Merge branch 'master' into gnome-team

.guix-authorizations

@@ -46,11 +46,15 @@
    (name "iyzsong"))
   ("1A85 8392 E331 EAFD B8C2  7FFB F3C1 A0D9 C1D6 5273"
    (name "janneke"))
+  ("3B1D 7F19 E36B B60C 0F5B  2CA9 A52A A2B4 77B6 DD35"
+   (name "jgart"))
   (;; primary: "1BA4 08C5 8BF2 0EA7 3179  635A 865D C0A3 DED9 B5D0"
    "E31D 9DDE EBA5 4A14 8A20  4550 DA45 97F9 47B4 1025"
    (name "jlicht"))
   ("8141 6036 E81A 5CF7 8F80  1071 ECFC 8398 8B4E 4B9F"
    (name "jonsger"))
+  ("3924 8CD8 41C6 3CC3 36DC  AF2F 505E 40B9 1617 1A8A"
+   (name "jpoiret"))
   ("017D 74E2 7F58 5696 3801  781D F663 943E 08D8 092A"
    (name "lbraun"))
   ("CA4F 8CF4 37D7 478F DA05  5FD4 4213 7701 1A37 8446"
@@ -102,4 +106,6 @@
    (name "vagrantc"))
   (;; primary: "C955 CC5D C048 7FB1 7966  40A9 199A F6A3 67E9 4ABB"
    "7238 7123 8EAC EB63 4548  5857 167F 8EA5 001A FA9C"
-   (name "wigust"))))
+   (name "wigust"))
+  ("705A 29B7 01EE 410E B6F9  236E 92F1 D22C 608E E7E5"
+   (name "zimoun"))))

Makefile.am

@@ -407,6 +407,10 @@ AUX_FILES =						\
   gnu/packages/aux-files/chromium/master-preferences.json		\
   gnu/packages/aux-files/emacs/guix-emacs.el		\
   gnu/packages/aux-files/guix.vim			\
+  gnu/packages/aux-files/linux-libre/6.3-arm.conf	\
+  gnu/packages/aux-files/linux-libre/6.3-arm64.conf	\
+  gnu/packages/aux-files/linux-libre/6.3-i686.conf	\
+  gnu/packages/aux-files/linux-libre/6.3-x86_64.conf	\
   gnu/packages/aux-files/linux-libre/6.2-arm.conf	\
   gnu/packages/aux-files/linux-libre/6.2-arm64.conf	\
   gnu/packages/aux-files/linux-libre/6.2-i686.conf	\

doc/build.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2019-2022 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2019-2023 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
 ;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;;
@@ -284,6 +284,9 @@ actual file name."
                      (loop rest))
                     ((('strong _ ...) _ ...)
                      #t)
+                    ((('span ('@ ('class "category")) ;raw Texinfo 6.8
+                             (? string-or-entity?) ...) rest ...)
+                     #t)
                     ((('span ('@ ('class "symbol-definition-category"))
                              (? string-or-entity?) ...) rest ...)
                      #t)
@@ -507,10 +510,16 @@ its <pre class=\"lisp\"> blocks (as produced by 'makeinfo --html')."
 
                   ;; Replace the ugly <strong> used for @deffn etc., which
                   ;; translate to <dt>, with more stylable markup.
-                  (('dt (@ ('id id)) category ... ('strong thing))
+                  (('dt ('@ ('id id))             ;raw Texinfo 6.8
+                        ('span ('@ ('class "category")) category ...)
+                        ('span ('strong thing)
+                               anchor))
                    (highlight-definition id category thing '()))
-                  (('dt (@ ('id id)) category ... ('strong thing)
+                  (('dt (@ ('id id))
-                        (? space?) ('em args ...))
+                        ('span ('@ ('class "category")) category ...)
+                        ('span ('strong thing)
+                               (? space?) ('em args ...)
+                               anchor))
                    (highlight-definition id category thing args))
 
                   ((tag ('@ attributes ...) body ...)

doc/contributing.texi

@@ -1529,7 +1529,7 @@ the patchset.
 
 @example
 $ git send-email -@var{NUMBER_COMMITS} -v@var{REVISION} \
-      --to @var{ISSUE_NUMBER}@@debbugs.gnu.org
+      --to=@var{ISSUE_NUMBER}@@debbugs.gnu.org
 @end example
 
 If need be, you may use @option{--cover-letter --annotate} to send
@@ -1561,7 +1561,7 @@ You can run the following command to have the @code{Mentors} team put in
 CC of a patch series:
 
 @example
-$ git send-email --to @var{ISSUE_NUMBER}@@debbugs.gnu.org \
+$ git send-email --to=@var{ISSUE_NUMBER}@@debbugs.gnu.org \
   --header-cmd='etc/teams.scm cc-mentors-header-cmd' *.patch
 @end example
 
@@ -1571,7 +1571,7 @@ current Git repository to review, you can run:
 
 @example
 $ guix shell -D guix
-[env]$ git send-email --to @var{ISSUE_NUMBER}@@debbugs.gnu.org -2
+[env]$ git send-email --to=@var{ISSUE_NUMBER}@@debbugs.gnu.org -2
 @end example
 
 @node Tracking Bugs and Patches

doc/guix.texi

@@ -113,7 +113,8 @@ Copyright @copyright{} 2022⁠–⁠2023 Bruno Victal@*
 Copyright @copyright{} 2022 Ivan Vilata-i-Balaguer@*
 Copyright @copyright{} 2023 Giacomo Leidi@*
 Copyright @copyright{} 2022 Antero Mejr@*
-Copyright @copyright{} 2023 Karl Hallsby
+Copyright @copyright{} 2023 Karl Hallsby@*
+Copyright @copyright{} 2023 Nathaniel Nicandro@*
 
 Permission is granted to copy, distribute and/or modify this document
 under the terms of the GNU Free Documentation License, Version 1.3 or
@@ -1558,16 +1559,33 @@ be used on Guix System.
 
 @subsubsection Installing the SELinux policy
 @cindex SELinux, policy installation
+
+@quotation Note
+The @code{guix-install.sh} binary installation script offers to perform
+the steps below for you (@pxref{Binary Installation}).
+@end quotation
+
 To install the policy run this command as root:
 
 @example
-semodule -i etc/guix-daemon.cil
+semodule -i /var/guix/profiles/per-user/root/current-guix/share/selinux/guix-daemon.cil
 @end example
 
-Then relabel the file system with @code{restorecon -vR /} or by a
+Then, as root, relabel the file system, possibly after making it
-different mechanism provided by your system.  You may need to remount
+writable:
-@file{/gnu/store} to make it writable first, e.g. with @code{mount -o
+
-remount,rw /gnu/store}.
+@example
+mount -o remount,rw /gnu/store
+restorecon -R /gnu /var/guix
+@end example
+
+At this point you can start or restart @command{guix-daemon}; on a
+distribution that uses systemd as its service manager, you can do that
+with:
+
+@example
+systemctl restart guix-daemon
+@end example
 
 Once the policy is installed, the file system has been relabeled, and
 the daemon has been restarted, it should be running in the
@@ -7784,6 +7802,24 @@ The exact set of supported keywords depends on the build system
 @code{#:phases}.  The @code{#:phases} keyword in particular lets you
 modify the set of build phases for your package (@pxref{Build Phases}).
 
+@quotation Compatibility Note
+Until version 1.3.0, the @code{arguments} field would typically use
+@code{quote} (@code{'}) or @code{quasiquote} (@code{`}) and no
+G-expressions, like so:
+
+@lisp
+(package
+  ;; several fields omitted
+  (arguments   ;old-style quoted arguments
+   '(#:tests? #f
+     #:configure-flags '("--enable-frobbing"))))
+@end lisp
+
+To convert from that style to the one shown above, you can run
+@code{guix style -S arguments @var{package}} (@pxref{Invoking guix
+style}).
+@end quotation
+
 @item @code{inputs} (default: @code{'()})
 @itemx @code{native-inputs} (default: @code{'()})
 @itemx @code{propagated-inputs} (default: @code{'()})
@@ -10379,7 +10415,9 @@ Alternatively, @var{file} may be a list of file names, in which case
 they are all subject to the substitutions.
 
 Be careful about using @code{$} to match the end of a line; by itself it
-won't match the terminating newline of a line.
+won't match the terminating newline of a line.  For example, to match a
+whole line ending with a backslash, one needs a regex like
+@code{"(.*)\\\\\n$"}.
 @end defmac
 
 @subsection File Search
@@ -12987,7 +13025,7 @@ builds @code{lapack}:
 
 @example
 guix build lapack \
-  --with-configure-flag=lapack=-DBUILD_COMPLEX=OFF
+  --with-configure-flag=lapack=-DBUILD_SHARED_LIBS=OFF
 @end example
 
 @quotation Note
@@ -14706,6 +14744,39 @@ Rewriting is done in a conservative way: preserving comments and bailing
 out if it cannot make sense of the code that appears in an inputs field.
 The @option{--input-simplification} option described below provides
 fine-grain control over when inputs should be simplified.
+
+@item arguments
+Rewrite package arguments to use G-expressions (@pxref{G-Expressions}).
+For example, consider this package definition:
+
+@lisp
+(define-public my-package
+  (package
+    ;; @dots{}
+    (arguments      ;old-style quoted arguments
+     '(#:make-flags '("V=1")
+       #:phases (modify-phases %standard-phases
+                  (delete 'build))))))
+@end lisp
+
+@noindent
+Running @command{guix style -S arguments} on this package would rewrite
+its @code{arguments} field like to:
+
+@lisp
+(define-public my-package
+  (package
+    ;; @dots{}
+    (arguments
+      (list #:make-flags #~'("V=1")
+            #:phases #~(modify-phases %standard-phases
+                         (delete 'build))))))
+@end lisp
+
+Note that changes made by the @code{arguments} rule do not entail a
+rebuild of the affected packages.  Furthermore, if a package definition
+happens to be using G-expressions already, @command{guix style} leaves
+it unchanged.
 @end table
 
 @item --list-stylings
@@ -17526,14 +17597,15 @@ hibernation via the @code{resume} kernel argument
                             file-systems)))))
 
 (kernel-arguments
-  (cons* "resume=/swapfile"
+  (cons* "resume=/dev/sda3"        ;device that holds /swapfile
-         "resume_offset=92514304"
+         "resume_offset=92514304"  ;offset of /swapfile on device
          %default-kernel-arguments))
 @end lisp
 
 This other snippet of @code{operating-system} enables the swap file
-@file{/swapfile} for hibernation by telling the kernel about the file
+@file{/swapfile} for hibernation by telling the kernel about the
-(@code{resume} argument) and its offset on disk (@code{resume_offset}
+partition containing it
+(@code{resume} argument) and its offset on that partition (@code{resume_offset}
 argument).  The latter value can be found in the output of the command
 @command{filefrag -e} as the first number right under the
 @code{physical_offset} column header (the second command extracts its
@@ -20000,6 +20072,12 @@ should listen on---e.g., @code{'("eno1")}.
 When set to @code{'all}, the DHCP client listens on all the available
 non-loopback interfaces that can be activated.  Otherwise the DHCP
 client listens only on the specified interfaces.
+
+@item @code{shepherd-requirement} (default: @code{'()})
+This option can be used to provide a list of symbols naming Shepherd services
+that this service will depend on, such as @code{'wpa-supplicant} or
+@code{'iwd} if you require authenticated access for encrypted WiFi or Ethernet
+networks.
 @end table
 @end deftp
 
@@ -20103,7 +20181,7 @@ Data Type representing the configuration of connman.
 @item @code{connman} (default: @var{connman})
 The connman package to use.
 
-@item @code{shepherd-requirement} (default: @code{()})
+@item @code{shepherd-requirement} (default: @code{'()})
 This option can be used to provide a list of symbols naming Shepherd services
 that this service will depend on, such as @code{'wpa-supplicant} or
 @code{'iwd} if you require authenticated access for encrypted WiFi or Ethernet
@@ -28709,6 +28787,243 @@ Extra options to pass to the Prometheus node exporter.
 @end table
 @end deftp
 
+@anchor{vnstat}
+@subsubheading vnStat Network Traffic Monitor
+@cindex vnstat
+
+vnStat is a network traffic monitor that uses interface statistics provided
+by the kernel rather than traffic sniffing.  This makes it a light resource
+monitor, regardless of network traffic rate.
+
+@defvar vnstat-service-type
+This is the service type for the @uref{https://humdi.net/vnstat/,vnStat} daemon
+and accepts a @code{vnstat-configuration} value.
+
+The following example will configure the service with default values:
+
+@lisp
+(service vnstat-service-type)
+@end lisp
+@end defvar
+
+@c %start of fragment
+@deftp {Data Type} vnstat-configuration
+Available @code{vnstat-configuration} fields are:
+
+@table @asis
+@item @code{package} (default: @code{vnstat}) (type: file-like)
+The vnstat package.
+
+@item @code{database-directory} (default: @code{"/var/lib/vnstat"}) (type: string)
+Specifies the directory where the database is to be stored.  A full path
+must be given and a leading '/' isn't required.
+
+@item @code{5-minute-hours} (default: @code{48}) (type: maybe-integer)
+Data retention duration for the 5 minute resolution entries.  The
+configuration defines for how many past hours entries will be stored.
+Set to @code{-1} for unlimited entries or to @code{0} to disable the
+data collection of this resolution.
+
+@item @code{64bit-interface-counters} (default: @code{-2}) (type: maybe-integer)
+Select interface counter handling.  Set to @code{1} for defining that
+all interfaces use 64-bit counters on the kernel side and @code{0} for
+defining 32-bit counter.  Set to @code{-1} for using the old style logic
+used in earlier versions where counter values within 32-bits are assumed
+to be 32-bit and anything larger is assumed to be a 64-bit counter.  This
+may produce false results if a 64-bit counter is reset within the
+32-bits.  Set to @code{-2} for using automatic detection based on
+available kernel datastructures.
+
+@item @code{always-add-new-interfaces?} (default: @code{#t}) (type: maybe-boolean)
+Enable or disable automatic creation of new database entries for
+interfaces not currently in the database even if the database file
+already exists when the daemon is started.  New database entries will
+also get created for new interfaces seen while the daemon is running.
+Pseudo interfaces @samp{lo}, @samp{lo0} and @samp{sit0} are always excluded from getting
+added.
+
+@item @code{bandwidth-detection?} (default: @code{#t}) (type: maybe-boolean)
+Try to automatically detect @var{max-bandwidth} value for each monitored
+interface.  Mostly only ethernet interfaces support this feature.
+@var{max-bandwidth} will be used as fallback value if detection fails.
+Any interface specific @var{max-BW} configuration will disable the
+detection for the specified interface.  In Linux, the detection is
+disabled for tun interfaces due to the Linux kernel always reporting 10
+Mbit regardless of the used real interface.
+
+@item @code{bandwidth-detection-interval} (default: @code{5}) (type: maybe-integer)
+How often in minutes interface specific detection of @var{max-bandwidth}
+is done for detecting possible changes when @var{bandwidth-detection} is
+enabled.  Can be disabled by setting to @code{0}.  Value range:
+@samp{0}..@samp{30}
+
+@item @code{boot-variation} (default: @code{15}) (type: maybe-integer)
+Time in seconds how much the boot time reported by system kernel can
+variate between updates.  Value range: @samp{0}..@samp{300}
+
+@item @code{check-disk-space?} (default: @code{#t}) (type: maybe-boolean)
+Enable or disable the availability check of at least some free disk
+space before a database write.
+
+@item @code{create-directories?} (default: @code{#t}) (type: maybe-boolean)
+Enable or disable the creation of directories when a configured path
+doesn't exist.  This includes @var{database-directory}.
+
+@item @code{daemon-group} (type: maybe-user-group)
+Specify the group to which the daemon process should switch during
+startup.  Set to @code{%unset-value} to disable group switching.
+
+@item @code{daemon-user} (type: maybe-user-account)
+Specify the user to which the daemon process should switch during
+startup.  Set to @code{%unset-value} to disable user switching.
+
+@item @code{daily-days} (default: @code{62}) (type: maybe-integer)
+Data retention duration for the one day resolution entries.  The
+configuration defines for how many past days entries will be stored.  Set
+to @code{-1} for unlimited entries or to @code{0} to disable the data
+collection of this resolution.
+
+@item @code{database-synchronous} (default: @code{-1}) (type: maybe-integer)
+Change the setting of the SQLite "synchronous" flag which controls how
+much care is taken to ensure disk writes have fully completed when
+writing data to the database before continuing other actions.  Higher
+values take extra steps to ensure data safety at the cost of slower
+performance.  A value of @code{0} will result in all handling being left
+to the filesystem itself.  Set to @code{-1} to select the default value
+according to database mode controlled by
+@var{database-write-ahead-logging} setting.  See SQLite documentation
+for more details regarding values from @code{1} to @code{3}.  Value
+range: @samp{-1}..@samp{3}
+
+@item @code{database-write-ahead-logging?} (default: @code{#f}) (type: maybe-boolean)
+Enable or disable SQLite Write-Ahead Logging mode for the database.  See
+SQLite documentation for more details and note that support for
+read-only operations isn't available in older SQLite versions.
+
+@item @code{hourly-days} (default: @code{4}) (type: maybe-integer)
+Data retention duration for the one hour resolution entries.  The
+configuration defines for how many past days entries will be stored.  Set
+to @code{-1} for unlimited entries or to @code{0} to disable the data
+collection of this resolution.
+
+@item @code{log-file} (type: maybe-string)
+Specify log file path and name to be used if @var{use-logging} is set to
+@code{1}.
+
+@item @code{max-bandwidth} (type: maybe-integer)
+Maximum bandwidth for all interfaces.  If the interface specific traffic
+exceeds the given value then the data is assumed to be invalid and
+rejected.  Set to 0 in order to disable the feature.  Value range:
+@samp{0}..@samp{50000}
+
+@item @code{max-bw} (type: maybe-alist)
+Same as @var{max-bandwidth} but can be used for setting individual
+limits for selected interfaces.  This is an association list of
+interfaces as strings to integer values.  For example,
+@lisp
+(max-bw `(("eth0" .  15000)
+          ("ppp0" .  10000)))
+@end lisp
+@var{bandwidth-detection} is disabled on an interface specific level for
+each @var{max-bw} configuration.  Value range: @samp{0}..@samp{50000}
+
+@item @code{monthly-months} (default: @code{25}) (type: maybe-integer)
+Data retention duration for the one month resolution entries.  The
+configuration defines for how many past months entries will be stored.
+Set to @code{-1} for unlimited entries or to @code{0} to disable the
+data collection of this resolution.
+
+@item @code{month-rotate} (default: @code{1}) (type: maybe-integer)
+Day of month that months are expected to change.  Usually set to 1 but
+can be set to alternative values for example for tracking monthly billed
+traffic where the billing period doesn't start on the first day.  For
+example, if set to 7, days of February up to and including the 6th will
+count for January.  Changing this option will not cause existing data to
+be recalculated.  Value range: @samp{1}..@samp{28}
+
+@item @code{month-rotate-affects-years?} (default: @code{#f}) (type: maybe-boolean)
+Enable or disable @var{month-rotate} also affecting yearly data.
+Applicable only when @var{month-rotate} has a value greater than one.
+
+@item @code{offline-save-interval} (default: @code{30}) (type: maybe-integer)
+How often in minutes cached interface data is saved to file when all
+monitored interfaces are offline.  Value range:
+@var{save-interval}..@samp{60}
+
+@item @code{pid-file} (default: @code{"/var/run/vnstatd.pid"}) (type: maybe-string)
+Specify pid file path and name to be used.
+
+@item @code{poll-interval} (default: @code{5}) (type: maybe-integer)
+How often in seconds interfaces are checked for status changes.  Value
+range: @samp{2}..@samp{60}
+
+@item @code{rescan-database-on-save?} (type: maybe-boolean)
+Automatically discover added interfaces from the database and start
+monitoring.  The rescan is done every @var{save-interval} or
+@var{offline-save-interval} minutes depending on the current activity
+state.
+
+@item @code{save-interval} (default: @code{5}) (type: maybe-integer)
+How often in minutes cached interface data is saved to file.  Value
+range: ( @var{update-interval} / 60 )..@samp{60}
+
+@item @code{save-on-status-change?} (default: @code{#t}) (type: maybe-boolean)
+Enable or disable the additional saving to file of cached interface data
+when the availability of an interface changes, i.e., when an interface
+goes offline or comes online.
+
+@item @code{time-sync-wait} (default: @code{5}) (type: maybe-integer)
+How many minutes to wait during daemon startup for system clock to sync
+if most recent database update appears to be in the future.  This may be
+needed in systems without a real-time clock (RTC) which require some
+time after boot to query and set the correct time.  @code{0} = wait
+disabled.  Value range: @samp{0}..@samp{60}
+
+@item @code{top-day-entries} (default: @code{20}) (type: maybe-integer)
+Data retention duration for the top day entries.  The configuration
+defines how many of the past top day entries will be stored.  Set to
+@code{-1} for unlimited entries or to @code{0} to disable the data
+collection of this resolution.
+
+@item @code{trafficless-entries?} (default: @code{#t}) (type: maybe-boolean)
+Create database entries even when there is no traffic during the entry's
+time period.
+
+@item @code{update-file-owner?} (default: @code{#t}) (type: maybe-boolean)
+Enable or disable the update of file ownership during daemon process
+startup.  During daemon startup, only database, log and pid files will
+be modified if the user or group change feature ( @var{daemon-user} or
+@var{daemon-group} ) is enabled and the files don't match the requested
+user or group.  During manual database creation, this option will cause
+file ownership to be inherited from the database directory if the
+directory already exists.  This option only has effect when the process
+is started as root or via sudo.
+
+@item @code{update-interval} (default: @code{20}) (type: maybe-integer)
+How often in seconds the interface data is updated.  Value range:
+@var{poll-interval}..@samp{300}
+
+@item @code{use-logging} (default: @code{2}) (type: maybe-integer)
+Enable or disable logging.  Accepted values are: @code{0} = disabled,
+@code{1} = logfile and @code{2} = syslog.
+
+@item @code{use-utc?} (type: maybe-boolean)
+Enable or disable using UTC as timezone in the database for all entries.
+When enabled, all entries added to the database will use UTC regardless
+of the configured system timezone.  When disabled, the configured system
+timezone will be used.  Changing this setting will not result in already
+existing data to be modified.
+
+@item @code{yearly-years} (default: @code{-1}) (type: maybe-integer)
+Data retention duration for the one year resolution entries.  The
+configuration defines for how many past years entries will be stored.
+Set to @code{-1} for unlimited entries or to @code{0} to disable the
+data collection of this resolution.
+
+@end table
+@end deftp
+@c %end of fragment
+
 @subsubheading Zabbix server
 @cindex zabbix zabbix-server
 Zabbix is a high performance monitoring system that can collect data from a
@@ -37557,6 +37872,9 @@ Number of cached nars to generate at a time.
 Location to fetch nars from when computing cached compressions.  By
 default, the storage location will be used.
 
+@item @code{extra-environment-variables} (default: @code{'()})
+Extra environment variables to set via the shepherd service.
+
 @end table
 @end deftp
 
@@ -38182,15 +38500,14 @@ The following is an example @code{dicod-service-type} configuration.
           (handlers (list
                      (dicod-handler
                       (name "wordnet")
-                      (module "dictorg")
+                      (module "wordnet")
                       (options
-                       (list #~(string-append "dbdir=" #$wordnet))))))
+                       (list #~(string-append "wnhome=" #$wordnet))))))
           (databases (list
                       (dicod-database
                        (name "wordnet")
                        (complex? #t)
-                       (handler "wordnet")
+                       (handler "wordnet"))
-                       (options '("database=wn")))
                       %dicod-database:gcide))))
 @end lisp
 
@@ -42660,9 +42977,11 @@ stateless: it can be replicated elsewhere or at another point in time.
 Preparing this list can be relatively tedious though, which is why
 @code{*unspecified*} is kept as a default.
 
-@item @code{authorized-keys} (default: @code{'()})
+@item @code{authorized-keys} (default: @code{#false})
-This must be a list of file-like objects, each of which containing an
+The default @code{#false} value means: Leave any
-SSH public key that should be authorized to connect to this machine.
+@file{~/.ssh/authorized_keys} file alone.  Otherwise, this must be a
+list of file-like objects, each of which containing an SSH public key
+that should be authorized to connect to this machine.
 
 Concretely, these files are concatenated and made available as
 @file{~/.ssh/authorized_keys}.  If an OpenSSH server, @command{sshd}, is
@@ -43084,8 +43403,10 @@ library is used by many applications to access fonts on the system.
 
 @defvar home-fontconfig-service-type
 This is the service type for generating configurations for Fontconfig.
-Its associated value is a list of strings (or gexps) pointing to fonts
+Its associated value is a list of either strings (or gexps) pointing to
-locations.
+fonts locations, or SXML (@pxref{SXML,,, guile, GNU Guile Reference
+Manual}) fragments to be converted into XML and put inside the main
+@code{fontconfig} node.
 
 Generally, it is better to extend this service than to directly
 configure it, as its default value is the default Guix Home's profile
@@ -43093,13 +43414,17 @@ font installation path (@file{~/.guix-home/profile/share/fonts}).  If
 you configure this service directly, be sure to include the above
 directory.
 
-A typical extension for adding an additional font directory might look
+A typical extension for adding an additional font directory and setting
-like this:
+a font as the default monospace font might look like this:
 
 @lisp
 (simple-service 'additional-fonts-service
                 home-fontconfig-service-type
-                (list "~/.nix-profile/share/fonts"))
+                (list "~/.nix-profile/share/fonts"
+                      '(alias
+                        (family "monospace")
+                        (prefer
+                         (family "Liberation Mono")))))
 @end lisp
 @end defvar
 

etc/git/gitconfig

@@ -1,6 +1,3 @@
-[commit]
-        gpgsign = true
-
 [diff "scheme"]
 	xfuncname = "^(\\(define.*)$"
 

etc/guix-daemon.cil.in

@@ -176,6 +176,11 @@
                 execute_no_trans read write open entrypoint map
                 getattr link unlink)))
 
+  ;; Remounting /gnu/store read-write.
+  (allow guix_daemon_t
+         fs_t
+         (filesystem (remount)))
+
   ;; TODO: unknown
   (allow guix_daemon_t
          root_t
@@ -223,6 +228,9 @@
   (allow guix_daemon_t
          tmpfs_t
          (file (create open read unlink write)))
+  (allow guix_daemon_t                          ;same as above, but with tmp_t
+         tmp_t
+         (file (create open read unlink write)))
   (allow guix_daemon_t
          tmpfs_t
          (dir (getattr add_name remove_name write)))

etc/guix-install.sh

@@ -606,6 +606,19 @@ fi
     _msg "${PAS}Bash shell prompt successfully customized for Guix"
 }
 
+sys_maybe_setup_selinux()
+{
+    if [ -f /sys/fs/selinux/policy ]
+    then
+	prompt_yes_no "Install SELinux policy required to run guix-daemon?" \
+	    || return
+
+	local var_guix=/var/guix/profiles/per-user/root/current-guix
+	semodule -i "${var_guix}/share/selinux/guix-daemon.cil"
+	restorecon -R /gnu /var/guix
+    fi
+}
+
 welcome()
 {
     local char
@@ -681,6 +694,7 @@ main()
 
     sys_create_store "${GUIX_BINARY_FILE_NAME}" "${tmp_path}"
     sys_create_build_user
+    sys_maybe_setup_selinux
     sys_enable_guix_daemon
     sys_authorize_build_farms
     sys_create_init_profile

etc/news.scm

@@ -26,6 +26,50 @@
 (channel-news
  (version 0)
 
+ (entry (commit "ba5da5125a81307500982517e2f458d57b024668")
+        (title
+         (en "New @code{arguments} rule for @command{guix style}")
+         (de "Neue Stilregel @code{arguments} für @command{guix style}")
+         (fr "Nouvelle règle @code{arguments} pour @command{guix style}"))
+        (body
+         (en "The @command{guix style} command has a new @dfn{styling rule}
+for package definitions.  Package writers may now run the following command:
+
+@example
+guix style -L /path/to/channel -S arguments @var{package}
+@end example
+
+This command rewrites the @code{arguments} field of @var{package} so that it
+uses G-expressions instead of classical quasiquotation.
+
+Run @command{info \"(guix) Invoking guix style\"} for more info.")
+         (de "Der Befehl @command{guix style} verfügt über eine neue @dfn{Stilregel}
+für Paketdefinitionen.  Paketautoren können jetzt folgenden Befehl benutzen:
+
+@example
+guix style -L /pfad/zum/kanal -S arguments @var{Paket}
+@end example
+
+Dadurch wird das Feld @code{arguments} in @var{Paket} so umgeschrieben, dass
+G-Ausdrücke (gexps) anstelle von klassischer Quasiquotierung verwendet
+werden.
+
+Führen Sie @command{info \"(guix.de) Aufruf von guix style\"} aus, um
+mehr Informationen zu erhalten.")
+         (fr "La commande @command{guix style} a une nouvelle @dfn{règle de
+style} pour les définitions de paquets.  Les auteurices de paquets peuvent
+maintenant lancer la commande suivante :
+
+@example
+guix style -L /chemin/vers/canal -S arguments @var{paquet}
+@end example
+
+Cette commande réécrit le champ @code{arguments} de @var{paquet} pour qu'il
+utilise des G-expressions plutôt que des quasicitations classiques.
+
+Lancer @command{info \"(guix.fr) Invoquer guix style\"} pour plus
+d'informations.")))
+
  (entry (commit "ae11fcb84ac478dfa56d322ef08890645183a087")
         (title
          (en "New @option{--with-configure-flag} transformation option")
@@ -39,7 +83,7 @@ the build system of the @code{lapack} package:
 
 @example
 guix build lapack \\
-  --with-configure-flag=lapack=-DBUILD_COMPLEX=OFF
+  --with-configure-flag=lapack=-DBUILD_SHARED_LIBS=OFF
 @end example
 
 Run @command{info \"(guix) Package Transformation Options\"} for more info.")
@@ -50,7 +94,7 @@ Befehlszeilenoption für configure mitzugeben.  Zum Beispiel können Sie dem
 
 @example
 guix build lapack \\
-  --with-configure-flag=lapack=-DBUILD_COMPLEX=OFF
+  --with-configure-flag=lapack=-DBUILD_SHARED_LIBS=OFF
 @end example
 
 Führen Sie für mehr Informationen @command{info \"(guix.de)
@@ -63,7 +107,7 @@ un drapeau à @command{cmake}, le système de construction du logiciel
 
 @example
 guix build lapack \\
-  --with-configure-flag=lapack=-DBUILD_COMPLEX=OFF
+  --with-configure-flag=lapack=-DBUILD_SHARED_LIBS=OFF
 @end example
 
 Voir @command{info \"(guix.fr) Options de transformation de paquets\"} pour

etc/teams.scm.in

@@ -208,7 +208,7 @@ packages (e.g. Astronomy, Chemistry, Math, Physics etc.)"
         #:scope (list "gnu/packages/algebra.scm"
                       "gnu/packages/astronomy.scm"
                       "gnu/packages/geo.scm"
-                      "gnu/packages/chemestry.scm"
+                      "gnu/packages/chemistry.scm"
                       "gnu/packages/maths.scm")))
 
 (define-team emacs
@@ -255,9 +255,16 @@ asdf-build-system."
                       "guix/scripts/import/go.scm"
                       "tests/go.scm")))
 
-(define-team embedded-bootstrap
+(define-team bootstrap
-  (team 'embedded-bootstrap
+  (team 'bootstrap
-        #:name "Embedded / Bootstrap"))
+        #:name "Bootstrap"
+        #:scope (list "gnu/packages/mes.scm")))
+
+(define-team embedded
+  (team 'embedded
+        #:name "Embedded"
+        #:scope (list "gnu/packages/bootloaders.scm"
+                      "gnu/packages/firmware.scm")))
 
 (define-team rust
   (team 'rust
@@ -480,7 +487,7 @@ GLib/GIO, GTK, GStreamer and Webkit."
 
 (define-member (person "Ludovic Courtès"
                        "ludo@gnu.org")
-  core home embedded-bootstrap mentors)
+  core home embedded bootstrap mentors)
 
 (define-member (person "Andreas Enge"
                        "andreas@enge.fr")
@@ -500,7 +507,7 @@ GLib/GIO, GTK, GStreamer and Webkit."
 
 (define-member (person "Efraim Flashner"
                        "efraim@flashner.co.il")
-  embedded-bootstrap julia rust science)
+  embedded bootstrap julia rust science)
 
 (define-member (person "jgart"
                        "jgart@dismail.de")
@@ -566,6 +573,10 @@ GLib/GIO, GTK, GStreamer and Webkit."
                        "iyzsong@envs.net")
   games localization lxqt xfce)
 
+(define-member (person "Vagrant Cascadian"
+                       "vagrant@debian.org")
+  embedded)
+
 (define-member (person "Vagrant Cascadian"
                        "vagrant@reproducible-builds.org")
   reproduciblebuilds)
@@ -605,24 +616,32 @@ of file names as string."
 (define (cc . teams)
   "Return arguments for `git send-email' to notify the members of the given
 TEAMS when a patch is received by Debbugs."
-  (format #true
+  (let ((members (append-map team-members teams)))
-          "~{--add-header=\"X-Debbugs-Cc: ~a\"~^ ~}"
+    (unless (null? members)
-          (map person-email
+      (format #true "--add-header=\"X-Debbugs-Cc: ~{~a~^, ~}\""
-               (delete-duplicates (append-map team-members teams) equal?))))
+              (map person-email (sort-members members))))))
+
+(define (sort-members members)
+  "Deduplicate and sort MEMBERS alphabetically by their name."
+  (sort (delete-duplicates members equal?)
+        (lambda (m1 m2)
+          (string<? (person-name m1) (person-name m2)))))
+
+(define (member->string member)
+  "Return the 'email <name>' string representation of MEMBER."
+  (let* ((name (person-name member))
+         (quoted-name/maybe (if (string-contains name ",")
+                                (string-append "\"" name "\"")
+                                name)))
+    (format #false "~a <~a>" quoted-name/maybe (person-email member))))
 
 (define* (list-members team #:optional port (prefix ""))
   "Print the members of the given TEAM."
   (define port* (or port (current-output-port)))
   (for-each
    (lambda (member)
-     (format port*
+     (format port* "~a~a~%" prefix (member->string member)))
-             "~a~a <~a>~%"
+   (sort-members (team-members team))))
-             prefix
-             (person-name member)
-             (person-email member)))
-   (sort
-    (team-members team)
-    (lambda (m1 m2) (string<? (person-name m1) (person-name m2))))))
 
 (define (list-teams)
   "Print all teams, their scope and their members."
@@ -716,13 +735,15 @@ and REV-END, two git revision strings."
      (apply cc (find-team-by-scope
                 (diff-revisions rev-start rev-end))))
     (("cc-members-header-cmd" patch-file)
-     (for-each (lambda (team-name)
+     (let* ((teams (map find-team (patch->teams patch-file)))
-                 (list-members (find-team team-name) (current-output-port)
+            (members (sort-members (append-map team-members teams))))
-                               "X-Debbugs-Cc: "))
+       (unless (null? members)
-               (patch->teams patch-file)))
+         (format #true "X-Debbugs-Cc: ~{~a~^, ~}"
+                 (map member->string members)))))
     (("cc-mentors-header-cmd" patch-file)
-     (list-members (find-team "mentors") (current-output-port)
+     (format #true "X-Debbugs-Cc: ~{~a~^, ~}"
-                   "X-Debbugs-Cc: "))
+             (map member->string
+                  (sort-members (team-members (find-team "mentors"))))))
     (("get-maintainer" patch-file)
      (apply main "list-members" (patch->teams patch-file)))
     (("list-teams" . args)

gnu/build/hurd-boot.scm

@@ -280,14 +280,14 @@ XXX TODO: use Linux xattr/setxattr to remove (settrans in) /libexec/RUNSYSTEM
             (system  (find-long-option "gnu.system" args))
             (to-load (find-long-option "gnu.load" args)))
 
-       (format #t "Setting-up essential translators...\n")
-       (setenv "PATH" (string-append system "/profile/bin"))
-       (set-hurd-device-translators)
-
        (false-if-exception (delete-file "/hurd"))
        (let ((hurd/hurd (readlink* (string-append system "/profile/hurd"))))
          (symlink hurd/hurd "/hurd"))
 
+       (format #t "Setting-up essential translators...\n")
+       (setenv "PATH" (string-append system "/profile/bin"))
+       (set-hurd-device-translators)
+
        (format #t "Starting pager...\n")
        (unless (zero? (system* "/hurd/mach-defpager"))
          (format #t "FAILED...Good luck!\n"))

gnu/home/services/fontutils.scm

@@ -2,6 +2,7 @@
 ;;; Copyright © 2021 Andrew Tropin <andrew@trop.in>
 ;;; Copyright © 2021 Xinglu Chen <public@yoctocell.xyz>
 ;;; Copyright © 2023 Giacomo Leidi <goodoldpaul@autistici.org>
+;;; Copyright © 2023 Andrew Patterson <andrewpatt7@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -23,6 +24,8 @@
   #:use-module (gnu packages fontutils)
   #:use-module (guix gexp)
   #:use-module (srfi srfi-1)
+  #:use-module (ice-9 match)
+  #:use-module (sxml simple)
 
   #:export (home-fontconfig-service-type))
 
@@ -35,17 +38,36 @@
 ;;;
 ;;; Code:
 
-(define (add-fontconfig-config-file directories)
+(define (write-fontconfig-doctype)
+  "Prints fontconfig's DOCTYPE to current-output-port."
+  ;; This is necessary because SXML doesn't seem to have a way to represent a doctype,
+  ;; but sxml->xml /does/ currently call any thunks in the SXML with the XML output port
+  ;; as current-output-port, allowing the output to include arbitrary text instead of
+  ;; just properly quoted XML.
+  (format #t "<!DOCTYPE fontconfig SYSTEM 'fonts.dtd'>"))
+
+(define (config->sxml config)
+  "Converts a <home-fontconfig-configuration> record into the SXML representation
+of fontconfig's fonts.conf file."
+  (define (snippets->sxml snippet)
+    (match snippet
+      ((or (? string? dir)
+           (? gexp? dir))
+       `(dir ,dir))
+      ((? list?)
+       snippet)))
+  `(*TOP* (*PI* xml "version='1.0'")
+          ,write-fontconfig-doctype
+          (fontconfig
+           ,@(map snippets->sxml config))))
+
+(define (add-fontconfig-config-file config)
   `(("fontconfig/fonts.conf"
      ,(mixed-text-file
        "fonts.conf"
-       (apply string-append
+       (call-with-output-string
-              `("<?xml version='1.0'?>
+         (lambda (port)
-<!DOCTYPE fontconfig SYSTEM 'fonts.dtd'>
+           (sxml->xml (config->sxml config) port)))))))
-<fontconfig>\n" ,@(map (lambda (directory)
-                         (string-append "  <dir>" directory "</dir>\n"))
-                       directories)
-                "</fontconfig>\n"))))))
 
 (define (regenerate-font-cache-gexp _)
   `(("profile/share/fonts"

gnu/home/services/shepherd.scm

@@ -52,7 +52,7 @@
   home-shepherd-configuration make-home-shepherd-configuration
   home-shepherd-configuration?
   (shepherd home-shepherd-configuration-shepherd
-            (default shepherd-0.9)) ; package
+            (default shepherd-0.10)) ; package
   (auto-start? home-shepherd-configuration-auto-start?
                (default #t))
   (daemonize? home-shepherd-configuration-daemonize?

gnu/home/services/ssh.scm

@@ -249,7 +249,7 @@ through before connecting to the server.")
   home-openssh-configuration make-home-openssh-configuration
   home-openssh-configuration?
   (authorized-keys home-openssh-configuration-authorized-keys ;list of file-like
-                   (default '()))
+                   (default #f))
   (known-hosts     home-openssh-configuration-known-hosts ;unspec | list of file-like
                    (default *unspecified*))
   (hosts           home-openssh-configuration-hosts   ;list of <openssh-host>
@@ -285,19 +285,21 @@ inserted after each of them."
                                      '#$files)))))))
 
 (define (openssh-configuration-files config)
-  (let ((config (plain-file "ssh.conf"
+  (let* ((ssh-config (plain-file "ssh.conf"
                                  (openssh-configuration->string config)))
          (known-hosts (home-openssh-configuration-known-hosts config))
-        (authorized-keys (file-join
+         (authorized-keys (home-openssh-configuration-authorized-keys config))
-                          "authorized_keys"
+         (authorized-keys (and
-                          (home-openssh-configuration-authorized-keys config)
+                           authorized-keys
-                          "\n")))
+                           (file-join "authorized_keys" authorized-keys "\n"))))
-    `((".ssh/authorized_keys" ,authorized-keys)
+    `(,@(if authorized-keys
+            `((".ssh/authorized_keys" ,authorized-keys))
+            '())
       ,@(if (unspecified? known-hosts)
             '()
             `((".ssh/known_hosts"
                ,(file-join "known_hosts" known-hosts "\n"))))
-      (".ssh/config" ,config))))
+      (".ssh/config" ,ssh-config))))
 
 (define openssh-activation
   (with-imported-modules (source-module-closure

gnu/local.mk

@@ -57,6 +57,7 @@
 # Copyright © 2022 ( <paren@disroot.org>
 # Copyright © 2022 jgart <jgart@dismail.de>
 # Copyright © 2023 Zheng Junjie <873216071@qq.com>
+# Copyright © 2023 Ivana Drazovic <iv.dra@hotmail.com>
 #
 # This file is part of GNU Guix.
 #
@@ -263,6 +264,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/forth.scm			\
   %D%/packages/freedesktop.scm			\
   %D%/packages/freeipmi.scm			\
+  %D%/packages/fsf.scm				\
   %D%/packages/ftp.scm				\
   %D%/packages/fribidi.scm			\
   %D%/packages/fvwm.scm				\
@@ -591,6 +593,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/suckless.scm			\
   %D%/packages/sugar.scm			\
   %D%/packages/swig.scm				\
+  %D%/packages/sycl.scm				\
   %D%/packages/sync.scm			\
   %D%/packages/syncthing.scm			\
   %D%/packages/synergy.scm			\
@@ -795,6 +798,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/tests/version-control.scm			\
   %D%/tests/virtualization.scm			\
   %D%/tests/vnc.scm				\
+  %D%/tests/vnstat.scm				\
   %D%/tests/web.scm
 
 INSTALLER_MODULES =                             \
@@ -1374,6 +1378,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/irrlicht-use-system-libs.patch		\
   %D%/packages/patches/irrlicht-link-against-needed-libs.patch	\
   %D%/packages/patches/isl-0.11.1-aarch64-support.patch	\
+  %D%/packages/patches/isync-openssl3-fix.patch			\
   %D%/packages/patches/itk-snap-alt-glibc-compat.patch		\
   %D%/packages/patches/jami-disable-integration-tests.patch	\
   %D%/packages/patches/jami-libjami-headers-search.patch	\
@@ -1433,6 +1438,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/kodi-mesa-eglchromium.patch		\
   %D%/packages/patches/kwayland-skip-flaky-test.patch		\
   %D%/packages/patches/laby-make-install.patch			\
+  %D%/packages/patches/laby-use-tmpdir-from-runtime.patch	\
   %D%/packages/patches/ldns-drill-examples.patch		\
   %D%/packages/patches/leela-zero-gtest.patch			\
   %D%/packages/patches/less-hurd-path-max.patch			\
@@ -1541,6 +1547,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/lvm2-static-link.patch			\
   %D%/packages/patches/mailutils-variable-lookup.patch		\
   %D%/packages/patches/make-impure-dirs.patch			\
+  %D%/packages/patches/mariadb-rocksdb-atomic-linking.patch	\
   %D%/packages/patches/mathjax-disable-webpack.patch			\
   %D%/packages/patches/mathjax-no-a11y.patch			\
   %D%/packages/patches/mathjax-3.1.2-no-a11y.patch		\
@@ -1559,7 +1566,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/memtest86+-build-reproducibly.patch	\
   %D%/packages/patches/mercurial-hg-extension-path.patch	\
   %D%/packages/patches/mercurial-openssl-compat.patch		\
-  %D%/packages/patches/mesa-opencl-all-targets.patch		\
   %D%/packages/patches/mhash-keygen-test-segfault.patch		\
   %D%/packages/patches/mia-fix-boost-headers.patch		\
   %D%/packages/patches/mia-vtk9.patch				\
@@ -1644,6 +1650,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/openjdk-10-setsignalhandler.patch        \
   %D%/packages/patches/openjdk-15-xcursor-no-dynamic.patch	\
   %D%/packages/patches/openmpi-mtl-priorities.patch		\
+  %D%/packages/patches/openmw-assume-nonconst-SIGSTKSZ.patch    \
   %D%/packages/patches/openssh-hurd.patch			\
   %D%/packages/patches/openssh-trust-guix-store-directory.patch	\
   %D%/packages/patches/openresolv-restartcmd-guix.patch	\
@@ -1958,6 +1965,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/tk-find-library.patch			\
   %D%/packages/patches/tla2tools-build-xml.patch		\
   %D%/packages/patches/tlf-support-hamlib-4.2+.patch		\
+  %D%/packages/patches/tofi-32bit-compat.patch			\
   %D%/packages/patches/tootle-glib-object-naming.patch		\
   %D%/packages/patches/tootle-reason-phrase.patch		\
   %D%/packages/patches/transcode-ffmpeg.patch	\
@@ -2072,6 +2080,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/xsane-tighten-default-umask.patch	\
   %D%/packages/patches/xterm-370-explicit-xcursor.patch		\
   %D%/packages/patches/xygrib-fix-finding-data.patch		\
+  %D%/packages/patches/xygrib-newer-proj.patch			\
   %D%/packages/patches/yggdrasil-extra-config.patch	\
   %D%/packages/patches/zig-do-not-link-against-librt.patch	\
   %D%/packages/patches/zig-use-system-paths.patch		\

gnu/packages/accessibility.scm

@@ -5,6 +5,7 @@
 ;;; Copyright © 2019 Andrew Miloradovsky <andrew@interpretmath.pw>
 ;;; Copyright © 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2022 Hunter Jozwiak <hunter.t.joz@gmail.com>
+;;; Copyright © 2023 Ivan Gankevich <igankevich@capybaramail.xyz>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -350,3 +351,38 @@ CONFIG_SPEAKUP=m
 CONFIG_SPEAKUP_SOFT=m
 @end itemize")
     (home-page "https://github.com/linux-speakup/espeakup")))
+
+(define-public mouseloupe
+  (package
+    (name "mouseloupe")
+    (version "0.6")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "mirror://sourceforge/" name "/" name "/v" version
+                            "/" name "-v" version ".tar.gz"))
+        (sha256 (base32 "0cvdkfakw7cix07j0c4iy10fkbqn6n8l1gr5dd3iy4f2d9bkza43"))))
+    (build-system gnu-build-system)
+    (arguments
+      `(#:tests? #f ; there are no tests
+        #:phases
+        (modify-phases %standard-phases
+          (delete 'configure)
+          (add-before 'build 'strtof
+            (lambda _
+              (substitute* "mouseloupe.c"
+                (("\\bstrtof\\b") "mouseloupe_strtof"))))
+          (replace 'install
+            (lambda _
+              (define out (assoc-ref %outputs "out"))
+              (install-file "mouseloupe" (string-append out "/bin"))
+              (install-file "mouseloupe.1.gz" (string-append out "/share/man/man1")))))))
+    (native-inputs
+      (list pkg-config))
+    (inputs
+      (list libx11 libxext libxcomposite libxdamage libxrender))
+    (synopsis "Screen magnifier tool for people with low vision")
+    (description "MouseLoupe is a kind of magnifying glass combined with the mouse pointer
+which allows an easy and pleasant web navigation.")
+    (home-page "https://sourceforge.net/projects/mouseloupe/")
+    (license license:gpl2+)))

gnu/packages/admin.scm

@@ -85,6 +85,7 @@
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system python)
+  #:use-module (guix build-system pyproject)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system ruby)
   #:use-module (guix build-system trivial)
@@ -367,11 +368,23 @@ interface and is based on GNU Guile.")
                          guile-fibers-1.1))       ;for cross-compilation
     (inputs (list guile-3.0-latest guile-fibers-1.1))))
 
+(define-public shepherd-0.10
+  (package
+    (inherit shepherd-0.9)
+    (version "0.10.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://gnu/shepherd/shepherd-"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "0dpbcq4jhqfv39jzc675ccidiyv8ziw5x9qv9kwxv132a5qf8phf"))))))
+
 (define-public shepherd shepherd-0.9)
 
 (define-public guile2.2-shepherd
   (package
-    (inherit shepherd-0.9)
+    (inherit shepherd-0.10)
     (name "guile2.2-shepherd")
     (native-inputs (list pkg-config guile-2.2))
     (inputs (list guile-2.2 guile2.2-fibers))))
@@ -4810,7 +4823,7 @@ LUKS volumes encrypted with the user's log-in password.")
 (define-public jc
   (package
     (name "jc")
-    (version "1.19.0")
+    (version "1.23.2")
     (source
      (origin
        ;; The PyPI tarball lacks the test suite.
@@ -4820,8 +4833,8 @@ LUKS volumes encrypted with the user's log-in password.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "021zk0y8kb6v3qf3hwfg8qjzzmrca039nz3fjywiy2njmbhr8hyi"))))
+        (base32 "17g2q0h3jwzfm80ldl8inpyh5y0qzzmgvyg10gkk1rp8i34wfgly"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
      (list #:phases
            #~(modify-phases %standard-phases
@@ -4830,6 +4843,7 @@ LUKS volumes encrypted with the user's log-in password.")
                  (lambda _
                    (substitute* (find-files "tests" "^test.*\\.py$")
                      (("America/Los_Angeles") "PST8PDT")))))))
+    (native-inputs (list python-pytest))
     (propagated-inputs
      (list python-pygments python-ruamel.yaml python-xmltodict))
     (home-page "https://github.com/kellyjonbrazil/jc")

gnu/packages/algebra.scm

@@ -133,7 +133,7 @@ greatest common divisor operations.")
 (define-public cm
   (package
    (name "cm")
-   (version "0.4.1")
+   (version "0.4.2")
    (source (origin
             (method url-fetch)
             (uri (string-append
@@ -141,7 +141,7 @@ greatest common divisor operations.")
                   version ".tar.gz"))
             (sha256
              (base32
-              "1avaw6a7lyc2833gr9b7zpk4blvrrrkz8r62sv1grh9xc9i4zg07"))))
+              "1c6m00wiw3rs5f0lq6c80rdr3dzklsvh69l8w3s7bj2r6yha6qbw"))))
    (build-system gnu-build-system)
    (propagated-inputs
      (list mpfrcx zlib)) ; Header files included from cm_common.h.

gnu/packages/astronomy.scm

@@ -476,17 +476,18 @@ in FITS files.")
        (modules '((guix build utils)))
        (snippet
         ;; Remove the bundled cfitsio
-        `(begin
+        #~(begin
             (delete-file-recursively "cfitsio3490")
             (substitute* "MANIFEST.in"
               (("recursive-include cfitsio3490.*$\n") ""))))))
     (build-system python-build-system)
     (arguments
-     `(#:phases
+     (list
-       (modify-phases %standard-phases
+      #:phases
+      #~(modify-phases %standard-phases
           (add-after 'unpack 'unbundle-cfitsio
-           (lambda* (#:key inputs #:allow-other-keys)
+            (lambda _
-             (let* ((cfitsio (assoc-ref inputs "cfitsio"))
+              (let* ((cfitsio #$(this-package-input "cfitsio"))
                      (includedir (string-append "\"" cfitsio "/include\""))
                      (libdir (string-append "\"" cfitsio "/lib\"")))
                 ;; Use Guix' cfitsio instead of the bundled one
@@ -1242,23 +1243,19 @@ astronomy and astrophysics.")
        (uri (pypi-uri "astropy_healpix" version))
        (sha256
         (base32 "1n1svmd41iv944zf4anbnsigd47zr4dfjf49vrc7m6928gmq9hw8"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
+     (list
-       (modify-phases %standard-phases
+      #:phases
+      #~(modify-phases %standard-phases
           ;; This file is opened in both install and check phases.
           (add-before 'install 'writable-compiler
             (lambda _ (make-file-writable "astropy_healpix/_compiler.c")))
-         (add-before 'check 'writable-compiler
+          (add-before 'check 'prepare-test-environment
-           (lambda _ (make-file-writable "astropy_healpix/_compiler.c")))
+            (lambda _
-         (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-             (when tests?
-               (add-installed-pythonpath inputs outputs)
               ;; Extensions have to be rebuilt before running the tests.
               (invoke "python" "setup.py" "build_ext" "--inplace")
-               (invoke "python" "-m" "pytest"
+              (make-file-writable "astropy_healpix/_compiler.c"))))))
-                       "--pyargs" "astropy_healpix")))))))
     (native-inputs
      (list python-extension-helpers
            python-hypothesis
@@ -1283,15 +1280,14 @@ astronomy and astrophysics.")
         (base32 "1vhkzsqlgn3ji5by2rdf2gwklhbyzvpzb1iglalhqjkkrdaaaz1h"))))
     (build-system python-build-system)
     (arguments
-     `(#:phases
+     (list #:phases
-       (modify-phases %standard-phases
+           #~(modify-phases %standard-phases
                (add-before 'check 'writable-home
                  (lambda _              ; some tests need a writable home
                    (setenv "HOME" (getcwd))))
                (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+                 (lambda* (#:key tests? #:allow-other-keys)
                    (when tests?
-               (add-installed-pythonpath inputs outputs)
                      (invoke "python" "-m" "pytest" "--pyargs" "astroquery"
                              ;; Skip tests that require online data.
                              "-m" "not remote_data")))))))
@@ -1370,11 +1366,6 @@ specifically in the C code.")
        (sha256
         (base32 "0fy1sni87cr05dkljd8wb7vgh7z9agh8wv5kiagxcpbcf8l06jv1"))))
     (build-system pyproject-build-system)
-    (arguments
-     ;; FIXME: Test failed a lot with: DeprecationWarning: distutils Version
-     ;; classes are deprecated. Use packaging.version instead (see:
-     ;; https://github.com/astropy/ccdproc/issues/805).
-     (list #:tests? #f))
     (native-inputs (list python-memory-profiler python-pytest-astropy))
     (propagated-inputs
      (list python-astropy
@@ -1505,13 +1496,13 @@ used with local NetDRMS sites.")
 (define-public python-ephem
   (package
     (name "python-ephem")
-    (version "4.1.3")
+    (version "4.1.4")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "ephem" version))
               (sha256
                (base32
-                "0smmm3l8csnw9rrimh8mpyjrm80jaafjl184spnji98vk22qd8bz"))))
+                "0q67z79lgwdylxagbsjm42xvsmk5jmgvghy36m2n5lb2446rz9bk"))))
     (build-system python-build-system)
     (native-inputs (list tzdata))
     (home-page "https://rhodesmill.org/pyephem/")
@@ -1575,13 +1566,13 @@ the easy construction of interactive matplotlib widget based animations.")
 (define-public python-photutils
   (package
     (name "python-photutils")
-    (version "1.6.0")
+    (version "1.7.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "photutils" version))
        (sha256
-        (base32 "0w4kxl6aqjp2wv396krw30kwg6cmmska8gvgpihm2i2zxyzz39vd"))))
+        (base32 "1bq4ma402lpa5d6l85awlc23kasxf40nq8hgi3iyrilnfikan0jz"))))
     (build-system python-build-system)
     (arguments
      `(#:test-target "pytest"
@@ -1684,13 +1675,13 @@ Low-Earth Orbit (LEO).")
 (define-public python-poppy
   (package
     (name "python-poppy")
-    (version "1.0.3")
+    (version "1.1.1")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "poppy" version))
               (sha256
                (base32
-                "050cn6aabd1dxbi7zihbqnkl79hz6q6d5n6g25zmrpvc4sii171m"))))
+                "0s8rb61q8dz66s8d3qg44kb6bb5gi40zl41ik9wyccgb4kyf3brp"))))
     (build-system pyproject-build-system)
     (propagated-inputs
      ;; XXX: With python-synphot (marked as optional) package added to the list
@@ -1728,27 +1719,16 @@ interest, and which require portability between platforms or ease of scripting."
 (define-public python-pyvo
   (package
     (name "python-pyvo")
-    (version "1.2.1")
+    (version "1.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pyvo" version))
        (sha256
-        (base32 "1ri5yp6903386lkn79mdcmlax7zsfrrrjbcvb91wxydcc9yasc1n"))))
+        (base32 "17acv1yhz1jrsx9f35nr1vg276ibaivh4i243qkmp6abzvfyg907"))))
-    (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" "--pyargs" "pyvo" "-k"
-                       (string-append   ; these tests use the network
-                        "not test_access_with_string"
-                        " and not test_access_with_list"
-                        " and not test_access_with_expansion"))))))))
     (native-inputs
-     (list python-pytest-astropy python-requests-mock))
+     (list python-pytest-astropy python-requests-mock python-setuptools-scm))
     (propagated-inputs
      (list python-astropy python-mimeparse python-pillow python-requests))
     (home-page "https://github.com/astropy/pyvo")
@@ -1800,13 +1780,13 @@ Virtual observatory (VO) using Python.")
 (define-public python-reproject
   (package
     (name "python-reproject")
-    (version "0.9.1")
+    (version "0.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "reproject" version))
        (sha256
-        (base32 "1msysqbhkfi3bmw29wipk250a008bnng7din56md9ipbwiar8x55"))))
+        (base32 "1ha0a1ja7k09ysd05adffgsapfwzc6m6az34a0av2mhmlwy4zb1q"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -1856,13 +1836,13 @@ changing the pixel resolution, orientation, coordinate system.")
 (define-public python-sgp4
   (package
     (name "python-sgp4")
-    (version "2.21")
+    (version "2.22")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "sgp4" version))
        (sha256
-        (base32 "1vzcrlrlzmhbycdz16m8v241l8zx49vsy81wcd0yjxs80isvhyb1"))))
+        (base32 "1yc6gcbhz80i875j0wf6ikx7rzs0m7m1qp72dmdhdjidmpma5w0p"))))
     (build-system python-build-system)
     (propagated-inputs
      (list python-numpy))
@@ -1885,16 +1865,21 @@ orbits described in TLE files.")
 (define-public python-sunpy
   (package
     (name "python-sunpy")
-    (version "4.1.1")
+    (version "4.1.5")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "sunpy" version))
        (sha256
-        (base32 "1h8dnsic96bxm5l278vk6jj5h4bh1b143fghsvv5rhigk137vysp"))))
+        (base32 "1j5g0ivsrc5ji9s7jc3kcbi2injfs3y31pm3priycljwcsxspkpm"))))
     (build-system pyproject-build-system)
     (arguments
      (list
+      #:test-flags
+      #~(list "-k" (string-append
+                    ;; XXX: Failed: DID NOT RAISE <class 'ModuleNotFoundError'>
+                    "not test_main_nonexisting_module"
+                    " and not test_main_stdlib_module"))
       #:phases
       #~(modify-phases %standard-phases
           (add-before 'install 'writable-compiler
@@ -1902,26 +1887,10 @@ orbits described in TLE files.")
               (make-file-writable "sunpy/_compiler.c")))
           (add-before 'check 'prepare-test-environment
             (lambda _
-              (setenv "HOME" "/tmp")
+              (setenv "HOME" "/tmp"))))))
-              (make-file-writable "sunpy/_compiler.c")
-              ;; TODO: (Sharlatan-20221106T115800+0000): Review failing tests
-              (substitute* "sunpy/image/tests/test_transform.py"
-                (("def test_clipping") "def __off_test_clipping")
-                (("def test_nans") "def __off_test_nans")
-                (("def test_endian") "def __off_test_endian"))
-              (substitute* "sunpy/map/tests/test_mapbase.py"
-                (("def test_derotating_nonpurerotation_pcij")
-                 "def __off_test_derotating_nonpurerotation_pcij"))
-              (substitute* "sunpy/map/sources/tests/test_mdi_source.py"
-                (("def test_synoptic_source")
-                 "def __off_test_synoptic_source"))
-              (substitute* "sunpy/tests/tests/test_self_test.py"
-                (("def test_main_nonexisting_module")
-                 "def __off_test_main_nonexisting_module")
-                (("def test_main_stdlib_module")
-                 "def __off_test_main_stdlib_module")))))))
     (native-inputs
-     (list python-aiohttp
+     (list opencv ; For tests, includes OpenCV-Python
+           python-aiohttp
            python-extension-helpers
            python-hvpy
            python-packaging
@@ -1950,7 +1919,6 @@ orbits described in TLE files.")
            python-matplotlib
            python-mpl-animators
            python-numpy
-           ;; python-opencv-python ; not packed yet
            python-pandas
            python-reproject
            python-scikit-image
@@ -1969,24 +1937,55 @@ SolarSoft data analysis environment.")
 (define-public python-astral
   (package
     (name "python-astral")
-    (version "2.2")
+    (version "3.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astral" version))
        (sha256
-        (base32 "1gkggdibccmdy9glymw3kbrkzm6svvsg0lk56hhy92y4smkrj7g4"))))
+        (base32 "121xag65rmv6pszbi3d206yz3jfwmpkf0jxjrxrd2scy5r0knz4v"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
+     (list
-       (modify-phases %standard-phases
+      #:test-flags
-         (replace 'check
+      ;; XXX: Disable tests which require newer version of python-pytz.
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+      ;; No time zone found with key Pacific/Auckland
-             (when tests?
+      #~(list "-k" (string-append
-               (add-installed-pythonpath inputs outputs)
+                    "not test_TimezoneLookup"
-               (invoke "python" "-m" "pytest")))))))
+                    " and not test_Sun"
+                    " and not test_Dawn"
+                    " and not test_Sunrise"
+                    " and not test_SolarNoon"
+                    " and not test_Dusk"
+                    " and not test_Sunset"
+                    " and not test_SolarElevation"
+                    " and not test_SolarAzimuth"
+                    " and not test_TimeAtAltitude"
+                    " and not test_MoonNoDate"
+                    " and not test_lookup"
+                    " and not test_tzinfo"
+                    " and not test_australia"
+                    " and not test_adak"
+                    " and not test_australia"
+                    " and not test_Elevation_NonNaive"
+                    " and not test_Wellington"
+                    " and not test_Sun_Local_tzinfo"
+                    " and not test_Sun_Local_str"
+                    " and not test_SolarZenith_London"
+                    " and not test_SolarZenith_Riyadh"
+                    " and not test_moonrise_utc"
+                    " and not test_moonrise_wellington"
+                    " and not test_moonset_wellington"))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'prepare-test-environment
+            (lambda _
+              (setenv "HOME" "/tmp"))))))
     (native-inputs
-     (list python-freezegun python-setuptools-scm))
+     (list python-freezegun
+           python-poetry-core
+           python-pytest
+           python-setuptools-scm))
     (propagated-inputs
      (list python-dataclasses python-pytest python-pytz))
     (home-page "https://github.com/sffjunkie/astral")
@@ -1999,6 +1998,8 @@ elevation, solar azimuth, rahukaalam, and the phases of the moon.")
 (define-public python-spherical-geometry
   (package
     (name "python-spherical-geometry")
+    ;; XXX: Can't be updated to the latest see:
+    ;; https://github.com/spacetelescope/spherical_geometry/issues/227
     (version "1.2.22")
     (source
      (origin
@@ -2631,55 +2632,44 @@ functions, so that they can be called with scalar or array inputs.")
 (define-public python-pynbody
   (package
     (name "python-pynbody")
-    (version "1.2.3")
+    (version "1.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pynbody" version))
        (sha256
-        (base32 "1jxwk2s4qz1znvyak2lj7ld01kl1jh87xp81ki7a8dz1gcy93fkx"))))
+        (base32 "1yp7ja66zqmbnh7bbwbyimxq1nkrmjrcif2rzfm1hswm0fp2fbga"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     (list #:phases
+     (list #:test-flags #~(list
-           #~(modify-phases %standard-phases
+                           ;; Disable tests which need to download additional
-               (add-after 'unpack 'disable-tests-require-testdata
+                           ;; 1.0GiB+ of test data archive from
-                 (lambda _
-                   ;; Disable tests which need to download additional 1.0GiB+
-                   ;; of test data archive from
                            ;; http://star.ucl.ac.uk/~app/testdata.tar.gz
                            ;;    https://github.com/pynbody/pynbody/blob/ \
                            ;;    f4bd482dc47532831b3ec115c7cb07149d61bfc5/ \
                            ;;    .github/workflows/build-test.yaml#L41
-                   (with-directory-excursion "tests"
+                           "--ignore=tests/gravity_test.py"
-                     (for-each delete-file
+                           "--ignore=tests/adaptahop_test.py"
-                               '("gravity_test.py"
+                           "--ignore=tests/ahf_halos_test.py"
-                                 "adaptahop_test.py"
+                           "--ignore=tests/array_test.py"
-                                 "ahf_halos_test.py"
+                           "--ignore=tests/bridge_test.py"
-                                 "array_test.py"
+                           "--ignore=tests/family_test.py"
-                                 "bridge_test.py"
+                           "--ignore=tests/partial_tipsy_test.py"
-                                 "family_test.py"
+                           "--ignore=tests/snapshot_test.py"
-                                 "partial_tipsy_test.py"
+                           "--ignore=tests/test_profile.py"
-                                 "snapshot_test.py"
+                           "--ignore=tests/gadget_test.py"
-                                 "test_profile.py"
+                           "--ignore=tests/gadgethdf_test.py"
-                                 "gadget_test.py"
+                           "--ignore=tests/grafic_test.py"
-                                 "gadgethdf_test.py"
+                           "--ignore=tests/halotools_test.py"
-                                 "grafic_test.py"
+                           "--ignore=tests/nchilada_test.py"
-                                 "halotools_test.py"
+                           "--ignore=tests/ramses_new_ptcl_format_test.py"
-                                 "nchilada_test.py"
+                           "--ignore=tests/ramses_test.py"
-                                 "ramses_new_ptcl_format_test.py"
+                           "--ignore=tests/rockstar_test.py"
-                                 "ramses_test.py"
+                           "--ignore=tests/sph_image_test.py"
-                                 "rockstar_test.py"
+                           "--ignore=tests/sph_smooth_test.py"
-                                 "sph_image_test.py"
+                           "--ignore=tests/subfind_test.py"
-                                 "sph_smooth_test.py"
+                           "--ignore=tests/subfindhdf_gadget4_test.py"
-                                 "subfind_test.py"
+                           "--ignore=tests/tipsy_test.py")))
-                                 "subfindhdf_gadget4_test.py"
-                                 "tipsy_test.py")))))
-               (replace 'check
-                 (lambda* (#:key tests? inputs outputs #:allow-other-keys)
-                   (when tests?
-                     (add-installed-pythonpath inputs outputs)
-                     (setenv "HOME" "/tmp")
-                     (invoke "pytest" "-vv")))))))
     (native-inputs
      (list python-cython
            python-pandas
@@ -2736,23 +2726,24 @@ datetime object.")
 (define-public python-asdf
   (package
     (name "python-asdf")
-    (version "2.13.0")
+    (version "2.15.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "asdf" version))
        (sha256
-        (base32 "1zixzv4n2fryaszsfchqh2nvp0gzvarhz03fc721yw6iafdadqij"))))
+        (base32 "11s56797l5330kkhppkyz0bsvms016knmyswj4gx91zrxf8iqvv8"))))
     (build-system pyproject-build-system)
     (arguments
-     ;; FIXME: Tests fail a lot with
+     (list #:test-flags
-     ;;
+           #~(list "-k" (string-append
-     ;; ERROR  - _pytest.pathlib.ImportPathMismatchError:
+                         "not test_overwrite"
-     ;; ('asdf.conftest', '/gnu/sto...
+                         " and not test_tagging_scalars"
-     ;;
+                         " and not test_info_command"
-     `(#:tests? #f))
+                         " and not test_array_inline_threshold_recursive"))))
     (native-inputs
      (list python-astropy
+           python-fsspec
            python-packaging
            python-psutil
            python-pytest
@@ -2848,26 +2839,16 @@ package such as asdf-astropy.")
 (define python-asdf-coordinates-schemas
   (package
     (name "python-asdf-coordinates-schemas")
-    (version "0.1.0")
+    (version "0.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "asdf_coordinates_schemas" version))
        (sha256
-        (base32 "0ahwhsz5jzljnpkfd2kvspirg823lnj5ip9sfkd9cx09z1nlz8jg"))))
+        (base32 "1x6mipg76c6qldq8s2p2wpsq0cpr9b5krp62xskljdz1f84abyg3"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-             (when tests?
-               (add-installed-pythonpath inputs outputs)
-               (invoke "python" "-m" "pytest")))))))
     (native-inputs
-     (list python-pytest
+     (list python-pytest python-semantic-version python-setuptools-scm))
-           python-semantic-version
-           python-setuptools-scm))
     (propagated-inputs
      (list python-asdf))
     (home-page "https://github.com/asdf-format/asdf-coordinates-schemas")
@@ -2974,18 +2955,21 @@ install an implementation package such as asdf-astropy.")
 (define-public python-asdf-astropy
   (package
     (name "python-asdf-astropy")
-    (version "0.3.0")
+    (version "0.4.0")
     (source
      (origin
        (method url-fetch)
-       (uri (pypi-uri "asdf_astropy" version))
+       (uri (pypi-uri "asdf-astropy" version))
        (sha256
-        (base32 "1gp5iav0a9g9q0zb22vhzi3v9vwk5wn2nxvr3mvi3bsdcdj3h23v"))))
+        (base32 "1difb2y1hlalbhrw8znwmmc0vzgg44zfsay98lpllb7y0536fas6"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list #:phases #~(modify-phases %standard-phases
+                        (add-before 'check 'set-home-env
+                          (lambda _ (setenv "HOME" "/tmp"))))))
     (native-inputs
      (list python-coverage
            python-h5py
-           python-matplotlib
            python-pandas
            python-pytest-astropy
            python-scipy
@@ -3015,19 +2999,9 @@ Astropy objects.")
        (uri (pypi-uri "asdf_wcs_schemas" version))
        (sha256
         (base32 "0khyab9mnf2lv755as8kwhk3lqqpd3f4291ny3b9yp3ik86fzhz1"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-             (when tests?
-               (add-installed-pythonpath inputs outputs)
-               (invoke "python" "-m" "pytest")))))))
     (native-inputs
-     (list python-pytest
+     (list python-pytest python-setuptools-scm python-semantic-version))
-           python-setuptools-scm
-           python-semantic-version))
     (propagated-inputs
      (list python-asdf))
     (home-page "https://github.com/asdf-format/asdf-wcs-schemas")
@@ -3041,13 +3015,13 @@ install an implementation package such as gwcs.")
 (define-public python-gwcs
   (package
     (name "python-gwcs")
-    (version "0.18.2")
+    (version "0.18.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "gwcs" version))
        (sha256
-        (base32 "0v9qcq6zl74d6s882s6xmas144jfalvll6va8rvrxmvpx4vqjzhg"))))
+        (base32 "0mgyk5mgmj242g8nl7glcj689vry3ncwf04b8q3hasjcc9bs0rm4"))))
     (build-system pyproject-build-system)
     (native-inputs
      (list python-jsonschema

gnu/packages/audio.scm

@@ -32,7 +32,7 @@
 ;;; Copyright © 2020, 2021 Guillaume Le Vaillant <glv@posteo.net>
 ;;; Copyright © 2020 Jonathan Frederickson <jonathan@terracrypt.net>
 ;;; Copyright © 2020 Giacomo Leidi <goodoldpaul@autistici.org>
-;;; Copyright © 2020, 2021 Vinicius Monego <monego@posteo.net>
+;;; Copyright © 2020, 2021, 2023 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2020 Michael Rohleder <mike@rohleder.de>
 ;;; Copyright © 2021 jgart <jgart@dismail.de>
 ;;; Copyright © 2021 Aleksandr Vityazev <avityazev@posteo.org>
@@ -3233,7 +3233,7 @@ lv2-c++-tools.")
              (lambda* (#:key inputs #:allow-other-keys)
                (let ((waf (assoc-ref inputs "python-waf")))
                  (copy-file (string-append waf "/bin/waf") "waf")))))))
-      (inputs (list boost gtkmm lv2))
+      (inputs (list boost gtkmm-2 lv2))
       (native-inputs (list pkg-config python-waf))
       (home-page "https://github.com/lvtk/lvtk")
       (synopsis "C++ libraries for LV2 plugins")
@@ -3322,22 +3322,19 @@ buffers, and audio capture.")
 (define-public patchage
   (package
     (name "patchage")
-    (version "1.0.4")
+    (version "1.0.10")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://download.drobilla.net/patchage-"
-                                  version
+                                  version ".tar.xz"))
-                                  ".tar.bz2"))
               (sha256
                (base32
-                "0gbakiw3mikgbvy3pssrmqmn7z5c7kp4vyaxj5rs4jnkscxgw9vw"))))
+                "1m472rkvv7kr57xnvmvds3iq3fj129mbw878427djc21rfg2lq80"))))
-    (build-system waf-build-system)
+    (build-system meson-build-system)
-    (arguments
+    (arguments `(#:tests? #f))                    ;no check target
-     `(#:tests? #f))                    ; no check target
     (inputs
      (list alsa-lib
-           boost
+           jack-2
-           jack-1
            ganv
            glibmm
            gtkmm-2
@@ -3443,7 +3440,7 @@ background file post-processing.")
 (define-public supercollider
   (package
     (name "supercollider")
-    (version "3.12.1")
+    (version "3.13.0")
     (source
      (origin
        (method git-fetch)
@@ -3455,14 +3452,14 @@ background file post-processing.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0id522338a464j1slcspajwc7klypbc9qpigw5mqjhrw970wij5z"))
+         "1dkpnaly4m2j41ypy7xj5m2yhbl4ykw3vbnam345z4dk6qhyj9b1"))
        (modules '((guix build utils)
                   (ice-9 ftw)))
        (snippet
         ;; The build system doesn't allow us to unbundle the following
         ;; libraries.  hidapi is also heavily patched and upstream not
         ;; actively maintained.
-        '(let ((keep-dirs '("nova-simd" "nova-tt" "hidapi"
+        #~(let ((keep-dirs '("nova-simd" "nova-tt" "hidapi"
                              "TLSF-2.4.6" "oscpack_1_1_0" "." "..")))
             (with-directory-excursion "./external_libraries"
               (for-each
@@ -3482,7 +3479,9 @@ link REQUIRED)"))))))
      '("out"                            ;core language
        "ide"))                          ;qt ide
     (arguments
-     `(#:configure-flags '("-DSYSTEM_BOOST=ON"
+     (list
+      #:configure-flags
+      #~(list "-DSYSTEM_BOOST=ON"
               "-DSYSTEM_YAMLCPP=ON"
               "-DSC_QT=ON"
               "-DCMAKE_BUILD_TYPE=Release"
@@ -3490,7 +3489,7 @@ link REQUIRED)"))))))
               "-DLIBSCSYNTH=ON"
               "-DSC_EL=OFF")      ;scel is packaged individually as emacs-scel
       #:phases
-       (modify-phases %standard-phases
+      #~(modify-phases %standard-phases
           ;; HOME must be defined otherwise supercollider throws a "ERROR:
           ;; Primitive '_FileMkDir' failed." error when generating the doc.
           ;; The graphical tests also hang without it.
@@ -3498,10 +3497,9 @@ link REQUIRED)"))))))
             (lambda _
               (setenv "HOME" (getcwd))))
           (add-after 'unpack 'patch-scclass-dir
-           (lambda* (#:key outputs #:allow-other-keys)
+            (lambda _
-             (let* ((out (assoc-ref outputs "out"))
+              (let* ((scclass-dir
-                    (scclass-dir
+                      (string-append #$output
-                     (string-append out
                                      "/share/SuperCollider/SCClassLibrary")))
                 (substitute* "lang/LangSource/SC_LanguageConfig.cpp"
                   (((string-append
@@ -3509,7 +3507,7 @@ link REQUIRED)"))))))
                      "\\(DirName::Resource\\) / CLASS_LIB_DIR_NAME"))
                    (string-append "Path(\"" scclass-dir "\")"))))))
           (add-after 'patch-scclass-dir 'fix-struct-SOUNDFILE-tag
-           (lambda* _
+            (lambda _
               (display (getcwd)) (newline)
               (substitute* "include/plugin_interface/SC_SndBuf.h"
                 (("SNDFILE_tag")
@@ -3519,9 +3517,8 @@ link REQUIRED)"))))))
               (system "Xvfb &")
               (setenv "DISPLAY" ":0")))
           (add-before 'install 'install-ide
-           (lambda* (#:key outputs #:allow-other-keys)
+            (lambda _
-             (let* ((out (assoc-ref outputs "out"))
+              (let* ((ide #$output:ide)
-                    (ide (assoc-ref outputs "ide"))
                      (scide "editors/sc-ide/scide"))
                 (install-file scide
                               (string-append ide "/bin"))
@@ -3564,20 +3561,20 @@ using Guix System.")
 (define-public libshout-idjc
   (package
     (name "libshout-idjc")
-    (version "2.4.4")
+    (version "2.4.6")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "mirror://sourceforge/libshoutidjc.idjc.p"
                            "/libshout-idjc-" version ".tar.gz"))
        (sha256
-        (base32 "1r9z8ggxylr2ab0isaljbm574rplnlcb12758j994h54nh2vikwb"))))
+        (base32 "1cgbym1qms408l4anc0imlcf091yk9kic4s9n7zcri3xzbi8lv1z"))))
     (build-system gnu-build-system)
     (native-inputs
      (list pkg-config))
     (inputs
-     (list libogg libtheora libvorbis speex))
+     (list libogg libshout libtheora libvorbis speex))
-    (home-page "https://idjc.sourceforge.net/")
+    (home-page "https://idjc.sourceforge.io/")
     (synopsis "Broadcast streaming library with IDJC extensions")
     (description "This package provides libshout plus IDJC extensions.")
     ;; GNU Library (not Lesser) General Public License.
@@ -3965,8 +3962,8 @@ encode and decode wavpack files.")
 
 (define-public libmixed
   ;; Release is much outdated.
-  (let ((commit "91e6b9f2438bca41205fade02c9d8f4f938838b6")
+  (let ((commit "9b2668e0d85175b0e92864cfbf1b9e58f77c92e0")
-        (revision "0"))
+        (revision "1"))
     (package
       (name "libmixed")
       (version (git-version "2.0" revision commit))
@@ -3978,14 +3975,10 @@ encode and decode wavpack files.")
                (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-          (base32 "01vwgv8ivpg7a4y95krkgh656mmklsn1k3fmhwp474aj82grd3m4"))))
+          (base32 "0ql2h0hh4jl96sc9i6mk1d6qq261bvsfapinvzr9gx3lpzycpfb7"))))
       (build-system cmake-build-system)
       (arguments
        (list
-        ;; FIXME: (Sharlatan-20230326T121542+0100): Tests failed 1/34, 1 failed,
-        ;; 33 passed. There is not simple way to disable just one test.
-        ;; https://github.com/Shirakumo/libmixed/issues/13
-        #:tests? #f
         #:configure-flags
         #~(list "-DBUILD_STATIC=OFF"
                 "-DCMAKE_CXX_FLAGS=-O3 -fPIC"
@@ -5664,7 +5657,7 @@ with the provided metadata and adhere to well-known best practices.")
 (define-public ztoolkit
   (package
     (name "ztoolkit")
-    (version "0.1.1")
+    (version "0.1.2")
     (source
      (origin
        (method git-fetch)
@@ -5674,7 +5667,7 @@ with the provided metadata and adhere to well-known best practices.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "07xl3cmdaf7k9mm58m93cn8i1jvgimmiifdw1w7v2jl88nx60pm1"))))
+         "1k60zklrrnch4l0iyzwb4q0srdj3gggwq8cpldwgdhn26ddqkl0d"))))
     (build-system meson-build-system)
     (native-inputs
      (list pkg-config))
@@ -5692,6 +5685,16 @@ minimum.")
     (home-page "https://git.zrythm.org/zrythm/ztoolkit")
     (license license:agpl3+)))
 
+(define-public ztoolkit-rsvg
+  (package/inherit ztoolkit
+    (name "ztoolkit-rsvg")
+    (arguments
+     (list #:configure-flags '(list "-Denable_rsvg=true")))
+    (propagated-inputs
+     (modify-inputs (package-propagated-inputs ztoolkit)
+       (prepend (librsvg-for-system))))
+    (synopsis "ZToolkit with SVG support")))
+
 (define-public libinstpatch
   (package
     (name "libinstpatch")
@@ -5723,16 +5726,6 @@ an object framework (based on GObject) to load patch files, which can then be
 edited, converted, compressed and saved.")
     (license license:lgpl2.1)))
 
-(define-public ztoolkit-rsvg
-  (package/inherit ztoolkit
-    (name "ztoolkit-rsvg")
-    (arguments
-     `(#:configure-flags `("-Denable_rsvg=true")))
-    (propagated-inputs
-     `(("librsvg" ,librsvg)
-       ,@(package-propagated-inputs ztoolkit)))
-    (synopsis "ZToolkit with SVG support")))
-
 (define-public lsp-dsp-lib
   (package
     (name "lsp-dsp-lib")

gnu/packages/autotools.scm

@@ -10,7 +10,7 @@
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2019 Pierre-Moana Levesque <pierre.moana.levesque@gmail.com>
-;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
+;;; Copyright © 2020, 2023 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2022 Marius Bakke <marius@gnu.org>
 ;;;
@@ -72,7 +72,7 @@
       #:phases
       #~(modify-phases %standard-phases
           #$@(if (%current-target-system)
-                 '((add-after 'install 'patch-non-shebang-references
+                 #~((add-after 'install 'patch-non-shebang-references
                       (lambda* (#:key build inputs #:allow-other-keys)
                         ;; `patch-shebangs' patches shebangs only, and the Perl
                         ;; scripts use a re-exec feature that references the
@@ -369,7 +369,7 @@ output is indexed in many ways to simplify browsing.")
                  (string-append "exit 77\n" all "\n")))))
 
           #$@(if (%current-target-system)
-                 '((add-after 'install 'patch-non-shebang-references
+                 #~((add-after 'install 'patch-non-shebang-references
                       (lambda* (#:key inputs #:allow-other-keys)
                         ;; `patch-shebangs' patches shebangs only, and the Perl
                         ;; scripts use a re-exec feature that references the

gnu/packages/barrier.scm

@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2022 Mathieu Othacehe <othacehe@gnu.org>
+;;; Copyright © 2023 Simon Tournier <zimon.toutoune@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -19,6 +20,7 @@
 (define-module (gnu packages barrier)
   #:use-module (guix build-system cmake)
   #:use-module (guix utils)
+  #:use-module (guix gexp)
   #:use-module (guix git-download)
   #:use-module (guix download)
   #:use-module ((guix licenses) #:prefix license:)
@@ -48,9 +50,17 @@
         (base32 "19bwa9qidq2mxv1fkyxxc1xdmv3jx6bj35bkaaw70jzkblnfmlfs"))))
     (build-system cmake-build-system)
     (arguments
-     '(#:configure-flags
+     (list
-       (list "-DBARRIER_USE_EXTERNAL_GTEST=ON")
+      #:configure-flags
-       #:tests? #f)) ;tests require a running x server
+      #~(list "-DBARRIER_USE_EXTERNAL_GTEST=ON")
+      #:tests? #f ;; tests require a running x server
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'fix-null
+            (lambda _
+              (substitute* "src/lib/base/Event.h"
+                (("#include \"common/stdmap\\.h\"")
+                 "#include \"common/stdmap.h\"\n#include <cstddef>")))))))
     (native-inputs
      (list googletest pkg-config))
     (inputs

gnu/packages/bioconductor.scm

@@ -4897,6 +4897,50 @@ makes available functions for visualization and exploration of the data and
 results.")
     (license license:gpl3+)))
 
+(define-public r-dropletutils
+  (package
+    (name "r-dropletutils")
+    (version "1.20.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "DropletUtils" version))
+       (sha256
+        (base32 "09xwfb4ihpsp465vb1zbcwm6ww6qi3spn9d8p4i1gczyc0p9pf1y"))))
+    (properties `((upstream-name . "DropletUtils")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-beachmat
+           r-bh
+           r-biocgenerics
+           r-biocparallel
+           r-delayedarray
+           r-delayedmatrixstats
+           r-dqrng
+           r-edger
+           r-genomicranges
+           r-hdf5array
+           r-iranges
+           r-matrix
+           r-r-utils
+           r-rcpp
+           r-rhdf5
+           r-rhdf5lib
+           r-s4vectors
+           r-scuttle
+           r-singlecellexperiment
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/DropletUtils")
+    (synopsis "Utilities for handling single-cell droplet data")
+    (description
+     "This package provides a number of utility functions for handling
+single-cell RNA-seq data from droplet technologies such as 10X Genomics.  This
+includes data loading from count matrices or molecule information files,
+identification of cells from empty droplets, removal of barcode-swapped
+pseudo-cells, and downsampling of the count matrix.")
+    (license license:gpl3)))
+
 (define-public r-dss
   (package
     (name "r-dss")

gnu/packages/bioinformatics.scm

@@ -1152,20 +1152,19 @@ cpp.find_library('hdf5_cpp', dirs : '~a'), "
                 "0ykjbps1y3z3085q94npw8i9x5gldc6shy8vlc08v76zljsm07hv"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:phases
+     (list
-       (modify-phases %standard-phases
+      #:phases
+      #~(modify-phases %standard-phases
           (add-after 'install 'wrap-executables
-           (lambda* (#:key inputs outputs #:allow-other-keys)
+            (lambda _
-             (let* ((out (assoc-ref outputs "out")))
               (for-each
                (lambda (script)
-                  (wrap-program (string-append out "/bin/" script)
+                 (wrap-program (string-append #$output "/bin/" script)
                    `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))))
                '("create_annotations_files.bash"
                  "create_metaplots.bash"
                  "Ribotaper_ORF_find.sh"
-                  "Ribotaper.sh")))
+                 "Ribotaper.sh")))))))
-             #t)))))
     (inputs
      (list bedtools-2.18
            samtools-0.1
@@ -2475,7 +2474,7 @@ package provides command line tools using the Bio++ library.")
 (define-public blast+
   (package
     (name "blast+")
-    (version "2.11.0")
+    (version "2.14.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2483,7 +2482,7 @@ package provides command line tools using the Bio++ library.")
                     version "/ncbi-blast-" version "+-src.tar.gz"))
               (sha256
                (base32
-                "0m0r9vkw631ky1za1wilsfk9k9spwqh22nkrb9a57rbwmrc1i3nq"))
+                "003mn7m4y306k7visv3in3ikfgm8m41z0jq9lyvz10iv1hdpyixz"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -2519,7 +2518,8 @@ package provides command line tools using the Bio++ library.")
                     (("cksum") "cksum >/dev/null"))))))
     (build-system gnu-build-system)
     (arguments
-     `(;; There are two(!) tests for this massive library, and both fail with
+     (list
+      ;; There are two(!) tests for this massive library, and both fail with
       ;; "unparsable timing stats".
       ;; ERR [127] --  [serial/datatool] datatool.sh     (unparsable timing stats)
       ;; ERR [127] --  [serial/datatool] datatool_xml.sh     (unparsable timing stats)
@@ -2527,12 +2527,12 @@ package provides command line tools using the Bio++ library.")
       #:out-of-source? #t
       #:parallel-build? #f              ;not supported
       #:phases
-       (modify-phases %standard-phases
+      #~(modify-phases %standard-phases
           (add-before 'configure 'set-HOME
             ;; $HOME needs to be set at some point during the configure phase
-          (lambda _ (setenv "HOME" "/tmp") #t))
+            (lambda _ (setenv "HOME" "/tmp")))
           (add-after 'unpack 'enter-dir
-          (lambda _ (chdir "c++") #t))
+            (lambda _ (chdir "c++")))
           (add-after 'enter-dir 'fix-build-system
             (lambda _
               (define (which* cmd)
@@ -2545,7 +2545,7 @@ package provides command line tools using the Bio++ library.")
                        (format (current-error-port)
                                "WARNING: Unable to find absolute path for ~s~%"
                                cmd)
-                     #f)))
+                       #false)))
 
               ;; Rewrite hardcoded paths to various tools
               (substitute* (append '("src/build-system/configure.ac"
@@ -2564,7 +2564,7 @@ package provides command line tools using the Bio++ library.")
                                      "src/build-system/Makefile.requirements"
                                      "src/build-system/Makefile.rules_with_autodep.in")
                                    (find-files "scripts/common/check" "\\.sh$"))
-              (("(/usr/bin/|/bin/)([a-z][-_.a-z]*)" all dir cmd)
+                (("(/usr/bin/|/bin/)([a-z][-_.a-z]*(\\+\\+)?)" all dir cmd)
                  (or (which* cmd) all)))
 
               (substitute* (find-files "src/build-system" "^config.*")
@@ -2579,43 +2579,40 @@ package provides command line tools using the Bio++ library.")
               (substitute* (find-files "scripts/common/impl/" "\\.sh$")
                 (("^ *PATH=.*") "")
                 (("action=/bin/") "action=")
-              (("export PATH") ":"))
+                (("export PATH") ":"))))
-            #t))
           (replace 'configure
-           (lambda* (#:key inputs outputs #:allow-other-keys)
+            (lambda _
-             (let ((out     (assoc-ref outputs "out"))
+              (let ((lib     (string-append #$output:lib "/lib"))
-                   (lib     (string-append (assoc-ref outputs "lib") "/lib"))
+                    (include (string-append #$output:include
-                   (include (string-append (assoc-ref outputs "include")
                                             "/include/ncbi-tools++")))
                 ;; The 'configure' script doesn't recognize things like
                 ;; '--enable-fast-install'.
                 (invoke "./configure.orig"
                         (string-append "--with-build-root=" (getcwd) "/build")
-                       (string-append "--prefix=" out)
+                        (string-append "--prefix=" #$output)
                         (string-append "--libdir=" lib)
                         (string-append "--includedir=" include)
                         (string-append "--with-bz2="
-                                      (assoc-ref inputs "bzip2"))
+                                       #$(this-package-input "bzip2"))
                         (string-append "--with-z="
-                                      (assoc-ref inputs "zlib"))
+                                       #$(this-package-input "zlib"))
                         (string-append "--with-pcre="
-                                      (assoc-ref inputs "pcre"))
+                                       #$(this-package-input "pcre"))
                         ;; Each library is built twice by default, once
                         ;; with "-static" in its name, and again
                         ;; without.
                         "--without-static"
-                       "--with-dll")
+                        "--with-dll")))))))
-               #t))))))
     (outputs '("out"       ;  21 MB
                "lib"       ; 226 MB
                "include")) ;  33 MB
     (inputs
-     `(("bzip2" ,bzip2)
+     (list bzip2
-       ("lmdb" ,lmdb)
+           lmdb
-       ("zlib" ,zlib)
+           zlib
-       ("pcre" ,pcre)
+           pcre
-       ("perl" ,perl)
+           perl
-       ("python" ,python-wrapper)))
+           python-wrapper))
     (native-inputs
      (list cpio))
     (home-page "https://blast.ncbi.nlm.nih.gov")
@@ -3449,31 +3446,31 @@ setup"))))
                 "0115hkjflsnfzn36xppwf9h9avfxlavr43djqmshkkzbgjzsz60i"))))
     (build-system gnu-build-system)
     (arguments
-     '(#:tests? #f ; no "check" target
+     (list
+      #:tests? #f                       ;no "check" target
       #:phases
-       (modify-phases %standard-phases
+      #~(modify-phases %standard-phases
           (delete 'configure)
           (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
+            (lambda _
-             (let* ((out (assoc-ref outputs "out"))
+              (let ((bin (string-append #$output "/bin"))
-                    (bin (string-append out "/bin"))
+                    (doc (string-append #$output "/share/doc/codingquarry")))
-                    (doc (string-append out "/share/doc/codingquarry")))
                 (install-file "INSTRUCTIONS.pdf" doc)
                 (copy-recursively "QuarryFiles"
-                                 (string-append out "/QuarryFiles"))
+                                  (string-append #$output
+                                                 "/share/codingquarry/QuarryFiles"))
                 (install-file "CodingQuarry" bin)
-               (install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin))
+                (install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin)))))))
-             #t)))))
+    ;; TODO: This package also needs a Python 2 variant of biopython
-    (inputs (list openmpi))
+    (inputs (list openmpi python-2)) ;Only Python 2 is supported
     (native-search-paths
      (list (search-path-specification
             (variable "QUARRY_PATH")
-            (files '("QuarryFiles")))))
+            (files '("share/codingquarry/QuarryFiles")))))
-    (native-inputs `(("python" ,python-2))) ; Only Python 2 is supported
+    (home-page "https://sourceforge.net/projects/codingquarry/")
     (synopsis "Fungal gene predictor")
     (description "CodingQuarry is a highly accurate, self-training GHMM fungal
 gene predictor designed to work with assembled, aligned RNA-seq transcripts.")
-    (home-page "https://sourceforge.net/projects/codingquarry/")
     (license license:gpl3+)))
 
 (define-public clustal-omega
@@ -3682,28 +3679,26 @@ files.")
 (define-public python-pybigwig
   (package
     (name "python-pybigwig")
-    (version "0.3.17")
+    (version "0.3.22")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "pyBigWig" version))
               (sha256
                (base32
-                "157x6v48y299zm382krf1dw08fdxg95im8lnabhp5vc94s04zxj1"))
+                "0hr25lkp26mk0fp7irdjdrdsd5lann9kyv0xq9npyyxxakvjci2x"))
               (modules '((guix build utils)))
               (snippet
-               '(begin
                ;; Delete bundled libBigWig sources
-                  (delete-file-recursively "libBigWig")
+               '(delete-file-recursively "libBigWig"))))
-                  #t))))
+    (build-system pyproject-build-system)
-    (build-system python-build-system)
     (arguments
-     `(#:phases
+     '(#:tests? #false      ;only one test exists and it needs internet access
+       #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'link-with-libBigWig
-           (lambda* (#:key inputs #:allow-other-keys)
+           (lambda _
              (substitute* "setup.py"
-               (("libs=\\[") "libs=[\"BigWig\", "))
+               (("libs=\\[") "libs=[\"BigWig\", ")))))))
-             #t)))))
     (propagated-inputs
      (list python-numpy))
     (inputs
@@ -4032,25 +4027,23 @@ with Python.")
                (base32 "1ibnplgfzj96w8glkx17v7sld3pm402fr5ybmf3h0rlcryabxrqy"))
               (modules '((guix build utils)))
               (snippet
-               '(begin
+               '(delete-file-recursively "src/htslib"))))
-                  (delete-file-recursively "src/htslib")
-                  #t))))
     (build-system gnu-build-system)
     (arguments
-     `(#:tests? #f ; There are no tests to run.
+     (list
+      #:tests? #f                       ;There are no tests to run.
       #:make-flags
-       ,#~(list "PARALLEL=1"           ; Allow parallel execution at run-time.
+      #~(list "PARALLEL=1"             ; Allow parallel execution at run-time.
               (string-append "prefix=" #$output))
       #:phases
-       (modify-phases %standard-phases
+      #~(modify-phases %standard-phases
           (delete 'configure)           ; There is no configure phase.
           (add-after 'install 'install-templates
-           (lambda* (#:key outputs #:allow-other-keys)
+            (lambda _
-             (let ((templates (string-append (assoc-ref outputs "out")
+              (let ((templates (string-append #$output
                                               "/share/delly/templates")))
                 (mkdir-p templates)
-               (copy-recursively "excludeTemplates" templates)
+                (copy-recursively "excludeTemplates" templates)))))))
-               #t))))))
     (inputs
      (list boost bzip2 htslib zlib))
     (home-page "https://github.com/dellytools/delly")
@@ -4219,7 +4212,7 @@ bases are detected.")
 (define-public diamond
   (package
     (name "diamond")
-    (version "0.9.30")
+    (version "2.1.6")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -4228,18 +4221,11 @@ bases are detected.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0k6f3kb6cniw11xw6763kkbs1sl0yack7xsy7q5fl5v170ssphq4"))))
+                "0kb17jwlsrvgswfahzznrffv1i6ybwwmq99qs7iga5yzbx64jp6q"))))
     (build-system cmake-build-system)
     (arguments
-     '(#:tests? #f ; no "check" target
+     (list #:configure-flags '(list "-DX86=OFF"))) ;avoid SSE4 and AVX2
-       #:phases
+    (inputs (list zlib))
-       (modify-phases %standard-phases
-         (add-after 'unpack 'remove-native-compilation
-           (lambda _
-             (substitute* "CMakeLists.txt" (("-march=native") ""))
-             #t)))))
-    (inputs
-     (list zlib))
     (home-page "https://github.com/bbuchfink/diamond")
     (synopsis "Accelerated BLAST compatible local sequence aligner")
     (description
@@ -4248,7 +4234,7 @@ translated DNA query sequences against a protein reference database (BLASTP
 and BLASTX alignment mode).  The speedup over BLAST is up to 20,000 on short
 reads at a typical sensitivity of 90-99% relative to BLAST depending on the
 data and settings.")
-    (license license:agpl3+)))
+    (license license:gpl3+)))
 
 (define-public discrover
   (package
@@ -4270,7 +4256,7 @@ data and settings.")
        #:phases
        (modify-phases %standard-phases
          (add-before 'build 'set-force-source-date
-           ;; for reproducible dates, texlive needs this to respect respect
+           ;; for reproducible dates, texlive needs this to respect
            ;; SOURCE_DATE_EPOCH
            (lambda _
              (setenv "FORCE_SOURCE_DATE" "1")))
@@ -4301,7 +4287,8 @@ data and settings.")
     (inputs
      (list boost cairo rmath-standalone))
     (native-inputs
-     `(("texlive" ,(texlive-updmap.cfg (list texlive-cm
+     (list (texlive-updmap.cfg
+            (list texlive-cm
                   texlive-amsfonts
                   texlive-doi
                   texlive-fonts-ec
@@ -4311,8 +4298,8 @@ data and settings.")
                   texlive-latex-natbib
                   texlive-bibtex        ;style files used by natbib
                   texlive-pgf           ;tikz
-                                             texlive-latex-verbatimbox)))
+                  texlive-latex-verbatimbox))
-       ("imagemagick" ,imagemagick)))
+           imagemagick))
     (home-page "https://dorina.mdc-berlin.de/public/rajewsky/discrover/")
     (synopsis "Discover discriminative nucleotide sequence motifs")
     (description "Discrover is a motif discovery method to find binding sites
@@ -5653,8 +5640,7 @@ VCF.")
                '(begin
                   ;; Delete pre-built binaries.
                   (delete-file-recursively "lib")
-                  (mkdir-p "lib")
+                  (mkdir-p "lib")))))
-                  #t))))
     (build-system ant-build-system)
     (arguments
      `(#:build-target "picard-jar"
@@ -5684,8 +5670,7 @@ VCF.")
                (("name=\"test\" depends=\"compile, ")
                 "name=\"test\" depends=\"compile-tests, ")
                (("name=\"compile\" depends=\"compile-src, compile-tests\"")
-                "name=\"compile\" depends=\"compile-src\""))
+                "name=\"compile\" depends=\"compile-src\""))))
-             #t))
          (add-after 'unpack 'fix-deflater-path
            (lambda* (#:key outputs #:allow-other-keys)
              (substitute* "src/java/net/sf/samtools/Defaults.java"
@@ -5693,8 +5678,7 @@ VCF.")
                 (string-append "getStringProperty(\"intel_deflater_so_path\", \""
                                (assoc-ref outputs "out")
                                "/lib/jni/libIntelDeflater.so"
-                               "\")")))
+                               "\")")))))
-             #t))
          ;; Build the deflater library, because we've previously deleted the
          ;; pre-built one.  This can only be built with access to the JDK
          ;; sources.
@@ -5717,31 +5701,27 @@ VCF.")
                        "-c" "-O3" "-fPIC" "IntelDeflater.c")
                (invoke "gcc" "-shared"
                        "-o" "../../../lib/jni/libIntelDeflater.so"
-                       "IntelDeflater.o" "-lz" "-lstdc++"))
+                       "IntelDeflater.o" "-lz" "-lstdc++"))))
-             #t))
          ;; We can only build everything else after building the JNI library.
          (add-after 'build-jni 'build-rest
            (lambda* (#:key make-flags #:allow-other-keys)
-             (apply invoke `("ant" "all" ,@make-flags))
+             (apply invoke `("ant" "all" ,@make-flags))))
-             #t))
          (add-before 'build 'set-JAVA6_HOME
            (lambda _
-             (setenv "JAVA6_HOME" (getenv "JAVA_HOME"))
+             (setenv "JAVA6_HOME" (getenv "JAVA_HOME"))))
-             #t))
          (replace 'install (install-jars "dist"))
          (add-after 'install 'install-jni-lib
            (lambda* (#:key outputs #:allow-other-keys)
              (let ((jni (string-append (assoc-ref outputs "out")
                                        "/lib/jni")))
                (mkdir-p jni)
-               (install-file "lib/jni/libIntelDeflater.so" jni)
+               (install-file "lib/jni/libIntelDeflater.so" jni)))))))
-               #t))))))
     (inputs
-     `(("java-snappy-1" ,java-snappy-1)
+     (list java-snappy-1
-       ("java-commons-jexl-2" ,java-commons-jexl-2)
+           java-commons-jexl-2
-       ("java-cofoja" ,java-cofoja)
+           java-cofoja
-       ("ant" ,ant/java8) ; for bzip2 support at runtime
+           ant/java8                    ;for bzip2 support at runtime
-       ("zlib" ,zlib)))
+           zlib))
     (native-inputs
      `(("ant-apache-bcel" ,ant-apache-bcel)
        ("ant-junit" ,ant-junit)
@@ -7561,35 +7541,34 @@ simultaneously.")
                 "0m8hlxscidsfqm9x9fyi62q6lpf1dv5115kgjjgnrkl49q9c27m6"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:parallel-build? #f ; not supported
+     (list
+      #:parallel-build? #f              ; not supported
       #:tests? #f                       ; no "check" target
-       #:make-flags '("HAVE_HDF5=1")
+      #:make-flags '(list "HAVE_HDF5=1")
       #:phases
-       (modify-phases %standard-phases
+      #~(modify-phases %standard-phases
+          #;
           (add-after 'unpack 'make-files-writable
-           (lambda _ (for-each make-file-writable (find-files "." ".*")) #t))
+            (lambda _ (for-each make-file-writable (find-files "." ".*"))))
           (add-before 'configure 'set-perl-search-path
             (lambda _
               ;; Work around "dotless @INC" build failure.
               (setenv "PERL5LIB"
                       (string-append (getcwd) "/setup:"
-                                    (getenv "PERL5LIB")))
+                                     (getenv "PERL5LIB")))))
-             #t))
           ;; See https://github.com/ncbi/ncbi-vdb/issues/14
           (add-after 'unpack 'patch-krypto-flags
             (lambda _
               (substitute* "libs/krypto/Makefile"
                 (("-Wa,-march=generic64\\+aes") "")
-               (("-Wa,-march=generic64\\+sse4") ""))
+                (("-Wa,-march=generic64\\+sse4") ""))))
-             #t))
           (replace 'configure
-           (lambda* (#:key inputs outputs #:allow-other-keys)
+            (lambda _
-             (let ((out (assoc-ref outputs "out")))
               ;; Override include path for libmagic
               (substitute* "setup/package.prl"
                 (("name => 'magic', Include => '/usr/include'")
                  (string-append "name=> 'magic', Include => '"
-                                 (assoc-ref inputs "libmagic")
+                                #$(this-package-input "file")
                                 "/include" "'")))
 
               ;; Install kdf5 library (needed by sra-tools)
@@ -7604,56 +7583,57 @@ simultaneously.")
               ;; Override search path for ngs-java
               (substitute* "setup/package.prl"
                 (("/usr/local/ngs/ngs-java")
-                  (assoc-ref inputs "java-ngs")))
+                 #$(this-package-input "java-ngs")))
 
               ;; The 'configure' script doesn't recognize things like
               ;; '--enable-fast-install'.
               (invoke "./configure"
                       (string-append "--build-prefix=" (getcwd) "/build")
-                       (string-append "--prefix=" (assoc-ref outputs "out"))
+                      (string-append "--prefix=" #$output)
                       (string-append "--debug")
                       (string-append "--with-xml2-prefix="
-                                      (assoc-ref inputs "libxml2"))
+                                     #$(this-package-input "libxml2"))
                       (string-append "--with-ngs-sdk-prefix="
-                                      (assoc-ref inputs "ngs-sdk"))
+                                     #$(this-package-input "ngs-sdk"))
                       (string-append "--with-hdf5-prefix="
-                                      (assoc-ref inputs "hdf5")))
+                                     #$(this-package-input "hdf5")))))
-               #t)))
           (add-after 'install 'install-interfaces
-           (lambda* (#:key outputs #:allow-other-keys)
+            (lambda _
               ;; Install interface libraries.  On i686 the interface libraries
               ;; are installed to "linux/gcc/i386", so we need to use the Linux
               ;; architecture name ("i386") instead of the target system prefix
               ;; ("i686").
-             (mkdir (string-append (assoc-ref outputs "out") "/ilib"))
+              (mkdir (string-append #$output "/ilib"))
               (copy-recursively (string-append
                                  "build/ncbi-vdb/linux/gcc/"
-                                ,(platform-linux-architecture
+                                 #$(platform-linux-architecture
                                     (lookup-platform-by-target-or-system
                                      (or (%current-target-system)
                                          (%current-system))))
                                  "/rel/ilib")
-                               (string-append (assoc-ref outputs "out")
+                                (string-append #$output "/ilib"))
-                                              "/ilib"))
               ;; Install interface headers
               (copy-recursively "interfaces"
-                               (string-append (assoc-ref outputs "out")
+                                (string-append #$output "/include"))))
-                                              "/include"))
+          (add-after 'install-interfaces 'install-libs
-             #t))
+            (lambda _
+              (copy-recursively (string-append
+                                 "build/ncbi-vdb/linux/gcc/"
+                                 #$(platform-linux-architecture
+                                    (lookup-platform-by-target-or-system
+                                     (or (%current-target-system)
+                                         (%current-system))))
+                                 "/rel/lib")
+                                (string-append #$output "/lib"))))
           ;; These files are needed by sra-tools.
           (add-after 'install 'install-configuration-files
-           (lambda* (#:key outputs #:allow-other-keys)
+            (lambda _
-             (let ((target (string-append (assoc-ref outputs "out") "/kfg")))
+              (let ((target (string-append #$output "/kfg")))
                 (mkdir target)
                 (install-file "libs/kfg/default.kfg" target)
-               (install-file "libs/kfg/certs.kfg" target))
+                (install-file "libs/kfg/certs.kfg" target)))))))
-             #t)))))
     (inputs
-     `(("libxml2" ,libxml2)
+     (list file hdf5 java-ngs libxml2 ngs-sdk ))
-       ("ngs-sdk" ,ngs-sdk)
-       ("java-ngs" ,java-ngs)
-       ("libmagic" ,file)
-       ("hdf5" ,hdf5)))
     (native-inputs (list perl))
     ;; NCBI-VDB requires SSE capability.
     (supported-systems '("i686-linux" "x86_64-linux"))
@@ -8013,10 +7993,11 @@ unique transcripts.")
          "1cr2mijkfs5sm35ffjs6861qsd1qkgnhnbavdv65zg5d655abbjf"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:parallel-build? #f             ; not supported
+     (list
+      #:parallel-build? #f             ; not supported
       #:tests? #f                      ; no "check" target
       #:make-flags
-       ,#~(list (string-append "DEFAULT_CRT="
+      #~(list (string-append "DEFAULT_CRT="
                              #$(this-package-input "ncbi-vdb")
                              "/kfg/certs.kfg")
               (string-append "DEFAULT_KFG="
@@ -8030,14 +8011,13 @@ unique transcripts.")
                                    "/lib64"
                                    "/lib32")))
        #:phases
-       (modify-phases %standard-phases
+       #~(modify-phases %standard-phases
            (add-before 'configure 'set-perl-search-path
              (lambda _
                ;; Work around "dotless @INC" build failure.
                (setenv "PERL5LIB"
                        (string-append (getcwd) "/setup:"
-                                    (getenv "PERL5LIB")))
+                                      (getenv "PERL5LIB")))))
-             #t))
            (replace 'configure
              (lambda* (#:key inputs outputs #:allow-other-keys)
                ;; The build system expects a directory containing the sources and
@@ -8061,38 +8041,40 @@ unique transcripts.")
                  (("CC\\?=gcc") "myCC=gcc")
                  (("\\(CC\\)") "(myCC)"))
 
+               ;; Don't link libxml2 statically
+               (substitute* "build/ld.linux.exe.sh"
+                 (("grep -q 'OS_DISTRIBUTOR = Ubuntu.*") "true\n"))
+
                ;; The 'configure' script doesn't recognize things like
                ;; '--enable-fast-install'.
                (invoke "./configure"
                        (string-append "--build-prefix=" (getcwd) "/build")
-                     (string-append "--prefix=" (assoc-ref outputs "out"))
+                       (string-append "--prefix=" #$output)
                        (string-append "--debug")
                        (string-append "--with-fuse-prefix="
-                                    (assoc-ref inputs "fuse"))
+                                      #$(this-package-input "fuse"))
                        (string-append "--with-magic-prefix="
-                                    (assoc-ref inputs "libmagic"))
+                                      #$(this-package-input "file"))
-                     ;; TODO: building with libxml2 fails with linker errors
-                     #;
                        (string-append "--with-xml2-prefix="
-                                    (assoc-ref inputs "libxml2"))
+                                      #$(this-package-input "libxml2"))
                        (string-append "--with-ncbi-vdb-sources="
-                                    (assoc-ref inputs "ncbi-vdb"))
+                                      #$(this-package-input "ncbi-vdb"))
                        (string-append "--with-ncbi-vdb-build="
-                                    (assoc-ref inputs "ncbi-vdb"))
+                                      #$(this-package-input "ncbi-vdb"))
                        (string-append "--with-ngs-sdk-prefix="
-                                    (assoc-ref inputs "ngs-sdk"))
+                                      #$(this-package-input "ngs-sdk"))
                        (string-append "--with-hdf5-prefix="
-                                    (assoc-ref inputs "hdf5")))
+                                      #$(this-package-input "hdf5"))))))))
-             #t)))))
     (native-inputs (list perl))
     (inputs
-     `(("ngs-sdk" ,ngs-sdk)
+     (list ngs-sdk
-       ("ncbi-vdb" ,ncbi-vdb)
+           ncbi-vdb
-       ("libmagic" ,file)
+           file
-       ("fuse" ,fuse)
+           fuse
-       ("hdf5" ,hdf5-1.10)
+           hdf5-1.10
-       ("zlib" ,zlib)
+           libxml2
-       ("python" ,python-wrapper)))
+           zlib
+           python-wrapper))
     (home-page
      "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software")
     (synopsis "Tools and libraries for reading and writing sequencing data")
@@ -12628,6 +12610,56 @@ single-cell RNA-seq data.")
 API services.")
     (license license:bsd-3)))
 
+(define-public python-mgatk
+  (package
+    (name "python-mgatk")
+    (version "0.6.7")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/caleblareau/mgatk")
+             ;; There is no tag for 0.6.7, but this is the commit
+             ;; corresponding to the version bump.
+             (commit "2633903acb1fb406bb58c787f320c3641f446ee7")))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "19iklfv1brwsfg1l5lrs3z8m343nskkn1998c1fs7fdn0lgrki2p"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; The md5 module has been removed in Python 3
+          (add-after 'unpack 'python3-compatibility
+            (lambda _
+              (substitute* "tests/test_cli.py"
+                (("import md5") "from hashlib import md5")
+                (("md5.new") "md5")
+                (("\\.digest") ".hexdigest")))))))
+    (propagated-inputs
+     (list python-biopython
+           python-click
+           python-numpy
+           python-optparse-pretty
+           python-pandas
+           python-pysam
+           python-regex
+           python-ruamel.yaml
+           snakemake))
+    (native-inputs
+     (list python-pytest))
+    (home-page "https://github.com/caleblareau/mgatk")
+    (synopsis "Mitochondrial genome analysis toolkit.")
+    (description "This package is a Python-based command line interface for
+processing .bam files with mitochondrial reads and generating high-quality
+heteroplasmy estimation from sequencing data.  The mgatk package places a
+special emphasis on mitochondrial genotypes generated from single-cell
+genomics data, primarily @acronym{mtscATAC-seq, mitochondrial single-cell
+ATAC-sequence}, but is generally applicable across other assays.")
+    (license license:expat)))
+
 (define-public python-multivelo
   (package
     (name "python-multivelo")
@@ -15811,16 +15843,16 @@ Barcoding Kit or Rapid Barcoding Kit.")
          "0bsa5mf9n9q5jz7mmacrra41l7r8rac5vgsn6wv1fb52ya58b970"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:tests? #f ; there are none
+     (list
+      #:tests? #f                       ;there are none
       #:phases
-       (modify-phases %standard-phases
+      #~(modify-phases %standard-phases
           (delete 'configure)
           (delete 'build)
           (replace 'install
-           (lambda* (#:key inputs outputs #:allow-other-keys)
+            (lambda _
-             (let* ((out (assoc-ref outputs "out"))
+              (let ((libexec (string-append #$output "/libexec/jamm"))
-                    (libexec (string-append out "/libexec/jamm"))
+                    (bin (string-append #$output "/bin")))
-                    (bin (string-append out "/bin")))
                 (substitute* '("JAMM.sh"
                                "SignalGenerator.sh")
                   (("^sPath=.*")
@@ -15843,14 +15875,13 @@ Barcoding Kit or Rapid Barcoding Kit.")
                    (install-file script bin)
                    (wrap-program (string-append bin "/" script)
                      `("PATH" ":" prefix
-                      (,(string-append (assoc-ref inputs "coreutils") "/bin")
+                       (,(string-append #$(this-package-input "coreutils") "/bin")
-                       ,(string-append (assoc-ref inputs "gawk") "/bin")
+                        ,(string-append #$(this-package-input "gawk") "/bin")
-                       ,(string-append (assoc-ref inputs "perl") "/bin")
+                        ,(string-append #$(this-package-input "perl") "/bin")
-                       ,(string-append (assoc-ref inputs "r-minimal") "/bin")))
+                        ,(string-append #$(this-package-input "r-minimal") "/bin")))
                      `("PERL5LIB" ":" prefix (,(getenv "PERL5LIB")))
                      `("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE")))))
-                (list "JAMM.sh" "SignalGenerator.sh")))
+                 (list "JAMM.sh" "SignalGenerator.sh"))))))))
-             #t)))))
     (inputs
      (list bash
            coreutils
@@ -16474,35 +16505,36 @@ includes a command line tool and an analysis pipeline.")
          "0jx9656ry766vb8z08m1c3im87b0c82qpnjby9wz4kcz8vn87dx2"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:tests? #f ; there are none
+     (list
+      #:tests? #f                       ;there are none
       #:phases
-       (modify-phases %standard-phases
+      #~(modify-phases %standard-phases
           (replace 'configure
             (lambda* (#:key inputs #:allow-other-keys)
-             (let ((htslib (assoc-ref inputs "htslib")))
               (substitute* "Makefile"
                 (("-I\\$\\(HTSLIB\\)/htslib")
-                  (string-append "-I" htslib "/include/htslib"))
+                 (string-append "-I"
+                                (search-input-directory inputs "/include/htslib")))
                 ((" \\$\\(HTSLIB\\)/libhts.a")
-                  (string-append " " htslib "/lib/libhts.so"))))
+                 (string-append " " (search-input-file inputs "/lib/libhts.so"))))
+              (let ((samtools (search-input-file inputs "/bin/samtools")))
                 (substitute* "run_arriba.sh"
-               (("^STAR ") (string-append (which "STAR") " "))
+                  (("^STAR ")
+                   (string-append (search-input-file inputs "/bin/STAR") " "))
                   (("samtools --version-only")
-                (string-append (which "samtools") " --version-only"))
+                   (string-append samtools " --version-only"))
                   (("samtools index")
-                (string-append (which "samtools") " index"))
+                   (string-append samtools " index"))
                   (("samtools sort")
-                (string-append (which "samtools") " sort")))
+                   (string-append samtools " sort"))))))
-             #t))
           (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
+            (lambda _
-             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+              (let ((bin (string-append #$output "/bin")))
                 (install-file "arriba" bin)
                 (install-file "run_arriba.sh" bin)
                 (install-file "draw_fusions.R" bin)
                 (wrap-program (string-append bin "/draw_fusions.R")
-                 `("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE")))))
+                  `("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE"))))))))))
-             #t)))))
     (inputs
      (list htslib
            r-minimal
@@ -17324,24 +17356,24 @@ significance profiles for each word studied across the sorted genelist.")
                     (commit (string-append "v" version))))
               (file-name (git-file-name name version))
               (sha256
-       (base32 "0ci5fqvmpamwgxvmyd79ygj6n3bnbl3vc7b6h1sxz58186sm3pfs"))))
+               (base32
+                "0ci5fqvmpamwgxvmyd79ygj6n3bnbl3vc7b6h1sxz58186sm3pfs"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:tests? #f ; Tests require node.
+     (list
+      #:tests? #f                       ;Tests require node.
       #:phases
-       (modify-phases %standard-phases
+      #~(modify-phases %standard-phases
           (delete 'configure)           ;There is no configure phase.
           (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
+            (lambda _
-             (let* ((out (assoc-ref outputs "out"))
+              (let ((bin (string-append #$output "/bin"))
-                    (bin (string-append out "/bin"))
+                    (include (string-append #$output "/include")))
-                    (include (string-append out "/include")))
                 ;; TODO: There are Python modules for these programs too.
                 (install-file "multichoose" bin)
                 (install-file "multipermute" bin)
                 (install-file "multichoose.h" include)
-               (install-file "multipermute.h" include))
+                (install-file "multipermute.h" include)))))))
-             #t)))))
     (home-page "https://github.com/ekg/multichoose")
     (synopsis "Efficient loopless multiset combination generation algorithm")
     (description "This library implements an efficient loopless multiset
@@ -17715,7 +17747,7 @@ length of a short-read sequencing alignment.")
 (define-public samblaster
   (package
     (name "samblaster")
-    (version "0.1.24")
+    (version "0.1.26")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -17724,18 +17756,17 @@ length of a short-read sequencing alignment.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-        "0iv2ddfw8363vb2x8gr3p8g88whb6mb9m0pf71i2cqsbv6jghap7"))))
+                "0g24fq5hplnfgqkh3xqpg3lgx3wmxwnh9c7m6yw7pbi40lmgl1jv"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:tests? #f ; there are none
+     (list
+      #:tests? #f                       ;there are none
       #:phases
-       (modify-phases %standard-phases
+      #~(modify-phases %standard-phases
           (delete 'configure)           ;There is no configure phase.
           (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
+            (lambda _
-             (install-file "samblaster"
+              (install-file "samblaster" (string-append #$output "/bin")))))))
-                           (string-append (assoc-ref outputs "out") "/bin"))
-             #t)))))
     (home-page "https://github.com/GregoryFaust/samblaster")
     (synopsis "Mark duplicates in paired-end SAM files")
     (description "Samblaster is a fast and flexible program for marking
@@ -17793,7 +17824,7 @@ patterns.")
 (define-public methyldackel
   (package
     (name "methyldackel")
-    (version "0.5.1")
+    (version "0.6.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -17802,28 +17833,28 @@ patterns.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1sfhf2ap75qxpnmy1ifgmxqs18rq8mah9mcgkby73vc6h0sw99ws"))))
+                "06kj76pyhzxfcjcpm840a3km3fa9994kfq4asglnb228pwak326z"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:test-target "test"
+     (list
+      #:test-target "test"
       #:make-flags
-       ,#~(list "CC=gcc"
+      #~(list "CC=gcc"
               "CFLAGS=-fcommon"
+              "LIBBIGWIG=-lBigWig"
               (string-append "prefix=" #$output "/bin/"))
       #:phases
-       (modify-phases %standard-phases
+      '(modify-phases %standard-phases
          (replace 'configure
-           (lambda* (#:key outputs #:allow-other-keys)
+           (lambda _
              (substitute* "Makefile"
-               (("-lhts ") "-lhts -lBigWig ")
                (("install MethylDackel \\$\\(prefix\\)" match)
                 (string-append "install -d $(prefix); " match))))))))
     (inputs
-     (list curl ; XXX: needed by libbigwig
+     (list curl htslib libbigwig zlib))
-           htslib-1.9 libbigwig zlib))
     ;; Needed for tests
     (native-inputs
-     `(("python" ,python-wrapper)))
+     (list python-wrapper))
     (home-page "https://github.com/dpryan79/MethylDackel")
     (synopsis "Universal methylation extractor for BS-seq experiments")
     (description
@@ -17851,11 +17882,11 @@ containing the reference genome as well.")
                 "10lpbllvny923jjbbyrpxahhd1m5h7sbj9gx7rd123rg10mlidki"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:make-flags
+     (list
-       ,#~(list "CC=gcc"
+      #:make-flags
-                (string-append "DESTDIR=" #$output))
+      #~(list "CC=gcc" (string-append "DESTDIR=" #$output))
       #:phases
-       (modify-phases %standard-phases
+      #~(modify-phases %standard-phases
           (replace 'configure
             (lambda* (#:key inputs outputs #:allow-other-keys)
               ;; Fix syntax
@@ -17864,7 +17895,7 @@ containing the reference genome as well.")
               (substitute* "Makefile"
                 (("CLAPACKPATH=/usr/lib")
                  (string-append "CLAPACKPATH="
-                               (assoc-ref inputs "clapack") "/lib")))
+                                #$(this-package-input "clapack") "/lib")))
               ;; Renaming the libraries is not necessary with our version of
               ;; CLAPACK.
               (substitute* "src/lib/Makefile"
@@ -17877,8 +17908,7 @@ containing the reference genome as well.")
                 (("libf2c.a") "libf2c.so"))
               (substitute* "src/Makefile"
                 (("/opt") "/share")
-               (("/usr/") "/"))
+                (("/usr/") "/"))))
-             #t))
           (replace 'check
             (lambda _
               (setenv "PATH"
@@ -20073,6 +20103,114 @@ handling.")))
      "Bíogo is a bioinformatics library for the Go language.")
     (license license:bsd-3)))
 
+(define-public python-gseapy
+  (package
+    (name "python-gseapy")
+    (version "1.0.4")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/zqfang/GSEApy")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "06gh09dwwj2xr5zx8i41smy8arx2pw7rll7sk50np28z419bnyz9"))))
+    (build-system cargo-build-system)
+    (arguments
+     (list
+      #:install-source? #false
+      #:features '(list "extension-module")
+      #:cargo-test-flags '(list "--features=extension-module")
+      #:cargo-inputs
+      `(("rust-csv" ,rust-csv-1)
+        ("rust-itertools" ,rust-itertools-0.10)
+        ("rust-pyo3" ,rust-pyo3-0.16)
+        ("rust-rand" ,rust-rand-0.8)
+        ("rust-rayon" ,rust-rayon-1)
+        ("rust-serde" ,rust-serde-1))
+      #:imported-modules
+      (append %cargo-build-system-modules
+              %pyproject-build-system-modules)
+      #:modules
+      '((guix build cargo-build-system)
+        ((guix build pyproject-build-system) #:prefix py:)
+        (guix build utils))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'install 'prepare-python-module
+            (lambda _
+              ;; We don't use maturin, nor do we use setuptools-rust.
+              (delete-file "pyproject.toml")
+              (call-with-output-file "pyproject.toml"
+                (lambda (port)
+                  (format port "\
+[build-system]
+build-backend = 'setuptools.build_meta'
+requires = ['setuptools']
+")))
+              (delete-file "setup.py")
+              (call-with-output-file "setup.cfg"
+                (lambda (port)
+                  (format port "\
+[metadata]
+name = gseapy
+version = ~a
+
+[options]
+packages = find:
+
+[options.packages.find]
+exclude =
+  src
+  docs
+  tests
+  Cargo.toml
+" #$version)))))
+          ;; We delete the Cargo checks but run the Python tests later.
+          ;; See https://github.com/zqfang/GSEApy/issues/207
+          (delete 'check)
+          (add-after 'prepare-python-module 'enable-bytecode-determinism
+            (assoc-ref py:%standard-phases 'enable-bytecode-determinism))
+          (add-after 'enable-bytecode-determinism 'build-python-module
+            (assoc-ref py:%standard-phases 'build))
+          (add-after 'build-python-module 'install-python-module
+            (assoc-ref py:%standard-phases 'install))
+          (add-after 'install-python-module 'install-python-library
+            (lambda _
+              (let ((site (string-append #$output "/lib/python"
+                                         #$(version-major+minor
+                                            (package-version python))
+                                         "/site-packages")))
+                (mkdir-p site)
+                (copy-file "target/release/libgse.so"
+                           (string-append site "/gseapy/gse.so")))))
+          (add-after 'install-python-library 'add-install-to-pythonpath
+            (assoc-ref py:%standard-phases 'add-install-to-pythonpath))
+          (add-after 'add-install-to-pythonpath 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (invoke "pytest" "-vv" "tests"
+                        ;; These tests need access to the internet
+                        "-k" "not test_enrichr and not test_prerank")))))))
+    (inputs
+     (list python-wrapper))
+    (native-inputs
+     (list python-pytest))
+    (propagated-inputs
+     (list python-numpy
+           python-scipy
+           python-pandas
+           python-matplotlib
+           python-requests))
+    (home-page "https://github.com/zqfang/gseapy")
+    (synopsis "Gene Set Enrichment Analysis in Python")
+    (description "GSEApy is a Python/Rust implementation for GSEA and wrapper
+for Enrichr.  GSEApy can be used for RNA-seq, ChIP-seq, Microarray data. It
+can be used for convenient GO enrichment and to produce publication quality
+figures in Python.")
+    (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

gnu/packages/bittorrent.scm

@@ -239,19 +239,21 @@ XML-RPC over SCGI.")
     (license l:gpl2+)))
 
 (define-public tremc
+  (let ((commit "6c15e3f5637c8f3641473328bd8c5b0cc122d930")
+        (revision "0"))
   (package
     (name "tremc")
-    (version "0.9.3")
+    (version (git-version "0.9.3" revision commit))
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/tremc/tremc")
-             (commit version)))
+             (commit commit)))
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "11izsgwj435skkgvw96an6ddcm1hk3ff1gji4ksnidlyv6g6npyv"))))
+         "1anlqzbwgmhrxlh20pfzf4iyw5l2w227h95rq6xf29ai7vddr82k"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; no test suite
@@ -268,7 +270,7 @@ XML-RPC over SCGI.")
     (description "Tremc is a console client, with a curses interface, for the
 Transmission BitTorrent daemon.")
     (home-page "https://github.com/tremc/tremc")
-    (license l:gpl3+)))
+    (license l:gpl3+))))
 
 (define-public aria2
   (package
@@ -500,6 +502,23 @@ qBittorrent is fast, stable and provides unicode support as well as many
 features.")
     (license l:gpl2+)))
 
+(define-public qbittorrent-nox
+  (let ((base qbittorrent))
+    (package
+      (inherit base)
+      (name "qbittorrent-nox")
+      (arguments
+       (substitute-keyword-arguments (package-arguments base)
+         ((#:configure-flags configure-flags)
+          #~(append #$configure-flags
+                    (list "--disable-gui")))
+         ((#:phases phases)
+          #~(modify-phases #$phases
+              (delete 'wrap-qt)))))
+      (inputs
+       (modify-inputs (package-inputs base)
+         (delete "qtsvg-5"))))))
+
 (define-public deluge
   (package
     (name "deluge")

gnu/packages/bootstrap.scm

@@ -325,14 +325,11 @@ or false to signal an error."
 
      ;; XXX: This one is used bare-bones, without a libc, so add a case
      ;; here just so we can keep going.
-     ((string=? system "arm-elf") "no-ld.so")
      ((string=? system "arm-eabi") "no-ld.so")
-     ((string=? system "xtensa-elf") "no-ld.so")
      ((string=? system "avr") "no-ld.so")
-     ((string=? system "propeller-elf") "no-ld.so")
      ((string=? system "i686-mingw") "no-ld.so")
      ((string=? system "x86_64-mingw") "no-ld.so")
-     ((string=? system "vc4-elf") "no-ld.so")
+     ((string-suffix? "-elf" system) "no-ld.so")
 
      (else (error "dynamic linker name not known for this system"
                   system)))))

gnu/packages/build-tools.scm

@@ -148,7 +148,7 @@ makes a few sacrifices to acquire fast full and incremental build times.")
      `(("c-ares" ,c-ares)
        ("fmt" ,fmt-8)
        ("grpc" ,grpc)
-       ("json-modern-cxx" ,json-modern-cxx)
+       ("nlohmann-json" ,nlohmann-json)
        ("protobuf" ,protobuf)
        ("python" ,python-wrapper)
        ("re2" ,re2)

gnu/packages/c.scm

@@ -17,6 +17,7 @@
 ;;; Copyright © 2022 Artyom V. Poptsov <poptsov.artyom@gmail.com>
 ;;; Copyright © 2022 Ekaitz Zarraga <ekaitz@elenq.tech>
 ;;; Copyright © 2022 ( <paren@disroot.org>
+;;; Copyright © 2023 zamfofex <zamfofex@twdb.moe>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -47,6 +48,7 @@
   #:use-module (guix store)
   #:use-module (gnu packages)
   #:use-module (gnu packages bash)
+  #:use-module (gnu packages bdw-gc)
   #:use-module (gnu packages bootstrap)
   #:use-module (gnu packages bison)
   #:use-module (gnu packages check)
@@ -57,7 +59,9 @@
   #:use-module (gnu packages guile)
   #:use-module (gnu packages llvm)
   #:use-module (gnu packages lua)
+  #:use-module (gnu packages m4)
   #:use-module (gnu packages multiprecision)
+  #:use-module (gnu packages ncurses)
   #:use-module (gnu packages pcre)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-xyz)
@@ -107,6 +111,30 @@ to this dialect as GNU C.  If you already know C, you can use this as a
 reference manual.")
       (license license:fdl1.3+))))
 
+(define-public c-rrb
+  (let ((commit "d908617ff84515af90c454ff4d0f98675ae6b456")
+        (revision "0"))
+    (package
+     (name "c-rrb")
+     (version (git-version "0.1.0" revision commit))
+     (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/hypirion/c-rrb")
+                    (commit commit)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32 "0zmha3xi80vgdcwzb4vwdllf97dvggjpjfgahrpsb5f5qi3yshxa"))))
+     (build-system gnu-build-system)
+     (inputs (list libgc))
+     (native-inputs (list autoconf automake libtool))
+     (home-page "https://github.com/hypirion/c-rrb")
+     (synopsis "Relaxed Radix Balanced Trees")
+     (description "Relaxed Radix Balanced Trees are an immutable vector-like
+data structure with good performance characteristics for concatenation and
+slicing.")
+     (license license:boost1.0))))
+
 (define-public cproc
   (let ((commit "70fe9ef1810cc6c05bde9eb0970363c35fa7e802")
         (revision "1"))
@@ -1424,3 +1452,65 @@ string.h, but with a utf8* prefix instead of the str* prefix.")
       (description
        "This package provides a header-only unit testing library for C/C++.")
       (license license:unlicense))))
+
+(define-public ispc
+  (package
+    (name "ispc")
+    (version "1.19.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/ispc/ispc")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0yhcgyzjlrgs920lm0l6kygj2skanfb6qkxbdgm69r8c2xkzkaa3"))))
+    (inputs (list ncurses))
+    (native-inputs (list bison clang flex m4 python))
+    (build-system cmake-build-system)
+    (supported-systems
+     '("x86_64-linux" "i686-linux" "aarch64-linux" "armhf-linux"))
+    (arguments
+     `(#:tests? #f
+       #:configure-flags
+       `(,,(string-append "-DCMAKE_C_COMPILER=" (cc-for-target))
+         ,,(string-append "-DCMAKE_CXX_COMPILER=" (cxx-for-target))
+         ,(string-append "-DCLANG_EXECUTABLE="
+                         (assoc-ref %build-inputs "clang")
+                         "/bin/clang")
+         ,(string-append "-DCLANGPP_EXECUTABLE="
+                         (assoc-ref %build-inputs "clang")
+                         "/bin/clang++"))
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'patch-curses-requirement
+           (lambda _
+             (substitute* "CMakeLists.txt"
+               (("\\bCURSES_CURSES_LIBRARY\\b")
+                "CURSES_LIBRARY"))))
+         ;; Note: This works around the following issue:
+         ;; <https://github.com/ispc/ispc/issues/1865>
+         ;; Because GCC in Guix does not have multilib support.
+         (add-before 'configure 'patch-target-archs
+           (lambda _
+             (substitute* "cmake/GenerateBuiltins.cmake"
+               (("\\bforeach \\(bit 32 64\\)")
+                ,(if (target-64bit?)
+                     "foreach (bit 64)"
+                     "foreach (bit 32)"))
+               (("\\bforeach \\(arch .*?\\)")
+                ,(if (target-x86?)
+                     "foreach (arch \"x86\")"
+                     "foreach (arch \"arm\")"))
+               (("\\bforeach \\(os_name \"windows\" .*?\\)")
+                "foreach (os_name \"linux\")")))))))
+    (synopsis "Implicit SPMD Program Compiler")
+    (description
+     "ISPC is a compiler for a variant of the C programming language, with
+extensions for single program, multiple data programming.  Under the SPMD
+model, the programmer writes a program that generally appears to be a regular
+serial program, though the execution model is actually that a number of
+program instances execute in parallel on the hardware.")
+    (home-page "https://github.com/ispc/ispc")
+    (license license:bsd-3)))

gnu/packages/code.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2015, 2018, 2020, 2021 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2015, 2018, 2020, 2021, 2023 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013, 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2015, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017, 2019-2023 Efraim Flashner <efraim@flashner.co.il>
@@ -182,14 +182,14 @@ highlighting your own code that seemed comprehensible when you wrote it.")
 (define-public global                             ; a global variable
   (package
     (name "global")
-    (version "6.6.9")
+    (version "6.6.10")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnu/global/global-"
                                  version ".tar.gz"))
              (sha256
               (base32
-               "1mgss7ch4izz7ibb23xah6h4iva77g9dq4pkc9g69jk0ipxa1jxa"))))
+               "1s6c9nzpp4jfq14l3mk9fnyipizljkka8hdr1wwh2g798nlydl9d"))))
     (build-system gnu-build-system)
     (arguments
      (list #:configure-flags
@@ -562,16 +562,19 @@ stack traces.")
                                          (assoc-ref %outputs "out")))
        #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'patch-pwd
+         (add-after 'unpack 'patch-references-to-commands
-           ;; Lift the requirement of having a shell in PATH.
+           (lambda* (#:key inputs #:allow-other-keys)
-           (lambda _
+             ;; Lift the requirement of having a shell and 'find' in PATH.
              (substitute* "bin/geninfo"
                (("qw/abs_path/")
                 "qw/abs_path getcwd/"))
              (substitute* '("bin/lcov" "bin/geninfo")
                (("`pwd`")
-                "getcwd()"))
+                "getcwd()")
-             #t))
+               (("`find ")
+                (string-append "`"
+                               (search-input-file inputs "/bin/find")
+                               " ")))))
          (delete 'configure)            ;no configure script
          (add-after 'install 'wrap
            (lambda* (#:key outputs #:allow-other-keys)

gnu/packages/cpp.scm

@@ -34,6 +34,7 @@
 ;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2023 Sughosha <Sughosha@proton.me>
 ;;; Copyright © 2023 Artyom V. Poptsov <poptsov.artyom@gmail.com>
+;;; Copyright © 2023 Liliana Marie Prikler <liliana.prikler@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -67,6 +68,8 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages assembly)
   #:use-module (gnu packages autotools)
+  #:use-module (gnu packages bdw-gc)
+  #:use-module (gnu packages benchmark)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages build-tools)
   #:use-module (gnu packages c)
@@ -100,6 +103,9 @@
   #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg)
+  ;; Using autoload to avoid a cycle.
+  ;; Note that (gnu packages serialization) has #:use-module (gnu packages cpp)
+  #:autoload   (gnu packages serialization) (cereal)
   #:use-module (ice-9 match))
 
 (define-public argagg
@@ -595,10 +601,10 @@ converting data between JSON representation and C++ structs.  DTO stands for
 data transfer object.")
     (license license:bsd-3)))
 
-(define-public json-modern-cxx
+(define-public nlohmann-json
   (package
-    (name "json-modern-cxx")
+    (name "nlohmann-json")
-    (version "3.10.5")
+    (version "3.11.2")
     (home-page "https://github.com/nlohmann/json")
     (source
      (origin
@@ -606,23 +612,24 @@ data transfer object.")
        (uri (git-reference (url home-page)
                            (commit (string-append "v" version))))
        (sha256
-        (base32 "1f9mi45ilwjc2w92grjc53sw038840bjpn8yjf6wc6bxs2nijfqd"))
+        (base32 "0g6rfsbkvrxmacchz4kbr741yybj7mls3r4hgyfdd3pdbqhn2is9"))
        (file-name (git-file-name name version))
        (modules '((guix build utils)))
        (snippet
-        '(begin
+        #~(begin
             ;; Delete bundled software.  Preserve doctest_compatibility.h, which
             ;; is a wrapper library added by this package.
-           (install-file "./test/thirdparty/doctest/doctest_compatibility.h" "/tmp")
+            (install-file "./tests/thirdparty/doctest/doctest_compatibility.h"
-           (for-each delete-file-recursively
+                          "/tmp")
-                     '("./third_party" "./test/thirdparty"))
+            (delete-file-recursively "./tests/thirdparty")
-           (install-file "/tmp/doctest_compatibility.h" "./test/thirdparty/doctest")
+            (install-file "/tmp/doctest_compatibility.h"
+                          "./tests/thirdparty/doctest")
 
             ;; Adjust for the unbundled fifo_map and doctest.
-           (substitute* "./test/thirdparty/doctest/doctest_compatibility.h"
+            (substitute* (find-files "./tests/" "\\.h(pp)?")
-             (("#include \"doctest\\.h\"")
+              (("#include \"doctest\\.h\"") "#include <doctest/doctest.h>")
-              "#include <doctest/doctest.h>"))
+              (("#include <doctest\\.h>") "#include <doctest/doctest.h>"))
-           (with-directory-excursion "test/src"
+            (with-directory-excursion "tests/src"
               (let ((files (find-files "." "\\.cpp$")))
                 (substitute* files
                   (("#include ?\"(fifo_map.hpp)\"" all fifo-map-hpp)
@@ -630,13 +637,15 @@ data transfer object.")
                     "#include <fifo_map/" fifo-map-hpp ">")))))))))
     (build-system cmake-build-system)
     (arguments
-     '(#:configure-flags
+     (list
-       (list "-DJSON_MultipleHeaders=ON" ; For json_fwd.hpp.
+      #:configure-flags
+      #~(list "-DJSON_MultipleHeaders=ON" ; For json_fwd.hpp.
               (string-append "-DJSON_TestDataDirectory="
                              (dirname
                               (search-input-directory %build-inputs
                                                       "json_nlohmann_tests"))))
-       #:phases (modify-phases %standard-phases
+      #:phases
+      #~(modify-phases %standard-phases
           (replace 'check
             (lambda* (#:key tests? parallel-tests? #:allow-other-keys)
               (if tests?
@@ -648,7 +657,7 @@ data transfer object.")
                   (format #t "test suite not run~%")))))))
     (native-inputs
      (list amalgamate
-           (let ((version "3.0.0"))
+           (let ((version "3.1.0"))
              (origin
                (method git-fetch)
                (uri (git-reference
@@ -657,14 +666,17 @@ data transfer object.")
                (file-name (git-file-name "json_test_data" version))
                (sha256
                 (base32
-                 "0nzsjzlvk14dazwh7k2jb1dinb0pv9jbx5jsyn264wvva0y7daiv"))))))
+                 "0nbirc428qx0lpi940p7y24fzdjbwl6xig3h5rdbihyymmdzhvbc"))))))
     (inputs
      (list doctest fifo-map))
     (synopsis "JSON parser and printer library for C++")
-    (description "JSON for Modern C++ is a C++ JSON library that provides
+    (description "@code{nlohmann::json} is a C++ JSON library that provides
 intuitive syntax and trivial integration.")
     (license license:expat)))
 
+(define-public json-modern-cxx
+  (deprecated-package "json-modern-cxx" nlohmann-json))
+
 (define-public xtl
   (package
     (name "xtl")
@@ -680,7 +692,7 @@ intuitive syntax and trivial integration.")
                 "134pgvmf9cx5dxs0m0m3qhp3m3r1gl86ic3xax21zc4sdj8sdq46"))
               (file-name (git-file-name name version))))
     (native-inputs
-     (list doctest googletest json-modern-cxx))
+     (list doctest googletest nlohmann-json))
     (arguments
      '(#:configure-flags
        '("-DBUILD_TESTS=ON")
@@ -1188,7 +1200,7 @@ algorithm called SAscan.")
 (define-public cxxopts
   (package
     (name "cxxopts")
-    (version "3.0.0")
+    (version "3.1.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1197,7 +1209,7 @@ algorithm called SAscan.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "08x7j168l1xwj0r3rv89cgghmfhsx98lpq35r3vkh504m1pd55a6"))))
+                "0d37qpsaq8ik7pl4vk8346vqcqyfzfbnpq8mhsa2gb2zf1lwr4wl"))))
     (build-system cmake-build-system)
     (synopsis "Lightweight C++ command line option parser")
     (description
@@ -1390,6 +1402,94 @@ provides a number of utilities to make coding with expected cleaner.")
     (home-page "https://tl.tartanllama.xyz/")
     (license license:cc0)))
 
+(define-public immer
+  (package
+   (name "immer")
+   (version "0.8.0")
+   (source (origin
+            (method git-fetch)
+            (uri (git-reference
+                  (url "https://github.com/arximboldi/immer")
+                  (commit (string-append "v" version))))
+            (file-name (git-file-name name version))
+            (sha256
+             (base32 "11km3l5h3rgsbj8yfyzk3fnx9na55l6zs2sxpx922yvlvs2blh27"))
+            (modules '((guix build utils)))
+            (snippet #~(begin
+                         (delete-file "tools/include/doctest.h")
+                         (delete-file "tools/include/catch.hpp")
+                         (substitute* (find-files "test" "\\.[cih]pp")
+                           (("<catch.hpp>") "<catch2/catch.hpp>")
+                           (("<doctest.h>") "<doctest/doctest.h>"))
+                         (substitute* (find-files "test/oss-fuzz" "\\.cpp")
+                           ;; someone used the wrong header :)
+                           (("<fmt/printf.h>") "<fmt/ostream.h>"))))))
+   (build-system cmake-build-system)
+   (arguments (list #:test-target "check"))
+   (inputs (list boost libgc c-rrb))
+   (native-inputs (list catch2 doctest fmt pkg-config))
+   (home-page "https://sinusoid.es/immer")
+   (synopsis "Immutable data structures")
+   (description "Immer is a library of persistent and immutable data structures
+written in C++.")
+   (license license:boost1.0)))
+
+(define-public zug
+  (let ((commit "d7e814b45fceceee3cb1442997d8b46cee4764ec")
+        (revision "0"))
+    (package
+     (name "zug")
+     (version (git-version "0.0.0" revision commit))
+     (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/arximboldi/zug")
+                    (commit commit)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32 "1ww4prh763n81kzzijak8z495varlvqml4ip7i09klqnw6ya72fc"))
+              (modules '((guix build utils)))
+              (snippet #~(delete-file-recursively "tools"))))
+     (build-system cmake-build-system)
+     (arguments (list #:test-target "check"))
+     (native-inputs (list boost catch2))
+     (home-page "https://sinusoid.es/zug")
+     (synopsis "Higher-order sequence transformers")
+     (description "Zug is a C++ library providing transducers, that is,
+composable sequential transformations.")
+     (license license:boost1.0))))
+
+(define-public lager
+  (let ((commit "2016df38be90ee176bcb73ea414be2318bc1ef31")
+        (revision "0"))
+    (package
+     (name "lager")
+     (version (git-version "0.0.0" revision commit))
+     (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/arximboldi/lager")
+                    (commit commit)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32 "1b7zxwqrbm7db7wxqbsrk7jjd3znvvi1cwj7jg6zkmf0199071a5"))))
+     (build-system cmake-build-system)
+     (arguments (list #:test-target "check"
+                      #:configure-flags #~(list "-Dlager_BUILD_EXAMPLES=no")
+                      #:phases
+                      #~(modify-phases %standard-phases
+                          (add-after 'unpack 'delete-failing-tests
+                            (lambda _
+                              (delete-file-recursively "test/event_loop"))))))
+     (inputs (list boost immer zug))
+     (native-inputs (list cereal))
+     (home-page "https://sinusoid.es/lager")
+     (synopsis "Library for value-oriented design")
+     (description "Lager is a library for value-oriented design implementing
+the unidirectional data-flow architecture.  Apart from a store and various
+event loops it also provides lenses and cursors.")
+     (license license:expat))))
+
 (define-public atomic-queue
   (package
     (name "atomic-queue")
@@ -1859,7 +1959,7 @@ of reading and writing XML.")
     (native-inputs
      (list googletest pkg-config))
     (inputs
-     (list json-modern-cxx))
+     (list nlohmann-json))
     (home-page "https://jsonnet.org/")
     (synopsis "Data templating language")
     (description "Jsonnet is a templating language extending JSON
@@ -2433,7 +2533,7 @@ queues, resource pools, strings, etc.
 (define-public ftxui
   (package
     (name "ftxui")
-    (version "3.0.0")
+    (version "4.0.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -2441,27 +2541,14 @@ queues, resource pools, strings, etc.
                     (commit (string-append "v" version))))
               (sha256
                (base32
-                "10a4yw2h29kixxyhll6cvrwyscsvz9asxry857a9l8nqvbhs946s"))
+                "01h59ln8amsj6ymxmsxhmslld2yp003n82fg3mphgkrh6lf22h6y"))
               (file-name (git-file-name name version))))
     (build-system cmake-build-system)
-    (native-inputs (list googletest))
+    (native-inputs (list googletest benchmark))
     (arguments
      (list #:configure-flags
            #~(list "-DFTXUI_BUILD_TESTS:BOOL=ON"
-                   "-DFTXUI_BUILD_TESTS_FUZZER:BOOL=OFF")
+                   "-DFTXUI_BUILD_TESTS_FUZZER:BOOL=OFF")))
-           #:phases
-           #~(modify-phases %standard-phases
-               (add-after 'unpack 'patch-cmake-tests
-                 (lambda _
-                   (substitute* "cmake/ftxui_test.cmake"
-                     (("NOT googletest_POPULATED")
-                      "FALSE"))
-                   ;; Disable benchmarks for a while as they require bundled Google
-                   ;; benchmark and when the 'googlebenchmark' is unbundled, there's
-                   ;; a CMake configuration error.
-                   (substitute* "cmake/ftxui_benchmark.cmake"
-                     (("NOT WIN32")
-                      "FALSE")))) )))
     (home-page "https://github.com/ArthurSonzogni/FTXUI")
     (synopsis "C++ Functional Terminal User Interface")
     (description

gnu/packages/cran.scm

@@ -17853,6 +17853,36 @@ visualization; flexible image manipulation; metadata and sparse image
 handling.")
     (license license:gpl2)))
 
+(define-public r-gridpattern
+  (package
+    (name "r-gridpattern")
+    (version "1.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "gridpattern" version))
+       (sha256
+        (base32 "13yypjsbpr61yn15y4cyz6s8jvcgg3mmr8rncskinpk8lsa8h2h4"))))
+    (properties `((upstream-name . "gridpattern")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-glue
+           r-memoise
+           r-png
+           r-rlang
+           r-sf))
+    (native-inputs (list r-knitr r-rmarkdown))
+    (home-page "https://trevorldavis.com/R/gridpattern/")
+    (synopsis "Grid pattern grobs")
+    (description
+     "This package provides grid grobs that fill in a user-defined area with
+various patterns.  It includes enhanced versions of the geometric and
+image-based patterns originally contained in the ggpattern package as well as
+original @code{pch}, @code{polygon_tiling}, @code{regular_polygon},
+@code{rose}, @code{text}, @code{wave}, and @code{weave} patterns plus support
+for custom user-defined patterns.")
+    (license license:expat)))
+
 (define-public r-gridsvg
   (package
     (name "r-gridsvg")
@@ -20162,6 +20192,36 @@ The flagship function is @code{ggMarginal()}, which can be used to add
 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
     (license license:expat)))
 
+(define-public r-ggpattern
+  (package
+    (name "r-ggpattern")
+    (version "1.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ggpattern" version))
+       (sha256
+        (base32 "1b9bfxlg64gr39bz58fp6jmg4nziwk8rk94rzpjsqhfhpwi2lrgr"))))
+    (properties `((upstream-name . "ggpattern")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-ggplot2
+           r-glue
+           r-gridpattern
+           r-rlang
+           r-scales))
+    (native-inputs (list r-knitr r-ragg r-rmarkdown))
+    (home-page "https://github.com/coolbutuseless/ggpattern")
+    (synopsis "Ggplot2 pattern geoms")
+    (description
+     "This package provides ggplot2 geoms filled with various patterns.
+It includes a patterned version of every ggplot2 geom that has a region that
+can be filled with a pattern.  It provides a suite of ggplot2 aesthetics and
+scales for controlling pattern appearances.  It supports over a dozen builtin
+patterns (every pattern implemented by gridpattern) as well as allowing custom
+user-defined patterns.")
+    (license license:expat)))
+
 (define-public r-minpack-lm
   (package
     (name "r-minpack-lm")

gnu/packages/crates-io.scm

@@ -6240,6 +6240,32 @@ portable \"best effort\" constant-time operation and embedded-friendly
     (description "This library provides for encoding and decoding any base.")
     (license license:expat)))
 
+(define-public rust-basic-toml-0.1
+  (package
+    (name "rust-basic-toml")
+    (version "0.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "basic-toml" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "1d2h378373x0i8j4mi4sfaq8np9hf5xqr2rh9pa7r5irfxk9p09f"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-serde" ,rust-serde-1))
+       #:cargo-development-inputs
+       (("rust-semver" ,rust-semver-1)
+        ("rust-serde" ,rust-serde-1)
+        ("rust-serde-derive" ,rust-serde-derive-1)
+        ("rust-serde-json" ,rust-serde-json-1))))
+    (home-page "https://github.com/dtolnay/basic-toml")
+    (synopsis "Minimal TOML library with few dependencies")
+    (description "This package provides minimal TOML library with few
+dependencies.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-bat-0.18
   (package
     (name "bat")
@@ -68124,24 +68150,25 @@ the Trust-DNS client to use rustls for TLS.")
 (define-public rust-trybuild-1
   (package
     (name "rust-trybuild")
-    (version "1.0.75")
+    (version "1.0.77")
     (source
      (origin
        (method url-fetch)
        (uri (crate-uri "trybuild" version))
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
-        (base32 "1wylxysdpbjz3cddaxvjnfk8vadi05chdivwg9l878c7b8hjq8gi"))))
+        (base32 "04rlcx55q7qbc17hv4znypwnm5n5d5ynbh5vsca8wk0nyakaakd4"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
-       (("rust-dissimilar" ,rust-dissimilar-1)
+       (("rust-basic-toml" ,rust-basic-toml-0.1)
+        ("rust-dissimilar" ,rust-dissimilar-1)
         ("rust-glob" ,rust-glob-0.3)
         ("rust-once-cell" ,rust-once-cell-1)
         ("rust-serde" ,rust-serde-1)
+        ("rust-serde-derive" ,rust-serde-derive-1)
         ("rust-serde-json" ,rust-serde-json-1)
-        ("rust-termcolor" ,rust-termcolor-1)
+        ("rust-termcolor" ,rust-termcolor-1))))
-        ("rust-toml" ,rust-toml-0.5))))
     (home-page "https://github.com/dtolnay/trybuild")
     (synopsis "Test harness for ui tests of compiler diagnostics")
     (description

gnu/packages/crypto.scm

@@ -25,6 +25,7 @@
 ;;; Copyright © 2022 Allan Adair <allan@adair.no>
 ;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2022 Denis 'GNUtoo' Carikli <GNUtoo@cyberdimension.org>
+;;; Copyright © 2023 Ivan Vilata-i-Balaguer <ivan@selidor.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -331,7 +332,7 @@ OpenBSD tool of the same name.")
        ("googletest-source" ,(package-source googletest))
        ("perl" ,perl)))
     (inputs
-     (list attr fuse openssl tinyxml2))
+     (list attr fuse openssl-1.1 tinyxml2))
     (arguments
      `(#:configure-flags (list "-DUSE_INTERNAL_TINYXML=OFF")
        #:phases

gnu/packages/cybersecurity.scm

@@ -89,7 +89,7 @@
     (native-inputs
      (list pkg-config))
     (inputs
-     (list argagg asmjit json-modern-cxx))
+     (list argagg asmjit nlohmann-json))
     (home-page "https://comsec.ethz.ch/research/dram/blacksmith")
     (synopsis "Rowhammer fuzzer with non-uniform and frequency-based patterns")
     (description

gnu/packages/databases.scm

@@ -10,7 +10,7 @@
 ;;; Copyright © 2015 Eric Dvorsak <eric@dvorsak.fr>
 ;;; Copyright © 2016, 2022 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2016 Christine Lemmer-Webber <cwebber@dustycloud.org>
-;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015-2023 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2017 Nikita <nikita@n0.is>
 ;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2016 David Craven <david@craven.ch>
@@ -968,6 +968,14 @@ Language.")
        #:parallel-tests? ,(target-x86-64?)
        #:phases
        (modify-phases %standard-phases
+         ;; TODO: Move this patch to the source field.
+         ,@(if (target-riscv64?)
+             `((add-after 'unpack 'patch-source
+                 (lambda* (#:key inputs native-inputs #:allow-other-keys)
+                   (invoke "patch" "-p1" "--force" "--input"
+                           (assoc-ref (or native-inputs inputs)
+                                      "patch-file")))))
+             '())
          (add-after 'unpack 'adjust-output-references
            (lambda _
              ;; The build system invariably prepends $CMAKE_INSTALL_PREFIX
@@ -1103,7 +1111,12 @@ Language.")
                 (("-lssl -lcrypto" all)
                  (string-append "-L" openssl " " all)))))))))
     (native-inputs
-     (list bison perl))
+     `(,@(if (target-riscv64?)
+           `(("patch" ,patch)
+             ("patch-file" ,(search-patch "mariadb-rocksdb-atomic-linking.patch")))
+           `())
+        ("bison" ,bison)
+        ("perl" ,perl)))
     (inputs
      (list fmt
            jemalloc
@@ -2646,7 +2659,11 @@ database and supports many programming languages.  It is a NoSQL database.")
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
-       (list "--enable-pthread" "--enable-off64" "--enable-fastest"
+       (list "--enable-pthread" "--enable-off64"
+             ,@(if (target-x86?)
+                 ;; Enables x86 specific cflags.
+                 '("--enable-fastest")
+                 '())
         (string-append "LDFLAGS=-Wl,-rpath="
                        (assoc-ref %outputs "out") "/lib"))))
     (inputs
@@ -3590,7 +3607,7 @@ text search extension.")
 (define-public python-sqlite-utils
   (package
     (name "python-sqlite-utils")
-    (version "3.30")
+    (version "3.32.1")
     (source (origin
               (method git-fetch)        ;for tests
               (uri (git-reference
@@ -3599,7 +3616,7 @@ text search extension.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1a58syvh5jp40vi5libsxkqy99z75kj4ckxqmylbhd342ppfy1wp"))))
+                "1qf9zwn9gdkx8825klicwkw8zj5wpidd8csdhjxvybq56nkgnrpm"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:phases #~(modify-phases %standard-phases
@@ -5013,7 +5030,7 @@ a Gtk.Grid Widget.")
     (build-system qt-build-system)
     (arguments
      (list #:configure-flags
-           ;; TODO: Unbundle json (json-modern-cxx).
+           ;; TODO: Unbundle json (nlohmann-json).
            #~(list (string-append "-DQSCINTILLA_INCLUDE_DIR="
                                   #$(this-package-input "qscintilla")
                                   "/include/Qsci")

gnu/packages/datastructures.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015, 2016, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2018, 2019, 2023 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017, 2019–2021 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Meiyo Peng <meiyo.peng@gmail.com>
 ;;; Copyright © 2019, 2020, 2022 Efraim Flashner <efraim@flashner.co.il>
@@ -444,11 +444,11 @@ better with a poor hash function.")
     (license license:expat)))
 
 (define-public zix
-  (let ((commit "56ec14c4369c591f5efbb500b0829b760bee7800")
+  (let ((commit "a13ae5ad9dc70075740f11139f1db96cc79faa59")
         (revision "0"))
     (package
       (name "zix")
-      (version (git-version "0.0.0" revision commit))
+      (version (git-version "0.3.3" revision commit))
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
@@ -457,7 +457,7 @@ better with a poor hash function.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "095b2vjmwh9swbwkkkjpcdhsi0c93lxrzd76k7hzdyyf7zb5rgdx"))))
+                  "1njyb8lz1d5qzf0k14pb3rq13xkxnddwbz090dj69138ymz1xgyl"))))
       (build-system meson-build-system)
       (arguments
        (list #:configure-flags #~(list "-Ddocs=disabled"))) ;needs "sphinxygen"

gnu/packages/debug.scm

@@ -12,6 +12,7 @@
 ;;; Copyright © 2022 Michael Rohleder <mike@rohleder.de>
 ;;; Copyright © 2022 Matthew James Kraai <kraai@ftbfs.org>
 ;;; Copyright © 2023 Andy Tai <atai@atai.org>
+;;; Copyright © 2023 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -688,8 +689,8 @@ fun.")
 
 (define-public libbacktrace
   ;; There are no releases nor tags.
-  (let ((revision "1")
+  (let ((revision "2")
-        (commit "5009c113981431ae1843ebd29d6ad24eb32fc1b2"))
+        (commit "cdb64b688dda93bbbacbc2b1ccf50ce9329d4748"))
     (package
       (name "libbacktrace")
       (version (git-version "1.0" revision commit))
@@ -701,10 +702,11 @@ fun.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "0663zjpfpnsyv9h3pbp7cgmg9gz79n68bqpdl97y6i0jsx93v1zg"))))
+                  "0iwd41pgr2nxlmghqdfwfwxac27jbqxwxp07jihhq85a8s3igjgr"))))
       (build-system gnu-build-system)
       (arguments
-       `(#:make-flags '("CFLAGS=-fPIC")))
+       `(#:parallel-tests? #f ;spurious failures when testing in parallel
+         #:make-flags '("CFLAGS=-fPIC")))
       (home-page "https://github.com/ianlancetaylor/libbacktrace")
       (synopsis "C library for producing symbolic backtraces")
       (description "The @code{libbacktrace} library can be linked into a C/C++
@@ -866,13 +868,13 @@ engineering.")
 (define-public ddd
   (package
     (name "ddd")
-    (version "3.3.12")
+    (version "3.4.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnu/ddd/ddd-" version ".tar.gz"))
               (sha256
                (base32
-                "0p5nx387857w3v2jbgvps2p6mlm0chajcdw5sfrddcglsxkwvmis"))))
+                "03sqsfiri5p130cmmzh2wikg0gisql496rvdhr1qaidh1f5bqk2x"))))
     (build-system gnu-build-system)
     (arguments
      (list #:tests? #f                  ;tests require manual intervention

gnu/packages/diffoscope.scm

@@ -74,7 +74,7 @@
 (define-public diffoscope
   (package
     (name "diffoscope")
-    (version "239")
+    (version "242")
     (source
      (origin
        (method git-fetch)
@@ -83,7 +83,7 @@
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1awxazbrqqzqr5x50kam50ibmnjvidynkzp2158rdx5gy5lmnwcy"))))
+        (base32 "1aa6cszav4bgiljhkly0l3bzn4kggkncrk1zbc6hdm361r8yrw34"))))
     (build-system python-build-system)
     (arguments
      `(#:phases (modify-phases %standard-phases

gnu/packages/dlang.scm

@@ -149,17 +149,18 @@ to a minimal test case.")
 (define ldc-bootstrap
   (package
     (name "ldc")
-    (version "1.30.0")
+    (version "1.32.2")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://github.com/ldc-developers/ldc/releases"
                            "/download/v" version "/ldc-" version "-src.tar.gz"))
        (sha256
-        (base32 "1kfs4fpr1525sv2ny10hlfppy8c075vjm8m649wr2b9411pkgfzx"))))
+        (base32 "15fdl7fy1ssjxpyb9g54ac4xzcirycly521whil142ijfkpam95z"))))
     (build-system cmake-build-system)
     (arguments
-     `(#:tests? #f                  ;skip in the bootstrap
+     `(#:disallowed-references (,tzdata-for-tests)
+       #:tests? #f                  ;skip in the bootstrap
        #:build-type "Release"
        #:configure-flags
         (list "-GNinja")
@@ -187,7 +188,6 @@ to a minimal test case.")
     (inputs
      `(("libconfig" ,libconfig)
        ("libedit" ,libedit)
-       ("tzdata" ,tzdata)
        ("zlib" ,zlib)))
     (native-inputs
      `(("lld-wrapper" ,(make-lld-wrapper lld-14 #:lld-as-ld? #t))
@@ -195,6 +195,7 @@ to a minimal test case.")
        ("ldc" ,gdmd)
        ("ninja" ,ninja)
        ("python-wrapper" ,python-wrapper)
+       ("tzdata" ,tzdata-for-tests)
        ("unzip" ,unzip)))
     (home-page "http://wiki.dlang.org/LDC")
     (synopsis "LLVM-based compiler for the D programming language")
@@ -263,11 +264,11 @@ bootstrapping more recent compilers written in D.")
                                    "/lib/linux\",\n"))))))
            (add-after 'unpack 'patch-paths-in-tests
              (lambda _
-               (substitute* "tests/d2/dmd-testsuite/Makefile"
+               (substitute* "tests/dmd/Makefile"
                  (("/bin/bash") (which "bash")))
                (substitute* "tests/linking/linker_switches.d"
                  (("echo") (which "echo")))
-               (substitute* "tests/d2/dmd-testsuite/dshell/test6952.d"
+               (substitute* "tests/dmd/dshell/test6952.d"
                  (("/usr/bin/env bash")
                   (which "bash")))))
            (add-after 'unpack 'disable-problematic-tests
@@ -280,8 +281,9 @@ bootstrapping more recent compilers written in D.")
                  ((" unittest") " version(skipunittest) unittest"))
                ;; The following tests plugins we don't have.
                (delete-file "tests/plugins/addFuncEntryCall/testPlugin.d")
+               (delete-file "tests/plugins/addFuncEntryCall/testPluginLegacy.d")
                ;; The following tests requires AVX instruction set in the CPU.
-               (substitute* "tests/d2/dmd-testsuite/runnable/cdvecfill.sh"
+               (substitute* "tests/dmd/runnable/cdvecfill.sh"
                  (("^// DISABLED: ") "^// DISABLED: linux64 "))
                ;; This unit test requires networking, fails with
                ;; "core.exception.RangeError@std/socket.d(778): Range
@@ -292,13 +294,13 @@ bootstrapping more recent compilers written in D.")
                ;; The GDB tests suite fails; there are a few bug reports about
                ;; it upstream.
                (for-each delete-file (find-files "tests" "gdb.*\\.(c|d|sh)$"))
-               (delete-file "tests/d2/dmd-testsuite/runnable/debug_info.d")
+               (delete-file "tests/dmd/runnable/debug_info.d")
-               (delete-file "tests/d2/dmd-testsuite/runnable/b18504.d")
+               (delete-file "tests/dmd/runnable/b18504.d")
                (substitute* "runtime/druntime/test/exceptions/Makefile"
                  ((".*TESTS\\+=rt_trap_exceptions_drt_gdb.*")
                   ""))
                ;; Drop gdb_dflags from the test suite.
-               (substitute* "tests/d2/CMakeLists.txt"
+               (substitute* "tests/dmd/CMakeLists.txt"
                  (("\\$\\{gdb_dflags\\}") ""))
                ;; The following tests fail on some systems, not all of
                ;; which are tested upstream.
@@ -314,10 +316,10 @@ bootstrapping more recent compilers written in D.")
                                  "instrument/xray_simple_execution.d"
                                  "sanitizers/msan_noerror.d"
                                  "sanitizers/msan_uninitialized.d"
-                                 "d2/dmd-testsuite/runnable_cxx/cppa.d")))
+                                 "dmd/runnable_cxx/cppa.d")))
                    (,(target-aarch64?)
                      (for-each delete-file
-                               '("d2/dmd-testsuite/runnable/ldc_cabi1.d"
+                               '("dmd/runnable/ldc_cabi1.d"
                                  "sanitizers/fuzz_basic.d"
                                  "sanitizers/msan_noerror.d"
                                  "sanitizers/msan_uninitialized.d")))

gnu/packages/education.scm

@@ -452,11 +452,11 @@ specialized device.")
   ;; The last release builds from qtwebkit, which has been removed from
   ;; Guix, so use the latest commit of the 1.7-dev branch, which builds with
   ;; qtwebengine-5.
-  (let ((commit "39e914f600d26565706f0e5b6ea2482b8b4038c7") ;1.6.2-rc0311
+  (let ((commit "47a96e1d6bbdc0250977d22f1b79f11fcc1cbeee")
-        (revision "1"))
+        (revision "0"))
     (package
       (name "openboard")
-      (version (git-version "1.6.1" revision commit))
+      (version (git-version "1.7-dev" revision commit))
       (source
        (origin
          (method git-fetch)
@@ -465,7 +465,7 @@ specialized device.")
                (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-          (base32 "1763l5dywirzidzc93726dggf9819p47hh6a7p7dwzd1bfq1wb2q"))))
+          (base32 "04pwmg41vlkwigym3zzkid6srh6f05b44g4mbihd6mhj6vsagx1f"))))
       (build-system qt-build-system)
       (arguments
        (list
@@ -500,7 +500,7 @@ specialized device.")
             (add-after 'unpack 'fix-library-path
               (lambda* (#:key inputs #:allow-other-keys)
                 (substitute* "OpenBoard.pro"
-                  (("/usr/include/quazip")
+                  (("/usr/include/quazip5")
                    (search-input-directory inputs "/include/quazip5"))
                   (("/usr/include/poppler")
                    (search-input-directory inputs "/include/poppler")))))

gnu/packages/emacs-xyz.scm

@@ -129,6 +129,8 @@
 ;;; Copyright © 2023 Evgeny Pisemsky <evgeny@pisemsky.com>
 ;;; Copyright © 2023 Gabriel Wicki <gabriel@erlikon.ch>
 ;;; Copyright © 2022-2023 Simon Josefsson <simon@josefsson.org>
+;;; Copyright © 2023 Fabio Natali <me@fabionatali.com>
+;;; Copyright © 2023 Arnaud Lechevallier <arnaud.lechevallier@free.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -450,7 +452,7 @@ e.g. emacs-geiser-guile for Guile.")
 (define-public emacs-gptel
   (package
     (name "emacs-gptel")
-    (version "0.3.5")
+    (version "0.3.6")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -459,7 +461,7 @@ e.g. emacs-geiser-guile for Guile.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1ymqx9m6ypxdqcc9y3d90ibs3d2n6lb9dg7fn7q30lz6qa5nsc94"))))
+                "1ykqq763sm0km167vyqxcg3jq4g1dzrvn9zwm9q927v83ijh6pf9"))))
     (build-system emacs-build-system)
     (arguments
      (list
@@ -737,10 +739,10 @@ configuration language which makes it trivial to write your own themes.")
     (license license:gpl3+)))
 
 (define-public emacs-inspector
-  (let ((commit "c328475aa433a39dd08702ff7daf5941a3a3efde")) ;version bump
+  (let ((commit "baa486ac2e4faed9a362322c0b2914d6f0c59ede")) ;version bump
     (package
       (name "emacs-inspector")
-      (version "0.29")
+      (version "0.31")
       (source
        (origin
          (uri (git-reference
@@ -748,18 +750,16 @@ configuration language which makes it trivial to write your own themes.")
                (commit commit)))
          (method git-fetch)
          (sha256
-          (base32 "0c9r8gk3ivrd9lpzjnf254ymmfnh4jnr1dcsbr0zmxrrpfsq3mym"))
+          (base32 "0xdgbs8kmsq1m9h9ykjkdvfn0xqf9gmhckr00lq8dxm0gab7x961"))
          (file-name (git-file-name name version))))
       (build-system emacs-build-system)
       (arguments
        (list
         #:tests? #t
         #:test-command #~(list "emacs" "-Q" "--batch"
-                               "-L" "."
+                               "-l" "inspector.el"
                                "-l" "inspector-tests.el"
-                               "-l" "tree-inspector-tests.el"
                                "-f" "ert-run-tests-batch-and-exit")))
-      (propagated-inputs (list emacs-treeview))
       (home-page "https://github.com/mmontone/emacs-inspector")
       (synopsis "Inspection tool for Emacs Lisp objects")
       (description
@@ -767,6 +767,38 @@ configuration language which makes it trivial to write your own themes.")
 Common Lisp or Smalltalk, but for Emacs Lisp.")
       (license license:gpl3+))))
 
+(define-public emacs-tree-inspector
+  (let ((commit "495ef1874fba9d75842087f4acf0ebd75cf09e97"))
+    (package
+      (name "emacs-tree-inspector")
+      (version "0.3")
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/mmontone/emacs-tree-inspector")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "011pk5gr2j9m4qnv70qz63bh58ga72nqahv0zkf2qpbr2a5df09c"))))
+      (build-system emacs-build-system)
+      (arguments
+       (list
+        #:tests? #true
+        #:test-command #~(list "emacs" "-Q" "--batch"
+                               "-L" "."
+                               "-l" "tree-inspector-tests.el"
+                               "-f" "ert-run-tests-batch-and-exit")))
+      (propagated-inputs (list emacs-treeview))
+      (home-page "https://github.com/mmontone/emacs-tree-inspector")
+      (synopsis "Inspection tool for Emacs Lisp objects that uses a tree view")
+      (description
+       "Tree Inspector is an inspection tool for Emacs Lisp objects that uses
+a tree view.  It works together with Emacs Inspector when it is loaded; when
+an object label is clicked on the tree, an inspector is opened on that
+object.")
+      (license license:gpl3+))))
+
 (define-public emacs-terminal-here
   (package
     (name "emacs-terminal-here")
@@ -1160,6 +1192,28 @@ and inserts a SpongeBob SquarePants ASCII art figure in the current
 buffer.")
       (license license:gpl3+))))
 
+(define-public emacs-prism
+  (package
+    (name "emacs-prism")
+    (version "0.3.2")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/alphapapa/prism.el")
+                    (commit version)))
+              (sha256
+               (base32
+                "0n2gf7302hqdnhsax1y3ahksfmmpd8cmiv1zgb7rjg8qhcs0iqp2"))))
+    (build-system emacs-build-system)
+    (propagated-inputs (list emacs-dash))
+    (home-page "https://github.com/alphapapa/prism.el")
+    (synopsis
+     "Disperses bracket-bounded syntax into a spectrum of color by depth")
+    (description
+     "Prism is a Rainbow Blocks-like mode for Emacs.  It preserves non-color
+face properties and allows configuration of faces and colors.")
+    (license license:gpl3+)))
+
 (define-public emacs-project
   (package
     (name "emacs-project")
@@ -1182,7 +1236,7 @@ some utility functions, and commands using that infrastructure.")
 (define-public git-modes
   (package
     (name "emacs-git-modes")
-    (version "1.4.0")
+    (version "1.4.1")
     (source
      (origin
        (method git-fetch)
@@ -1191,8 +1245,10 @@ some utility functions, and commands using that infrastructure.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0aqz65pcqc35h5z4s606f48iqn87h5v9nj3cp6n9yjxa2v7w5hfk"))))
+        (base32 "0b9fywqwccdvyg1cfnlzl61gq1gryjvzp32cw91l4igv7ppmq684"))))
     (build-system emacs-build-system)
+    (propagated-inputs
+     (list emacs-compat))
     (home-page "https://github.com/magit/git-modes")
     (synopsis "Emacs major modes for Git configuration files")
     (description
@@ -1204,7 +1260,7 @@ configuration files, such as @file{.gitattributes}, @file{.gitignore}, and
 (define-public emacs-with-editor
   (package
     (name "emacs-with-editor")
-    (version "3.2.0")
+    (version "3.3.0")
     (source
      (origin
        (method git-fetch)
@@ -1213,7 +1269,7 @@ configuration files, such as @file{.gitattributes}, @file{.gitignore}, and
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1d98hagpm6h5vgx80qlh3zrfcb6z000rfc707w9zzmh634dkg3xx"))))
+        (base32 "1p0mrx4cixjpw34x8m8f8wna5f9rh8h3s4kpsycyvzmpmz3jicr9"))))
     (build-system emacs-build-system)
     (arguments
      (list
@@ -1231,7 +1287,7 @@ configuration files, such as @file{.gitattributes}, @file{.gitignore}, and
     (native-inputs
      (list texinfo))
     (propagated-inputs
-     (list emacs-async))
+     (list emacs-async emacs-compat))
     (home-page "https://github.com/magit/with-editor")
     (synopsis "Emacs library for using Emacsclient as EDITOR")
     (description
@@ -1579,7 +1635,7 @@ purpose finder.")
 (define-public emacs-minions
   (package
     (name "emacs-minions")
-    (version "0.3.7")
+    (version "1.0.0")
     (source
      (origin
        (method git-fetch)
@@ -1588,10 +1644,10 @@ purpose finder.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1bzxxs8mxaihpjkbxgynhsi39lbbnij28grdc3sk9sq09j9752vw"))))
+        (base32 "0ralw9znj749ii046l0dfa3aacm05g1ix59rfsjafhky8fiwz37m"))))
     (build-system emacs-build-system)
     (propagated-inputs
-     (list emacs-dash))
+     (list emacs-compat emacs-dash))
     (home-page "https://github.com/tarsius/minions")
     (synopsis "Minor-mode menu for the mode line")
     (description
@@ -1635,7 +1691,7 @@ displayed at the bottom or at the top.")
 (define-public emacs-moody
   (package
     (name "emacs-moody")
-    (version "0.7.1")
+    (version "1.0.0")
     (source
      (origin
        (method git-fetch)
@@ -1644,8 +1700,10 @@ displayed at the bottom or at the top.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "09yyihx6cpa724z6cj2rqspajwj325ipgpmckklpgq6l4h5xnwy4"))))
+        (base32 "03rg1f8lnxc16cipadaxgvl9cdxlihn64xbww35n8cbkhgmmir5z"))))
     (build-system emacs-build-system)
+    (propagated-inputs
+     (list emacs-compat))
     (home-page "https://github.com/tarsius/moody")
     (synopsis "Tabs and ribbons for Emacs mode-line")
     (description
@@ -1905,7 +1963,7 @@ automatically opened with this mode.")
 (define-public emacs-ghq
   (package
     (name "emacs-ghq")
-    (version "0.1.2")
+    (version "0.2.0")
     (source
      (origin
        (method git-fetch)
@@ -1914,10 +1972,21 @@ automatically opened with this mode.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0rh2k93c3a0vl073a3s3a3h6gkw454v1lyd7y8l3pd24vw9hc628"))))
+        (base32 "10a7rxmijwmdkfb5rgavd8inc3a45q0m57dxdf6v62bcy00kmw4l"))))
     (build-system emacs-build-system)
-    (propagated-inputs
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'set-ghq-location
+            (lambda* (#:key inputs #:allow-other-keys)
+              (let ((ghq (search-input-file inputs "/bin/ghq")))
+                (substitute* "ghq.el"
+                  (("\"ghq") (string-append "\"" ghq)))))))))
+    (inputs
      (list ghq))
+    (propagated-inputs
+     (list emacs-dash emacs-s))
     (home-page "https://github.com/rcoedo/emacs-ghq")
     (synopsis "Emacs interface for @code{ghq} tool")
     (description
@@ -1928,7 +1997,7 @@ organizing remote Go repository clones.")
 (define-public emacs-ghub
   (package
     (name "emacs-ghub")
-    (version "3.5.6")
+    (version "3.6.0")
     (source
      (origin
        (method git-fetch)
@@ -1937,7 +2006,7 @@ organizing remote Go repository clones.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1pw1rjrvvanlcxv3rb64s2p646zfaipp7h7v8djlrrnlgy6mwbqd"))))
+        (base32 "11nrh2lr5179r0brd9vl7r0i0dpjxdr5frplxq6j2ca7l2vzwqyr"))))
     (build-system emacs-build-system)
     (arguments
      (list
@@ -1962,7 +2031,7 @@ organizing remote Go repository clones.")
     (native-inputs
      (list texinfo))
     (propagated-inputs
-     (list emacs-dash emacs-let-alist emacs-treepy))
+     (list emacs-compat emacs-dash emacs-let-alist emacs-treepy))
     (home-page "https://github.com/magit/ghub")
     (synopsis "Emacs client libraries for the APIs of various Git forges")
     (description
@@ -3238,15 +3307,15 @@ code completion and project management support.")
 (define-public emacs-auto-compile
   (package
     (name "emacs-auto-compile")
-    (version "1.7.2")
+    (version "1.8.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
-                    (url "https://github.com/emacscollective/auto-compile.git")
+                    (url "https://github.com/emacscollective/auto-compile")
                     (commit version)))
               (sha256
                (base32
-                "1njnyilv6lxnbvi6yrgzg6qjhf6vgh4fpag4hav1j45718y6kd31"))))
+                "1zkqpvnashwn721qwf9khwizfxq9g3dhhy1siyk1s2wq1a9li9wq"))))
     (build-system emacs-build-system)
     (propagated-inputs (list emacs-compat emacs-packed))
     (home-page "https://github.com/emacscollective/auto-compile")
@@ -5239,7 +5308,7 @@ kmonad's configuration files (@file{.kbd}).")
 (define-public emacs-keycast
   (package
     (name "emacs-keycast")
-    (version "1.2.0")
+    (version "1.3.0")
     (source
      (origin
        (method git-fetch)
@@ -5248,8 +5317,10 @@ kmonad's configuration files (@file{.kbd}).")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "01z20lsnjk8pwdsl4vx5dqdc4603bmb7fxan7n8j1fgvkvi63yzl"))))
+        (base32 "1hri91g6c0507vaisx3c0xr52xwy82j3vqk0irf30mcrv1j9a5hd"))))
     (build-system emacs-build-system)
+    (propagated-inputs
+     (list emacs-compat))
     (home-page "https://github.com/tarsius/keycast")
     (synopsis "Show current command and its key in the mode line")
     (description
@@ -6009,7 +6080,7 @@ intended to be.")
 (define-public emacs-ef-themes
   (package
     (name "emacs-ef-themes")
-    (version "0.11.0")
+    (version "1.0.0")
     (source
      (origin
        (method git-fetch)
@@ -6019,7 +6090,7 @@ intended to be.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1s03qdwb6wb1ddd2gmv4casdnr4mgxmifyhbzhvjdz7v50sdgq7k"))))
+         "0rq1cy9hg603wk7pnfj0zfc84h1l87rg8blk4x4b61x7bkc3dd7q"))))
     (build-system emacs-build-system)
     (home-page "https://git.sr.ht/~protesilaos/ef-themes")
     (synopsis "Colorful and legible themes")
@@ -6497,7 +6568,7 @@ Lisp.")
 (define-public emacs-paren-face
   (package
     (name "emacs-paren-face")
-    (version "1.0.8")
+    (version "1.1.0")
     (source
      (origin
        (method git-fetch)
@@ -6506,8 +6577,10 @@ Lisp.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "13d8psgd2j3vqmgwwf62gwyq7h6qlj8rrs31fxwjqmzzdblwqy1y"))))
+        (base32 "0ma2sxhds4b73zap8kyphbng7a77fsbwrzlybar11if4asd1dfba"))))
     (build-system emacs-build-system)
+    (propagated-inputs
+     (list emacs-compat))
     (home-page "https://github.com/tarsius/paren-face")
     (synopsis "Face for parentheses in Lisp modes")
     (description
@@ -6852,7 +6925,7 @@ allrecipes.com.")
 (define-public emacs-org-inline-pdf
   (package
     (name "emacs-org-inline-pdf")
-    (version "0.2")
+    (version "0.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -6861,18 +6934,19 @@ allrecipes.com.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1qc92xvgxmnwjixk8bxwbc1l1jj0qk9dg73jyaip6lk4g0wjk6xf"))))
+                "1i5hvdnd0bqr663i2ccdxba58ib0ixmc1y40mld6znmgc8p2973l"))))
     (build-system emacs-build-system)
     (inputs
      (list pdf2svg))
     (arguments
-     `(#:phases
+     (list
-       (modify-phases %standard-phases
+      #:phases
+      #~(modify-phases %standard-phases
           (add-after 'unpack 'patch-exec-paths
             (lambda* (#:key inputs #:allow-other-keys)
-             (let ((pdf2svg (assoc-ref inputs "pdf2svg")))
+              (let ((pdf2svg (search-input-file inputs "/bin/pdf2svg")))
                 (substitute* "org-inline-pdf.el"
-                 (("\"pdf2svg\"") (string-append "\"" pdf2svg "/bin/pdf2svg\"")))))))))
+                  (("\"pdf2svg\"") (string-append "\"" pdf2svg "\"")))))))))
     (home-page "https://github.com/shg/org-inline-pdf.el")
     (synopsis "Inline PDF previewing for Org")
     (description "This package provides a minor mode that enables
@@ -8143,20 +8217,18 @@ src blocks.")
     (license license:gpl3+)))
 
 (define-public emacs-ol-notmuch
-  (let ((commit "1a53d6c707514784cabf33d865b577bf77f45913")
-        (revision "0"))
   (package
     (name "emacs-ol-notmuch")
-      (version (git-version "2.0.0" revision commit))
+    (version "2.0.1")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://git.sr.ht/~tarsius/ol-notmuch")
-               (commit commit)))
+             (commit (string-append "v" version))))
        (sha256
         (base32
-           "16p7j51z8r047alwn2hkb6944f7ds29ckb97b4k8ia00vwch0d67"))
+         "1rlpl3kb709q5brkjrrpirdnhvyh447q93li9lgfz67yya29rfqd"))
        (file-name (git-file-name name version))))
     (build-system emacs-build-system)
     (propagated-inputs
@@ -8168,7 +8240,7 @@ src blocks.")
 Emacs' Org mode.  A search is a query to be performed by Notmuch; it is the
 equivalent to folders in other mail clients.  Similarly, mails are referred to
 by a query, so both a link can refer to several mails.")
-      (license license:gpl3+))))
+    (license license:gpl3+)))
 
 (define-public emacs-debbugs
   (package
@@ -8991,6 +9063,34 @@ one Emacs buffer.")
 comparing characters, removing cursors, and more.")
       (license license:bsd-2))))
 
+(define-public emacs-substitute
+  (let ((commit "b81bb7789847f3d1645a60422fa080c48b93dd47")) ;version bump
+    (package
+      (name "emacs-substitute")
+      (version "0.1.8")
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://git.sr.ht/~protesilaos/substitute")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0s1lgpwmdjz17rd4r6qp41agmpqwa9976v1pb55p648zjh0p2vlz"))))
+      (build-system emacs-build-system)
+      (home-page "https://git.sr.ht/~protesilaos/substitute")
+      (synopsis "Efficiently replace targets in the buffer or context")
+      (description
+       "Substitute is a set of commands that perform text replacement (i)
+throughout the buffer, (ii) limited to the current definition (per
+narrow-to-defun), (iii) from point to the end of the buffer, and (iv) from
+point to the beginning of the buffer.
+
+These substitutions are meant to be as quick as possible and, as such, differ
+from the standard @code{query-replace} tool.  The provided commands prompt for
+substitute text and perform the substitution outright.")
+      (license license:gpl3+))))
+
 (define-public emacs-typo
   (package
     (name "emacs-typo")
@@ -10440,7 +10540,7 @@ variants.")
 (define-public emacs-solarized-theme
   (package
     (name "emacs-solarized-theme")
-    (version "2.0.0")
+    (version "2.0.1")
     (source
      (origin
        (method git-fetch)
@@ -10449,7 +10549,7 @@ variants.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "17z6cj8ids88xj2i6zs1s0mxs0fhn3gr7g5nhhy8s8khnzmyy2vj"))))
+        (base32 "0l2lcdm2hsjasfkg4rmypa4mvbhglbkkyv0jg88ygc6py9klcccd"))))
     (build-system emacs-build-system)
     (propagated-inputs
      (list emacs-dash))
@@ -11343,7 +11443,7 @@ between symbols.")
 (define-public emacs-hl-todo
   (package
     (name "emacs-hl-todo")
-    (version "3.4.2")
+    (version "3.5.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -11352,8 +11452,10 @@ between symbols.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "03i3dvg7scvbxx6z07916zqc7p8w5s9nxv4v2phr68046zjz05dw"))))
+                "1d9mkbd33zyx540ilp1vz8fgckvxv0qd2vyjgz11zh1qv1pfk8gh"))))
     (build-system emacs-build-system)
+    (propagated-inputs
+     (list emacs-compat))
     (home-page "https://github.com/tarsius/hl-todo")
     (synopsis "Emacs mode to highlight TODO and similar keywords")
     (description
@@ -12691,7 +12793,7 @@ agree upon.")
 (define-public emacs-undohist-el
   (package
     (name "emacs-undohist-el")
-    (version "0.2.1")
+    (version "0.3.0")
     (source
      (origin
        (method git-fetch)
@@ -12700,7 +12802,7 @@ agree upon.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0hmx2b20nrxg2lb8vplgrzdh8chgxwlbmjvbq5scddggd302sd56"))))
+        (base32 "1s1574q85lflik7w983v859qgxy1sn6i09hspa78smiawfva1855"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/m2ym/undohist-el")
     (synopsis "Save undo history between sessions")
@@ -12782,7 +12884,7 @@ mode with the package emacs-julia-mode.")
 (define-public emacs-julia-snail
   (package
     (name "emacs-julia-snail")
-    (version "1.2.0")
+    (version "1.2.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -12791,7 +12893,7 @@ mode with the package emacs-julia-mode.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1m6hh041gc10dfc1q5vxrgv64s1240whc9igqjm7asmnprajdiab"))))
+                "1vbg97h2jvmkpyhdsra51ilimzvrqnpy8rf1bhxnnb54p2cgkpsr"))))
     (build-system emacs-build-system)
     (arguments
      (list
@@ -13240,7 +13342,7 @@ with Elfeed.")
 (define-public emacs-elfeed-score
   (package
     (name "emacs-elfeed-score")
-    (version "1.2.5")
+    (version "1.2.6")
     (source
      (origin
        (method git-fetch)
@@ -13249,7 +13351,7 @@ with Elfeed.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0slbmmcsf5pqbiq3nmna7wx9jvfgdgjp272qdqvmrv99jdj92cq6"))))
+        (base32 "0d0dxldafgk3knc0d8g8ghm24zsq5x2p1pswh2syyl33nqf61s8s"))))
     (build-system emacs-build-system)
     (arguments
      (list
@@ -13389,7 +13491,7 @@ maximizes flexibility (at the expense of conciseness).")
 (define-public emacs-find-file-in-project
   (package
     (name "emacs-find-file-in-project")
-    (version "6.2.0")
+    (version "6.2.1")
     (source
      (origin
        (method git-fetch)
@@ -13398,7 +13500,7 @@ maximizes flexibility (at the expense of conciseness).")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0sq8fyq19jw1hm0m6hiqnvzzvx0c3xigfx7x6i40ib5hnfjlqs0a"))))
+        (base32 "1vrr3fwifn3lpajh03rx5rzzgc5dks0p6154y1c7f49wqffds36p"))))
     (build-system emacs-build-system)
     (arguments
      `(#:tests? #t
@@ -15420,7 +15522,7 @@ passive voice.")
 (define-public emacs-org
   (package
     (name "emacs-org")
-    (version "9.6.5")
+    (version "9.6.6")
     (source
      (origin
        (method git-fetch)
@@ -15429,7 +15531,7 @@ passive voice.")
              (commit (string-append "release_" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1dpqds0cx56va8cpvvhiqi116h7c4msfqxzvhnamm99ab4ccck1a"))))
+        (base32 "1z3n2dzvgr225f33lvpwwdssrw32lsa1c27l2h9irzv7p33pl1zf"))))
     (build-system emacs-build-system)
     (arguments
      (list
@@ -16158,19 +16260,18 @@ using a convenient notation.")
                    license:fdl1.3+)))) ;GFDLv1.3+ for the manual
 
 (define-public emacs-beframe
-  (let ((commit "edfab6eefe4ac35cd8d1ed87fc7f670496d25e40")) ;version bump
   (package
     (name "emacs-beframe")
-      (version "0.2.0")
+    (version "0.3.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://git.sr.ht/~protesilaos/beframe")
-                      (commit commit)))
+                    (commit version)))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                  "0sd8r3icaj2gl7f62fyzlwkkb05mc3cwsqgicw0n1x07s5ir3129"))))
+                "1nblpac1pkhgwpbw0k0p9xx6yc5kiai4pznw39slx703mzzqzqyj"))))
     (build-system emacs-build-system)
     (arguments
      (list
@@ -16196,7 +16297,7 @@ call buffers that belong to frames ``beframed''.  Producing multiple frames
 does not generate multiple buffer lists.  There still is only one global list
 of buffers.  Beframing them simply filters the list.")
     (license (list license:gpl3+
-                     license:fdl1.3+))))) ; GFDLv1.3+ for the manual
+                   license:fdl1.3+)))) ; GFDLv1.3+ for the manual
 
 (define-public emacs-gn-mode
   (package
@@ -19194,7 +19295,7 @@ which avoids some of the issues with using Emacs’s built-in Url library.")
 (define-public emacs-ement
   (package
     (name "emacs-ement")
-    (version "0.8.3")
+    (version "0.9.3")
     (source
      (origin
        (method git-fetch)
@@ -19203,7 +19304,7 @@ which avoids some of the issues with using Emacs’s built-in Url library.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "17s3sl0dijgmhnaryw08g6vn6za46xz6a709rsfrdis8v1knqd7z"))))
+        (base32 "1fh592y4v6iybdfh0b55k8nknzgsbcmy9g62ymvqz0wlhwq4h5h9"))))
     (build-system emacs-build-system)
     (arguments
      (list #:emacs emacs))              ;need libxml support
@@ -20814,7 +20915,7 @@ highlighting and indentation support.")
 (define-public emacs-terraform-mode
   (package
     (name "emacs-terraform-mode")
-    (version "1.0.0")
+    (version "1.0.1")
     (source
      (origin
        (method git-fetch)
@@ -20823,7 +20924,7 @@ highlighting and indentation support.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0npmj39b74h1lmqbvnnwcy3jqnaifgawi9p4sb242fcngiy2ppxf"))))
+        (base32 "10wndnlsv7f2yn83n1wamnhiwyhxkdlmwld9yk0m2kkxx4pwfgfj"))))
     (build-system emacs-build-system)
     (propagated-inputs
      (list emacs-dash emacs-hcl-mode))
@@ -21869,7 +21970,7 @@ according to a parsing expression grammar.")
 (define-public emacs-eldev
   (package
     (name "emacs-eldev")
-    (version "1.3.1")
+    (version "1.4")
     (source
      (origin
        (method git-fetch)
@@ -21878,7 +21979,7 @@ according to a parsing expression grammar.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "14rrh5ycwd3r5k3df8aif4jii645m5jgplxky3hrjgr8vxd951h8"))))
+        (base32 "1cziz1a8mh24aj79jfnkjb0llh6a2raqnlcfyaswha80bwzwp4ph"))))
     (build-system emacs-build-system)
     (arguments
      (list
@@ -23018,19 +23119,18 @@ without disturbing alignment.")
     (license license:gpl3+)))
 
 (define-public emacs-macrostep
-  (let ((commit "424e3734a1ee526a1bd7b5c3cd1d3ef19d184267"))
   (package
     (name "emacs-macrostep")
-      (version (git-version "0.9" "1" commit))
+    (version "0.9.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
-                      (url "https://github.com/joddie/macrostep")
+                    (url "https://github.com/emacsorphanage/macrostep")
-                      (commit commit)))
+                    (commit version)))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                  "1fm40mxdn289cyzgw992223dgrjmwxn4q8svyyxfaxjrpb38jhjz"))))
+                "1sxvp1q8naf0328l9fs90nk8bzsv485sajx4khh77nwkz3v4sr9f"))))
     (build-system emacs-build-system)
     (arguments
      (list
@@ -23055,7 +23155,7 @@ without disturbing alignment.")
                 (invoke "emacs" "--batch" "-L" "."
                         "-l" "macrostep-test.el"
                         "-f" "ert-run-tests-batch-and-exit")))))))
-      (home-page "https://github.com/joddie/macrostep")
+    (home-page "https://github.com/emacsorphanage/macrostep")
     (synopsis "Interactive macro-expander for Emacs")
     (description "@code{macrostep} is an Emacs minor mode for interactively
 stepping through the expansion of macros in Emacs Lisp source code.  It lets
@@ -23064,7 +23164,7 @@ pretty-printing the expanded forms inline in the source buffer, which is
 temporarily read-only while macro expansions are visible.  You can expand and
 collapse macro forms one step at a time, and evaluate or instrument the
 expansions for debugging with Edebug as normal.")
-      (license license:gpl3+))))
+    (license license:gpl3+)))
 
 (define-public emacs-macrostep-geiser
   ;; XXX: Upstream does not tag commits (yet).  The commit below matches the
@@ -23812,7 +23912,7 @@ and doesn't require memorisation of commands.
 (define-public emacs-logview
   (package
     (name "emacs-logview")
-    (version "0.16")
+    (version "0.16.1")
     (source
      (origin
        (method git-fetch)
@@ -23821,7 +23921,7 @@ and doesn't require memorisation of commands.
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0vw6brs76z7fkvlazakwhhgdcydjc099j150c7503kwi2hmmp0p8"))))
+        (base32 "12m0wqzfbphpz88fnawn5kb7yaayxh3yajbf6zzzbnyc8rjajcr6"))))
     (propagated-inputs
      (list emacs-datetime emacs-extmap))
     (build-system emacs-build-system)
@@ -27068,7 +27168,7 @@ backends, including the @command{wordnet} offline backend.")
 (define-public emacs-editorconfig
   (package
     (name "emacs-editorconfig")
-    (version "0.9.1")
+    (version "0.10.1")
     (source
      (origin
        (method git-fetch)
@@ -27078,7 +27178,7 @@ backends, including the @command{wordnet} offline backend.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1v8x649r9b0ihnhddkkfb8ck21z2hr3swgczwgzwdk0ys6pl89my"))))
+         "1hwqhfm32sg4y0l0yn7378vjb6icgd92lkazy2z6dmnks5sbz0a3"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/editorconfig/editorconfig-emacs")
     (synopsis "Define and maintain consistent coding styles between different
@@ -28378,11 +28478,11 @@ a vterm buffer and back again.")
 
 (define-public emacs-simple-mpc
   ;; There have been no releases.
-  (let ((commit "bee8520e81292b4c7353e45b193f9a13b482f5b2")
+  (let ((commit "35923caf39d4bebeb0e49264a29441c22216f1ed")
         (revision "1"))
     (package
       (name "emacs-simple-mpc")
-      (version (git-version "0" revision commit))
+      (version (git-version "1.0" revision commit))
       (source
        (origin
          (method git-fetch)
@@ -28392,7 +28492,7 @@ a vterm buffer and back again.")
          (file-name (git-file-name name version))
          (sha256
           (base32
-           "1ja06pv007cmzjjgka95jlg31k7d29jrih1yxyblsxv85s9sg21q"))))
+           "0vnqnxw2qhxlzgyms220l9qcj1rvpyrmg1isri2l6hxk23ga89p9"))))
       (build-system emacs-build-system)
       (propagated-inputs (list emacs-s))
       (home-page "https://github.com/jorenvo/simple-mpc")
@@ -28654,7 +28754,7 @@ recursively.  The results are cached for speed.")
 (define-public emacs-orgit
   (package
     (name "emacs-orgit")
-    (version "1.8.0")
+    (version "1.9.0")
     (home-page "https://github.com/magit/orgit")
     (source (origin
               (method git-fetch)
@@ -28664,7 +28764,7 @@ recursively.  The results are cached for speed.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1hjfsj12qx06m8ji4l2sg502a55sabar4h6c2b2i9nmp1xf5889l"))))
+                "00fkj88yddan80q8zbx0jy66d958srkm06jiy1nraamxqr15mmyz"))))
     (build-system emacs-build-system)
     (propagated-inputs
      (list emacs-dash emacs-magit))
@@ -29347,7 +29447,7 @@ real search.")
 (define-public emacs-notmuch-maildir
   (package
     (name "emacs-notmuch-maildir")
-    (version "0.2.1")
+    (version "0.2.2")
     (source
      (origin
        (method git-fetch)
@@ -29356,10 +29456,10 @@ real search.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1fqnx6hhg0cqj82yjpl7llg6vvppc3y8q9k6g67mqr7z3712bw0x"))))
+        (base32 "09f5g2xll2wh9jkd8crgngnbhxxkiy1rqsjg5g4c0i3hdyk4c3s5"))))
     (build-system emacs-build-system)
     (propagated-inputs
-     (list emacs-notmuch))
+     (list emacs-compat emacs-notmuch))
     (home-page "https://git.sr.ht/~tarsius/notmuch-maildir")
     (synopsis "Visualize maildirs as a tree")
     (description
@@ -29391,23 +29491,18 @@ as Emacs Lisp.")
     (license license:gpl3+)))
 
 (define-public emacs-transient
-  ;; Use the latest commit as the latest release is getting old and has known
-  ;; problems, according to its one of its maintainers (see:
-  ;; https://github.com/magit/magit/issues/4676#issuecomment-1473912505).
-  (let ((commit "0ae0de43590b5b6984a83f9e044e7c426455ac6e")
-        (revision "1"))
   (package
     (name "emacs-transient")
-      (version (git-version "0.3.7" revision commit))
+    (version "0.4.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/magit/transient")
-                      (commit commit)))
+                    (commit (string-append "v" version))))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                  "01b60pj8k3vwvs2xsx5md2myz0l1dj1myh9jrdyaiyhcaacvlbq8"))))
+                "0c9bfn5jwwng98h7i9lx0q3vg00wd8w25cg8d3vyy2vqfbg80qhy"))))
     (build-system emacs-build-system)
     (arguments
      `(#:tests? #f                      ;no test suite
@@ -29432,7 +29527,7 @@ in Emacs, Transient implements a similar abstraction involving a prefix
 command, infix arguments and suffix commands.  We could call this abstraction
 a \"transient command\", but because it always involves at least two
 commands (a prefix and a suffix) we prefer to call it just a \"transient\".")
-      (license license:gpl3+))))
+    (license license:gpl3+)))
 
 (define-public emacs-forge
   (package
@@ -31124,6 +31219,25 @@ top of the old defadvice system, to help users of defadvice move to the new
 advice system without dropping support for Emacs<24.4.")
     (license license:gpl3+)))
 
+(define-public emacs-url-http-oauth
+  (package
+    (name "emacs-url-http-oauth")
+    (version "0.8.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://elpa.gnu.org/packages/url-http-oauth-" version
+             ".tar"))
+       (sha256 (base32
+                "1vcbx8rpzvx4v4g7iyja6kpsqidaiy2xzj7glrwwzhppkbp0xkvy"))))
+    (build-system emacs-build-system)
+    (home-page "https://elpa.gnu.org/packages/url-http-oauth.html")
+    (synopsis "OAuth 2.0 for URL library")
+    (description
+     "Url HTTP Oauth adds OAuth 2.0 support to Emacs's URL library.")
+    (license license:gpl3+)))
+
 (define-public emacs-url-http-ntlm
   (package
     (name "emacs-url-http-ntlm")
@@ -31145,14 +31259,14 @@ advice system without dropping support for Emacs<24.4.")
 (define-public emacs-soap-client
   (package
     (name "emacs-soap-client")
-    (version "3.2.1")
+    (version "3.2.3")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://elpa.gnu.org/packages/"
                            "soap-client-" version ".tar"))
        (sha256
-        (base32 "0ajv6l1p8dinnlybwzvv4c2i6291is6isjxb2h4apg27g66qbcki"))))
+        (base32 "0z6af253iwimam03jnpai2h989i6vyv05wdz7dadna6amdryfznc"))))
     (build-system emacs-build-system)
     (home-page "https://elpa.gnu.org/packages/soap-client.html")
     (synopsis "Access SOAP web services")
@@ -31181,17 +31295,20 @@ programming in Emacs Lisp easy and fun.")
 (define-public emacs-excorporate
   (package
     (name "emacs-excorporate")
-    (version "1.0.0")
+    (version "1.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://elpa.gnu.org/packages/"
                            "excorporate-" version ".tar"))
        (sha256
-        (base32 "1g0wc2kp15ra323b4rxvdh58q9c4h7m20grw6a0cs53m7l9xi62f"))))
+        (base32 "1il51gfgvkxjj7vdi5kdmzi87hl9853ck8s45p0cxrddlaiqbmwy"))))
     (build-system emacs-build-system)
     (propagated-inputs
-     (list emacs-fsm emacs-soap-client emacs-url-http-ntlm))
+     (list emacs-fsm
+           emacs-soap-client
+           emacs-url-http-oauth
+           emacs-url-http-ntlm))
     (home-page "https://elpa.gnu.org/packages/excorporate.html")
     (synopsis "Exchange integration")
     (description "This package provides Exchange integration for Emacs.")
@@ -31434,7 +31551,7 @@ it forcibly
 (define-public emacs-elpher
   (package
     (name "emacs-elpher")
-    (version "3.4.3")
+    (version "3.5.0")
     (source
      (origin
        (method git-fetch)
@@ -31443,7 +31560,7 @@ it forcibly
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "04m226by90mv4rxxy6is8appxnvxq4npr585k2y2l1vmrj0qwn49"))))
+        (base32 "0cxzv9nx5vshf45r7msaqnq8h7xwi4kd8pb3na3dljlrhwvgdrk6"))))
     (build-system emacs-build-system)
     (arguments
      (list
@@ -32498,6 +32615,30 @@ such as:
 @end itemize")
     (license license:gpl3+)))
 
+(define-public emacs-framemove
+  ;; Use the latest commit, as there are no tagged releases.
+  (let ((commit "0faa8a4937f398e4971fc877b1c294100506b645")
+        (revision "0"))
+    (package
+      (name "emacs-framemove")
+      (version (git-version "0.10" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/emacsmirror/framemove")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1z4xqx1cvllil03pdwsybsj5v9w7ggdrak1kxa856ki5mj1ja3gl"))))
+      (build-system emacs-build-system)
+      (home-page "https://www.emacswiki.org/emacs/framemove.el")
+      (synopsis "Directional frame selection routines")
+      (description "Framemove is similar to the Windmove library, but for
+frames.  It provides a simple set of keystrokes to move the input/focus
+between windows.")
+      (license license:gpl3))))
+
 (define-public emacs-flycheck-cpplint
   (package
     (name "emacs-flycheck-cpplint")
@@ -33867,7 +34008,7 @@ launching other commands/applications from within Emacs, similar to the
 (define-public emacs-no-littering
   (package
     (name "emacs-no-littering")
-    (version "1.3.0")
+    (version "1.4.0")
     (source
      (origin
        (method git-fetch)
@@ -33876,7 +34017,7 @@ launching other commands/applications from within Emacs, similar to the
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1vkypj2mm428kmawxnyaqg3v5xpcs5hkbmyvjkib8ib02psshxd7"))))
+        (base32 "1i5fcci8fg14hbd4cjb84q3mx6rfwhbwkw0g21v25dal61kw4yvb"))))
     (build-system emacs-build-system)
     (propagated-inputs
      (list emacs-compat))
@@ -34950,7 +35091,7 @@ displayed for sharing.")
 (define-public emacs-orglink
   (package
     (name "emacs-orglink")
-    (version "1.2.0")
+    (version "1.2.1")
     (source
      (origin
        (method git-fetch)
@@ -34959,8 +35100,10 @@ displayed for sharing.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1619ly90vh2lla5rbw87a4n0rfal3wpbf7005jjiyv2ay88nc7l9"))))
+        (base32 "05x8alv4a8c1g9l8v8p319vcr0y7w1i2r6ipj0v3dy4n2gh7v822"))))
     (build-system emacs-build-system)
+    (propagated-inputs
+     (list emacs-compat))
     (home-page "https://github.com/tarsius/orglink")
     (synopsis "Use Org mode links in other modes")
     (description "This library implements support for some Org mode link types
@@ -36591,14 +36734,14 @@ projects.")
 (define-public emacs-vundo
   (package
     (name "emacs-vundo")
-    (version "2.0.0")
+    (version "2.1.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://elpa.gnu.org/packages/vundo-"
                                   version ".tar"))
               (sha256
                (base32
-                "032aqcqq2xhh12qcpp8p3qldv0r9cnqr2y11jk1m5cvgal1cbb68"))))
+                "1inm6kvh5j47nsrmq6wpf30dqmx0arzdpa6vdcn834g50i4fh8kc"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/casouri/vundo")
     (synopsis "Visualize the undo tree")

gnu/packages/engineering.scm

@@ -20,7 +20,7 @@
 ;;; Copyright © 2020, 2021 Ekaitz Zarraga <ekaitz@elenq.tech>
 ;;; Copyright © 2020 B. Wilson <elaexuotee@wilsonb.com>
 ;;; Copyright © 2020, 2021, 2022, 2023 Vinicius Monego <monego@posteo.net>
-;;; Copyright © 2020, 2021 Morgan Smith <Morgan.J.Smith@outlook.com>
+;;; Copyright © 2020, 2021, 2023 Morgan Smith <Morgan.J.Smith@outlook.com>
 ;;; Copyright © 2021 qblade <qblade@protonmail.com>
 ;;; Copyright © 2021 Gerd Heber <gerd.heber@gmail.com>
 ;;; Copyright © 2021, 2022 Guillaume Le Vaillant <glv@posteo.net>
@@ -908,45 +908,89 @@ fonts to gEDA.")
       (build-system cmake-build-system)
       (arguments
        (list
+        #:imported-modules `((guix build guile-build-system)
+                             ,@%cmake-build-system-modules)
+        #:modules '((guix build cmake-build-system)
+                    ((guix build guile-build-system) #:prefix guile:)
+                    (guix build utils))
         #:test-target "libfive-test"
-        #:configure-flags
+        #:configure-flags #~(list
-        #~(list (string-append "-DGUILE_CCACHE_DIR="
+                             (string-append
-                               #$output "/lib/guile/3.0/site-ccache"))
+                              "-DPYTHON_SITE_PACKAGES_DIR="
+                              #$output "/lib/python"
+                              #$(version-major+minor
+                                 (package-version
+                                  (this-package-input "python-wrapper")))
+                              "/site-packages"))
         #:phases
         #~(modify-phases %standard-phases
-            (add-after 'unpack 'fix-autocompilation
-              (lambda _ (setenv "HOME" "/tmp")))
             (add-after 'unpack 'remove-native-compilation
               (lambda _
                 (substitute* "CMakeLists.txt" (("-march=native") ""))))
+            (add-after 'unpack 'remove-environment-variable-override
+              (lambda _
+                (substitute* "studio/src/guile/interpreter.cpp"
+                  (("qputenv\\(\"GUILE_LOAD_COMPILED_PATH\".*") ""))))
             (add-after 'unpack 'fix-library-location
               (lambda _
                 (substitute* "libfive/bind/guile/libfive/lib.scm"
                   (("\\(get-environment-variable \"LIBFIVE_FRAMEWORK_DIR\"\\)" m)
                    (string-append m "\n\"" #$output "/lib/\""))
                   (("\\(get-environment-variable \"LIBFIVE_STDLIB_DIR\"\\)" m)
-                   (string-append m "\n\"" #$output "/lib/\"")))))
+                   (string-append m "\n\"" #$output "/lib/\"")))
-            (add-after 'install 'install-scm-files
+                (substitute* "libfive/bind/python/libfive/ffi.py"
+                  (("os.environ.get\\('LIBFIVE_FRAMEWORK_DIR'\\)" m)
+                   (string-append m " or \"" #$output "/lib/\"")))))
+            (add-before 'build 'generate-bindings
               (lambda _
-                (for-each
+                ;; These files already exist but we regenerate them from source
-                 (lambda (file)
+                (with-directory-excursion "../source/libfive/stdlib"
-                   (install-file file
+                  (substitute* '("gen_scm.py" "gen_c.py" "gen_py.py")
-                                 (string-append #$output
+                    (("datetime.now\\(\\)\\.strftime\\([^)]+)") "\"N/A\"")
-                                                "/share/guile/site/3.0/libfive")))
+                    (("os\\.getlogin\\(\\)") "\"guix\""))
-                 (find-files "../source/libfive/bind/guile/libfive"
+                  (invoke "python" "gen_scm.py")
-                             "\\.scm$")))))))
+                  (invoke "python" "gen_c.py")
+                  (invoke "python" "gen_py.py"))))
+            (add-after 'unpack 'do-not-build-guile-bindings
+              (lambda _
+                (delete-file "libfive/bind/guile/CMakeLists.txt")
+                (call-with-output-file
+                    "libfive/bind/guile/CMakeLists.txt"
+                  (lambda (port)
+                    (display "add_custom_target(libfive-guile)\n" port)))))
+            (add-after 'build 'guile-build
+              (lambda args
+                (apply (assoc-ref guile:%standard-phases 'build)
+                       #:source-directory "../source/libfive/bind/guile"
+                       args)))
+            (add-after 'install 'wrap-studio
+              (lambda _
+                (let* ((effective-version (guile:target-guile-effective-version))
+                       (scm (string-append #$output "/share/guile/site/"
+                                           effective-version))
+                       (go (string-append #$output "/lib/guile/"
+                                          effective-version "/site-ccache"))
+                       (py (string-append #$output "/lib/python"
+                                          #$(version-major+minor
+                                             (package-version
+                                              (this-package-input "python-wrapper")))
+                                          "/site-packages")))
+                  (wrap-program (string-append #$output "/bin/Studio")
+                    `("GUILE_LOAD_PATH" ":" prefix (,scm))
+                    `("GUILE_LOAD_COMPILED_PATH" ":" prefix (,go))
+                    `("GUIX_PYTHONPATH" ":" prefix (,py)))))))))
       (native-inputs
        (list pkg-config))
       (inputs
-       (list boost libpng qtbase-5 eigen guile-3.0))
+       (list bash-minimal boost eigen guile-3.0 libpng python-wrapper qtbase))
       (home-page "https://libfive.com")
       (synopsis "Tool for programmatic computer-aided design")
       (description
        "Libfive is a tool for programmatic computer-aided design (CAD).  In
-libfive, solid models are defined as Scheme scripts, and there are no opaque
+libfive, solid models are defined as Scheme or Python scripts, and there are
-function calls into the geometry kernel: everything is visible to the user.
+no opaque function calls into the geometry kernel: everything is visible to
-Even fundamental, primitive shapes are represented as code in the user-level
+the user.  Even fundamental, primitive shapes are represented as code in the
-language.")
+user-level language.")
       (license (list license:mpl2.0               ;library
                      license:gpl2+))              ;Guile bindings and GUI
 
@@ -2497,7 +2541,7 @@ measurement devices and test equipment via GPIB, RS232, Ethernet or USB.")
 (define-public python-scikit-rf
   (package
     (name "python-scikit-rf")
-    (version "0.26.0")
+    (version "0.27.1")
     (source (origin
               (method git-fetch) ;PyPI misses some files required for tests
               (uri (git-reference
@@ -2505,7 +2549,7 @@ measurement devices and test equipment via GPIB, RS232, Ethernet or USB.")
                     (commit (string-append "v" version))))
               (sha256
                (base32
-                "1v7dag6sm96b18y4p46cjjyqnq9r2r7qmiy0xvdwy3js4zf4iwcv"))
+                "1rh2hq050439azlglqb54cy3jc1ir5y1ps55as4d5j619a7mq9x0"))
               (file-name (git-file-name name version))))
     (build-system pyproject-build-system)
     (propagated-inputs (list python-matplotlib
@@ -3023,13 +3067,13 @@ program that can perform mesh processing tasks in batch mode, without a GUI.")
 (define-public poke
   (package
     (name "poke")
-    (version "3.1")
+    (version "3.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnu/poke/poke-" version
                                   ".tar.gz"))
               (sha256
-               (base32 "0gziizzpdwg1h4znndhapx4ybjqhxycgxdh0f1qyq5h9h6xac1gl"))
+               (base32 "15qd9z3wv7jrdlh6f9hwgni54ssdz8hzrn4lxiacwv1sslfmb3km"))
               (modules '((guix build utils)))
               (snippet
                '(begin

gnu/packages/finance.scm

@@ -123,6 +123,7 @@
   #:use-module (gnu packages readline)
   #:use-module (gnu packages security-token)
   #:use-module (gnu packages sphinx)
+  #:use-module (gnu packages sqlite)
   #:use-module (gnu packages tex)
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages textutils)
@@ -133,10 +134,12 @@
   #:use-module (gnu packages xml)
   #:use-module (gnu packages gnuzilla))
 
-(define-public bitcoin-core-23.0
+(define-public bitcoin-core
+  ;; The support lifetimes for bitcoin-core versions can be found in
+  ;; <https://bitcoincore.org/en/lifecycle/#schedule>.
   (package
     (name "bitcoin-core")
-    (version "23.0")
+    (version "24.1")
     (source (origin
               (method url-fetch)
               (uri
@@ -144,7 +147,7 @@
                               version "/bitcoin-" version ".tar.gz"))
               (sha256
                (base32
-                "01fcb90pqip3v77kljykx51cmg7jdg2cmp7ys0a40svdkps8nx16"))))
+                "0kmgpzknbykgwb8vd7hj3j1xxn35785gf4vii5705k6rnarks2la"))))
     (build-system gnu-build-system)
     (native-inputs
      (list autoconf
@@ -160,7 +163,8 @@
            libevent
            miniupnpc
            openssl
-           qtbase-5))
+           qtbase-5
+           sqlite))
     (arguments
      `(#:configure-flags
        (list
@@ -211,11 +215,6 @@ of the bitcoin protocol.  This package provides the Bitcoin Core command
 line client and a client based on Qt.")
     (license license:expat)))
 
-;; The support lifetimes for bitcoin-core versions can be found in
-;; <https://bitcoincore.org/en/lifecycle/#schedule>.
-
-(define-public bitcoin-core bitcoin-core-23.0)
-
 (define-public ghc-hledger
   (package
     (name "ghc-hledger")
@@ -289,14 +288,14 @@ Accounting.")
 (define-public homebank
   (package
     (name "homebank")
-    (version "5.6.2")
+    (version "5.6.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://homebank.free.fr/public/sources/"
                                   "homebank-" version ".tar.gz"))
               (sha256
                (base32
-                "1w8nafqr54i3gksd2s0n246ip178qikn0jcmdx4ihg2dw1cdxsqj"))))
+                "0a1qhbnifqs0j59m1w5wfj1ix8iywmy1kc8185zvxndvckspb521"))))
     (build-system glib-or-gtk-build-system)
     (native-inputs
      (list pkg-config intltool))
@@ -1684,72 +1683,6 @@ trezord as a regular user instead of needing to it run as root.")
 Trezor wallet.")
     (license license:lgpl3+)))
 
-(define-public bitcoin-abc
-  (package
-    (name "bitcoin-abc")
-    (version "0.21.12")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://download.bitcoinabc.org/"
-                                  version "/src/bitcoin-abc-"
-                                  version ".tar.gz"))
-              (sha256
-               (base32
-                "1amzwy3gpl8ai90dsy7g0z51qq8vxfzbf642wn4bfynb8jmw3kx5"))))
-    (build-system cmake-build-system)
-    (native-inputs
-     (list pkg-config
-           python ; for the tests
-           util-linux ; provides the hexdump command for tests
-           qttools-5))
-    (inputs
-     (list bdb-5.3
-           boost
-           jemalloc
-           libevent
-           miniupnpc
-           openssl
-           protobuf
-           qrencode
-           qtbase-5
-           zeromq
-           zlib))
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-before 'configure 'make-qt-deterministic
-           (lambda _
-             ;; Make Qt deterministic.
-             (setenv "QT_RCC_SOURCE_DATE_OVERRIDE" "1")
-             #t))
-         (add-before 'check 'set-home
-           (lambda _
-             (setenv "HOME" (getenv "TMPDIR")) ; tests write to $HOME
-             #t))
-         (add-after 'check 'check-functional
-           (lambda _
-             (invoke
-              "python3" "./test/functional/test_runner.py"
-              (string-append "--jobs=" (number->string (parallel-job-count)))
-              ;; TODO: find why the abc-miner-fund test fails.
-              "--exclude=abc-miner-fund")
-             #t)))))
-    (home-page "https://www.bitcoinabc.org/")
-    (synopsis "Bitcoin ABC peer-to-peer full node for the Bitcoin Cash protocol")
-    (description
-     "Bitcoin Cash brings sound money to the world, fulfilling the original
-promise of Bitcoin as Peer-to-Peer Electronic Cash.  Merchants and users are
-empowered with low fees and reliable confirmations is a digital currency that
-enables instant payments to anyone anywhere in the world.  It uses
-peer-to-peer technology to operate without central authority: managing
-transactions and issuing money are carried out collectively by the network.
-As a fork it implemented changes lowering the time between blocks and now
-offers confimations after less than 5 seconds and have significantly lower
-fees that BTC.  Bitcoin ABC is the reference implementation of the Bitcoin
-Cash protocol.  This package provides the Bitcoin Cash command line client and
-a client based on Qt.  This is a fork of Bitcoin Core.")
-    (license license:expat)))
-
 (define-public libofx
   (package
     (name "libofx")
@@ -1799,7 +1732,7 @@ following three utilities are included with the library:
 (define-public bitcoin-unlimited
   (package
     (name "bitcoin-unlimited")
-    (version "1.10.0.0")
+    (version "2.0.0.0")
     (source
      (origin
        (method git-fetch)
@@ -1808,7 +1741,7 @@ following three utilities are included with the library:
              (commit (string-append "BCHunlimited" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "12yb2rbd6hsns43qyxc5dm7h5k4sph9sb64q7kkbqi3xhgrrsjdq"))))
+        (base32 "0s4iyjfhjx21xa3z7433m4skfr115565k0ckza87ha2d4nl8kz5h"))))
     (build-system gnu-build-system)
     (native-inputs
      (list autoconf
@@ -1860,7 +1793,12 @@ following three utilities are included with the library:
              ;; an expired SSL certificate.
              (substitute* "src/qt/test/test_main.cpp"
                (("if \\(QTest::qExec\\(&test2\\) != 0\\)")
-                "if (QTest::qExec(&test2) == 0)"))))
+                "if (QTest::qExec(&test2) == 0)"))
+             ;; The following test passes with OpenSSL 1.1, but fails with
+             ;; OpenSSL 3.
+             (substitute* "src/secp256k1/src/tests.c"
+               (("run_ecdsa_der_parse\\(\\);")
+                ""))))
          (add-before 'check 'set-home
            (lambda _
              ;; Tests write to $HOME
@@ -2261,7 +2199,7 @@ and manipulation.")
 (define-public xmrig
   (package
     (name "xmrig")
-    (version "6.19.0")
+    (version "6.19.2")
     (source
      (origin
        (method git-fetch)
@@ -2269,7 +2207,7 @@ and manipulation.")
              (url "https://github.com/xmrig/xmrig")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
-       (sha256 (base32 "10vaq6ld4sddnpmv9dg71fjvw1jrfaddrp3bq6p3dxhsl153khm4"))
+       (sha256 (base32 "1hgcfq79d5060iryr34bpwf1dvgqmbmn9mm4ccfvp896r10j482h"))
        (modules '((guix build utils)))
        (snippet
         ;; TODO: Try to use system libraries instead of bundled ones in
@@ -2303,16 +2241,15 @@ and manipulation.")
     (home-page "https://xmrig.com/")
     (synopsis "Monero miner")
     (description
-     "XMRig is a high performance, cross platform RandomX, KawPow,
+     "XMRig is a high-performance, cross-platform RandomX, KawPow,
-CryptoNight, AstroBWT and GhostRider unified CPU/GPU miner and RandomX
+CryptoNight and GhostRider unified CPU/GPU miner and RandomX benchmark.
-benchmark.
 
 Warning: upstream, by default, receives a percentage of the mining time.  This
-anti-functionality has been neutralised in Guix, but possibly not in all other
+anti-functionality has been neutralized in Guix, but possibly not in all other
 distributions.
 
-Warning: this software, because of it's nature, has high energy consumption.
+Warning: this software, because of its nature, has high energy consumption.
-Also, the energy expenses might be higher that the cryptocurrency gained by
+Also, the energy expenses might be higher than the cryptocurrency gained by
 mining.")
     (license license:gpl3+)))
 

gnu/packages/firmware.scm

@@ -481,7 +481,7 @@ provide OpenFirmware functionality on top of an already running system.")
 (define* (make-opensbi-package platform name #:optional (arch "riscv64"))
   (package
     (name name)
-    (version "1.1")
+    (version "1.2")
     (source
      (origin
        (method git-fetch)
@@ -490,14 +490,16 @@ provide OpenFirmware functionality on top of an already running system.")
              (commit (string-append "v" version))))
        (file-name (git-file-name "opensbi" version))
        (sha256
-        (base32 "0xlnhl965286kvizyjm571qbhj3l5n71a02dmbmgxzcqapzgi9wk"))))
+        (base32 "13k76ngmbs6xk8wm0vhc3fjs5w82g34wxs2zf4r27jd79m47xjb5"))))
     (build-system gnu-build-system)
     (native-inputs
-     `(,@(if (and (not (string-prefix? "riscv64" (%current-system)))
+     (append
+       (if (and (not (string-prefix? "riscv64" (%current-system)))
                 (string-prefix? "riscv64" arch))
-           `(("cross-gcc" ,(cross-gcc "riscv64-linux-gnu"))
+         (list (cross-gcc "riscv64-linux-gnu")
-             ("cross-binutils" ,(cross-binutils "riscv64-linux-gnu")))
+               (cross-binutils "riscv64-linux-gnu"))
-           '())))
+         '())
+       (list python)))
     (arguments
      `(#:tests? #f ; no check target
        #:make-flags (list (string-append "PLATFORM=" ,platform)
@@ -523,8 +525,7 @@ provide OpenFirmware functionality on top of an already running system.")
                (for-each
                  (lambda (file)
                    (install-file file out))
-                 bin))
+                 bin)))))))
-             #t)))))
     (home-page "https://github.com/riscv-software-src/opensbi")
     (synopsis "RISC-V @acronym{SBI, Supervisor Binary Interface} implementation")
     (description

gnu/packages/fonts.scm

@@ -11,7 +11,7 @@
 ;;; Copyright © 2016 Jookia <166291@gmail.com>
 ;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2016 Dmitry Nikolaev <cameltheman@gmail.com>
-;;; Copyright © 2016-2022 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016-2023 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2020 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2016 Toni Reina <areina@riseup.net>
 ;;; Copyright © 2017–2022 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -53,6 +53,8 @@
 ;;; Copyright © 2022 Hilton Chain <hako@ultrarare.space>
 ;;; Copyright © 2022 Nguyễn Gia Phong <mcsinyx@disroot.org>
 ;;; Copyright © 2023 Nicolas Graves <ngraves@ngraves.fr>
+;;; Copyright © 2023 Ahmad Draidi <a.r.draidi@redscript.org>
+;;; Copyright © 2023 Arnaud Lechevallier <arnaud.lechevallier@free.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -919,7 +921,8 @@ for use at smaller text sizes")))
        (snippet
         '(begin
            (use-modules (guix build utils))
-           (delete-file-recursively "font/precompiled")))))
+           (delete-file-recursively "font/precompiled")
+           (delete-file-recursively "hangul/precompiled")))))
     (build-system gnu-build-system)
     (outputs '("out"   ; TrueType/OpenType version
                "pcf"   ; PCF (bitmap) version
@@ -1809,6 +1812,25 @@ programming.  Iosevka is completely generated from its source code.")
        (sha256
         (base32 "1h5jfrpply7ypc4h6ivxs30qkrbni51zkj78xz6nz4zbnp923yi0"))))))
 
+(define-public font-iosevka-comfy
+  (package
+    (inherit font-iosevka)
+    (name "font-iosevka-comfy")
+    (version "1.2.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://git.sr.ht/~protesilaos/iosevka-comfy")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32 "1gccv28avxlkicl6rcsn6i23pdn0nrk91zhcyzwwc3nyzm2w8w40"))))
+    (home-page "https://git.sr.ht/~protesilaos/iosevka-comfy")
+    (description
+     "Iosevka Comfy is a TTF font derived from Iosevka.  It is a slightly tweaked
+     version of the original, designed for enhanced readability.")
+    (license license:silofl1.1)))
+
 (define-public font-sarasa-gothic
   (package
     (name "font-sarasa-gothic")
@@ -3049,3 +3071,161 @@ prevalent typefaces in Traditional Chinese regions.")
 Kong variant of Adobe’s Source Han Sans.  The font aims at providing a modern,
 region-agnostic glyph set adopting the “modern” glyph style that is similar to
 prevalent typefaces in Traditional Chinese regions.")))
+
+(define-public font-spleen
+  (package
+    (name "font-spleen")
+    (version "1.9.3")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/fcambus/spleen/releases/download/"
+                    version "/spleen-" version ".tar.gz"))
+              (sha256
+               (base32
+                "09bbwza14pl70cxbr09f9m8522s5p1p04kx9gh8svpd50bdixbdp"))))
+    (build-system font-build-system)
+    (outputs '("out" ;OTB
+               "bdf" "otf" "pcf" "psf"))
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'install
+            (lambda* (#:key outputs #:allow-other-keys)
+              (let* ((otb (assoc-ref outputs "out"))
+                     (bdf (assoc-ref outputs "bdf"))
+                     (otf (assoc-ref outputs "otf"))
+                     (pcf (assoc-ref outputs "pcf"))
+                     (psf (assoc-ref outputs "psf"))
+                     (otb-font-dir (string-append (assoc-ref outputs
+                                                             "out")
+                                                  "/share/fonts/misc"))
+                     (bdf-font-dir (string-append (assoc-ref outputs
+                                                             "bdf")
+                                                  "/share/fonts/misc"))
+                     (otf-font-dir (string-append (assoc-ref outputs
+                                                             "otf")
+                                                  "/share/fonts/opentype"))
+                     (pcf-font-dir (string-append (assoc-ref outputs
+                                                             "pcf")
+                                                  "/share/fonts/misc"))
+                     (psf-font-dir (string-append (assoc-ref outputs
+                                                             "psf")
+                                                  "/share/consolefonts")))
+                (mkdir-p otb-font-dir)
+                (mkdir-p bdf-font-dir)
+                (mkdir-p otf-font-dir)
+                (mkdir-p pcf-font-dir)
+                (mkdir-p psf-font-dir)
+                (for-each (lambda (otb)
+                            (install-file otb otb-font-dir))
+                          (find-files "." "\\.otb$"))
+                (for-each (lambda (bdf)
+                            (install-file bdf bdf-font-dir))
+                          (find-files "." "\\.bdf$"))
+                (for-each (lambda (otf)
+                            (install-file otf otf-font-dir))
+                          (find-files "." "\\.otf$"))
+                (for-each (lambda (pcf)
+                            (install-file pcf pcf-font-dir))
+                          (find-files "." "\\.pcf$"))
+                (for-each (lambda (psf)
+                            (install-file psf psf-font-dir))
+                          (find-files "." "\\.psfu$"))) #t)))))
+    (home-page "https://www.cambus.net/spleen-monospaced-bitmap-fonts/")
+    (synopsis "Monospaced bitmap font for consoles and terminals")
+    (description
+     "Spleen is a monospaced bitmap font available in 6 sizes:
+ 5x8, 6x12, 8x16, 12x24, 16x32, 32x64.
+
+All sizes are provided in the Glyph Bitmap Distribution Format (BDF),
+ PCF, PSF (for the Linux console), and OTB formats.  All sizes, except
+ 5x8, are provided in OTF format also.
+
+All font sizes, except 5x8 and 6x12, contain all ISO/IEC 8859-1
+ characters (Basic Latin and Latin-1 Supplement Unicode block), Latin
+ Extended-A characters, as well as Box Drawing, Block Elements, and
+ Braille Patterns Unicode blocks.
+
+The 5x8 and 6x12 versions only contain printable ASCII characters,
+ the Braille Patterns Unicode block, and light Box Drawing characters.
+
+Spleen also has support for Powerline symbols out of the box.")
+    (license license:bsd-2)))
+
+(define-public font-scientifica
+  (package
+    (name "font-scientifica")
+    (version "2.3")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/nerdypepper/scientifica/releases/download/"
+                    "v" version "/scientifica.tar"))
+              (sha256
+               (base32
+                "0zwa3s75lvbky2vn73i1fmxa37hi3zfm7f6wfpqwcip8l1lpi1gh"))))
+    (build-system font-build-system)
+    (outputs '("out" ;OTB
+               "bdf" "ttf"))
+    (arguments
+     (list #:phases #~(modify-phases %standard-phases
+                        (replace 'install
+                          (lambda* (#:key outputs #:allow-other-keys)
+                            (let* ((otb (assoc-ref outputs "out"))
+                                   (bdf (assoc-ref outputs "bdf"))
+                                   (ttf (assoc-ref outputs "ttf"))
+                                   (otb-font-dir (string-append (assoc-ref
+                                                                 outputs "out")
+                                                  "/share/fonts/misc"))
+                                   (ttf-font-dir (string-append (assoc-ref
+                                                                 outputs "ttf")
+                                                  "/share/fonts/truetype"))
+                                   (bdf-font-dir (string-append (assoc-ref
+                                                                 outputs "bdf")
+                                                  "/share/fonts/misc")))
+                              (mkdir-p otb-font-dir)
+                              (mkdir-p bdf-font-dir)
+                              (mkdir-p ttf-font-dir)
+                              (for-each (lambda (otb)
+                                          (install-file otb otb-font-dir))
+                                        (find-files "." "\\.otb$"))
+                              (for-each (lambda (bdf)
+                                          (install-file bdf bdf-font-dir))
+                                        (find-files "." "\\.bdf$"))
+                              (for-each (lambda (ttf)
+                                          (install-file ttf ttf-font-dir))
+                                        (find-files "." "\\.ttf$"))) #t)))))
+    (home-page "https://github.com/nerdypepper/scientifica")
+    (synopsis "Tall and condensed bitmap font for geeks")
+    (description
+     "@code{scientifica} is largely based on
+@url{https://github.com/romeovs/creep, @code{creep}}, with a number of
+minor tweaks to improve readability (a matter of taste of course).
+Most characters are just 4px wide, which is brilliant for low dpi(90-120) displays.")
+    (license license:silofl1.1)))
+
+(define-public font-recursive
+  (package
+    (name "font-recursive")
+    (version "1.085")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/arrowtype/recursive/"
+                                  "releases/download/v"
+                                  version
+                                  "/ArrowType-Recursive-"
+                                  version
+                                  ".zip"))
+              (sha256
+               (base32
+                "00ns6zwizp0wyxyrf7fxqmxm4gl7ygarxq1mj952h78q1rxdzjyb"))))
+    (build-system font-build-system)
+    (home-page "https://www.recursive.design/")
+    (synopsis "Variable font family for code & UI")
+    (description "Recursive Sans & Mono is a variable type family built for
+better code & UI.  It is inspired by casual script signpainting, but designed
+primarily to meet the needs of programming environments and application
+interfaces.")
+    (license license:silofl1.1)))

gnu/packages/freedesktop.scm

@@ -32,6 +32,7 @@
 ;;; Copyright © 2022 Wamm K. D. <jaft.r@outlook.com>
 ;;; Copyright © 2022 Petr Hodina <phodina@protonmail.com>
 ;;; Copyright © 2022 muradm <mail@muradm.net>
+;;; Copyright © 2023 Alex Devaure <ajadevaure@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -2086,6 +2087,9 @@ that wish to perform colour calibration.")
      (list #:configure-flags
            #~(list (string-append "-Dudev_hwdb_dir=" #$output
                                   "/lib/udev/hwdb.d")
+                   (string-append "-Dc_link_args=-Wl,-rpath="
+                                  (search-input-directory %build-inputs
+                                                          "lib/nss"))
                    (string-append "-Dudev_rules_dir=" #$output
                                   "/lib/udev/rules.d"))))
     (native-inputs

gnu/packages/fsf.scm

@@ -0,0 +1,72 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2023 宋文武 <iyzsong@envs.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 fsf)
+  #:use-module (gnu packages tex)
+  #:use-module (guix build-system copy)
+  #:use-module (guix download)
+  #:use-module (guix gexp)
+  #:use-module (guix packages)
+  #:use-module ((guix licenses) #:prefix license:))
+
+(define-public book-faif
+  (package
+    (name "book-faif")
+    (version "2.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://www.fsf.org/faif/faif-" version
+                                  ".tar.bz2"))
+              (sha256
+               (base32
+                "0qf14d0n6k1dn9z0fdnx9qkhn4iq685xd443w7l7w54bm931p7dw"))))
+    (build-system copy-build-system)
+    (native-inputs
+     (list (texlive-updmap.cfg
+            (list
+             texlive-caption
+             texlive-endnotes
+             texlive-fonts-ec
+             texlive-helvetic
+             texlive-hyperref
+             texlive-latex-fncychap
+             texlive-latex-geometry
+             texlive-latex-ucs
+             texlive-times))))
+    (arguments
+     (list
+      #:install-plan #~'(("faif-2.0.pdf" "share/doc/faif/"))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'install 'build
+            (lambda _
+              (invoke "pdflatex" "faif-2.0.tex"))))))
+    (home-page "https://www.fsf.org/faif")
+    (synopsis "Free as in Freedom (2.0)")
+    (description
+     "In 2002, Sam Williams wrote Free as in Freedom, a biography of Richard
+M. Stallman.  In its epilogue, Williams expressed hope that choosing to
+distribute his book under the GNU Free Documentation License would enable and
+encourage others to share corrections and their own perspectives through
+modifications to his work.  Free as in Freedom (2.0) is Stallman's revision of
+the original biography.  While preserving Williams's viewpoint, it includes
+factual corrections and extensive new commentary by Stallman, as well as new
+prefaces by both authors written for the occasion.  It is a rare kind of
+biography, where the reader has the benefit of both the biographer's original
+words and the subject's response.")
+    (license license:fdl1.3+)))

gnu/packages/game-development.scm

@@ -59,6 +59,7 @@
   #:use-module (guix build-system python)
   #:use-module (guix build-system scons)
   #:use-module (gnu packages)
+  #:use-module (gnu packages assembly)
   #:use-module (gnu packages audio)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages base)
@@ -1775,7 +1776,8 @@ of use.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "19mcbnjl4279qalb97msf965bjax48mx1r1qczyvwhn28h6n3bsy"))))
+         "19mcbnjl4279qalb97msf965bjax48mx1r1qczyvwhn28h6n3bsy"))
+       (patches (search-patches "openmw-assume-nonconst-SIGSTKSZ.patch"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f                      ; No test target
@@ -2066,14 +2068,14 @@ a 2D editor view.")
 (define-public guile-chickadee
   (package
     (name "guile-chickadee")
-    (version "0.9.0")
+    (version "0.10.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://files.dthompson.us/chickadee/"
                                   "chickadee-" version ".tar.gz"))
               (sha256
                (base32
-                "0b92lld7kj629mvq44vgd8vmf9h7s5gkdawb35vkzlx5q03wjfvk"))))
+                "0x8g0bsvir2z3876ynslfgnmfr5p92ic4666v73526lswnv56bqk"))))
     (build-system gnu-build-system)
     (arguments
      '(#:make-flags '("GUILE_AUTO_COMPILE=0")))
@@ -2803,8 +2805,8 @@ much more.")
 
 (define-public recastnavigation
   ;; We follow master since there hasn't been a release since 1.5.1 in 2016.
-  (let ((commit "c5cbd53024c8a9d8d097a4371215e3342d2fdc87")
+  (let ((commit "6d1f9711b3b71f28c2c1c0742d76e0ef8766cf91")
-        (revision "1"))
+        (revision "2"))
     (package
       (name "recastnavigation")
       (version (git-version "1.5.1" revision commit))
@@ -2816,7 +2818,7 @@ much more.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "034bm47gc3r285w1pnvkhmm74zz99d204b1r865gisaiq4qfbza0"))))
+                  "0cqp0sbm0ixqnxqz6gf2gybh5l4az91mdsd8b5bgxs1wpl2jmnga"))))
       (build-system cmake-build-system)
       (arguments
        `(#:configure-flags (list "-DBUILD_SHARED_LIBS=ON"
@@ -2853,7 +2855,7 @@ progresses the level, or you may regenerate tiles as the world changes.")
 (define-public raylib
   (package
     (name "raylib")
-    (version "4.2.0")
+    (version "4.5.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -2863,19 +2865,27 @@ progresses the level, or you may regenerate tiles as the world changes.")
               ;; TODO: Unbundle src/external
               (sha256
                (base32
-                "14v5iwxh8grywiyw9agpd2sfpyriq1rwwkd9f2s4iihh0z5j7hk8"))))
+                "00y8fsa4g9fk93s3wihbxl929m84hw3fflr0h409s3i1kfmv7ajj"))))
     (build-system cmake-build-system)
     (arguments
      (list #:tests? #f  ;no test
            #:configure-flags
-           #~(list "-DBUILD_SHARED_LIBS=ON" )))
+           #~(list "-DBUILD_SHARED_LIBS=ON"
-    (inputs (list alsa-lib
+                   "-DUSE_EXTERNAL_GLFW=ON"
-                  libx11
+                   "-DCMAKE_C_FLAGS=-lpulse")
-                  libxrandr
+           #:phases
-                  libxi
+           #~(modify-phases %standard-phases
-                  libxinerama
+               (add-before 'configure 'configure-miniaudio
-                  libxcursor
+                 ;; Use PulseAudio as raudio backend.
-                  mesa))
+                 (lambda _
+                   (substitute* "src/raudio.c"
+                     (("^#include \"external/miniaudio\\.h\"") "
+#define MA_NO_RUNTIME_LINKING
+#define MA_ENABLE_ONLY_SPECIFIC_BACKENDS
+#define MA_ENABLE_PULSEAUDIO
+#include \"external/miniaudio.h\"
+")))))))
+    (inputs (list glfw pulseaudio))
     (native-inputs (list pkg-config))
     (synopsis "C library for videogame programming")
     (description
@@ -2884,3 +2894,74 @@ progresses the level, or you may regenerate tiles as the world changes.")
   writing your game.")
     (home-page "https://www.raylib.com/")
     (license license:zlib)))
+
+(define-public bbcsdl
+  (package
+    (name "bbcsdl")
+    (version "1.35a")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/rtrussell/BBCSDL/")
+                    (commit "b9b2a3eb438cb799edb2766055b3c38e9518e3e3")))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1d03xmhrl6ba6w0vwfk46mpyc9d0w3bixxj2d4irx7wl7bh3bfic"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:tests? #f                       ; XXX: tests not automated
+      #:phases
+      #~(modify-phases %standard-phases
+          (delete 'configure)           ; no configure script
+          (replace 'build
+            (lambda* (#:key outputs #:allow-other-keys)
+              ;; 'makefile' expects the source directory to be named 'BBCSDL'.
+              (symlink "source" "../BBCSDL")
+              ;; 'bbcsdl' finds 'libstb.so' in its RPATH.
+              (substitute* "bin/linux/makefile"
+                (("-Wl,-R,'\\$\\$ORIGIN'")
+                 (string-append "-Wl,-rpath="
+                                (assoc-ref outputs "out") "/opt/bbcsdl")))
+              ;; Build 'bbcbasic' and 'bbcsdl'.
+              (invoke "make" "-C" "console/linux")
+              (invoke "make" "-C" "bin/linux")))
+          (replace 'install
+            (lambda* (#:key inputs outputs #:allow-other-keys)
+              (let* ((out (assoc-ref outputs "out"))
+                     (opt (string-append out "/opt/bbcsdl"))
+                     (bin (string-append out "/bin")))
+                (for-each
+                 (lambda (f)
+                   (copy-recursively f (string-append opt "/" f)))
+                 ;; Those files need to be installed into the same difertory.
+                 '("lib" "examples" "bbcsdl.bbc"
+                   "libstb.so" "bbcsdl" "bbcbasic"))
+                ;; Replace bundled fonts.
+                (for-each
+                 (lambda (font)
+                   (delete-file (string-append opt "/lib/" font))
+                   (symlink
+                    (search-input-file
+                     inputs (string-append "share/fonts/truetype/" font))
+                    (string-append opt "/lib/" font)))
+                 '("DejaVuSans.ttf" "DejaVuSansMono.ttf"
+                   "FreeSans.ttf" "FreeMono.ttf" "FreeSerif.ttf"))
+                (mkdir bin)
+                (symlink (string-append opt "/bbcsdl")
+                         (string-append bin "/bbcsdl"))
+                (symlink (string-append opt "/bbcbasic")
+                         (string-append bin "/bbcbasic"))))))))
+    (native-inputs (list nasm))
+    (inputs (list sdl2 sdl2-ttf sdl2-net font-dejavu font-gnu-freefont))
+    (synopsis "BBC BASIC for SDL 2.0")
+    (home-page "https://www.bbcbasic.co.uk/bbcsdl/")
+    (description
+     "BBC BASIC is the programming language originally specified and adopted
+by the British Broadcasting Corporation for its groundbreaking Computer
+Literacy Project of the early 1980s.  BBC BASIC for SDL 2.0 combines the
+simplicity of BASIC with the sophistication of a modern structured language,
+allowing you to write utilities and games, use sound and graphics, perform
+calculations and create complete applications.")
+    (license license:zlib)))

gnu/packages/games.scm

@@ -76,6 +76,8 @@
 ;;; Copyright © 2022 Hendursaga <hendursaga@aol.com>
 ;;; Copyright © 2022 Parnikkapore <poomklao@yahoo.com>
 ;;; Copyright © 2023 Zheng Junjie <873216071@qq.com>
+;;; Copyright © 2023 Florian Pelz <pelzflorian@pelzflorian.de>
+;;; Copyright © 2023 Ivana Drazovic <iv.dra@hotmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -217,6 +219,7 @@
   #:use-module (gnu packages xml)
   #:use-module (guix build-system copy)
   #:use-module (guix build-system cmake)
+  #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
   #:use-module (guix build-system meson)
@@ -4890,7 +4893,7 @@ Transport Tycoon Deluxe.")
               ("freetype" ,freetype)
               ("icu4c" ,icu4c)
               ("jansson" ,jansson)
-              ("json-modern-cxx" ,json-modern-cxx)
+              ("nlohmann-json" ,nlohmann-json)
               ("libpng" ,libpng)
               ("libzip" ,libzip)
               ("mesa" ,mesa)
@@ -5898,22 +5901,37 @@ Linux / Mac OS X servers, and an auto mapper with a VT100 map display.")
              (sha256
               (base32
                "1y6nfxcjhqg9bb81hs0wijg7kcwk5kff81rgd8bsv5ps7ia9nj6b"))
-             (patches (search-patches "laby-make-install.patch"))))
+             (patches (search-patches "laby-make-install.patch"
-    (build-system gnu-build-system)
+                                      "laby-use-tmpdir-from-runtime.patch"))))
+    (build-system glib-or-gtk-build-system)
     (inputs
-     (list lablgtk3 ocaml-lablgtk3-sourceview3 ocaml ocaml-findlib ocamlbuild))
+     (list gdk-pixbuf
+           lablgtk3
+           (librsvg-for-system)
+           ocaml-lablgtk3-sourceview3
+           ocaml
+           ocaml-findlib
+           ocamlbuild))
     (arguments
-     '(#:phases
+     (list #:phases
-       (modify-phases %standard-phases
+           #~(modify-phases %standard-phases
                (delete 'configure)
                (add-before 'build 'set-library-path
                  (lambda* (#:key inputs #:allow-other-keys)
-             (let ((lablgtk (assoc-ref inputs "lablgtk")))
+                   (let ((lablgtk #$(this-package-input "lablgtk")))
                      (setenv "LD_LIBRARY_PATH"
-                       (string-append lablgtk "/lib/ocaml/stublibs"))))))
+                             (string-append lablgtk "/lib/ocaml/stublibs")))))
+               (add-after 'glib-or-gtk-wrap 'wrap-pixbuf
+                  (lambda* (#:key outputs #:allow-other-keys)
+                    (let ((laby (string-append #$output "/bin/laby")))
+                      (wrap-program laby
+                        ;; Wrapping GDK_PIXBUF_MODULE_FILE allows laby to
+                        ;; function in pure environments.
+                        `("GDK_PIXBUF_MODULE_FILE" =
+                          (,(getenv "GDK_PIXBUF_MODULE_FILE"))))))))
            #:tests? #f ; no 'check' target
            #:make-flags
-       (list (string-append "PREFIX=" (assoc-ref %outputs "out")) "all")))
+           #~(list (string-append "PREFIX=" #$output) "all")))
     (home-page "https://sgimenez.github.io/laby/")
     (synopsis "Programming game")
     (description "Learn programming, playing with ants and spider webs ;-)

gnu/packages/gcc.scm

@@ -1043,12 +1043,12 @@ as the 'native-search-paths' field."
           (srfi srfi-26)
           (ice-9 regex)))
        ((#:configure-flags flags)
-        `(cons (string-append "--enable-languages="
+        #~(cons (string-append "--enable-languages="
-                              ,(string-join languages ","))
+                               #$(string-join languages ","))
                 (remove (cut string-match "--enable-languages.*" <>)
-                       ,flags)))
+                        #$flags)))
        ((#:phases phases)
-        `(modify-phases ,phases
+        #~(modify-phases #$phases
             (add-after 'install 'remove-broken-or-conflicting-files
               (lambda* (#:key outputs #:allow-other-keys)
                 (for-each
@@ -1156,7 +1156,7 @@ provides the GNU compiler for the Go programming language.")
       (arguments
        (substitute-keyword-arguments (package-arguments gccgo)
          ((#:phases phases)
-          `(modify-phases ,phases
+          #~(modify-phases #$phases
               (add-after 'install 'wrap-go-with-tool-path
                 (lambda* (#:key outputs #:allow-other-keys)
                   (let* ((out (assoc-ref outputs "out"))
@@ -1177,7 +1177,7 @@ provides the GNU compiler for the Go programming language.")
                   (substitute* "libgo/Makefile.in"
                     (("(GccgoToolDir = \\\")[^\\\"]+" _ start)
                      (string-append start "/nonexistent"))
-                   ,@(if (version>=? (package-version gccgo) "12.0")
+                    #$@(if (version>=? (package-version gccgo) "12.0")
                            '((("(defaultGOROOT = `)[^`]+" _ start)
                               (string-append start "/nonexistent")))
                            '((("(DefaultGoroot = \\\")[^\\\"]+" _ start)

gnu/packages/geo.scm

@@ -8,7 +8,7 @@
 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;; Copyright © 2018, 2019, 2020, 2021 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2019-2023 Guillaume Le Vaillant <glv@posteo.net>
-;;; Copyright © 2019-2022 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2019-2023 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2019, 2021 Wiktor Żelazny <wzelazny@vurv.cz>
 ;;; Copyright © 2019, 2020 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2020, 2022 Marius Bakke <marius@gnu.org>
@@ -1651,10 +1651,11 @@ map display.  Downloads map data from a number of websites, including
                      (url "https://github.com/opengribs/XyGrib")
                      (commit (string-append "v" version))))
               (file-name (git-file-name name version))
-              (patches (search-patches "xygrib-fix-finding-data.patch"))
               (sha256
                (base32
                 "0xzsm8pr0zjk3f8j880fg5n82jyxn8xf1330qmmq1fqv7rsrg9ia"))
+              (patches (search-patches "xygrib-fix-finding-data.patch"
+                                       "xygrib-newer-proj.patch"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -1663,11 +1664,13 @@ map display.  Downloads map data from a number of websites, including
                   ;; Upstream link: https://github.com/opengribs/XyGrib/pull/255
                   (substitute* "src/SkewT.h"
                     (("QMessageBox>") "QMessageBox>\n#include <QPainterPath>"))
-                  #t))))
+                  ;; Accept newer versions of openjpeg
+                  ;; https://github.com/opengribs/XyGrib/pull/298
+                  (substitute* "CMakeLists.txt"
+                    (("openjpeg-2.4") "openjpeg-2.5 openjpeg-2.4"))))))
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags (list "-DGNU_PACKAGE=ON")
-
        #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'patch-directories
@@ -1693,7 +1696,7 @@ map display.  Downloads map data from a number of websites, including
            libnova
            libpng
            openjpeg
-           proj-7
+           proj
            qtbase-5
            zlib))
     (native-search-paths

gnu/packages/gl.scm

@@ -530,9 +530,7 @@ from software emulation to complete hardware acceleration for modern GPUs.")
   (package/inherit mesa
     (name "mesa-opencl")
     (source (origin
-              (inherit (package-source mesa))
+              (inherit (package-source mesa))))
-              (patches (cons (search-patch "mesa-opencl-all-targets.patch")
-                             (origin-patches (package-source mesa))))))
     (arguments
      (substitute-keyword-arguments (package-arguments mesa)
        ((#:configure-flags flags)
@@ -679,25 +677,19 @@ extension functionality is exposed in a single header file.")
 (define-public guile-opengl
   (package
     (name "guile-opengl")
-    (version "0.1.0")
+    (version "0.2.0")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnu/guile-opengl/guile-opengl-"
                                  version ".tar.gz"))
              (sha256
               (base32
-               "13qfx4xh8baryxqrv986l848ygd0piqwm6s2s90pxk9c0m9vklim"))))
+               "0rbc2wf9x63ilj3n85h8wyllzc2b22abmhs2p2ghjgc253n8gw5q"))))
     (build-system gnu-build-system)
     (native-inputs (list pkg-config))
     (inputs (list guile-2.2 mesa glu freeglut))
     (arguments
      '(#:phases (modify-phases %standard-phases
-                 (add-after 'configure 'patch-makefile
-                   (lambda _
-                     ;; Install compiled Guile files in the expected place.
-                     (substitute* '("Makefile")
-                       (("^godir = .*$")
-                        "godir = $(moddir)\n"))))
                  (add-before 'build 'patch-dynamic-link
                    (lambda* (#:key inputs outputs #:allow-other-keys)
                      (substitute* "gl/runtime.scm"
@@ -728,16 +720,6 @@ OpenGL graphics API.")
   (package
     (inherit guile-opengl)
     (name "guile3.0-opengl")
-    (arguments
-     (substitute-keyword-arguments (package-arguments guile-opengl)
-       ((#:phases phases)
-        `(modify-phases ,phases
-           (add-after 'unpack 'build-with-guile-3.0
-             (lambda _
-               (substitute* "configure"
-                 (("_guile_versions_to_search=\"")
-                  "_guile_versions_to_search=\"3.0 "))
-               #t))))))
     (inputs
      (list guile-3.0 mesa glu freeglut))))
 

gnu/packages/gnome.scm

@@ -74,6 +74,8 @@
 ;;; Copyright © 2022 Alexandros Theodotou <alex@zrythm.org>
 ;;; Copyright © 2022 Arjan Adriaanse <arjan@adriaan.se>
 ;;; Copyright © 2023 Kaelyn Takata <kaelyn.alexi@protonmail.com>
+;;; Copyright © 2023 Juliana Sims <juli@incana.org>
+;;; Copyright © 2023 Dominik Delgado Steuter <d@delgado.nrw>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1951,8 +1953,8 @@ and system administrators.")
   ;; recent versions of the build tools.  The latest activity on the
   ;; pre-GNOME version has been in 2014, while GNOME has continued applying
   ;; fixes since.
-  (let ((commit "0997887d97f01be28bf3886dfd3e2002de437930")
+  (let ((commit "b903dd83aa5aab1b41c7864dd5027d1b6a0a190c")
-        (revision "3"))
+        (revision "4"))
     (package
       (name "dia")
       (version (git-version "0.97.3" revision commit))
@@ -1964,7 +1966,7 @@ and system administrators.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "199b4n1jydg1g9lnz0r8xx67h7s2ac2lfj89zp015lbs0qqfkmsh"))))
+                  "0j5q7whwpzzfsinjryp3g0xh3cyy88drwyr0w8x0666mj6h70h6a"))))
       (build-system meson-build-system)
       ;; XXX: Parallel builds may cause: [74/566] [...]
       ;; fatal error: dia-lib-enums.h: No such file or directory
@@ -10408,6 +10410,45 @@ to perfectly fit the GNOME desktop.")
 (define-public gnome-todo
   (deprecated-package "gnome-todo" endeavour))
 
+(define-public dialect
+  (package
+    (name "dialect")
+    (version "2.1.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/dialect-app/dialect")
+                    (commit version)
+                    (recursive? #t))) ;po module
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0wac9r33zslyhvadyj7iaapskk7f9pfvia7zlqfksfhkaji6gmna"))))
+    (build-system meson-build-system)
+    (arguments
+     `(#:glib-or-gtk? #t))
+    (native-inputs (list blueprint-compiler
+                         desktop-file-utils
+                         `(,glib "bin")
+                         gnu-gettext
+                         gobject-introspection
+                         `(,gtk "bin")
+                         pkg-config))
+    (propagated-inputs (list gstreamer
+                             libadwaita
+                             libsoup
+                             python
+                             python-gtts
+                             python-pygobject
+                             python-requests))
+    (home-page "https://apps.gnome.org/app/app.drey.Dialect")
+    (synopsis "Translation application for GNOME")
+    (description
+     "Dialect is a simple translation application that uses Google Translate
+(default), LibreTranslate or Lingva Translate.  It includes features
+like automatic language detection, text-to-speech and clipboard buttons.")
+    (license license:gpl3+)))
+
 (define-public gnome-dictionary
   (package
     (name "gnome-dictionary")
@@ -12305,42 +12346,29 @@ non-privileged user.")
 (define-public geary
   (package
     (name "geary")
-    (version "40.0")
+    (version "43.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://gitlab.gnome.org/GNOME/geary.git")
-                    (commit (string-append "gnome-" version))))
+                    (commit version)))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "04hvw86r8sczvjm1z3ls5y5y5h6nyfb648rjkfx05ib00mqq5v1x"))))
+                "05b8c5ljzx1ly7wq8jzpv8psxmsdlz395sr17xwj49nh495nflz5"))))
     (build-system meson-build-system)
     (arguments
-     `(#:glib-or-gtk? #t
+     (list #:glib-or-gtk? #t
            #:configure-flags
-       '("-Dprofile=release")
+           #~(list "-Dprofile=release")
-       #:phases (modify-phases %standard-phases
+           #:phases
-                  (add-after 'unpack 'disable-failing-tests
+           #~(modify-phases %standard-phases
+               (add-after 'unpack 'skip-gtk-update-icon-cache
+                 ;; Don't create 'icon-theme.cache'.
                  (lambda _
-                      (substitute* "test/test-client.vala"
+                   (substitute* "meson.build"
-                        (("client.add_suite\\(new Application.CertificateManagerTest\\(\\).suite\\);")
+                     (("gtk_update_icon_cache: true")
-                         ""))))
+                      "gtk_update_icon_cache: false"))))
-                  (add-after 'unpack 'generate-vapis
-                    (lambda* (#:key inputs #:allow-other-keys)
-                      ;; It’s not possible to generate the GMime vapi, because
-                      ;; there’s custom metadata that gmime didn’t
-                      ;; install. Thus, the vapi should be built and installed
-                      ;; with gmime.
-                      (define gmime
-                        (assoc-ref inputs "gmime"))
-                      (copy-file (string-append gmime "/share/vala/vapi/gmime-3.0.vapi")
-                                 "bindings/vapi/gmime-3.0.vapi")))
-                  (add-after 'unpack 'disable-postinstall-script
-                    (lambda _
-                      (substitute* "build-aux/post_install.py"
-                        (("gtk-update-icon-cache")
-                         "true"))))
                (add-before 'check 'setup-home
                  (lambda _
                    ;; Tests require a writable HOME.
@@ -12351,11 +12379,11 @@ non-privileged user.")
                    (setenv "DISPLAY" ":1"))))))
     (inputs
      (list enchant
-           folks-with-libsoup2
+           folks
            gcr
            glib
            gmime
-           gnome-online-accounts-3.44
+           gnome-online-accounts
            gsettings-desktop-schemas
            gspell
            gsound
@@ -12370,18 +12398,16 @@ non-privileged user.")
            libstemmer
            libunwind
            sqlite
-           webkitgtk-with-libsoup2
+           webkitgtk
            ytnef))
     (native-inputs
      (list appstream-glib
            cmake-minimal
            desktop-file-utils
            gettext-minimal
-           glib
            `(,glib "bin")
-           gmime
+           gnutls                       ; for certtool
            gobject-introspection
-           gsettings-desktop-schemas
            itstool
            libarchive
            libxml2

gnu/packages/graphics.scm

@@ -2328,7 +2328,9 @@ Features include:
                              "cmd/generate_density_map/main.cpp"
                              "cmd/generate_sdf/main.cpp")
                 (("^#include <cxxopts/cxxopts\\.hpp>")
-                 "#include <cxxopts.hpp>"))))))
+                 "#include <cxxopts.hpp>")
+                (("cxxopts::OptionException")
+                 "cxxopts::exceptions::parsing"))))))
       (build-system cmake-build-system)
       (outputs '("out" "bin"))
       (arguments
@@ -2481,7 +2483,7 @@ a tetrahedral mesh, isovalue discretization and Lagrangian movement;
 (define-public f3d
   (package
     (name "f3d")
-    (version "1.3.1")
+    (version "2.0.0")
     (source
      (origin
        (method git-fetch)
@@ -2490,16 +2492,21 @@ a tetrahedral mesh, isovalue discretization and Lagrangian movement;
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0hdfgwf5d24ykab634xg4vv9r09nh96ss7hhnqnh5nmw4abhxzg7"))
+        (base32 "1gcwpdkz3ylaxi133zri1cxkvj6za5s1hbgqqc8fn10q2dkkdd44"))
        (modules '((guix build utils)))
        (snippet
         #~(begin
-            (delete-file "application/cxxopts.hpp")
+            (delete-file "external/cxxopts.hpp")
-            (delete-file "application/json.hpp")
+            (delete-file "external/json.hpp")
             (substitute* "application/F3DOptionsParser.cxx"
               (("^#include \"cxxopts\\.hpp\"")
                "#include <cxxopts.hpp>")
               (("^#include \"json\\.hpp\"")
+               "#include <nlohmann/json.hpp>")
+              (("cxxopts::OptionException")
+               "cxxopts::exceptions::parsing"))
+            (substitute* "library/src/engine.cxx"
+              (("^#include <json\\.hpp>")
                "#include <nlohmann/json.hpp>"))))))
     (build-system cmake-build-system)
     ;; The package cannot easily be split into out and lib outputs because
@@ -2535,7 +2542,7 @@ a tetrahedral mesh, isovalue discretization and Lagrangian movement;
     (native-inputs
      (list cxxopts
            help2man
-           json-modern-cxx))
+           nlohmann-json))
     (inputs
      (list alembic
            assimp

gnu/packages/graphviz.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2015, 2021 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2015, 2021, 2023 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015, 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Theodoros Foradis <theodoros@foradis.org>
 ;;; Copyright © 2017, 2018, 2019, 2022 Ricardo Wurmus <rekado@elephly.net>
@@ -124,6 +124,13 @@ interfaces for other technical domains.")
      '((release-monitoring-url . "https://graphviz.org/download/source/")))
     (license license:epl1.0)))
 
+(define-public graphviz-minimal
+  (package/inherit graphviz
+    (name "graphviz-minimal")
+    (inputs (modify-inputs (package-inputs graphviz)
+              (delete "libxrender" "libx11" "pango" "libxaw")))
+    (synopsis "Graph visualization software (without X11 support)")))
+
 (define-public python-graphviz
   (package
     (name "python-graphviz")

gnu/packages/guile-xyz.scm

@@ -733,7 +733,7 @@ you send to a FIFO file.")
 (define-public guile-dsv
   (package
     (name "guile-dsv")
-    (version "0.5.2")
+    (version "0.6.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -742,7 +742,7 @@ you send to a FIFO file.")
               (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "056wab749fyabklp4srai72dwzihlm6hkcdy1da7d4gh8iqsyqpi"))))
+                "0llivcgb7idglsapcmvb2qscds7768f2xfgr4lns8mzl2xf5hwvv"))))
     (build-system gnu-build-system)
     (native-inputs
      (list autoconf automake pkg-config texinfo help2man))
@@ -2034,7 +2034,7 @@ provides tight coupling to Guix.")
 (define-public guile-ics
   (package
     (name "guile-ics")
-    (version "0.4.0")
+    (version "0.5.0")
     (source
      (origin
        (method git-fetch)
@@ -2044,7 +2044,7 @@ provides tight coupling to Guix.")
        (file-name (string-append name "-" version "-checkout"))
        (sha256
         (base32
-         "1wjkba135iipwqrp14c3q6wpbjhglp9d12is16lj8l81xyv8gjn3"))))
+         "1ipryn69ad4viqai9pnwhkqqpf9wgw0m2qxrwkfrpm1bfdyilw9w"))))
     (build-system gnu-build-system)
     (arguments
      (list #:phases #~(modify-phases %standard-phases
@@ -3843,7 +3843,7 @@ debugging code.")
 (define-public guile-png
   (package
     (name "guile-png")
-    (version "0.3.0")
+    (version "0.4.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -3852,22 +3852,19 @@ debugging code.")
               (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "1lv2cjzgrr0yshqng96l6bnn8pjmljv8qcn4w3wldh97ns7qigds"))))
+                "1vkhv0dip0na6d9g478i587n5y6046vn5rsjmfnbibi9yx4rkrf8"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:make-flags '("GUILE_AUTO_COMPILE=0") ;to prevent guild warnings
+     `(#:make-flags '("GUILE_AUTO_COMPILE=0"))) ;to prevent guild warnings
-       #:phases
+    (native-inputs (list autoconf
-       (modify-phases %standard-phases
+                         automake
-         ;; Guile-PNG tries to log parser messages to the syslog which is not
+                         pkg-config
-         ;; available during the build.
+                         texinfo
-         (add-after 'unpack 'fix-tests
+                         ;; needed when cross-compiling.
-           (lambda* (#:key inputs outputs #:allow-other-keys)
+                         guile-3.0
-             (substitute* "tests/graphics.scm"
+                         guile-lib
-               (("             \\(png graphics\\)\\)")
+                         guile-zlib
-                (string-append "             (png graphics)\n"
+                         guile-smc))
-                               "             (png fsm context))\n"
-                               "(log-clear-handlers!)"))))))))
-    (native-inputs (list autoconf automake pkg-config texinfo))
     (inputs (list bash-minimal guile-3.0 guile-lib guile-zlib))
     (propagated-inputs (list guile-smc))
     (home-page "https://github.com/artyom-poptsov/guile-png")
@@ -5208,7 +5205,7 @@ locations.")
 (define-public guile-netlink
   (package
     (name "guile-netlink")
-    (version "1.1.1")
+    (version "1.1.2")
     (source
      (origin
        (method git-fetch)
@@ -5218,7 +5215,7 @@ locations.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0jcl6mzqy04if5drflmygmggbgzsxa42mlmskqb3cfqmksq0zj0y"))))
+         "1s06xbyj0yd49aivfpc9l73c8c12r3zjmskkyislrfwkbpd74hjr"))))
     (build-system gnu-build-system)
     (inputs
      (list guile-3.0))
@@ -5304,7 +5301,7 @@ GitLab instance.")
 (define-public guile-smc
   (package
     (name "guile-smc")
-    (version "0.5.2")
+    (version "0.6.0")
     (source
      (origin
        (method git-fetch)
@@ -5314,7 +5311,7 @@ GitLab instance.")
        (file-name (string-append name "-" version))
        (sha256
         (base32
-         "05q20vi59whjs7jb8bgcxnnfy6c3wx26m5ps2fwlsz52nggarxzb"))))
+         "15b8m30kjl46p44xjd65vv1bv60hy130zfskkcsrj10fzahyk9zd"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags '("GUILE_AUTO_COMPILE=0")     ;to prevent guild warnings
@@ -5344,7 +5341,15 @@ GitLab instance.")
                    (,(string-append out go)
                     ,(string-append guile-lib go))))))))))
     (native-inputs
-     (list autoconf automake pkg-config texinfo help2man which))
+     (list autoconf
+           automake
+           pkg-config
+           texinfo
+           help2man
+           which
+           ;; needed when cross-compiling.
+           guile-3.0
+           guile-lib))
     (inputs
      (list bash-minimal guile-3.0 guile-lib inetutils))
     (home-page "https://github.com/artyom-poptsov/guile-smc")
@@ -5375,7 +5380,7 @@ with a FSM is being built (for example, from a Makefile.)")
 (define-public guile-ini
   (package
     (name "guile-ini")
-    (version "0.5.2")
+    (version "0.5.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -5384,13 +5389,20 @@ with a FSM is being built (for example, from a Makefile.)")
               (file-name (string-append name "-" version))
               (sha256
                (base32
-                "17fbys3gsfyx4f77a2fswirx76dlr57il2z27z77wljaz777jk36"))))
+                "03pdbas7f6r2q3jbcn68xpm57hika3byb4rhsf0544kw6yk3bm8q"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags '("GUILE_AUTO_COMPILE=0") ;to prevent guild warnings
        #:phases (modify-phases %standard-phases
                   (delete 'strip))))
-    (native-inputs (list autoconf automake pkg-config texinfo))
+    (native-inputs (list autoconf
+                         automake
+                         pkg-config
+                         texinfo
+                         ;; needed when cross-compiling.
+                         guile-3.0
+                         guile-lib
+                         guile-smc))
     (inputs (list bash-minimal guile-3.0 guile-lib))
     (propagated-inputs (list guile-smc))
     (home-page "https://github.com/artyom-poptsov/guile-ini")

gnu/packages/hardware.scm

@@ -1059,7 +1059,7 @@ technology, such as head mounted displays with built in head tracking.")
                   (string-append #$(this-package-input "hueplusplus")
                                  "/include/hueplusplus"))
                  (("dependencies/json")
-                  (string-append #$(this-package-input "json-modern-cxx")
+                  (string-append #$(this-package-input "nlohmann-json")
                                  "/include/nlohmann")))))
            ;; Call qmake instead of configure to create a Makefile.
            (replace 'configure
@@ -1067,7 +1067,7 @@ technology, such as head mounted displays with built in head tracking.")
     (inputs
      (list hidapi
            hueplusplus
-           json-modern-cxx
+           nlohmann-json
            libusb
            mbedtls-apache
            qtbase-5))

gnu/packages/haskell-apps.scm

@@ -294,13 +294,13 @@ to @code{cabal repl}).")
 (define-public git-annex
   (package
     (name "git-annex")
-    (version "10.20230321")
+    (version "10.20230407")
     (source
      (origin
        (method url-fetch)
        (uri (hackage-uri "git-annex" version))
        (sha256
-        (base32 "1lbv0jzfr6knjcqd2ik4k2dw7brsnjmn33qwijpgivnsbf1q0ibz"))))
+        (base32 "19500i3xcmxbh990kmdqimknlpk55z5iz9lnm3w35g8hmrpfh0d0"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "git-annex")))
     (arguments

gnu/packages/haskell-check.scm

@@ -148,7 +148,13 @@ contains the correct result for the test.")
                 "006bf4gyc30i2gvb17hj1mzrh1kwnwf7l050x3f72wi6c2axl87l"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "tasty")))
-    (inputs (list ghc-tagged ghc-optparse-applicative ghc-ansi-terminal))
+    (inputs
+      (append
+        (list ghc-tagged ghc-optparse-applicative ghc-ansi-terminal)
+        ;; TODO: Add ghc-unbounded-delays unconditionally on next rebuild cycle.
+        (if (member (%current-system) '("i686-linux"))
+            (list ghc-unbounded-delays)
+            '())))
     (home-page "https://github.com/UnkindPartition/tasty")
     (synopsis "Modern and extensible testing framework")
     (description

gnu/packages/image-processing.scm

@@ -1213,7 +1213,7 @@ in 3D or programmatically using ParaView’s batch processing capabilities.")
            glew
            gmsh
            hdf5
-           ;;json-modern-cxx              ;For ParFlow; build fails
+           ;;nlohmann-json                ;For ParFlow; build fails
            jsoncpp
            libjpeg-turbo
            libogg

gnu/packages/image-viewers.scm

@@ -112,7 +112,7 @@
 (define-public ytfzf
   (package
     (name "ytfzf")
-    (version "2.5.2")
+    (version "2.6.0")
     (home-page "https://github.com/pystardust/ytfzf")
     (source
      (origin
@@ -123,7 +123,7 @@
          (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "138rqjjyh6ar951v0v5sl1v000ja8zznn141qqw8ymx5h2z44r6w"))))
+        (base32 "19wmzpbc23515ab4v4pw792x68y7bgsqhd2pmlqiq6bp6jxfrykg"))))
     (build-system gnu-build-system)
     (arguments
      (list
@@ -829,14 +829,14 @@ with tiling window managers.  Features include:
 (define-public qiv
   (package
     (name "qiv")
-    (version "2.3.2")
+    (version "2.3.3")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "http://spiegl.de/qiv/download/qiv-"
                            version ".tgz"))
        (sha256
-        (base32 "1mc0f2nnas4q0d7zc9r6g4z93i32xlx0p9hl4fn5zkyml24a1q28"))
+        (base32 "011pad6gvmpphiv85yq820w3m79m3spfafarcsrhb2ylwbymy27g"))
        (modules '((guix build utils)))
        (snippet
         '(begin

gnu/packages/image.scm

@@ -2043,7 +2043,7 @@ identical visual appearance.")
 (define-public slurp
   (package
    (name "slurp")
-   (version "1.3.2")
+   (version "1.4.0")
    (source
     (origin
      (method git-fetch)
@@ -2052,7 +2052,7 @@ identical visual appearance.")
            (commit (string-append "v" version))))
      (file-name (git-file-name name version))
      (sha256
-      (base32 "00dx6ds1227qnxqrw58k0am78q8fa49rgp1zingrkjcbpbi7g475"))))
+      (base32 "1i6g4dfiv2mwkjvvrx3wizb1n05xmd4j9nkhdii4klwd1gdrhjwd"))))
    (build-system meson-build-system)
    (native-inputs
     (list pkg-config scdoc))

gnu/packages/irc.scm

@@ -155,7 +155,7 @@ irssi, but graphical.")
 (define-public irssi
   (package
     (name "irssi")
-    (version "1.4.3")
+    (version "1.4.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/irssi/irssi/"
@@ -163,7 +163,7 @@ irssi, but graphical.")
                                   version ".tar.xz"))
               (sha256
                (base32
-                "0d04bam0lrk66wi7ygd5si5y6adf2ajhh6mn89zyc8m34d972gxr"))))
+                "1bby23mn7318dmxf8aw9ahs6j4mbc0ilm4swji4m8ixiqz49xzpy"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases

gnu/packages/irods.scm

@@ -143,7 +143,7 @@
        ("boost" ,boost-for-irods)
        ("cppzmq" ,cppzmq)
        ("fmt" ,fmt-6)
-       ("json" ,json-modern-cxx)
+       ("json" ,nlohmann-json)
        ("libarchive" ,libarchive)
        ("libcxxabi" ,libcxxabi-6) ; we need this for linking with -lc++abi
        ("linux-pam" ,linux-pam)
@@ -247,7 +247,7 @@ stored.")
        ("cppzmq" ,cppzmq)
        ("fmt" ,fmt-6)
        ("irods" ,irods)
-       ("json" ,json-modern-cxx)
+       ("json" ,nlohmann-json)
        ("libarchive" ,libarchive)
        ("libcxxabi" ,libcxxabi-6)     ; we need this for linking with -lc++abi
        ("mit-krb5" ,mit-krb5)

gnu/packages/jupyter.scm

@@ -196,7 +196,7 @@ Messaging Protocol}.")
            python-jupyter-client))
     (inputs
      (list xtl
-           json-modern-cxx
+           nlohmann-json
            cppzmq
            zeromq
            openssl

gnu/packages/linux.scm

@@ -66,7 +66,7 @@
 ;;; Copyright © 2022 Artyom V. Poptsov <poptsov.artyom@gmail.com>
 ;;; Copyright © 2022 Rene Saavedra <nanuui@protonmail.com>
 ;;; Copyright © 2022 muradm <mail@muradm.net>
-;;; Copyright © 2022 Denis 'GNUtoo' Carikli <GNUtoo@cyberdimension.org>
+;;; Copyright © 2022, 2023 Denis 'GNUtoo' Carikli <GNUtoo@cyberdimension.org>
 ;;; Copyright © 2022 Hunter Jozwiak <hunter.t.joz@gmail.com>
 ;;; Copyright © 2022 Hilton Chain <hako@ultrarare.space>
 ;;; Copyright © 2022 Stefan <stefan-guix@vodafonemail.de>
@@ -485,32 +485,47 @@ 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-6.2-version "6.2.14")
+(define-public linux-libre-6.3-version "6.3.3")
+(define-public linux-libre-6.3-gnu-revision "gnu")
+(define deblob-scripts-6.3
+  (linux-libre-deblob-scripts
+   linux-libre-6.3-version
+   linux-libre-6.3-gnu-revision
+   (base32 "01ivgzq18fwas87q84jx9jipcw58kwdnch7ylwg06d98ncga27px")
+   (base32 "10n0ya7y4k96hggylcmymwfj1d07vhpzkz7qamqz7n96jqj1fnpi")))
+(define-public linux-libre-6.3-pristine-source
+  (let ((version linux-libre-6.3-version)
+        (hash (base32 "1ra4kr9bp1s9d7amvz6ik1q3chwps5lysn37b28770pfdim22xc9")))
+   (make-linux-libre-source version
+                            (%upstream-linux-source version hash)
+                            deblob-scripts-6.3)))
+
+(define-public linux-libre-6.2-version "6.2.16")
 (define-public linux-libre-6.2-gnu-revision "gnu")
 (define deblob-scripts-6.2
   (linux-libre-deblob-scripts
    linux-libre-6.2-version
    linux-libre-6.2-gnu-revision
-   (base32 "15wrksnimwb099qgqc631rp8dgv5b61l6s5kknk23frqdwkp4shp")
+   (base32 "03jd3ijbdql44m89fnzwp3mlygs735n4ga7mighlfbdybfjzwfyj")
-   (base32 "0560xc8l2z79qk2dnv15i0m4igw9mq2ymv2a40nw2z3lcqygcs5x")))
+   (base32 "15q27ji6k67a1m94lj0hs47sd072fmb1p575r7g6mq8pl9yynbrl")))
 (define-public linux-libre-6.2-pristine-source
   (let ((version linux-libre-6.2-version)
-        (hash (base32 "0ab756x6baza5wmi0r836g7z0hkvby65g0k6n1sd95nl16irzg0f")))
+        (hash (base32 "04w76lfkfiq7z4dl3cnq6yiqmiwjayhw3n7n81hv8d3919w0vzq6")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-6.2)))
 
-(define-public linux-libre-6.1-version "6.1.27")
+(define-public linux-libre-6.1-version "6.1.29")
 (define-public linux-libre-6.1-gnu-revision "gnu")
 (define deblob-scripts-6.1
   (linux-libre-deblob-scripts
    linux-libre-6.1-version
    linux-libre-6.1-gnu-revision
-   (base32 "10igxhqvlh5ar98i68xf5w9ywfb9l05vg20s8yxmgc62pj72h0yi")
+   (base32 "1b96867b46m36l88qnq2d4i9y43ghw97z9jajrh11cvb6kq4xi67")
-   (base32 "0cchdhjra74zanyk14brv2l2dvxpg8dn58rn477lgfb44mcnhq33")))
+   (base32 "12p6z91fmdqwnmkw0cjha4gl7kzija8fk7yxciznz1raxix6bq57")))
 (define-public linux-libre-6.1-pristine-source
   (let ((version linux-libre-6.1-version)
-        (hash (base32 "01grx5y48scyyihpj176knn5yvgpxv2gfkli03rwj31xvnb4pdy2")))
+        (hash (base32 "1yzwp0496j63c6lhvsni1ynr8b2cpn552pli3nd3fdk0pp4nqwqy")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-6.1)))
@@ -518,67 +533,67 @@ 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-5.15-version "5.15.110")
+(define-public linux-libre-5.15-version "5.15.112")
 (define-public linux-libre-5.15-gnu-revision "gnu")
 (define deblob-scripts-5.15
   (linux-libre-deblob-scripts
    linux-libre-5.15-version
    linux-libre-5.15-gnu-revision
-   (base32 "0vj60bra81fmbx3lz924czbhxs4dmvd4d584g9mcs80b7c4q52kg")
+   (base32 "0w5wyw8zp124nwydjvpnih7q3lp7gadlgsw60syw45nqq0afvlz3")
-   (base32 "03hwhwbcicwyx5i30d6m715kwgrxz4h21xhk55wnawlk8zhx3r35")))
+   (base32 "00n8c7ghfs36bvz0yjw6w9daf5zcgj94kxxn27bfyfm274rkddmz")))
 (define-public linux-libre-5.15-pristine-source
   (let ((version linux-libre-5.15-version)
-        (hash (base32 "0nqbhgafl513pdfn55j608829bsw8kn0v616gblxqy4rgg3zqacq")))
+        (hash (base32 "0lfnd8mpb3nzvd0gk0jbls3zx7y5kskc4kgccjgkc34flgdyps5h")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.15)))
 
-(define-public linux-libre-5.10-version "5.10.179")
+(define-public linux-libre-5.10-version "5.10.180")
 (define-public linux-libre-5.10-gnu-revision "gnu1")
 (define deblob-scripts-5.10
   (linux-libre-deblob-scripts
    linux-libre-5.10-version
    linux-libre-5.10-gnu-revision
    (base32 "0mw7qn77y9c6wrnw4rjvf75cpm1w6n1aqqhf8cnghcb97p2yxxrf")
-   (base32 "1g4vabfswxzf9ahxc06k2ffksf84kcr2csx4m5kx680w0jqqnk80")))
+   (base32 "12jhak2bw1jy2jk70vrm66kjvh0cd6c8f2qiy2bk40rq7bf62mr6")))
 (define-public linux-libre-5.10-pristine-source
   (let ((version linux-libre-5.10-version)
-        (hash (base32 "0abylcqbzpxxh45kmvd9i2cig64aajz87j5c8vm3w1ab2mf49g8v")))
+        (hash (base32 "0a8cicvcyl5w4vi7gxhgd59ny44gj9cbv4z5pnwn9jgny55rm0ys")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.10)))
 
-(define-public linux-libre-5.4-version "5.4.242")
+(define-public linux-libre-5.4-version "5.4.243")
 (define-public linux-libre-5.4-gnu-revision "gnu1")
 (define deblob-scripts-5.4
   (linux-libre-deblob-scripts
    linux-libre-5.4-version
    linux-libre-5.4-gnu-revision
    (base32 "1nlgk8ajb5wl3aa96h9a0pb9j5a5wmrbpk63varn557x1d00r7wj")
-   (base32 "1d6as1yk9svysh07hdybs8glvn8s9f8gwlbjl7f9m920pdam2r60")))
+   (base32 "070j069sj6spy2wkzfzm1d5jd7pffm0s1m917wblc8d3x8pbgvf8")))
 (define-public linux-libre-5.4-pristine-source
   (let ((version linux-libre-5.4-version)
-        (hash (base32 "0a7wfi84p74qsnbj1vamz4qxzp94v054jp1csyfl0blz3knrlbql")))
+        (hash (base32 "017b1xhmjpmiq48pzzx36wn6jwwgaq2kgia51h7pxr7fxr7ndky3")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.4)))
 
-(define-public linux-libre-4.19-version "4.19.282")
+(define-public linux-libre-4.19-version "4.19.283")
 (define-public linux-libre-4.19-gnu-revision "gnu1")
 (define deblob-scripts-4.19
   (linux-libre-deblob-scripts
    linux-libre-4.19-version
    linux-libre-4.19-gnu-revision
    (base32 "06pqv050bkii0hc2v7ymny5264w1bca8db0dp1pw9mfmjg865am5")
-   (base32 "1q0fgpbdwc21wj9wnjjb49dp84ch6ymd5na3iaabadwjs2nmb6bd")))
+   (base32 "05yqb59gj7mq5ha9xg045bz517sdg6janfa2yjq70qa6ahpc5fac")))
 (define-public linux-libre-4.19-pristine-source
   (let ((version linux-libre-4.19-version)
-        (hash (base32 "02z20879xl4ya957by1p35vi1a7myzxwiqd9cnvm541sgnci99a3")))
+        (hash (base32 "1x2irhiv20aq2mrgqyz18d147shbmghwfxq4qi0sv5vc1k91cwq4")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.19)))
 
-(define-public linux-libre-4.14-version "4.14.314")
+(define-public linux-libre-4.14-version "4.14.315")
 (define-public linux-libre-4.14-gnu-revision "gnu1")
 (define deblob-scripts-4.14
   (linux-libre-deblob-scripts
@@ -588,7 +603,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
    (base32 "1ccggm19nl7pdcxmsm08fkqy8phz8rqfmww5ypizibdmnrmpn2v9")))
 (define-public linux-libre-4.14-pristine-source
   (let ((version linux-libre-4.14-version)
-        (hash (base32 "0lwiykv2ci7lrjvvykbiqavzzizdkf8xxqlybixi9l1as7q02v47")))
+        (hash (base32 "17f9cbinysazllrxkv1qlhgi3x61isi7jqrv0qlfpjh69k1waim3")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.14)))
@@ -621,6 +636,11 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
     (patches (append (origin-patches source)
                      patches))))
 
+(define-public linux-libre-6.3-source
+  (source-with-patches linux-libre-6.3-pristine-source
+                       (list %boot-logo-patch
+                             %linux-libre-arm-export-__sync_icache_dcache-patch)))
+
 (define-public linux-libre-6.2-source
   (source-with-patches linux-libre-6.2-pristine-source
                        (list %boot-logo-patch
@@ -737,6 +757,11 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
     (description "Headers of the Linux-Libre kernel.")
     (license license:gpl2)))
 
+(define-public linux-libre-headers-6.3
+  (make-linux-libre-headers* linux-libre-6.3-version
+                             linux-libre-6.3-gnu-revision
+                             linux-libre-6.3-source))
+
 (define-public linux-libre-headers-6.2
   (make-linux-libre-headers* linux-libre-6.2-version
                              linux-libre-6.2-gnu-revision
@@ -1080,6 +1105,14 @@ Linux kernel.  It has been modified to remove all non-free binary blobs.")
 ;;; Generic kernel packages.
 ;;;
 
+(define-public linux-libre-6.3
+  (make-linux-libre* linux-libre-6.3-version
+                     linux-libre-6.3-gnu-revision
+                     linux-libre-6.3-source
+                     '("x86_64-linux" "i686-linux" "armhf-linux"
+                       "aarch64-linux" "powerpc64le-linux" "riscv64-linux")
+                     #:configuration-file kernel-config))
+
 (define-public linux-libre-6.2
   (make-linux-libre* linux-libre-6.2-version
                      linux-libre-6.2-gnu-revision
@@ -1088,11 +1121,11 @@ Linux kernel.  It has been modified to remove all non-free binary blobs.")
                        "aarch64-linux" "powerpc64le-linux" "riscv64-linux")
                      #:configuration-file kernel-config))
 
-(define-public linux-libre-version         linux-libre-6.2-version)
+(define-public linux-libre-version         linux-libre-6.3-version)
-(define-public linux-libre-gnu-revision    linux-libre-6.2-gnu-revision)
+(define-public linux-libre-gnu-revision    linux-libre-6.3-gnu-revision)
-(define-public linux-libre-pristine-source linux-libre-6.2-pristine-source)
+(define-public linux-libre-pristine-source linux-libre-6.3-pristine-source)
-(define-public linux-libre-source          linux-libre-6.2-source)
+(define-public linux-libre-source          linux-libre-6.3-source)
-(define-public linux-libre                 linux-libre-6.2)
+(define-public linux-libre                 linux-libre-6.3)
 
 (define-public linux-libre-6.1
   (make-linux-libre* linux-libre-6.1-version
@@ -1323,9 +1356,9 @@ Linux kernel.  It has been modified to remove all non-free binary blobs.")
 (define-public linux-libre-with-bpf
   (let ((base-linux-libre
          (make-linux-libre*
-          linux-libre-6.2-version
+          linux-libre-6.3-version
-          linux-libre-6.2-gnu-revision
+          linux-libre-6.3-gnu-revision
-          linux-libre-6.2-source
+          linux-libre-6.3-source
           '("x86_64-linux" "i686-linux" "armhf-linux"
             "aarch64-linux" "powerpc64le-linux" "riscv64-linux")
           #:extra-version "bpf"
@@ -1336,7 +1369,10 @@ Linux kernel.  It has been modified to remove all non-free binary blobs.")
     (package
       (inherit base-linux-libre)
       (inputs (modify-inputs (package-inputs base-linux-libre)
-                (prepend cpio))))))
+                (prepend cpio)))
+      (synopsis "Linux-libre with BPF support")
+      (description "This package provides GNU Linux-Libre with support
+for @acronym{BPF, the Berkeley Packet Filter}."))))
 
 
 ;;;
@@ -5880,24 +5916,33 @@ and copy/paste text in the console and in xterm.")
 (define-public btrfs-progs
   (package
     (name "btrfs-progs")
-    (version "6.1.2")
+    (version "6.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://kernel.org/linux/kernel/"
-                                  "people/kdave/btrfs-progs/"
+                                  "people/kdave/btrfs-progs/" "btrfs-progs-v"
-                                  "btrfs-progs-v" version ".tar.xz"))
+                                  version ".tar.xz"))
               (sha256
                (base32
-                "0ylxszcsm0jqsa5glccd1pv3rcfk1f5wjcf3ayxc0r9xgzcngrkb"))))
+                "0zbampc47nq3h8as3rda2apns5sj93ywxnrkal74kjvyg3zvv820"))))
     (build-system gnu-build-system)
-    (outputs '("out"
+    (outputs '("out" "static")) ;static versions of the binaries in "out"
-               "static"))      ; static versions of the binaries in "out"
     (arguments
-     '(#:configure-flags
+     (list
+      #:configure-flags
+      #~(append
+         ;; Without --disable-documentation, it complains about missing
+         ;; python-sphinx on systems where this package isn't available
+         ;; (because it requires Rust).
+         (if #$@(member (%current-system)
+                        (package-transitive-supported-systems
+                         python-sphinx))
+             '()
+             (list "--disable-documentation"))
          ;; The ‘Python support’ was never actually installed by previous
          ;; versions of this package, but did prevent cross-compilation.
-       (list "--disable-python")
+         (list "--disable-python"))
-       #:phases (modify-phases %standard-phases
+      #:phases #~(modify-phases %standard-phases
                    (add-after 'unpack 'patch-makefile
                      (lambda* (#:key outputs #:allow-other-keys)
                        (substitute* "Makefile"
@@ -5905,16 +5950,19 @@ and copy/paste text in the console and in xterm.")
                           (string-append (assoc-ref outputs "out")
                                          "/lib/udev/rules.d")))))
                    (add-after 'build 'build-static
-                   (lambda _ (invoke "make" "static")))
+                     (lambda _
+                       (invoke "make" "static")))
                    (add-after 'install 'install-bash-completion
                      (lambda* (#:key outputs #:allow-other-keys)
                        (let* ((out (assoc-ref outputs "out"))
-                            (bashcomp (string-append out "/etc/bash_completion.d")))
+                              (bashcomp (string-append out
+                                                       "/etc/bash_completion.d")))
                          (mkdir-p bashcomp)
                          (copy-file "btrfs-completion"
                                     (string-append bashcomp "/btrfs")))))
                    (add-after 'install 'install-static
-                   (let ((staticbin (string-append (assoc-ref %outputs "static")
+                     (let ((staticbin (string-append (assoc-ref %outputs
+                                                                "static")
                                                      "/bin")))
                        (lambda _
                          (invoke "make"
@@ -5923,29 +5971,34 @@ and copy/paste text in the console and in xterm.")
        #:tests? #f ;XXX: require the 'btrfs' kernel module.
        #:test-target "test"
        #:parallel-tests? #f)) ;tests fail when run in parallel
-    (inputs `(("e2fsprogs" ,e2fsprogs)  ; for btrfs-convert
+    (inputs (list e2fsprogs   ;for btrfs-convert
-              ("eudev" ,eudev)
+                  eudev
-              ("lzo" ,lzo)
+                  lzo
-              ("util-linux:lib" ,util-linux "lib")       ;for libblkid and libuuid
+                  `(,util-linux "lib")            ;for libblkid and libuuid
-              ("util-linux:static" ,util-linux "static") ;ditto
+                  `(,util-linux "static")         ;ditto
-              ("zlib" ,zlib)
+                  zlib
-              ("zlib:static" ,zlib "static")
+                  `(,zlib "static")
-              ("zstd" ,zstd "lib")
+                  `(,zstd "lib")
-              ("zstd:static" ,zstd "static")))
+                  `(,zstd "static")))
-    (native-inputs `(("pkg-config" ,pkg-config)
+    (native-inputs
-                     ;; For building documentation.
+     (append
-                     ("python-sphinx" ,python-sphinx)
+      ;; For building documentation.  Since python-sphinx requires Rust, add
-                     ;; For tests.
+      ;; it conditionally depending on such support.
-                     ("acl" ,acl)
+      (if (supported-package? python-sphinx)
-                     ("dmsetup" ,lvm2)
+          (list python-sphinx)
-                     ("grep" ,grep)     ; need Perl regexp support
+          '())
-                     ("libaio" ,libaio)
+      (list pkg-config
-                     ("liburing" ,liburing)
+            acl                                   ;for tests
-                     ("util-linux" ,util-linux) ; for fallocate
+            lvm2                                  ;for dmsetup
-                     ("which" ,which)))
+            grep                                  ;need Perl regexp support
+            libaio
+            liburing
+            util-linux                            ;for fallocate
+            which)))
     (home-page "https://btrfs.wiki.kernel.org/index.php/Main_Page")
     (synopsis "Create and manage btrfs copy-on-write file systems")
-    (description "Btrfs is a @acronym{CoW, copy-on-write} file system for Linux
+    (description
+     "Btrfs is a @acronym{CoW, copy-on-write} file system for Linux
 aimed at implementing advanced features while focusing on fault tolerance,
 repair and easy administration.")
     ;; GPL2+: crc32.c, radix-tree.c, raid6.c, rbtree.c.
@@ -8986,7 +9039,7 @@ the superuser to make device nodes.")
 (define-public fakeroot
   (package
     (name "fakeroot")
-    (version "1.30.1")
+    (version "1.31")
     (source
      (origin
        ;; There are no tags in the repository, so take this snapshot.
@@ -8995,7 +9048,7 @@ the superuser to make device nodes.")
                            "fakeroot/fakeroot_" version ".orig.tar.gz"))
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
-        (base32 "0xba5gfh7ygv6na8n1ckqd2jnpdr9q88qan385qxp85c47sb3srj"))
+        (base32 "0br0gvvribfs2kpkhwr51lsinhl6l36334wx1cbwfmhww50nv233"))
        (modules '((guix build utils)
                   (ice-9 ftw)))
        (snippet

gnu/packages/lisp-xyz.scm

@@ -9769,8 +9769,8 @@ implementation specific equivalent.")
   (sbcl-package->ecl-package sbcl-trivial-macroexpand-all))
 
 (define-public sbcl-serapeum
-  (let ((commit "ce6c3b320cde38767caea2b86afa87ff280b9c11")
+  (let ((commit "47217ab69f76673db7e1fa65665ab804fb46d974")
-        (revision "9"))
+        (revision "11"))
     (package
       (name "sbcl-serapeum")
       (version (git-version "0.0.0" revision commit))
@@ -9783,7 +9783,7 @@ implementation specific equivalent.")
                (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-          (base32 "0vpxgvxniyn12wkhmav2iq4x4bj12hjrsf2ajwcapp0sh06qg1j9"))))
+          (base32 "1mr868z1za6vfhb7gq3j7c1rb606gqfzschxdy7wcqx5xv3ndgpa"))))
       (build-system asdf-build-system/sbcl)
       (inputs
        (list sbcl-alexandria
@@ -18512,20 +18512,18 @@ protocol for Mastodon.")
   (sbcl-package->cl-source-package sbcl-tooter))
 
 (define-public sbcl-croatoan
-  (let ((commit "42e474f4dffe2f4e429905a612be5736c2c3e374")
-        (revision "7"))
   (package
     (name "sbcl-croatoan")
-      (version (git-version "0.0.1" revision commit))
+    (version "0.1")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/McParen/croatoan")
-               (commit commit)))
+             (commit (string-append "v" version))))
        (file-name (git-file-name "cl-croatoan" version))
        (sha256
-          (base32 "12hnj8gwk2600j3kn778xvvpx3y6z0428v5dq2qbf4vbzj66vcxj"))))
+        (base32 "1whbvwc4df7zz0002xy3aczrpf4s3vk6kmyh9wydgwl112h060pd"))))
     (build-system asdf-build-system/sbcl)
     (arguments
      '(#:phases
@@ -18544,7 +18542,7 @@ protocol for Mastodon.")
     (description "Croatoan provides high-level Common Lisp CLOS bindings for
 the ncurses terminal library.")
     (home-page "https://github.com/McParen/croatoan")
-      (license license:expat))))
+    (license license:expat)))
 
 (define-public ecl-croatoan
   (sbcl-package->ecl-package sbcl-croatoan))
@@ -25547,7 +25545,7 @@ access lexicographic data from WordNet.")
 (define-public sbcl-nfiles
   (package
    (name "sbcl-nfiles")
-   (version "1.1.2")
+   (version "1.1.3")
    (source
     (origin
      (method git-fetch)
@@ -25557,7 +25555,7 @@ access lexicographic data from WordNet.")
      (file-name (git-file-name "cl-nfiles" version))
      (sha256
       (base32
-       "1z6xxkr5q325zhpiyy3z03mv663jz85k844cczym4869b845rib2"))
+       "1rndrxqb16wfbi5zkg8gbqm163xhs31ka0algsxvrhb9kf2j8c4q"))
      (modules '((guix build utils)))
      (snippet
       `(begin
@@ -25626,10 +25624,10 @@ change since last write.
            (package-inputs sbcl-nfiles)))))
 
 (define-public sbcl-nasdf
-  (let ((commit "c63a6ff12239f132844cc0703e79ea3b33dae630"))
+  (let ((commit "5d823d97282e11cecd8da9bcb255c4a8ead1ba93"))
     (package
       (name "sbcl-nasdf")
-      (version "0.1.2")
+      (version "0.1.5")
       (source
        (origin
          (method git-fetch)
@@ -25639,7 +25637,7 @@ change since last write.
          (file-name (git-file-name "cl-ntemplate" version))
          (sha256
           (base32
-           "1b57jkyrvr3n0c66lih4m34fqzw3s5yqlk91v7hg2gchcn3v9glg"))))
+           "0vs40ndfyhpx3nj9fc505apk98qgp0pq3cdmqpf67jqkrpcdmnvx"))))
       (build-system asdf-build-system/sbcl)
       (arguments
        `(#:phases
@@ -26404,7 +26402,7 @@ instead of #'FOO.
 (define-public sbcl-njson
   (package
     (name "sbcl-njson")
-    (version "1.0.0")
+    (version "1.1.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -26413,12 +26411,12 @@ instead of #'FOO.
               (file-name (git-file-name "cl-njson" version))
               (sha256
                (base32
-                "1apwccrvivrq57rlrw6vffrn3a5hikk10s0dndszjw5ri29b3qyd"))))
+                "02m9l77am2rlkg83dyp3jvb76ifw1y84xh3wpz6cx7h2wkxkjnl5"))))
     (build-system asdf-build-system/sbcl)
-    (inputs (list sbcl-cl-json))
+    (inputs (list sbcl-cl-json sbcl-jzon))
     (native-inputs (list sbcl-lisp-unit2))
     (arguments
-     '(#:asd-systems '("njson" "njson/cl-json")))
+     '(#:asd-systems '("njson" "njson/cl-json" "njson/jzon")))
     (home-page "https://github.com/atlas-engineer/njson")
     (synopsis "JSON handling framework for Common Lisp")
     (description
@@ -26426,8 +26424,8 @@ instead of #'FOO.
 and process JSON data, in the minimum keystrokes/minutes possible.
 
 NJSON is parser-independent, with existing Common Lisp JSON parsers being
-loadable as additional system.  @code{cl-json} is included by default, though.
+loadable as additional system.  @code{jzon} and @code{cl-json} backends are
-Conveniences that NJSON provides are:
+included by default, though.  Conveniences that NJSON provides are:
 
 @itemize
 @item @code{encode} and @code{decode} as single entry points for JSON reading
@@ -26457,7 +26455,7 @@ forms conveniently accessible as @code{j:rem}, @code{j:get},
 (define-public sbcl-nactivitypub
   (package
     (name "sbcl-nactivitypub")
-    (version "0.0.4")
+    (version "0.0.5")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -26466,7 +26464,7 @@ forms conveniently accessible as @code{j:rem}, @code{j:get},
               (file-name (git-file-name "cl-nactivitypub" version))
               (sha256
                (base32
-                "06vzaqwwc9j8r89ld3fd6bbbfd5bl0jh132rlf9wxmr0xcaqwkrl"))))
+                "0m2vwi11zp0bpvr0hglq1svdxlp3cc70yvix30yksfzp6kk3amyn"))))
     (build-system asdf-build-system/sbcl)
     (inputs (list sbcl-cl-str
                   sbcl-dexador

gnu/packages/machine-learning.scm

@@ -18,6 +18,8 @@
 ;;; Copyright © 2020, 2021, 2022, 2023 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2020, 2021, 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2022, 2023 Nicolas Graves <ngraves@ngraves.fr>
+;;; Copyright © 2023 zamfofex <zamfofex@twdb.moe>
+;;; Copyright © 2023 Navid Afkhami <navid.afkhami@mdc-berlin.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1360,7 +1362,7 @@ for k-neighbor-graph construction and approximate nearest neighbor search.")
 (define-public python-opentsne
   (package
     (name "python-opentsne")
-    (version "0.6.1")
+    (version "0.7.1")
     (source
      (origin
        (method git-fetch) ; no tests in PyPI release
@@ -1369,27 +1371,23 @@ for k-neighbor-graph construction and approximate nearest neighbor search.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "124nid27lfq1ipfjd2gkynqcmb4khisjb4r05jv42ckfkk4dbsxs"))))
+        (base32 "12wp98mh67v6v683yi7wbv8zhpafrfz21z349bww4wgi2q7bl3il"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
        (modify-phases %standard-phases
          ;; Benchmarks require the 'macosko2015' data files.
          (add-after 'unpack 'delete-benchmark
-           (lambda _
+           (lambda _ (delete-file-recursively "benchmarks")))
-             (delete-file-recursively "benchmarks")))
          (add-after 'unpack 'skip-test
            (lambda _ ;; TODO: figure out why this test fails.
              (substitute* "tests/test_correctness.py"
                (("def test_iris\\(self\\)") "def _test_iris(self)"))))
          ;; Numba needs a writable dir to cache functions.
          (add-before 'check 'set-numba-cache-dir
-           (lambda _
+           (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
-             (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
+    (native-inputs (list python-cython))
-    (native-inputs
+    (inputs (list fftw))
-     (list python-cython))
-    (inputs
-     (list fftw))
     (propagated-inputs
      (list python-numpy python-pynndescent python-scikit-learn
            python-scipy))
@@ -1523,23 +1521,20 @@ and a few related numerical optimization tools.")
 (define-public python-cmaes
   (package
     (name "python-cmaes")
-    (version "0.8.2")
+    (version "0.9.1")
     (source
      (origin
        (method git-fetch) ;no tests in PyPI
        (uri (git-reference
-             (url "https://github.com/CyberAgent/cmaes")
+             (url "https://github.com/CyberAgentAILab/cmaes")
              (commit (string-append "v" version))))
        (sha256
-        (base32 "1jyckaifir528dz6m95nvky8hvqmz5gz6dlp65baahhbca0danzb"))
+        (base32 "1f3143w8ii6i93bdh65iazrq1lryccd805ndnqww5l8h7qnnzpkm"))
        (file-name (git-file-name name version))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
-    (native-inputs
+    (native-inputs (list python-hypothesis))
-     (list python-setuptools ;build fails without this
+    (propagated-inputs (list python-numpy))
-           python-wheel))
+    (home-page "https://github.com/CyberAgentAILab/cmaes")
-    (propagated-inputs
-     (list python-numpy))
-    (home-page "https://github.com/CyberAgent/cmaes")
     (synopsis "CMA-ES implementation for Python")
     (description "This package provides provides an implementation of the
 Covariance Matrix Adaptation Evolution Strategy (CMA-ES) for Python.")
@@ -1836,7 +1831,7 @@ written in C++.")
       (license license:asl2.0))))
 
 (define kaldi-for-vosk
-  (let* ((commit "6417ac1dece94783e80dfbac0148604685d27579")
+  (let* ((commit "a25f216f5ce4eec5e45a6ab7651e20c9840a05cd")
          (revision "0")
          (openfst openfst-for-vosk))
     (package
@@ -1851,13 +1846,13 @@ written in C++.")
                (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-          (base32 "04xw2dpfvpla8skpk08azmgr9k97cd8hn83lj4l85q165gbzql4s"))))
+          (base32 "16w90za8narkfi590cxj4p7vc1f5sdxc927g5hk6kh4l3mf6iisl"))))
       (inputs
        (list alsa-lib
-             lapack ;; compared to base kaldi, replacing `(,gfortran "lib")
+             lapack ;compared to base kaldi, replacing `(,gfortran "lib")
              glib
              gstreamer
-             jack-1
+             jack-2
              openblas
              openfst
              portaudio
@@ -1865,14 +1860,14 @@ written in C++.")
       (arguments
        (list
         #:test-target "test"
-        #:make-flags ''("online2" "lm" "rnnlm")
+        #:make-flags '(list "online2" "lm" "rnnlm")
         #:phases
         #~(modify-phases %standard-phases
             (add-after 'unpack 'chdir
               (lambda _ (chdir "src")))
             (replace 'configure
               (lambda _
-                (let* ((portaudio #$(this-package-input "portaudio"))
+                (let ((portaudio #$(this-package-input "portaudio"))
                       (lapack    #$(this-package-input "lapack"))
                       (openfst   #$(this-package-input "openfst"))
                       (openblas  #$(this-package-input "openblas")))
@@ -1892,6 +1887,8 @@ written in C++.")
                      portaudio))
                   (substitute* "matrix/Makefile"     ;temporary test bypass
                     (("matrix-lib-test sparse-matrix-test") ""))
+                  (substitute* "cudamatrix/Makefile"
+                    ((" cu-array-test") ""))
 
                   ;; This `configure' script doesn't support variables passed as
                   ;; arguments, nor does it support "prefix".
@@ -1918,7 +1915,7 @@ written in C++.")
               (lambda _ (substitute* "kaldi.mk" ((" -O1") " -O3"))))
             (replace 'install
               (lambda _
-                (let* ((inc (string-append #$output "/include"))
+                (let ((inc (string-append #$output "/include"))
                       (lib (string-append #$output "/lib")))
                   ;; The build phase installed symlinks to the actual
                   ;; libraries.  Install the actual targets.
@@ -3113,6 +3110,46 @@ These include a barrier, broadcast, and allreduce.")
       (home-page "https://github.com/facebookincubator/gloo")
       (license license:bsd-3))))
 
+(define-public python-tensorly
+  (package
+    (name "python-tensorly")
+    (version "0.8.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/tensorly/tensorly")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "184mvs1gwycsh2f8jgdyc3jyhiylbn4xw2srpjd264dz2l9ms2l7"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      '(list
+        ;; These tests fail due to missing example, documentation, or tutorial files.
+        "--ignore=doc/sphinx_ext/sphinx_gallery/tests/test_gen_rst.py"
+        ;; XXX There is no "get_marker" method.
+        "--ignore=doc/sphinx_ext/sphinx_gallery/tests/test_gen_gallery.py"
+        "-k"
+        (string-append
+         ;; tutorials/plot_parse.py is not included
+         "not test_jupyter_notebook"
+         ;; nor is examples/plot_quantum.py
+         " and not test_file_is_generated"))))
+    (propagated-inputs (list python-jsmin python-numpy python-scipy))
+    (native-inputs (list python-pytest python-pytest-cov python-sphinx))
+    (home-page "https://github.com/tensorly/tensorly")
+    (synopsis "Tensor learning in Python")
+    (description
+     "This is a Python library that aims at making tensor learning simple and
+accessible.  It allows performing tensor decomposition, tensor learning and
+tensor algebra easily.  Its backend system allows seamlessly perform
+computation with NumPy, PyTorch, JAX, MXNet, TensorFlow or CuPy and run
+methodxs at scale on CPU or GPU.")
+    (license license:bsd-3)))
+
 (define-public python-umap-learn
   (package
     (name "python-umap-learn")
@@ -3431,7 +3468,7 @@ Note: currently this package does not provide GPU support.")
                 "0mqrhq3s23mn8n4i0q791pshn3dgplp0h9ny0pmmp798q0798dzs"))))
     (build-system pyproject-build-system)
     (propagated-inputs (list python-click
-                             python-fastapi
+                             python-fastapi-for-pytorch-lightning
                              python-multipart
                              python-pyjwt
                              python-requests
@@ -4117,7 +4154,7 @@ simple speech recognition.")
                   "library_dirs=["
                   "'" #$vosk-api "/lib'"
                   "],\n\t"
-                  "libraries=['vosk', 'python3.9'],\n\t"
+                  "libraries=['vosk', 'python3.10'],\n\t"
                   "include_dirs=["
                   "'" #$vosk-api "/src'" "])")))
               (substitute* "vosk/__init__.py"
@@ -4303,3 +4340,23 @@ easily extensible.")
 Brian 2 simulator.")
     (license license:cecill)))
 
+(define-public oneapi-dnnl
+  (package
+    (name "oneapi-dnnl")
+    (version "3.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/oneapi-src/oneDNN")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1jgmb5kl0bf4a2zfn94zlb117672r9lvvkkmwl86ihlyr1mpr3d0"))))
+    (build-system cmake-build-system)
+    (home-page "https://github.com/oneapi-src/oneDNN")
+    (synopsis "Deep Neural Network Library")
+    (description
+     "OneAPI Deep Neural Network Library (oneDNN) is a cross-platform
+performance library of basic building blocks for deep learning applications.")
+    (license license:asl2.0)))

gnu/packages/mail.scm

@@ -602,7 +602,7 @@ aliasing facilities to work just as they would on normal mail.")
 (define-public mutt
   (package
     (name "mutt")
-    (version "2.2.9")
+    (version "2.2.10")
     (source (origin
              (method url-fetch)
              (uri (list
@@ -612,7 +612,7 @@ aliasing facilities to work just as they would on normal mail.")
                                    version ".tar.gz")))
              (sha256
               (base32
-               "1yyg49sgghi7pgw7xr3cnzgypa9yd0kdc3nsrqq1zzjq3liinlzs"))
+               "121xrns9b0n5cdjb7nv5a6idjjk58pp7pdclgdphjy9g88i3yxsd"))
              (patches (search-patches "mutt-store-references.patch"))))
     (build-system gnu-build-system)
     (inputs
@@ -2233,7 +2233,10 @@ hashing scheme (such as scrypt) plug-in for @code{Dovecot}.")
        (uri (string-append "mirror://sourceforge/isync/isync/"
                            version "/isync-" version ".tar.gz"))
        (sha256 (base32
-                "1zq0wwvmqsl9y71546dr0aygzn9gjjfiw19hlcq87s929y4p6ckw"))))
+                "1zq0wwvmqsl9y71546dr0aygzn9gjjfiw19hlcq87s929y4p6ckw"))
+       (patches
+        ;; Likely to be included in next version
+        (search-patches "isync-openssl3-fix.patch"))))
     (build-system gnu-build-system)
     (native-inputs
      (list perl))

gnu/packages/messaging.scm

@@ -1225,6 +1225,7 @@ of xmpppy.")
            python-css-parser
            python-dbus
            python-gssapi
+           python-idna
            python-keyring
            python-nbxmpp
            python-packaging
@@ -1454,14 +1455,14 @@ Qt-based XMPP library QXmpp.")
 (define-public prosody
   (package
     (name "prosody")
-    (version "0.12.2")
+    (version "0.12.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://prosody.im/downloads/source/"
                                   "prosody-" version ".tar.gz"))
               (sha256
                (base32
-                "05ma72wr6iypr62vq748jhzx8i3lmgnsjshrx6w0z7sg24jfhqmn"))))
+                "0091vc0v8xnxkpdi4qpy4dirn92y4pa09q1qssi40q7l3w1hvnim"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ;tests require "busted"
@@ -2325,7 +2326,7 @@ QMatrixClient project.")
      (list boost
            coeurl
            curl
-           json-modern-cxx
+           nlohmann-json
            libevent
            libsodium
            olm
@@ -2408,7 +2409,7 @@ for the Matrix protocol.  It is built on to of @code{Boost.Asio}.")
            gst-plugins-base
            gst-plugins-bad              ; sdp & webrtc for voip
            gst-plugins-good-qt          ; rtpmanager for voip
-           json-modern-cxx
+           nlohmann-json
            libevent
            libnice                      ; for voip
            olm
@@ -3382,7 +3383,7 @@ Weechat communicate over the Matrix protocol.")
              (when tests?
                (invoke "pytest")))))))
     (inputs
-     (list python-websocket-client))
+     (list python-mock python-websocket-client))
     (native-inputs
      (list python-pytest))
     (home-page "https://github.com/wee-slack/wee-slack")

gnu/packages/mpd.scm

@@ -600,7 +600,7 @@ mpdevil loads all tags and covers on demand.")
 (define-public mympd
   (package
     (name "mympd")
-    (version "10.2.6")
+    (version "10.3.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -609,7 +609,7 @@ mpdevil loads all tags and covers on demand.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1adi1pdygj7wlfi6k3978b6ny2cziai4f761a61j9vxa2ywf7wbb"))))
+                "04mpj0qikdg7nqp8rvwr83bx3544qy2ha0sjj4cnpjknka6p8xan"))))
     (build-system cmake-build-system)
     (arguments
      (list #:tests? #f)) ; no test target

gnu/packages/mpi.scm

@@ -399,13 +399,13 @@ only provides @code{MPI_THREAD_FUNNELED}.")))
 (define-public python-mpi4py
   (package
     (name "python-mpi4py")
-    (version "3.0.3")
+    (version "3.1.4")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "mpi4py" version))
        (sha256
-        (base32 "07ssbhssv27rrjx1c5vd3vsr31vay5d8xcf4zh9yblcyidn72b81"))))
+        (base32 "101lz7bnm9l17nrkbg6497kxscyh53aah7qd2b820ck2php8z18p"))))
     (build-system python-build-system)
     (arguments
      `(#:phases

gnu/packages/music.scm

@@ -674,6 +674,7 @@ It is a fork of Clementine aimed at music collectors and audiophiles.")
     (inputs
      (list alsa-lib
            ao
+           elogind ;for MPRIS support
            faad2
            ffmpeg
            flac
@@ -2268,7 +2269,7 @@ a JACK session.")
 (define-public mixxx
   (package
     (name "mixxx")
-    (version "2.3.4")
+    (version "2.3.5")
     (source
      (origin
        (method git-fetch)
@@ -2280,7 +2281,7 @@ a JACK session.")
         (search-patches "mixxx-link-qtscriptbytearray-qtscript.patch"
                         "mixxx-system-googletest-benchmark.patch"))
        (sha256
-        (base32 "056zn0nxl7xrmg467ljdszsycrszsrzsc8k4s39mp4qxyd9qq4yn"))
+        (base32 "0142xcq5ahk50kzc06s13xilj8m4p0spmd5hqd8s08qjhr37n2il"))
        (modules '((guix build utils)))
        (snippet
         ;; Delete libraries that we already have or don't need.
@@ -3538,16 +3539,15 @@ follows a traditional multi-track tape recorder control paradigm.")
              (unless (or (string-prefix? "x86_64" system)
                          (string-prefix? "i686" system))
                (substitute* "wscript"
-                 (("'-msse', '-mfpmath=sse', ") "")))
+                 (("'-msse', '-mfpmath=sse', ") ""))))))
-             #t)))
        #:tests? #f))                    ;no tests
     (inputs
-     `(("cairo" ,cairo)
+     (list cairo
-       ("fftw" ,fftw)
+           fftw
-       ("gtk" ,gtk+-2)
+           gtk+-2
-       ("gtkmm" ,gtkmm-2)
+           gtkmm-2
-       ("lv2" ,lv2)
+           lv2
-       ("lvtk" ,lvtk)))
+           lvtk))
     (native-inputs
      (list pkg-config))
     (home-page "https://github.com/blablack/ams-lv2")
@@ -6176,6 +6176,42 @@ audio and MIDI plugins that can also run as standalone JACK applications.")
     (home-page "https://x42-plugins.com/x42/")
     (license license:gpl2+)))
 
+(define-public xuidesigner
+  (package
+    (name "xuidesigner")
+    (version "0.9")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/brummer10/XUiDesigner")
+                    (commit (string-append "v" version))
+                    ;; For libxputty
+                    (recursive? #true)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32 "1ap6g2j9lr4x9gpnavdhs4qa3z4dw100xgknpi6ysj0rmzc220mi"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:tests? #f                       ;no "check" target
+      #:make-flags
+      #~(list (string-append "PREFIX=" #$output)
+              (string-append "CC=" #$(cc-for-target)))
+      #:phases
+      #~(modify-phases %standard-phases
+          (delete 'configure))))
+    (inputs
+     (list cairo libx11 lilv))
+    (native-inputs
+     (list pkg-config which xxd))
+    (home-page "https://github.com/brummer10/XUiDesigner")
+    (synopsis "GUI generator tool to create X11 UIs for LV2 plugins")
+    (description "XUiDesigner parses an LV2 plugin's ttl file and generates
+the needed controller widgets.  The created GUI can be saved as UI-Bundle,
+which then could be built and installed.  For later editing of the UI, a JSON
+file is added, which you could load per drag 'n drop into XUiDesigner.")
+    (license license:bsd-0)))
+
 (define-public zam-plugins
   (package
     (name "zam-plugins")
@@ -6452,7 +6488,7 @@ and as an LV2 plugin.")
     ;; distros to make necessary changes to integrate the software into the
     ;; distribution.
     (name "zrythm")
-    (version "1.0.0-beta.4.5.62")
+    (version "1.0.0-beta.4.9.1")
     (source
      (origin
        (method url-fetch)
@@ -6460,11 +6496,10 @@ and as an LV2 plugin.")
                            version ".tar.xz"))
        (sha256
         (base32
-         "1nfb3h3aky8f8xslx6qzvcgcfrhlqa1v50kzanmpjxrx9dcllin7"))))
+         "0skdb4bpw4v5175yw9wijrc6j36mxjq8i7p8nn9650lipxg6bshd"))))
     (build-system meson-build-system)
     (arguments
-     (list #:tests? #f             ;123 pass, 3 fail. Appears network-related.
+     (list #:glib-or-gtk? #t
-           #:glib-or-gtk? #t
            #:configure-flags
            #~(list "-Dtests=true"
                    "-Dmanpage=false"    ;fish-completions breaks this
@@ -6477,6 +6512,40 @@ and as an LV2 plugin.")
                    "-Dsdl=enabled")     ;for SDL audio backend (which uses ALSA)
            #:phases
            #~(modify-phases %standard-phases
+               (add-after 'unpack 'patch-tests
+                 (lambda _
+                   ;; io_mkdir must be called with a GError value, not plain
+                   ;; NULL, or else the assertion in io_mkdir segfaults.
+                   (substitute* "tests/helpers/zrythm.h"
+                     (("success = io_mkdir \\(tmp_log_dir, NULL\\);" m)
+                      (string-append "err = NULL;
+success = io_mkdir (tmp_log_dir, &err);")))
+
+                   ;; zrythm: fails because curl wants to access the internet.
+                   ;; project: unknown failure XXX
+                   ;; The other tests fail with this error:
+                   ;;     error: attempt to map invalid URI `'
+                   ;; This means that lilv is given an empty LV2 plugin URI.
+                   ;; This is probably because we don't provide all LV2
+                   ;; plugins that are needed for running the tests.
+                   (substitute* "tests/meson.build"
+                     (("foreach name, info : tests")
+                      "\
+  disabled_tests = {
+    'zrythm': 0,
+    'project': 0,
+    'audio/midi_track': 0,
+    'integration/recording': 0,
+    'actions/mixer_selections_action': 0,
+    'actions/tracklist_selections': 0
+  }
+  enabled_tests = {}
+  foreach name, info : tests
+    if name not in disabled_tests
+      enabled_tests += {name: info}
+    endif
+  endforeach
+  foreach name, info : enabled_tests"))))
                (add-before 'build 'disable-guile-auto-compilation
                  (lambda _
                    (setenv "GUILE_AUTO_COMPILE" "0")))
@@ -6498,11 +6567,10 @@ and as an LV2 plugin.")
            font-dseg
            gettext-minimal
            glib
-           glibc
            graphviz
            gtk
            gtksourceview
-           guile-2.2
+           guile-3.0
            jack-2
            json-glib
            libadwaita
@@ -6607,7 +6675,7 @@ as JACK standalone applications.")
 (define-public zplugins
   (package
     (name "zplugins")
-    (version "0.2.4")
+    (version "0.2.5")
     (source
      (origin
        (method git-fetch)
@@ -6618,10 +6686,10 @@ as JACK standalone applications.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0l6cm6y8j1417mwspraldzixpnps8scx81wd36n2xpx60v4iqss0"))))
+         "0xsnq8kg57pdswqi9yy5nrpjbfgmym2m1qi3cj3hki33kwzx2nn1"))))
     (build-system meson-build-system)
     (inputs
-      (list guile-2.2 libsndfile lv2 ztoolkit-rsvg))
+      (list guile-3.0 libsndfile lv2 ztoolkit-rsvg))
     (native-inputs
       (list pkg-config))
     (synopsis "Audio plugin collection")

gnu/packages/networking.scm

@@ -488,7 +488,7 @@ GLib-based library, libnice, as well as GStreamer elements to use it.")
 (define-public librecast
   (package
     (name "librecast")
-    (version "0.5.1")
+    (version "0.6.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -497,7 +497,7 @@ GLib-based library, libnice, as well as GStreamer elements to use it.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1zzdxawzsj0lxyxm8c2wdqx3b633f8ybvlg6szs4v0y42xg4a829"))))
+                "1kixnm7pn8345wp0klhnpw5x992cqbqx3bhc01j8xhqf6irlzdm3"))))
     (build-system gnu-build-system)
     (arguments
      `(#:parallel-tests? #f

gnu/packages/package-management.scm

@@ -68,6 +68,7 @@
   #:use-module (gnu packages flex)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gettext)
+  #:use-module (gnu packages ghostscript)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gnupg)
@@ -273,6 +274,13 @@ $(prefix)/etc/openrc\n")))
                               (("\"[^\"]*/bin//xz")
                                (string-append "\"" xz "/bin/xz")))))
                         #t))
+                    (add-before 'build 'set-font-path
+                      (lambda* (#:key inputs #:allow-other-keys)
+                        ;; Tell 'dot' where to look for fonts.
+                        (setenv "XDG_DATA_DIRS"
+                                (dirname
+                                 (search-input-directory inputs
+                                                         "share/fonts")))))
                     (add-before 'check 'copy-bootstrap-guile
                       (lambda* (#:key system target inputs #:allow-other-keys)
                         ;; Copy the bootstrap guile tarball in the store
@@ -431,7 +439,8 @@ $(prefix)/etc/openrc\n")))
                        ("automake" ,automake)
                        ("gettext" ,gettext-minimal)
                        ("texinfo" ,texinfo)
-                       ("graphviz" ,graphviz)
+                       ("graphviz" ,graphviz-minimal)
+                       ("font-ghostscript" ,font-ghostscript) ;fonts for 'dot'
                        ("help2man" ,help2man)
                        ("po4a" ,po4a)))
       (inputs
@@ -527,7 +536,7 @@ the Nix package manager.")
     ;; Use a minimum set of dependencies.
     (native-inputs
      (modify-inputs (package-native-inputs guix)
-       (delete "po4a" "graphviz" "help2man")))
+       (delete "po4a" "graphviz" "font-ghostscript" "help2man")))
     (inputs
      (modify-inputs (package-inputs guix)
        (delete "boot-guile" "boot-guile/i686" "util-linux")
@@ -546,6 +555,7 @@ the Nix package manager.")
         #f)
        ((#:phases phases '%standard-phases)
         `(modify-phases ,phases
+           (delete 'set-font-path)
            (add-after 'unpack 'change-default-guix
              (lambda _
                ;; We need to tell 'guix-daemon' which 'guix' command to use.
@@ -1378,8 +1388,8 @@ environments.")
                   "0k9zkdyyzir3fvlbcfcqy17k28b51i20rpbjwlx2i1mwd2pw9cxc")))))))
 
 (define-public guix-build-coordinator
-  (let ((commit "3f6473c0d296ed6efab1feebcacd76fc597bb6ef")
+  (let ((commit "99981dc3270d79ae0b83f94386e26cc75a7162b3")
-        (revision "81"))
+        (revision "84"))
     (package
       (name "guix-build-coordinator")
       (version (git-version "0" revision commit))
@@ -1390,7 +1400,7 @@ environments.")
                       (commit commit)))
                 (sha256
                  (base32
-                  "0c2k2v15ga4bdmm74f4h385pwjimvsvrgjzsfd04il9a6r4qg319"))
+                  "047qqqhpcg5rrzgpp2qlijn6rhlm2ipqhqr1yj1lrnx12dld2kqk"))
                 (file-name (string-append name "-" version "-checkout"))))
       (build-system gnu-build-system)
       (arguments
@@ -1474,15 +1484,11 @@ environments.")
              guile-lib
              (first (assoc-ref (package-native-inputs guix) "guile"))))
       (inputs
-       (append
        (list (first (assoc-ref (package-native-inputs guix) "guile"))
              sqlite
-              bash-minimal)
+             bash-minimal
-        (if (hurd-target?)
+             sqitch))
-            '()
-            (list sqitch))))
       (propagated-inputs
-       (append
        (list guile-prometheus
              guile-gcrypt
              guile-json-4
@@ -1491,10 +1497,8 @@ environments.")
              guile-zlib
              guile-sqlite3
              guix
-              guile-gnutls)
+             guile-gnutls
-        (if (hurd-target?)
+             guile-fibers-next))
-            '()
-            (list guile-fibers-next))))
       (home-page "https://git.cbaines.net/guix/build-coordinator/")
       (synopsis "Tool to help build derivations")
       (description
@@ -1507,63 +1511,6 @@ outputs of those builds.")
   (package
     (inherit guix-build-coordinator)
     (name "guix-build-coordinator-agent-only")
-    (arguments
-     `(#:modules (((guix build guile-build-system)
-                   #:select (target-guile-effective-version))
-                  ,@%gnu-build-system-modules)
-       #:imported-modules ((guix build guile-build-system)
-                           ,@%gnu-build-system-modules)
-       #:phases
-       (modify-phases %standard-phases
-         (add-before 'build 'set-GUILE_AUTO_COMPILE
-           (lambda _
-             ;; To avoid warnings relating to 'guild'.
-             (setenv "GUILE_AUTO_COMPILE" "0")
-             #t))
-         (add-after 'install 'wrap-executable
-           (lambda* (#:key inputs outputs target #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (bin (string-append out "/bin"))
-                    (guile (assoc-ref inputs "guile"))
-                    (version (target-guile-effective-version))
-                    (scm (string-append out "/share/guile/site/" version))
-                    (go  (string-append out "/lib/guile/" version "/site-ccache")))
-               (for-each
-                (lambda (file)
-                  (simple-format (current-error-port) "wrapping: ~A\n" file)
-                  (let ((guile-inputs (list
-                                       "guile-json"
-                                       "guile-gcrypt"
-                                       "guix"
-                                       "guile-prometheus"
-                                       "guile-lib"
-                                       "guile-lzlib"
-                                       "guile-zlib"
-                                       "guile-sqlite3"
-                                       "guile-gnutls")))
-                    (wrap-program file
-                      `("PATH" ":" prefix (,bin))
-                      `("GUILE_LOAD_PATH" ":" prefix
-                        (,scm ,(string-join
-                                (map (lambda (input)
-                                       (simple-format
-                                        #f "~A/share/guile/site/~A"
-                                        (assoc-ref inputs input)
-                                        version))
-                                     guile-inputs)
-                                ":")))
-                      `("GUILE_LOAD_COMPILED_PATH" ":" prefix
-                        (,go ,(string-join
-                               (map (lambda (input)
-                                      (simple-format
-                                       #f "~A/lib/guile/~A/site-ccache"
-                                       (assoc-ref inputs input)
-                                       version))
-                                    guile-inputs)
-                               ":"))))))
-                (find-files bin)))
-             #t))
-         (delete 'strip))))             ; As the .go files aren't compatible
     (native-inputs
      (list pkg-config
            autoconf
@@ -1581,7 +1528,6 @@ outputs of those builds.")
      (list (first (assoc-ref (package-native-inputs guix) "guile"))
            bash-minimal))
     (propagated-inputs
-     (append
      (list guile-prometheus
            guile-gcrypt
            guile-json-4
@@ -1589,7 +1535,7 @@ outputs of those builds.")
            guile-lzlib
            guile-zlib
            guix
-               guile-gnutls)))
+           guile-gnutls))
     (description
      "The Guix Build Coordinator helps with performing lots of builds across
 potentially many machines, and with doing something with the results and
@@ -1687,8 +1633,8 @@ in an isolated environment, in separate namespaces.")
     (license license:gpl3+)))
 
 (define-public nar-herder
-  (let ((commit "659543cd9ad78f712b4b067863db0613423dd23b")
+  (let ((commit "efaf8fa580ad197d74ff375ca50bddf9c8ac3a86")
-        (revision "18"))
+        (revision "19"))
     (package
       (name "nar-herder")
       (version (git-version "0" revision commit))
@@ -1699,7 +1645,7 @@ in an isolated environment, in separate namespaces.")
                       (commit commit)))
                 (sha256
                  (base32
-                  "09ghbbrk5gazkpqxcvfnn56pp11sndn7hw00ipc8d95wqk53g9qg"))
+                  "169cz6xwx4klcsx0769807yjk0xnck73q4hyrsv289nfgfd9x8a2"))
                 (file-name (string-append name "-" version "-checkout"))))
       (build-system gnu-build-system)
       (arguments

gnu/packages/patches/isync-openssl3-fix.patch

@@ -0,0 +1,81 @@
+Upstream status: Taken from master branch.  Likely included in versions > 1.4.4
+
+Fixes issues with OpenSSL3.  See related thread:
+https://sourceforge.net/p/isync/mailman/isync-devel/thread/Y2jnr8hESp1PUW+6@bulldog/
+
+From b6c36624f04cd388873785c0631df3f2f9ac4bf0 Mon Sep 17 00:00:00 2001
+From: Oswald Buddenhagen <ossi@users.sf.net>
+Date: Mon, 6 Jun 2022 11:55:37 +0200
+Subject: [PATCH] work around "unexpected EOF" error messages at end of SSL
+ connections
+
+gmail apparently doesn't send a close notification (SSL_shutdown())
+before closing the TCP socket.
+---
+ src/drv_imap.c | 7 +++++--
+ src/socket.c   | 9 +++++++++
+ src/socket.h   | 1 +
+ 3 files changed, 15 insertions(+), 2 deletions(-)
+
+diff --git a/src/drv_imap.c b/src/drv_imap.c
+index fb8d165..6286045 100644
+--- a/src/drv_imap.c
++++ b/src/drv_imap.c
+@@ -1620,6 +1620,7 @@ imap_socket_read( void *aux )
+ 					error( "IMAP error: unexpected BYE response: %s\n", cmd );
+ 					/* We just wait for the server to close the connection now. */
+ 					ctx->expectEOF = 1;
++					socket_expect_eof( &ctx->conn );
+ 				} else {
+ 					/* We still need to wait for the LOGOUT's tagged OK. */
+ 				}
+@@ -1882,10 +1883,12 @@ static void
+ imap_cleanup_p2( imap_store_t *ctx,
+                  imap_cmd_t *cmd ATTR_UNUSED, int response )
+ {
+-	if (response == RESP_NO)
++	if (response == RESP_NO) {
+ 		imap_cancel_store( &ctx->gen );
+-	else if (response == RESP_OK)
++	} else if (response == RESP_OK) {
+ 		ctx->expectEOF = 1;
++		socket_expect_eof( &ctx->conn );
++	}
+ }
+ 
+ /******************* imap_open_store *******************/
+diff --git a/src/socket.c b/src/socket.c
+index ac3c847..892cece 100644
+--- a/src/socket.c
++++ b/src/socket.c
+@@ -810,6 +810,15 @@ socket_expect_activity( conn_t *conn, int expect )
+ 		conf_wakeup( &conn->fd_timeout, expect ? conn->conf->timeout : -1 );
+ }
+ 
++void
++socket_expect_eof( conn_t *sock )
++{
++#ifdef SSL_OP_IGNORE_UNEXPECTED_EOF  // implies HAVE_LIBSSL
++	if (sock->ssl)
++		SSL_set_options( sock->ssl, SSL_OP_IGNORE_UNEXPECTED_EOF );
++#endif
++}
++
+ int
+ socket_read( conn_t *conn, char *buf, uint len )
+ {
+diff --git a/src/socket.h b/src/socket.h
+index 5b1edd0..af679aa 100644
+--- a/src/socket.h
++++ b/src/socket.h
+@@ -142,6 +142,7 @@ void socket_start_tls(conn_t *conn, void (*cb)( int ok, void *aux ) );
+ void socket_start_deflate( conn_t *conn );
+ void socket_close( conn_t *sock );
+ void socket_expect_activity( conn_t *sock, int expect );
++void socket_expect_eof( conn_t *sock );
+ int socket_read( conn_t *sock, char *buf, uint len ); /* never waits */
+ char *socket_read_line( conn_t *sock ); /* don't free return value; never waits */
+ typedef enum { KeepOwn = 0, GiveOwn } ownership_t;
+-- 
+2.39.2
+

gnu/packages/patches/laby-use-tmpdir-from-runtime.patch

@@ -0,0 +1,39 @@
+Reported as <https://github.com/sgimenez/laby/pull/68>
+
+diff --git a/build b/build
+index 992a9e3..0df74d9 100755
+--- a/build
++++ b/build
+@@ -7,7 +7,6 @@ source build.conf || exit 1
+ 
+ export PREFIX=${PREFIX-/usr}
+ export DATADIR=${DATADIR-${PREFIX}/share}
+-export TMPDIR=${TMPDIR-/tmp}
+ 
+ export PROJECT_NAME=${PROJECT_NAME-unknown}
+ export PROJECT_VERSION=${PROJECT_VERSION-unknown}
+diff --git a/src/config.sh b/src/config.sh
+index 19d4160..9338aad 100644
+--- a/src/config.sh
++++ b/src/config.sh
+@@ -29,5 +29,4 @@ let build_ocaml = "${OCAML_VERSION}"
+ let build_lablgtk = "${BUILD_LABLGTK}"
+ let build_lablgtk_sourceview = "${BUILD_LABLGTKSV}"
+ let _ = Res.sys_data_dir := "${DATADIR}"
+-let _ = Res.sys_tmp_dir := "${TMPDIR}"
+ EOF
+diff --git a/src/laby.ml b/src/laby.ml
+index b77f2b2..e17acb9 100644
+--- a/src/laby.ml
++++ b/src/laby.ml
+@@ -48,6 +48,7 @@ let opts =
+ 
+ let _ =
+   Printexc.record_backtrace true;
++  Res.sys_tmp_dir := Filename.get_temp_dir_name ();
+   Run.init
+     ~name:Config.project_name
+     ~conf:(conf, ["conf"])
+-- 
+2.34.1
+

gnu/packages/patches/mariadb-rocksdb-atomic-linking.patch

@@ -0,0 +1,54 @@
+https://github.com/MariaDB/server/pull/2477
+https://github.com/MariaDB/server/commit/195c0e81493c41f1d20b91a5bcc6aaaf4979d781.patch
+
+From 195c0e81493c41f1d20b91a5bcc6aaaf4979d781 Mon Sep 17 00:00:00 2001
+From: Daniel Black <daniel@mariadb.org>
+Date: Fri, 3 Feb 2023 11:51:20 +1100
+Subject: [PATCH] MDEV-30554 RockDB libatomic linking on riscv64
+
+The existing storage/rocksdb/CMakeCache.txt defined
+ATOMIC_EXTRA_LIBS when atomics where required. This was
+determined by the toplevel configure.cmake test
+(HAVE_GCC_C11_ATOMICS_WITH_LIBATOMIC).
+
+As build_rocksdb.cmake is included after ATOMIC_EXTRA_LIBS
+was set, we just need to use it. As such no riscv64
+specific macro is needed in build_rocksdb.cmake.
+
+As highlighted by Gianfranco Costamagna (@LocutusOfBorg)
+in #2472 overwriting SYSTEM_LIBS was problematic.
+This is corrected in case in future SYSTEM_LIBS is changed
+elsewhere.
+
+Closes #2472.
+---
+ storage/rocksdb/build_rocksdb.cmake | 8 ++------
+ 1 file changed, 2 insertions(+), 6 deletions(-)
+
+diff --git a/storage/rocksdb/build_rocksdb.cmake b/storage/rocksdb/build_rocksdb.cmake
+index e23862ee65901..647e51e2f90d9 100644
+--- a/storage/rocksdb/build_rocksdb.cmake
++++ b/storage/rocksdb/build_rocksdb.cmake
+@@ -129,10 +129,6 @@ if(CMAKE_SYSTEM_PROCESSOR MATCHES "ppc64")
+   ADD_DEFINITIONS(-DHAVE_POWER8 -DHAS_ALTIVEC)
+ endif(CMAKE_SYSTEM_PROCESSOR MATCHES "ppc64")
+ 
+-if(CMAKE_SYSTEM_PROCESSOR STREQUAL "riscv64")
+- set(SYSTEM_LIBS ${SYSTEM_LIBS} -latomic)
+-endif()
+-
+ option(WITH_FALLOCATE "build with fallocate" ON)
+ 
+ if(WITH_FALLOCATE AND UNIX)
+@@ -161,9 +157,9 @@ include_directories(SYSTEM ${ROCKSDB_SOURCE_DIR}/third-party/gtest-1.7.0/fused-s
+ 
+ find_package(Threads REQUIRED)
+ if(WIN32)
+-  set(SYSTEM_LIBS ${SYSTEM_LIBS} Shlwapi.lib Rpcrt4.lib)
++  set(SYSTEM_LIBS ${SYSTEM_LIBS} ${ATOMIC_EXTRA_LIBS} Shlwapi.lib Rpcrt4.lib)
+ else()
+-  set(SYSTEM_LIBS ${CMAKE_THREAD_LIBS_INIT} ${LIBRT} ${CMAKE_DL_LIBS})
++  set(SYSTEM_LIBS ${SYSTEM_LIBS} ${CMAKE_THREAD_LIBS_INIT} ${LIBRT} ${CMAKE_DL_LIBS} ${ATOMIC_EXTRA_LIBS})
+ endif()
+ 
+ set(ROCKSDB_LIBS rocksdblib})

gnu/packages/patches/mesa-opencl-all-targets.patch

@@ -1,25 +0,0 @@
-This patch restores LLVM targets needed for OpenCL, *reverting* this
-upstream commit:
-
-  From 80817b6e344258ac9b955f824ebf9019a0fc1610 Mon Sep 17 00:00:00 2001
-  From: Jesse Natalie <jenatali@microsoft.com>
-  Date: Wed, 18 Nov 2020 18:30:30 -0800
-  Subject: [PATCH] meson: Adjust Clover's required LLVM modules
-
-diff --git a/meson.build b/meson.build
-index 6d1607c35a3..f828eb80faa 100644
---- b/meson.build
-+++ a/meson.build
-@@ -1479,10 +1479,9 @@
- endif
- if with_gallium_opencl
-   llvm_modules += [
--    'linker', 'coverage', 'instrumentation', 'ipo', 'irreader',
--    'lto', 'option', 'objcarcopts', 'profiledata'
-+    'all-targets', 'linker', 'coverage', 'instrumentation', 'ipo', 'irreader',
-+    'lto', 'option', 'objcarcopts', 'profiledata',
-   ]
--  llvm_optional_modules += ['frontendopenmp']
- endif
- if with_microsoft_clc
-   llvm_modules += ['target', 'linker', 'irreader', 'option', 'libdriver']

gnu/packages/patches/openmw-assume-nonconst-SIGSTKSZ.patch

@@ -0,0 +1,39 @@
+From 98a7d90ee258ceef9c70b0b2955d0458ec46f048 Mon Sep 17 00:00:00 2001
+From: elsid <elsid.mail@gmail.com>
+Date: Fri, 24 Sep 2021 19:40:29 +0200
+Subject: [PATCH] Assume SIGSTKSZ is not a constant
+
+SIGSTKSZ is not defined as constant since glibc 2.34:
+https://sourceware.org/git/?p=glibc.git;a=commit;h=6c57d320484988e87e446e2e60ce42816bf51d53
+---
+ components/crashcatcher/crashcatcher.cpp | 5 ++---
+ 1 file changed, 2 insertions(+), 3 deletions(-)
+
+diff --git a/components/crashcatcher/crashcatcher.cpp b/components/crashcatcher/crashcatcher.cpp
+index 86571e1e3a..c828e1ca81 100644
+--- a/components/crashcatcher/crashcatcher.cpp
++++ b/components/crashcatcher/crashcatcher.cpp
+@@ -56,8 +56,6 @@ static const char exec_err[] = "!!! Failed to exec debug process\n";
+
+ static char argv0[PATH_MAX];
+
+-static char altstack[SIGSTKSZ];
+-
+
+ static struct {
+     int signum;
+@@ -475,9 +473,10 @@ int crashCatcherInstallHandlers(int argc, char **argv, int num_signals, int *sig
+
+     /* Set an alternate signal stack so SIGSEGVs caused by stack overflows
+      * still run */
++    static char* altstack = new char [SIGSTKSZ];
+     altss.ss_sp = altstack;
+     altss.ss_flags = 0;
+-    altss.ss_size = sizeof(altstack);
++    altss.ss_size = SIGSTKSZ;
+     sigaltstack(&altss, nullptr);
+
+     memset(&sa, 0, sizeof(sa));
+--
+GitLab
+

gnu/packages/patches/tofi-32bit-compat.patch

@@ -0,0 +1,87 @@
+This patch is from upstream and shouldn't be needed in the next release.
+https://github.com/philj56/tofi/commit/667075f0920da3c2b353fbce54b6430c195ef031.patch
+
+From 667075f0920da3c2b353fbce54b6430c195ef031 Mon Sep 17 00:00:00 2001
+From: Phil Jones <philj56@gmail.com>
+Date: Sun, 30 Apr 2023 20:08:57 +0100
+Subject: [PATCH] Replace `strto[u]l` with `strto[u]ll`.
+
+On 32-bit systems, using `strtoul` was causing negative values for
+unsigned options to be treated as valid, as the value was being parsed
+as a 32-bit unsigned int, then cast to a 64-bit signed int, which
+remained positive.
+---
+ src/color.c  | 8 ++++----
+ src/config.c | 6 +++---
+ 2 files changed, 7 insertions(+), 7 deletions(-)
+
+diff --git a/src/color.c b/src/color.c
+index 4b6b356..b1d5e90 100644
+--- a/src/color.c
++++ b/src/color.c
+@@ -22,7 +22,7 @@ struct color hex_to_color(const char *hex)
+ 			hex[2], hex[2],
+ 			'\0'};
+ 		char *endptr;
+-		tmp = strtol(str, &endptr, 16);
++		tmp = strtoll(str, &endptr, 16);
+ 		if (errno || *endptr != '\0' || tmp < 0) {
+ 			return (struct color) { -1, -1, -1, -1 };
+ 		}
+@@ -37,14 +37,14 @@ struct color hex_to_color(const char *hex)
+ 			hex[3], hex[3],
+ 			'\0'};
+ 		char *endptr;
+-		tmp = strtol(str, &endptr, 16);
++		tmp = strtoll(str, &endptr, 16);
+ 		if (errno || *endptr != '\0' || tmp < 0) {
+ 			return (struct color) { -1, -1, -1, -1 };
+ 		}
+ 		val = tmp;
+ 	} else if (len == 6) {
+ 		char *endptr;
+-		tmp = strtol(hex, &endptr, 16);
++		tmp = strtoll(hex, &endptr, 16);
+ 		if (errno || *endptr != '\0' || tmp < 0) {
+ 			return (struct color) { -1, -1, -1, -1 };
+ 		}
+@@ -53,7 +53,7 @@ struct color hex_to_color(const char *hex)
+ 		val |= 0xFFu;
+ 	} else if (len == 8) {
+ 		char *endptr;
+-		tmp = strtol(hex, &endptr, 16);
++		tmp = strtoll(hex, &endptr, 16);
+ 		if (errno || *endptr != '\0' || tmp < 0) {
+ 			return (struct color) { -1, -1, -1, -1 };
+ 		}
+diff --git a/src/config.c b/src/config.c
+index 2b85028..556199d 100644
+--- a/src/config.c
++++ b/src/config.c
+@@ -1027,7 +1027,7 @@ uint32_t parse_uint32(const char *filename, size_t lineno, const char *str, bool
+ {
+ 	errno = 0;
+ 	char *endptr;
+-	int64_t ret = strtoul(str, &endptr, 0);
++	int64_t ret = strtoull(str, &endptr, 0);
+ 	if (endptr == str || *endptr != '\0') {
+ 		PARSE_ERROR(filename, lineno, "Failed to parse \"%s\" as unsigned int.\n", str);
+ 		if (err) {
+@@ -1046,7 +1046,7 @@ int32_t parse_int32(const char *filename, size_t lineno, const char *str, bool *
+ {
+ 	errno = 0;
+ 	char *endptr;
+-	int64_t ret = strtol(str, &endptr, 0);
++	int64_t ret = strtoll(str, &endptr, 0);
+ 	if (endptr == str || *endptr != '\0') {
+ 		PARSE_ERROR(filename, lineno, "Failed to parse \"%s\" as int.\n", str);
+ 		if (err) {
+@@ -1065,7 +1065,7 @@ struct uint32_percent parse_uint32_percent(const char *filename, size_t lineno,
+ {
+ 	errno = 0;
+ 	char *endptr;
+-	int64_t val = strtoul(str, &endptr, 0);
++	int64_t val = strtoull(str, &endptr, 0);
+ 	bool percent = false;
+ 	if (endptr == str || (*endptr != '\0' && *endptr != '%')) {
+ 		PARSE_ERROR(filename, lineno, "Failed to parse \"%s\" as unsigned int.\n", str);

gnu/packages/patches/xfce4-settings-defaults.patch

@@ -1,17 +1,18 @@
-This patch make Xfce use "gnome" as the default icon theme and enable font antialias.
+This patch make Xfce use "elementary-xfce-dark" as the default icon theme, "Greybird" as
+the default GTK theme and enable font antialias.
 
-Taken from ArchLinux.
 
-diff -upr xfce4-settings-4.12.0.orig/xfsettingsd/xsettings.xml xfce4-settings-4.12.0/xfsettingsd/xsettings.xml
+diff -upr xfce4-settings-4.18.2.orig/xfsettingsd/xsettings.xml xfce4-settings-4.18.2/xfsettingsd/xsettings.xml
---- xfce4-settings-4.12.0.orig/xfsettingsd/xsettings.xml	2015-02-24 03:33:11.000000000 +0200
+--- xfce4-settings-4.18.2.orig/xfsettingsd/xsettings.xml	2023-02-11 16:55:53.000000000 +0800
-+++ xfce4-settings-4.12.0/xfsettingsd/xsettings.xml	2015-03-01 09:52:24.376869688 +0200
++++ xfce4-settings-4.18.2/xfsettingsd/xsettings.xml	2023-05-14 19:20:43.919701586 +0800
 @@ -6,8 +6,8 @@
- <?xml version="1.0" encoding="UTF-8"?>
+ 
  <channel name="xsettings" version="1.0">
    <property name="Net" type="empty">
-     <property name="ThemeName" type="empty"/>
+-    <property name="ThemeName" type="empty"/>
 -    <property name="IconThemeName" type="empty"/>
-+    <property name="IconThemeName" type="string" value="gnome"/>
++    <property name="ThemeName" type="string" value="Greybird"/>
++    <property name="IconThemeName" type="string" value="elementary-xfce-dark"/>
      <property name="DoubleClickTime" type="int" value="400"/>
      <property name="DoubleClickDistance" type="int" value="5"/>
      <property name="DndDragThreshold" type="int" value="8"/>

gnu/packages/patches/xygrib-newer-proj.patch

@@ -0,0 +1,600 @@
+These two patches are already applied upstream.
+https://patch-diff.githubusercontent.com/raw/opengribs/XyGrib/pull/289.patch
+
+removing cmake/FindPROJ4.cmake removed since it didn't apply cleanly.
+
+From 95aa7b47bfe83ee276806acd8ce08867fd7a28d9 Mon Sep 17 00:00:00 2001
+From: Fyleo <fyleo45@gmail.com>
+Date: Tue, 7 Sep 2021 18:10:39 +0200
+Subject: [PATCH 1/2] port to PROJ 8.0 API
+
+---
+ CMakeLists.txt                 | 14 +++----
+ cmake/FindPROJ4.cmake          | 77 ----------------------------------
+ cmake/FindPROJ8.cmake          | 76 +++++++++++++++++++++++++++++++++
+ src/CMakeLists.txt             |  2 +-
+ src/map/Projection.h           |  7 +---
+ src/map/Projection_libproj.cpp | 30 ++++++-------
+ 6 files changed, 101 insertions(+), 105 deletions(-)
+ delete mode 100644 cmake/FindPROJ4.cmake
+ create mode 100644 cmake/FindPROJ8.cmake
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index b066a044..77633a21 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -122,22 +122,22 @@ find_path(OPENJPEG_INCLUDE_DIR
+ include_directories(${OPENJPEG_INCLUDE_DIR})
+ 
+ if(NOT WIN32)
+-    include(cmake/FindPROJ4.cmake)
+-    if(NOT PROJ4_FOUND)
+-      message(FATAL_ERROR "PROJ.4 library not found!")
++    include(cmake/FindPROJ8.cmake)
++    if(NOT PROJ8_FOUND)
++      message(FATAL_ERROR "PROJ.8 library not found!")
+     endif()
+-    include_directories(${PROJ4_INCLUDE_DIRS})
++    include_directories(${PROJ8_INCLUDE_DIRS})
+ endif()
+ if(WIN32)
+-    find_library(PROJ4_LIBRARIES
++    find_library(PROJ8_LIBRARIES
+         NAME "libproj.a"
+         PATHS
+         $ENV{EXTERNLIBS}/lib
+          /opt/lib
+         REQUIRED
+     )
+-    find_path(PROJ4_INCLUDE_DIRS
+-         NAMES "proj_api.h"
++    find_path(PROJ8_INCLUDE_DIRS
++         NAMES "proj.h"
+          PATHS
+          $ENV{EXTERNLIBS}/include
+          /opt/include
+diff --git a/cmake/FindPROJ8.cmake b/cmake/FindPROJ8.cmake
+new file mode 100644
+index 00000000..33470ac2
+--- /dev/null
++++ b/cmake/FindPROJ8.cmake
+@@ -0,0 +1,76 @@
++# - Find PROJ8
++# Find the PROJ8 includes and library
++#
++#  PROJ8_INCLUDE_DIR - Where to find PROJ8 includes
++#  PROJ8_LIBRARIES   - List of libraries when using PROJ8
++#  PROJ8_FOUND       - True if PROJ8 was found
++
++IF(PROJ8_INCLUDE_DIR)
++  SET(PROJ8_FIND_QUIETLY TRUE)
++ENDIF(PROJ8_INCLUDE_DIR)
++
++FIND_PATH(PROJ8_INCLUDE_DIR "proj.h"
++  PATHS
++  $ENV{EXTERNLIBS}/include
++  $ENV{EXTERNLIBS}/PROJ8/include
++  ~/Library/Frameworks/include
++  /Library/Frameworks/include
++  /usr/local/include
++  /usr/include
++  /sw/include # Fink
++  /opt/local/include # DarwinPorts
++  /opt/csw/include # Blastwave
++  /opt/include
++  DOC "PROJ8 - Headers"
++)
++
++SET(PROJ8_NAMES PROJ8 proj proj_8_0)
++SET(PROJ8_DBG_NAMES PROJ8D projD proj_8_0_1)
++
++FIND_LIBRARY(PROJ8_LIBRARY NAMES ${PROJ8_NAMES}
++  PATHS
++  $ENV{EXTERNLIBS}
++  $ENV{EXTERNLIBS}/PROJ8
++  ~/Library/Frameworks
++  /Library/Frameworks
++  /usr/local
++  /usr
++  /sw
++  /opt/local
++  /opt/csw
++  /opt
++  PATH_SUFFIXES lib lib64
++  DOC "PROJ8 - Library"
++)
++
++INCLUDE(FindPackageHandleStandardArgs)
++
++IF(MSVC)
++  # VisualStudio needs a debug version
++  FIND_LIBRARY(PROJ8_LIBRARY_DEBUG NAMES ${PROJ8_DBG_NAMES}
++    PATHS
++    $ENV{EXTERNLIBS}/PROJ8/lib
++    DOC "PROJ8 - Library (Debug)"
++  )
++  
++  IF(PROJ8_LIBRARY_DEBUG AND PROJ8_LIBRARY)
++    SET(PROJ8_LIBRARIES optimized ${PROJ8_LIBRARY} debug ${PROJ8_LIBRARY_DEBUG})
++  ENDIF(PROJ8_LIBRARY_DEBUG AND PROJ8_LIBRARY)
++
++  FIND_PACKAGE_HANDLE_STANDARD_ARGS(PROJ8 DEFAULT_MSG PROJ8_LIBRARY PROJ8_LIBRARY_DEBUG PROJ8_INCLUDE_DIR)
++
++  MARK_AS_ADVANCED(PROJ8_LIBRARY PROJ8_LIBRARY_DEBUG PROJ8_INCLUDE_DIR)
++  
++ELSE(MSVC)
++  # rest of the world
++  SET(PROJ8_LIBRARIES ${PROJ8_LIBRARY})
++
++  FIND_PACKAGE_HANDLE_STANDARD_ARGS(PROJ8 DEFAULT_MSG PROJ8_LIBRARY PROJ8_INCLUDE_DIR)
++  
++  MARK_AS_ADVANCED(PROJ8_LIBRARY PROJ8_INCLUDE_DIR)
++  
++ENDIF(MSVC)
++
++IF(PROJ8_FOUND)
++  SET(PROJ8_INCLUDE_DIRS ${PROJ8_INCLUDE_DIR})
++ENDIF(PROJ8_FOUND)
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index 2e5dbde4..9c96d49f 100644
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -118,7 +118,7 @@ include_directories(${CMAKE_CURRENT_SOURCE_DIR}/util)
+ include_directories(${CMAKE_CURRENT_SOURCE_DIR}/map ${MAP_GENERATED_HEADERS})
+ include_directories(${CMAKE_CURRENT_SOURCE_DIR}/GUI ${GUI_GENERATED_HEADERS})
+ 
+-target_link_libraries(${CMAKE_PROJECT_NAME} g2clib gui util map ${LIBNOVA_LIBRARY} ${OPENJPEG_LIBRARIES} ${Qt5Core_LIBRARIES} ${Qt5Gui_LIBRARIES} ${Qt5Widgets_LIBRARIES} ${Qt5Network_LIBRARIES} ${Qt5Xml_LIBRARIES} ${Qt5PrintSupport_LIBRARIES} ${BZIP2_LIBRARIES} ${ZLIB_LIBRARIES} ${PROJ4_LIBRARIES} ${PNG_LIBRARIES})
++target_link_libraries(${CMAKE_PROJECT_NAME} g2clib gui util map ${LIBNOVA_LIBRARY} ${OPENJPEG_LIBRARIES} ${Qt5Core_LIBRARIES} ${Qt5Gui_LIBRARIES} ${Qt5Widgets_LIBRARIES} ${Qt5Network_LIBRARIES} ${Qt5Xml_LIBRARIES} ${Qt5PrintSupport_LIBRARIES} ${BZIP2_LIBRARIES} ${ZLIB_LIBRARIES} ${PROJ8_LIBRARIES} ${PNG_LIBRARIES})
+ 
+ # Sanitizers, part 2/2
+ if ( CMAKE_VERSION VERSION_GREATER 3.4 )
+diff --git a/src/map/Projection.h b/src/map/Projection.h
+index b4ca7f5b..d482e0dd 100644
+--- a/src/map/Projection.h
++++ b/src/map/Projection.h
+@@ -21,10 +21,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ #include <QObject>
+ #include <cstdio>
+ 
+-#ifndef ACCEPT_USE_OF_DEPRECATED_PROJ_API_H
+-#define ACCEPT_USE_OF_DEPRECATED_PROJ_API_H
+-#endif
+-#include "proj_api.h"
++#include "proj.h"
+ 
+ class Projection : public QObject
+ {
+@@ -141,7 +138,7 @@ class Projection_libproj : public Projection
+ 		int   getProjection()   {return currentProj;}
+ 
+ 	private :
+-		projPJ libProj;
++		PJ * libProj;
+ 		int  currentProj;
+ };
+ 
+diff --git a/src/map/Projection_libproj.cpp b/src/map/Projection_libproj.cpp
+index 1dcbd540..0299714e 100644
+--- a/src/map/Projection_libproj.cpp
++++ b/src/map/Projection_libproj.cpp
+@@ -93,9 +93,9 @@ void Projection_libproj::setProjection(int code)
+     params[nbpar++] = "no_defs";
+     params[nbpar++] = "over";	// allow longitude > 180°
+     // XXX ouch pj_init
+-    libProj = pj_init(nbpar, (char **)params);
++    libProj = proj_create_argv(PJ_DEFAULT_CTX, nbpar, (char **)params);
+ 	if (!libProj)
+-		printf("proj error: %s\n", pj_strerrno(pj_errno));
++		printf("proj error: %s\n", proj_errno_string(proj_errno(libProj)));
+ 	assert(libProj);
+ 	currentProj = code;
+ //	libProj->over = 1;		// allow longitude > 180°
+@@ -106,23 +106,23 @@ void Projection_libproj::setProjection(int code)
+ Projection_libproj::~Projection_libproj()
+ {
+     if (libProj != nullptr) {
+-		pj_free(libProj);
++		proj_destroy(libProj);
+ 	}
+ }
+ 
+ //-------------------------------------------------------------------------------
+ void Projection_libproj::map2screen(double x, double y, int *i, int *j) const
+ {
+-	projUV data, res;
++	PJ_COORD data, res;
+ 	if (y <= -90.0)
+ 		y = -90.0+1e-5;
+ 	if (y >= 90.0)
+ 		y = 90.0-1e-5;
+-	data.v =  y * DEG_TO_RAD;
+-	data.u =  x * DEG_TO_RAD;
+-	res = pj_fwd(data, libProj);
+-	*i =  (int) (W/2.0 + scale * (res.u/111319.0-CX) + 0.5);
+-	*j =  (int) (H/2.0 - scale * (res.v/111319.0-CY) + 0.5);
++	data.uv.v =  y;
++	data.uv.u =  x;
++	res = proj_trans(libProj, PJ_FWD, data);
++	*i =  (int) (W/2.0 + scale * (res.uv.u/111319.0-CX) + 0.5);
++	*j =  (int) (H/2.0 - scale * (res.uv.v/111319.0-CY) + 0.5);
+ 	//printf("PROJ   map2screen (%f %f) -> (%3d %3d)\n", x,y, *i,*j);
+ }
+ 
+@@ -130,12 +130,12 @@ void Projection_libproj::map2screen(double x, double y, int *i, int *j) const
+ //-------------------------------------------------------------------------------
+ void Projection_libproj::screen2map(int i, int j, double *x, double *y) const
+ {
+-	projUV data, res;
+-	data.u =  ((i-W/2.0)/scale+ CX)*111319.0 ;
+-	data.v =  ((H/2.0-j)/scale+ CY)*111319.0 ;
+-	res = pj_inv(data, libProj);
+-	*x = (double)(res.u*RAD_TO_DEG);
+-	*y = (double)(res.v*RAD_TO_DEG);
++	PJ_COORD data, res;
++	data.uv.u =  ((i-W/2.0)/scale+ CX)*111319.0 ;
++	data.uv.v =  ((H/2.0-j)/scale+ CY)*111319.0 ;
++	res = proj_trans(libProj, PJ_INV, data);
++	*x = (double)(res.uv.u);
++	*y = (double)(res.uv.v);
+ 	//printf("PROJ   screen2map (%3d %3d) -> (%f %f)\n", i,j, *x,*y);
+ }
+ //--------------------------------------------------------------
+
+From 720a2db307f5c93c0079f9811a3c35cfe8bb12f5 Mon Sep 17 00:00:00 2001
+From: didier <didier@users.sourceforge.net>
+Date: Mon, 24 Jan 2022 13:13:42 +0100
+Subject: [PATCH 2/2] Use new libproj API if available
+
+---
+ CMakeLists.txt                 | 12 ++---
+ cmake/FindPROJ.cmake           | 96 ++++++++++++++++++++++++++++++++++
+ cmake/FindPROJ8.cmake          | 76 ---------------------------
+ src/CMakeLists.txt             |  2 +-
+ src/map/Projection.h           |  9 ++++
+ src/map/Projection_libproj.cpp | 32 +++++++++++-
+ 6 files changed, 143 insertions(+), 84 deletions(-)
+ create mode 100644 cmake/FindPROJ.cmake
+ delete mode 100644 cmake/FindPROJ8.cmake
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 77633a21..358a87a2 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -122,21 +122,21 @@ find_path(OPENJPEG_INCLUDE_DIR
+ include_directories(${OPENJPEG_INCLUDE_DIR})
+ 
+ if(NOT WIN32)
+-    include(cmake/FindPROJ8.cmake)
+-    if(NOT PROJ8_FOUND)
+-      message(FATAL_ERROR "PROJ.8 library not found!")
++    include(cmake/FindPROJ.cmake)
++    if(NOT PROJ_FOUND)
++      message(FATAL_ERROR "PROJ library not found!")
+     endif()
+-    include_directories(${PROJ8_INCLUDE_DIRS})
++    include_directories(${PROJ_INCLUDE_DIRS})
+ endif()
+ if(WIN32)
+-    find_library(PROJ8_LIBRARIES
++    find_library(PROJ_LIBRARIES
+         NAME "libproj.a"
+         PATHS
+         $ENV{EXTERNLIBS}/lib
+          /opt/lib
+         REQUIRED
+     )
+-    find_path(PROJ8_INCLUDE_DIRS
++    find_path(PROJ_INCLUDE_DIRS
+          NAMES "proj.h"
+          PATHS
+          $ENV{EXTERNLIBS}/include
+diff --git a/cmake/FindPROJ.cmake b/cmake/FindPROJ.cmake
+new file mode 100644
+index 00000000..33b53000
+--- /dev/null
++++ b/cmake/FindPROJ.cmake
+@@ -0,0 +1,96 @@
++# - Find PROJ
++# Find the PROJ includes and library
++#
++#  PROJ_INCLUDE_DIR - Where to find PROJ includes
++#  PROJ_LIBRARIES   - List of libraries when using PROJ
++#  PROJ_FOUND       - True if PROJ was found
++
++IF(PROJ_INCLUDE_DIR)
++  SET(PROJ_FIND_QUIETLY TRUE)
++ENDIF(PROJ_INCLUDE_DIR)
++
++FIND_PATH(PROJ_INCLUDE_DIR "proj.h"
++  PATHS
++  $ENV{EXTERNLIBS}/include
++  $ENV{EXTERNLIBS}/PROJ/include
++  ~/Library/Frameworks/include
++  /Library/Frameworks/include
++  /usr/local/include
++  /usr/include
++  /sw/include # Fink
++  /opt/local/include # DarwinPorts
++  /opt/csw/include # Blastwave
++  /opt/include
++  DOC "PROJ - Headers"
++)
++
++IF(PROJ_INCLUDE_DIR)
++    SET(PROJ_NAMES PROJ proj proj_8_0)
++    SET(PROJ_DBG_NAMES PROJD projD proj_8_0_1)
++ELSE(PROJ_INCLUDE_DIR)
++    FIND_PATH(PROJ_INCLUDE_DIR "proj_api.h"
++      PATHS
++      $ENV{EXTERNLIBS}/include
++      $ENV{EXTERNLIBS}/PROJ/include
++      ~/Library/Frameworks/include
++      /Library/Frameworks/include
++      /usr/local/include
++      /usr/include
++      /sw/include # Fink
++      /opt/local/include # DarwinPorts
++      /opt/csw/include # Blastwave
++      /opt/include
++      DOC "PROJ - Headers"
++    )
++    ADD_DEFINITIONS(-DACCEPT_USE_OF_DEPRECATED_PROJ_API_H=1)
++    SET(PROJ_NAMES PROJ proj proj_4_9)
++    SET(PROJ_DBG_NAMES PROJD projD proj_4_9_D)
++ENDIF(PROJ_INCLUDE_DIR)
++
++FIND_LIBRARY(PROJ_LIBRARY NAMES ${PROJ_NAMES}
++  PATHS
++  $ENV{EXTERNLIBS}
++  $ENV{EXTERNLIBS}/PROJ
++  ~/Library/Frameworks
++  /Library/Frameworks
++  /usr/local
++  /usr
++  /sw
++  /opt/local
++  /opt/csw
++  /opt
++  PATH_SUFFIXES lib lib64
++  DOC "PROJ - Library"
++)
++
++INCLUDE(FindPackageHandleStandardArgs)
++
++IF(MSVC)
++  # VisualStudio needs a debug version
++  FIND_LIBRARY(PROJ_LIBRARY_DEBUG NAMES ${PROJ_DBG_NAMES}
++    PATHS
++    $ENV{EXTERNLIBS}/PROJ/lib
++    DOC "PROJ - Library (Debug)"
++  )
++  
++  IF(PROJ_LIBRARY_DEBUG AND PROJ_LIBRARY)
++    SET(PROJ_LIBRARIES optimized ${PROJ_LIBRARY} debug ${PROJ_LIBRARY_DEBUG})
++  ENDIF(PROJ_LIBRARY_DEBUG AND PROJ_LIBRARY)
++
++  FIND_PACKAGE_HANDLE_STANDARD_ARGS(PROJ DEFAULT_MSG PROJ_LIBRARY PROJ_LIBRARY_DEBUG PROJ_INCLUDE_DIR)
++
++  MARK_AS_ADVANCED(PROJ_LIBRARY PROJ_LIBRARY_DEBUG PROJ_INCLUDE_DIR)
++  
++ELSE(MSVC)
++  # rest of the world
++  SET(PROJ_LIBRARIES ${PROJ_LIBRARY})
++
++  FIND_PACKAGE_HANDLE_STANDARD_ARGS(PROJ DEFAULT_MSG PROJ_LIBRARY PROJ_INCLUDE_DIR)
++  
++  MARK_AS_ADVANCED(PROJ_LIBRARY PROJ_INCLUDE_DIR)
++  
++ENDIF(MSVC)
++
++IF(PROJ_FOUND)
++  SET(PROJ_INCLUDE_DIRS ${PROJ_INCLUDE_DIR})
++ENDIF(PROJ_FOUND)
+diff --git a/cmake/FindPROJ8.cmake b/cmake/FindPROJ8.cmake
+deleted file mode 100644
+index 33470ac2..00000000
+--- a/cmake/FindPROJ8.cmake
++++ /dev/null
+@@ -1,76 +0,0 @@
+-# - Find PROJ8
+-# Find the PROJ8 includes and library
+-#
+-#  PROJ8_INCLUDE_DIR - Where to find PROJ8 includes
+-#  PROJ8_LIBRARIES   - List of libraries when using PROJ8
+-#  PROJ8_FOUND       - True if PROJ8 was found
+-
+-IF(PROJ8_INCLUDE_DIR)
+-  SET(PROJ8_FIND_QUIETLY TRUE)
+-ENDIF(PROJ8_INCLUDE_DIR)
+-
+-FIND_PATH(PROJ8_INCLUDE_DIR "proj.h"
+-  PATHS
+-  $ENV{EXTERNLIBS}/include
+-  $ENV{EXTERNLIBS}/PROJ8/include
+-  ~/Library/Frameworks/include
+-  /Library/Frameworks/include
+-  /usr/local/include
+-  /usr/include
+-  /sw/include # Fink
+-  /opt/local/include # DarwinPorts
+-  /opt/csw/include # Blastwave
+-  /opt/include
+-  DOC "PROJ8 - Headers"
+-)
+-
+-SET(PROJ8_NAMES PROJ8 proj proj_8_0)
+-SET(PROJ8_DBG_NAMES PROJ8D projD proj_8_0_1)
+-
+-FIND_LIBRARY(PROJ8_LIBRARY NAMES ${PROJ8_NAMES}
+-  PATHS
+-  $ENV{EXTERNLIBS}
+-  $ENV{EXTERNLIBS}/PROJ8
+-  ~/Library/Frameworks
+-  /Library/Frameworks
+-  /usr/local
+-  /usr
+-  /sw
+-  /opt/local
+-  /opt/csw
+-  /opt
+-  PATH_SUFFIXES lib lib64
+-  DOC "PROJ8 - Library"
+-)
+-
+-INCLUDE(FindPackageHandleStandardArgs)
+-
+-IF(MSVC)
+-  # VisualStudio needs a debug version
+-  FIND_LIBRARY(PROJ8_LIBRARY_DEBUG NAMES ${PROJ8_DBG_NAMES}
+-    PATHS
+-    $ENV{EXTERNLIBS}/PROJ8/lib
+-    DOC "PROJ8 - Library (Debug)"
+-  )
+-  
+-  IF(PROJ8_LIBRARY_DEBUG AND PROJ8_LIBRARY)
+-    SET(PROJ8_LIBRARIES optimized ${PROJ8_LIBRARY} debug ${PROJ8_LIBRARY_DEBUG})
+-  ENDIF(PROJ8_LIBRARY_DEBUG AND PROJ8_LIBRARY)
+-
+-  FIND_PACKAGE_HANDLE_STANDARD_ARGS(PROJ8 DEFAULT_MSG PROJ8_LIBRARY PROJ8_LIBRARY_DEBUG PROJ8_INCLUDE_DIR)
+-
+-  MARK_AS_ADVANCED(PROJ8_LIBRARY PROJ8_LIBRARY_DEBUG PROJ8_INCLUDE_DIR)
+-  
+-ELSE(MSVC)
+-  # rest of the world
+-  SET(PROJ8_LIBRARIES ${PROJ8_LIBRARY})
+-
+-  FIND_PACKAGE_HANDLE_STANDARD_ARGS(PROJ8 DEFAULT_MSG PROJ8_LIBRARY PROJ8_INCLUDE_DIR)
+-  
+-  MARK_AS_ADVANCED(PROJ8_LIBRARY PROJ8_INCLUDE_DIR)
+-  
+-ENDIF(MSVC)
+-
+-IF(PROJ8_FOUND)
+-  SET(PROJ8_INCLUDE_DIRS ${PROJ8_INCLUDE_DIR})
+-ENDIF(PROJ8_FOUND)
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index 9c96d49f..d1c42f95 100644
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -118,7 +118,7 @@ include_directories(${CMAKE_CURRENT_SOURCE_DIR}/util)
+ include_directories(${CMAKE_CURRENT_SOURCE_DIR}/map ${MAP_GENERATED_HEADERS})
+ include_directories(${CMAKE_CURRENT_SOURCE_DIR}/GUI ${GUI_GENERATED_HEADERS})
+ 
+-target_link_libraries(${CMAKE_PROJECT_NAME} g2clib gui util map ${LIBNOVA_LIBRARY} ${OPENJPEG_LIBRARIES} ${Qt5Core_LIBRARIES} ${Qt5Gui_LIBRARIES} ${Qt5Widgets_LIBRARIES} ${Qt5Network_LIBRARIES} ${Qt5Xml_LIBRARIES} ${Qt5PrintSupport_LIBRARIES} ${BZIP2_LIBRARIES} ${ZLIB_LIBRARIES} ${PROJ8_LIBRARIES} ${PNG_LIBRARIES})
++target_link_libraries(${CMAKE_PROJECT_NAME} g2clib gui util map ${LIBNOVA_LIBRARY} ${OPENJPEG_LIBRARIES} ${Qt5Core_LIBRARIES} ${Qt5Gui_LIBRARIES} ${Qt5Widgets_LIBRARIES} ${Qt5Network_LIBRARIES} ${Qt5Xml_LIBRARIES} ${Qt5PrintSupport_LIBRARIES} ${BZIP2_LIBRARIES} ${ZLIB_LIBRARIES} ${PROJ_LIBRARIES} ${PNG_LIBRARIES})
+ 
+ # Sanitizers, part 2/2
+ if ( CMAKE_VERSION VERSION_GREATER 3.4 )
+diff --git a/src/map/Projection.h b/src/map/Projection.h
+index d482e0dd..9ac13426 100644
+--- a/src/map/Projection.h
++++ b/src/map/Projection.h
+@@ -20,8 +20,13 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ #define PROJECTION_H
+ #include <QObject>
+ #include <cstdio>
++//#define ACCEPT_USE_OF_DEPRECATED_PROJ_API_H
+ 
++#ifdef ACCEPT_USE_OF_DEPRECATED_PROJ_API_H
++#include "proj_api.h"
++#else
+ #include "proj.h"
++#endif
+ 
+ class Projection : public QObject
+ {
+@@ -138,7 +143,11 @@ class Projection_libproj : public Projection
+ 		int   getProjection()   {return currentProj;}
+ 
+ 	private :
++#ifdef ACCEPT_USE_OF_DEPRECATED_PROJ_API_H
++		projPJ libProj;
++#else
+ 		PJ * libProj;
++#endif
+ 		int  currentProj;
+ };
+ 
+diff --git a/src/map/Projection_libproj.cpp b/src/map/Projection_libproj.cpp
+index 0299714e..e2ea525c 100644
+--- a/src/map/Projection_libproj.cpp
++++ b/src/map/Projection_libproj.cpp
+@@ -92,10 +92,15 @@ void Projection_libproj::setProjection(int code)
+     params[nbpar++] = "ellps=WGS84";
+     params[nbpar++] = "no_defs";
+     params[nbpar++] = "over";	// allow longitude > 180°
+-    // XXX ouch pj_init
++#ifdef ACCEPT_USE_OF_DEPRECATED_PROJ_API_H
++    libProj = pj_init(nbpar, (char **)params);
++	if (!libProj)
++		printf("proj error: %s\n", pj_strerrno(pj_errno));
++#else
+     libProj = proj_create_argv(PJ_DEFAULT_CTX, nbpar, (char **)params);
+ 	if (!libProj)
+ 		printf("proj error: %s\n", proj_errno_string(proj_errno(libProj)));
++#endif
+ 	assert(libProj);
+ 	currentProj = code;
+ //	libProj->over = 1;		// allow longitude > 180°
+@@ -106,23 +111,39 @@ void Projection_libproj::setProjection(int code)
+ Projection_libproj::~Projection_libproj()
+ {
+     if (libProj != nullptr) {
++#ifdef ACCEPT_USE_OF_DEPRECATED_PROJ_API_H
++		pj_free(libProj);
++#else
+ 		proj_destroy(libProj);
++#endif
+ 	}
+ }
+ 
+ //-------------------------------------------------------------------------------
+ void Projection_libproj::map2screen(double x, double y, int *i, int *j) const
+ {
++#ifdef ACCEPT_USE_OF_DEPRECATED_PROJ_API_H
++	projUV data, res;
++#else
+ 	PJ_COORD data, res;
++#endif
+ 	if (y <= -90.0)
+ 		y = -90.0+1e-5;
+ 	if (y >= 90.0)
+ 		y = 90.0-1e-5;
++#ifdef ACCEPT_USE_OF_DEPRECATED_PROJ_API_H
++	data.v =  y * DEG_TO_RAD;
++	data.u =  x * DEG_TO_RAD;
++	res = pj_fwd(data, libProj);
++	*i =  (int) (W/2.0 + scale * (res.u/111319.0-CX) + 0.5);
++	*j =  (int) (H/2.0 - scale * (res.v/111319.0-CY) + 0.5);
++#else
+ 	data.uv.v =  y;
+ 	data.uv.u =  x;
+ 	res = proj_trans(libProj, PJ_FWD, data);
+ 	*i =  (int) (W/2.0 + scale * (res.uv.u/111319.0-CX) + 0.5);
+ 	*j =  (int) (H/2.0 - scale * (res.uv.v/111319.0-CY) + 0.5);
++#endif
+ 	//printf("PROJ   map2screen (%f %f) -> (%3d %3d)\n", x,y, *i,*j);
+ }
+ 
+@@ -130,12 +151,21 @@ void Projection_libproj::map2screen(double x, double y, int *i, int *j) const
+ //-------------------------------------------------------------------------------
+ void Projection_libproj::screen2map(int i, int j, double *x, double *y) const
+ {
++#ifdef ACCEPT_USE_OF_DEPRECATED_PROJ_API_H
++	projUV data, res;
++	data.u =  ((i-W/2.0)/scale+ CX)*111319.0 ;
++	data.v =  ((H/2.0-j)/scale+ CY)*111319.0 ;
++	res = pj_inv(data, libProj);
++	*x = (double)(res.u*RAD_TO_DEG);
++	*y = (double)(res.v*RAD_TO_DEG);
++#else
+ 	PJ_COORD data, res;
+ 	data.uv.u =  ((i-W/2.0)/scale+ CX)*111319.0 ;
+ 	data.uv.v =  ((H/2.0-j)/scale+ CY)*111319.0 ;
+ 	res = proj_trans(libProj, PJ_INV, data);
+ 	*x = (double)(res.uv.u);
+ 	*y = (double)(res.uv.v);
++#endif
+ 	//printf("PROJ   screen2map (%3d %3d) -> (%f %f)\n", i,j, *x,*y);
+ }
+ //--------------------------------------------------------------

gnu/packages/python-check.scm

@@ -2530,7 +2530,7 @@ parametrize.  This plugin allows you to use all four.")
 (define-public python-pytest-httpx
   (package
     (name "python-pytest-httpx")
-    (version "0.21.0")
+    (version "0.22.0")
     (source
      (origin
        ;; pypi package doesn't include the tests
@@ -2540,16 +2540,8 @@ parametrize.  This plugin allows you to use all four.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "12mcy1f5d5cq3rqrqgi2ar0qvzw62ibys17hw6dsdfd0j2syck4r"))))
+        (base32 "1ncpd74hmsz4sadvjg99fnfscxpgh3mc2siini0dhxzwgwdkk5i7"))))
-    (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?
-               (setenv "PYTHONPATH" (getcwd))
-               (invoke "pytest" "-vv")))))))
     (propagated-inputs (list python-httpx))
     (native-inputs (list python-pytest python-pytest-asyncio))
     (home-page "https://colin-b.github.io/pytest_httpx/")
@@ -2607,3 +2599,36 @@ the X11 display server protocol.  It runs in memory and does not require a
 physical display.  Only a network layer is necessary.  Xvfb is useful for
 running acceptance tests on headless servers.")
     (license license:expat)))
+
+(define-public python-vulture
+  (package
+    (name "python-vulture")
+    (version "2.7")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "vulture" version))
+              (sha256
+               (base32
+                "0cl0v3dadxvff0pgq1j120m064a3nmnbjjylkmcxp7zd2jh81yv7"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list #:phases #~(modify-phases %standard-phases
+                        (replace 'check
+                          (lambda* (#:key tests? #:allow-other-keys)
+                            (when tests?
+                              (invoke "pytest" "-vv" "tests" "-k"
+                                      ;; skip test that uses python-pint
+                                      ;; pint has many dependencies
+                                      "not test_whitelists_with_python")))))))
+    (native-inputs (list python-pytest python-pytest-cov))
+    (propagated-inputs (list python-toml))
+    (home-page "https://github.com/jendrikseipp/vulture")
+    (synopsis "Find dead Python code")
+    (description
+     "Vulture finds unused code in Python programs.  This is useful for
+cleaning up and finding errors in large code bases.  If you run Vulture on
+both your library and test suite you can find untested code.  Due to Python's
+dynamic nature, static code analyzers like Vulture are likely to miss some
+dead code.  Also, code that is only called implicitly may be reported as
+unused.")
+    (license license:expat)))

gnu/packages/python-crypto.scm

@@ -27,6 +27,7 @@
 ;;; Copyright © 2021, 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2021 Maxime Devos <maximedevos@telenet.be>
 ;;; Copyright © 2022 Antero Mejr <antero@mailbox.org>
+;;; Copyright © 2023 Juliana Sims <juli@incana.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -800,6 +801,32 @@ Networking and Cryptography library.  These libraries have a stated goal
 of improving usability, security and speed.")
     (license license:asl2.0)))
 
+(define-public python-crcmod
+  (package
+    (name "python-crcmod")
+    (version "1.7")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "crcmod" version))
+              (sha256
+               (base32
+                "07k0hgr42vw2j92cln3klxka81f33knd7459cn3d8aszvfh52w6w"))))
+    (build-system python-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                ;; As per the Unit Testing subsection in the README.
+                (invoke "python" "-m" "crcmod.test")))))))
+    (synopsis "CRC generator for Python")
+    (description "Python module for generating objects that compute the
+Cyclic Redundancy Check.")
+    (home-page "https://crcmod.sourceforge.net/")
+    (license license:expat)))
+
 (define-public python-blurhash
   (package
     (name "python-blurhash")
@@ -1246,27 +1273,41 @@ Password-Authenticated Key Exchange algorithm.")
 (define-public python-txtorcon
   (package
     (name "python-txtorcon")
-    (version "19.0.0")
+    (version "23.0.0")
-    (source
+    (source (origin
-      (origin
               (method url-fetch)
               (uri (pypi-uri "txtorcon" version))
               (sha256
                (base32
-          "0fxzhsc62bhmr730vj9pzallmw56gz6iykvl28a5agrycm0bfc9p"))))
+                "09a3k4g90pvs0q006ighka7xic39nnnk9bfrka23g4b8cynzy982"))))
     (build-system python-build-system)
     (arguments
-      ;; The tests fail immediately due to a missing file. Reported upstream:
+     (list #:phases #~(modify-phases %standard-phases
-      ;; <https://github.com/meejah/txtorcon/issues/330>
+                        (add-before 'check 'disable-failing-tests
-     `(#:tests? #f))
+                          (lambda _
-    (propagated-inputs
+                            ;; These tests fail
-     (list python-automat
+                            (substitute* "test/test_router.py"
+                              (("\\W+def test_countrycode\\(self\\):" all)
+                               (string-append
+                                "    from unittest import skip as _skip\n"
+                                "    @_skip('Fails during Guix build')\n" all))
+                              (("\\W+def test_get_location_private\\(self\\):"
+                                all)
+                               (string-append
+                                "    @_skip('Fails during Guix build')\n" all)))
+                            ;; This test errors out
+                            (substitute* "test/test_util.py"
+                              (("\\W+def test_real_addr\\(self\\):" all)
+                               (string-append
+                                "    @_skip('Fails during Guix build')\n" all))))))))
+    (propagated-inputs (list python-automat
                              python-idna
                              python-incremental
                              python-pyopenssl
                              python-service-identity
                              python-twisted
                              python-zope-interface))
+    (native-inputs (list python-mock))
     (home-page "https://github.com/meejah/txtorcon")
     (synopsis "Twisted-based Tor controller client")
     (description "This package provides a Twisted-based Tor controller client,

gnu/packages/python-science.scm

@@ -1020,7 +1020,7 @@ Mathematics (GLM) library to Python.")
 (define-public python-distributed
   (package
     (name "python-distributed")
-    (version "2022.05.2")
+    (version "2023.4.1")
     (source
      (origin
        ;; The test files are not included in the archive on pypi
@@ -1031,58 +1031,12 @@ Mathematics (GLM) library to Python.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "009jrlk7kmazrd3nkl217cl3x5ddg7kw9mqdgq1z9knv5h1rm8qv"))
+         "164xp2dxac95nngmgdhlk0vwnnvbmajqliz994bdvw72xnv1ya18"))))
-       ;; Delete bundled copy of python-versioneer.
-       (snippet '(delete-file "versioneer.py"))))
     (build-system pyproject-build-system)
     (arguments
-     '(#:phases
+     (list
-       (modify-phases %standard-phases
+      #:test-flags
-         (add-after 'unpack 'versioneer
+      '(list "-x" "-m"
-           (lambda _
-             (invoke "versioneer" "install")))
-         (add-after 'unpack 'fix-references
-           (lambda* (#:key outputs #:allow-other-keys)
-             (substitute* '("distributed/comm/tests/test_ucx_config.py"
-                            "distributed/tests/test_client.py"
-                            "distributed/tests/test_queues.py"
-                            "distributed/tests/test_variable.py"
-                            "distributed/cli/tests/test_tls_cli.py"
-                            "distributed/cli/tests/test_dask_spec.py"
-                            "distributed/cli/tests/test_dask_worker.py"
-                            "distributed/cli/tests/test_dask_scheduler.py")
-               (("\"dask-scheduler\"")
-                (format #false "\"~a/bin/dask-scheduler\""
-                        (assoc-ref outputs "out")))
-               (("\"dask-worker\"")
-                (format #false "\"~a/bin/dask-worker\""
-                        (assoc-ref outputs "out"))))))
-         ;; ERROR: distributed==2022.5.2
-         ;; ContextualVersionConflict (locket 0.2.0
-         ;; (/gnu/store/...-python-locket-0.2.0/lib/python3.9/site-packages),
-         ;; Requirement.parse('locket>=1.0.0'), {'distributed'})
-         (delete 'sanity-check)
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               (substitute* "setup.cfg"
-                 (("ignore:There is no current event loop:DeprecationWarning" m)
-                  (string-append m "
-    ignore:clear_current is deprecated:DeprecationWarning
-    ignore:make_current is deprecated.*:DeprecationWarning")))
-               (setenv "DISABLE_IPV6" "1")
-               ;; The integration tests are all problematic to some
-               ;; degree.  They either require network access or some
-               ;; other setup.  We only run the tests in
-               ;; distributed/tests.
-               (for-each (lambda (dir)
-                           (delete-file-recursively
-                            (string-append "distributed/" dir "/tests")))
-                         (list "cli" "comm" "dashboard" "deploy" "diagnostics"
-                               "http" "http/scheduler" "http/worker"
-                               "protocol" "shuffle"))
-               (invoke "python" "-m" "pytest" "-vv" "distributed"
-                       "-m"
              (string-append "not slow"
                             " and not flaky"
                             " and not gpu"
@@ -1101,6 +1055,7 @@ Mathematics (GLM) library to Python.")
                 "test_async_context_manager"
                 "test_async_with"
                 "test_client_repr_closed_sync"
+                "test_client_is_quiet_cluster_close"
                 "test_close_closed"
                 "test_close_fast_without_active_handlers"
                 "test_close_grace_period_for_handlers"
@@ -1121,10 +1076,13 @@ Mathematics (GLM) library to Python.")
                 "test_dashboard_link_inproc"
                 "test_deserialize_error"
                 "test_dont_override_default_get"
+                "test_ensure_no_new_clients"
                 "test_errors"
                 "test_fail_to_pickle_target_2"
+                "test_failure_doesnt_crash"
                 "test_file_descriptors_dont_leak"
                 "test_finished"
+                "test_freeze_batched_send"
                 "test_get_client_functions_spawn_clusters"
                 "test_host_uses_scheduler_protocol"
                 "test_identity_inproc"
@@ -1133,6 +1091,7 @@ Mathematics (GLM) library to Python.")
                 "test_locked_comm_drop_in_replacement"
                 "test_locked_comm_intercept_read"
                 "test_locked_comm_intercept_write"
+                "test_mixing_clients_different_scheduler"
                 "test_multiple_listeners"
                 "test_no_dangling_asyncio_tasks"
                 "test_plugin_exception"
@@ -1183,24 +1142,79 @@ Mathematics (GLM) library to Python.")
               ;; These fail because it doesn't find dask[distributed]
               " and not test_quiet_close_process"
 
-                        ;; This one fails because of a silly assert failure:
+              ;; There is no distributed.__git_revision__ property.
-                        ;; '2022.05.2' == '2022.5.2'
-                        " and not test_version"
               " and not test_git_revision"
 
+              ;; The system monitor did not return a dictionary containing
+              ;; "host_disk_io.read_bps".
+              " and not test_disk_config"
+
               ;; These fail because the exception text format
               ;; appears to have changed.
               " and not test_exception_text"
               " and not test_worker_bad_args"
-                        " and not test_run_spec_deserialize_fail"
-
-                        ;; Recursion stack failure.  No idea what they
-                        ;; expected to happen.
-                        " and not test_stack_overflow"
 
               ;; These tests are rather flaky
               " and not test_quiet_quit_when_cluster_leaves"
-                        " and not multiple_clients_restart"))))))))
+              " and not multiple_clients_restart"))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'versioneer
+            (lambda _
+              ;; Our version of versioneer needs setup.cfg.  This is adapted
+              ;; from pyproject.toml.
+              (with-output-to-file "setup.cfg"
+                (lambda ()
+                  (display "\
+[versioneer]
+VCS = git
+style = pep440
+versionfile_source = distributed/_version.py
+versionfile_build = distributed/_version.py
+tag_prefix =
+parentdir_prefix = distributed-
+")))
+              (invoke "versioneer" "install")
+              (substitute* "setup.py"
+                (("versioneer.get_version\\(\\)")
+                 (string-append "\"" #$version "\"")))))
+          (add-after 'unpack 'fix-pytest-config
+            (lambda _
+              ;; This option is not supported by our version of pytest.
+              (substitute* "pyproject.toml"
+                (("--cov-config=pyproject.toml.*") ""))))
+          (add-after 'unpack 'fix-references
+            (lambda* (#:key outputs #:allow-other-keys)
+              (substitute* '("distributed/comm/tests/test_ucx_config.py"
+                             "distributed/tests/test_client.py"
+                             "distributed/tests/test_queues.py"
+                             "distributed/tests/test_variable.py"
+                             "distributed/cli/tests/test_tls_cli.py"
+                             "distributed/cli/tests/test_dask_spec.py"
+                             "distributed/cli/tests/test_dask_worker.py"
+                             "distributed/cli/tests/test_dask_scheduler.py")
+                (("\"dask-scheduler\"")
+                 (format #false "\"~a/bin/dask-scheduler\"" #$output))
+                (("\"dask-worker\"")
+                 (format #false "\"~a/bin/dask-worker\"" #$output)))))
+          (add-before 'check 'pre-check
+            (lambda _
+              (setenv "DISABLE_IPV6" "1")
+              ;; The integration tests are all problematic to some
+              ;; degree.  They either require network access or some
+              ;; other setup.  We only run the tests in
+              ;; distributed/tests.
+              (for-each (lambda (dir)
+                          (delete-file-recursively
+                           (string-append "distributed/" dir "/tests")))
+                        (list "cli" "comm" "dashboard" "deploy" "diagnostics"
+                              "http" "http/scheduler" "http/worker"
+                              "protocol" "shuffle"))))
+          ;; We need to use "." here.
+          (replace 'check
+            (lambda* (#:key tests? test-flags #:allow-other-keys)
+              (when tests?
+                (apply invoke "python" "-m" "pytest" "." "-vv" test-flags)))))))
     (propagated-inputs
      (list python-click
            python-cloudpickle
@@ -1217,7 +1231,8 @@ Mathematics (GLM) library to Python.")
            python-urllib3
            python-zict))
     (native-inputs
-     (list python-pytest
+     (list python-importlib-metadata
+           python-pytest
            python-pytest-timeout
            python-flaky
            python-versioneer))

gnu/packages/python-web.scm

@@ -59,6 +59,7 @@
 ;;; Copyright © 2022 Michael Rohleder <mike@rohleder.de>
 ;;; Copyright © 2022 Baptiste Strazzulla <bstrazzull@hotmail.fr>
 ;;; Copyright © 2023 John Kehayias <john.kehayias@protonmail.com>
+;;; Copyright © 2023 Ivan Vilata-i-Balaguer <ivan@selidor.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -119,6 +120,7 @@
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages time)
+  #:use-module (gnu packages version-control)
   #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
   #:use-module ((guix licenses) #:prefix license:)
@@ -142,6 +144,8 @@
      (list python-distro
            python-httplib2
            python-oauthlib
+           python-pyparsing
+           python-six
            python-wadllib))
     (home-page "https://launchpad.net/lazr.restfulclient")
     (synopsis "Web client Python library extending wadlib")
@@ -1752,6 +1756,54 @@ BOM detection, but the actual implementation for encoders and decoders
 is Python’s.")
     (license license:bsd-3)))
 
+(define-public python-omnipath
+  (package
+    (name "python-omnipath")
+    (version "1.0.6")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "omnipath" version))
+              (sha256
+               (base32
+                "01hmcp1202g5drs8dkxnyyb5v14g503dj4zfiqypghmigi9ipw86"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      '(modify-phases %standard-phases
+         (add-after 'unpack 'relax
+           (lambda _
+             (substitute* "requirements.txt"
+               (("wrapt>=1.12.0")
+                "wrapt>=1.11.0"))))
+         (add-after 'unpack 'set-home
+           (lambda _ (setenv "HOME" "/tmp"))))))
+    (propagated-inputs
+     (list python-attrs
+           python-docrep
+           python-inflect
+           python-networkx
+           python-packaging
+           python-pandas
+           python-requests
+           python-tqdm
+           python-typing-extensions
+           python-urllib3
+           python-wrapt))
+    (native-inputs
+     (list python-bump2version
+           python-pre-commit
+           python-pytest
+           python-pytest-mock
+           python-requests-mock
+           python-setuptools-scm
+           python-tox))
+    (home-page "https://omnipathdb.org/")
+    (synopsis "Python client for the OmniPath web service")
+    (description "This package provides a Python client for the OmniPath web
+service.")
+    (license license:expat)))
+
 (define-public python-openapi-schema-validator
   (package
     (name "python-openapi-schema-validator")
@@ -1929,20 +1981,29 @@ for clients and servers.")
 (define-public python-cssutils
   (package
     (name "python-cssutils")
-    (version "1.0.2")
+    (version "2.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "cssutils" version))
        (sha256
         (base32
-          "1bxchrbqzapwijap0yhlxdil1w9bmwvgx77aizlkhc2mcxjg1z52"))))
+         "13l1y0xr3fgbl95w3pinb5av5dqk2ip39pih6vgrz47c3hyd5p7p"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
-    (native-inputs
-     (list unzip))               ; for unpacking the source
     (arguments
-     `(#:tests? #f))                    ; tests require python-pbr < 1.7.0
+     (list
-    (home-page "https://cthedot.de/cssutils/")
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'check
+            (lambda _
+              (invoke "pytest" "-vv" "-k"
+                      ;; disable tests requiring network
+                      (string-append "not test_parseUrl "
+                                     "and not encutils "
+                                     "and not website.logging")))))))
+    (native-inputs
+     (list python-pytest python-jaraco-test))
+    (home-page "https://github.com/jaraco/cssutils")
     (synopsis
       "CSS Cascading Style Sheets library for Python")
     (description
@@ -2435,14 +2496,14 @@ conforming to a given API or contract.")
 (define-public python-zope-exceptions
   (package
     (name "python-zope-exceptions")
-    (version "4.4")
+    (version "4.6")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "zope.exceptions" version))
        (sha256
         (base32
-         "1nkgfwawswmyc6i0b8g3ymvja4mb507m8yhid8s4rbxq3dmqhwhd"))))
+         "1kc3hql2i35ys5alkj9csiaz2s9bx0rff585vnrrgvavqsj297b1"))))
     (build-system python-build-system)
     (arguments
      '(#:phases
@@ -2566,14 +2627,14 @@ internationalized messages within program source text.")
 (define-public python-zope-schema
   (package
     (name "python-zope-schema")
-    (version "6.0.0")
+    (version "7.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "zope.schema" version))
        (sha256
         (base32
-          "09jg47bxhfg1ahr1jxb5y0cbiszyk1j6fn1r1r7s6svjl3lbryr0"))))
+          "1fgvx7nim9plxnyiq6vmah1dji7ba5290fws1i0lwk9m0g5xpm7a"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -6119,24 +6180,22 @@ major web browsers.")
         (modules '((guix build utils)))
         (snippet
          '(delete-file-recursively "rapidjson"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     `(#:configure-flags
+     (list
-       (list (string-append "--rj-include-dir="
+      #:test-flags '(list "tests")
-                            (assoc-ref %build-inputs "rapidjson")
-                            "/include/rapidjson"))
       #:phases
-       (modify-phases %standard-phases
+      #~(modify-phases %standard-phases
-         (replace 'build
+          ;; We cannot seem to use #:configure-flags with the
-           (lambda* (#:key inputs #:allow-other-keys)
+          ;; pyproject-build-system to override rj_include_dir.
-             (invoke "python" "setup.py" "build"
+          (add-after 'unpack 'override-rapidjson-sources
-                     (string-append "--rj-include-dir="
+            (lambda _
-                                    (assoc-ref %build-inputs "rapidjson")
+              (substitute* "setup.py"
-                                    "/include/rapidjson"))))
+                (("^rj_include_dir =.*")
-         (replace 'check
+                 (string-append "rj_include_dir = '"
-           (lambda* (#:key tests? #:allow-other-keys)
+                                #$(this-package-native-input "rapidjson")
-             (when tests?
+                                "/include/rapidjson" "'"))
-               (invoke "python" "-m" "pytest" "tests")))))))
+                (("if not os.path.isdir.*") "if False:")))))))
     (native-inputs
      (list rapidjson python-pytest python-pytz))
     (home-page "https://github.com/python-rapidjson/python-rapidjson")

gnu/packages/python-xyz.scm

@@ -59,14 +59,14 @@
 ;;; Copyright © 2019, 2020 Brett Gilio <brettg@gnu.org>
 ;;; Copyright © 2019 Sam <smbaines8@gmail.com>
 ;;; Copyright © 2019, 2023 Jack Hill <jackhill@jackhill.us>
-;;; Copyright © 2019, 2020, 2021, 2022 Guillaume Le Vaillant <glv@posteo.net>
+;;; Copyright © 2019-2023, Guillaume Le Vaillant <glv@posteo.net>
 ;;; Copyright © 2019, 2020 Alex Griffin <a@ajgrf.com>
 ;;; Copyright © 2019, 2020, 2021, 2022 Pierre Langlois <pierre.langlois@gmx.com>
 ;;; Copyright © 2019 Jacob MacDonald <jaccarmac@gmail.com>
 ;;; Copyright © 2019, 2020, 2021 Giacomo Leidi <goodoldpaul@autistici.org>
 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
 ;;; Copyright © 2019, 2020, 2021, 2022 Tanguy Le Carrour <tanguy@bioneland.org>
-;;; Copyright © 2019, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2019, 2021-2023 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;; Copyright © 2020 Riku Viitanen <riku.viitanen@protonmail.com>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;; Copyright © 2020 sirgazil <sirgazil@zoho.com>
@@ -583,6 +583,26 @@ and variables you'll need already imported and created.
 scipy and numpy of negative binomial maximum likelihood estimation.")
     (license license:gpl3+)))
 
+(define-public python-docrep
+  (package
+    (name "python-docrep")
+    (version "0.3.2")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "docrep" version))
+              (sha256
+               (base32
+                "0523jrzjj29kxpdllmfhrfj9kysi9mphp2m7ippjkn5b07i1g2pd"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-six))
+    (native-inputs (list python-pytest python-pytest-runner))
+    (home-page "https://github.com/Chilipp/docrep")
+    (synopsis "Python package for docstring repetition")
+    (description "Docrep is the documentation repetition module.  This module
+targets developers that develop complex and nested Python APIs and helps them
+to create a well-documented piece of software.")
+    (license license:asl2.0)))
+
 (define-public python-dotmap
   (package
     (name "python-dotmap")
@@ -621,6 +641,29 @@ remembers the order in which the items were inserted and supports almost all the
 features of the Python's built-in dict.")
     (license license:unlicense)))
 
+(define-public python-adjusttext
+  (package
+    (name "python-adjusttext")
+    (version "0.8")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "adjustText" version))
+              (sha256
+               (base32
+                "05zf0xn7ab40dan213fwbp1z4rybih8dphf9mzb2ddmbafxq41mv"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-matplotlib python-numpy))
+    (home-page "https://github.com/Phlya/adjustText")
+    (synopsis "Adjust text position in matplotlib plots to minimize overlaps")
+    (description
+     "Often when we want to label multiple points on a graph the text will
+start heavily overlapping with both other labels and data points.  This can be
+a major problem requiring manual solution.  However this can be largely
+automatized by smart placing of the labels (difficult) or iterative adjustment
+of their positions to minimize overlaps (relatively easy).  This library
+implements the latter option to help with matplotlib graphs.")
+    (license license:expat)))
+
 (define-public python-argopt
   (package
    (name "python-argopt")
@@ -1141,6 +1184,67 @@ commits.")
 generator MkDocs.")
     (license license:expat)))
 
+(define-public python-skranger
+  (package
+    (name "python-skranger")
+    (version "0.8.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/crflynn/skranger")
+                    (commit version)
+                    (recursive? #true)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0njy4xbc98l295k92nyk93njv1348vd1il5pdyrnk8nnzc2anzf0"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:modules '((guix build pyproject-build-system)
+                  (guix build utils)
+                  (ice-9 match))
+      #:test-flags
+      ;; "from sklearn.datasets import load_boston" fails because it has been
+      ;; removed from scikit-learn since version 1.2.
+      '(list "--ignore=tests/conftest.py"
+             "--ignore=tests/test_tools.py"
+             "--ignore=tests/tree/test_regressor.py"
+             "--ignore=tests/ensemble/test_regressor.py")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'fix-tests
+            (lambda _
+              (substitute* "tests/conftest.py"
+                (("from sklearn.datasets import load_boston") "")
+                (("^_boston_X.*") "_boston_X, _boston_Y = (True, True)\n"))))
+          (add-before 'check 'build-extensions
+            (lambda _
+              ;; Cython extensions have to be built before running the tests.
+              (invoke "python" "buildpre.py")
+              (invoke "python" "build.py" "build_ext" "--inplace")
+              (let ((site (string-append #$output "/lib/python"
+                                         #$(version-major+minor
+                                            (package-version python))
+                                         "/site-packages/skranger"))
+                    (lib (match (find-files "build" "\\.so")
+                           ((the-lib) the-lib)
+                           (_ (error "could not find .so")))))
+                (mkdir-p site)
+                (install-file lib site)))))))
+    (propagated-inputs (list python-scikit-learn))
+    (native-inputs
+     (list python-cython
+           python-matplotlib
+           python-pandas
+           python-poetry-core
+           python-pytest))
+    (home-page "https://github.com/crflynn/skranger")
+    (synopsis "Python bindings for C++ ranger random forests")
+    (description "This package provides scikit-learn compatible Python
+bindings to the C++ random forest implementation, ranger, using Cython.")
+    (license license:gpl3+)))
+
 (define-public python-slixmpp
   (package
     (name "python-slixmpp")
@@ -2690,6 +2794,26 @@ a library.")
     (description "DiskCache is a disk and file backed persistent cache.")
     (license license:asl2.0)))
 
+(define-public python-optparse-pretty
+  (package
+    (name "python-optparse-pretty")
+    (version "0.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "optparse-pretty" version))
+       (sha256
+        (base32 "1920wbh2b7a8qn7zx2iiqbcdaax335l81a73x9pp8h11yzs2jdmh"))))
+    (build-system pyproject-build-system)
+    (arguments (list #:tests? #false))  ;There are none
+    (home-page "https://github.com/gvalkov/optparse-pretty")
+    (synopsis "Compact help formatter for optparse")
+    (description
+     "This module provides two help formatters for optparse.  They provide
+terser and more customizable option formatting in comparison to the default
+help formatter.")
+    (license license:bsd-3)))
+
 (define-public python-orjson
   (package
     (name "python-orjson")
@@ -2703,9 +2827,14 @@ a library.")
     (build-system cargo-build-system)
     (arguments
      (list
+      #:imported-modules `(,@%cargo-build-system-modules
+                           ,@%pyproject-build-system-modules)
+      #:modules '((guix build cargo-build-system)
+                  ((guix build pyproject-build-system) #:prefix py:)
+                  (guix build utils))
       #:phases
       #~(modify-phases %standard-phases
-          (add-after 'install 'build-python-module
+          (add-after 'install 'prepare-python-module
             (lambda _
               ;; We don't use maturin.
               (delete-file "pyproject.toml")
@@ -2719,10 +2848,9 @@ requires = ['setuptools']
               (call-with-output-file "setup.cfg"
                 (lambda (port)
                   (format port "\
-
 [metadata]
 name = orjson
-version = '~a'
+version = ~a
 
 [options]
 packages = find:
@@ -2733,15 +2861,11 @@ exclude =
   integration
   test
   Cargo.toml
-" #$version)))
+" #$version)))))
-              ;; ZIP does not support timestamps before 1980.
+          (add-after 'prepare-python-module 'build-python-module
-              (setenv "SOURCE_DATE_EPOCH" "315532800")
+            (assoc-ref py:%standard-phases 'build))
-              (invoke "python" "-m" "build" "--wheel" "--no-isolation" ".")))
           (add-after 'build-python-module 'install-python-module
-            (lambda* (#:key outputs #:allow-other-keys)
+            (assoc-ref py:%standard-phases 'install))
-              (let ((whl (car (find-files "dist" "\\.whl$"))))
-                (invoke "pip" "--no-cache-dir" "--no-input"
-                        "install" "--no-deps" "--prefix" #$output whl))))
           (add-after 'install-python-module 'install-python-library
             (lambda _
               (let ((site (string-append #$output "/lib/python"
@@ -4870,22 +4994,8 @@ recognition library with full Unicode support.  It has features like:
               (sha256
                (base32
                 "1nh75i72584r70alhqc479gys04s5m5g3vq601yf2njbs7z5jzng"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
-    (arguments
+    (arguments (list #:tests? #f))      ;pypi source does not contains tests
-     (list
-      #:tests? #f                       ;pypi source does not contains tests
-      #:phases
-      #~(modify-phases %standard-phases
-          (replace 'build
-            (lambda _ (invoke "flit" "build")))
-          (replace 'install
-            (lambda* (#:key inputs outputs #:allow-other-keys)
-              (add-installed-pythonpath inputs outputs)
-              (for-each
-               (lambda (wheel)
-                 (invoke "python" "-m" "pip" "install"
-                         wheel (string-append "--prefix=" #$output)))
-               (find-files "dist" "\\.whl$")))))))
     (native-inputs (list python-flit))
     (propagated-inputs
      (list python-mdurl
@@ -9588,6 +9698,37 @@ module with a few extra procedures.")
 releases.")
     (license license:expat)))
 
+(define-public python-jaraco-test
+  (package
+    (name "python-jaraco-test")
+    (version "5.3.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "jaraco.test" version))
+              (sha256
+               (base32
+                "0h0x8qmvfkfqvwdx2m7kwhn53sg26k8gkaas7s1730ak772zqrvz"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases #~(modify-phases %standard-phases
+                   (replace 'check
+                     (lambda _
+                       (invoke "pytest" "-vv" "-k" "http"))))))
+    (propagated-inputs (list python-jaraco-context python-jaraco-functools))
+    (native-inputs (list python-flake8
+                         python-pytest
+                         python-pytest-black
+                         python-pytest-checkdocs
+                         python-pytest-cov
+                         python-pytest-enabler
+                         python-pytest-flake8
+                         python-pytest-mypy))
+    (home-page "https://github.com/jaraco/jaraco.test")
+    (synopsis "Testing support by jaraco")
+    (description "This package provides testing support by jaraco.")
+    (license license:expat)))
+
 (define-public python-simplegeneric
   (package
     (name "python-simplegeneric")
@@ -11094,27 +11235,7 @@ SVG, EPS, PNG and terminal output.")
               (sha256
                (base32
                 "08vvnp4ps86857imxz2l5xi2vir5xdcdp3apq4badb4b5llifgw9"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
-    (arguments
-     (list #:modules '((guix build python-build-system)
-                       (guix build utils)
-                       (ice-9 match))
-           #:phases #~(modify-phases %standard-phases
-                        (replace 'build
-                          (lambda _
-                            (invoke "python" "-m" "build" "--wheel"
-                                    "--no-isolation" ".")))
-                        (replace 'install
-                          (lambda _
-                            (match (find-files "dist" "\\.whl$")
-                              ((wheel _ ...)
-                               (invoke "python" "-m" "pip" "install"
-                                       (string-append "--prefix=" #$output)
-                                       wheel)))))
-                        (replace 'check
-                          (lambda* (#:key tests? #:allow-other-keys)
-                            (when tests?
-                              (invoke "pytest" "-vv")))))))
     (propagated-inputs (list python-pandas python-matplotlib python-numpy
                              python-scipy))
     (native-inputs (list python-flit-core python-pypa-build python-pytest))
@@ -11127,7 +11248,6 @@ with the PyData stack, including support for numpy and pandas data structures
 and statistical routines from scipy and statsmodels.")
     (license license:bsd-3)))
 
-
 (define-public python-session-info
   (package
     (name "python-session-info")
@@ -11716,7 +11836,37 @@ you do not want to store entirely on disk or on memory.")
                         " and not test_httplib_misuse"
                         ;; Fails with IndexError.
                         " and not test_session_mode_defaults_to"
-                        "_request_mode_in_wsgi_handler"))))))))
+                        "_request_mode_in_wsgi_handler"
+                        ;; Tests below fail with pytest 7
+                        " and not test_leaks"
+                        " and not test_basic"
+                        " and not test_keyboard_interrupt_is_captured"
+                        " and not test_transaction_with_error"
+                        " and not test_transaction_no_error"
+                        " and not test_start_span_to_start_transaction"
+                        " and not test_tracestate_computation"
+                        " and not test_doesnt_add_new_tracestate_to_transaction_when_none_given"
+                        " and not test_adds_tracestate_to_transaction_when_to_traceparent_called"
+                        " and not test_adds_tracestate_to_transaction_when_getting_trace_context"
+                        " and not test_tracestate_is_immutable_once_set"
+                        " and not test_to_traceparent"
+                        " and not test_to_tracestate"
+                        " and not test_sentrytrace_extraction"
+                        " and not test_tracestate_extraction"
+                        " and not test_iter_headers"
+                        " and not test_tracestate_reinflation"
+                        " and not test_continue_from_headers"
+                        " and not test_memory_usage"
+                        " and not test_transactions_do_not_go_through_before_send"
+                        " and not test_start_span_after_finish"
+                        " and not test_span_trimming"
+                        " and not test_transaction_naming"
+                        " and not test_start_transaction"
+                        " and not test_finds_transaction_on_scope"
+                        " and not test_finds_transaction_when_descendent_span_is_on_scope"
+                        " and not test_finds_orphan_span_on_scope"
+                        " and not test_finds_non_orphan_span_on_scope"
+                        " and not test_circular_references"))))))))
     (native-inputs
      (list python-django
            python-executing
@@ -11809,31 +11959,7 @@ plugin for flake8 to check PEP-8 naming conventions.")
        (sha256
         (base32
          "00zahgw9zjfqwf0218bj5k732aibnn68cq1p8f0wmbirb7fy5k31"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          ;; XXX: PEP 517 manual build/install procedures copied from
-          ;; python-isort.
-          (replace 'build
-            (lambda _
-              ;; ZIP does not support timestamps before 1980.
-              (setenv "SOURCE_DATE_EPOCH" "315532800")
-              (invoke "python" "-m" "build" "--wheel" "--no-isolation" ".")))
-          (replace 'check
-            (lambda* (#:key tests? inputs outputs #:allow-other-keys)
-              (when tests?
-                (invoke "pytest" "-vv"
-                        ;; Two parameterized test_load tests are currently
-                        ;; failing (see:
-                        ;; https://github.com/FFY00/python-pep621/issues/14).
-                        "-k" "not test_load"))))
-          (replace 'install
-            (lambda* (#:key outputs #:allow-other-keys)
-              (let ((whl (car (find-files "dist" "\\.whl$"))))
-                (invoke "pip" "--no-cache-dir" "--no-input"
-                        "install" "--no-deps" "--prefix" #$output whl)))))))
     (propagated-inputs (list python-packaging))
     (native-inputs (list python-pypa-build python-pytest python-tomli))
     (home-page "https://github.com/FFY00/python-pyproject-metadata")
@@ -16860,13 +16986,13 @@ ISO 8859, etc.).")
 (define-public python-anyqt
   (package
     (name "python-anyqt")
-    (version "0.0.13")
+    (version "0.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "AnyQt" version))
        (sha256
-        (base32 "0z7myf0mp1qx4gza6ncqyq9whk67vblmh9n3klk19dv4aakjml2f"))))
+        (base32 "0fvnhdk0nzhlm1xydisvdq1w7lwaakdkbwb1rkyz4vd232wji4jb"))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #f ;there are no tests
@@ -17254,6 +17380,36 @@ can also be used to get the exact location, font or color of the text.")
 is made as zipfile like as possible.")
     (license license:isc)))
 
+(define-public python-slugid
+  (package
+    (name "python-slugid")
+    (version "2.0.0")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+              (url "https://github.com/taskcluster/slugid.py")
+              (commit (string-append "v" version))))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "1h64p2jlqv6lsmw8h2j203kx3bhv72cwzpk5gdhsaamw30cp3h1i"))))
+    (build-system python-build-system)
+    (native-inputs (list python-nose))
+    (arguments
+      (list #:phases
+        #~(modify-phases %standard-phases
+            (replace 'check
+              (lambda* (#:key inputs tests? #:allow-other-keys)
+                (when tests?
+                  ;; The project uses tox to run the tests via nose.
+                  (invoke "nosetests" "-v" "test.py")))))))
+    (home-page "http://taskcluster.github.io/slugid.py")
+    (synopsis "Module for Base64 encoded UUID v4 slugs")
+    (description "This package provides a module for generating v4
+UUIDs and encoding them into 22 character URL-safe base64 slug
+representation.")
+    (license license:mpl2.0)))
+
 (define-public python-rich
   (package
     (name "python-rich")
@@ -18131,6 +18287,65 @@ specified in POSIX.1-2001 and POSIX.1-2008.")
 objects, patterned after the Mocha library for Ruby.")
     (license license:bsd-3)))
 
+(define-public python-inflect
+  (package
+    (name "python-inflect")
+    (version "6.0.4")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "inflect" version))
+              (sha256
+               (base32
+                "1sqj4svg2vbn4vq332nxnvky2433rgxbvjd529lddjmn2yd68hhq"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      '(list "--ignore=_custom_build/backend.py"
+             "-k" "not mypy-status")
+      #:phases
+      '(modify-phases %standard-phases
+         ;; The build system insists on ignoring the existing environment and
+         ;; running "pip install".
+         (add-after 'unpack 'do-not-use-pip-install
+           (lambda _
+             (substitute* "pyproject.toml"
+               (("^build-backend.*") "\
+build-backend = \"backend\"
+backend_path = [\"_custom_build\"]\n")
+               (("requires = .*") "requires = []\n"))
+             (mkdir-p "_custom_build")
+             (with-output-to-file "_custom_build/backend.py"
+               (lambda _
+                 (display "\
+from setuptools import build_meta as _orig
+from setuptools.build_meta import *
+def get_requires_for_build_wheel(config_settings=None):
+    return []
+def get_requires_for_build_sdist(config_settings=None):
+    return []
+")))
+             (setenv "PYTHONPATH"
+                     (string-append (getcwd) "/_custom_build")))))))
+    (propagated-inputs (list python-pydantic))
+    (native-inputs (list python-flake8
+                         python-pygments
+                         python-pytest
+                         python-pytest-black
+                         python-pytest-checkdocs
+                         python-pytest-cov
+                         python-pytest-enabler
+                         python-pytest-flake8
+                         python-pytest-mypy
+                         ;; For the version number
+                         python-setuptools-scm))
+    (home-page "https://github.com/jaraco/inflect")
+    (synopsis "Correctly generate plurals, singular nouns, ordinals, indefinite articles")
+    (description
+     "This Python module lets you correctly generate plurals, singular nouns,
+ordinals, indefinite articles; it also can convert numbers to words.")
+    (license license:expat)))
+
 (define-public python-inflection
   (package
     (name "python-inflection")
@@ -22049,14 +22264,14 @@ functionality like full case-folding for case-insensitive matches in Unicode.")
 (define-public python-pyopengl
   (package
     (name "python-pyopengl")
-    (version "3.1.5")
+    (version "3.1.6")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "PyOpenGL" version))
        (sha256
         (base32
-         "091lp9bpqi8yf1nmyg19xmvw611lrzq2q94cl1k5gnlh0c6vl1s1"))))
+         "09syrsfrcknr1k2wmj05gfd5d0dyjfxzbipzbd0agv9775vwi9lf"))))
     (build-system python-build-system)
     (inputs
      (list mesa freeglut glu))
@@ -22094,14 +22309,14 @@ library.")
   (package
     (inherit python-pyopengl)
     (name "python-pyopengl-accelerate")
-    (version "3.1.5")
+    (version "3.1.6")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "PyOpenGL-accelerate" version))
        (sha256
         (base32
-         "01iggy5jwxv7lxnj51zbmlbhag9wcb7dvrbwgi97i90n0a5m3r8j"))))
+         "1hydrpdn4p4z6mlczcg1y4s0z8si3rs6zq8x4ql558pcaq1312md"))))
     (inputs
      (list mesa python-numpy)) ; for cython module
                                         ; numpy_formathandler, thus not propagated
@@ -22727,19 +22942,27 @@ queue.")
 (define-public python-zict
   (package
     (name "python-zict")
-    (version "2.0.0")
+    (version "3.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "zict" version))
        (sha256
         (base32
-         "05pd1hyhqvpw87rnbvl3vdyf619snpyccbswaxisdj17frwnjacf"))))
+         "19gvr41xi5fazkzkg33kwrk70sv50hygng0cg70ayym9nriy48g3"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      ;; This uses "importorskip", but it won't skip.
+      '(list "--ignore=tests/test_lmdb.py")))
     (propagated-inputs
      (list python-heapdict))
     (native-inputs
-     (list python-pytest))
+     (list python-pytest
+           python-pytest-asyncio
+           python-pytest-repeat
+           python-pytest-timeout))
     (home-page "https://zict.readthedocs.io/en/latest/")
     (synopsis "Composable mutable mapping tools")
     (description "This package provides abstract @code{MutableMapping} classes
@@ -22806,13 +23029,13 @@ user's @file{~/Trash} directory.")
 (define-public python-yamllint
   (package
     (name "python-yamllint")
-    (version "1.26.1")
+    (version "1.31.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "yamllint" version))
        (sha256
-        (base32 "090krlxj7az0d9yl8i20vjrqi66dfxx7y5xakjhxzsfp7qmldnc7"))))
+        (base32 "0rbs7xq7y7bp3k75z7jamrdrrfyp95hifsz0hwm1cgkk5z8z30rd"))))
     (build-system python-build-system)
     (propagated-inputs
      (list python-pathspec python-pyyaml python-setuptools))
@@ -24787,16 +25010,38 @@ append on old values.  Partd excels at shuffling operations.")
 (define-public python-fsspec
   (package
     (name "python-fsspec")
-    (version "2022.5.0")
+    (version "2023.5.0")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (pypi-uri "fsspec" version))
+       (uri (git-reference
+             (url "https://github.com/fsspec/filesystem_spec")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1d43qiz8g395042a52yswz6j7q41gvrv3k53wvxn1rs4bk3mjm3s"))))
+         "0c0brw5s4330rj0yjcrqi56hanvaahn43854jai70qzqg1qvyl88"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
-    (arguments '(#:tests? #f))          ; there are none
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'fix-version
+            (lambda _
+              (substitute* "fsspec/__init__.py"
+                (("__version__ = .*")
+                 (string-append "__version__ = \"" #$version "\"")))
+              (substitute* "setup.py"
+                (("versioneer.get_version\\(\\)")
+                 (string-append "\"" #$version "\""))))))
+      #:test-flags
+      '(list
+        ;; requires internet access
+        "--ignore=fsspec/implementations/tests/test_dbfs.py")))
+    (propagated-inputs
+     (list python-aiohttp python-libarchive-c python-requests python-tqdm))
+    (native-inputs
+     (list python-pytest python-pytest-mock python-numpy))
     (home-page "https://github.com/intake/filesystem_spec")
     (synopsis "File-system specification")
     (description "The purpose of this package is to produce a template or
@@ -24810,29 +25055,61 @@ decisions with any given backend.")
 (define-public python-dask
   (package
     (name "python-dask")
-    (version "2022.05.2")
+    (version "2023.4.1")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/dask/dask/")
-             (commit "8db1597c9745543df3129399bead5fbc95a54571")))
+             (commit "a69a808f75a961504a9ba18058bff5e458be97fb")))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1xfk3wml972z502w5ii5mn03ls3rg5p4hqgl0hkicgpmzlyz9kph"))
+        (base32 "089kz6hcgl4yxwx99br1124sg1gkdy554hf120z9a5cfbrf0ah9y"))))
-       (snippet
+    (build-system pyproject-build-system)
-        ;; Delete generated copy of python-versioneer.  We recreate it below.
-        '(delete-file "versioneer.py"))))
-    (build-system python-build-system)
     (arguments
-     `(#:phases
+     (list
-       (modify-phases %standard-phases
+      ;; Avoid coverage
+      #:test-flags
+      #~(list "-m" "not gpu and not slow and not network"
+              "-k" (string-append
+                    ;; This one cannot be interrupted.
+                    "not test_interrupt"
+                    ;; This one expects a deprecation warning that never
+                    ;; comes.
+                    " and not test_RandomState_only_funcs")
+              ;; Tests must run from the output directory, because otherwise
+              ;; it complains about the difference between the target
+              ;; directory embedded in the pyc files and the source directory
+              ;; from which we run tests.
+              (getcwd))
+      #:phases
+      #~(modify-phases %standard-phases
           (add-after 'unpack 'versioneer
             (lambda _
-             (invoke "versioneer" "install")))
+              ;; Our version of versioneer needs setup.cfg.  This is adapted
-         (replace 'check
+              ;; from pyproject.toml.
-           (lambda* (#:key tests? #:allow-other-keys)
+              (with-output-to-file "setup.cfg"
-             (when tests? (invoke "pytest" "-vv")))))))
+                (lambda ()
+                  (display "\
+[versioneer]
+VCS = git
+style = pep440
+versionfile_source = dask/_version.py
+versionfile_build = dask/_version.py
+tag_prefix =
+parentdir_prefix = dask-
+")))
+              (invoke "versioneer" "install")
+              (substitute* "setup.py"
+                (("versioneer.get_version\\(\\)")
+                 (string-append "\"" #$version "\"")))))
+          (add-after 'unpack 'fix-pytest-config
+            (lambda _
+              ;; This option is not supported by our version of pytest.
+              (substitute* "pyproject.toml"
+                (("--cov-config=pyproject.toml") ""))))
+          (add-before 'check 'pre-check
+            (lambda _ (chdir "/tmp"))))))
     (propagated-inputs
      (list python-cloudpickle
            python-fsspec
@@ -24843,7 +25120,9 @@ decisions with any given backend.")
            python-toolz
            python-pyyaml))
     (native-inputs
-     (list python-pytest python-pytest-runner python-pytest-rerunfailures
+     (list python-click
+           python-importlib-metadata
+           python-pytest python-pytest-runner python-pytest-rerunfailures
            python-versioneer))
     (home-page "https://github.com/dask/dask/")
     (synopsis "Parallel computing with task scheduling")
@@ -27270,7 +27549,7 @@ information for your operating system.")
        (uri (pypi-uri "canonicaljson" version))
        (sha256
         (base32 "0j5lq191jkd483q6xzc16c9fahxf15lrv03mvah9ka3lq85pcnfa"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
      (list
       #:phases
@@ -27279,21 +27558,7 @@ information for your operating system.")
            (lambda _
              ;; Permit newer versions of setuptools_scm
              (substitute* "pyproject.toml"
-               ((">= 2.0.0, <3") ">= 2.0.0"))))
+               ((">= 2.0.0, <3") ">= 2.0.0")))))))
-          (replace 'build
-            (lambda _
-              ;; ZIP does not support timestamps before 1980.
-              (setenv "SOURCE_DATE_EPOCH" "315532800")
-              (invoke "python" "-m" "build" "--wheel" "--no-isolation" ".")))
-          (replace 'check
-            (lambda* (#:key tests? #:allow-other-keys)
-              (when tests?
-                (invoke "pytest"))))
-          (replace 'install
-            (lambda _
-              (let ((whl (car (find-files "dist" "\\.whl$"))))
-                (invoke "pip" "--no-cache-dir" "--no-input"
-                        "install" "--no-deps" "--prefix" #$output whl)))))))
     (native-inputs
      (list python-pypa-build python-pytest python-setuptools python-setuptools-scm))
     (propagated-inputs
@@ -32614,24 +32879,7 @@ Storage}.")
               (sha256
                (base32
                 "1f3qrygj16y767q2c7pn9j6m95ggcmj9s5cx9v92ygygly4mr3jp"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (replace 'check
-            (lambda* (#:key tests? #:allow-other-keys)
-              (when tests?
-                (invoke "pytest" "-v" "tests"))))
-          ;; XXX: PEP 517 manual build copied from python-isort.
-          (replace 'build
-            (lambda _
-              (invoke "python" "-m" "build" "--wheel" "--no-isolation" ".")))
-          (replace 'install
-            (lambda _
-              (let ((whl (car (find-files "dist" "\\.whl$"))))
-                (invoke "pip" "--no-cache-dir" "--no-input"
-                        "install" "--no-deps" "--prefix" #$output whl)))))))
     (native-inputs
      (list python-click
            python-poetry-core

gnu/packages/rdf.scm

@@ -33,6 +33,7 @@
   #:use-module (guix download)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system meson)
   #:use-module (guix build-system python)
   #:use-module (guix build-system waf)
   #:use-module (gnu packages)
@@ -278,26 +279,24 @@ and triple stores.")
 (define-public serd
   (package
     (name "serd")
-    (version "0.30.8")
+    (version "0.30.16")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://download.drobilla.net/serd-"
-                                 version ".tar.bz2"))
+                                 version ".tar.xz"))
              (sha256
               (base32
-               "11zs53yx40mv62vxsl15mvdh7s17y5v6lgcgahdvzxgnan7w8bk7"))))
+               "0ilimkczibiwwvc12i14b8zi6ng42hjf9j907g8dik8rlmnlh3zm"))))
-    (build-system waf-build-system)
+    (build-system meson-build-system)
     (arguments
-     `(#:tests? #f                      ; no check target
+     (list
+      #:tests? #f                       ; no check target
       #:phases
-       (modify-phases %standard-phases
+      #~(modify-phases %standard-phases
-         (add-before
+          (add-before 'configure 'set-ldflags
-          'configure 'set-ldflags
+            (lambda _
-          (lambda* (#:key outputs #:allow-other-keys)
               (setenv "LDFLAGS"
-                    (string-append "-Wl,-rpath="
+                      (string-append "-Wl,-rpath=" #$output "/lib")))))))
-                                   (assoc-ref outputs "out") "/lib"))
-            #t)))))
     (home-page "https://drobilla.net/software/serd/")
     (synopsis "Library for RDF syntax supporting Turtle and NTriples")
     (description
@@ -312,26 +311,24 @@ ideal (e.g. in LV2 implementations or embedded applications).")
 (define-public sord
   (package
     (name "sord")
-    (version "0.16.8")
+    (version "0.16.14")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://download.drobilla.net/sord-"
-                                 version ".tar.bz2"))
+                                 version ".tar.xz"))
              (sha256
               (base32
-               "052y7zllrg0bzyky2rmrrwnnf16p6bk7q40rq9mgm0mzm8p9sa3w"))))
+               "06vkqk3dnn15zdnzklahib2pvbfspy2zcrnvhmxnw8fbbxyxj3r2"))))
-    (build-system waf-build-system)
+    (build-system meson-build-system)
     (arguments
-     `(#:tests? #f                      ; no check target
+     (list
+      #:tests? #f                       ; no check target
       #:phases
-       (modify-phases %standard-phases
+      #~(modify-phases %standard-phases
-         (add-before
+          (add-before 'configure 'set-ldflags
-          'configure 'set-ldflags
+            (lambda _
-          (lambda* (#:key outputs #:allow-other-keys)
               (setenv "LDFLAGS"
-                    (string-append "-Wl,-rpath="
+                      (string-append "-Wl,-rpath=" #$output "/lib")))))))
-                                   (assoc-ref outputs "out") "/lib"))
-            #t)))))
     (inputs
      (list pcre))
     (native-inputs

gnu/packages/ruby.scm

@@ -29,7 +29,7 @@
 ;;; Copyright © 2020 Tomás Ortín Fernández <tomasortin@mailbox.org>
 ;;; Copyright © 2021 Giovanni Biscuolo <g@xelera.eu>
 ;;; Copyright © 2022 Philip McGrath <philip@philipmcgrath.com>
-;;; Copyright © 2022 Remco van 't Veer <remco@remworks.net>
+;;; Copyright © 2022, 2023 Remco van 't Veer <remco@remworks.net>
 ;;; Copyright © 2022 Taiju HIGASHI <higashi@taiju.info>
 ;;; Copyright © 2023 Yovan Naumovski <yovan@gorski.stream>
 ;;;
@@ -163,6 +163,7 @@ a focus on simplicity and productivity.")
   (package
     (inherit ruby-2.6)
     (version "2.7.6")
+    (replacement ruby-2.7-fixed) ; security fixes
     (source
      (origin
        (inherit (package-source ruby-2.6))
@@ -200,7 +201,7 @@ a focus on simplicity and productivity.")
 (define ruby-2.7-fixed
   (package
     (inherit ruby-2.7)
-    (version "2.7.7")
+    (version "2.7.8")
     (source
      (origin
        (inherit (package-source ruby-2.7))
@@ -209,12 +210,12 @@ a focus on simplicity and productivity.")
                            "/ruby-" version ".tar.gz"))
        (sha256
         (base32
-         "143vih5jzmrd2r5h94pa3qzml0ldii0qzs6g09jg6zqxd7djf0g1"))))))
+         "182vni66djmiqagwzfsd0za7x9k3zag43b88c590aalgphybdnn2"))))))
 
 (define-public ruby-3.0
   (package
     (inherit ruby-2.7)
-    (version "3.0.5")
+    (version "3.0.6")
     (source
      (origin
        (method url-fetch)
@@ -223,7 +224,7 @@ a focus on simplicity and productivity.")
                            "/ruby-" version ".tar.xz"))
        (sha256
         (base32
-         "1pnxbdkkh2miq9nqfq2qscvh76nprzg0r620d9ckdzih42xbaz6g"))))
+         "1lfvgm6jbspmwmc3haww83l1l8vl1airzi08ljrcz19dws9yxjxm"))))
     (inputs
      (modify-inputs (package-inputs ruby-2.7)
        (replace "openssl" openssl)))))
@@ -231,7 +232,7 @@ a focus on simplicity and productivity.")
 (define-public ruby-3.1
   (package
     (inherit ruby-3.0)
-    (version "3.1.3")
+    (version "3.1.4")
     (source
      (origin
        (method url-fetch)
@@ -240,12 +241,12 @@ a focus on simplicity and productivity.")
                            "/ruby-" version ".tar.xz"))
        (sha256
         (base32
-         "06ipqz45qcs0y1273gk2gwslxwd7jgighz3mzbddzg16k29n3qaf"))))))
+         "0kzr792rk9n9yrqlyrkc1a0cmbk5y194f7v7p4vwjdk0ww860v8v"))))))
 
 (define-public ruby-3.2
   (package
     (inherit ruby-3.1)
-    (version "3.2.1")
+    (version "3.2.2")
     (source
      (origin
        (method url-fetch)
@@ -254,7 +255,7 @@ a focus on simplicity and productivity.")
                            "/ruby-" version ".tar.xz"))
        (sha256
         (base32
-         "0333xln2jkqdfk5zwxas6rpyd4rff2910z99qnyrqi15mrhqcv3l"))))
+         "08wy2ishjwbccfsrd0iwmyadbwjzrpyxnk74wcrf7163gq7jsdab"))))
     (inputs
      (modify-inputs (package-inputs ruby-3.1)
        (prepend libyaml)))))

gnu/packages/scheme.scm

@@ -639,7 +639,8 @@ threads.")
                                  ""))))
                           (add-before 'install 'build
                             (lambda _
-                              (invoke "makeinfo" "--output=sicp.info"
+                              (invoke "makeinfo" "--no-split"
+                                      "--output=sicp.info"
                                       "sicp-pocket.texi"))))))
       (home-page "https://sarabander.github.io/sicp")
       (synopsis "Structure and Interpretation of Computer Programs")

gnu/packages/search.scm

@@ -735,14 +735,14 @@ bibliographic data and simple document and bibtex retrieval.")
 (define-public ugrep
   (package
     (name "ugrep")
-    (version "3.11.0")
+    (version "3.11.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/Genivia/ugrep")
                     (commit (string-append "v" version))))
               (sha256
-               (base32 "1sibd44ky7xqfmrfvi09h5ignn7i3v1fjxnfvybp3cjfm08yxacy"))
+               (base32 "0k0dzdyif9lpk0avjk02xkd6bjg9km4spr3p4hzls88y9hwgcc9l"))
               (file-name (git-file-name name version))
               (modules '((guix build utils)))
               (snippet

gnu/packages/shells.scm

@@ -535,14 +535,14 @@ ksh, and tcsh.")
 (define-public xonsh
   (package
     (name "xonsh")
-    (version "0.13.4")
+    (version "0.14.0")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "xonsh" version))
         (sha256
           (base32
-           "19r1g8i8k6ds7ncvqdh58vkm4m5hz4w9zbglmg1mi7xcdqp4ax8h"))
+           "1wcv1sk8igs5kb9fqb8njbxwiqbwzpn0kdx9xkaddq3wn6msma25"))
         (modules '((guix build utils)))
         (snippet
          #~(begin
@@ -851,7 +851,7 @@ Shell (pdksh).")
 (define-public oil
   (package
     (name "oil")
-    (version "0.14.2")
+    (version "0.15.0")
     (source
      ;; oil's sources contain a modified version of CPython 2.7.13.
      ;; According to https://www.oilshell.org/blog/2017/05/05.html
@@ -864,7 +864,7 @@ Shell (pdksh).")
        (uri (string-append "https://www.oilshell.org/download/oil-"
                            version ".tar.gz"))
        (sha256
-        (base32 "0qsfkav6a70nvp27ilab7zilmihw4ygga48a0dkxa14q9giwlgwr"))))
+        (base32 "1yy4523lbwkb0abnnvp4v08nv94isxb16wjryrp820idb90c1zfb"))))
     (build-system gnu-build-system)
     (arguments
      (list #:strip-binaries? #f         ; strip breaks the binary

gnu/packages/speech.scm

@@ -4,7 +4,7 @@
 ;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2018, 2020–2022 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2016 Kei Kebreau <kkebreau@posteo.net>
-;;; Copyright © 2019, 2021, 2022 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2019, 2021, 2022, 2023 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2020 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2021 qblade <qblade@protonmail.com>
@@ -608,7 +608,7 @@ recognition engine.")
 (define-public ekho
   (package
     (name "ekho")
-    (version "8.4")
+    (version "8.6")
     (source
      (origin
        (method url-fetch)
@@ -616,7 +616,7 @@ recognition engine.")
         (string-append "mirror://sourceforge/e-guidedog/Ekho/"
                        version "/ekho-" version ".tar.xz"))
        (sha256
-        (base32 "1v476kpw09ljj8mavasj4hya2w11jwlx7q22rh1lsn9jkkam5i2a"))))
+        (base32 "1hxdh8bs4zs83w19z897wb4n8n0kyv0ycjfwbi5w0j7mcxsqwh27"))))
     (native-inputs
      (list pkg-config))
     (inputs

gnu/packages/sphinx.scm

@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014 David Thompson <davet@gnu.org>
-;;; Copyright © 2015, 2017, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2017, 2019, 2020, 2021, 2023 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015, 2016, 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2016-2019, 2022 Marius Bakke <marius@gnu.org>
@@ -368,15 +368,8 @@ Blog, News or Announcements section to a Sphinx website.")
         (file-name (git-file-name name version))
         (sha256
          (base32 "1ivqz6yv96a2jp59kylg1gbkrmzq6zwilppz3ij0zrkjn25zb97k"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
-    (arguments
+    (propagated-inputs (list python-docutils-0.15 python-sphinx-4))
-     '(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               (invoke "pytest")))))))
-    (propagated-inputs (list python-docutils python-sphinx-4))
     (native-inputs
      (list python-pytest
            python-pytest-regressions))

gnu/packages/sssd.scm

@@ -27,6 +27,7 @@
   #:use-module (guix download)
   #:use-module (guix gexp)
   #:use-module (guix git-download)
+  #:use-module (guix modules)
   #:use-module (guix utils)
   #:use-module (guix build utils)
   #:use-module (guix build-system gnu)
@@ -151,6 +152,8 @@ fundamental object types for C.")
     (build-system gnu-build-system)
     (arguments
      (list
+      #:imported-modules (source-module-closure
+                          '((guix build python-build-system)))
       #:make-flags
       #~(list (string-append "CFLAGS=-DRENEWAL_PROG_PATH=\\\""
                              #$(this-package-input "adcli") "/sbin/adcli"
@@ -184,6 +187,8 @@ fundamental object types for C.")
                              "/xml/dtd/docbook/catalog.xml"))
       #:phases
       #~(modify-phases %standard-phases
+          (add-after 'unpack 'ensure-no-mtimes-pre-1980
+            (@@ (guix build python-build-system) ensure-no-mtimes-pre-1980))
           (add-after 'patch-source-shebangs 'patch-more-shebangs
             (lambda _
               (substitute* '("src/tools/analyzer/sss_analyze"
@@ -266,8 +271,8 @@ fundamental object types for C.")
            p11-kit ; for PKCS#11 support
            pcre2
            popt
-           python
+           python ; for wrap-program phase
-           samba
+           samba/pinned
            talloc
            tdb
            tevent))
@@ -286,6 +291,7 @@ fundamental object types for C.")
            libxslt
            openssh ; for tests
            pkg-config
+           python-toolchain
            po4a
            softhsm ; for tests
            `(,util-linux "lib"))) ; for uuid.h, reqired for KCM