@@ -39078,7 +39079,7 @@ Emacs.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "0cxrzgxflwgz9wsim84vrliwvkf53v242di4dvn2dfh65gccwqjx"))))
+                  "18km8jdxjcqnh378xxd7ivvvcxzrif8zpq9zgki9i7f0q8lsx677"))))
       (build-system emacs-build-system)
       (propagated-inputs (list emacs-flim-lb))
       (inputs (list emacs-bbdb-vcard))
@@ -39092,8 +39093,8 @@ EasyPG and latest Emacs.")
 
 (define-public emacs-wanderlust
   ;; No release since Jan 15, 2010.
-  (let ((commit "3e8cf26abd9c5c8e4fc611032e259ca930665641")
+  (let ((commit "9fd2c65e8d690625f35035a71e73f51f740dbe04")
-        (revision "803"))
+        (revision "818"))
     (package
       (name "emacs-wanderlust")
       (version (git-version "2.15.9" revision commit))
@@ -39114,7 +39115,7 @@ EasyPG and latest Emacs.")
                            (("package-user-dir") "NONE"))))
                 (sha256
                  (base32
-                  "0k9r3j7pcnvnnj0km8ggjdrf2nfgn1mfq7r7267bk3r3x92cvqh9"))))
+                  "034zrl54ql3ddaj5vl62bjzf2a5hvrq5gd9kynmyp0skgk8i6dr2"))))
       (build-system emacs-build-system)
       (arguments
        (list #:phases

gnu/packages/emulators.scm

@@ -14,7 +14,7 @@
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;; Copyright © 2020 Christopher Howard <christopher@librehacker.com>
 ;;; Copyright © 2021 Felipe Balbi <balbi@kernel.org>
-;;; Copyright © 2021 Felix Gruber <felgru@posteo.net>
+;;; Copyright © 2021, 2024 Felix Gruber <felgru@posteo.net>
 ;;; Copyright © 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net>
 ;;; Copyright © 2023 c4droid <c4droid@foxmail.com>
@@ -351,7 +351,7 @@ console.")
              libxi
              libxrandr
              lzo
-             mbedtls-apache
+             mbedtls-lts
              mesa
              miniupnpc
              openal
@@ -791,7 +791,7 @@ and Game Boy Color games.")
 (define-public sameboy
   (package
     (name "sameboy")
-    (version "0.15.8")
+    (version "0.16.2")
     (source
      (origin
        (method git-fetch)
@@ -800,7 +800,7 @@ and Game Boy Color games.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "11qz5lamwxgvlh4dc95xd4m8hrypjj3bvha51zg9l454hxlvw4j8"))))
+        (base32 "1ckx5dm57h7ncvfqqqb2mdl5dcmhkardcn78zv965h6w1yxg0ii8"))))
     (build-system gnu-build-system)
     (native-inputs
      (list rgbds pkg-config))
@@ -1433,7 +1433,7 @@ as RetroArch.")
 (define-public retroarch
   (package
     (name "retroarch")
-    (version "1.16.0.3")
+    (version "1.17.0")
     (source
      (origin
        (method git-fetch)
@@ -1442,7 +1442,7 @@ as RetroArch.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1nvvd78hx1s73nif7g02pqms29b9v072mxnld0vmsh78236qngq5"))))
+        (base32 "1mf511wh7kpj29vv7rgngamvmfs151n8j4dls7jbqasdj5hik3zi"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; no tests
@@ -1490,7 +1490,7 @@ as RetroArch.")
            libxml2
            libxrandr
            libxv
-           mbedtls-apache
+           mbedtls-lts
            mesa
            openal
            openssl

gnu/packages/file-systems.scm

@@ -12,7 +12,8 @@
 ;;; Copyright © 2021, 2023 Kaelyn Takata <kaelyn.alexi@protonmail.com>
 ;;; Copyright © 2022 Brian Cully <bjc@spork.org>
 ;;; Copyright © 2023 Aaron Covrig <aaron.covrig.us@ieee.org>
-;;;
+;;; Copyright © 2024 Ahmad Draidi <a.r.draidi@redscript.org>
+;;
 ;;; This file is part of GNU Guix.
 ;;;
 ;;; GNU Guix is free software; you can redistribute it and/or modify it
@@ -71,6 +72,7 @@
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
   #:use-module (gnu packages golang-check)
   #:use-module (gnu packages golang-crypto)
   #:use-module (gnu packages guile)
@@ -582,98 +584,98 @@ from a mounted file system.")
     (license license:gpl2+)))
 
 (define-public bcachefs-tools
-  (let ((commit "1e358401ecdf1963e5799de19ab69111e82e5ebc")
+  (package
-        (revision "0"))
+    (name "bcachefs-tools")
-    (package
+    (version "1.4.1")
-      (name "bcachefs-tools")
+    (source
-      (version (git-version "1.2" revision commit))
+     (origin
-      (source
+       (method git-fetch)
-       (origin
+       (uri (git-reference
-         (method git-fetch)
+             (url "https://evilpiepirate.org/git/bcachefs-tools.git")
-         (uri (git-reference
+             (commit (string-append "v" version))))
-               (url "https://evilpiepirate.org/git/bcachefs-tools.git")
+       (file-name (git-file-name name version))
-               (commit commit)))
+       (sha256
-         (file-name (git-file-name name version))
+        (base32 "0axwbckqrw1v3v50nzhpkvpyjbjwy3rq5bv23db84x3xia497apq"))))
-         (sha256
+    (build-system gnu-build-system)
-          (base32 "0bflgqb3q9jikyyrv6hywv6m1fapzzn874hlhf86pn6abxrlf5fa"))))
+    (arguments
-      (build-system gnu-build-system)
+     (list #:make-flags
-      (arguments
+           #~(list (string-append "VERSION=" #$version) ; ‘v…-nogit’ otherwise
-       (list #:make-flags
+                   (string-append "PREFIX=" #$output)
-             #~(list (string-append "VERSION=" #$version) ; ‘v…-nogit’ otherwise
+                   "INITRAMFS_DIR=$(PREFIX)/share/initramfs-tools"
-                     (string-append "PREFIX=" #$output)
+                   "PKGCONFIG_UDEVRULESDIR=$(PREFIX)/lib/udev/rules.d"
-                     "INITRAMFS_DIR=$(PREFIX)/share/initramfs-tools"
+                   (string-append "CC=" #$(cc-for-target))
-                     (string-append "CC=" #$(cc-for-target))
+                   (string-append "PKG_CONFIG=" #$(pkg-config-for-target))
-                     (string-append "PKG_CONFIG=" #$(pkg-config-for-target))
+                   ;; ‘This will be less of an option in the future, as more
-                     ;; ‘This will be less of an option in the future, as more
+                   ;; code gets rewritten in Rust.’
-                     ;; code gets rewritten in Rust.’
+                   "NO_RUST=better")
-                     "NO_RUST=better")
+           #:phases
-             #:phases
+           #~(modify-phases %standard-phases
-             #~(modify-phases %standard-phases
+               (delete 'configure)    ; no configure script
-                 (delete 'configure)    ; no configure script
+               (replace 'check
-                 (replace 'check
+                 ;; The test suite is moribund upstream (‘never been useful’),
-                   ;; The test suite is moribund upstream (‘never been useful’),
+                 ;; but let's keep running it as a sanity check until then.
-                   ;; but let's keep running it as a sanity check until then.
+                 (lambda* (#:key tests? make-flags #:allow-other-keys)
-                   (lambda* (#:key tests? make-flags #:allow-other-keys)
+                   (when tests?
-                     (when tests?
+                     ;; We must manually build the test_helper first.
-                       ;; We must manually build the test_helper first.
+                     (apply invoke "make" "tests" make-flags)
-                       (apply invoke "make" "tests" make-flags)
+                     (invoke (string-append
-                       (invoke (string-append
+                              #$(this-package-native-input "python-pytest")
-                                #$(this-package-native-input "python-pytest")
+                              "/bin/pytest") "-k"
-                                "/bin/pytest") "-k"
+                              ;; These fail (‘invalid argument’) on kernels
-                                ;; These fail (‘invalid argument’) on kernels
+                              ;; with a previous bcachefs version.
-                                ;; with a previous bcachefs version.
+                              (string-append "not test_format and "
-                                (string-append "not test_format and "
+                                             "not test_fsck and "
-                                               "not test_fsck and "
+                                             "not test_list and "
-                                               "not test_list and "
+                                             "not test_list_inodes and "
-                                               "not test_list_inodes and "
+                                             "not test_list_dirent")))))
-                                               "not test_list_dirent")))))
+               (add-after 'install 'promote-mount.bcachefs.sh
-                 (add-after 'install 'promote-mount.bcachefs.sh
+                 ;; The (optional) ‘mount.bcachefs’ requires rust:cargo.
-                   ;; The (optional) ‘mount.bcachefs’ requires rust:cargo.
+                 ;; This shell alternative does the job well enough for now.
-                   ;; This shell alternative does the job well enough for now.
+                 (lambda* (#:key inputs #:allow-other-keys)
-                   (lambda* (#:key inputs #:allow-other-keys)
+                   (define (whence file)
-                     (define (whence file)
+                     (dirname (search-input-file inputs file)))
-                       (dirname (search-input-file inputs file)))
+                   (let ((mount (string-append #$output
-                     (let ((mount (string-append #$output
+                                               "/sbin/mount.bcachefs")))
-                                                 "/sbin/mount.bcachefs")))
+                     (delete-file mount) ; symlink to ‘bcachefs’
-                       (delete-file mount) ; symlink to ‘bcachefs’
+                     (copy-file "mount.bcachefs.sh" mount)
-                       (copy-file "mount.bcachefs.sh" mount)
+                     ;; WRAP-SCRIPT causes bogus ‘Insufficient arguments’ errors.
-                       ;; WRAP-SCRIPT causes bogus ‘Insufficient arguments’ errors.
+                     (wrap-program mount
-                       (wrap-program mount
+                       `("PATH" ":" prefix
-                         `("PATH" ":" prefix
+                         ,(list (getcwd)
-                           ,(list (getcwd)
+                                (whence "bin/tail")
-                                  (whence "bin/tail")
+                                (whence "bin/awk")
-                                  (whence "bin/awk")
+                                (whence "bin/mount"))))))))))
-                                  (whence "bin/mount"))))))))))
+    (native-inputs
-      (native-inputs
+     (cons* pkg-config
-       (cons* pkg-config
+            ;; For generating documentation with rst2man.
-              ;; For generating documentation with rst2man.
+            python
-              python
+            python-docutils
-              python-docutils
+            ;; For tests.
-              ;; For tests.
+            python-pytest
-              python-pytest
+            (if (member (%current-system) (package-supported-systems valgrind))
-              (if (member (%current-system) (package-supported-systems valgrind))
+                (list valgrind)
-                  (list valgrind)
+                '())))
-                  '())))
+    (inputs
-      (inputs
+     (list eudev
-       (list eudev
+           keyutils
-             keyutils
+           libaio
-             libaio
+           libscrypt
-             libscrypt
+           libsodium
-             libsodium
+           liburcu
-             liburcu
+           `(,util-linux "lib")
-             `(,util-linux "lib")
+           lz4
-             lz4
+           zlib
-             zlib
+           `(,zstd "lib")
-             `(,zstd "lib")
 
-             ;; Only for mount.bcachefs.sh.
+           ;; Only for mount.bcachefs.sh.
-             coreutils-minimal
+           bash-minimal
-             gawk
+           coreutils-minimal
-             util-linux))
+           gawk
-      (home-page "https://bcachefs.org/")
+           util-linux))
-      (synopsis "Tools to create and manage bcachefs file systems")
+    (home-page "https://bcachefs.org/")
-      (description
+    (synopsis "Tools to create and manage bcachefs file systems")
-       "The bcachefs-tools are command-line utilities for creating, checking,
+    (description
+     "The bcachefs-tools are command-line utilities for creating, checking,
 and otherwise managing bcachefs file systems.
 
 Bcachefs is a @acronym{CoW, copy-on-write} file system supporting native
@@ -683,7 +685,7 @@ multiple block devices for replication and/or performance, similar to RAID.
 In addition, bcachefs provides all the functionality of bcache, a block-layer
 caching system, and lets you assign different roles to each device based on its
 performance and other characteristics.")
-      (license license:gpl2+))))
+    (license license:gpl2+)))
 
 (define-public bcachefs-tools/static
   (package

gnu/packages/fonts.scm

@@ -58,7 +58,7 @@
 ;;; Copyright © 2023 gemmaro <gemmaro.dev@gmail.com>
 ;;; Copyright © 2023 Denis 'GNUtoo' Carikli <GNUtoo@cyberdimension.org>
 ;;; Copyright © 2023 chris <chris@bumblehead.com>
-;;; Copyright © 2023 Luis Felipe López Acevedo <sirgazil@zoho.com>
+;;; Copyright © 2023, 2024 Luis Felipe López Acevedo <sirgazil@zoho.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1975,7 +1975,7 @@ weights and five widths in both Roman and Italic, plus variable fonts.")
 (define-public font-sarasa-gothic
   (package
     (name "font-sarasa-gothic")
-    (version "1.0.3")
+    (version "1.0.5")
     (source
      (origin
        (method url-fetch)
@@ -1983,7 +1983,7 @@ weights and five widths in both Roman and Italic, plus variable fonts.")
                            "/releases/download/v" version
                            "/Sarasa-TTC-" version ".7z"))
        (sha256
-        (base32 "1cgqf15fhg567s2bwjpal3xfcdnbgyy0iav5181zkn6b4k56dgl4"))))
+        (base32 "0sfmqrjfzjy2zxd26kjrdbp59ahxj7p2qr1z5qy512j2cgl1gyiq"))))
     (build-system font-build-system)
     (arguments
      `(#:phases (modify-phases %standard-phases
@@ -3521,3 +3521,31 @@ for display purposes.  It features four weights (light, medium, bold,
 and black), a stylistic alternative, small caps, and many alternate
 glyphs.")
       (license license:silofl1.1))))
+
+(define-public font-oswald
+  (let ((version "0")
+        (commit "6e65651c229e897dc55fb8d17097ee7f75b2769b")
+        (revision "0"))
+    (package
+      (name "font-oswald")
+      (version (git-version version revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/googlefonts/OswaldFont")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "0m5c98crw6df6hbhxv4smh6ldzk5fx434fyri8xgnsjjcrkqxy0h"))))
+      (build-system font-build-system)
+      (home-page "https://github.com/googlefonts/OswaldFont")
+      (synopsis "Gothic typeface")
+      (description "Oswald is a reworking of the classic gothic typeface
+style historically represented by designs such as 'Alternate Gothic'.
+The characters of Oswald have been re-drawn and reformed to better fit
+the pixel grid of standard digital screens.  Oswald is designed to be
+used freely across the internet by web browsers on desktop computers,
+laptops and mobile devices.")
+      (license license:silofl1.1))))

gnu/packages/fontutils.scm

@@ -19,6 +19,7 @@
 ;;; Copyright © 2023 John Kehayias <john.kehayias@protonmail.com>
 ;;; Copyright © 2023 Janneke Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2023 pinoaffe <pinoaffe@gmail.com>
+;;; Copyright © 2024 Sören Tempel <soeren@soeren-tempel.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -73,6 +74,7 @@
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg)
   #:use-module (gnu packages tex)
+  #:use-module (gnu packages textutils)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix gexp)
   #:use-module (guix packages)
@@ -1911,6 +1913,7 @@ maintain the Noto Fonts project.")
      (list check pkg-config scdoc))
     (propagated-inputs
      (list ;; Required by fcft.pc.
+           utf8proc
            fontconfig
            freetype
            harfbuzz

gnu/packages/fpga.scm

@@ -425,7 +425,7 @@ a hardware description and verification language.")
 (define-public nvc
   (package
     (name "nvc")
-    (version "1.9.2")
+    (version "1.11.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -434,7 +434,7 @@ a hardware description and verification language.")
               (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "0zifyn7fr4k73ga6iwvsbsl6gi5106vlv5mkmqs0svi0sqx847f4"))))
+                "0rh6xwzr1drgwa04gx6w4r968yxlvfkvzg92950akf7wyxf331k7"))))
     (build-system gnu-build-system)
     (arguments
      `(#:out-of-source? #t
@@ -457,7 +457,8 @@ a hardware description and verification language.")
     (inputs
      (list elfutils
            llvm-9
-           libffi))
+           libffi
+           `(,zstd "lib")))
     (synopsis "VHDL compiler and simulator")
     (description "This package provides a VHDL compiler and simulator.")
     (home-page "https://www.nickg.me.uk/nvc/")

gnu/packages/game-development.scm

@@ -1344,7 +1344,7 @@ and multimedia programs in the Python language.")
 
 (define-public python-pygame-sdl2
   (let ((real-version "2.1.0")
-        (renpy-version "8.2.0"))
+        (renpy-version "8.1.3"))
     (package
       (inherit python-pygame)
       (name "python-pygame-sdl2")
@@ -1354,7 +1354,7 @@ and multimedia programs in the Python language.")
          (method url-fetch)
          (uri (string-append "https://www.renpy.org/dl/" renpy-version
                              "/pygame_sdl2-" version ".tar.gz"))
-         (sha256 (base32 "17mc39c7ha83kzv2wmq61a15mn6p8wh2y33ixhf5sb4bvyr48mhy"))
+         (sha256 (base32 "0qlprs9n3w254ilizqzvr6s01zx72gh7an0bgwxsq4hm22qypdws"))
          (modules '((guix build utils)))
          (snippet
           '(begin
@@ -1395,7 +1395,7 @@ developed mainly for Ren'py.")
 (define-public python-renpy
   (package
     (name "python-renpy")
-    (version "8.2.0")
+    (version "8.1.3")
     (source
      (origin
        (method url-fetch)
@@ -1403,7 +1403,7 @@ developed mainly for Ren'py.")
                            "/renpy-" version "-source.tar.bz2"))
        (sha256
         (base32
-         "02v54qqjjigfqhdr50kzhkdvplk56bvprq65jl57kcs1qhvlf5s9"))
+         "1g6fz5dxp7yxhgv6q4brzf5hpfqq3l1g3dfv3fsiwwn6mj0b01z2"))
        (modules '((guix build utils)))
        (snippet
         #~(begin
@@ -2038,7 +2038,7 @@ games.")
            libxi
            libxinerama
            libxrandr
-           mbedtls-apache
+           mbedtls-lts
            mesa
            opusfile
            pcre2
@@ -2280,7 +2280,7 @@ scripted in a Python-like language.")
            libxinerama
            libxkbcommon
            libxrandr
-           mbedtls-apache
+           mbedtls-lts
            mesa
            openxr
            opusfile

gnu/packages/games.scm

@@ -60,7 +60,7 @@
 ;;; Copyright © 2021 Olivier Rojon <o.rojon@posteo.net>
 ;;; Copyright © 2021 Stefan Reichör <stefan@xsteve.at>
 ;;; Copyright © 2021, 2022 Greg Hogan <code@greghogan.com>
-;;; Copyright © 2021 David Pflug <david@pflug.io>
+;;; Copyright © 2021, 2024 David Pflug <david@pflug.io>
 ;;; Copyright © 2021, 2022 Felix Gruber <felgru@posteo.net>
 ;;; Copyright © 2021 Solene Rapenne <solene@perso.pw>
 ;;; Copyright © 2021, 2022 Noisytoot <ron@noisytoot.org>
@@ -80,6 +80,7 @@
 ;;; Copyright © 2023 Ivana Drazovic <iv.dra@hotmail.com>
 ;;; Copyright © 2023, 2024 gemmaro <gemmaro.dev@gmail.com>
 ;;; Copyright © 2023 Wilko Meyer <w@wmeyer.eu>
+;;; Copyright © 2024 Vagrant Cascadian <vagrant@debian.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -149,6 +150,7 @@
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages gnuzilla)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
   #:use-module (gnu packages gperf)
   #:use-module (gnu packages graphics)
   #:use-module (gnu packages graphviz)
@@ -8095,26 +8097,49 @@ Strife, Chex Quest, and fan-created games like Harmony, Hacx and Freedoom.")
 (define-public odamex
   (package
     (name "odamex")
-    (version "0.9.5")
+    (version "10.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (string-append
              "mirror://sourceforge/odamex/Odamex/" version "/"
-             "odamex-src-" version ".tar.bz2"))
+             "odamex-src-" version ".tar.xz"))
        (sha256
-        (base32 "1x0c9vnwn336inkfamh4na8xjyfjmzfxfn49j4snqymkypjqw6jq"))))
+        (base32 "1isrmki18471yry48mmm7lxzp1kiqma9cc7fx38cvpm2mpgfyvzk"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           ;; XXX: Unbundle more, they are not replaced by the ones provided
+           ;; in inputs: fltk, jsoncpp, miniupnp, protobuf.
+           ;;
+           ;; Remove some bundled libraries.
+           (with-directory-excursion "libraries"
+             (for-each delete-file-recursively
+                       '("curl" "libpng" "portmidi" "zlib")))))))
     (build-system cmake-build-system)
-    (arguments `(#:tests? #f))          ; no tests
+    (arguments
+     (list
+      #:tests? #f ; no tests
+      #:configure-flags
+      #~(list "-DBUILD_CLIENT=1"
+              "-DBUILD_MASTER=1"
+              "-DBUILD_SERVER=1"
+              "-DUSE_INTERNAL_LIBS=0"
+              "-DUSE_INTERNAL_MINIUPNP=0")))
     (native-inputs
-     (list deutex))
+     (list deutex pkg-config))
     (inputs
-     `(("sdl" ,sdl2)
+     (list alsa-lib
-       ("sdl-mixer" ,sdl2-mixer)
+           curl
-       ("zlib" ,zlib)
+           fltk
-       ("libpng" ,libpng)
+           jsoncpp
-       ("curl" ,curl)
+           libpng
-       ("alsa-lib" ,alsa-lib)))
+           miniupnpc
+           portmidi
+           protobuf
+           sdl2
+           sdl2-mixer
+           zlib))
     (home-page "https://odamex.net/")
     (synopsis "Multiplayer Doom port")
     (description "Odamex is a modification of the Doom engine that
@@ -11322,7 +11347,7 @@ disassembly of the DOS version, extended with new features.")
 (define-public fheroes2
   (package
     (name "fheroes2")
-    (version "1.0.5")
+    (version "1.0.11")
     (source
      (origin
        (method git-fetch)
@@ -11331,7 +11356,7 @@ disassembly of the DOS version, extended with new features.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0v7dxzb5cfjb55jydd8f61zzlvxq9mrgdy51hq19b06dmrx1dnc7"))))
+        (base32 "1i1a4dynlb5kl55rmfmib2jha1b2igw5jyiiyla1fxgkbkjnbf27"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f                      ; no tests

gnu/packages/geo.scm

@@ -13,7 +13,7 @@
 ;;; Copyright © 2019, 2020 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2020, 2022 Marius Bakke <marius@gnu.org>
 ;;; Copyright © 2020 Christopher Baines <mail@cbaines.net>
-;;; Copyright © 2020, 2021, 2022, 2023 Felix Gruber <felgru@posteo.net>
+;;; Copyright © 2020–2024 Felix Gruber <felgru@posteo.net>
 ;;; Copyright © 2021, 2023, 2024 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;; Copyright © 2021, 2023, 2024 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2021 Clément Lassieur <clement@lassieur.org>
@@ -434,7 +434,7 @@ OpenStreetMap written in C using eXpat, Cairo and GLib.")
 (define-public geos
   (package
     (name "geos")
-    (version "3.11.2")
+    (version "3.12.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://download.osgeo.org/geos/geos-"
@@ -442,7 +442,7 @@ OpenStreetMap written in C using eXpat, Cairo and GLib.")
                                   ".tar.bz2"))
               (sha256
                (base32
-                "1k744nwfa5sj4amzsdjxgac83wh6xfb9xi7z5bka7ic1jik7gw5i"))))
+                "00qdk9a4048pzfj2rhzkfw3lvm642znf6kr4x29i3d94494pxsnn"))))
     (build-system cmake-build-system)
     (arguments `(#:phases
                  (modify-phases %standard-phases
@@ -450,7 +450,7 @@ OpenStreetMap written in C using eXpat, Cairo and GLib.")
                     'unpack 'patch-test-shebangs
                     (lambda _
                       (substitute* '("tests/xmltester/testrunner.sh"
-                                     "tests/geostest/testrunner.sh")
+                                     "tests/xmltester/safe_to_xml.sh")
                         (("/bin/sh") (which "sh"))))))))
     (inputs
      (list glib))
@@ -547,7 +547,11 @@ and driving.")
        (method url-fetch)
        (uri (string-append "http://download.osgeo.org/geotiff/libgeotiff/libgeotiff-"
                            version ".tar.gz"))
-       (patches (search-patches "libgeotiff-fix-tests-with-proj-9.1.1.patch"))
+       (patches
+         (search-patches "libgeotiff-fix-tests-with-proj-9.1.1.patch"
+                         "libgeotiff-fix-tests-with-proj-9.3.0.patch"
+                         "libgeotiff-fix-tests-with-proj-9.3.1.patch"
+                         "libgeotiff-fix-tests-on-i386.patch"))
        (sha256
         (base32 "1mjmgv48x51ppax5dnb6lq7z600czxll53bx6jbzqwd4m93i7aq5"))
        (modules '((guix build utils)))
@@ -739,7 +743,7 @@ fully fledged Spatial SQL capabilities.")
 (define-public proj
   (package
     (name "proj")
-    (version "9.2.0")
+    (version "9.3.1")
     (source
      (origin
        (method url-fetch)
@@ -747,7 +751,7 @@ fully fledged Spatial SQL capabilities.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "03nm1sgvh237my7ss6kayn6887cbnayvjxrrxsrfcakkmbsida6y"))))
+         "1g0hkpiablvhsmw0kn5frwgdir3q7avc45p6lc1zhhhzkv5ikydh"))))
     (build-system cmake-build-system)
     (native-inputs (list googletest pkg-config))
     (propagated-inputs (list curl libtiff sqlite)) ;required by proj.pc
@@ -843,31 +847,36 @@ projections.")
 (define-public python-pyproj
   (package
     (name "python-pyproj")
-    (version "3.5.0")
+    (version "3.6.1")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "pyproj" version))
         (sha256
           (base32
-            "1xhvr0n5gb7v6x0wd7cqmc0zrky2fag7bq2shx6l2qqq3icx2ncq"))))
+            "1gq1spm5zdq9k8kl9cb31b9m08ybyrdggfw3sjrqyz9b9iq7raj4"))))
     (build-system python-build-system)
     (arguments
-     `(#:phases
+     (list
-       (modify-phases %standard-phases
+      #:phases
-         (add-after 'unpack 'set-proj-path
+      #~(modify-phases %standard-phases
-           (lambda* (#:key inputs #:allow-other-keys)
+          (add-after 'unpack 'set-proj-path
-             (let ((proj (assoc-ref inputs "proj")))
+            (lambda* (#:key #:allow-other-keys)
-               (setenv "PROJ_DIR" proj)
+              (let ((proj #$(this-package-input "proj")))
-               (substitute* "pyproj/datadir.py"
+                (setenv "PROJ_DIR" proj)
-                 (("(internal_datadir = ).*$" all var)
+                (substitute* "pyproj/datadir.py"
-                  (string-append var "Path(\"" proj "/share/proj\")\n")))))))))
+                  (("(internal_datadir = ).*$" all var)
+                   (string-append var "Path(\"" proj
+                                  "/share/proj\")\n")))))))))
     (inputs
       (list proj))
     (propagated-inputs
       (list python-certifi))
     (native-inputs
-      (list python-cython python-numpy python-pandas python-pytest
+      (list python-cython
+            python-numpy
+            python-pandas
+            python-pytest
             python-xarray))
     (home-page "https://github.com/pyproj4/pyproj")
     (synopsis
@@ -1313,7 +1322,7 @@ utilities for data translation and processing.")
 (define-public python-pyshp
   (package
     (name "python-pyshp")
-    (version "2.1.3")
+    (version "2.3.1")
     (source
      (origin
        (method git-fetch)
@@ -1322,8 +1331,13 @@ utilities for data translation and processing.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0jsraqzq82pw19wvx84x7w5cs8agr44a9b5y0jjw540wim4xa73r"))))
+        (base32 "02pbr091p8v4kfv1p6p2aa4asgm9r74dc12r35lvgmhs9y163z69"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      ;; This test requires internet access.
+      '(list "--deselect" "test_shapefile.py::test_reader_url")))
     (native-inputs
      (list python-pytest python-pytest-runner))
     (home-page "https://github.com/GeospatialPython/pyshp")
@@ -2572,7 +2586,7 @@ orienteering sport.")
     (license license:gpl3+)))
 
 (define-public grass
-  (let* ((version "7.8.7")
+  (let* ((version "7.8.8")
          (majorminor (string-join (list-head (string-split version #\.) 2) ""))
          (grassxx (string-append "grass" majorminor)))
     (package
@@ -2584,7 +2598,7 @@ orienteering sport.")
          (uri (string-append "https://grass.osgeo.org/" grassxx
                              "/source/grass-" version ".tar.gz"))
          (sha256
-          (base32 "0sbz0ba9p963phvd0gmvfqq1fg4ixpipzcjbf20ys86qavjppzsg"))))
+          (base32 "1gpfbppfajc8d6b9alw9fdzgaa83w26kl6fff1395bc9gal215ms"))))
       (build-system gnu-build-system)
       (inputs
        `(("bzip2" ,bzip2)
@@ -2858,6 +2872,7 @@ growing set of geoscientific methods.")
                              "test_core_pointcloudlayerexporter"
                              "test_core_projectstorage"
                              "test_core_coordinatereferencesystem"
+                             "test_core_overlayexpression"
                              "test_gui_queryresultwidget"
                              "test_provider_copcprovider"
                              "test_provider_eptprovider"
@@ -2881,6 +2896,7 @@ growing set of geoscientific methods.")
                              "PyQgsOGRProviderGpkg"
                              "PyQgsProcessExecutablePt1"
                              "PyQgsProcessExecutablePt2"
+                             "PyQgsProjectionSelectionWidgets"
                              "PyQgsProviderConnectionGpkg"
                              "PyQgsProviderConnectionSpatialite"
                              "PyQgsOGRProvider"
@@ -3089,6 +3105,30 @@ path loss.")
      "This is a python implementation of the geodesic routines in GeographicLib.")
     (license license:expat)))
 
+(define-public python-geoip2fast
+  (package
+    (name "python-geoip2fast")
+    (version "1.2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "geoip2fast" version))
+       (sha256
+        (base32 "1cmdjlwjd4pg3qvsb8d4vghqj1im58npxb6dmrd5q90wjga4rfvm"))))
+    (build-system pyproject-build-system)
+    ;; The tests are speed tests or development tests to compare results with
+    ;; a different library.
+    (arguments (list #:tests? #false))
+    (home-page "https://github.com/rabuchaim/geoip2fast")
+    (synopsis
+     "Fast GeoIP2 country/city/asn lookup library")
+    (description
+     "@code{GeoIP2Fast} is a fast @code{GeoIP2} country/city/asn lookup
+library that supports IPv4 and IPv6.  A search takes less than 0.00003
+seconds.  It has its own data file updated twice a week with
+Maxmind-Geolite2-CSV, supports IPv4/IPv6 and is pure Python.")
+    (license license:expat)))
+
 (define-public python-geopy
   (package
     (name "python-geopy")

gnu/packages/gnome.scm

@@ -8,7 +8,7 @@
 ;;; Copyright © 2015 Mathieu Lirzin <mthl@openmailbox.org>
 ;;; Copyright © 2015, 2017 Andy Wingo <wingo@igalia.com>
 ;;; Copyright © 2015 David Hashe <david.hashe@dhashe.com>
-;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2023 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015-2020, 2023, 2024 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015, 2016, 2017, 2018, 2021 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 David Thompson <davet@gnu.org>
 ;;; Copyright © 2015-2024 Efraim Flashner <efraim@flashner.co.il>
@@ -7943,7 +7943,17 @@ to display dialog boxes from the commandline and shell scripts.")
               ;; let's disable them as well.
               ;; See <https://gitlab.gnome.org/GNOME/mutter/-/issues/2125>
               (substitute* "src/tests/clutter/conform/meson.build"
-                (("'timeline.*',") ""))))
+                (("'timeline.*',") ""))
+
+              ;; On i686-linux this test fails with a dbus error.  This seems
+              ;; to be fine in later versions, so this workaround can probably
+              ;; be removed soon.
+              #$@(if (string=? "i686-linux" (or (%current-target-system)
+                                                (%current-system)))
+                     #~((substitute* "src/tests/wayland-unit-tests.c"
+                          (("g_test_add_func \\(\"/wayland/toplevel/activation\",") "")
+                          (("^                   toplevel_activation\\);") "")))
+                     #~())))
           (replace 'check
             (lambda* (#:key tests? test-options parallel-tests?
                       #:allow-other-keys)

gnu/packages/gnupg.scm

@@ -346,11 +346,33 @@ compatible to GNU Pth.")
            zlib))
     (arguments
      (list
-      #:configure-flags #~'(;; Otherwise, the test suite looks for the `gpg`
+      #:configure-flags
-                            ;; executable in its installation directory in
+      ;; Always use quasiquote on the next core-updates cycle.
-                            ;; /gnu/store before it has been installed.
+      #~(#$(if (%current-target-system)
-                            "--enable-gnupg-builddir-envvar"
+               #~quasiquote
-                            "--enable-all-tests")
+               #~quote)
+         (#$@(if (%current-target-system)
+                 #~(,(string-append
+                      "--with-libgpg-error-prefix="
+                      #$(this-package-input "libgpg-error"))
+                    ,(string-append
+                      "--with-libgcrypt-prefix="
+                      #$(this-package-input "libgcrypt"))
+                    ,(string-append
+                      "--with-libassuan-prefix="
+                      #$(this-package-input "libassuan"))
+                    ,(string-append
+                      "--with-ksba-prefix="
+                      #$(this-package-input "libksba"))
+                    ,(string-append
+                      "--with-npth-prefix="
+                      #$(this-package-input "npth")))
+                 #~())
+          ;; Otherwise, the test suite looks for the `gpg`
+          ;; executable in its installation directory in
+          ;; /gnu/store before it has been installed.
+          "--enable-gnupg-builddir-envvar"
+          "--enable-all-tests"))
       #:phases
       #~(modify-phases %standard-phases
           (add-before 'configure 'patch-paths

gnu/packages/golang-build.scm

@@ -0,0 +1,506 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com>
+;;; Copyright © 2019, 2020 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2020 Danny Milosavljevic <dannym@scratchpost.org>
+;;; Copyright © 2020 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2020 HiPhish <hiphish@posteo.de>
+;;; Copyright © 2020 Oleg Pykhalov <go.wigust@gmail.com>
+;;; Copyright © 2020 Ryan Prior <rprior@protonmail.com>
+;;; Copyright © 2020 Vagrant Cascadian <vagrant@debian.org>
+;;; Copyright © 2021 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2021 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2021 Sarah Morgensen <iskarian@mgsn.dev>
+;;; Copyright © 2021 hackeryarn <artemchernyak@gmail.com>
+;;; Copyright © 2023 Artyom V. Poptsov <poptsov.artyom@gmail.com>
+;;; Copyright © 2023 Felix Lechner <felix.lechner@lease-up.com>
+;;; Copyright © 2023 Katherine Cox-Buday <cox.katherine.e@gmail.com>
+;;; Copyright © 2023 Nicolas Graves <ngraves@ngraves.fr>
+;;; Copyright © 2023 Timo Wilken <guix@twilken.net>
+;;;
+;;; 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 golang-build)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix build-system go)
+  #:use-module (guix gexp)
+  #:use-module (guix git-download)
+  #:use-module (guix packages)
+  #:use-module (guix utils)
+  #:use-module (gnu packages))
+
+;;; Commentary:
+;;;
+;;; Modules (libraries) which are part of the Golang project but outside the
+;;; main Golang tree, see <https://pkg.go.dev/golang.org/x>
+;;;
+;;; Since they are bound to be relied on by many, their dependencies should be
+;;; kept minimal, and this module should not depend on other modules
+;;; containing Golang packages.
+;;;
+;;; Please: Try to add new module packages in alphabetic order.
+;;;
+;;; Code:
+
+(define-public go-github-com-yuin-goldmark
+  (package
+    (name "go-github-com-yuin-goldmark")
+    (version "1.2.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/yuin/goldmark")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "12rsnsf65drcp0jfw2jl9w589vsn3pxdk1zh3v9q908iigngrcmy"))))
+    (build-system go-build-system)
+    (arguments
+     `(#:import-path "github.com/yuin/goldmark"))
+    (home-page "https://github.com/yuin/goldmark/")
+    (synopsis "Markdown parser")
+    (description "This package provides a markdown parser.")
+    (license license:expat)))
+
+(define-public go-golang-org-x-crypto
+  (package
+    (name "go-golang-org-x-crypto")
+    (version "0.4.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://go.googlesource.com/crypto")
+             (commit (string-append "v" version))))
+       (file-name (string-append "go.googlesource.com-crypto-"
+                                 version "-checkout"))
+       (sha256
+        (base32 "13i0yz4hvc4qdr438nmzilvl5ns73v3910bakcddny3jbzq72i2m"))))
+    (build-system go-build-system)
+    (arguments
+     '(#:import-path "golang.org/x/crypto"
+       ;; Source-only package
+       #:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         ;; Source-only package
+         (delete 'build))))
+    (propagated-inputs
+     (list go-golang-org-x-sys))
+    (home-page "https://go.googlesource.com/crypto/")
+    (synopsis "Supplementary cryptographic libraries in Go")
+    (description "This package provides supplementary cryptographic libraries
+for the Go language.")
+    (license license:bsd-3)))
+
+(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-image
+  (let ((commit "58c23975cae11f062d4b3b0c143fe248faac195d")
+        (revision "1"))
+    (package
+      (name "go-golang-org-x-image")
+      (version (git-version "0.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://go.googlesource.com/image")
+               (commit commit)))
+         (file-name (string-append "go.googlesource.com-image-"
+                                   version "-checkout"))
+         (sha256
+          (base32 "0i2p2girc1sfcic6xs6vrq0fp3szfx057xppksb67kliywjjrm5x"))))
+      (build-system go-build-system)
+      (arguments
+       `(#:import-path "golang.org/x/image"
+         ;; Source-only package
+         #:tests? #f
+         #:phases
+         (modify-phases %standard-phases
+           (delete 'build))))
+      (home-page "https://go.googlesource.com/image")
+      (synopsis "Supplemental Go image libraries")
+      (description "This package provides supplemental Go libraries for image
+processing.")
+      (license license:bsd-3))))
+
+(define-public go-golang-org-x-mod
+  (let ((commit "7c05a442b7c1d1a107879b4a090bb5a38d3774a1")
+        (revision "0"))
+    (package
+      (name "go-golang-org-x-mod")
+      (version (git-version "0.7.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/golang/mod")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "14r24fq3kn84k2y2jvvg8hwpy52a3q429pimrdwl5zwknbr2awmh"))))
+      (build-system go-build-system)
+      (arguments
+       '(#:import-path "golang.org/x/mod/"
+         #:tests? #f
+         #:phases (modify-phases %standard-phases
+                    ;; Source-only package
+                    (delete 'build))))
+      (home-page "https://golang.org/x/mod")
+      (synopsis "Tools to work directly with Go module mechanics")
+      (description
+       "This repository holds packages for writing tools that work directly
+with Go module mechanics.  That is, it is for direct manipulation of Go
+modules themselves.
+
+The specific case of loading packages should still be done by invoking the
+@command{go} command, which remains the single point of truth for package
+loading algorithms.")
+      (license license:bsd-3))))
+
+(define-public go-golang-org-x-net
+  (let ((commit "8e0e7d8d38f2b6d21d742845570dde2902d06a1d")
+        (revision "0"))
+    (package
+      (name "go-golang-org-x-net")
+      (version (git-version "0.5.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://go.googlesource.com/net")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1fidlcn3vcz42v2lc0rpmqh3bz08bcklj6jvnmz2vvgc481ci5hy"))))
+      (build-system go-build-system)
+      (arguments
+       (list
+        #:import-path "golang.org/x/net"
+        ;; Source-only package
+        #:tests? #f
+        #:phases
+        #~(modify-phases %standard-phases
+            ;; Source-only package
+            (delete 'build))))
+      (home-page "https://go.googlesource.com/net")
+      (synopsis "Go supplemental networking libraries")
+      (description "This package provides supplemental Go networking libraries.")
+      (license license:bsd-3))))
+
+;; XXX: Not in use by any other packages, consider to remove or merge with
+;; go-golang-org-x-net.
+(define-public go-golang-org-x-net-0.17
+  (let ((commit "b225e7ca6dde1ef5a5ae5ce922861bda011cfabd")
+        (revision "0"))
+    (package
+      (inherit go-golang-org-x-net)
+      (name "go-golang-org-x-net")
+      (version (git-version "0.17.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://go.googlesource.com/net")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "17zhim2m0r8nyy18g2lsawxm4rawix2qbjyn80x9vc6jc8fv05m9")))))))
+
+(define-public go-golang-org-x-net-html
+  (package
+    (inherit go-golang-org-x-net)
+    (name "go-golang-org-x-net-html")
+    (arguments
+     '(#:import-path "golang.org/x/net/html"
+       #:unpack-path "golang.org/x/net"))
+    (home-page "https://godoc.org/golang.org/x/net/html")
+    (synopsis "HTML5-compliant tokenizer and parser")
+    (description
+     "This package provides an HTML5-compliant tokenizer and parser.")))
+
+(define-public go-golang-org-x-sync
+  (let ((commit "8fcdb60fdcc0539c5e357b2308249e4e752147f1")
+        (revision "1"))
+    (package
+      (name "go-golang-org-x-sync")
+      (version (git-version "0.1.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://go.googlesource.com/sync")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "07qrhni6f5hh5p95k1yk6s4wsj341q663irvx6rllrxfsymj6a0z"))))
+      (build-system go-build-system)
+      (arguments
+       `(#:import-path "golang.org/x/sync"
+         #:tests? #f
+         ;; Source-only package
+         #:phases (modify-phases %standard-phases
+                    (delete 'build))))
+      (home-page "https://go.googlesource.com/sync/")
+      (synopsis "Additional Go concurrency primitives")
+      (description "This package provides Go concurrency primitives in
+addition to the ones provided by the language and “sync” and “sync/atomic”
+packages.")
+      (license license:bsd-3))))
+
+(define-public go-golang.org-x-sync-errgroup
+  (let ((commit "cd5d95a43a6e21273425c7ae415d3df9ea832eeb")
+        (revision "0"))
+    (package
+      (name "go-golang.org-x-sync-errgroup")
+      (version (git-version "0.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://go.googlesource.com/sync")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1nqkyz2y1qvqcma52ijh02s8aiqmkfb95j08f6zcjhbga3ds6hds"))))
+      (build-system go-build-system)
+      (arguments
+       '(#:import-path "golang.org/x/sync/errgroup"
+         #:unpack-path "golang.org/x/sync"))
+      (home-page "https://godoc.org/golang.org/x/sync/errgroup")
+      (synopsis "Synchronization, error propagation, and Context cancellation
+for groups of goroutines working on subtasks of a common task")
+      (description "This package provides synchronization, error
+propagation, and Context cancellation for groups of goroutines working on
+subtasks of a common task.")
+      (license license:bsd-3))))
+
+(define-public go-golang.org-x-sync-semaphore
+  (package
+    (inherit go-golang.org-x-sync-errgroup)
+    (name "go-golang.org-x-sync-semaphore")
+    (arguments
+     '(#:import-path "golang.org/x/sync/semaphore"
+       #:unpack-path "golang.org/x/sync"))
+    (home-page "https://godoc.org/golang.org/x/sync/semaphore")
+    (synopsis "Weighted semaphore implementation in Go")
+    (description "Weighted semaphore implementation in Go.")))
+
+(define-public go-golang-org-x-sys
+  (let ((commit "ca59edaa5a761e1d0ea91d6c07b063f85ef24f78")
+        (revision "0"))
+    (package
+      (name "go-golang-org-x-sys")
+      (version (git-version "0.8.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://go.googlesource.com/sys")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1p81niiin8dwyrjl2xsc95136w3vdw4kmj0w3mlh0vh5v134s4xq"))))
+      (build-system go-build-system)
+      (arguments
+       (list
+        #:import-path "golang.org/x/sys"
+        ;; Source-only package
+        #:tests? #f
+        #:phases
+        #~(modify-phases %standard-phases
+            ;; Source-only package
+            (delete 'build))))
+      (home-page "https://go.googlesource.com/sys")
+      (synopsis "Go support for low-level system interaction")
+      (description "This package provides supplemental libraries offering Go
+support for low-level interaction with the operating system.")
+      (license license:bsd-3))))
+
+(define-public go-golang-org-x-term
+  (package
+    (name "go-golang-org-x-term")
+    (version "0.3.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://go.googlesource.com/term")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "16s3d62fgdhiqvcib61s5pwxp08hhrmzx8bdv5zk1w1krjizdarl"))))
+    (build-system go-build-system)
+    (arguments '(#:import-path "golang.org/x/term"))
+    (propagated-inputs
+     (list go-golang-org-x-sys))
+    (home-page "https://pkg.go.dev/golang.org/x/term")
+    (synopsis "Go terminal/console support")
+    (description "@code{term} provides support functions for dealing with
+terminals, as commonly found on Unix systems.")
+    (license license:bsd-3)))
+
+(define-public go-golang-org-x-text
+  (package
+    (name "go-golang-org-x-text")
+    (version "0.3.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://go.googlesource.com/text")
+             (commit (string-append "v" version))))
+       (file-name (string-append "go.googlesource.com-text-"
+                                 version "-checkout"))
+       (sha256
+        (base32 "0flv9idw0jm5nm8lx25xqanbkqgfiym6619w575p7nrdh0riqwqh"))))
+    (build-system go-build-system)
+    (arguments
+     `(#:import-path "golang.org/x/text"
+       ;; Source-only package
+       #:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'build))))
+    (home-page "https://go.googlesource.com/text")
+    (synopsis "Supplemental Go text processing libraries")
+    (description "This package provides supplemental Go libraries for text
+processing.")
+    (license license:bsd-3)))
+
+(define-public go-golang-org-x-time
+  (let ((commit "9d24e82272b4f38b78bc8cff74fa936d31ccd8ef")
+        (revision "2"))
+    (package
+      (name "go-golang-org-x-time")
+      (version (git-version "0.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://go.googlesource.com/time")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1f5nkr4vys2vbd8wrwyiq2f5wcaahhpxmia85d1gshcbqjqf8dkb"))))
+      (build-system go-build-system)
+      (arguments
+       `(#:import-path "golang.org/x/time"
+         ;; Source-only package
+         #:tests? #f
+         #:phases
+         (modify-phases %standard-phases
+         ;; Source-only package
+           (delete 'build))))
+      (home-page "https://godoc.org/golang.org/x/time/rate")
+      (synopsis "Supplemental Go time libraries")
+      (description "This package provides supplemental Go libraries related to
+time.")
+      (license license:bsd-3))))
+
+(define-public go-golang-org-x-tools
+  (package
+    (name "go-golang-org-x-tools")
+    (version "0.5.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://go.googlesource.com/tools")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "08kx2nndq3sr6xai7403mbsqvz5shxmp2icylfr2fmwagr59cb2n"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           ;; gopls versions are tagged separately, and it is a
+           ;; 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
+         (delete 'build))))
+    (propagated-inputs
+     (list go-github-com-yuin-goldmark
+           go-golang-org-x-mod
+           go-golang-org-x-net
+           go-golang-org-x-sys))
+    (home-page "https://go.googlesource.com/tools/")
+    (synopsis "Tools that support the Go programming language")
+    (description "This package provides miscellaneous tools that support the
+Go programming language.")
+    (license license:bsd-3)))
+
+(define-public go-golang-org-x-xerrors
+  (let ((commit "5ec99f83aff198f5fbd629d6c8d8eb38a04218ca")
+        (revision "0"))
+    (package
+      (name "go-golang-org-x-xerrors")
+      (version (git-version "0.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://go.googlesource.com/xerrors")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1dbzc3gmf2haazpv7cgmv97rq40g2xzwbglc17vas8dwhgwgwrzb"))))
+      (build-system go-build-system)
+      (arguments
+       '(#:import-path "golang.org/x/xerrors"))
+      (home-page "https://godoc.org/golang.org/x/xerrors")
+      (synopsis "Go 1.13 error values")
+      (description "This package holds the transition packages for the new Go
+1.13 error values.")
+      (license license:bsd-3))))
+
+;;;
+;;; Avoid adding new packages to the end of this file. To reduce the chances
+;;; of a merge conflict, place them above by existing packages with similar
+;;; functionality or similar names.
+;;;

gnu/packages/golang-check.scm

@@ -14,6 +14,7 @@
 ;;; Copyright © 2021 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2022 ( <paren@disroot.org>
 ;;; Copyright © 2022 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2023 Benjamin <benjamin@uvy.fr>
 ;;; Copyright © 2023 Felix Lechner <felix.lechner@lease-up.com>
 ;;; Copyright © 2023 Hilton Chain <hako@ultrarare.space>
 ;;; Copyright © 2023 Katherine Cox-Buday <cox.katherine.e@gmail.com>
@@ -40,7 +41,9 @@
   #:use-module (guix gexp)
   #:use-module (guix git-download)
   #:use-module (gnu packages)
-  #:use-module (gnu packages golang))
+  #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
+  #:use-module (gnu packages golang-xyz))
 
 ;;; Commentary:
 ;;;
@@ -122,6 +125,44 @@
 @end itemize\n")
       (license license:expat))))
 
+(define-public go-github-com-davecgh-go-spew
+  (package
+    (name "go-github-com-davecgh-go-spew")
+    (version "1.1.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/davecgh/go-spew")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0hka6hmyvp701adzag2g26cxdj47g21x6jz4sc6jjz1mn59d474y"))))
+    (build-system go-build-system)
+    (arguments
+     '(#:unpack-path "github.com/davecgh/go-spew"
+       #:import-path "github.com/davecgh/go-spew/spew"))
+    (home-page "https://github.com/davecgh/go-spew")
+    (synopsis "Deep pretty printer for Go data structures to aid in debugging")
+    (description "Package @command{spew} implements a deep pretty printer
+for Go data structures to aid in debugging.
+
+A quick overview of the additional features spew provides over the built-in
+printing facilities for Go data types are as follows:
+
+@itemize
+@item Pointers are dereferenced and followed.
+@item Circular data structures are detected and handled properly.
+@item Custom Stringer/error interfaces are optionally invoked, including on
+unexported types.
+@item Custom types which only implement the Stringer/error interfaces via a
+pointer receiver are optionally invoked when passing non-pointer variables.
+@item Byte arrays and slices are dumped like the hexdump -C command which
+includes offsets, byte values in hex, and ASCII output (only when using Dump
+style).
+@end itemize")
+    (license license:isc)))
+
 (define-public go-github-com-frankban-quicktest
   (package
     (name "go-github-com-frankban-quicktest")
@@ -351,6 +392,30 @@ builds on top of Go's builtin @code{testing} library and is complemented by the
 Gomega matcher library.")
     (license license:expat)))
 
+(define-public go-github-com-prashantv-gostub
+  (package
+    (name "go-github-com-prashantv-gostub")
+    (version "1.1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/prashantv/gostub")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "035xf5w4fqlicdbbjcflsqflc0z5gmrn6wr7q41xwqfwfpraf9ah"))))
+    (build-system go-build-system)
+    (arguments
+     '(#:import-path "github.com/prashantv/gostub"))
+    (native-inputs (list go-github-com-stretchr-testify))
+    (home-page "https://github.com/prashantv/gostub")
+    (synopsis "Stubbing library for Go")
+    (description
+     "Package gostub is used for stubbing variables in tests, and resetting the
+original value once the test has been run.")
+    (license license:expat)))
+
 (define-public go-github-com-stretchr-testify
   (package
     (name "go-github-com-stretchr-testify")

gnu/packages/golang-compression.scm

@@ -0,0 +1,144 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2020 Danny Milosavljevic <dannym@scratchpost.org>
+;;; Copyright © 2021 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2021 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2022 Sharlatan Hellseher <sharlatanus@gmail.com>
+;;;
+;;; 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 golang-compression)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix build-system go)
+  #:use-module (guix gexp)
+  #:use-module (guix git-download)
+  #:use-module (guix packages)
+  #:use-module (guix utils)
+  #:use-module (gnu packages))
+
+;;; Commentary:
+;;;
+;;; Please: Try to add new module packages in alphabetic order.
+;;;
+;;; Code:
+
+(define-public go-github-com-andybalholm-brotli
+  (package
+    (name "go-github-com-andybalholm-brotli")
+    (version "1.0.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/andybalholm/brotli")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1zvmj7gbnkq9xwv1bvcxk9acxl06y902148qwbd2kqwgs52wy2c0"))))
+    (build-system go-build-system)
+    (arguments
+     `(#:import-path "github.com/andybalholm/brotli"))
+    (home-page "https://github.com/andybalholm/brotli")
+    (synopsis "Pure Go Brotli encoder and decoder")
+    (description
+     "This package is a brotli compressor and decompressor implemented in Go.
+It was translated from the reference implementation
+(@url{https://github.com/google/brotli,https://github.com/google/brotli}) with
+the @code{c2go} tool at
+@url{https://github.com/andybalholm/c2go,https://github.com/andybalholm/c2go}.")
+    (license license:expat)))
+
+(define-public go-github-com-golang-snappy
+  (package
+    (name "go-github-com-golang-snappy")
+    (version "0.0.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/golang/snappy")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "004cw699yz3pdpawhjhpa0y94c4w479nw1rf39zj6h6027kpwv2j"))
+       (patches (search-patches "go-github-com-golang-snappy-32bit-test.patch"))))
+    (build-system go-build-system)
+    (arguments
+     `(#:import-path "github.com/golang/snappy"))
+    (home-page "https://github.com/golang/snappy")
+    (synopsis "Snappy compression format in the Go programming language")
+    (description "This package provides a Go implementation of the Snappy
+compression format.")
+    (license license:bsd-3)))
+
+(define-public go-github-com-klauspost-compress
+  (package
+    (name "go-github-com-klauspost-compress")
+    (version "1.13.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/klauspost/compress")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0ydnf9rizlhm8rilh14674qqx272sbwbkjx06xn9pqvy6mmn2r3r"))))
+    (build-system go-build-system)
+    (arguments
+     `(#:import-path "github.com/klauspost/compress"
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'reset-gzip-timestamps 'fix-permissions
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; Provide write permissions on gzip files so that
+             ;; reset-gzip-timestamps has sufficient permissions.
+             (for-each make-file-writable
+                       (find-files (assoc-ref outputs "out") ".gz$")))))))
+    (propagated-inputs
+     (list go-github-com-golang-snappy))
+    (home-page "https://github.com/klauspost/compress")
+    (synopsis "Go compression library")
+    (description "@code{compress} provides various compression algorithms.")
+    (license license:bsd-3)))
+
+(define-public go-github.com-ulikunitz-xz
+  (package
+    (name "go-github.com-ulikunitz-xz")
+    (version "0.5.8")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/ulikunitz/xz.git")
+             (commit (string-append "v" version))))
+       (file-name (string-append name "-" version "-checkout"))
+       (sha256
+        (base32 "1xnsymi5fmmm734bi4c6z57p5cvnyxlpi29yxs4v21w5k763aypd"))))
+    (build-system go-build-system)
+    (arguments
+     `(#:import-path "github.com/ulikunitz/xz"))
+    (home-page "https://github.com/ulikunitz/xz")
+    (synopsis "Read and write xz compressed streams in Go")
+    (description "This package provides a library to read and write xz
+compressed streams in Go.")
+    (license license:bsd-3)))
+
+;;;
+;;; Avoid adding new packages to the end of this file. To reduce the chances
+;;; of a merge conflict, place them above by existing packages with similar
+;;; functionality or similar names.
+;;;

gnu/packages/golang-crypto.scm

@@ -15,6 +15,7 @@
 ;;; Copyright © 2022 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2022, 2023 Nicolas Graves <ngraves@ngraves.fr>
 ;;; Copyright © 2023 Artyom V. Poptsov <poptsov.artyom@gmail.com>
+;;; Copyright © 2023 Benjamin <benjamin@uvy.fr>
 ;;; Copyright © 2023 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2023 Felix Lechner <felix.lechner@lease-up.com>
 ;;; Copyright © 2023 Jack Hill <jackhill@jackhill.us>
@@ -43,7 +44,9 @@
   #:use-module (guix utils)
   #:use-module (gnu packages)
   #:use-module (gnu packages golang)
-  #:use-module (gnu packages golang-check))
+  #:use-module (gnu packages golang-build)
+  #:use-module (gnu packages golang-check)
+  #:use-module (gnu packages golang-compression))
 
 ;;; Commentary:
 ;;;
@@ -580,6 +583,55 @@ library's internal ChaCha20 package.")
 the Go standard library's TLS 1.3 implementation.")
     (license license:bsd-3)))
 
+(define-public go-github-com-nats-io-jwt-v2
+  (package
+    (name "go-github-com-nats-io-jwt-v2")
+    (version "2.5.3")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/nats-io/jwt")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0wcqbfyd3b4qdspmf72cpsbi0y2a4b1qd0cv3qvhh17d1h1a6zib"))))
+    (build-system go-build-system)
+    (arguments
+     (list #:import-path "github.com/nats-io/jwt/v2"
+           #:unpack-path "github.com/nats-io/jwt"))
+    (propagated-inputs (list go-github-com-nats-io-nkeys))
+    (home-page "https://github.com/nats-io/jwt")
+    (synopsis "Go library signing JWT tokens with NKeys for the NATS ecosystem")
+    (description
+     "This library is a JWT implementation that uses nkeys to digitally sign
+JWT tokens.  Nkeys use Ed25519 to provide authentication of JWT claims.")
+    (license license:asl2.0)))
+
+(define-public go-github-com-nats-io-nkeys
+  (package
+    (name "go-github-com-nats-io-nkeys")
+    (version "0.4.7")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/nats-io/nkeys")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0779m4nn6n0ql23wnk50ybddslvb84mwx036gf7yw6ckmm4yybxs"))))
+    (build-system go-build-system)
+    (arguments
+     '(#:import-path "github.com/nats-io/nkeys"))
+    (propagated-inputs (list go-golang-org-x-crypto))
+    (home-page "https://github.com/nats-io/nkeys")
+    (synopsis "Go library implementing public-key system for NATS ecosystem")
+    (description
+     "This package is an Ed25519 based public-key signature system that
+simplifies keys and seeds and performs signing and verification.")
+    (license license:asl2.0)))
+
 (define-public go-github-com-minio-blake2b-simd
   (let ((commit "3f5f724cb5b182a5c278d6d3d55b40e7f8c2efb4")
         (revision "0"))
@@ -611,6 +663,31 @@ performance is obtained with AVX2 which gives roughly a 4X performance
 increase approaching hashing speeds of 1GB/sec on a single core.")
       (license license:asl2.0))))
 
+(define-public go-github-com-minio-highwayhash
+  (package
+    (name "go-github-com-minio-highwayhash")
+    (version "1.0.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/minio/highwayhash")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1inrix7720273ccynxcyi7xsgc55cskxrw7gwn08qkmdj9xdxqai"))))
+    (build-system go-build-system)
+    (arguments
+     '(#:import-path "github.com/minio/highwayhash"))
+    (propagated-inputs (list go-golang-org-x-sys))
+    (home-page "https://github.com/minio/highwayhash")
+    (synopsis "HighwayHash library for Go")
+    (description
+     "This package implements the pseudo-random-function (PRF) HighwayHash.
+HighwayHash is a fast hash function designed to defend hash-flooding attacks
+or to authenticate short-lived messages.")
+    (license license:asl2.0)))
+
 (define-public go-github-com-minio-sha256-simd
   (package
     (name "go-github-com-minio-sha256-simd")
@@ -699,6 +776,8 @@ Architecture Processors\" by J. Guilford et al.")
                (delete-file-recursively
                 (string-append "src/" import-path "/testdata"))
                #t)))))
+      (native-inputs
+       (list go-golang-org-x-crypto))
       (home-page "https://github.com/OperatorFoundation/ed25519")
       (synopsis "Ed25519 for go")
       (description "Package ed25519 implements the Ed25519 signature

gnu/packages/golang-web.scm

@@ -48,7 +48,9 @@
   #:use-module (guix utils)
   #:use-module (gnu packages)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
   #:use-module (gnu packages golang-check)
+  #:use-module (gnu packages golang-compression)
   #:use-module (gnu packages golang-crypto)
   #:use-module (gnu packages golang-xyz)
   #:use-module (gnu packages tls)
@@ -1081,6 +1083,7 @@ Microsoft AD PAC authorization data.")
     (native-inputs
      (list go-github-com-davecgh-go-spew
            go-github-com-pmezard-go-difflib
+           go-github-com-stretchr-objx
            go-gopkg-in-yaml-v2))
     (home-page "https://github.com/jmespath/go-jmespath")
     (synopsis "Golang implementation of JMESPath")

gnu/packages/golang-xyz.scm

@@ -1,5 +1,13 @@
 ;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2017, 2018, 2019 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr>
+;;; Copyright © 2020 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2022 Dominic Martinez <dom@dominicm.dev>
+;;; Copyright © 2023 Benjamin <benjamin@uvy.fr>
+;;; Copyright © 2023 Katherine Cox-Buday <cox.katherine.e@gmail.com>
+;;; Copyright © 2023 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;; Copyright © 2023 Thomas Ieong <th.ieong@free.fr>
+;;; Copyright © 2024 Artyom V. Poptsov <poptsov.artyom@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -24,7 +32,11 @@
   #:use-module (guix packages)
   #:use-module (guix utils)
   #:use-module (gnu packages)
-  #:use-module (gnu packages golang-check))
+  #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
+  #:use-module (gnu packages golang-check)
+  #:use-module (gnu packages golang-compression)
+  #:use-module (gnu packages golang-crypto))
 
 ;;; Commentary:
 ;;;
@@ -34,6 +46,193 @@
 ;;;
 ;;; Code:
 
+(define-public go-github-com-anmitsu-go-shlex
+  (package
+    (name "go-github-com-anmitsu-go-shlex")
+    (version "0.0.0-20200514113438-38f4b401e2be")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/anmitsu/go-shlex")
+               (commit (go-version->git-ref version))))
+        (file-name (git-file-name name version))
+        (sha256
+          (base32 "17iz68yzbnr7y4s493asbagbv79qq8hvl2pkxvm6bvdkgphj8w1g"))))
+    (build-system go-build-system)
+    (arguments '(#:import-path "github.com/anmitsu/go-shlex"))
+    (home-page "https://github.com/anmitsu/go-shlex")
+    (synopsis "Simple shell-like lexical analyzer for Go")
+    (description "This package provides a simple lexical analyzer to parse
+shell-like commands.")
+    (license license:expat)))
+
+(define-public go-github-com-armon-go-radix
+  (package
+    (name "go-github-com-armon-go-radix")
+    (version "1.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/armon/go-radix")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1m1k0jz9gjfrk4m7hjm7p03qmviamfgxwm2ghakqxw3hdds8v503"))))
+    (build-system go-build-system)
+    (arguments '(#:import-path "github.com/armon/go-radix"))
+    (home-page "https://github.com/armon/go-radix")
+    (synopsis "Go implementation of Radix trees")
+    (description "This package provides a single @code{Tree} implementation,
+optimized for sparse nodes of
+@url{http://en.wikipedia.org/wiki/Radix_tree,radix tree}.")
+    (license license:expat)))
+
+(define-public go-github-com-bitly-go-hostpool
+  (package
+    (name "go-github-com-bitly-go-hostpool")
+    (version "0.1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/bitly/go-hostpool")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1iibj7dwymczw7cknrh6glc6sdpp4yap2plnyr8qphynwrzlz73w"))))
+    (build-system go-build-system)
+    (arguments
+     '(#:import-path "github.com/bitly/go-hostpool"))
+    (native-inputs (list go-github-com-stretchr-testify))
+    (home-page "https://github.com/bitly/go-hostpool")
+    (synopsis "Pool among multiple hosts from Golang")
+    (description
+     "This package provides a Go package to intelligently and flexibly pool among
+multiple hosts from your Go application.  Host selection can operate in round
+robin or epsilon greedy mode, and unresponsive hosts are avoided.")
+    (license license:expat)))
+
+(define-public go-github-com-bitly-timer-metrics
+  (package
+    (name "go-github-com-bitly-timer-metrics")
+    (version "1.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/bitly/timer_metrics")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "02fhx8hx8126m2cgxw9fm8q2401r7zfann8b5zy5yyark1sgkrb4"))))
+    (build-system go-build-system)
+    (arguments
+     '(#:import-path "github.com/bitly/timer_metrics"))
+    (home-page "https://github.com/bitly/timer_metrics")
+    (synopsis "Capture timings and enable periodic metrics every @var{n} events")
+    (description "This package provides an efficient way to capture timing
+information and periodically output metrics")
+    (license license:expat)))
+
+(define-public go-github-com-blang-semver
+  (let ((commit "60ec3488bfea7cca02b021d106d9911120d25fe9")
+        (revision "0"))
+    (package
+      (name "go-github-com-blang-semver")
+      (version (git-version "0.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/blang/semver")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "19pli07y5592g4dyjyj0jq5rn548vc3fz0qg3624vm1j5828p1c2"))))
+      (build-system go-build-system)
+      (arguments
+       '(#:import-path "github.com/blang/semver"))
+      (home-page "https://github.com/blang/semver")
+      (synopsis "Semantic versioning library written in Go")
+      (description
+       "Semver is a library for Semantic versioning written in Go.")
+      (license license:expat))))
+
+(define-public go-github-com-bmizerany-perks-quantile
+  (package
+    (name "go-github-com-bmizerany-perks-quantile")
+    (version "0.0.0-20230307044200-03f9df79da1e")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/bmizerany/perks")
+             (commit (go-version->git-ref version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1f2a99v3618bz2mf61iwhdjm3xi1gam6v4apqgcrz71gj7ba9943"))))
+    (build-system go-build-system)
+    (arguments
+     (list #:unpack-path "github.com/bmizerany/perks"
+           #:import-path "github.com/bmizerany/perks/quantile"))
+    (home-page "https://github.com/bmizerany/perks")
+    (synopsis "Library for computing quantiles")
+    (description
+     "Perks contains the Go package @code{quantile} that computes approximate
+quantiles over an unbounded data stream within low memory and CPU bounds.")
+    (license license:bsd-2)))
+
+(define-public go-github-com-burntsushi-toml
+  (package
+    (name "go-github-com-burntsushi-toml")
+    (version "1.2.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/BurntSushi/toml")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1v9czq4hsyvdz7yx70y6sgq77wmrgfmn09r9cj4w85z38jqnamv7"))))
+    (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 is
+similar to Go's standard library @code{json} and @code{xml} package.")
+    (license license:expat)))
+
+(define-public go-github-com-cyberdelia-go-metrics-graphite
+  (package
+    (name "go-github-com-cyberdelia-go-metrics-graphite")
+    (version "0.0.0-20161219230853-39f87cc3b432")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/cyberdelia/go-metrics-graphite")
+               (commit (go-version->git-ref version))))
+        (file-name (git-file-name name version))
+        (sha256
+          (base32 "1nnpwryw8i110laffyavvhx38gcd1jnpdir69y6fxxzpx06d094w"))))
+    (build-system go-build-system)
+    (propagated-inputs
+     (list go-github-com-rcrowley-go-metrics))
+    (arguments
+     '(#:tests? #f ; Tests require network interface access
+       #:import-path "github.com/cyberdelia/go-metrics-graphite"))
+    (home-page "https://github.com/cyberdelia/go-metrics-graphite")
+    (synopsis "Graphite client for go-metrics")
+    (description "This package provides a reporter for the
+@url{https://github.com/rcrowley/go-metrics,go-metrics} library which posts
+metrics to Graphite.")
+    (license license:bsd-2)))
+
 (define-public go-github-com-djherbis-atime
   (package
     (name "go-github-com-djherbis-atime")
@@ -56,6 +255,57 @@
 atimes for files.")
     (license license:expat)))
 
+(define-public go-github-com-gabriel-vasile-mimetype
+  (package
+    (name "go-github-com-gabriel-vasile-mimetype")
+    (version "1.4.3")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/gabriel-vasile/mimetype")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "11swnjczhrza0xi8q2wlk056nnbcghm44vqs52zfv6rwqvy6imhj"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:go go-1.20
+      #:import-path "github.com/gabriel-vasile/mimetype"
+      #:phases #~(modify-phases %standard-phases
+                   (add-before 'check 'add-supported-mimes-md
+                     (lambda* (#:key import-path #:allow-other-keys)
+                       ;; This file needs to be available for writing during the
+                       ;; tests otherwise they will fail.
+                       (let ((file (format #f "src/~a/supported_mimes.md"
+                                           import-path)))
+                         (invoke "touch" file)
+                         (chmod file #o644)))))))
+    (propagated-inputs (list go-golang-org-x-net))
+    (home-page "https://github.com/gabriel-vasile/mimetype")
+    (synopsis "Golang library for media type and file extension detection")
+    (description
+     "This package provides a Golang module that uses magic number signatures
+to detect the MIME type of a file.
+
+Main features:
+@itemize
+@item Fast and precise MIME type and file extension detection.
+@item Supports
+@url{https://github.com/gabriel-vasile/mimetype/blob/master/supported_mimes.md,
+many MIME types}.
+@item Allows to
+@url{https://pkg.go.dev/github.com/gabriel-vasile/mimetype#example-package-Extend,
+extend} with other file formats.
+@item Common file formats are prioritized.
+@item
+@url{https://pkg.go.dev/github.com/gabriel-vasile/mimetype#example-package-TextVsBinary,
+Differentiation between text and binary files}.
+@item Safe for concurrent usage.
+@end itemize")
+    (license license:expat)))
+
 (define-public go-github-com-matryer-try
   (package
     (name "go-github-com-matryer-try")
@@ -90,6 +340,366 @@ atimes for files.")
     (description "This package provides an idiomatic Go retry module.")
     (license license:expat)))
 
+(define-public go-github-com-miekg-dns
+  (package
+    (name "go-github-com-miekg-dns")
+    (version "1.1.48")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/miekg/dns")
+               (commit (string-append "v" version))))
+        (file-name (git-file-name name version))
+        (sha256
+          (base32 "14m4wnbgmc1prj4ds1fsz1nwb1awaq365lhbp8clzsidxmhjf3hl"))))
+    (build-system go-build-system)
+    (arguments '(#:import-path "github.com/miekg/dns"))
+    (propagated-inputs
+     (list go-golang-org-x-tools
+           go-golang-org-x-sys
+           go-golang-org-x-sync
+           go-golang-org-x-net))
+    (home-page "https://github.com/miekg/dns")
+    (synopsis "Domain Name Service library in Go")
+    (description
+      "This package provides a fully featured interface to the @acronym{DNS,
+Domain Name System}.  Both server and client side programming is supported.
+The package allows complete control over what is sent out to the @acronym{DNS,
+Domain Name Service}.  The API follows the less-is-more principle, by
+presenting a small interface.")
+    (license license:bsd-3)))
+
+(define-public go-github-com-mreiferson-go-options
+  (package
+    (name "go-github-com-mreiferson-go-options")
+    (version "1.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/mreiferson/go-options")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1pxs9ybrh196qy14ijn4zn51h2z28lj31y6vxrz2xxhgvpmfmxyl"))))
+    (build-system go-build-system)
+    (arguments
+     '(#:import-path "github.com/mreiferson/go-options"))
+    (home-page "https://github.com/mreiferson/go-options")
+    (synopsis "Go package to structure and resolve options")
+    (description
+     "The @code{options} Go package resolves configuration values set via
+command line flags, config files, and default struct values.")
+    (license license:expat)))
+
+(define-public go-github-com-mreiferson-go-svc
+  ;; NSQ specific fork of github.com/judwhite/go-svc, as Guix go build system
+  ;; does not support go.mod with `replace' statement.
+  (let ((commit "7a96e00010f68d9436e3de53a70c53f209a0c244")
+        (revision "0"))
+    (package
+      (name "go-github-com-mreiferson-go-svc")
+      (version (git-version "1.2.1" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/mreiferson/go-svc")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1acgb0n3svhnraqj1fz5qc5n3b4vc5ffwyk9vfi6gcfkibm0hgmd"))))
+      (build-system go-build-system)
+      (arguments
+       '(#:import-path "github.com/judwhite/go-svc"))
+      (propagated-inputs (list go-golang-org-x-sys))
+      (home-page "https://github.com/mreiferson/go-svc")
+      (synopsis "Go Windows Service wrapper for GNU/Linux")
+      (description
+       "Go Windows Service wrapper compatible with GNU/Linux.  Windows tests
+@url{https://github.com/judwhite/go-svc/raw/master/svc/svc_windows_test.go,here}.")
+      (license license:expat))))
+
+(define-public go-github-com-nats-io-nats-go
+  (package
+    (name "go-github-com-nats-io-nats-go")
+    (version "1.32.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/nats-io/nats.go")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "08b3n5mdpxvn9hipz0j001bp5r67i43cqji9x9dyzikypqdfg38k"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:go go-1.20
+      #:import-path "github.com/nats-io/nats.go"))
+    (propagated-inputs (list go-golang-org-x-text
+                         go-github-com-nats-io-nuid
+                         go-github-com-nats-io-nkeys
+                         go-github-com-klauspost-compress))
+    (home-page "https://github.com/nats-io/nats.go")
+    (synopsis "Go Client for NATS server")
+    (description
+     "This package provides a Go client for the NATS messaging system.")
+    (license license:asl2.0)))
+
+(define-public go-github-com-nats-io-nuid
+  (package
+    (name "go-github-com-nats-io-nuid")
+    (version "1.0.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/nats-io/nuid")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "11zbhg4kds5idsya04bwz4plj0mmiigypzppzih731ppbk2ms1zg"))))
+    (build-system go-build-system)
+    (arguments
+     '(#:import-path "github.com/nats-io/nuid"))
+    (home-page "https://github.com/nats-io/nuid")
+    (synopsis "Go library implementing identifier generator for NATS ecosystem")
+    (description
+     "This package provides a unique identifier generator that is high performance,
+very fast, and tries to be entropy pool friendly.")
+    (license license:asl2.0)))
+
+(define-public go-github-com-nbrownus-go-metrics-prometheus
+  (package
+    (name "go-github-com-nbrownus-go-metrics-prometheus")
+    (version "0.0.0-20210712211119-974a6260965f")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/nbrownus/go-metrics-prometheus")
+               (commit (go-version->git-ref version))))
+        (file-name (git-file-name name version))
+        (sha256
+          (base32 "1kl9l08aas544627zmhkgp843qx94sxs4inxm20nw1hx7gp79dz0"))))
+    (build-system go-build-system)
+    (arguments '(#:import-path "github.com/nbrownus/go-metrics-prometheus"))
+    (propagated-inputs
+     (list go-github-com-stretchr-testify
+           go-github-com-rcrowley-go-metrics
+           go-github-com-prometheus-client-golang))
+    (home-page "https://github.com/nbrownus/go-metrics-prometheus")
+    (synopsis "Prometheus support for go-metrics")
+    (description "This package provides a reporter for the @code{go-metrics}
+library which posts the metrics to the Prometheus client registry and just
+updates the registry.")
+    (license license:asl2.0)))
+
+(define-public go-github-com-nsqio-go-diskqueue
+  (package
+    (name "go-github-com-nsqio-go-diskqueue")
+    (version "1.1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/nsqio/go-diskqueue")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1hp66hkmfn0nyf3c53a40f94ah11a9rj01r5zp3jph9p54j8rany"))))
+    (build-system go-build-system)
+    (arguments
+     '(#:import-path "github.com/nsqio/go-diskqueue"))
+    (home-page "https://github.com/nsqio/go-diskqueue")
+    (synopsis "Go package providing a file system backed FIFO queue")
+    (description
+     "The @code{diskqueue} Go package provides a file system backed FIFO
+queue.")
+    (license license:expat)))
+
+(define-public go-github-com-nsqio-go-nsq
+  (package
+    (name "go-github-com-nsqio-go-nsq")
+    (version "1.1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/nsqio/go-nsq")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1h9z3z225sdgg7fl3l7x11xn5ch6lm5flgmcj046cdp453qj2qhf"))))
+    (build-system go-build-system)
+    (arguments
+     (list #:tests? #f                  ;tests require networking
+           #:import-path "github.com/nsqio/go-nsq"))
+    (propagated-inputs (list go-github-com-golang-snappy))
+    (home-page "https://github.com/nsqio/go-nsq")
+    (synopsis "Consumer/producer library for NSQ")
+    (description
+     "The @code{nsq} Go module provides a high-level @code{Consumer} and
+@code{Producer} types as well as low-level functions to communicate over the
+NSQ protocol @url{https://nsq.io/}.")
+    (license license:expat)))
+
+(define-public go-github-com-prometheus-client-model
+  (let ((commit "14fe0d1b01d4d5fc031dd4bec1823bd3ebbe8016")
+        (revision "2"))
+    (package
+      (name "go-github-com-prometheus-client-model")
+      (version (git-version "0.0.2" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/prometheus/client_model")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0zdmk6rbbx39cvfz0r59v2jg5sg9yd02b4pds5n5llgvivi99550"))))
+      (build-system go-build-system)
+      (arguments
+       '(#:import-path "github.com/prometheus/client_model"
+         #:tests? #f
+         #:phases
+         (modify-phases %standard-phases
+           ;; Source-only package
+           (delete 'build))))
+      (propagated-inputs
+       (list go-github-com-golang-protobuf-proto))
+      (synopsis "Data model artifacts for Prometheus")
+      (description "This package provides data model artifacts for Prometheus.")
+      (home-page "https://github.com/prometheus/client_model")
+      (license license:asl2.0))))
+
+(define-public go-github-com-rcrowley-go-metrics
+  (let ((commit "cac0b30c2563378d434b5af411844adff8e32960")
+        (revision "2"))
+    (package
+      (name "go-github-com-rcrowley-go-metrics")
+      (version (git-version "0.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/rcrowley/go-metrics")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1hfxffnpaw49pr3wrkbzq3pnv3nyzsvk5dxndv0yz70xlrbg8a04"))))
+      (build-system go-build-system)
+      (arguments
+       ;; Arbitrary precision tests are known to be broken on aarch64, ppc64le
+       ;; and s390x. See: https://github.com/rcrowley/go-metrics/issues/249
+       `(#:tests? ,(not (string-prefix? "aarch64" (or (%current-target-system)
+                                                      (%current-system))))
+         #:import-path "github.com/rcrowley/go-metrics"))
+      (propagated-inputs
+       (list go-github-com-stathat-go))
+      (synopsis "Go port of Coda Hale's Metrics library")
+      (description "This package provides a Go implementation of Coda Hale's
+Metrics library.")
+      (home-page "https://github.com/rcrowley/go-metrics")
+      (license license:bsd-2))))
+
+(define-public go-github-com-skip2-go-qrcode
+  (package
+    (name "go-github-com-skip2-go-qrcode")
+    (version "0.0.0-20200617195104-da1b6568686e")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/skip2/go-qrcode")
+             (commit (go-version->git-ref version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0pghd6y2x8a5fqy4rjn4d8j5jcslb236naycdza5an7vyvinsgs9"))
+       (patches (search-patches "go-github-com-skip2-go-qrcode-fix-tests.patch"))))
+    (build-system go-build-system)
+    (arguments '(#:import-path "github.com/skip2/go-qrcode"))
+    (home-page "https://github.com/skip2/go-qrcode")
+    (synopsis "QR code encoder")
+    (description "This package provides a QR code encoder for the Goloang.")
+    (license license:expat)))
+
+(define-public go-github-com-songgao-water
+  (package
+    (name "go-github-com-songgao-water")
+    (version "0.0.0-20200317203138-2b4b6d7c09d8")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/songgao/water")
+               (commit (go-version->git-ref version))))
+        (file-name (git-file-name name version))
+        (sha256
+          (base32 "1k5aildfszp6x66jzar4y36lic8ijkb5020hfaivpvq3bnwdiikl"))))
+    (build-system go-build-system)
+    (arguments '(#:tests? #f ; Tests require network interface access
+                 #:import-path "github.com/songgao/water"))
+    (home-page "https://github.com/songgao/water")
+    (synopsis "Simple network TUN/TAP library")
+    (description
+      "This package provides a simple TUN/TAP interface library for Go that
+efficiently works with standard packages like @code{io}, @code{bufio}, etc..
+Use waterutil with it to work with TUN/TAP packets/frames.")
+    (license license:bsd-3)))
+
+(define-public go-github-com-stathat-go
+  (let ((commit "74669b9f388d9d788c97399a0824adbfee78400e")
+        (revision "0"))
+    (package
+      (name "go-github-com-stathat-go")
+      (version (git-version "0.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/stathat/go")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1zzlsl24dyr202qkr2pay22m6d0gb7ssms77wgdx0r0clgm7dihw"))))
+      (build-system go-build-system)
+      (arguments
+       `(#:import-path "github.com/stathat/go"))
+      (synopsis "Post statistics to StatHat")
+      (description "This is a Go package for posting to a StatHat account.")
+      (home-page "https://github.com/stathat/go")
+      (license license:expat))))
+
+(define-public go-go-uber-org-automaxprocs
+  (package
+    (name "go-go-uber-org-automaxprocs")
+    (version "1.5.3")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/uber-go/automaxprocs")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "03arxcfaj7k6iwfdk0liaynxf9rjfj9m5glsjp7ws01xjkgrdpbc"))))
+    (build-system go-build-system)
+    (arguments
+     '(#:import-path "go.uber.org/automaxprocs"))
+    (native-inputs (list go-github-com-stretchr-testify
+                         go-github-com-prashantv-gostub))
+    (home-page "https://github.com/uber-go/automaxprocs")
+    (synopsis "CPU-count detection library for Go")
+    (description
+     "This package automatically set GOMAXPROCS to match Linux container
+CPU quota.")
+    (license license:expat)))
+
 ;;;
 ;;; Avoid adding new packages to the end of this file. To reduce the chances
 ;;; of a merge conflict, place them above by existing packages with similar

gnu/packages/gps.scm

@@ -7,6 +7,7 @@
 ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
 ;;; Copyright © 2020 Marius Bakke <marius@gnu.org>
 ;;; Copyright © 2021 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
+;;; Copyright © 2024 Andy Tai <atai@atai.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -139,7 +140,7 @@ between two other data points.")
 (define-public gama
   (package
     (name "gama")
-    (version "2.27")
+    (version "2.28")
     (source
       (origin
         (method url-fetch)
@@ -147,7 +148,7 @@ between two other data points.")
                             version ".tar.gz"))
         (sha256
          (base32
-          "0h9kwgzz9ijzx6jcpc37qhadc41k1jdcv0s2wcpsz6zjmx63p2wk"))
+          "06kblr43yxkn5y77nigwy42r81cmi5pxz3kp50z271vvj3h3zisx"))
         (modules '((guix build utils)))
         (snippet
          '(begin

gnu/packages/guile-xyz.scm

@@ -38,7 +38,7 @@
 ;;; Copyright © 2021 Leo Le Bouter <lle-bout@zaclys.net>
 ;;; Copyright © 2021 Zelphir Kaltstahl <zelphirkaltstahl@posteo.de>
 ;;; Copyright © 2021 Oleg Pykhalov <go.wigust@gmail.com>
-;;; Copyright © 2021, 2022 Artyom V. Poptsov <poptsov.artyom@gmail.com>
+;;; Copyright © 2021, 2022, 2024 Artyom V. Poptsov <poptsov.artyom@gmail.com>
 ;;; Copyright © 2022 Maxime Devos <maximedevos@telenet.be>
 ;;; Copyright © 2022 Zhu Zihao <all_but_last@163.com>
 ;;; Copyright © 2022 Antero Mejr <antero@mailbox.org>
@@ -1853,7 +1853,7 @@ library}.")
 (define-public guile-yamlpp
   (package
     (name "guile-yamlpp")
-    (version "0.2")
+    (version "0.3")
     (source
      (origin
        (method git-fetch)
@@ -1862,7 +1862,7 @@ library}.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "14mlqi7hw7pi9scwk1g432issnqcn185pd8na2plijxq55cy0iq7"))))
+        (base32 "0ik69y0vddg0myp0zdbkmklma0qkkrqzwlqwkij1zirklz6hl1ss"))))
     (build-system gnu-build-system)
     (native-inputs (list autoconf automake libtool pkg-config))
     (inputs (list guile-3.0 yaml-cpp))
@@ -2175,7 +2175,7 @@ provides tight coupling to Guix.")
 (define-public guile-ics
   (package
     (name "guile-ics")
-    (version "0.5.0")
+    (version "0.6.0")
     (source
      (origin
        (method git-fetch)
@@ -2185,7 +2185,7 @@ provides tight coupling to Guix.")
        (file-name (string-append name "-" version "-checkout"))
        (sha256
         (base32
-         "1ipryn69ad4viqai9pnwhkqqpf9wgw0m2qxrwkfrpm1bfdyilw9w"))))
+         "1gkz19iz3ncf9ddr731lsaw12ca7ygj3dxziz54s9xpp5cw19r0v"))))
     (build-system gnu-build-system)
     (arguments
      (list #:phases #~(modify-phases %standard-phases
@@ -2196,8 +2196,12 @@ provides tight coupling to Guix.")
            texinfo
            gettext-minimal ;Gettext brings 'AC_LIB_LINKFLAGS_FROM_LIBS'.
            help2man
-           pkg-config))
+           pkg-config
-    (inputs (list guile-3.0 which))
+           ;; needed when cross-compiling.
+           guile-3.0
+           guile-lib
+           guile-smc))
+    (inputs (list guile-3.0))
     (propagated-inputs (list guile-lib guile-smc guile-dsv))
     (home-page "https://github.com/artyom-poptsov/guile-ics")
     (synopsis "Guile parser library for the iCalendar format")
@@ -2213,7 +2217,12 @@ The library is shipped with documentation in Info format and usage examples.")
   (package
     (inherit guile-ics)
     (name "guile2.2-ics")
-    (inputs (list guile-2.2 which))
+    (native-inputs
+     (modify-inputs (package-native-inputs guile-ics)
+       (replace "guile" guile-2.2)
+       (replace "guile-lib" guile2.2-lib)
+       (replace "guile-smc" guile2.2-smc)))
+    (inputs (list guile-2.2))
     (propagated-inputs (list guile2.2-lib guile2.2-dsv guile2.2-smc))))
 
 (define-public guile-imanifest
@@ -4202,7 +4211,7 @@ debugging code.")
 (define-public guile-png
   (package
     (name "guile-png")
-    (version "0.7.1")
+    (version "0.7.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -4211,7 +4220,7 @@ debugging code.")
               (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "0y65795s9bs69msqvdbq8h34n00bkfs5v1d44wz21nwdffvq6557"))))
+                "1ad03r84j17rwfxbxqb0qmf70ggqs01kjyman3x1581lm5dk1757"))))
     (build-system gnu-build-system)
     (arguments
      (list

gnu/packages/guile.scm

@@ -17,7 +17,7 @@
 ;;; Copyright © 2019 Taylan Kammer <taylan.kammer@gmail.com>
 ;;; Copyright © 2020-2023 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2021 Maxime Devos <maximedevos@telenet.be>
-;;; Copyright © 2021 Timothy Sample <samplet@ngyro.com>
+;;; Copyright © 2021, 2024 Timothy Sample <samplet@ngyro.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -999,4 +999,26 @@ library.  It exposes an interface similar to other Guile compression
 libraries, like Guile-zlib.")
     (license license:gpl3+)))
 
+(define-public guile-bzip2
+  (package
+    (name "guile-bzip2")
+    (version "0.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://files.ngyro.com/guile-bzip2/guile-bzip2-"
+                           version ".tar.gz"))
+       (sha256
+        (base32 "1qnxk5fzg8m9ik1ckhjvi22kkhd810mrg8jzxiizhk920b69wbdh"))))
+    (build-system gnu-build-system)
+    (native-inputs (list guile-3.0 guile-bytestructures pkg-config))
+    (inputs (list guile-3.0 bzip2))
+    (propagated-inputs (list guile-bytestructures))
+    (home-page "https://ngyro.com/software/guile-bzip2.html")
+    (synopsis "Guile bindings for libbzip2")
+    (description "Guile-bzip2 is a Guile wrapper for the libbzip2
+library.  It exposes an interface similar to other Guile compression
+libraries, like Guile-zlib.")
+    (license license:gpl3+)))
+
 ;;; guile.scm ends here

gnu/packages/hardware.scm

@@ -703,7 +703,7 @@ battery state, controlling LEDs, and setting the inactive time.")
     (arguments
      `(#:tests? #f)) ;; Tests require Google's gtest and gmock
     (inputs
-     (list mbedtls-apache))
+     (list mbedtls-lts))
     (synopsis "C++ library to control Philips Hue lights")
     (description "Hueplusplus is a library for controlling Philips Hue lights.
 Features:
@@ -1112,7 +1112,7 @@ technology, such as head mounted displays with built in head tracking.")
            hueplusplus
            nlohmann-json
            libusb
-           mbedtls-apache
+           mbedtls-lts
            qtbase-5))
     (native-inputs
      (list pkg-config

gnu/packages/haxe.scm

@@ -78,7 +78,7 @@
                   apr-util
                   gtk+-2
                   libgc
-                  mbedtls-apache
+                  mbedtls-lts
                   (list mariadb "dev")
                   (list mariadb "lib")
                   openssl
@@ -171,7 +171,7 @@ interactive languages.")
                  (lambda _
                    (invoke "make" "install"))))))
     (inputs (list libuv
-                  mbedtls-apache
+                  mbedtls-lts
                   neko
                   ocaml-extlib
                   ocaml-luv
@@ -255,7 +255,7 @@ includes the compiler and library manager.")
                   libpng
                   libuv
                   libvorbis
-                  mbedtls-apache
+                  mbedtls-lts
                   mikktspace
                   minimp3
                   openal

gnu/packages/high-availability.scm

@@ -2,6 +2,7 @@
 ;;; Copyright © 2020 Brice Waegeneire <brice@waegenei.re>
 ;;; Copyright © 2020, 2022 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2022 Sharlatan Hellseher <sharlatanus@gmail.com>
+;;; Copyright © 2023 Benjamin <benjamin@uvy.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -35,7 +36,12 @@
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
+  #:use-module (gnu packages golang-check)
+  #:use-module (gnu packages golang-compression)
+  #:use-module (gnu packages golang-crypto)
   #:use-module (gnu packages golang-web)
+  #:use-module (gnu packages golang-xyz)
   #:use-module (gnu packages hardware)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages lua)
@@ -45,7 +51,6 @@
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
   #:use-module (gnu packages rsync)
-  #:use-module (gnu packages syncthing)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages valgrind)
   #:use-module (gnu packages version-control)
@@ -194,6 +199,47 @@ applications.")
  in general better performances compared to the old network protocol.")
     (license (list license:gpl2+ license:lgpl2.1+))))
 
+(define-public nats-server
+  (package
+    (name "nats-server")
+    (version "2.10.10")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/nats-io/nats-server")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1sn8a3xfs1s9jc5fphrnc0ahh83h7ma2ckg2x447gdhg1p7pf9gn"))))
+    (build-system go-build-system)
+    (inputs
+     (list go-github-com-klauspost-compress
+           go-github-com-minio-highwayhash
+           go-github-com-nats-io-jwt-v2
+           go-github-com-nats-io-nats-go
+           go-github-com-nats-io-nkeys
+           go-github-com-nats-io-nuid
+           go-go-uber-org-automaxprocs
+           go-golang-org-x-crypto
+           go-golang-org-x-sys
+           go-golang-org-x-time))
+    (arguments
+     (list
+      #:go go-1.20
+      #:import-path "github.com/nats-io/nats-server"
+      #:install-source? #f))
+    (home-page "https://github.com/nats-io/nats-server")
+    (synopsis "High performance message broker")
+    (description
+     "NATS is a simple, secure and performant communications system for digital
+systems, services and devices.  NATS is part of the Cloud Native Computing
+Foundation (CNCF).  NATS has over 40 client language implementations, and its
+server can run on-premise, in the cloud, at the edge, and even on a Raspberry
+Pi.  NATS can secure and simplify design and operation of modern distributed
+systems.")
+    (license license:asl2.0)))
+
 (define-public nsq
   (package
     (name "nsq")
@@ -240,7 +286,7 @@ applications.")
            go-github-com-bmizerany-perks-quantile
            go-github-com-burntsushi-toml
            go-github-com-davecgh-go-spew
-           go-github-com-golang-snappy ; Move to (gnu packages golang)
+           go-github-com-golang-snappy
            go-github-com-julienschmidt-httprouter
            go-github-com-mreiferson-go-options
            go-github-com-mreiferson-go-svc

gnu/packages/image-processing.scm

@@ -13,7 +13,7 @@
 ;;; Copyright © 2020 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;; Copyright © 2020 Brendan Tildesley <mail@brendan.scot>
 ;;; Copyright © 2021 Oleh Malyi <astroclubzp@gmail.com>
-;;; Copyright © 2021, 2022 Felix Gruber <felgru@posteo.net>
+;;; Copyright © 2021, 2022, 2024 Felix Gruber <felgru@posteo.net>
 ;;; Copyright © 2021 Andy Tai <atai@atai.org>
 ;;; Copyright © 2021 Ekaitz Zarraga <ekaitz@elenq.tech>
 ;;; Copyright © 2021 Paul Garlick <pgarlick@tourbillion-technology.com>
@@ -494,7 +494,7 @@ integrates with various databases on GUI toolkits such as Qt and Tk.")
 (define-public opencv
   (package
     (name "opencv")
-    (version "4.8.0")
+    (version "4.8.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -534,7 +534,7 @@ integrates with various databases on GUI toolkits such as Qt and Tk.")
                   (for-each delete-file (find-files "." "\\.jar$"))))
               (sha256
                (base32
-                "14bjpb0ahhaqnim8g6vs0gyd6jgnmly1amx25a0rk1a6ii2aiywn"))))
+                "1alvfqacbmrn7s6rbx0r150fg0lmsg13s887gn289vdawgrd7k04"))))
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags
@@ -1240,7 +1240,7 @@ programmatically.")
 (define-public vxl
   (package
     (name "vxl")
-    (version "2.0.2")
+    (version "3.5.0")
     (source
      (origin
        (method git-fetch)
@@ -1249,7 +1249,7 @@ programmatically.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0949hw57szq8943f1whwqaz591xjmb19kj803hcv74hdai2b0ycg"))
+        (base32 "0iqq4lm51l5gvkax6r79ypifqmgir3p3vman9gsc2085d2agjvbs"))
        (modules '((guix build utils)))
        ;; TODO: vxl includes an old version of dcmtk.  It won't build with
        ;; version 3.6.x.

gnu/packages/image-viewers.scm

@@ -77,6 +77,7 @@
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages graphics)
   #:use-module (gnu packages image)

gnu/packages/ipfs.scm

@@ -29,9 +29,12 @@
   #:use-module (guix download)
   #:use-module (guix build-system go)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
   #:use-module (gnu packages golang-check)
+  #:use-module (gnu packages golang-compression)
   #:use-module (gnu packages golang-crypto)
   #:use-module (gnu packages golang-web)
+  #:use-module (gnu packages golang-xyz)
   #:use-module (gnu packages python)
   #:use-module (gnu packages shells)
   #:use-module (gnu packages syncthing))
@@ -224,7 +227,7 @@ written in Go.")
 (define-public kubo
   (package
     (name "kubo")
-    (version "0.18.0")
+    (version "0.19.0")
     (source
      (origin
        (method url-fetch/tarbomb)
@@ -232,7 +235,7 @@ written in Go.")
              "https://dist.ipfs.io/kubo/v" version
              "/kubo-source.tar.gz"))
        (sha256
-        (base32 "0fx5a974hyg29xvwwsmh3zz3nk3391ifyk3l0wl36xskfdqdwg5a"))
+        (base32 "0k0mw44fq6306pmfp6v4wawgigry9plnl2ij8i5f46606j55c31w"))
        (file-name (string-append name "-" version "-source"))
        (modules '((guix build utils)))
        (snippet '(for-each delete-file-recursively
@@ -287,7 +290,7 @@ written in Go.")
      (list
       #:unpack-path "github.com/ipfs/kubo"
       #:import-path "github.com/ipfs/kubo/cmd/ipfs"
-      #:go go-1.18
+      #:go go-1.20
       #:phases
       #~(modify-phases %standard-phases
           ;; https://github.com/ipfs/kubo/blob/master/docs/command-completion.md

gnu/packages/irc.scm

@@ -67,6 +67,7 @@
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
   #:use-module (gnu packages golang-check)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages guile)
@@ -912,7 +913,7 @@ but can also be used independently as a logging bot.")
      (list argon2
            gnutls
            libmaxminddb
-           mbedtls-apache
+           mbedtls-lts
            (list mariadb "dev")
            openldap
            openssl

gnu/packages/julia-jll.scm

@@ -1399,11 +1399,11 @@ build tree Yggdrasil.")
                   (("generate_wrapper_header.*")
                    (string-append
                     "generate_wrapper_header(\"MbedTLS\", \""
-                    (assoc-ref inputs "mbedtls-apache") "\")\n"))))
+                    (assoc-ref inputs "mbedtls") "\")\n"))))
               ;; There's a Julia file for each platform, override them all
               (find-files "src/wrappers/" "\\.jl$"))
              #t)))))
-    (inputs (list mbedtls-apache))
+    (inputs (list mbedtls-lts))
     (propagated-inputs (list julia-jllwrappers))
     (home-page "https://github.com/JuliaBinaryWrappers/MbedTLS_jll.jl")
     (synopsis "Apache's mbed TLS binary wrappers")

gnu/packages/julia.scm

@@ -186,7 +186,7 @@ libraries.  It is also a bit like @code{ldd} and @code{otool -L}.")
                                          "gmp" "lapack"
                                          "libssh2" "libnghttp2" "libgit2"
                                          "libblastrampoline"
-                                         "mbedtls-apache" "mpfr"
+                                         "mbedtls" "mpfr"
                                          "openblas" "openlibm" "pcre2"
                                          "suitesparse" "gfortran:lib"))
                                   ":"))))
@@ -263,9 +263,9 @@ libraries.  It is also a bit like @code{ldd} and @code{otool -L}.")
                (substitute* (jlpath "MPFR")
                  (((from "libmpfr")) (to "mpfr" "libmpfr")))
                (substitute* (jlpath "MbedTLS")
-                 (((from "libmbedcrypto")) (to "mbedtls-apache" "libmbedcrypto"))
+                 (((from "libmbedcrypto")) (to "mbedtls" "libmbedcrypto"))
-                 (((from "libmbedtls")) (to "mbedtls-apache" "libmbedtls"))
+                 (((from "libmbedtls")) (to "mbedtls" "libmbedtls"))
-                 (((from "libmbedx509")) (to "mbedtls-apache" "libmbedx509")))
+                 (((from "libmbedx509")) (to "mbedtls" "libmbedx509")))
                (substitute* (jlpath "nghttp2")
                  (((from "libnghttp2")) (to "libnghttp2" "libnghttp2")))
                (substitute* (jlpath "OpenBLAS")
@@ -318,7 +318,7 @@ libraries.  It is also a bit like @code{ldd} and @code{otool -L}.")
              (substitute* "stdlib/PCRE2_jll/test/runtests.jl"
                (("10.40.0") ,(package-version (this-package-input "pcre2"))))
              (substitute* "stdlib/MbedTLS_jll/test/runtests.jl"
-               (("2.28.0") ,(package-version (this-package-input "mbedtls-apache"))))
+               (("2.28.0") ,(package-version (this-package-input "mbedtls"))))
              (substitute* "stdlib/MPFR_jll/test/runtests.jl"
                (("4.1.0") ,(package-version (this-package-input "mpfr"))))
              (substitute* "stdlib/GMP_jll/test/runtests.jl"
@@ -515,7 +515,7 @@ using Dates: @dateformat_str, Date, DateTime, DateFormat, Time"))
        ("libunwind" ,libunwind-julia)
        ("libuv" ,libuv-julia)
        ("llvm" ,llvm-julia)
-       ("mbedtls-apache" ,mbedtls-apache)
+       ("mbedtls" ,mbedtls-lts)
        ("mpfr" ,mpfr)
        ,@(if (target-x86-64?)
              `(("openblas" ,openblas-ilp64))

gnu/packages/jupyter.scm

@@ -804,7 +804,13 @@ JupyterLab.")
          (replace 'check
            (lambda* (#:key tests? #:allow-other-keys)
              (when tests?
-               (invoke "pytest" "-v")))))))
+               (invoke
+                "pytest" "-v"
+                ;; Disable failing tests.
+                "-k" (string-append
+                      "not test_dataunion_constricts_widget_data"
+                      " and not test_dataunion_widget_change_notified"
+                      " and not test_datawidget_creation_blank_comm"))))))))
     (propagated-inputs
      (list python-ipywidgets python-numpy python-six python-traittypes))
     (native-inputs

gnu/packages/linphone.scm

@@ -184,7 +184,7 @@ writing, administering, and running unit tests in C.")
                (with-directory-excursion "tester"
                  (invoke "./bctoolbox_tester"))))))))
     (inputs
-     (list bcunit libdecaf mbedtls-apache))
+     (list bcunit libdecaf mbedtls-lts))
     (synopsis "Belledonne Communications Tool Box")
     (description "BcToolBox is an utilities library used by Belledonne
 Communications software like belle-sip, mediastreamer2 and linphone.")

gnu/packages/linux.scm

@@ -134,6 +134,7 @@
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
   #:use-module (gnu packages gperf)
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages gstreamer)
@@ -495,17 +496,17 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
 
 ;; The current "mainline" kernel.
 
-(define-public linux-libre-6.7-version "6.7.2")
+(define-public linux-libre-6.7-version "6.7.4")
 (define-public linux-libre-6.7-gnu-revision "gnu")
 (define deblob-scripts-6.7
   (linux-libre-deblob-scripts
    linux-libre-6.7-version
    linux-libre-6.7-gnu-revision
-   (base32 "0hwashmml56r74kgjb637b3ln2d7f9vgfl18sxvczyl84xlbcncj")
+   (base32 "1ddngihfmwffgvxxv8xsppi76r6grvdxr6zzfzvgl9qw07a6c9fd")
    (base32 "1vb2pd0wdfl9p5qi8hj1i5xg1p4pyrp01iqhap9xbb2yai4l80j5")))
 (define-public linux-libre-6.7-pristine-source
   (let ((version linux-libre-6.7-version)
-        (hash (base32 "0wd6pxh7wy9bzjzwd0rdsdnghpr53qbs722fhg07bi19m8dy8kf3")))
+        (hash (base32 "036nk3h7vqzd7gnxan2173kpss5qm2pci1lvd58gh90azigrz3gn")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-6.7)))
@@ -513,17 +514,17 @@ 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-6.6-version "6.6.14")
+(define-public linux-libre-6.6-version "6.6.16")
 (define-public linux-libre-6.6-gnu-revision "gnu")
 (define deblob-scripts-6.6
   (linux-libre-deblob-scripts
    linux-libre-6.6-version
    linux-libre-6.6-gnu-revision
-   (base32 "0g8m0rb15b0231dv8ji456s75a67szsaim71may3yprplycz6pav")
+   (base32 "1qm8f3fq4yx59f7b6yky5ryyf229ypxnry922sr8cy0s7mp62cmv")
    (base32 "0kavbby960k7wg355p3hjb9v1c4gnk8dv3lkfhpz44ayhv7kihg5")))
 (define-public linux-libre-6.6-pristine-source
   (let ((version linux-libre-6.6-version)
-        (hash (base32 "110mz8fjlg1j9wnhhq2ik5alayhf61adajd8jqmcsqprncnnpsgv")))
+        (hash (base32 "0c5a9agdr27bwd1z6790whczb858z8i34hhn548lzbdylfamf7dj")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-6.6)))
@@ -531,7 +532,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
 ;; 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-6.1-version "6.1.75")
+(define-public linux-libre-6.1-version "6.1.77")
 (define-public linux-libre-6.1-gnu-revision "gnu")
 (define deblob-scripts-6.1
   (linux-libre-deblob-scripts
@@ -541,7 +542,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
    (base32 "1jg2v1nxd6i5x536vmd1l14xhpzrcimpmjfipb1zkrwil102y25f")))
 (define-public linux-libre-6.1-pristine-source
   (let ((version linux-libre-6.1-version)
-        (hash (base32 "0mis14ll6xmhw71vfpw1aahi5z207qysha7x316fq4qc6c899lbc")))
+        (hash (base32 "07grng6rrgpy6c3465hwqhn3gcdam1c8rwya30vgpk8nfxbfqm1v")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-6.1)))
@@ -2335,7 +2336,7 @@ by Robert Shea and Robert Anton Wilson.")
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f)) ;no test suite
-    (inputs (list fuse-2 mbedtls-apache))
+    (inputs (list fuse-2 mbedtls-lts))
     (synopsis "FUSE driver to read/write Windows BitLocker drives")
     (description
      "This package provides means to to read BitLocker encrypted
@@ -10331,25 +10332,25 @@ text-based database (@file{$XDG_CONFIG_HOME/modprobed-db}), which can be read
 directly by @code{make localmodconfig} as described above.")
     (license license:expat)))
 
-(define-public kconfig-hardened-check
+(define-public kernel-hardening-checker
   (package
-    (name "kconfig-hardened-check")
+    (name "kernel-hardening-checker")
-    (version "0.6.1")
+    (version "0.6.6")
     (source (origin
               (method git-fetch)
               (uri (git-reference
-                    (url "https://github.com/a13xp0p0v/kconfig-hardened-check")
+                    (url "https://github.com/a13xp0p0v/kernel-hardening-checker")
                     (commit (string-append "v" version))))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0bpdy2a7l75y5cqzzc92nh4gapzgza8ml5i8ximr6brf6pr3681z"))))
+                "1w9xx3xvx4wrfdkdwkfzjlfichgkvacil9b8s1fcgla63z65m5f6"))))
     (build-system python-build-system)
-    (home-page "https://github.com/a13xp0p0v/kconfig-hardened-check")
+    (home-page "https://github.com/a13xp0p0v/kernel-hardening-checker")
     (synopsis
      "Tool for checking the security hardening options of the Linux kernel")
     (description
-     "@code{kconfig-hardened-check} is a tool for checking the security
+     "@code{kernel-hardening-checker} is a tool for checking the security
 hardening options of the Linux kernel.  Provided preferences are based on
 suggestions from various sources, including:
 
@@ -10363,6 +10364,9 @@ suggestions from various sources, including:
 This tool supports checking Kconfig options and kernel cmdline parameters.")
     (license license:gpl3)))
 
+(define-public kconfig-hardened-check
+  (deprecated-package "kconfig-hardened-check" kernel-hardening-checker))
+
 (define-public firejail
   (package
     (name "firejail")

gnu/packages/lisp-xyz.scm

@@ -1073,7 +1073,7 @@ options, e.g., by looking up an external key/value store
 (define-public sbcl-command-line-args
   (package
     (name "sbcl-command-line-args")
-    (version "0.1.0")
+    (version "0.1.1")
     (source
      (origin
        (method git-fetch)
@@ -1082,7 +1082,7 @@ options, e.g., by looking up an external key/value store
              (commit (string-append "v" version))))
        (file-name (git-file-name "cl-command-line-args" version))
        (sha256
-        (base32 "0ncw32qaak878xg68p42m2sh0qv19hg1va9wrh74d92v7cqz08kw"))))
+        (base32 "140xnz2v0v3hfg3dp2fhidw8ns6lxd3a5knm07wqdp48ksg119wy"))))
     (build-system asdf-build-system/sbcl)
     (arguments
      '(#:asd-systems '("whereiseveryone.command-line-args")))
@@ -11551,6 +11551,42 @@ may contain sets, maps may be keyed by sets, etc.")
      ;; Tests fails on ECL with "The function FSET::MAKE-CHAR is undefined".
      '(#:tests? #f))))
 
+(define-public sbcl-modf
+  (let ((commit "dea93fe62c6bf7f66f32f52ac0c555aedbf7abad")
+        (revision "0"))
+    (package
+      (name "sbcl-modf")
+      (version (git-version "0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/smithzvk/modf")
+               (commit commit)))
+         (file-name (git-file-name "cl-modf" version))
+         (sha256
+          (base32
+           "1aap7ldy7lv942khp026pgndgdzfkkqa9xcq1ykinrmflrgdazay"))))
+      (build-system asdf-build-system/sbcl)
+      (inputs
+       (list sbcl-alexandria
+             sbcl-closer-mop
+             sbcl-iterate))
+      (native-inputs
+       (list sbcl-stefil))
+      (home-page "https://github.com/smithzvk/modf")
+      (synopsis "SETF like macro for functional programming in Common Lisp")
+      (description "This library simplifies functional programming in Common
+Lisp by making it easier to make new data structures with specified changes in
+place.")
+      (license license:bsd-3))))
+
+(define-public cl-modf
+  (sbcl-package->cl-source-package sbcl-modf))
+
+(define-public ecl-modf
+  (sbcl-package->ecl-package sbcl-modf))
+
 (define-public sbcl-cl-cont
   (let ((commit "fc1fa7e6eb64894fdca13e688e6015fad5290d2a")
         (revision "1"))
@@ -21876,8 +21912,8 @@ Common Lisp.")
   (sbcl-package->cl-source-package sbcl-metacopy))
 
 (define-public sbcl-legit
-  (let ((commit "5f8a2d4c4f5fb8e53340eeef600433ee20e03fbe")
+  (let ((commit "9c677b9b798803d37ab6f5e0e0705441872f7230")
-        (revision "2"))
+        (revision "3"))
     (package
       (name "sbcl-legit")
       (version (git-version "1.0.0" revision commit))
@@ -21887,9 +21923,9 @@ Common Lisp.")
          (uri (git-reference
                (url "https://github.com/Shinmera/legit")
                (commit commit)))
-         (file-name (git-file-name name version))
+         (file-name (git-file-name "cl-legit" version))
          (sha256
-          (base32 "0crr7ya7dg15di7glk3w9sgf6j8dmny347gynmxxrdvjj9pa906m"))))
+          (base32 "0jy021ywrbnkgbgb63ip6j7kr40m4wz2pz1v5ybn6xkkn6dyprsz"))))
       (build-system asdf-build-system/sbcl)
       (arguments
        `(#:phases

gnu/packages/lisp.scm

@@ -1242,7 +1242,7 @@ including a built-in database engine and a GUI system.")
 (define-public janet
   (package
     (name "janet")
-    (version "1.32.1")
+    (version "1.33.0")
     (source
      (origin
        (method git-fetch)
@@ -1251,7 +1251,7 @@ including a built-in database engine and a GUI system.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1nnqbpql6749597m0lp56i2zqm003pg690399l0g8kb9kwvpv1yv"))))
+        (base32 "16wgljca7hp29fz5p2dnvy2cbscjx4imf85rhjwc1jkgdjswjxli"))))
     (build-system gnu-build-system)
     (arguments
      (list #:make-flags

gnu/packages/llvm.scm

@@ -22,7 +22,7 @@
 ;;; Copyright © 2021 Lars-Dominik Braun <lars@6xq.net>
 ;;; Copyright © 2021, 2022 Guillaume Le Vaillant <glv@posteo.net>
 ;;; Copyright © 2021, 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
-;;; Copyright © 2022 Greg Hogan <code@greghogan.com>
+;;; Copyright © 2022, 2024 Greg Hogan <code@greghogan.com>
 ;;; Copyright © 2022 John Kehayias <john.kehayias@protonmail.com>
 ;;; Copyright © 2022 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2022 Zhu Zihao <all_but_last@163.com>
@@ -1709,7 +1709,7 @@ misuse of libraries outside of the store.")))
 (define-public lldb
   (package
     (name "lldb")
-    (version (package-version llvm-15))
+    (version (package-version llvm-17))
     (source (llvm-monorepo version))
     (build-system cmake-build-system)
     (arguments
@@ -1723,8 +1723,8 @@ misuse of libraries outside of the store.")))
     (native-inputs
      (list pkg-config swig))
     (inputs
-     (list clang-15
+     (list clang-17
-           llvm-15
+           llvm-17
            ;; Optional (but recommended) inputs.
            ncurses
            libedit

gnu/packages/logging.scm

@@ -213,7 +213,7 @@ output in multiple windows in a terminal.")
 (define-public spdlog
   (package
     (name "spdlog")
-    (version "1.12.0")
+    (version "1.13.0")
     (source
      (origin
        (method git-fetch)
@@ -221,9 +221,8 @@ output in multiple windows in a terminal.")
              (url "https://github.com/gabime/spdlog")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
-       (patches (search-patches "spdlog-fix-tests.patch"))
        (sha256
-        (base32 "0yyncv6wjs5rqm76rkqyxpfbsingk1dq5zfcqhy1a7fpw8xdl53k"))))
+        (base32 "0zgdmdgnp2y36jrlk85d4fiyjkjd6anly8pambyc3f3v6sg02zyy"))))
     (build-system cmake-build-system)
     ;; TODO run benchmark. Currently not possible, as adding
     ;; (gnu packages benchmark) forms a dependency cycle

gnu/packages/machine-learning.scm

@@ -24,6 +24,7 @@
 ;;; Copyright © 2023 Zheng Junjie <873216071@qq.com>
 ;;; Copyright © 2023 Troy Figiel <troy@troyfigiel.com>
 ;;; Copyright © 2024 Sharlatan Hellseher <sharlatanus@gmail.com>
+;;; Copyright © 2024 David Pflug <david@pflug.io>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -73,6 +74,7 @@
   #:use-module (gnu packages cran)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages dejagnu)
+  #:use-module (gnu packages documentation)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gettext)
@@ -660,6 +662,53 @@ networks) based on simulation of (stochastic) flow in graphs.")
 algorithm.")
     (license license:gpl3)))
 
+(define-public openmm
+  (package
+    (name "openmm")
+    (version "8.1.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/openmm/openmm")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "064vv6zaci30pj38z5lwfqscxssm67jqxkz30hcya9vm4ng831d5"))))
+    (build-system cmake-build-system)
+    (arguments
+     (list
+      #:configure-flags
+      '(list "-DOPENMM_BUILD_SHARED_LIB=TRUE"
+             "-DOPENMM_BUILD_C_AND_FORTRAN_WRAPPERS=TRUE"
+             "-DOPENMM_BUILD_PYTHON_WRAPPERS=TRUE"
+             "-DOPENMM_BUILD_CUDA_LIB=FALSE")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'patch-python-build-system
+            (lambda _
+              (substitute* "wrappers/python/CMakeLists.txt"
+                (("install --root=\\\\\\$ENV\\{DESTDIR\\}/")
+                 (string-append "install --prefix=" #$output
+                                " --root=/ --single-version-externally-managed")))))
+          (add-after 'install 'install-python
+            (lambda _
+              (invoke "make" "PythonInstall"))))))
+    (inputs
+     (list python-wrapper))
+    (propagated-inputs
+     (list python-numpy))
+    (native-inputs
+     (list doxygen gfortran opencl-headers python-cython swig))
+    (home-page "https://github.com/openmm/openmm/")
+    (synopsis "Toolkit for molecular simulation")
+    (description
+     "OpenMM is a toolkit for molecular simulation.  It can be used either as
+a stand-alone application for running simulations, or as a library you call
+from your own code.")
+    ;; See https://github.com/openmm/openmm/issues/4278#issuecomment-1772982471
+    (license license:expat)))
+
 (define-public randomjungle
   (package
     (name "randomjungle")
@@ -5317,3 +5366,23 @@ Brian 2 simulator.")
      "OneAPI Deep Neural Network Library (oneDNN) is a cross-platform
 performance library of basic building blocks for deep learning applications.")
     (license license:asl2.0)))
+
+(define-public python-gguf
+  (package
+    (name "python-gguf")
+    (version "0.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "gguf" version))
+       (sha256
+        (base32 "0rbyc2h3kpqnrvbyjvv8a69l577jv55a31l12jnw21m1lamjxqmj"))))
+    (build-system pyproject-build-system)
+    (arguments
+      (list #:tests? #false))
+    (inputs (list poetry python-pytest))
+    (propagated-inputs (list python-numpy))
+    (home-page "https://ggml.ai")
+    (synopsis "Read and write ML models in GGUF for GGML")
+    (description "A Python library for reading and writing GGUF & GGML format ML models.")
+    (license license:expat)))

gnu/packages/mail.scm

@@ -108,6 +108,7 @@
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
   #:use-module (gnu packages golang-check)
   #:use-module (gnu packages golang-crypto)
   #:use-module (gnu packages golang-web)
@@ -247,15 +248,15 @@ mail client.")
     (name "anubis")
     ;; This 4.2.90 alpha release adds support for Guile 3 and has fixes for
     ;; other issues.
-    (version "4.2.90")
+    (version "4.3")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://alpha.gnu.org/gnu/anubis/anubis-"
+       (uri (string-append "mirror://gnu/anubis/anubis-"
              version ".tar.gz"))
        (sha256
         (base32
-         "0dvm6acl32dv8bixx9z50gzwfp6kj4kxnn1j3dcwjlp7sasjp41s"))))
+         "0b5ghaccy09l6fv0bg4my3yrxbw807wpwk14xvjih8j6ghrz62pz"))))
     (build-system gnu-build-system)
     (native-inputs
      (list automake autoconf gettext-minimal m4))                     ;for the test suite

gnu/packages/maths.scm

@@ -28,7 +28,7 @@
 ;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com>
 ;;; Copyright © 2018, 2020-2022 Marius Bakke <marius@gnu.org>
 ;;; Copyright © 2018 Eric Brown <brown@fastmail.com>
-;;; Copyright © 2018, 2021 Julien Lepiller <julien@lepiller.eu>
+;;; Copyright © 2018, 2021, 2024 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2018 Amin Bandali <bandali@gnu.org>
 ;;; Copyright © 2019, 2021-2023 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2019 Steve Sprang <scs@stevesprang.com>
@@ -93,6 +93,7 @@
   #:use-module (guix build-system ant)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system copy)
+  #:use-module (guix build-system dune)
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
@@ -184,6 +185,7 @@
   #:use-module (gnu packages tcl)
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages tex)
+  #:use-module (gnu packages time)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages version-control)
   #:use-module (gnu packages wxwidgets)
@@ -9355,7 +9357,7 @@ numeric differences and differences in numeric formats.")
 (define-public why3
   (package
     (name "why3")
-    (version "1.4.1")
+    (version "1.6.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -9364,7 +9366,7 @@ numeric differences and differences in numeric formats.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1yca6mx8bjm8x0i594ivh31aw45s6fbimmwfj8g2v9zwrgmr1i4s"))))
+                "0k3y98xzhrl44vwzq2m6k4nrllrwp3ll69lc2gfl8d77w0wg7gkp"))))
     (build-system ocaml-build-system)
     (native-inputs
      (list autoconf automake coq ocaml which))
@@ -9412,36 +9414,38 @@ of C, Java, or Ada programs.")
 (define-public frama-c
   (package
     (name "frama-c")
-    (version "24.0")
+    (version "27.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://frama-c.com/download/frama-c-"
-                                  version "-Chromium.tar.gz"))
+                                  version "-Cobalt.tar.gz"))
               (sha256
                (base32
-                "0x1xgip50jdz1phsb9rzwf2ra8lshn1hmd9g967xia402wrg3sjf"))))
+                "1lirkvhf5m53d33l0aw5jzc1fyzkwx5fkgh9g71732d52r55f4sv"))))
-    (build-system ocaml-build-system)
+    (build-system dune-build-system)
     (arguments
-     `(#:tests? #f; no test target in Makefile
+      `(#:phases
-       #:configure-flags
+        (modify-phases %standard-phases
-       (list "--enable-verbosemake")    ; to aid debugging
+          (add-before 'build 'set-env
-       #:phases
+            (lambda _
-       (modify-phases %standard-phases
+              (setenv "CC" "gcc"))))))
-         (add-before 'configure 'export-shell
-           (lambda* (#:key inputs #:allow-other-keys)
-             (setenv "CONFIG_SHELL"
-                     (search-input-file inputs "/bin/sh")))))))
     (inputs
      (list gmp zlib))
-    (propagated-inputs
+    (propagated-inputs (list
-     (list ocaml-biniou
+                         graphviz
-           ocaml-easy-format
+                         lablgtk3
-           ocaml-graph
+                         ocaml-graph
-           ocaml-yojson
+                         ocaml-odoc
-           ocaml-zarith
+                         ocaml-lablgtk3-sourceview3
-           ocaml-lablgtk3-sourceview3
+                         ocaml-yaml
-           lablgtk3
+                         ocaml-yojson
-           why3))
+                         ocaml-zarith
+                         ocaml-ppx-deriving
+                         ocaml-ppx-deriving-yojson
+                         ocaml-ppx-deriving-yaml
+                         ocaml-ppx-import
+                         why3))
+    (native-inputs (list dune-site time ocaml-menhir ocaml-graph))
     (native-search-paths
      (list (search-path-specification
             (variable "FRAMAC_SHARE")

gnu/packages/medical.scm

@@ -83,32 +83,34 @@ Health Federation.")
 
 (define-public openmolar-1
   (package
-   (name "openmolar")
+    (name "openmolar")
-   (version "1.0.15-gd81f9e5")
+    (version "1.1.6-g81838c85")
-   (source (origin
+    (source
-             (method url-fetch)
+     (origin
-             (uri (string-append
+       (method url-fetch)
-                   "https://static.openmolar.com/om1/releases/openmolar-"
+       (uri (string-append
-                   version ".tar.gz"))
+             "https://static.openmolar.com/om1/releases/openmolar-" version
-             (sha256
+             ".tar.gz"))
-              (base32
+       (sha256
-               "1cfdzfbi6wslw7k0dc6ad6xrgs75iwsl91cg73w4myswaqqkfk3z"))))
+        (base32 "09vrfqn511vswnj2q9m7srlwdgz066qvqpmja6sg1yl1ibh3cbpr"))))
-   (build-system python-build-system)
+    (build-system python-build-system)
-   (arguments
+    (arguments
-    `(#:use-setuptools? #f
+     `(#:use-setuptools? #f
-      #:phases
+       #:phases (modify-phases %standard-phases
-      (modify-phases %standard-phases
+                  (add-after 'unpack 'patch-/usr
-        (add-after 'unpack 'patch-/usr
+                    (lambda* (#:key outputs #:allow-other-keys)
-          (lambda* (#:key outputs #:allow-other-keys)
+                      (substitute* '("setup.py"
-            (substitute* "setup.py"
+                                     "src/openmolar/settings/localsettings.py")
-              (("/usr") (assoc-ref outputs "out")))
+                        (("/usr")
-            #t)))))
+                         (assoc-ref outputs "out"))) #t)))))
-   (inputs
+    (inputs (list python-pyqtwebengine python-pyqt+qscintilla
-    (list python-pyqt+qscintilla python-mysqlclient qscintilla))
+                  python-mysqlclient qscintilla))
-   (home-page "https://openmolar.com/om1")
+    (propagated-inputs (list qtwebengine-5))
-   (synopsis "Dental practice management software")
+    (home-page "https://openmolar.com/om1")
-   (description "Openmolar is a dental practice management suite.  Its
+    (synopsis "Dental practice management software")
+    (description
+     "Openmolar is a dental practice management suite.  Its
 functionality includes appointments, patient records, treatment planning,
 billing etc.  It is a full featured, reliable and thoroughly tested
 application and has been translated into many languages.")
-   (license gpl3+)))
+    (license gpl3+)))

gnu/packages/messaging.scm

@@ -86,6 +86,7 @@
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
   #:use-module (gnu packages gperf)
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages gstreamer)
@@ -2636,11 +2637,11 @@ replacement.")
     (license license:gpl2+)))
 
 (define-public tdlib
-  (let ((commit "27c3eaeb4964bd5f18d8488e354abde1a4383e49")
+  (let ((commit "c5c55092dd61b9eb15d6bbfd0f02c04c593450e7")
         (revision "0"))
     (package
       (name "tdlib")
-      (version (git-version "1.8.23" revision commit))
+      (version (git-version "1.8.24" revision commit))
       (source
        (origin
          (method git-fetch)
@@ -2648,7 +2649,7 @@ replacement.")
                (url "https://github.com/tdlib/td")
                (commit commit)))
          (sha256
-          (base32 "14f65dfmg2p5hyvi3lffvvazwcd3i3jrrw3c2pwrc5yfgxk3662g"))
+          (base32 "1kwbp4ay4zvk9jscp0xv9rv4jz2krm9jya8q81wnvn9qd0ybg94f"))
          (file-name (git-file-name name version))))
       (build-system cmake-build-system)
       (arguments

gnu/packages/moe.scm

@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014, 2015, 2017 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2016, 2019, 2021, 2023 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2024 Andy Tai <atai@atai.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -28,14 +29,14 @@
 (define-public moe
   (package
     (name "moe")
-    (version "1.13")
+    (version "1.14")
     (source
      (origin
       (method url-fetch)
       (uri (string-append "mirror://gnu/moe/moe-"
                           version ".tar.lz"))
       (sha256
-       (base32 "0sql4r5g60k3rsz8vsr04rl5b873rwli1x75333xd29ga6y5g9a3"))))
+       (base32 "17cw43zsahisz5msqdv366np3zrdschgnm1lk1pm26dfw1nbvfpl"))))
     (build-system gnu-build-system)
     (native-inputs (list lzip))
     (inputs (list ncurses))

gnu/packages/music.scm

@@ -52,7 +52,7 @@
 ;;; Copyright © 2022 jgart <jgart@dismail.de>
 ;;; Copyright © 2023 Jonathan Brielmaier <jonathan.brielmaier@web.de>
 ;;; Copyright © 2023 Antero Mejr <antero@mailbox.org>
-;;; Copyright © 2023 Sharlatan Hellseher <sharlatanus@gmail.com>
+;;; Copyright © 2023, 2024 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;; Copyright © 2023 Yovan Naumovski <yovan@gorski.stream>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -1673,15 +1673,7 @@ typographic detail of symbols on the page.")
        (sha256
         (base32
          "0wma9vzn42h1rhbzh2dwjsrzjhsi1yqdgn6wx1dfk78vaki6prd8"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               (invoke "python" "-m" "pytest" ".")
-               #t))))))
     (native-inputs
      (list lilypond
            python-black
@@ -1691,7 +1683,8 @@ typographic detail of symbols on the page.")
            python-mypy
            python-pytest
            python-pytest-cov
-           python-pytest-helpers-namespace))
+           python-pytest-helpers-namespace
+           python-sphinx-autodoc-typehints))
     (propagated-inputs
      (list abjad))
     (home-page "https://abjad.github.io")
@@ -1715,15 +1708,7 @@ and manipulating rhythms such as accelerandi, taleas, and more.")
        (sha256
         (base32
          "05hr2lr6myzi493k8vc19cqzraxxnbdwlckwbnras19l5g5ns38x"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               (invoke "python" "-m" "pytest" "tests")
-               #t))))))
     (native-inputs
      (list lilypond
            python-black
@@ -1733,7 +1718,8 @@ and manipulating rhythms such as accelerandi, taleas, and more.")
            python-mypy
            python-pytest
            python-pytest-cov
-           python-pytest-helpers-namespace))
+           python-pytest-helpers-namespace
+           python-sphinx-autodoc-typehints))
     (propagated-inputs
      (list abjad))
     (home-page "https://abjad.github.io")
@@ -3821,7 +3807,7 @@ event-based scripts for scrobbling, notifications, etc.")
 (define-public picard
   (package
     (name "picard")
-    (version "2.10")
+    (version "2.11")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -3829,7 +3815,7 @@ event-based scripts for scrobbling, notifications, etc.")
                     "picard/picard-" version ".tar.gz"))
               (sha256
                (base32
-                "0f9rvif9m83jhal9n9x8kks17c0cgcipi1hjqmki7a296lz175ss"))))
+                "0ppq2n9jf8c8r8p9dkpcyipd2psr9hg0zbd5hcdsicili25336j4"))))
     (build-system python-build-system)
     (arguments
      (list

gnu/packages/networking.scm

@@ -62,6 +62,8 @@
 ;;; Copyright © 2023 Zheng Junjie <873216071@qq.com>
 ;;; Copyright © 2023 Artyom V. Poptsov <poptsov.artyom@gmail.com>
 ;;; Copyright © 2024 Tomas Volf <~@wolfsden.cz>
+;;; Copyright © 2022 Dominic Martinez <dom@dominicm.dev>
+;;; Copyright © 2024 Alexey Abramov <levenson@mmer.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -125,7 +127,11 @@
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
+  #:use-module (gnu packages golang-check)
+  #:use-module (gnu packages golang-crypto)
   #:use-module (gnu packages golang-web)
+  #:use-module (gnu packages golang-xyz)
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages gstreamer)
   #:use-module (gnu packages gtk)
@@ -832,7 +838,7 @@ at the link-layer level.")
              (substitute* "src/supplemental/websocket/CMakeLists.txt"
                (("nng_test\\(wssfile_test\\)") "")))))))
     (native-inputs (list oksh))
-    (inputs (list mbedtls-apache))
+    (inputs (list mbedtls-lts))
     (synopsis "Lightweight messaging library")
     (description "NNG project is a rewrite of the scalability protocols library
 known as libnanomsg, and adds significant new capabilities, while retaining
@@ -4551,7 +4557,7 @@ network.")
 (define-public ngtcp2
   (package
     (name "ngtcp2")
-    (version "1.1.0")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
@@ -4559,7 +4565,7 @@ network.")
                            "releases/download/v" version "/"
                            "ngtcp2-" version ".tar.xz"))
        (sha256
-        (base32 "1pppl6s25hz91w6321g1q7dqvfy4vccz9mmc5r8sfdvdc95fngl0"))))
+        (base32 "158acn01df6sxqjqx4h948phpcgc2da88aiqn9p2jqgqph48brxh"))))
     (build-system gnu-build-system)
     (arguments
      (list
@@ -4670,6 +4676,91 @@ IPv6 Internet connectivity - it also works over IPv4.")
      ;; which apply to the Application, with which you must still comply
      license:lgpl3)))
 
+(define-public nebula
+  (package
+    (name "nebula")
+    (version "1.8.2")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/slackhq/nebula")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0ly1axgmskrkmxhzymqis6gxf2wd7rvhycm94wfb8k0hirndvg5m"))
+              ;; Remove windows-related binary blobs and files
+              (snippet
+               #~(begin
+                   (use-modules (guix build utils))
+                   (delete-file-recursively "dist/windows")
+                   (delete-file-recursively "wintun")))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:go go-1.20
+      #:import-path "github.com/slackhq/nebula"
+      #:install-source? #f
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'build
+            (lambda* (#:key import-path #:allow-other-keys)
+              ;; Suggested option to provide build time flags is not supported
+              ;; in Guix for go-build-system.
+              ;; -ldflags "-X main.Build=SOMEVERSION"
+              (substitute* (string-append "src/" import-path "/cmd/nebula/main.go")
+                (("Version: ")
+                 (string-append "Version: " #$version)))
+              ;; Build nebula and nebula-cert
+              (let* ((dir "github.com/slackhq/nebula")
+                     (nebula-cmd (string-append dir "/cmd/nebula"))
+                     (cert-cmd (string-append dir "/cmd/nebula-cert")))
+                (invoke "go" "build" nebula-cmd)
+                (invoke "go" "build" cert-cmd))))
+          (replace 'install
+            (lambda _
+              (let* ((out #$output)
+                     (bindir (string-append out "/bin")))
+                (install-file "nebula" bindir)
+                (install-file "nebula-cert" bindir)))))))
+    (inputs
+     (list go-dario-cat-mergo
+           go-github-com-anmitsu-go-shlex
+           go-github-com-armon-go-radix
+           go-github-com-cespare-xxhash
+           go-github-com-cyberdelia-go-metrics-graphite
+           go-github-com-flynn-noise
+           go-github-com-gogo-protobuf
+           go-github-com-google-gopacket
+           go-github-com-miekg-dns
+           go-github-com-nbrownus-go-metrics-prometheus
+           go-github-com-prometheus-client-golang
+           go-github-com-prometheus-client-model
+           go-github-com-prometheus-procfs
+           go-github-com-rcrowley-go-metrics
+           go-github-com-sirupsen-logrus
+           go-github-com-skip2-go-qrcode
+           go-github-com-songgao-water
+           go-github-com-stretchr-testify
+           go-golang-org-x-crypto
+           go-golang-org-x-net
+           go-golang-org-x-sys
+           go-golang-org-x-term
+           go-google-golang-org-protobuf
+           go-gopkg-in-yaml-v2
+           go-netlink
+           go-netns))
+    (home-page "https://github.com/slackhq/nebula")
+    (synopsis "Scalable, peer-to-peer overlay networking tool")
+    (description
+     "Nebula is a peer-to-peer networking tool based on the
+@url{https://noiseprotocol.org/, Noise Protocol Framework}.  It is not a fully
+decentralized network, but instead uses central discovery nodes and a
+certificate authority to facilitate direct, encrypted peer-to-peer connections
+from behind most firewalls and @acronym{NAT, Network Address Translation}
+layers.")
+    (license license:expat)))
+
 (define-public netdiscover
   (package
    (name "netdiscover")
@@ -4701,7 +4792,7 @@ on hub/switched networks.  It is based on @acronym{ARP} packets, it will send
 (define-public phantomsocks
   (package
     (name "phantomsocks")
-    (version "0.0.0-20231031033204-8b0ac27fc450")
+    (version "0.0.0-20240125140126-2576269ca69a")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -4710,10 +4801,10 @@ on hub/switched networks.  It is based on @acronym{ARP} packets, it will send
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1q4i8pgj6hzry9wzlczx729dmmgqdqfb26rfaim2ngmp1dyy9drl"))))
+                "1kbcr6580a9pi0a3wssnfr3mnxqq2k9w1fg4khikn82lqaljab2f"))))
     (build-system go-build-system)
     (arguments
-     (list #:go go-1.20
+     (list #:go go-1.21
            #:install-source? #f
            #:import-path "github.com/macronut/phantomsocks"
            #:build-flags #~'("-tags" #$(if (target-linux?)
@@ -4779,6 +4870,7 @@ implementations.")
     (home-page "https://www.chiark.greenend.org.uk/~sgtatham/putty/")
     (license license:expat)))
 
+
 (define-public vnstat
   (package
    (name "vnstat")

gnu/packages/node-xyz.scm

@@ -702,6 +702,32 @@ Subsequent calls will either return the cached previous value or throw an error
 if desired.")
     (license license:isc)))
 
+(define-public node-path-key
+  (package
+    (name "node-path-key")
+    (version "4.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/sindresorhus/path-key")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "09f4rf70qhq234fcc3pw9nrqic8cb75pk2b6wfnpr96v0r1h8d8g"))))
+    (build-system node-build-system)
+    (arguments
+     '(#:tests? #f
+       #:phases (modify-phases %standard-phases
+                  (add-after 'patch-dependencies 'delete-dependencies
+                    (lambda _
+                      (delete-dependencies '("@types/node" "ava" "tsd" "xo")))))))
+    (home-page "https://github.com/sindresorhus/path-key")
+    (synopsis "Cross-platform utility to compute the PATH environment variable key")
+    (description "@code{path-key} provides an implementation to compute the
+particular cross-platform spellings of the PATH environment variable key.")
+    (license license:expat)))
+
 (define-public node-ieee754
   (package
     (name "node-ieee754")

gnu/packages/ocr.scm

@@ -3,7 +3,7 @@
 ;;; Copyright © 2016, 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Alex Vong <alexvong1995@gmail.com>
-;;; Copyright © 2021 Andy Tai <atai@atai.org>
+;;; Copyright © 2021, 2024 Andy Tai <atai@atai.org>
 ;;; Copyright © 2021, 2022 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;;
@@ -56,14 +56,14 @@
 (define-public ocrad
   (package
     (name "ocrad")
-    (version "0.28")
+    (version "0.29")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnu/ocrad/ocrad-"
                                  version ".tar.lz"))
              (sha256
               (base32
-               "0bmzpcv7sjf8f5pvd9wwh9yp6s7zqd226876g5csmbdxdmbymk1l"))))
+               "1sfrs9jg102malg09cnjdji7lkv9xxccpp3j9a41dfmpn330q80i"))))
     (build-system gnu-build-system)
     (native-inputs (list libpng lzip))
     (home-page "https://www.gnu.org/software/ocrad/")

gnu/packages/package-management.scm

@@ -411,11 +411,12 @@ $(prefix)/etc/openrc\n")))
                                (ssh    (assoc-ref inputs "guile-ssh"))
                                (gnutls (assoc-ref inputs "guile-gnutls"))
                                (disarchive (assoc-ref inputs "disarchive"))
+                               (bzip2 (assoc-ref inputs "guile-bzip2"))
                                (lzma (assoc-ref inputs "guile-lzma"))
                                (locales (assoc-ref inputs "glibc-utf8-locales"))
                                (deps   (list gcrypt json sqlite gnutls git
                                              bs ssh zlib lzlib zstd guile-lib
-                                             disarchive lzma))
+                                             disarchive bzip2 lzma))
                                (deps*  (if avahi (cons avahi deps) deps))
                                (effective
                                 (read-line
@@ -520,6 +521,7 @@ $(prefix)/etc/openrc\n")))
          ("bootstrap/xz" ,(bootstrap-executable "xz" (%current-system)))
 
          ("disarchive" ,disarchive)               ;for 'guix perform-download'
+         ("guile-bzip2" ,guile-bzip2)             ;for Disarchive
          ("guile-lzma" ,guile-lzma)               ;for Disarchive
 
          ("git-minimal" ,git-minimal)             ;for 'guix perform-download'

gnu/packages/parallel.scm

@@ -64,14 +64,14 @@
 (define-public parallel
   (package
     (name "parallel")
-    (version "20231222")
+    (version "20240122")
     (source
      (origin
       (method url-fetch)
       (uri (string-append "mirror://gnu/parallel/parallel-"
                           version ".tar.bz2"))
       (sha256
-       (base32 "1alvva2dlnlq5rbbklzc2a7l84mg550l1xc632zdgfx9dzf6sihr"))
+       (base32 "17s4bdywswgrib6zzj2wcmzf792aw85rcavbn6vdf734np5qi5l5"))
       (snippet
        '(begin
           (use-modules (guix build utils))

gnu/packages/password-utils.scm

@@ -91,6 +91,7 @@
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
   #:use-module (gnu packages golang-crypto)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages guile)
@@ -852,7 +853,7 @@ key URIs using the standard otpauth:// scheme.")
 (define-public qtpass
   (package
     (name "qtpass")
-    (version "1.3.2")
+    (version "1.4.0")
     (source
      (origin
        (method git-fetch)
@@ -861,65 +862,37 @@ key URIs using the standard otpauth:// scheme.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32
+        (base32 "10ixahm4ap0l1rrz4cyswblm22ns9z1baf5lv3dn23wprfdcp8m0"))))
-         "0748hjvhjrybi33ci3c8hcr74k9pdrf5jv8npf9hrsrmdyy1kr9x"))))
+    (build-system qt-build-system)
-    (build-system gnu-build-system)
     (arguments
-     `(#:modules ((guix build gnu-build-system)
+     (list
-                  (guix build qt-utils)
+      #:test-target "check"
-                  (guix build utils))
+      #:phases
-       #:imported-modules (,@%gnu-build-system-modules
+      #~(modify-phases %standard-phases
-                            (guix build qt-utils))
+          (replace 'configure
-       #:phases
+            (lambda _
-       (modify-phases %standard-phases
+              (invoke "qmake"
-         (replace 'configure
+                      "QMAKE_LRELEASE=lrelease"
-           (lambda* (#:key inputs outputs #:allow-other-keys)
+                      "QMAKE_LUPDATE=lupdate"
-             (let ((out (assoc-ref outputs "out")))
+                      (string-append "PREFIX=" #$output))))
-               ;; lupdate/lrelease need to find qmake.
+          (add-before 'check 'pre-check
-               (setenv "QMAKE" "qmake")
+            ;; Fontconfig needs a writable cache.
-               ;; qmake needs to find lrelease/lupdate.
+            (lambda _ (setenv "HOME" "/tmp")))
-               (invoke "qmake"
+          (add-after 'install 'install-auxilliary
-                       "QMAKE_LRELEASE=lrelease"
+            ;; Install man-page, icon and .desktop file.
-                       "QMAKE_LUPDATE=lupdate"
+            (lambda _
-                       (string-append "PREFIX=" out)))))
+              (let ((applications (string-append #$output "/share/applications"))
-         (add-after 'configure 'reset-resource-timestamps
+                    (icons (string-append #$output "/share/icons/hicolor/scalable/apps"))
-           ;; Reset timestamps on localization files for a reproducible build.
+                    (man (string-append #$output "/share/man/man1")))
-           (lambda _
+                (install-file "qtpass.desktop" applications)
-             (with-directory-excursion "localization"
+                (install-file "artwork/icon.svg" icons)
-               (for-each (lambda (file)
+                (rename-file (string-append icons "/icon.svg")
-                           (let* ((base (basename file ".qm"))
+                             (string-append icons "/qtpass-icon.svg"))
-                                  (src (string-append base ".ts"))
+                (install-file "qtpass.1" man)))))))
-                                  (st (stat src)))
-                             (set-file-time file st)))
-                         (find-files "." ".*\\.qm")))
-             #t))
-         (add-after 'install 'install-auxilliary
-           ;; Install man-page, icon and .desktop file.
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (applications (string-append out "/share/applications"))
-                    (icons (string-append out "/share/icons/hicolor/scalable/apps"))
-                    (man (string-append out "/share/man/man1")))
-               (install-file "qtpass.desktop" applications)
-               (install-file "artwork/icon.svg" icons)
-               (rename-file (string-append icons "/icon.svg")
-                            (string-append icons "/qtpass-icon.svg"))
-               (install-file "qtpass.1" man)
-               #t)))
-         (add-after 'install 'wrap-qt
-           (lambda* (#:key outputs inputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out")))
-               (wrap-qt-program "qtpass" #:output out #:inputs inputs))
-             #t))
-         (add-before 'check 'check-setup
-           ;; Make Qt render "offscreen", required for tests.
-           (lambda _
-             (setenv "QT_QPA_PLATFORM" "offscreen")
-             #t)))))
     (native-inputs
      (list qttools-5))
     (inputs
-     (list qtbase-5 qtsvg-5))
+     (list qtsvg-5))
     (home-page "https://qtpass.org")
     (synopsis "GUI for password manager password-store")
     (description

gnu/packages/patches/avalon-toolkit-rdkit-fixes.patch

@@ -0,0 +1,110 @@
+Patches taken from the rdkit fork at this commit (there version
+AvalonToolkit_2.0.6-pre.2):
+https://github.com/rdkit/ava-formake/commit/d05bee0382b8f4696b2b4b05b0038fb7d559520a
+
+diff -ur a/src/main/C/common/reaccsio.c b/src/main/C/common/reaccsio.c
+--- a/src/main/C/common/reaccsio.c
++++ b/src/main/C/common/reaccsio.c
+@@ -322,34 +322,49 @@
+       fprintf(fp,"\n");
+ }
+ 
++#define MAX_BONDLINE_FIELDS 7
++#define BONDLINE_FIELD_LEN 3
++
+ int ReadREACCSBond(Fortran_FILE *fp, struct reaccs_bond_t *bp)
+ {
+-   int nitems, i;
+-   char buffer[MAX_BUFFER+1];
++   int nitems, i, j, k;
++   int bond_line_len, n_chars, pos;
++   int *ptrarray[MAX_BONDLINE_FIELDS];
++   char c;
++   char buffer[BONDLINE_FIELD_LEN+1];
+ 
+    if (fp->status != FORTRAN_NORMAL) return(fp->status);
+ 
+-   strncpy(buffer,fp->buffer,MAX_BUFFER);
+-   /* zero pad only atom numbers! */
+-   for (i=0; i<6; i++) if (buffer[i] == ' ') buffer[i] = '0';
+-
+    bp->stereo_symbol = 0;
+    bp->dummy = 0;
+    bp->topography = 0;
+    bp->reaction_mark = NONE;
+-   // make sure spaces are interpreted the Fortran-way
+-   for (i=9; i<strlen(buffer)  &&  i<21; i+=3)
+-   {
+-       if ((i+1)<strlen(buffer)  &&  buffer[i+1]==' ') buffer[i+1] = '0';
+-       if ((i+2)<strlen(buffer)  &&  buffer[i+2]==' ') buffer[i+2] = '0';
++   ptrarray[0] = &bp->atoms[0];
++   ptrarray[1] = &bp->atoms[1];
++   ptrarray[2] = &bp->bond_type;
++   ptrarray[3] = &bp->stereo_symbol;
++   ptrarray[4] = &bp->dummy;
++   ptrarray[5] = &bp->topography;
++   ptrarray[6] = &bp->reaction_mark;
++   bond_line_len = strlen(fp->buffer);
++   nitems = bond_line_len ? (bond_line_len - 1) / BONDLINE_FIELD_LEN + 1 : 0;
++   if (nitems > MAX_BONDLINE_FIELDS)
++      nitems = MAX_BONDLINE_FIELDS;
++   for (i = 0; i < nitems; ++i)
++   {
++      pos = i * BONDLINE_FIELD_LEN;
++      memset(buffer, 0, BONDLINE_FIELD_LEN + 1);
++      n_chars = bond_line_len - pos;
++      if (n_chars > BONDLINE_FIELD_LEN)
++         n_chars = BONDLINE_FIELD_LEN;
++      for (j = 0, k = 0; j < n_chars; ++j)
++      {
++         c = fp->buffer[pos + j];
++         if (c != ' ')
++            buffer[k++] = c;
++      }
++      sscanf(buffer, "%3d", ptrarray[i]);
+    }
+-   nitems = sscanf(buffer,
+-                   "%3d%3d%3d%3d%3d%3d%3d",
+-                   &bp->atoms[0],   &bp->atoms[1],
+-                   &bp->bond_type,  &bp->stereo_symbol,
+-                   &bp->dummy,
+-                   &bp->topography, &bp->reaction_mark);
+-
+    if (nitems >= 3)
+    {
+       GetBuffer(fp);
+@@ -1582,6 +1597,8 @@
+ 
+    PrintREACCSMolecule(fp, mp,"");
+ 
++   fputc('\0', fp);
++   fflush(fp);
+    rewind(fp);
+ 
+    MolStr = _ReadFile(fp);
+diff -ur a/src/main/C/programs/struchk.c b/src/main/C/programs/struchk.c
+--- a/src/main/C/programs/struchk.c
++++ b/src/main/C/programs/struchk.c
+@@ -1581,6 +1581,22 @@
+ 
+    if ((result & SIZE_CHECK_FAILED) == 0)
+    {
++      for (i = 0; i < mp->n_bonds; ++i) {
++         for (j = 0; j < 2; ++j) {
++            if (mp->bond_array[i].atoms[j] < 1 || mp->bond_array[i].atoms[j] > mp->n_atoms)
++            {
++               snprintf(msg_buffer, MAXMSG,
++                  "%10s    : illegal atom # (%d, max allowed is %d) in bond %d",
++                  mp->name, mp->bond_array[i].atoms[j], mp->n_atoms, i + 1);
++               AddMsgToList(msg_buffer);
++               result |= SIZE_CHECK_FAILED;
++            }
++         }
++      }
++   }
++
++   if ((result & SIZE_CHECK_FAILED) == 0)
++   {
+       if (convert_atom_texts)
+       {
+          tmp = ConvertAtomAliases(mp);

gnu/packages/patches/coq-fix-envvars.patch

@@ -1,53 +0,0 @@
-From 0e76cda958a4d3e4bcbb96e171c26b6b3478c6c2 Mon Sep 17 00:00:00 2001
-From: Julien Lepiller <julien@lepiller.eu>
-Date: Thu, 10 Feb 2022 16:44:10 +0100
-Subject: [PATCH] Fix environment variable usage.
-
----
- boot/env.ml | 26 +++++++++++++++++++-------
- 1 file changed, 19 insertions(+), 7 deletions(-)
-
-diff --git a/boot/env.ml b/boot/env.ml
-index e8521e7..d834a3a 100644
---- a/boot/env.ml
-+++ b/boot/env.ml
-@@ -32,17 +32,29 @@ let fail_msg =
- 
- let fail s = Format.eprintf "%s@\n%!" fail_msg; exit 1
- 
-+let path_to_list p =
-+  let sep = if String.equal Sys.os_type "Win32" then ';' else ':' in
-+    String.split_on_char sep p
-+
- (* This code needs to be refactored, for now it is just what used to be in envvars  *)
- let guess_coqlib () =
-   Util.getenv_else "COQLIB" (fun () ->
-   let prelude = "theories/Init/Prelude.vo" in
--  Util.check_file_else
--    ~dir:Coq_config.coqlibsuffix
--    ~file:prelude
--    (fun () ->
--      if Sys.file_exists (Filename.concat Coq_config.coqlib prelude)
--      then Coq_config.coqlib
--      else fail ()))
-+  let coqlibpath = Util.getenv_else "COQLIBPATH" (fun () -> Coq_config.coqlibsuffix) in
-+  let paths = path_to_list coqlibpath in
-+  let valid_paths =
-+    List.filter
-+      (fun dir -> (Util.check_file_else ~dir:dir ~file:prelude (fun () -> "")) <> "")
-+      paths in
-+  match valid_paths with
-+  | [] ->
-+    if Sys.file_exists (Filename.concat Coq_config.coqlib prelude)
-+    then Coq_config.coqlib
-+    else
-+      fail "cannot guess a path for Coq libraries; please use -coqlib option \
-+            or ensure you have installed the package containing Coq's stdlib (coq-stdlib in OPAM) \
-+            If you intend to use Coq without a standard library, the -boot -noinit options must be used."
-+  | p::_ -> p)
- 
- (* Build layout uses coqlib = coqcorelib *)
- let guess_coqcorelib lib =
--- 
-2.34.0
-

gnu/packages/patches/go-github-com-skip2-go-qrcode-fix-tests.patch

@@ -0,0 +1,37 @@
+From dd203f29a36bf518deacbc03e8562b0195c8345f Mon Sep 17 00:00:00 2001
+From: Dominic Martinez <dom@dominicm.dev>
+Date: Mon, 4 Apr 2022 12:06:03 -0400
+Subject: [PATCH] Fix failing qr decode test
+
+First convert integers into runes before performing a string conversion.
+---
+ qrcode_decode_test.go | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/qrcode_decode_test.go b/qrcode_decode_test.go
+index 1f4b1d3..2b0756b 100644
+--- a/qrcode_decode_test.go
++++ b/qrcode_decode_test.go
+@@ -122,7 +122,7 @@ func TestDecodeAllCharacters(t *testing.T) {
+ 
+ 	// zbarimg has trouble with null bytes, hence start from ASCII 1.
+ 	for i := 1; i < 256; i++ {
+-		content += string(i)
++		content += string(rune(i))
+ 	}
+ 
+ 	q, err := New(content, Low)
+@@ -154,7 +154,7 @@ func TestDecodeFuzz(t *testing.T) {
+ 		for j := 0; j < len; j++ {
+ 			// zbarimg seems to have trouble with special characters, test printable
+ 			// characters only for now.
+-			content += string(32 + r.Intn(94))
++			content += string(rune(32 + r.Intn(94)))
+ 		}
+ 
+ 		for _, level := range []RecoveryLevel{Low, Medium, High, Highest} {
+
+base-commit: da1b6568686e89143e94f980a98bc2dbd5537f13
+-- 
+2.34.0
+

gnu/packages/patches/libgeotiff-fix-tests-on-i386.patch

@@ -0,0 +1,35 @@
+From 9990160268fafb71751d4f3a9ad724df70cb9451 Mon Sep 17 00:00:00 2001
+From: Bas Couwenberg <sebastic@xs4all.nl>
+Date: Fri, 1 Dec 2023 10:35:46 +0100
+Subject: [PATCH] Fix test failure on i386.
+
+---
+https://github.com/OSGeo/libgeotiff/pull/107
+
+ test/testlistgeo | 6 ++++++
+ 1 file changed, 6 insertions(+)
+
+diff --git a/test/testlistgeo b/test/testlistgeo
+index 48e92eb..ceec2e6 100755
+--- a/test/testlistgeo
++++ b/test/testlistgeo
+@@ -218,6 +218,9 @@ echo "" >>${OUT}
+ sed "s/ETRS89-extended/ETRS89/g" < ${OUT} > ${OUT}.tmp
+ mv ${OUT}.tmp ${OUT}
+ 
++sed "s/ProjCenterLongGeoKey: 46.437229 ( 46d26'14.02\"E)/ProjCenterLongGeoKey: 46.437229 ( 46d26'14.03\"E)/" < ${OUT} > ${OUT}.tmp
++mv ${OUT}.tmp ${OUT}
++
+ sed "s/ETRS89-extended/ETRS89/g" < ${TEST_CLI_DIR}/testlistgeo_out.dist > testlistgeo_out.dist.normalized
+ 
+ sed "s/GCS: 4053\/Unspecified datum based upon the International 1924 Authalic Sphere/GCS: 10346\/NSIDC Authalic Sphere/g" < ${OUT} > ${OUT}.tmp
+@@ -230,6 +233,9 @@ mv testlistgeo_out.dist.normalized.tmp testlistgeo_out.dist.normalized
+ sed "s/Datum: 6053\/Not specified (based on International 1924 Authalic Sphere)/Datum: 1360\/NSIDC International 1924 Authalic Sphere/g" < testlistgeo_out.dist.normalized > testlistgeo_out.dist.normalized.tmp
+ mv testlistgeo_out.dist.normalized.tmp testlistgeo_out.dist.normalized
+ 
++sed "s/ProjCenterLongGeoKey: 46.437229 ( 46d26'14.02\"E)/ProjCenterLongGeoKey: 46.437229 ( 46d26'14.03\"E)/" < testlistgeo_out.dist.normalized > testlistgeo_out.dist.normalized.tmp
++mv testlistgeo_out.dist.normalized.tmp testlistgeo_out.dist.normalized
++
+ # do 'diff' with distribution results
+ # after cleaning for avoid spurios result due 
+ # to different build dir

gnu/packages/patches/libgeotiff-fix-tests-with-proj-9.3.0.patch

@@ -0,0 +1,51 @@
+From 3806fdab4a17f44641a2113faec778e756e2be3d Mon Sep 17 00:00:00 2001
+From: Even Rouault <even.rouault@spatialys.com>
+Date: Tue, 29 Aug 2023 19:04:25 +0200
+Subject: [PATCH] Fix 'make check' to pass with PROJ 9.3 (fixes #89)
+
+---
+https://github.com/OSGeo/libgeotiff/pull/90
+
+ test/testlistgeo | 16 +++++++++++++---
+ 1 file changed, 13 insertions(+), 3 deletions(-)
+
+diff --git a/test/testlistgeo b/test/testlistgeo
+index 9a41e74..48e92eb 100755
+--- a/test/testlistgeo
++++ b/test/testlistgeo
+@@ -218,14 +218,24 @@ echo "" >>${OUT}
+ sed "s/ETRS89-extended/ETRS89/g" < ${OUT} > ${OUT}.tmp
+ mv ${OUT}.tmp ${OUT}
+ 
+-sed "s/ETRS89-extended/ETRS89/g" < ${TEST_CLI_DIR}/testlistgeo_out.dist > testlistgeo_out.dist.tmp
++sed "s/ETRS89-extended/ETRS89/g" < ${TEST_CLI_DIR}/testlistgeo_out.dist > testlistgeo_out.dist.normalized
++
++sed "s/GCS: 4053\/Unspecified datum based upon the International 1924 Authalic Sphere/GCS: 10346\/NSIDC Authalic Sphere/g" < ${OUT} > ${OUT}.tmp
++mv ${OUT}.tmp ${OUT}
++sed "s/Datum: 6053\/Not specified (based on International 1924 Authalic Sphere)/Datum: 1360\/NSIDC International 1924 Authalic Sphere/g" < ${OUT} > ${OUT}.tmp
++mv ${OUT}.tmp ${OUT}
++
++sed "s/GCS: 4053\/Unspecified datum based upon the International 1924 Authalic Sphere/GCS: 10346\/NSIDC Authalic Sphere/g" < testlistgeo_out.dist.normalized > testlistgeo_out.dist.normalized.tmp
++mv testlistgeo_out.dist.normalized.tmp testlistgeo_out.dist.normalized
++sed "s/Datum: 6053\/Not specified (based on International 1924 Authalic Sphere)/Datum: 1360\/NSIDC International 1924 Authalic Sphere/g" < testlistgeo_out.dist.normalized > testlistgeo_out.dist.normalized.tmp
++mv testlistgeo_out.dist.normalized.tmp testlistgeo_out.dist.normalized
+ 
+ # do 'diff' with distribution results
+ # after cleaning for avoid spurios result due 
+ # to different build dir
+ sed -e "s/Testing listgeo .*test/Testing listgeo ..\/test/"  -i ${OUT}
+ echo "diff ${OUT} with testlistgeo_out.dist"
+-diff -u ${OUT} testlistgeo_out.dist.tmp
++diff -u ${OUT} testlistgeo_out.dist.normalized
+ if [ $? -ne 0 ] ; then
+     echo  ""
+     echo "PROBLEMS HAVE OCCURRED"
+@@ -236,7 +246,7 @@ else
+     echo "TEST OK"
+     echo "test file ${OUT} removed"
+     echo
+-    rm testlistgeo_out.dist.tmp
++    rm testlistgeo_out.dist.normalized
+     /bin/rm -f ${OUT}
+     exit 0
+ fi

gnu/packages/patches/libgeotiff-fix-tests-with-proj-9.3.1.patch

@@ -0,0 +1,40 @@
+From 4f90e57fa1cac7afdd57e5f649775cb24aa15612 Mon Sep 17 00:00:00 2001
+From: Bas Couwenberg <sebastic@xs4all.nl>
+Date: Fri, 1 Dec 2023 08:23:20 +0100
+Subject: [PATCH] Fix test failure with PROJ 9.3.1.
+
+Closes: #104
+---
+https://github.com/OSGeo/libgeotiff/pull/105
+
+ test/testlistgeo | 10 ++++++++++
+ 1 file changed, 10 insertions(+)
+
+diff --git a/test/testlistgeo b/test/testlistgeo
+index 48e92eb..4331cc3 100755
+--- a/test/testlistgeo
++++ b/test/testlistgeo
+@@ -218,6 +218,11 @@ echo "" >>${OUT}
+ sed "s/ETRS89-extended/ETRS89/g" < ${OUT} > ${OUT}.tmp
+ mv ${OUT}.tmp ${OUT}
+ 
++sed "s/Projection = 15914 (BLM zone 14N (US survey .*))/Projection = 15914 (BLM zone 14N)/g" < ${OUT} > ${OUT}.tmp
++mv ${OUT}.tmp ${OUT}
++sed "s/Projection = 6753 (Oregon Columbia River West zone (.*))/Projection = 6753 (Oregon Columbia River West zone)/" < ${OUT} > ${OUT}.tmp
++mv ${OUT}.tmp ${OUT}
++
+ sed "s/ETRS89-extended/ETRS89/g" < ${TEST_CLI_DIR}/testlistgeo_out.dist > testlistgeo_out.dist.normalized
+ 
+ sed "s/GCS: 4053\/Unspecified datum based upon the International 1924 Authalic Sphere/GCS: 10346\/NSIDC Authalic Sphere/g" < ${OUT} > ${OUT}.tmp
+@@ -230,6 +235,11 @@ mv testlistgeo_out.dist.normalized.tmp testlistgeo_out.dist.normalized
+ sed "s/Datum: 6053\/Not specified (based on International 1924 Authalic Sphere)/Datum: 1360\/NSIDC International 1924 Authalic Sphere/g" < testlistgeo_out.dist.normalized > testlistgeo_out.dist.normalized.tmp
+ mv testlistgeo_out.dist.normalized.tmp testlistgeo_out.dist.normalized
+ 
++sed "s/Projection = 15914 (BLM zone 14N (US survey .*))/Projection = 15914 (BLM zone 14N)/" < testlistgeo_out.dist.normalized > testlistgeo_out.dist.normalized.tmp
++mv testlistgeo_out.dist.normalized.tmp testlistgeo_out.dist.normalized
++sed "s/Projection = 6753 (Oregon Columbia River West zone (.*))/Projection = 6753 (Oregon Columbia River West zone)/" < testlistgeo_out.dist.normalized > testlistgeo_out.dist.normalized.tmp
++mv testlistgeo_out.dist.normalized.tmp testlistgeo_out.dist.normalized
++
+ # do 'diff' with distribution results
+ # after cleaning for avoid spurios result due 
+ # to different build dir

gnu/packages/patches/ocaml-dose3-Fix-for-ocaml-4.06.patch

@@ -1,52 +0,0 @@
-From aeca7656f499d7f4595319858f242276920e31bb Mon Sep 17 00:00:00 2001
-From: Louis Gesbert <louis.gesbert@ocamlpro.com>
-Date: Sat, 2 Dec 2017 12:51:01 +0100
-Subject: [PATCH] Fix for ocaml 4.06
-
----
- common/criteria_lexer.mll | 8 ++++----
- common/util.ml            | 2 +-
- 2 files changed, 5 insertions(+), 5 deletions(-)
-
-diff --git a/common/criteria_lexer.mll b/common/criteria_lexer.mll
-index 71f9178..fc4eae3 100644
---- a/common/criteria_lexer.mll
-+++ b/common/criteria_lexer.mll
-@@ -18,7 +18,7 @@
-     let c = Lexing.lexeme_char lexbuf 2 in (* the delimiter can be any character *)
-     (* find the terminating delimiter *)
-     let endpos =
--      try String.index_from lexbuf.lex_buffer (lexbuf.lex_start_pos + 3) c with
-+      try Bytes.index_from lexbuf.lex_buffer (lexbuf.lex_start_pos + 3) c with
-       |Invalid_argument _ ->
-           raise (Format822.Syntax_error (
-             Format822.error lexbuf "String too short"))
-@@ -27,9 +27,9 @@
-             Format822.error lexbuf (Printf.sprintf "cannot find: %c" c)))
-     in
-     let len = endpos - (lexbuf.lex_start_pos + 3) in
--    let s = String.sub lexbuf.lex_buffer (lexbuf.lex_start_pos + 3) len in
--    lexbuf.Lexing.lex_curr_pos <- lexbuf.Lexing.lex_start_pos + ((String.length s)+4);
--    s
-+    let s = Bytes.sub lexbuf.lex_buffer (lexbuf.lex_start_pos + 3) len in
-+    lexbuf.Lexing.lex_curr_pos <- lexbuf.Lexing.lex_start_pos + ((Bytes.length s)+4);
-+    Bytes.to_string s
- 
- }
- 
-diff --git a/common/util.ml b/common/util.ml
-index 598f266..36ca3d1 100644
---- a/common/util.ml
-+++ b/common/util.ml
-@@ -87,7 +87,7 @@ module MakeMessages(X : sig val label : string end) = struct
-   let clean label =
-     try 
-       let s = Filename.chop_extension (Filename.basename label) in
--      String.capitalize s
-+      String.capitalize_ascii s
-     with Invalid_argument _ -> label
- 
-   let create ?(enabled=false) label =
--- 
-2.11.0
-

gnu/packages/patches/ocaml-dose3-Install-mli-cmx-etc.patch

@@ -1,133 +0,0 @@
-From b5314c20d8e3caf62fe0dc96ad937a2950158b23 Mon Sep 17 00:00:00 2001
-From: Louis Gesbert <louis.gesbert@ocamlpro.com>
-Date: Thu, 2 Mar 2017 12:19:56 +0100
-Subject: [PATCH] Install mli, cmx, etc.
-
----
- Makefile | 26 +++++++++++++-------------
- 1 file changed, 13 insertions(+), 13 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 09464ff..5044d7f 100644
---- a/Makefile
-+++ b/Makefile
-@@ -56,7 +56,7 @@ $(DOSELIBS)/cudf.%:
- 	@for i in _build/cudf/cudf.*; do \
- 	  if [ -e $$i ]; then \
- 	  cp $$i $(DOSELIBS) ; \
--	  rm -f $(DOSELIBS)/*.mlpack $(DOSELIBS)/*.cmx ; \
-+	  rm -f $(DOSELIBS)/*.mlpack ; \
- 	  fi ; \
- 	done
- 
-@@ -67,7 +67,7 @@ $(DOSELIBS)/common.%: common/*.ml common/*.mli
- 	  if [ -e $$i ]; then \
- 	  cp $$i $(DOSELIBS) ; \
- 		rm $$i ;\
--	  rm -f $(DOSELIBS)/*.mlpack $(DOSELIBS)/*.cmx ; \
-+	  rm -f $(DOSELIBS)/*.mlpack ; \
- 	  fi ; \
- 	done
- 
-@@ -78,7 +78,7 @@ $(DOSELIBS)/versioning.%: versioning/*.ml versioning/*.mli
- 	  if [ -e $$i ]; then \
- 	  cp $$i $(DOSELIBS) ; \
- 		rm $$i ;\
--	  rm -f $(DOSELIBS)/*.mlpack $(DOSELIBS)/*.cmx ; \
-+	  rm -f $(DOSELIBS)/*.mlpack ; \
- 	  fi ; \
- 	done
- 
-@@ -88,7 +88,7 @@ $(DOSELIBS)/algo.%: algo/*.ml algo/*.mli $(DOSELIBS)/common.%
- 	  if [ -e $$i ]; then \
- 	  cp $$i $(DOSELIBS) ; \
- 		rm $$i ;\
--	  rm -f $(DOSELIBS)/*.mlpack $(DOSELIBS)/*.cmx ; \
-+	  rm -f $(DOSELIBS)/*.mlpack ; \
- 	  fi ; \
- 	done
- 
-@@ -98,7 +98,7 @@ $(DOSELIBS)/debian.%: deb/*.ml deb/*.mli $(DOSELIBS)/pef.%
- 	  if [ -e $$i ]; then \
- 	  cp $$i $(DOSELIBS) ; \
- 		rm $$i ;\
--	  rm -f $(DOSELIBS)/*.mlpack $(DOSELIBS)/*.cmx ; \
-+	  rm -f $(DOSELIBS)/*.mlpack ; \
- 	  fi ; \
- 	done
- 
-@@ -108,7 +108,7 @@ $(DOSELIBS)/opam.%: opam/*.ml opam/*.mli $(DOSELIBS)/pef.%
- 	  if [ -e $$i ]; then \
- 	  cp $$i $(DOSELIBS) ; \
- 		rm $$i ;\
--	  rm -f $(DOSELIBS)/*.mlpack $(DOSELIBS)/*.cmx ; \
-+	  rm -f $(DOSELIBS)/*.mlpack ; \
- 	  fi ; \
- 	done
- 
-@@ -118,7 +118,7 @@ $(DOSELIBS)/npm.%: npm/*.ml npm/*.mli $(DOSELIBS)/versioning.% $(DOSELIBS)/pef.%
- 	  if [ -e $$i ]; then \
- 	  cp $$i $(DOSELIBS) ; \
- 		rm $$i ;\
--	  rm -f $(DOSELIBS)/*.mlpack $(DOSELIBS)/*.cmx ; \
-+	  rm -f $(DOSELIBS)/*.mlpack ; \
- 	  fi ; \
- 	done
- 
-@@ -128,7 +128,7 @@ $(DOSELIBS)/rpm.%: rpm/*.ml $(DOSELIBS)/algo.%
- 	  if [ -e $$i ]; then \
- 	  cp $$i $(DOSELIBS) ; \
- 		rm $$i ;\
--	  rm -f $(DOSELIBS)/*.mlpack $(DOSELIBS)/*.cmx ; \
-+	  rm -f $(DOSELIBS)/*.mlpack ; \
- 	  fi ; \
- 	done
- 
-@@ -138,7 +138,7 @@ $(DOSELIBS)/pef.%: pef/*.ml pef/*.mli
- 	  if [ -e $$i ]; then \
- 	  cp $$i $(DOSELIBS) ; \
- 		rm $$i ;\
--	  rm -f $(DOSELIBS)/*.mlpack $(DOSELIBS)/*.cmx ; \
-+	  rm -f $(DOSELIBS)/*.mlpack ; \
- 	  fi ; \
- 	done
- 
-@@ -148,7 +148,7 @@ $(DOSELIBS)/csw.%: opencsw/*.ml $(DOSELIBS)/versioning.%
- 	  if [ -e $$i ]; then \
- 	  cp $$i $(DOSELIBS) ; \
- 		rm $$i ;\
--	  rm -f $(DOSELIBS)/*.mlpack $(DOSELIBS)/*.cmx ; \
-+	  rm -f $(DOSELIBS)/*.mlpack ; \
- 	  fi ; \
- 	done
- 
-@@ -158,7 +158,7 @@ $(DOSELIBS)/doseparse.%: $(DOSELIBS)/pef.% $(DOSELIBS)/debian.%
- 	  if [ -e $$i ]; then \
- 	  cp $$i $(DOSELIBS) ; \
- 		rm $$i ;\
--	  rm -f $(DOSELIBS)/*.mlpack $(DOSELIBS)/*.cmx $(DOSELIBS)/*.ml ; \
-+	  rm -f $(DOSELIBS)/*.mlpack $(DOSELIBS)/*.ml ; \
- 	  fi ; \
- 	done
- 
-@@ -168,7 +168,7 @@ $(DOSELIBS)/doseparseNoRpm.%: $(DOSELIBS)/pef.% $(DOSELIBS)/debian.%
- 	  if [ -e $$i ]; then \
- 			cp $$i $(DOSELIBS) ;\
- 			rm $$i ;\
--			rm -f $(DOSELIBS)/*.mlpack $(DOSELIBS)/*.cmx ;\
-+			rm -f $(DOSELIBS)/*.mlpack ;\
- 	  fi ; \
- 	done
- 
-@@ -223,7 +223,7 @@ INSTALL_STUFF_ = META
- INSTALL_STUFF_ += $(wildcard _build/doselibs/*.cma _build/doselibs/*.cmi)
- INSTALL_STUFF_ += $(wildcard _build/doselibs/*.cmxa _build/doselibs/*.cmxs)
- INSTALL_STUFF_ += $(wildcard _build/doselibs/*.a)
--#INSTALL_STUFF_ += $(wildcard _build/*/*.mli)
-+INSTALL_STUFF_ += $(wildcard _build/doselibs/*.mli) $(wildcard _build/doselibs/*.cmti) $(wildcard _build/doselibs/*.cmx)
- INSTALL_STUFF_ += $(wildcard _build/rpm/*.so)
- 
- exclude_cudf = $(wildcard _build/doselibs/*cudf* _build/cudf/*)
--- 
-2.11.0
-

gnu/packages/patches/ocaml-dose3-add-unix-dependency.patch

@@ -1,25 +0,0 @@
-From b94cf24739818e5aff397e0a83b19ea32dc81f42 Mon Sep 17 00:00:00 2001
-From: Louis Gesbert <louis.gesbert@ocamlpro.com>
-Date: Tue, 6 Feb 2018 10:15:45 +0100
-Subject: [PATCH 3/3] Add "unix" as dependency to dose3.common in META.in
-
----
- META.in | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/META.in b/META.in
-index aa2cd8d..0f9d337 100644
---- a/META.in
-+++ b/META.in
-@@ -8,7 +8,7 @@ package "common" (
- version = "@PACKAGE_VERSION@"
- archive(byte) = "common.cma"
- archive(native) = "common.cmxa"
--requires = "extlib, re.pcre, cudf, @ZIP@, @BZ2@"
-+requires = "extlib, re.pcre, cudf, unix, @ZIP@, @BZ2@"
- )
- 
- package "algo" (
--- 
-2.11.0
-

gnu/packages/patches/ocaml-dose3-dont-make-printconf.patch

@@ -1,9 +0,0 @@
---- a/configure
-+++ b/configure
-@@ -6552,6 +6552,3 @@ if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then
-   { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5
- $as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;}
- fi
--
--
--make printconf

gnu/packages/patches/rdkit-unbundle-external-dependencies.patch

@@ -58,100 +58,83 @@ diff --git a/External/AvalonTools/CMakeLists.txt b/External/AvalonTools/CMakeLis
 index 3e31195fc..314ba35b5 100644
 --- a/External/AvalonTools/CMakeLists.txt
 +++ b/External/AvalonTools/CMakeLists.txt
-@@ -2,107 +2,14 @@ if(NOT RDK_BUILD_AVALON_SUPPORT)
+@@ -2,90 +2,8 @@ if(NOT RDK_BUILD_AVALON_SUPPORT)
    return()
  endif(NOT RDK_BUILD_AVALON_SUPPORT)
  
+-set(AVALON_VERSION "2.0.5-pre.3")
 -if(NOT DEFINED AVALONTOOLS_DIR)
--  set(AVALONTOOLS_DIR "${CMAKE_CURRENT_SOURCE_DIR}/SourceDistribution")
+-  set(AVALONTOOLS_DIR "${CMAKE_CURRENT_SOURCE_DIR}/ava-formake-AvalonToolkit_${AVALON_VERSION}")
--  set(fileToPatch "${CMAKE_CURRENT_SOURCE_DIR}/SourceDistribution/common/reaccsio.c")
+-  set(fileToCheck "${AVALONTOOLS_DIR}/src/main/C/common/reaccsio.c")
 -  set(needDownload "TRUE")
--  if(EXISTS "${fileToPatch}")
+-  if(EXISTS "${fileToCheck}")
--    file(READ "${fileToPatch}" buffer)
+-    set(needDownload "FALSE")
--    if("${buffer}" MATCHES "//MyFree\\(\\(char \\*\\)tempdir\\);")
--      set(needDownload "FALSE")
--    endif()
 -  endif()
 -else()
 -  string(REGEX REPLACE "\\\\" "/" AVALONTOOLS_DIR ${AVALONTOOLS_DIR})
 -  set(needDownload "FALSE")
 -endif()
 -
--set(AVALON_SRC_PATH ${AVALONTOOLS_DIR}/common)
+-set(AVALON_SRC_PATH "${AVALONTOOLS_DIR}/src/main/C")
+-set(AVALON_COMMON_PATH "${AVALON_SRC_PATH}/common")
+-set(AVALON_INCLUDE_PATH "${AVALON_SRC_PATH}/include")
+-set(AVALON_PROGRAMS_PATH "${AVALON_SRC_PATH}/programs")
 -
 -if(needDownload)
 -  if(NOT DEFINED AVALONTOOLS_URL)
--    set(AVALONTOOLS_URL "https://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.2/AvalonToolkit_1.2.0.source.tar")
+-    set(AVALONTOOLS_URL "https://github.com/rdkit/ava-formake/archive/refs/tags/AvalonToolkit_${AVALON_VERSION}.tar.gz")
 -  endif()
 -  if(NOT DEFINED AVALONTOOLS_MD5SUM)
--    set(AVALONTOOLS_MD5SUM "092a94f421873f038aa67d4a6cc8cb54")
+-    set(AVALONTOOLS_MD5SUM "7a20c25a7e79f3344e0f9f49afa03351")
 -  endif()
 -  if(NOT DEFINED AVALONTOOLS_BASE)
 -    string(REGEX REPLACE "^.*/" "" AVALONTOOLS_BASE "${AVALONTOOLS_URL}")
 -  endif()
 -  downloadAndCheckMD5(${AVALONTOOLS_URL} "${CMAKE_CURRENT_SOURCE_DIR}/${AVALONTOOLS_BASE}" ${AVALONTOOLS_MD5SUM})
--  execute_process(COMMAND ${CMAKE_COMMAND} -E tar xf
+-  execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf
--    ${CMAKE_CURRENT_SOURCE_DIR}/AvalonToolkit_1.2.0.source.tar
+-    ${CMAKE_CURRENT_SOURCE_DIR}/AvalonToolkit_${AVALON_VERSION}.tar.gz
 -    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
--  # apply patch to AvalonTools
--  configure_file("${fileToPatch}" "${fileToPatch}.orig" COPYONLY)
--  file(READ "${fileToPatch}" buffer)
--  string(REGEX REPLACE "MyFree\\(\\(char \\*\\)tempdir\\);"
--    "//MyFree((char *)tempdir);" buffer "${buffer}")
--  file(WRITE "${fileToPatch}" "${buffer}")
 -endif()
- 
+-
- if (MSVC)
+-if(CMAKE_C_COMPILER_ID STREQUAL "GNU")
-   add_definitions("/D_CRT_SECURE_NO_WARNINGS")
+-  add_compile_options(-Wno-format-security -Wformat=0 -Wstringop-overflow=0 -Wformat-overflow=0 -Wno-unused-result )
-   add_compile_options(/wd4224 /wd4101 /wd4018 /wd4996 /wd4244 /wd4305 /wd4013 /wd4146 /wd4334 /wd4715 /wd4715 /nologo)
+-endif()
- endif(MSVC)
+-if(CMAKE_C_COMPILER_ID STREQUAL "Clang")
- 
+-  add_compile_options(-Wno-absolute-value -Wno-return-type -Wno-tautological-overlap-compare)
--set(avalon_clib_srcs ${AVALON_SRC_PATH}/layout.c
+-endif()
--	${AVALON_SRC_PATH}/symboltable.c
+-if (MSVC)
--	${AVALON_SRC_PATH}/patclean.c
+-  add_definitions("/D_CRT_SECURE_NO_WARNINGS")
--	${AVALON_SRC_PATH}/utilities.c
+-  add_compile_options(/wd4018 /wd4101 /wd4146 /wd4334 /wd4477 /wd4715 /wd4716 /wd4996 /nologo)
--	${AVALON_SRC_PATH}/symbol_lists.c
+-endif(MSVC)
--	${AVALON_SRC_PATH}/stereo.c
+-
--	${AVALON_SRC_PATH}/set.c
+-set(avalon_clib_srcs ${AVALON_COMMON_PATH}/layout.c
--	${AVALON_SRC_PATH}/perceive.c
+-	${AVALON_COMMON_PATH}/symboltable.c
--	${AVALON_SRC_PATH}/local.c
+-	${AVALON_COMMON_PATH}/patclean.c
--	${AVALON_SRC_PATH}/graph.c
+-	${AVALON_COMMON_PATH}/utilities.c
--	${AVALON_SRC_PATH}/geometry.c
+-	${AVALON_COMMON_PATH}/symbol_lists.c
--	${AVALON_SRC_PATH}/forio.c
+-	${AVALON_COMMON_PATH}/stereo.c
--	${AVALON_SRC_PATH}/depictutil.c
+-	${AVALON_COMMON_PATH}/set.c
--	${AVALON_SRC_PATH}/denormal.c
+-	${AVALON_COMMON_PATH}/perceive.c
--	${AVALON_SRC_PATH}/casutils.c
+-	${AVALON_COMMON_PATH}/local.c
--	${AVALON_SRC_PATH}/ssmatch.c
+-	${AVALON_COMMON_PATH}/graph.c
--	${AVALON_SRC_PATH}/rtutils.c
+-	${AVALON_COMMON_PATH}/geometry.c
--	${AVALON_SRC_PATH}/smi2mol.c
+-	${AVALON_COMMON_PATH}/forio.c
--	${AVALON_SRC_PATH}/didepict.c
+-	${AVALON_COMMON_PATH}/depictutil.c
--	${AVALON_SRC_PATH}/pattern.c
+-	${AVALON_COMMON_PATH}/denormal.c
--	${AVALON_SRC_PATH}/canonizer.c
+-	${AVALON_COMMON_PATH}/casutils.c
--	${AVALON_SRC_PATH}/aacheck.c
+-	${AVALON_COMMON_PATH}/ssmatch.c
--	${AVALON_SRC_PATH}/fixcharges.c
+-	${AVALON_COMMON_PATH}/rtutils.c
--	${AVALON_SRC_PATH}/struchk.c
+-	${AVALON_COMMON_PATH}/smi2mol.c
--	${AVALON_SRC_PATH}/reaccsio.c
+-	${AVALON_COMMON_PATH}/didepict.c
--	${AVALON_SRC_PATH}/hashcode.c
+-	${AVALON_COMMON_PATH}/pattern.c
+-	${AVALON_COMMON_PATH}/canonizer.c
+-	${AVALON_COMMON_PATH}/aacheck.c
+-	${AVALON_COMMON_PATH}/fixcharges.c
+-	${AVALON_PROGRAMS_PATH}/struchk.c
+-	${AVALON_COMMON_PATH}/reaccsio.c
+-	${AVALON_COMMON_PATH}/hashcode.c
 -  )
 -
--# we need this to ensure that builds continue
--# to work on linux systems with older versions
--# of glibc when we're building with gcc-4.1.
--# Without this flag, we'll endup requiring
--# glibc 2.7.
--if(CMAKE_SYSTEM_NAME STREQUAL "Linux")
--    add_definitions(-D_GNU_SOURCE=1)
--endif()
--
--if(CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
--  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-return-type -Wno-implicit-function-declaration -Wno-absolute-value -Wno-parentheses -Wno-logical-op-parentheses -Wno-dangling-else -Wno-format")
--endif()
--if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
--  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-unused-result -Wformat-overflow=0 -Wformat=0 -Wno-format-security -Wno-implicit-function-declaration")
--endif()
--
--
--
 -rdkit_library(avalon_clib ${avalon_clib_srcs})
 -target_compile_definitions(avalon_clib PRIVATE RDKIT_AVALONLIB_BUILD)
 -if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32))
@@ -159,11 +142,11 @@ index 3e31195fc..314ba35b5 100644
 -endif()
 -
 -include_directories(${CMAKE_CURRENT_SOURCE_DIR})
--include_directories(${AVALON_SRC_PATH})
+-include_directories(${AVALON_INCLUDE_PATH})
 -
  rdkit_library(AvalonLib AvalonTools.cpp SHARED 
 -     LINK_LIBRARIES avalon_clib SubstructMatch FileParsers SmilesParse GraphMol DataStructs  )
-+     LINK_LIBRARIES -lavalontoolkit SubstructMatch FileParsers SmilesParse GraphMol DataStructs  )
++     LINK_LIBRARIES -lavalon4rdkit SubstructMatch FileParsers SmilesParse GraphMol DataStructs  )
  target_compile_definitions(AvalonLib PRIVATE RDKIT_AVALONLIB_BUILD)
  rdkit_headers(AvalonTools.h DEST GraphMol)
  rdkit_test(testAvalonLib1 test1.cpp
@@ -278,7 +261,7 @@ diff --git a/External/RingFamilies/CMakeLists.txt b/External/RingFamilies/CMakeL
 index 08dd1fe04..66ecd5834 100644
 --- a/External/RingFamilies/CMakeLists.txt
 +++ b/External/RingFamilies/CMakeLists.txt
-@@ -1,47 +1,6 @@
+@@ -1,47 +1,7 @@
 -add_custom_target(ringdecomposerlib_support ALL)
 -
  if(NOT RDK_USE_URF)
@@ -324,10 +307,9 @@ index 08dd1fe04..66ecd5834 100644
 -rdkit_headers(${URFLIB_DIR}/RingDecomposerLib.h DEST "")
 -
 -
--set(RDK_URF_LIBS RingDecomposerLib
--    CACHE STRING "the libraries for the URF calculation" FORCE)
 +rdkit_library(RingDecomposerLib dummy.cpp SHARED LINK_LIBRARIES -lRingDecomposerLib)
-+set(RDK_URF_LIBS RingDecomposerLib CACHE STRING "" FORCE)
+ set(RDK_URF_LIBS RingDecomposerLib
+     CACHE STRING "the libraries for the URF calculation" FORCE)
 diff --git a/External/RingFamilies/dummy.cpp b/External/RingFamilies/dummy.cpp
 new file mode 100644
 index 000000000..e69de29bb
@@ -335,40 +317,60 @@ diff --git a/External/YAeHMOP/CMakeLists.txt b/External/YAeHMOP/CMakeLists.txt
 index f1027b3bd..8bee2f910 100644
 --- a/External/YAeHMOP/CMakeLists.txt
 +++ b/External/YAeHMOP/CMakeLists.txt
-@@ -18,32 +18,8 @@ endif()
+@@ -4,52 +4,7 @@ endif(NOT RDK_BUILD_YAEHMOP_SUPPORT)
  
- include_directories( ${RDKit_ExternalDir}/YAeHMOP )
+ add_definitions(-DRDK_BUILD_YAEHMOP_SUPPORT)
  
--ExternalProject_Add(yaehmop_project
+-if(NOT DEFINED YAEHMOP_DIR)
--  GIT_REPOSITORY https://github.com/greglandrum/yaehmop.git
+-  set(YAEHMOP_DIR "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop")
--  GIT_TAG master
+-endif()
--  UPDATE_COMMAND ""
+-
--  PATCH_COMMAND ""
+-if(NOT EXISTS "${YAEHMOP_DIR}/tightbind/bind.h")
--  PREFIX ${CMAKE_CURRENT_SOURCE_DIR}
+-    set(RELEASE_NO "2023.03.1")
--  SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop"
+-    set(MD5 "e6450f13e02c54d024233b993c3c7ff6")
--  SOURCE_SUBDIR "tightbind"
+-    downloadAndCheckMD5("https://github.com/greglandrum/yaehmop/archive/refs/tags/v${RELEASE_NO}.tar.gz"
--  CMAKE_ARGS -DUSE_BLAS_LAPACK=OFF -DCMAKE_INSTALL_PREFIX=${PROJECT_BINARY_DIR} -DCMAKE_C_FLAGS=${CMAKE_C_FLAGS} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+-          "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop-${RELEASE_NO}.tar.gz" ${MD5})
--  TEST_COMMAND "")
+-    execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
+-      ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop-${RELEASE_NO}.tar.gz
+-      WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+-
+-    file(RENAME "yaehmop-${RELEASE_NO}" "${YAEHMOP_DIR}")
+-else()
+-  message("-- Found YAeHMOP source in ${YAEHMOP_DIR}")
+-endif()
+-
+-set(yaehmop_INCLUDE_DIRS ${YAEHMOP_DIR}/..
+-     CACHE STRING "yaehmop Include File" FORCE)
+-include_directories(${yaehmop_INCLUDE_DIRS})
+-
+-if(CMAKE_COMPILER_IS_GNUCXX AND NOT CYGWIN)
+-    SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC")
+-endif()
+-if(CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
+-    SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC")
+-endif()
+-
+-# bring in the eHT code, but skip the targets (we'll get yaehmop_eht anyway because it's a dependency)
+-add_subdirectory(yaehmop/tightbind EXCLUDE_FROM_ALL True)
+-
+-# set install dir for the yaehmop library:
+-INSTALL(TARGETS yaehmop_eht EXPORT rdkit-targets
+-        DESTINATION ${RDKit_LibDir}/${RDKLIB_DEST}
+-        COMPONENT runtime )
+-
+-
 -
--include_directories(${PROJECT_BINARY_DIR}/include)
--link_directories(${PROJECT_BINARY_DIR}/lib)
--link_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build)
 -
 -set(EHT_PARAM_FILE ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop/tightbind/eht_parms.dat )
 -install(FILES ${EHT_PARAM_FILE}
 -        DESTINATION ${RDKit_ShareDir}/Data
 -        COMPONENT data)
 -
--message("YAeHMOP include_dirs: ${PROJECT_BINARY_DIR}/include")
--message("YAeHMOP link_dirs: ${PROJECT_BINARY_DIR}/lib ${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build")
--
 -rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES yaehmop_eht GraphMol )
 +rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES -lyaehmop_eht GraphMol )
  target_compile_definitions(EHTLib PRIVATE RDKIT_EHTLIB_BUILD)
--add_dependencies(EHTLib yaehmop_project)
  rdkit_headers(EHTTools.h DEST GraphMol)
  rdkit_catch_test(testEHTLib1 test1.cpp
-            LINK_LIBRARIES EHTLib FileParsers SmilesParse )
 diff --git a/External/YAeHMOP/EHTTools.cpp b/External/YAeHMOP/EHTTools.cpp
 index 7a229f51f..71033dc5c 100644
 --- a/External/YAeHMOP/EHTTools.cpp
@@ -382,3 +384,23 @@ index 7a229f51f..71033dc5c 100644
  }
  
  namespace RDKit {
+@@ -160,4 +160,4 @@ bool runMol(const ROMol &mol, EHTResults &results, int confId,
+ }
+ 
+ }  // end of namespace EHTTools
+-}  // end of namespace RDKit
+\ No newline at end of file
++}  // end of namespace RDKit
+diff --git a/External/YAeHMOP/Wrap/CMakeLists.txt b/External/YAeHMOP/Wrap/CMakeLists.txt
+index 759a9f360..114d24532 100644
+--- a/External/YAeHMOP/Wrap/CMakeLists.txt
++++ b/External/YAeHMOP/Wrap/CMakeLists.txt
+@@ -4,6 +4,8 @@ rdkit_python_extension(rdEHTTools
+                        DEST Chem
+                        LINK_LIBRARIES
+                        EHTLib )
++
++target_include_directories(rdEHTTools PRIVATE ${RDKit_ExternalDir}/YAeHMOP)
+                        
+ add_pytest(pyEHTTools
+          ${CMAKE_CURRENT_SOURCE_DIR}/testEHTTools.py)

gnu/packages/patches/spdlog-fix-tests.patch

@@ -1,26 +0,0 @@
-Remove after next release and package update:
-https://github.com/gabime/spdlog/commit/2ee8bac78e6525a8ad9a9196e65d502ce390d83a
-
-From 2ee8bac78e6525a8ad9a9196e65d502ce390d83a Mon Sep 17 00:00:00 2001
-From: xvitaly <vitaly@easycoding.org>
-Date: Sun, 23 Jul 2023 10:15:25 +0200
-Subject: [PATCH] Added missing square bracket to fix the level_to_string_view
- test. (#2827)
-
----
- tests/test_misc.cpp | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/tests/test_misc.cpp b/tests/test_misc.cpp
-index 9f3cb1744..6199641ff 100644
---- a/tests/test_misc.cpp
-+++ b/tests/test_misc.cpp
-@@ -43,7 +43,7 @@ TEST_CASE("log_levels", "[log_levels]")
-     REQUIRE(log_info("Hello", spdlog::level::trace) == "Hello");
- }
- 
--TEST_CASE("level_to_string_view", "[convert_to_string_view")
-+TEST_CASE("level_to_string_view", "[convert_to_string_view]")
- {
-     REQUIRE(spdlog::level::to_string_view(spdlog::level::trace) == "trace");
-     REQUIRE(spdlog::level::to_string_view(spdlog::level::debug) == "debug");

gnu/packages/patches/tinydir-fix-cbehave-test.patch

@@ -2,10 +2,22 @@ Make test work with upstream cbehave
 (tinydir bundles a modified version)
 
 diff --git a/tests/file_open_test.c b/tests/file_open_test.c
-index 3e659bc..9f6f88d 100644
+index 09b856e..92b13ca 100644
 --- a/tests/file_open_test.c
 +++ b/tests/file_open_test.c
-@@ -19,4 +19,7 @@ FEATURE(file_open, "File open")
+@@ -4,6 +4,11 @@
+ #include "cbehave.h"
+ #include "util.h"
+ 
++#define ASSERT(cond, ret) \
++if (!(cond)) {\
++    cbehave_feature_return(__FILE__, __LINE__, ret, _state); \
++    goto _feature_over; \
++}\
+ 
+ FEATURE(file_open, "File open")
+ 	SCENARIO("Open file in current directory")
+@@ -34,4 +39,7 @@ FEATURE(file_open, "File open")
  	SCENARIO_END
  FEATURE_END
  

gnu/packages/patool.scm

@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2024 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -20,7 +21,7 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix git-download)
   #:use-module (guix packages)
-  #:use-module (guix build-system python)
+  #:use-module (guix build-system pyproject)
   #:use-module (gnu packages)
   #:use-module (gnu packages backup)
   #:use-module (gnu packages cdrom)
@@ -35,7 +36,7 @@
 (define-public patool
   (package
     (name "patool")
-    (version "1.12")
+    (version "2.1.1")
     (source
      (origin
        (method git-fetch)               ;no test data in PyPI archive
@@ -45,14 +46,20 @@
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0zgvgx9549rvb57rgkpjalydz46k71gibfs6ab3b3sy439s0ay4h"))))
+         "09il0gq1xxlism30hx1aa06alz1xhrnhhwcjzx1znical0bp3q1r"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases (modify-phases %standard-phases
+     (list
-                  (replace 'check
+      #:test-flags
-                    (lambda* (#:key tests? #:allow-other-keys)
+      '(list "-k" (string-append
-                      (when tests?
+                   ;; Disable failing tests.
-                        (invoke "pytest")))))))
+                   "not test_mime_file_compress"
+                   " and not test_mime_file_gzip"
+                   " and not test_mime_file_lzip"
+                   " and not test_bsdtar_gz_file"
+                   " and not test_py_tarfile_gz_file"
+                   " and not test_tar_gz_file"
+                   " and not test_tar_lzip_file"))))
     (native-inputs
      (list bzip2
            cabextract

gnu/packages/pdf.scm

@@ -19,7 +19,7 @@
 ;;; Copyright © 2019,2020 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2020-2023 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2020, 2022 Michael Rohleder <mike@rohleder.de>
-;;; Copyright © 2020 Timotej Lazar <timotej.lazar@araneo.si>
+;;; Copyright © 2020, 2024 Timotej Lazar <timotej.lazar@araneo.si>
 ;;; Copyright © 2020, 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2021 Maxime Devos <maximedevos@telenet.be>
 ;;; Copyright © 2022 Paul A. Patience <paul@apatience.com>
@@ -842,14 +842,14 @@ and based on PDF specification 1.7.")
 (define-public mupdf
   (package
     (name "mupdf")
-    (version "1.23.7")
+    (version "1.23.10")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://mupdf.com/downloads/archive/"
                            "mupdf-" version "-source.tar.lz"))
        (sha256
-        (base32 "0d0ig1amxyy50jvfbn6rz49zd0980p6syqzcx5v7wg0c3pl2iwwm"))
+        (base32 "0p0smyfcziqrnp391l0pmpjca07075km0xlw20kd3hqa919lhq0i"))
        (modules '((guix build utils)
                   (ice-9 ftw)
                   (srfi srfi-1)))

gnu/packages/pretty-print.scm

@@ -172,14 +172,14 @@ different programming languages.")
 (define-public fmt-10
   (package
     (name "fmt")
-    (version "10.1.1")
+    (version "10.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://github.com/fmtlib/fmt/releases/download/"
                            version "/fmt-" version ".zip"))
        (sha256
-        (base32 "06wxxn9yxw44nskdnpwyl6y4j27ssmw5d3d4rnb03df922imhkmq"))))
+        (base32 "1j8nln7rql2nxkhdlgpmx1c1dp6dyxnar1n5r7sjg0rws6i5289i"))))
     (build-system cmake-build-system)
     (arguments '(#:configure-flags '("-DBUILD_SHARED_LIBS=ON")))
     (native-inputs (list unzip))