Merge branch 'master' into emacs-team

Makefile.am

@@ -140,6 +140,7 @@ MODULES =					\
   guix/platforms/arm.scm                        \
   guix/platforms/avr.scm                        \
   guix/platforms/mips.scm                       \
+  guix/platforms/or1k.scm                       \
   guix/platforms/powerpc.scm                    \
   guix/platforms/riscv.scm                      \
   guix/platforms/x86.scm                        \
@@ -453,9 +454,6 @@ AUX_FILES =						\
   gnu/packages/aux-files/linux-libre/4.19-arm64.conf	\
   gnu/packages/aux-files/linux-libre/4.19-i686.conf	\
   gnu/packages/aux-files/linux-libre/4.19-x86_64.conf	\
-  gnu/packages/aux-files/linux-libre/4.14-arm.conf	\
-  gnu/packages/aux-files/linux-libre/4.14-i686.conf	\
-  gnu/packages/aux-files/linux-libre/4.14-x86_64.conf	\
   gnu/packages/aux-files/pack-audit.c			\
   gnu/packages/aux-files/python/sanity-check.py		\
   gnu/packages/aux-files/python/sitecustomize.py	\

doc/contributing.texi

@@ -2111,9 +2111,15 @@ they are ready to become a committer.  Commit access should not be
 thought of as a ``badge of honor'' but rather as a responsibility a
 contributor is willing to take to help the project.  It is expected from
 all contributors, and even more so from committers, to help build
-consensus and make decisions based on consensus.  To learn what
+consensus and make decisions based on consensus.  By using consensus, we
-consensus decision making means and understand its finer details, you
+are committed to finding solutions that everyone can live with.  It
-are encouraged to read
+implies that no decision is made against significant concerns and these
+concerns are actively resolved with proposals that work for everyone.  A
+contributor (which may or may not have commit access) wishing to block a
+proposal bears a special responsibility for finding alternatives,
+proposing ideas/code or explain the rationale for the status quo to
+resolve the deadlock.  To learn what consensus decision making means and
+understand its finer details, you are encouraged to read
 @url{https://www.seedsforchange.org.uk/consensus}.
 
 The following sections explain how to get commit access, how to be ready
@@ -2328,7 +2334,7 @@ Perhaps the biggest action you can do to help GNU Guix grow as a project
 is to review the work contributed by others.  You do not need to be a
 committer to do so; applying, reading the source, building, linting and
 running other people's series and sharing your comments about your
-experience will give some confidence to committers.  Basically, you gmust
+experience will give some confidence to committers.  Basically, you must
 ensure the check list found in the @ref{Submitting Patches} section has
 been correctly followed.  A reviewed patch series should give the best
 chances for the proposed change to be merged faster, so if a change you

doc/guix.texi

@@ -22,7 +22,7 @@
 @set SUBSTITUTE-URLS https://@value{SUBSTITUTE-SERVER-1} https://@value{SUBSTITUTE-SERVER-2}
 
 @copying
-Copyright @copyright{} 2012-2023 Ludovic Courtès@*
+Copyright @copyright{} 2012-2024 Ludovic Courtès@*
 Copyright @copyright{} 2013, 2014, 2016 Andreas Enge@*
 Copyright @copyright{} 2013 Nikita Karetnikov@*
 Copyright @copyright{} 2014, 2015, 2016 Alex Kost@*
@@ -43,7 +43,7 @@ Copyright @copyright{} 2016, 2017, 2018, 2019, 2020, 2021 Christopher Baines@*
 Copyright @copyright{} 2017, 2018, 2019 Clément Lassieur@*
 Copyright @copyright{} 2017, 2018, 2020, 2021, 2022 Mathieu Othacehe@*
 Copyright @copyright{} 2017 Federico Beffa@*
-Copyright @copyright{} 2017, 2018 Carlo Zancanaro@*
+Copyright @copyright{} 2017, 2018, 2024 Carlo Zancanaro@*
 Copyright @copyright{} 2017 Thomas Danckaert@*
 Copyright @copyright{} 2017 humanitiesNerd@*
 Copyright @copyright{} 2017, 2021 Christine Lemmer-Webber@*
@@ -124,6 +124,7 @@ Copyright @copyright{} 2023 Thomas Ieong@*
 Copyright @copyright{} 2023 Saku Laesvuori@*
 Copyright @copyright{} 2023 Graham James Addis@*
 Copyright @copyright{} 2023 Tomas Volf@*
+Copyright @copyright{} 2024 Herman Rimm@*
 
 Permission is granted to copy, distribute and/or modify this document
 under the terms of the GNU Free Documentation License, Version 1.3 or
@@ -732,14 +733,17 @@ ready to use it.
 
 @cindex installing Guix from binaries
 @cindex installer script
-This section describes how to install Guix on an arbitrary system from a
+This section describes how to install Guix from a self-contained tarball
-self-contained tarball providing binaries for Guix and for all its
+providing binaries for Guix and for all its dependencies.  This is often
-dependencies.  This is often quicker than installing from source, which
+quicker than installing from source, which is described in the next
-is described in the next sections.  The only requirement is to have
+sections.  Binary installation requires a system using a Hurd or Linux
-GNU@tie{}tar and Xz.
+kernel; the GNU@tie{}tar and Xz commands must also be available.
+
+@quotation Important
+This section only applies to systems without Guix.  Following it for
+existing Guix installations will overwrite important system files.
 
 @c Note duplicated from the ``Installation'' node.
-@quotation Note
 We recommend the use of this
 @uref{https://git.savannah.gnu.org/cgit/guix.git/plain/etc/guix-install.sh,
 shell installer script}.  The script automates the download, installation, and
@@ -1297,6 +1301,11 @@ environment variable is set to the non-existent
 @file{/homeless-shelter}.  This helps to highlight inappropriate uses of
 @env{HOME} in the build scripts of packages.
 
+All this usually enough to ensure details of the environment do not
+influence build processes.  In some exceptional cases where more control
+is needed---typically over the date, kernel, or CPU---you can resort to
+a virtual build machine (@pxref{build-vm, virtual build machines}).
+
 You can influence the directory where the daemon stores build trees
 @i{via} the @env{TMPDIR} environment variable.  However, the build tree
 within the chroot is always called @file{/tmp/guix-build-@var{name}.drv-0},
@@ -9850,7 +9859,7 @@ MbedTLS package:
                   (("generate_wrapper_header.*")
                    (string-append
                     "generate_wrapper_header(\"MbedTLS\", \""
-                    (assoc-ref inputs "mbedtls-apache") "\")\n"))))
+                    (assoc-ref inputs "mbedtls") "\")\n"))))
               ;; There's a Julia file for each platform, override them all.
               (find-files "src/wrappers/" "\\.jl$"))))
 @end lisp
@@ -14021,6 +14030,9 @@ the certificates of X.509 authorities from the directory pointed to by
 the @env{SSL_CERT_DIR} environment variable (@pxref{X.509
 Certificates}), unless @option{--no-check-certificate} is used.
 
+Alternatively, @command{guix download} can also retrieve a Git
+repository, possibly a specific commit, tag, or branch.
+
 The following options are available:
 
 @table @code
@@ -14045,6 +14057,26 @@ URL, which makes you vulnerable to ``man-in-the-middle'' attacks.
 @itemx -o @var{file}
 Save the downloaded file to @var{file} instead of adding it to the
 store.
+
+@item --git
+@itemx -g
+Checkout the Git repository at the latest commit on the default branch.
+
+@item --commit=@var{commit-or-tag}
+Checkout the Git repository at @var{commit-or-tag}.
+
+@var{commit-or-tag} can be either a tag or a commit defined in the Git
+repository.
+
+@item --branch=@var{branch}
+Checkout the Git repository at @var{branch}.
+
+The repository will be checked out at the latest commit of @var{branch},
+which must be a valid branch of the Git repository.
+
+@item --recursive
+@itemx -r
+Recursively clone the Git repository.
 @end table
 
 @node Invoking guix hash
@@ -14155,12 +14187,21 @@ is a package definition, or a template thereof, in the format we know
 The general syntax is:
 
 @example
-guix import @var{importer} @var{options}@dots{}
+guix import [@var{global-options}@dots{}] @var{importer} @var{package} [@var{options}@dots{}]
 @end example
 
 @var{importer} specifies the source from which to import package
 metadata, and @var{options} specifies a package identifier and other
-options specific to @var{importer}.
+options specific to @var{importer}. @command{guix import} itself has the
+following @var{global-options}:
+
+@table @code
+@item --insert=@var{file}
+@itemx -i @var{file}
+Insert the package definition(s) that the @var{importer} generated into the
+specified @var{file}, either in alphabetical order among existing package
+definitions, or at the end of the file otherwise.
+@end table
 
 Some of the importers rely on the ability to run the @command{gpgv} command.
 For these, GnuPG must be installed and in @code{$PATH}; run @code{guix install
@@ -14311,7 +14352,7 @@ statistical and graphical environment}.
 
 Information is extracted from the @file{DESCRIPTION} file of the package.
 
-The command command below imports metadata for the Cairo R package:
+The command below imports metadata for the Cairo R package:
 
 @example
 guix import cran Cairo
@@ -14371,10 +14412,10 @@ Information about the package is obtained from the TeX Live package
 database, a plain text file that is included in the
 @code{texlive-scripts} package.  The source code is downloaded from
 possibly multiple locations in the SVN repository of the Tex Live
-project.
+project.  Note that therefore SVN must be installed and in @code{$PATH};
+run @code{guix install subversion} if needed.
 
-The command command below imports metadata for the @code{fontspec}
+The command below imports metadata for the @code{fontspec} TeX package:
-TeX package:
 
 @example
 guix import texlive fontspec
@@ -16721,6 +16762,20 @@ guix package}).
 This option can be repeated several times, in which case the manifests
 are concatenated.
 
+@item --expression=@var{expr}
+@itemx -e @var{expr}
+Consider the package @var{expr} evaluates to.
+
+A typical use case for this option is specifying a package that is
+hidden and thus cannot be referred to in the usual way, as in this
+example:
+
+@example
+guix weather -e '(@@@@ (gnu packages rust) rust-bootstrap)'
+@end example
+
+This option can be repeated.
+
 @item --coverage[=@var{count}]
 @itemx -c [@var{count}]
 Report on substitute coverage for packages: list packages with at least
@@ -16903,6 +16958,7 @@ The available targets are:
    - i686-linux-gnu
    - i686-w64-mingw32
    - mips64el-linux-gnu
+   - or1k-elf
    - powerpc-linux-gnu
    - powerpc64le-linux-gnu
    - riscv64-linux-gnu
@@ -20948,9 +21004,214 @@ networks.
 @item @code{disable-vpn?} (default: @code{#f})
 When true, disable connman's vpn plugin.
 
+@item @code{general-configuration} (default: @code{(connman-general-configuration)})
+Configuration serialized to @file{main.conf} and passed as @option{--config}
+to @command{connmand}.
+
 @end table
 @end deftp
 
+@c %start of fragment
+
+@deftp {Data Type} connman-general-configuration
+Available @code{connman-general-configuration} fields are:
+
+@table @asis
+@item @code{input-request-timeout} (type: maybe-number)
+Set input request timeout.  Default is 120 seconds.  The request for
+inputs like passphrase will timeout after certain amount of time.  Use
+this setting to increase the value in case of different user interface
+designs.
+
+@item @code{browser-launch-timeout} (type: maybe-number)
+Set browser launch timeout.  Default is 300 seconds.  The request for
+launching a browser for portal pages will timeout after certain amount
+of time.  Use this setting to increase the value in case of different
+user interface designs.
+
+@item @code{background-scanning?} (type: maybe-boolean)
+Enable background scanning.  Default is true.  If wifi is disconnected,
+the background scanning will follow a simple back off mechanism from 3s
+up to 5 minutes.  Then, it will stay in 5 minutes unless user
+specifically asks for scanning through a D-Bus call.  If so, the
+mechanism will start again from 3s.  This feature activates also the
+background scanning while being connected, which is required for roaming
+on wifi.  When @code{background-scanning?} is false, ConnMan will not
+perform any scan regardless of wifi is connected or not, unless it is
+requested by the user through a D-Bus call.
+
+@item @code{use-gateways-as-timeservers?} (type: maybe-boolean)
+Assume that service gateways also function as timeservers.  Default is
+false.
+
+@item @code{fallback-timeservers} (type: maybe-list)
+List of Fallback timeservers.  These timeservers are used for NTP sync
+when there are no timeservers set by the user or by the service, and
+when @code{use-gateways-as-timeservers?} is @code{#f}.  These can
+contain a mixed combination of fully qualified domain names, IPv4 and
+IPv6 addresses.
+
+@item @code{fallback-nameservers} (type: maybe-list)
+List of fallback nameservers appended to the list of nameservers given
+by the service.  The nameserver entries must be in numeric format, host
+names are ignored.
+
+@item @code{default-auto-connect-technologies} (type: maybe-list)
+List of technologies that are marked autoconnectable by default.  The
+default value for this entry when empty is @code{"ethernet"},
+@code{"wifi"}, @code{"cellular"}.  Services that are automatically
+connected must have been set up and saved to storage beforehand.
+
+@item @code{default-favourite-technologies} (type: maybe-list)
+List of technologies that are marked favorite by default.  The default
+value for this entry when empty is @code{"ethernet"}.  Connects to
+services from this technology even if not setup and saved to storage.
+
+@item @code{always-connected-technologies} (type: maybe-list)
+List of technologies which are always connected regardless of
+preferred-technologies setting (@code{auto-connect?} @code{#t}).  The
+default value is empty and this feature is disabled unless explicitly
+enabled.
+
+@item @code{preferred-technologies} (type: maybe-list)
+List of preferred technologies from the most preferred one to the least
+preferred one.  Services of the listed technology type will be tried one
+by one in the order given, until one of them gets connected or they are
+all tried.  A service of a preferred technology type in state 'ready'
+will get the default route when compared to another preferred type
+further down the list with state 'ready' or with a non-preferred type; a
+service of a preferred technology type in state 'online' will get the
+default route when compared to either a non-preferred type or a
+preferred type further down in the list.
+
+@item @code{network-interface-blacklist} (type: maybe-list)
+List of blacklisted network interfaces.  Found interfaces will be
+compared to the list and will not be handled by ConnMan, if their first
+characters match any of the list entries.  Default value is
+@code{"vmnet"}, @code{"vboxnet"}, @code{"virbr"}, @code{"ifb"}.
+
+@item @code{allow-hostname-updates?} (type: maybe-boolean)
+Allow ConnMan to change the system hostname.  This can happen for
+example if we receive DHCP hostname option.  Default value is @code{#t}.
+
+@item @code{allow-domainname-updates?} (type: maybe-boolean)
+Allow connman to change the system domainname.  This can happen for
+example if we receive DHCP domainname option.  Default value is
+@code{#t}.
+
+@item @code{single-connected-technology?} (type: maybe-boolean)
+Keep only a single connected technology at any time.  When a new service
+is connected by the user or a better one is found according to
+preferred-technologies, the new service is kept connected and all the
+other previously connected services are disconnected.  With this setting
+it does not matter whether the previously connected services are in
+'online' or 'ready' states, the newly connected service is the only one
+that will be kept connected.  A service connected by the user will be
+used until going out of network coverage.  With this setting enabled
+applications will notice more network breaks than normal.  Note this
+options can't be used with VPNs.  Default value is @code{#f}.
+
+@item @code{tethering-technologies} (type: maybe-list)
+List of technologies that are allowed to enable tethering.  The default
+value is @code{"wifi"}, @code{"bluetooth"}, @code{"gadget"}.  Only those
+technologies listed here are used for tethering.  If one wants to tether
+ethernet, then add @code{"ethernet"} in the list.  Note that if ethernet
+tethering is enabled, then a DHCP server is started on all ethernet
+interfaces.  Tethered ethernet should never be connected to corporate or
+home network as it will disrupt normal operation of these networks.  Due
+to this ethernet is not tethered by default.  Do not activate ethernet
+tethering unless you really know what you are doing.
+
+@item @code{persistent-tethering-mode?} (type: maybe-boolean)
+Restore earlier tethering status when returning from offline mode,
+re-enabling a technology, and after restarts and reboots.  Default value
+is @code{#f}.
+
+@item @code{enable-6to4?} (type: maybe-boolean)
+Automatically enable anycast 6to4 if possible.  This is not recommended,
+as the use of 6to4 will generally lead to a severe degradation of
+connection quality.  See RFC6343.  Default value is @code{#f} (as
+recommended by RFC6343 section 4.1).
+
+@item @code{vendor-class-id} (type: maybe-string)
+Set DHCP option 60 (Vendor Class ID) to the given string.  This option
+can be used by DHCP servers to identify specific clients without having
+to rely on MAC address ranges, etc.
+
+@item @code{enable-online-check?} (type: maybe-boolean)
+Enable or disable use of HTTP GET as an online status check.  When a
+service is in a READY state, and is selected as default, ConnMan will
+issue an HTTP GET request to verify that end-to-end connectivity is
+successful.  Only then the service will be transitioned to ONLINE state.
+If this setting is false, the default service will remain in READY
+state.  Default value is @code{#t}.
+
+@item @code{online-check-ipv4-url} (type: maybe-string)
+IPv4 URL used during the online status check.  Please refer to the
+README for more detailed information.  Default value is
+@uref{http://ipv4.connman.net/online/status.html}.
+
+@item @code{online-check-ipv6-url} (type: maybe-string)
+IPv6 URL used during the online status check.  Please refer to the
+README for more detailed information.  Default value is
+@uref{http://ipv6.connman.net/online/status.html}.
+
+@item @code{online-check-initial-interval} (type: maybe-number)
+Range of intervals between two online check requests.  Please refer to
+the README for more detailed information.  Default value is @samp{1}.
+
+@item @code{online-check-max-interval} (type: maybe-number)
+Range of intervals between two online check requests.  Please refer to
+the README for more detailed information.  Default value is @samp{1}.
+
+@item @code{enable-online-to-ready-transition?} (type: maybe-boolean)
+WARNING: This is an experimental feature.  In addition to
+@code{enable-online-check} setting, enable or disable use of HTTP GET to
+detect the loss of end-to-end connectivity.  If this setting is
+@code{#f}, when the default service transitions to ONLINE state, the
+HTTP GET request is no more called until next cycle, initiated by a
+transition of the default service to DISCONNECT state.  If this setting
+is @code{#t}, the HTTP GET request keeps being called to guarantee that
+end-to-end connectivity is still successful.  If not, the default
+service will transition to READY state, enabling another service to
+become the default one, in replacement.  Default value is @code{#f}.
+
+@item @code{auto-connect-roaming-services?} (type: maybe-boolean)
+Automatically connect roaming services.  This is not recommended unless
+you know you won't have any billing problem.  Default value is
+@code{#f}.
+
+@item @code{address-conflict-detection?} (type: maybe-boolean)
+Enable or disable the implementation of IPv4 address conflict detection
+according to RFC5227.  ConnMan will send probe ARP packets to see if an
+IPv4 address is already in use before assigning the address to an
+interface.  If an address conflict occurs for a statically configured
+address, an IPv4LL address will be chosen instead (according to
+RFC3927).  If an address conflict occurs for an address offered via
+DHCP, ConnMan sends a DHCP DECLINE once and for the second conflict
+resorts to finding an IPv4LL address.  Default value is @code{#f}.
+
+@item @code{localtime} (type: maybe-string)
+Path to localtime file.  Defaults to @file{/etc/localtime}.
+
+@item @code{regulatory-domain-follows-timezone?} (type: maybe-boolean)
+Enable regulatory domain to be changed along timezone changes.  With
+this option set to true each time the timezone changes the first present
+ISO3166 country code is read from
+@file{/usr/share/zoneinfo/zone1970.tab} and set as regulatory domain
+value.  Default value is @code{#f}.
+
+@item @code{resolv-conf} (type: maybe-string)
+Path to resolv.conf file.  If the file does not exist, but intermediate
+directories exist, it will be created.  If this option is not set, it
+tries to write into @file{/var/run/connman/resolv.conf} if it fails
+(@file{/var/run/connman} does not exist or is not writeable).  If you do
+not want to update resolv.conf, you can set @file{/dev/null}.
+
+@end table
+
+@end deftp
+
 @cindex WPA Supplicant
 @defvar wpa-supplicant-service-type
 This is the service type to run @url{https://w1.fi/wpa_supplicant/,WPA
@@ -25555,6 +25816,9 @@ The @code{(gnu services databases)} module provides the following services.
 
 @subsubheading PostgreSQL
 
+@defvar postgresql-service-type
+The service type for the PostgreSQL database server.  Its value should
+be a valid @code{postgresql-configuration} object, documented below.
 The following example describes a PostgreSQL service with the default
 configuration.
 
@@ -25581,6 +25845,7 @@ sudo -u postgres -s /bin/sh
 createuser --interactive
 createdb $MY_USER_LOGIN      # Replace appropriately.
 @end example
+@end defvar
 
 @deftp {Data Type} postgresql-configuration
 Data type representing the configuration for the
@@ -27888,7 +28153,7 @@ Prosodyctl will also help you to import certificates from the
 them.  See @url{https://prosody.im/doc/letsencrypt}.
 
 @example
-prosodyctl --root cert import /etc/letsencrypt/live
+prosodyctl --root cert import /etc/certs
 @end example
 
 The available configuration parameters follow.  Each parameter
@@ -28354,10 +28619,11 @@ services:
 
 @subsubheading Jami
 
-@cindex jami, service
+@defvar jami-service-type
-
+The service type for running Jami as a service.  It takes a
-This section describes how to configure a Jami server that can be used
+@code{jami-configuration} object as a value, documented below.  This
-to host video (or audio) conferences, among other uses.  The following
+section describes how to configure a Jami server that can be used to
+host video (or audio) conferences, among other uses.  The following
 example demonstrates how to specify Jami account archives (backups) to
 be provisioned automatically:
 
@@ -28485,6 +28751,7 @@ Account_username: f3345f2775ddfe07a4b0d95daea111d15fbc1199
 The remaining actions should be self-explanatory.
 
 The complete set of available configuration options is detailed below.
+@end defvar
 
 @c TODO: Ideally, the following fragments would be auto-generated at
 @c build time, so that they needn't be manually duplicated.
@@ -28581,6 +28848,12 @@ account fingerprint for a registered username.
 This section describes how to set up and run a
 @uref{https://mumble.info, Mumble} server (formerly known as Murmur).
 
+@defvar mumble-server-service-type
+
+This is the service to run a Mumble server.  It takes a
+@code{mumble-server-configuration} object as its value, defined below.
+@end defvar
+
 @deftp {Data Type} mumble-server-configuration
 The service type for the Mumble server.  An example configuration can
 look like this:
@@ -28591,8 +28864,8 @@ look like this:
           (welcome-text
             "Welcome to this Mumble server running on Guix!")
           (cert-required? #t) ;disallow text password logins
-          (ssl-cert "/etc/letsencrypt/live/mumble.example.com/fullchain.pem")
+          (ssl-cert "/etc/certs/mumble.example.com/fullchain.pem")
-          (ssl-key "/etc/letsencrypt/live/mumble.example.com/privkey.pem")))
+          (ssl-key "/etc/certs/mumble.example.com/privkey.pem")))
 @end lisp
 
 After reconfiguring your system, you can manually set the mumble-server
@@ -28710,12 +28983,12 @@ Should logged ips be obfuscated to protect the privacy of users.
 File name of the SSL/TLS certificate used for encrypted connections.
 
 @lisp
-(ssl-cert "/etc/letsencrypt/live/example.com/fullchain.pem")
+(ssl-cert "/etc/certs/example.com/fullchain.pem")
 @end lisp
 @item @code{ssl-key} (default: @code{#f})
 Filepath to the ssl private key used for encrypted connections.
 @lisp
-(ssl-key "/etc/letsencrypt/live/example.com/privkey.pem")
+(ssl-key "/etc/certs/example.com/privkey.pem")
 @end lisp
 
 @item @code{ssl-dh-params} (default: @code{#f})
@@ -31603,6 +31876,50 @@ Additional arguments to pass to the @command{varnishd} process.
 @end table
 @end deftp
 
+@subheading Whoogle Search
+@cindex Whoogle Search
+
+@uref{https://github.com/benbusby/whoogle-search, Whoogle Search} is a
+self-hosted, ad-free, privacy-respecting meta search engine that collects
+and displays Google search results.  By default, you can configure it by
+adding this line to the @code{services} field of your operating system
+declaration:
+
+@lisp
+(service whoogle-service-type)
+@end lisp
+
+As a result, Whoogle Search runs as local Web server, which you can
+access by opening @indicateurl{http://localhost:5000} in your browser.
+The configuration reference is given below.
+
+@defvar whoogle-service-type
+Service type for Whoogle Search.  Its value must be a
+@code{whoogle-configuration} record---see below.
+@end defvar
+
+@deftp {Data Type} whoogle-configuration
+Data type representing Whoogle Search service configuration.
+
+@table @asis
+@item @code{package} (default: @code{whoogle-search})
+The Whoogle Search package to use.
+
+@item @code{host} (default: @code{"127.0.0.1"})
+The host address to run Whoogle on.
+
+@item @code{port} (default: @code{5000})
+The port where Whoogle will be exposed.
+
+@item @code{environment-variables} (default: @code{'()})
+A list of strings with the environment variables to configure Whoogle.
+You can consult
+@uref{https://github.com/benbusby/whoogle-search/blob/main/whoogle.template.env,
+its environment variables template} for the list of available options.
+
+@end table
+@end deftp
+
 @subsubheading Patchwork
 @cindex Patchwork
 Patchwork is a patch tracking system.  It can collect patches sent to a
@@ -32307,21 +32624,13 @@ A service type for the @code{certbot} Let's Encrypt client.  Its value
 must be a @code{certbot-configuration} record as in this example:
 
 @lisp
-(define %certbot-deploy-hook
-  (program-file "certbot-deploy-hook.scm"
-    (with-imported-modules '((gnu services herd))
-      #~(begin
-          (use-modules (gnu services herd))
-          (with-shepherd-action 'nginx ('reload) result result)))))
-
 (service certbot-service-type
          (certbot-configuration
           (email "foo@@example.net")
           (certificates
            (list
             (certificate-configuration
-             (domains '("example.net" "www.example.net"))
+             (domains '("example.net" "www.example.net")))
-             (deploy-hook %certbot-deploy-hook))
             (certificate-configuration
              (domains '("bar.example.net")))))))
 @end lisp
@@ -32435,12 +32744,18 @@ certificates and keys; the shell variable @code{$RENEWED_DOMAINS} will
 contain a space-delimited list of renewed certificate domains (for
 example, @samp{"example.com www.example.com"}.
 
+@item @code{start-self-signed?} (default: @code{#t})
+Whether to generate an initial self-signed certificate during system
+activation.  This option is particularly useful to allow @code{nginx} to
+start before @code{certbot} has run, because @code{certbot} relies on
+@code{nginx} running to perform HTTP challenges.
+
 @end table
 @end deftp
 
 For each @code{certificate-configuration}, the certificate is saved to
-@code{/etc/letsencrypt/live/@var{name}/fullchain.pem} and the key is
+@code{/etc/certs/@var{name}/fullchain.pem} and the key is
-saved to @code{/etc/letsencrypt/live/@var{name}/privkey.pem}.
+saved to @code{/etc/certs/@var{name}/privkey.pem}.
 @node DNS Services
 @subsection DNS Services
 @cindex DNS (domain name system)
@@ -36081,6 +36396,142 @@ host.  If empty, QEMU uses a default file name.
 @end deftp
 
 
+@anchor{build-vm}
+@subsubheading Virtual Build Machines
+
+@cindex virtual build machines
+@cindex build VMs
+@cindex VMs, for offloading
+@dfn{Virtual build machines} or ``build VMs'' let you offload builds to
+a fully controlled environment.  ``How can it be more controlled than
+regular builds?  And why would it be useful?'', you ask.  Good
+questions.
+
+Builds spawned by @code{guix-daemon} indeed run in a controlled
+environment; specifically the daemon spawns build processes in separate
+namespaces and in a chroot, such as that build processes only see their
+declared dependencies and a well-defined subset of the file system tree
+(@pxref{Build Environment Setup}, for details).  A few aspects of the
+environments are not controlled though: the operating system kernel, the
+CPU model, and the date.  Most of the time, these aspects have no impact
+on the build process: the level of isolation @code{guix-daemon} provides
+is ``good enough''.
+
+@cindex time traps
+However, there are occasionally cases where those aspects @emph{do}
+influence the build process.  A typical example is @dfn{time traps}:
+build processes that stop working after a certain date@footnote{The most
+widespread example of time traps is test suites that involve checking
+the expiration date of a certificate.  Such tests exists in TLS
+implementations such as OpenSSL and GnuTLS, but also in high-level
+software such as Python.}.  Another one is software that optimizes for
+the CPU microarchitecture it is built on or, worse, bugs that manifest
+only on specific CPUs.
+
+To address that, @code{virtual-build-machine-service-type} lets you add
+a virtual build machine on your system, as in this example:
+
+@lisp
+(use-modules (gnu services virtualization))
+
+(operating-system
+  ;; @dots{}
+  (services (append (list (service virtual-build-machine-service-type))
+                    %base-services)))
+@end lisp
+
+By default, you have to explicitly start the build machine when you need
+it, at which point builds may be offloaded to it (@pxref{Daemon Offload
+Setup}):
+
+@example
+herd start build-vm
+@end example
+
+With the default setting shown above, the build VM runs with its clock
+set to a date several years in the past, and on a CPU model that
+corresponds to that date---a model possibly older than that of your
+machine.  This lets you rebuild today software from the past that would
+otherwise fail to build due to a time trap or other issues in its build
+process.  You can view the VM's config like this:
+
+@example
+herd configuration build-vm
+@end example
+
+You can configure the build VM, as in this example:
+
+@lisp
+(service virtual-build-machine-service-type
+         (virtual-build-machine
+          (cpu "Westmere")
+          (cpu-count 8)
+          (memory-size (* 1 1024))
+          (auto-start? #t)))
+@end lisp
+
+The available options are shown below.
+
+@defvar virtual-build-machine-service-type
+This is the service type to run @dfn{virtual build machines}.  Virtual
+build machines are configured so that builds are offloaded to them when
+they are running.
+@end defvar
+
+@deftp {Data Type} virtual-build-machine
+This is the data type specifying the configuration of a build machine.
+It contains the fields below:
+
+@table @asis
+@item @code{name} (default: @code{'build-vm})
+The name of this build VM.  It is used to construct the name of its
+Shepherd service.
+
+@item @code{image}
+The image of the virtual machine (@pxref{System Images}).  This notably
+specifies the virtual disk size and the operating system running into it
+(@pxref{operating-system Reference}).  The default value is a minimal
+operating system image.
+
+@item @code{qemu} (default: @code{qemu-minimal})
+The QEMU package to run the image.
+
+@item @code{cpu}
+The CPU model being emulated as a string denoting a model known to QEMU.
+
+The default value is a model that matches @code{date} (see below).  To
+see what CPU models are available, run, for example:
+
+@example
+qemu-system-x86_64 -cpu help
+@end example
+
+@item @code{cpu-count} (default: @code{4})
+The number of CPUs emulated by the virtual machine.
+
+@item @code{memory-size} (default: @code{2048})
+Size in mebibytes (MiB) of the virtual machine's main memory (RAM).
+
+@item @code{date} (default: a few years ago)
+Date inside the virtual machine when it starts; this must be a SRFI-19
+date object (@pxref{SRFI-19 Date,,, guile, GNU Guile Reference Manual}).
+
+@item @code{port-forwardings} (default: 11022 and 11004)
+TCP ports of the virtual machine forwarded to the host.  By default, the
+SSH and secrets ports are forwarded into the host.
+
+@item @code{systems} (default: @code{(list (%current-system))})
+List of system types supported by the build VM---e.g.,
+@code{"x86_64-linux"}.
+
+@item @code{auto-start?} (default: @code{#f})
+Whether to start the virtual machine when the system boots.
+@end table
+@end deftp
+
+In the next section, you'll find a variant on this theme: GNU/Hurd
+virtual machines!
+
 @anchor{hurd-vm}
 @subsubheading The Hurd in a Virtual Machine
 
@@ -37126,9 +37577,9 @@ serve the default @file{/srv/git} over HTTPS might be:
              (listen '("443 ssl"))
              (server-name "git.my-host.org")
              (ssl-certificate
-              "/etc/letsencrypt/live/git.my-host.org/fullchain.pem")
+              "/etc/certs/git.my-host.org/fullchain.pem")
              (ssl-certificate-key
-              "/etc/letsencrypt/live/git.my-host.org/privkey.pem")
+              "/etc/certs/git.my-host.org/privkey.pem")
              (locations
               (list
                (git-http-nginx-location-configuration
@@ -38253,9 +38704,9 @@ footers.
            (nginx-server-block
              (nginx-server-configuration
                (ssl-certificate
-                 "/etc/letsencrypt/live/myweb.site/fullchain.pem")
+                 "/etc/certs/myweb.site/fullchain.pem")
                (ssl-certificate-key
-                 "/etc/letsencrypt/live/myweb.site/privkey.pem")
+                 "/etc/certs/myweb.site/privkey.pem")
                (listen '("443 ssl http2" "[::]:443 ssl http2"))
                (locations
                  (list
@@ -40060,16 +40511,31 @@ After @command{guix system reconfigure} configure Nix for your user:
 
 @itemize
 @item Add a Nix channel and update it.  See
-@url{https://nixos.org/nix/manual/, Nix Package Manager Guide}.
+@url{https://nixos.wiki/wiki/Nix_channels, Nix channels} for more
+information about the available channels.  If you would like to use the
+unstable Nix channel you can do this by running:
+
+@example
+$ nix-channel --add https://nixos.org/channels/nixpkgs-unstable
+$ nix-channel --update
+@end example
+
+@item Create your Nix profile directory:
+
+@example
+$ sudo mkdir -p /nix/var/nix/profiles/per-user/$USER
+$ sudo chown $USER:root /nix/var/nix/profiles/per-user/$USER
+@end example
 
 @item Create a symlink to your profile and activate Nix profile:
-@end itemize
 
 @example
 $ ln -s "/nix/var/nix/profiles/per-user/$USER/profile" ~/.nix-profile
 $ source /run/current-system/profile/etc/profile.d/nix.sh
 @end example
 
+@end itemize
+
 @end defvar
 
 @deftp {Data Type} nix-configuration
@@ -42888,6 +43354,15 @@ shepherd, The GNU Shepherd Manual}, for more info.
 Whether to restart the service when it stops, for instance when the
 underlying process dies.
 
+@item @code{respawn-limit} (default: @code{#f})
+Set a limit on how many times and how frequently a service may be
+restarted by Shepherd before it is disabled.  @xref{Defining
+Services,,, shepherd, The GNU Shepherd Manual}, for details.
+
+@item @code{respawn-delay} (default: @code{#f})
+When true, this is the delay in seconds before restarting a failed
+service.
+
 @item @code{start}
 @itemx @code{stop} (default: @code{#~(const #f)})
 The @code{start} and @code{stop} fields refer to the Shepherd's
@@ -43120,7 +43595,7 @@ A clause has the following form:
 the generated record.
 
 @var{type-decl} is either @code{@var{type}} for fields that require a
-value to be set or @code{(@var{type} @var{default})} otherwise.
+value to be set or @code{(@var{type} @var{default-value})} otherwise.
 
 @var{type} is the type of the value corresponding to @var{field-name};
 since Guile is untyped, a predicate
@@ -43961,6 +44436,116 @@ to use alternative services to implement more advanced use cases like
 read-only home.  Feel free to experiment and share your results.
 @end defvar
 
+@cindex dot files in Guix Home
+It is often the case that Guix Home users already have a setup for versioning
+their user configuration files (also known as @emph{dot files}) in a single
+directory, and some way of automatically deploy changes to their user home.
+
+@cindex Stow-like dot file management
+The @code{home-dotfiles-service-type} from @code{(gnu home services dotfiles)}
+is designed to ease the way into using Guix Home for this kind of users,
+allowing them to point the service to their dotfiles directory, which must
+follow the layout suggested by
+@uref{https://www.gnu.org/software/stow/, GNU Stow},
+and have their dotfiles automatically deployed to their user home, without
+migrating them to Guix native configurations.
+
+The dotfiles directory layout is expected to be structured as follows. Please
+keep in mind that it is advisable to keep your dotfiles directories under
+version control, for example in the same repository where you'd track your
+Guix Home configuration.
+
+@example
+~$ tree -a ./dotfiles/
+dotfiles/
+├── git
+│   └── .gitconfig
+├── gpg
+│   └── .gnupg
+│       ├── gpg-agent.conf
+│       └── gpg.conf
+├── guile
+│   └── .guile
+├── guix
+│   └── .config
+│       └── guix
+│           └── channels.scm
+├── nix
+│   ├── .config
+│   │   └── nixpkgs
+│   │       └── config.nix
+│   └── .nix-channels
+├── tmux
+│   └── .tmux.conf
+└── vim
+    └── .vimrc
+
+13 directories, 10 files
+@end example
+
+For an informal specification please refer to the Stow manual
+(@pxref{Top,,, stow, Introduction}). A suitable configuration would then
+be:
+
+@lisp
+(home-environment
+  ;; @dots{}
+  (services
+    (service home-dotfiles-service-type
+             (home-dotfiles-configuration
+               (directories (list "./dotfiles"))))))
+@end lisp
+
+The expected home directory state would then be:
+
+@example
+.
+├── .config
+│   ├── guix
+│   │   └── channels.scm
+│   └── nixpkgs
+│       └── config.nix
+├── .gitconfig
+├── .gnupg
+│   ├── gpg-agent.conf
+│   └── gpg.conf
+├── .guile
+├── .nix-channels
+├── .tmux.conf
+└── .vimrc
+@end example
+
+@defvar home-dotfiles-service-type
+Return a service which is very similiar to @code{home-files-service-type}
+(and actually extends it), but designed to ease the way into using Guix
+Home for users that already track their dotfiles under some kind of version
+control.  This service allows users to point Guix Home to their dotfiles
+directory and have their files automatically deployed to their home directory
+just like Stow would, without migrating all of their dotfiles to Guix native
+configurations.
+@end defvar
+
+@deftp {Data Type} home-dotfiles-configuration
+Available @code{home-dotfiles-configuration} fields are:
+
+@table @asis
+@item @code{source-directory} (default: @code{(current-source-directory)})
+The path where dotfile directories are resolved. By default dotfile directories
+are resolved relative the source location where
+@code{home-dotfiles-configuration} appears.
+
+@item @code{directories} (type: list-of-strings)
+The list of dotfiles directories where @code{home-dotfiles-service-type} will
+look for application dotfiles.
+
+@item @code{exclude} (default: @code{'(".*~" ".*\\.swp" "\\.git" "\\.gitignore")})
+The list of file patterns @code{home-dotfiles-service-type} will exclude while
+visiting each one of the @code{directories}.
+
+@end table
+
+@end deftp
+
 @defvar home-xdg-configuration-files-service-type
 The service is very similar to @code{home-files-service-type} (and
 actually extends it), but used for defining files, which will go to
@@ -46167,6 +46752,11 @@ Platform targeting AVR CPUs without an operating system, with run-time support
 from AVR Libc.
 @end defvar
 
+@defvar or1k-elf
+Platform targeting OpenRISC 1000 CPU without an operating system and without a
+C standard library.
+@end defvar
+
 @node System Images
 @chapter Creating System Images
 

doc/package-hello.json

@@ -6,7 +6,7 @@
     "build-system": "gnu",
     "arguments": {
       "tests?": false
-    }
+    },
     "home-page": "https://www.gnu.org/software/hello/",
     "synopsis": "Hello, GNU world: An example GNU package",
     "description": "GNU Hello prints a greeting.",
@@ -16,11 +16,11 @@
   {
     "name": "greeter",
     "version": "1.0",
-    "source": "https://example.com/greeter-1.0.tar.gz",
+    "source": "mirror://gnu/hello/hello-2.10.tar.gz",
     "build-system": "gnu",
     "arguments": {
       "test-target": "foo",
-      "parallel-build?": false,
+      "parallel-build?": false
     },
     "home-page": "https://example.com/",
     "synopsis": "Greeter using GNU Hello",

etc/disarchive-manifest.scm

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

etc/git/gitconfig

@@ -20,6 +20,7 @@
 [b4]
         attestation-check-dkim = off
         attestation-policy = off
+        shazam-am-flags = --signoff --3way
         linkmask = https://yhetil.org/guix/%s
         linktrailermask = https://yhetil.org/guix/%s
         midmask = https://yhetil.org/guix/%s

etc/news.scm

@@ -19,6 +19,7 @@
 ;; Copyright © 2021, 2023 Jonathan Brielmaier <jonathan.brielmaier@web.de>
 ;; Copyright © 2022 Thiago Jung Bauermann <bauermann@kolabnow.com>
 ;; Copyright © 2024 Oleg Pykhalov <go.wigust@gmail.com>
+;; Copyright © 2024 Wilko Meyer <w@wmeyer.eu>
 ;;
 ;; Copying and distribution of this file, with or without modification, are
 ;; permitted in any medium without royalty provided the copyright notice and
@@ -27,6 +28,18 @@
 (channel-news
  (version 0)
 
+ (entry (commit "10a193596368443f441077525ebbddf787d91e4b")
+        (title
+          (en "Linux-libre 4.14 removed due to end of upstream support")
+          (de "Linux-libre 4.14 wurde entfernt"))
+        (body
+          (en "The linux-libre 4.14 kernel series has reached the end of
+             its life, and is no longer supported upstream.  For this
+             reason, it has been removed from GNU Guix.")
+          (de "Die @code{linux-libre} 4.14-Versionsreihe hat ihr
+Supportende erreicht und wird nicht mehr unterstützt („end of life“). Daher ist die
+Versionsreihe aus GNU Guix entfernt worden.")))
+
  (entry (commit "519e1e3eb88ec532fc83ebb742d9919269b57c87")
         (title
          (de "Neue Option @samp{--max-layers=N} für den Befehl @command{guix pack}")

etc/teams.scm

@@ -8,7 +8,7 @@ exec $pre_inst_env_maybe guix repl -- "$0" "$@"
 !#
 
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2022, 2023 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2022-2024 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2022 Mathieu Othacehe <othacehe@gnu.org>
 ;;; Copyright © 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2022 Simon Tournier <zimon.toutoune@gmail.com>
@@ -176,6 +176,13 @@ and the r-build-system."
                       "guix/scripts/import/cran.scm"
                       "tests/cran.scm")))
 
+(define-team sugar
+  (team 'sugar
+        #:name "Sugar team"
+        #:description
+        "Everything related to the Sugar Desktop and learning environment."
+        #:scope (list "gnu/packages/sugar.scm")))
+
 (define-team telephony
   (team 'telephony
         #:name "Telephony team"
@@ -299,10 +306,12 @@ asdf-build-system."
 (define-team go
   (team 'go
         #:name "Go team"
-        #:scope (list "gnu/packages/golang.scm"
+        #:scope (list "gnu/packages/configuration-management.scm"
-                      "gnu/packages/golang-check.scm"
+                      "gnu/packages/golang(-.+|)\\.scm$"
-                      "guix/build/go-build-system.scm"
+                      "gnu/packages/syncthing.scm"
+                      "gnu/packages/terraform.scm"
                       "guix/build-system/go.scm"
+                      "guix/build/go-build-system.scm"
                       "guix/import/go.scm"
                       "guix/scripts/import/go.scm"
                       "tests/go.scm")))
@@ -495,7 +504,8 @@ asdf-build-system."
 and Thunderbird."
         #:scope (list "gnu/build/icecat-extension.scm"
                       "gnu/packages/browser-extensions.scm"
-                      "gnu/packages/gnuzilla.scm")))
+                      "gnu/packages/gnuzilla.scm"
+                      "gnu/packages/tor-browsers.scm")))
 
 (define-team racket
   (team 'racket
@@ -592,7 +602,7 @@ GLib/GIO, GTK, GStreamer and Webkit."
 
 (define-member (person "Efraim Flashner"
                        "efraim@flashner.co.il")
-  embedded bootstrap julia rust science)
+  embedded bootstrap julia rust)
 
 (define-member (person "jgart"
                        "jgart@dismail.de")
@@ -624,7 +634,7 @@ GLib/GIO, GTK, GStreamer and Webkit."
 
 (define-member (person "Ricardo Wurmus"
                        "rekado@elephly.net")
-  r core mentors tex)
+  core mentors r sugar tex)
 
 (define-member (person "Christopher Baines"
                        "guix@cbaines.net")
@@ -710,6 +720,10 @@ GLib/GIO, GTK, GStreamer and Webkit."
                        "w@wmeyer.eu")
   kernel)
 
+(define-member (person "Mark H Weaver"
+                       "mhw@netris.org")
+  mozilla)
+
 
 (define (find-team name)
   (or (hash-ref %teams (string->symbol name))

gnu/build/activation.scm

@@ -8,6 +8,7 @@
 ;;; Copyright © 2021 Maxime Devos <maximedevos@telenet.be>
 ;;; Copyright © 2020 Christine Lemmer-Webber <cwebber@dustycloud.org>
 ;;; Copyright © 2021 Brice Waegeneire <brice@waegenei.re>
+;;; Copyright © 2024 Nicolas Graves <ngraves@ngraves.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -408,6 +409,7 @@ improvement."
 
   (format #t "making '~a' the current system...~%" system)
 
+  (mkdir-p "/run")
   ;; Atomically make SYSTEM current.
   (let ((new (string-append %current-system ".new")))
     (symlink system new)

gnu/build/file-systems.scm

@@ -7,6 +7,7 @@
 ;;; Copyright © 2019 David C. Trudgian <dave@trudgian.net>
 ;;; Copyright © 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2022 Oleg Pykhalov <go.wigust@gmail.com>
+;;; Copyright © 2024 Nicolas Graves <ngraves@ngraves.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1021,8 +1022,8 @@ were found."
 
 (define (canonicalize-device-spec spec)
   "Return the device name corresponding to SPEC, which can be a <uuid>, a
-<file-system-label>, or a string (typically a /dev file name or an nfs-root
+<file-system-label>, the string 'none' or another string (typically a /dev
-containing ':/')."
+file name or an nfs-root containing ':/')."
   (define max-trials
     ;; Number of times we retry partition label resolution, 1 second per
     ;; trial.  Note: somebody reported a delay of 16 seconds (!) before their
@@ -1046,8 +1047,8 @@ containing ':/')."
 
   (match spec
     ((? string?)
-     (if (string-contains spec ":/")
+     (if (or (string-contains spec ":/") (string=? spec "none"))
-         spec                  ; do not resolve NFS devices
+         spec                  ; do not resolve NFS / tmpfs devices
          ;; Nothing to do, but wait until SPEC shows up.
          (resolve identity spec identity)))
     ((? file-system-label?)

gnu/build/install.scm

@@ -2,6 +2,7 @@
 ;;; Copyright © 2013-2020, 2022 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016 Chris Marusich <cmmarusich@gmail.com>
 ;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2024 Nicolas Graves <ngraves@ngraves.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -134,8 +135,6 @@ STORE."
     (directory "/var/guix/gcroots")
     (directory "/var/empty")                        ; for no-login accounts
     (directory "/var/db")                           ; for dhclient, etc.
-    (directory "/var/run")
-    (directory "/run")
     (directory "/mnt")
     (directory "/var/guix/profiles/per-user/root" 0 0)
 

gnu/build/marionette.scm

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

gnu/build/secret-service.scm

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

gnu/ci.scm

@@ -191,6 +191,7 @@ SYSTEM."
   (define (pointless? target)
     ;; Return #t if it makes no sense to cross-build to TARGET from SYSTEM.
     (or (string=? target "avr") ; Nothing for AVR at this time.
+        (string=? target "or1k-elf") ;; Nothing for or1k-elf at this time.
         (match system
           ((or "x86_64-linux" "i686-linux")
            (if (string-contains target "mingw")

gnu/home/services.scm

@@ -37,6 +37,7 @@
   #:use-module (guix memoization)
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-9)
+  #:use-module (srfi srfi-34)
   #:use-module (ice-9 match)
   #:use-module (ice-9 vlist)
 

gnu/home/services/dotfiles.scm

@@ -0,0 +1,117 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2024 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2024 Giacomo Leidi <goodoldpaul@autistici.org>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu home services dotfiles)
+  #:use-module (gnu home services)
+  #:use-module (gnu services)
+  #:autoload   (guix build utils) (find-files)
+  #:use-module (guix gexp)
+  #:use-module (guix records)
+  #:use-module ((guix utils) #:select (current-source-directory))
+  #:use-module (srfi srfi-1)
+  #:use-module (ice-9 ftw)
+  #:use-module (ice-9 regex)
+  #:export (home-dotfiles-service-type
+            home-dotfiles-configuration
+            home-dotfiles-configuration?
+            home-dotfiles-configuration-source-directory
+            home-dotfiles-configuration-directories
+            home-dotfiles-configuration-excluded))
+
+(define %home-dotfiles-excluded
+  '(".*~"
+    ".*\\.swp"
+    "\\.git"
+    "\\.gitignore"))
+
+(define-record-type* <home-dotfiles-configuration>
+  home-dotfiles-configuration make-home-dotfiles-configuration
+  home-dotfiles-configuration?
+  (source-directory  home-dotfiles-configuration-source-directory
+                     (default (current-source-directory))
+                     (innate))
+  (directories       home-dotfiles-configuration-directories       ;list of strings
+                     (default '()))
+  (excluded          home-dotfiles-configuration-excluded       ;list of strings
+                     (default %home-dotfiles-excluded)))
+
+(define (import-dotfiles directory files)
+  "Return a list of objects compatible with @code{home-files-service-type}'s
+value.  Each object is a pair where the first element is the relative path
+of a file and the second is a gexp representing the file content.  Objects are
+generated by recursively visiting DIRECTORY and mapping its contents to the
+user's home directory, excluding files that match any of the patterns in EXCLUDED."
+  (define (strip file)
+    (string-drop file (+ 1 (string-length directory))))
+
+  (define (format file)
+    ;; Remove from FILE characters that cannot be used in the store.
+    (string-append
+     "home-dotfiles-"
+     (string-map (lambda (chr)
+                   (if (and (char-set-contains? char-set:ascii chr)
+                            (char-set-contains? char-set:graphic chr)
+                            (not (memv chr '(#\. #\/ #\space))))
+                       chr
+                       #\-))
+                 file)))
+
+  (map (lambda (file)
+         (let ((stripped (strip file)))
+           (list stripped
+                 (local-file file (format stripped)
+                             #:recursive? #t))))
+       files))
+
+(define (home-dotfiles-configuration->files config)
+  "Return a list of objects compatible with @code{home-files-service-type}'s
+value, generated following GNU Stow's algorithm for each of the
+directories in CONFIG, excluding files that match any of the patterns configured."
+  (define excluded
+    (home-dotfiles-configuration-excluded config))
+  (define exclusion-rx
+    (make-regexp (string-append "^.*(" (string-join excluded "|") ")$")))
+
+  (define (directory-contents directory)
+    (find-files directory
+                (lambda (file stat)
+                  (not (regexp-exec exclusion-rx
+                                    (basename file))))))
+
+  (define (resolve directory)
+    ;; Resolve DIRECTORY relative to the 'source-directory' field of CONFIG.
+    (if (string-prefix? "/" directory)
+        directory
+        (in-vicinity (home-dotfiles-configuration-source-directory config)
+                     directory)))
+
+  (append-map (lambda (directory)
+                (let* ((directory (resolve directory))
+                       (contents  (directory-contents directory)))
+                  (import-dotfiles directory contents)))
+              (home-dotfiles-configuration-directories config)))
+
+(define-public home-dotfiles-service-type
+  (service-type (name 'home-dotfiles)
+                (extensions
+                 (list (service-extension home-files-service-type
+                                          home-dotfiles-configuration->files)))
+                (default-value (home-dotfiles-configuration))
+                (description "Files that will be put in the user's home directory
+following GNU Stow's algorithm, and further processed during activation.")))

gnu/home/services/symlink-manager.scm

@@ -2,6 +2,7 @@
 ;;; Copyright © 2021 Andrew Tropin <andrew@trop.in>
 ;;; Copyright © 2021 Xinglu Chen <public@yoctocell.xyz>
 ;;; Copyright © 2022 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2024 Nicolas Graves <ngraves@ngraves.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -157,6 +158,12 @@ subdirectory from XDG_CONFIG_HOME to generate a target path."
                            #t
                            (G_ "Skipping ~a (not an empty directory)... done\n")
                            directory))
+                         ;; This happens when the directory is a mounted device.
+                         ((= EBUSY errno)
+                          (format
+                           #t
+                           (G_ "Skipping ~a (underlying device is busy)... done\n")
+                           directory))
                          ((= ENOENT errno) #t)
                          ((= ENOTDIR errno) #t)
                          (else

gnu/local.mk

@@ -1,6 +1,6 @@
 # GNU Guix --- Functional package management for GNU
 # Copyright © 2012-2024 Ludovic Courtès <ludo@gnu.org>
-# Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2022, 2023 Andreas Enge <andreas@enge.fr>
+# Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2022, 2023, 2024 Andreas Enge <andreas@enge.fr>
 # Copyright © 2016 Mathieu Lirzin <mthl@gnu.org>
 # Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021 Mark H Weaver <mhw@netris.org>
 # Copyright © 2016 Chris Marusich <cmmarusich@gmail.com>
@@ -13,7 +13,7 @@
 # Copyright © 2016-2023 Efraim Flashner <efraim@flashner.co.il>
 # Copyright © 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
 # Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
-# Copyright © 2017, 2018, 2023 Clément Lassieur <clement@lassieur.org>
+# Copyright © 2017, 2018, 2023, 2024 Clément Lassieur <clement@lassieur.org>
 # Copyright © 2017, 2020 Mathieu Othacehe <m.othacehe@gmail.com>
 # Copyright © 2017, 2018, 2019 Gábor Boskovits <boskovits@gmail.com>
 # Copyright © 2018 Amirouche Boubekki <amirouche@hypermove.net>
@@ -56,13 +56,14 @@
 # Copyright © 2022 Alex Griffin <a@ajgrf.com>
 # Copyright © 2022 ( <paren@disroot.org>
 # Copyright © 2022 jgart <jgart@dismail.de>
-# Copyright © 2023 Zheng Junjie <873216071@qq.com>
+# Copyright © 2023, 2024 Zheng Junjie <873216071@qq.com>
 # Copyright © 2023 Ivana Drazovic <iv.dra@hotmail.com>
 # Copyright © 2023 Andy Tai <atai@atai.org>
 # Copyright © 2023 B. Wilson <elaexuotee@wilsonb.com>
 # Copyright © 2023 gemmaro <gemmaro.dev@gmail.com>
 # Copyright © 2023 Herman Rimm <herman@rimm.ee>
 # Copyright © 2023 Troy Figiel <troy@troyfigiel.com>
+# Copyright © 2024 David Elsing <david.elsing@posteo.net>
 #
 # This file is part of GNU Guix.
 #
@@ -96,6 +97,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/home/services.scm			\
   %D%/home/services/desktop.scm			\
   %D%/home/services/dict.scm			\
+  %D%/home/services/dotfiles.scm		\
   %D%/home/services/symlink-manager.scm		\
   %D%/home/services/fontutils.scm		\
   %D%/home/services/gnupg.scm			\
@@ -199,9 +201,15 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/cpp.scm 				\
   %D%/packages/cppi.scm				\
   %D%/packages/cran.scm				\
+  %D%/packages/crates-apple.scm		\
+  %D%/packages/crates-crypto.scm		\
   %D%/packages/crates-io.scm			\
   %D%/packages/crates-graphics.scm		\
   %D%/packages/crates-gtk.scm			\
+  %D%/packages/crates-tls.scm			\
+  %D%/packages/crates-vcs.scm			\
+  %D%/packages/crates-web.scm			\
+  %D%/packages/crates-windows.scm		\
   %D%/packages/cross-base.scm			\
   %D%/packages/cross-toolchain.scm		\
   %D%/packages/crypto.scm			\
@@ -306,8 +314,12 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/gnu-pw-mgr.scm			\
   %D%/packages/gobby.scm			\
   %D%/packages/golang.scm			\
+  %D%/packages/golang-build.scm		\
   %D%/packages/golang-check.scm		\
+  %D%/packages/golang-compression.scm		\
+  %D%/packages/golang-crypto.scm	      	\
   %D%/packages/golang-web.scm	        	\
+  %D%/packages/golang-xyz.scm	        	\
   %D%/packages/gperf.scm			\
   %D%/packages/gpodder.scm			\
   %D%/packages/gps.scm				\
@@ -543,6 +555,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/toys.scm				\
   %D%/packages/tryton.scm			\
   %D%/packages/qt.scm				\
+  %D%/packages/quantum.scm			\
   %D%/packages/racket.scm			\
   %D%/packages/radio.scm			\
   %D%/packages/ragel.scm			\
@@ -629,6 +642,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/tls.scm				\
   %D%/packages/tmux.scm				\
   %D%/packages/toolkits.scm			\
+  %D%/packages/tor-browsers.scm			\
   %D%/packages/tor.scm				\
   %D%/packages/tree-sitter.scm			\
   %D%/packages/tv.scm				\
@@ -927,7 +941,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/apr-skip-getservbyname-test.patch	\
   %D%/packages/patches/aria2-unbundle-wslay.patch		\
   %D%/packages/patches/ark-skip-xar-test.patch			\
-  %D%/packages/patches/arpack-ng-propagate-rng-state.patch	\
   %D%/packages/patches/asli-use-system-libs.patch		\
   %D%/packages/patches/aspell-CVE-2019-25051.patch		\
   %D%/packages/patches/aspell-default-dict-dir.patch		\
@@ -952,6 +965,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/audiofile-function-signature.patch	\
   %D%/packages/patches/automake-skip-amhello-tests.patch	\
   %D%/packages/patches/avahi-localstatedir.patch		\
+  %D%/packages/patches/avalon-toolkit-rdkit-fixes.patch		\
   %D%/packages/patches/avidemux-install-to-lib.patch		\
   %D%/packages/patches/awesome-reproducible-png.patch		\
   %D%/packages/patches/awesome-4.3-fno-common.patch		\
@@ -965,7 +979,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/bazaar-CVE-2017-14176.patch		\
   %D%/packages/patches/bc-fix-cross-compilation.patch		\
   %D%/packages/patches/bdb-5.3-atomics-on-gcc-9.patch		\
-  %D%/packages/patches/bind-re-add-attr-constructor-priority.patch	\
   %D%/packages/patches/brightnessctl-elogind-support.patch	\
   %D%/packages/patches/bsd-games-2.17-64bit.patch		\
   %D%/packages/patches/bsd-games-add-configure-config.patch	\
@@ -1051,7 +1064,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/converseen-hide-non-free-pointers.patch	\
   %D%/packages/patches/cool-retro-term-wctype.patch		\
   %D%/packages/patches/coreutils-gnulib-tests.patch		\
-  %D%/packages/patches/coq-fix-envvars.patch			\
   %D%/packages/patches/cppcheck-disable-char-signedness-test.patch	\
   %D%/packages/patches/cpuinfo-system-libraries.patch		\
   %D%/packages/patches/cpulimit-with-glib-2.32.patch		\
@@ -1134,7 +1146,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/emacs-wordnut-require-adaptive-wrap.patch	\
   %D%/packages/patches/emacs-xelb-ignore-length-element.patch	\
   %D%/packages/patches/emacs-yasnippet-fix-empty-snippet-next.patch	\
-  %D%/packages/patches/emacs-yasnippet-fix-tests.patch	\
   %D%/packages/patches/enblend-enfuse-reproducible.patch	\
   %D%/packages/patches/enjarify-setup-py.patch			\
   %D%/packages/patches/enlightenment-fix-setuid-path.patch	\
@@ -1301,6 +1312,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/ghostscript-no-header-id.patch		\
   %D%/packages/patches/ghostscript-no-header-uuid.patch		\
   %D%/packages/patches/ghostscript-no-header-creationdate.patch \
+  %D%/packages/patches/git-filter-repo-generate-doc.patch	\
   %D%/packages/patches/gitg-fix-positional-argument.patch	\
   %D%/packages/patches/gklib-suitesparse.patch			\
   %D%/packages/patches/glib-appinfo-watch.patch			\
@@ -1399,7 +1411,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/guile-fibers-libevent-timeout.patch	\
   %D%/packages/patches/guile-fix-invalid-unicode-handling.patch \
   %D%/packages/patches/guile-gdbm-ffi-support-gdbm-1.14.patch	\
-  %D%/packages/patches/guile-git-adjust-for-libgit2-1.2.0.patch \
   %D%/packages/patches/guile-hurd-posix-spawn.patch		\
   %D%/packages/patches/guile-present-coding.patch		\
   %D%/packages/patches/guile-rsvg-pkgconfig.patch		\
@@ -1505,8 +1516,10 @@ dist_patch_DATA =						\
   %D%/packages/patches/julia-Use-MPFR-4.2.patch	                \
   %D%/packages/patches/libftdi-fix-paths-when-FTDIPP-set.patch	\
   %D%/packages/patches/libgeotiff-fix-tests-with-proj-9.1.1.patch	\
+  %D%/packages/patches/libgeotiff-fix-tests-with-proj-9.3.0.patch	\
+  %D%/packages/patches/libgeotiff-fix-tests-with-proj-9.3.1.patch	\
+  %D%/packages/patches/libgeotiff-fix-tests-on-i386.patch	\
   %D%/packages/patches/libobjc2-unbundle-robin-map.patch	\
-  %D%/packages/patches/librime-fix-build-with-gcc10.patch	\
   %D%/packages/patches/libvirt-add-install-prefix.patch	\
   %D%/packages/patches/libziparchive-add-includes.patch		\
   %D%/packages/patches/lightdm-arguments-ordering.patch		\
@@ -1646,6 +1659,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/lua-liblua-so.patch                      \
   %D%/packages/patches/lua-5.4-pkgconfig.patch			\
   %D%/packages/patches/lua-5.4-liblua-so.patch			\
+  %D%/packages/patches/lugaru-fix-sound.patch			\
   %D%/packages/patches/luit-posix.patch				\
   %D%/packages/patches/mactelnet-remove-init.patch		\
   %D%/packages/patches/mailutils-variable-lookup.patch		\
@@ -1715,7 +1729,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/network-manager-meson.patch		\
   %D%/packages/patches/nginx-socket-cloexec.patch		\
   %D%/packages/patches/nnpack-system-libraries.patch		\
-  %D%/packages/patches/notmuch-emacs-test-output.patch		\
   %D%/packages/patches/nsis-env-passthru.patch			\
   %D%/packages/patches/nss-getcwd-nonnull.patch			\
   %D%/packages/patches/nss-increase-test-timeout.patch		\
@@ -1725,10 +1738,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/nvi-db4.patch				\
   %D%/packages/patches/nyacc-binary-literals.patch		\
   %D%/packages/patches/obs-modules-location.patch		\
-  %D%/packages/patches/ocaml-dose3-add-unix-dependency.patch	\
-  %D%/packages/patches/ocaml-dose3-Fix-for-ocaml-4.06.patch	\
-  %D%/packages/patches/ocaml-dose3-dont-make-printconf.patch	\
-  %D%/packages/patches/ocaml-dose3-Install-mli-cmx-etc.patch	\
   %D%/packages/patches/ocaml-multiple-definitions.patch		\
   %D%/packages/patches/ocaml-4.07-dynamically-allocate-signal-stack.patch	\
   %D%/packages/patches/ocaml-4.09-dynamically-allocate-signal-stack.patch	\
@@ -1805,7 +1814,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-sip-include-dirs.patch	\
   %D%/packages/patches/python-sgmllib3k-assertions.patch	\
   %D%/packages/patches/python-sphinx-prompt-docutils-0.19.patch	\
-  %D%/packages/patches/python-telingo-fix-comparison.patch	\
   %D%/packages/patches/python-typeguard-python3.10.patch	\
   %D%/packages/patches/python-uqbar-python3.10.patch	        \
   %D%/packages/patches/python-wxwidgets-type-errors.patch	\
@@ -1914,7 +1922,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-piexif-fix-tests-with-pillow-7.2.patch	\
   %D%/packages/patches/python-pillow-CVE-2022-45199.patch	\
   %D%/packages/patches/python-pyfakefs-remove-bad-test.patch	\
-  %D%/packages/patches/python-flint-includes.patch		\
   %D%/packages/patches/python-libxml2-utf8.patch		\
   %D%/packages/patches/python-memcached-syntax-warnings.patch	\
   %D%/packages/patches/python-mox3-python3.6-compat.patch	\
@@ -1961,7 +1968,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/qtwayland-cleanup-callbacks.patch	\
   %D%/packages/patches/ragel-char-signedness.patch		\
   %D%/packages/patches/randomjungle-disable-static-build.patch	\
-  %D%/packages/patches/range-v3-build-with-gcc10.patch	\
   %D%/packages/patches/raptor2-heap-overflow.patch		\
   %D%/packages/patches/ratpoints-sturm_and_rp_private.patch	\
   %D%/packages/patches/ratpoison-shell.patch			\
@@ -1971,6 +1977,8 @@ dist_patch_DATA =						\
   %D%/packages/patches/renpy-use-system-fribidi.patch		\
   %D%/packages/patches/reposurgeon-add-missing-docbook-files.patch	\
   %D%/packages/patches/r-httpuv-1.6.6-unvendor-libuv.patch	\
+  %D%/packages/patches/r-sapa-lapack.patch			\
+  %D%/packages/patches/r-sgloptim.patch				\
   %D%/packages/patches/ri-li-modernize_cpp.patch		\
   %D%/packages/patches/ripperx-missing-file.patch		\
   %D%/packages/patches/rpcbind-CVE-2017-8779.patch		\
@@ -1980,6 +1988,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/racket-rktio-bin-sh.patch		\
   %D%/packages/patches/racket-zuo-bin-sh.patch			\
   %D%/packages/patches/remake-impure-dirs.patch			\
+  %D%/packages/patches/restartd-update-robust.patch             \
   %D%/packages/patches/restic-0.9.6-fix-tests-for-go1.15.patch	\
   %D%/packages/patches/rng-tools-revert-build-randstat.patch	\
   %D%/packages/patches/rocclr-5.6.0-enable-gfx800.patch		\
@@ -1997,17 +2006,20 @@ dist_patch_DATA =						\
   %D%/packages/patches/rustc-1.54.0-src.patch			\
   %D%/packages/patches/rust-1.64-fix-riscv64-bootstrap.patch	\
   %D%/packages/patches/rust-1.70-fix-rustix-build.patch	\
-  %D%/packages/patches/rust-ring-0.16-missing-files.patch	\
+  %D%/packages/patches/rust-cargo-edit-remove-ureq.patch	\
-  %D%/packages/patches/rust-ring-0.16-test-files.patch		\
+  %D%/packages/patches/rust-ring-0.17-ring-core.patch		\
-  %D%/packages/patches/i3status-rust-enable-unstable-features.patch	\
   %D%/packages/patches/rust-ndarray-remove-blas-src-dep.patch	\
   %D%/packages/patches/rust-ndarray-0.13-remove-blas-src.patch	\
   %D%/packages/patches/rust-ndarray-0.14-remove-blas-src.patch	\
   %D%/packages/patches/rust-nettle-disable-vendor.patch		 \
+  %D%/packages/patches/rust-rspec-1-remove-clippy.patch	\
+  %D%/packages/patches/rust-trash-2-update-windows.patch	\
   %D%/packages/patches/rust-webbrowser-remove-unsupported-os.patch	\
   %D%/packages/patches/rust-wl-clipboard-rs-newer-wl.patch      \
   %D%/packages/patches/rw-igraph-0.10.patch			\
   %D%/packages/patches/rxvt-unicode-fix-cursor-position.patch	\
+  %D%/packages/patches/s7-flint-3.patch                      	\
+  %D%/packages/patches/sajson-for-gemmi-numbers-as-strings.patch	\
   %D%/packages/patches/sbc-fix-build-non-x86.patch		\
   %D%/packages/patches/sbcl-aserve-add-HTML-5-elements.patch	\
   %D%/packages/patches/sbcl-aserve-fix-rfe12668.patch	\
@@ -2043,7 +2055,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/source-highlight-gcc-compat.patch	\
   %D%/packages/patches/softhsm-fix-openssl3-tests.patch		\
   %D%/packages/patches/spectre-meltdown-checker-externalize-fwdb.patch \
-  %D%/packages/patches/spdlog-fix-tests.patch			\
   %D%/packages/patches/sphinxbase-fix-doxygen.patch		\
   %D%/packages/patches/sssd-system-directories.patch		\
   %D%/packages/patches/steghide-fixes.patch			\
@@ -2171,6 +2182,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/webrtc-audio-processing-big-endian.patch	\
   %D%/packages/patches/webrtc-for-telegram-desktop-unbundle-libsrtp.patch \
   %D%/packages/patches/websocketpp-fix-for-cmake-3.15.patch	\
+  %D%/packages/patches/wlroots-hwdata-fallback.patch		\
   %D%/packages/patches/wmctrl-64-fix.patch			\
   %D%/packages/patches/wmfire-update-for-new-gdk-versions.patch	\
   %D%/packages/patches/wordnet-CVE-2008-2149.patch			\

gnu/machine/ssh.scm

@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2019 Jakob L. Kreuze <zerodaysfordays@sdf.org>
 ;;; Copyright © 2020-2023 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2024 Ricardo <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -537,6 +538,8 @@ failed to switch systems while deploying '~a':~%~{~s ~}")
                                         host
                                         (inferior-exception-arguments c))))
                               os))
+          (parameterize ((%current-system system)
+                         (%current-target-system #f))
             (with-roll-back #t
               (mbegin %store-monad
                 (upgrade-shepherd-services (eval/error-handling c
@@ -552,7 +555,7 @@ an error occurred while upgrading services on '~a':~%~{~s ~}~%")
 failed to install bootloader on '~a':~%~{~s ~}~%")
                                               host
                                               (inferior-exception-arguments c))))
-                                  bootloader-configuration bootcfg))))))))
+                                    bootloader-configuration bootcfg)))))))))
 
 
 ;;;

gnu/packages/admin.scm

@@ -62,6 +62,8 @@
 ;;; Copyright © 2023 Bruno Victal <mirai@makinata.eu>
 ;;; Copyright © 2023 Tobias Kortkamp <tobias.kortkamp@gmail.com>
 ;;; Copyright © 2023 Jaeme Sifat <jaeme@runbox.com>
+;;; Copyright © 2023 Nicolas Graves <ngraves@ngraves.fr>
+;;; Copyright © 2023 Tomás Ortín Fernández <tomasortin@mailbox.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -112,6 +114,7 @@
   #:use-module (gnu packages compression)
   #:use-module (gnu packages crates-graphics)
   #:use-module (gnu packages crates-io)
+  #:use-module (gnu packages crates-windows)
   #:use-module (gnu packages crypto)
   #:use-module (gnu packages cryptsetup)
   #:use-module (gnu packages curl)
@@ -130,6 +133,8 @@
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
+  #:use-module (gnu packages golang-compression)
   #:use-module (gnu packages groff)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages guile)
@@ -149,6 +154,7 @@
   #:use-module (gnu packages mcrypt)
   #:use-module (gnu packages mpi)
   #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages nettle)
   #:use-module (gnu packages networking)
   #:use-module (gnu packages openldap)
   #:use-module (gnu packages package-management)
@@ -4907,6 +4913,33 @@ It can mount all local file systems supported by @command{mount}, as well as
 LUKS volumes encrypted with the user's log-in password.")
     (license (list license:gpl2+ license:lgpl2.1+))))
 
+(define-public pam-uaccess
+  (let ((commit "54fbf043c63cc500b4850b0b4a12ea14078f2b53")
+        (revision "0"))
+    (package
+      (name "pam-uaccess")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://git.sr.ht/~kennylevinsen/pam_uaccess")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "08068cw4nvcanym8b5dyccnnb3qc3f09pbvi6fcfiz227yx73npc"))))
+      (build-system meson-build-system)
+      (native-inputs (list pkg-config))
+      (inputs (list acl eudev linux-pam))
+      (home-page "https://git.sr.ht/~kennylevinsen/pam_uaccess")
+      (synopsis
+       "PAM module that grants access to devices tagged @code{uaccess} in udev")
+      (description
+       "@code{pam_uaccess} is a PAM module that grants access to devices tagged
+@code{uaccess} in udev for the duration of the users' session, replacing
+elogind's uaccess feature.")
+      (license license:expat))))
+
 (define-public jc
   (package
     (name "jc")
@@ -5814,6 +5847,57 @@ up services to use only two factor, or public/private authentication
 mechanisms if you really want to protect services.")
     (license license:gpl2+)))
 
+(define-public restartd
+  (let* ((commit "7044125ac55056f2663536f7137170edf92ebd75")
+         ;; Version is 0.2.4 in the version file in the repo
+         ;; but not in github tags.
+         ;; It is released as 0.2.3-1.1 for other distributions.
+         ;; Probably because of the lack of activity upstream.
+         (revision "1"))
+    (package
+      (name "restartd")
+      (version (git-version "0.2.3" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/ajraymond/restartd")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "1m1np00b4zvvwx63gzysbi38i5vj1jsjvh2s0p9czl6dzyz582z0"))
+         (patches (search-patches "restartd-update-robust.patch"))))
+      (build-system gnu-build-system)
+      (arguments
+       (list
+        #:tests? #f ; no tests
+        #:make-flags
+        #~(list (string-append "CC=" #$(cc-for-target)))
+        #:phases
+        #~(modify-phases %standard-phases
+            (delete  'configure)
+            (replace 'install
+              (lambda _
+                (install-file "restartd.conf" (string-append #$output "/etc"))
+                (install-file "restartd" (string-append #$output "/sbin"))
+                (install-file "restartd.8"
+                              (string-append #$output "/share/man/man8"))
+                (mkdir-p (string-append #$output "/share/man/fr/man8"))
+                (copy-file
+                 "restartd.fr.8"
+                 (string-append #$output "/share/man/fr/man8/restartd.8")))))))
+      (home-page "https://launchpad.net/debian/+source/restartd")
+      (synopsis "Daemon for restarting processes")
+      (description "This package provides a daemon for checking running and
+not running processes.  It reads the @file{/proc} directory every @var{n}
+seconds and does a POSIX regexp on the process names.  The daemon runs a
+user-provided script when it detects a program in the running processes, or an
+alternate script if it doesn't detect the program.  The daemon can only be
+called by the root user, but can use @command{sudo -u user} in the process
+called if needed.")
+      (license license:gpl2+))))
+
 (define-public rex
   (package
     (name "rex")
@@ -6038,3 +6122,34 @@ breadth-first rather than depth-first.  It is otherwise compatible with many
 versions of @command{find}, including POSIX, GNU, and *BSD find.")
     (home-page "https://tavianator.com/projects/bfs.html")
     (license license:bsd-0)))
+
+(define-public rdfind
+  (package
+    (name "rdfind")
+    (version "1.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://rdfind.pauldreik.se/" name "-" version
+                           ".tar.gz"))
+       (sha256
+        (base32 "0y9j1w3nbgjks0k4kgm6qq92yrwgv66n212ncmlmhsl8y676wh3s"))))
+    (build-system gnu-build-system)
+    (native-inputs (list which))
+    (inputs (list nettle))
+    (arguments
+     (list
+      #:phases #~(modify-phases %standard-phases
+                   (add-before 'check 'patch-tests
+                     (lambda _
+                       (display (which "echo"))
+                       (substitute* "testcases/common_funcs.sh"
+                         (("/bin/echo")
+                          (which "echo"))))))))
+    (home-page "https://rdfind.pauldreik.se")
+    (synopsis "Find duplicate files")
+    (description
+     "Rdfind is a command line tool that finds duplicate files based on
+their content instead of their file names.  It is useful for compressing
+backup directories or just finding duplicate files.")
+    (license license:gpl2+)))

gnu/packages/algebra.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2022 Andreas Enge <andreas@enge.fr>
+;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2022, 2023, 2024 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2013, 2015, 2017, 2018, 2021 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016-2023 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2014, 2018 Mark H Weaver <mhw@netris.org>
@@ -133,25 +133,26 @@ greatest common divisor operations.")
 (define-public cm
   (package
    (name "cm")
-   (version "0.4.2")
+   (version "0.4.3")
    (source (origin
             (method url-fetch)
             (uri (string-append
-                  "http://www.multiprecision.org/downloads/cm-"
+                  "https://www.multiprecision.org/downloads/cm-"
                   version ".tar.gz"))
             (sha256
              (base32
-              "1c6m00wiw3rs5f0lq6c80rdr3dzklsvh69l8w3s7bj2r6yha6qbw"))))
+              "01dha0hl0daappjiydpk4ngl9nxkxli6a48jp6d7v85yjjykac5j"))))
    (build-system gnu-build-system)
    (propagated-inputs
-     (list mpfrcx zlib)) ; Header files included from cm_common.h.
+     (list mpfrcx zlib)) ; Header files included from lib/cm.h.
    (inputs
-     (list pari-gp))
+     (list flint pari-gp))
    (synopsis "CM constructions for elliptic curves")
    (description
     "The CM software implements the construction of ring class fields of
 imaginary quadratic number fields and of elliptic curves with complex
-multiplication via floating point approximations.  It consists of libraries
+multiplication via floating point approximations, and the elliptic curve
+primality proving algorithm (ECPP).  It consists of libraries
 that can be called from within a C program and of executable command
 line applications.")
    (license license:gpl3+)
@@ -295,6 +296,34 @@ GP2C, the GP to C compiler, translates GP scripts to PARI programs.")
    (license license:gpl2)
    (home-page "https://pari.math.u-bordeaux.fr/")))
 
+(define-public paritwine
+  (package
+    (name "paritwine")
+    (version "0.2.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://www.multiprecision.org/downloads/" name
+                    "-" version
+                    ".tar.gz"))
+              (sha256
+               (base32
+                "15m5jxmhx5zivk1k9wxpmzs8kqva3kvgxizdrkrmmp1qycn85n23"))))
+    (build-system gnu-build-system)
+    (propagated-inputs (list pari-gp
+                             gmp
+                             mpfr
+                             mpc
+                             cmh
+                             flint)) ; referenced in src/paritwine.h
+    (synopsis "Glue library between PARI/GP and other mathematics libraries")
+    (description
+     "PariTwine is a glue library between the system for computer algebra
+and number theory PARI/GP and a number of other mathematics libraries,
+currently GMP, GNU MPFR, GNU MPC, FLINT and CMH.")
+    (license license:gpl2+)
+    (home-page "https://www.multiprecision.org/paritwine/index.html")))
+
 (define-public cmh
   (package
     (name "cmh")
@@ -417,41 +446,20 @@ or text interfaces) or as a C++ library.")
 (define-public flint
   (package
    (name "flint")
-   (version "2.9.0")
+   (version "3.0.1")
    (source
     (origin
       (method url-fetch)
-      (uri (string-append "http://flintlib.org/flint-" version ".tar.gz"))
+      (uri (string-append "https://flintlib.org/flint-" version ".tar.gz"))
       (sha256
-       (base32 "0sp79ixaawjzna79afrlwlx9hg55jxil03f1wq435j9k23ar1h1g"))))
+       (base32 "1d4lawfvmjd4n7rp4z9xkwwjjbrjhkmxnxw1xf0ki1isa001lcbv"))))
    (build-system gnu-build-system)
    (inputs
     (list ntl))
    (propagated-inputs
     (list gmp mpfr)) ; header files from both are included by flint/arith.h
    (arguments
-    `(#:parallel-tests? #f              ; seems to be necessary on arm
+    `(#:parallel-tests? #f))            ; seems to be necessary on arm
-      #:phases
-       (modify-phases %standard-phases
-         (add-before 'configure 'newer-c++
-           (lambda _
-             (substitute* "configure"
-               (("-ansi") ""))
-             #t))
-         (replace 'configure
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out"))
-                   (gmp (assoc-ref inputs "gmp"))
-                   (mpfr (assoc-ref inputs "mpfr"))
-                   (ntl (assoc-ref inputs "ntl")))
-               ;; Do not pass "--enable-fast-install", which makes the
-               ;; homebrew configure process fail.
-               (invoke "./configure"
-                       (string-append "--prefix=" out)
-                       (string-append "--with-gmp=" gmp)
-                       (string-append "--with-mpfr=" mpfr)
-                       (string-append "--with-ntl=" ntl))
-               #t))))))
    (synopsis "Fast library for number theory")
    (description
     "FLINT is a C library for number theory.  It supports arithmetic
@@ -470,52 +478,12 @@ fast arithmetic.")
     '((release-monitoring-url . "http://flintlib.org/downloads.html")))))
 
 (define-public arb
-  (package
+  (deprecated-package "arb" flint))
-    (name "arb")
-    (version "2.23.0")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/fredrik-johansson/arb")
-                    (commit version)))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "1m9vskyf857gbm0cbh3z8c8m6cqkqa765wb9hqmsv7yzfmklzpvn"))))
-    (build-system gnu-build-system)
-    (propagated-inputs
-     (list flint))               ; flint.h is included by arf.h
-    (inputs
-     (list gmp mpfr))
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (replace 'configure
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out"))
-                   (flint (assoc-ref inputs "flint"))
-                   (gmp (assoc-ref inputs "gmp"))
-                   (mpfr (assoc-ref inputs "mpfr")))
-               ;; Do not pass "--enable-fast-install", which makes the
-               ;; homebrew configure process fail.
-               (invoke "./configure"
-                       (string-append "--prefix=" out)
-                       (string-append "--with-flint=" flint)
-                       (string-append "--with-gmp=" gmp)
-                       (string-append "--with-mpfr=" mpfr))))))))
-    (home-page "https://arblib.org")
-    (synopsis "Arbitrary precision floating-point ball arithmetic")
-    (description
-     "Arb is a C library for arbitrary-precision floating-point ball
-arithmetic.  It supports efficient high-precision computation with
-polynomials, power series, matrices and special functions over the
-real and complex numbers, with automatic, rigorous error control.")
-    (license license:lgpl2.1+)))
 
 (define-public python-flint
   (package
     (name "python-flint")
-    (version "0.3.0")
+    (version "0.5.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -524,15 +492,14 @@ real and complex numbers, with automatic, rigorous error control.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1v0anazbj1cfi68nl2j6dbd31kgkc1563xmr0zk5xk3xj78569pw"))
+                "10370kqik6q6vdqrqv3gbznsyaxbgqb3rbrff4alpw0sqr5s07c7"))))
-              (patches (search-patches "python-flint-includes.patch"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-cython))
+     (list python-cython-3))
     (propagated-inputs
      (list python-numpy))
     (inputs
-     (list arb flint))
+     (list flint))
     (synopsis "Python module wrapping ARB and FLINT")
     (description
      "Python-flint is a Python extension module wrapping FLINT
@@ -592,12 +559,12 @@ matrices, and polynomials over the integers and over finite fields.")
 (define-public singular
   (package
    (name "singular")
-   (version "4.2.1")
+   (version "4.3.2p10")
    (source
     (origin
       (method url-fetch)
       (uri
-       (string-append "http://www.mathematik.uni-kl.de/ftp/pub/Math/"
+       (string-append "https://www.singular.uni-kl.de/ftp/pub/Math/"
                       "Singular/SOURCES/"
                       (string-join
                        (string-split
@@ -607,7 +574,7 @@ matrices, and polynomials over the integers and over finite fields.")
                         #\.) "-")
                       "/singular-" version ".tar.gz"))
              (sha256 (base32
-                      "13gy1gdng8zijwlr1fn5sixw53z0zf9czzlg0vh1dcc59zw6v998"))))
+                      "1a2j2pkp73rb1xdd5623gkk1snwd85yimssnz86y0m79zvyckhi8"))))
    (build-system gnu-build-system)
    (native-inputs
     (list doxygen graphviz perl))

gnu/packages/android.scm

@@ -36,6 +36,7 @@
   #:use-module (guix git-download)
   #:use-module (guix build-system android-ndk)
   #:use-module (guix build-system cmake)
+  #:use-module (guix build-system emacs)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
   #:use-module (guix build-system python)
@@ -1224,6 +1225,36 @@ connected devices via ADB.")
     (home-page "https://github.com/mvdan/fdroidcl")
     (license license:bsd-3)))
 
+(define-public emacs-fdroid
+  (package
+    (name "emacs-fdroid")
+    (version "0.1.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/migalmoreno/fdroid.el")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1gv4kfir12bbi17cm5hpx197m8dbw1xwqp0z6qb3vc0fdnyis35j"))))
+    (build-system emacs-build-system)
+    (arguments
+     (list
+      #:phases #~(modify-phases %standard-phases
+                   (add-after 'unpack 'patch-file-name
+                     (lambda* (#:key inputs #:allow-other-keys)
+                       (emacs-substitute-variables "fdroid.el"
+                         ("fdroid-program"
+                          (search-input-file inputs "/bin/fdroidcl"))))))))
+    (inputs (list fdroidcl))
+    (home-page "https://github.com/migalmoreno/fdroid.el")
+    (synopsis "Manage F-Droid packages from Emacs")
+    (description "This package is an Emacs interface to F-Droid.  Its purpose
+is to aid in the management of F-Droid packages for an Android device or an
+emulator inside the comfort of Emacs.")
+    (license license:gpl3+)))
+
 (define-public enjarify
   (package
     (name "enjarify")
@@ -1277,7 +1308,7 @@ Java bytecode, which simplifies the analysis of Android applications.")
 (define-public android-file-transfer
   (package
     (name "android-file-transfer")
-    (version "4.2")
+    (version "4.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1287,7 +1318,7 @@ Java bytecode, which simplifies the analysis of Android applications.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "125rq8ji83nw6chfw43i0h9c38hjqh1qjibb0gnf9wrigar9zc8b"))))
+                "1ianph8ivj0fxg1l7llid7gv4pbfb5j23b33j9gan6x7scr13q2h"))))
     (build-system cmake-build-system)
     (arguments
      (list #:tests? #f)) ;there are no tests

gnu/packages/antivirus.scm

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

gnu/packages/audio.scm

@@ -1424,6 +1424,35 @@ performances.  The plugins include a cellular automaton synthesizer, an
 envelope follower, distortion effects, tape effects and more.")
     (license license:gpl2+)))
 
+(define-public omins-lv2
+  (let ((commit "058f341053067b69a84d4081107fda5058290ff9")
+	(revision "1"))
+    (package
+      (name "omins-lv2")
+      ;; No release despite being perfectly usable. 0.0.0 seems to be the only
+      ;; version the author ever specified:
+      (version (git-version "0.0.0" revision commit))
+      (source
+       (origin (method git-fetch)
+	       (uri
+	        (git-reference
+	         (url "https://git.drobilla.net/cgit.cgi/omins.lv2.git/")
+	         (commit commit)))
+	       (file-name (git-file-name name version))
+	       (sha256
+	        (base32
+                 "01hnx4hhbz3ap3bw15s42q4q1mw1mhdjwygq4550wvjfg6k4ga8w"))))
+      (build-system waf-build-system)
+      (arguments (list #:tests? #false)) ;There are no tests.
+      (inputs (list lv2))
+      (native-inputs (list pkg-config))
+      (home-page "https://git.drobilla.net/cgit.cgi/omins.lv2.git/")
+      (synopsis "LV2 audio plugins for modular synthesis")
+      (description
+       "Omins-lv2 is a small collection of LV2 audio plugins for modular
+synthesis.")
+      (license license:gpl2+))))
+
 (define-public snapcast
   (package
     (name "snapcast")
@@ -6311,7 +6340,7 @@ and DSD streams.")
 (define-public qpwgraph
   (package
     (name "qpwgraph")
-    (version "0.6.0")
+    (version "0.6.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -6320,7 +6349,7 @@ and DSD streams.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "17jl347rwagdyx6pgnp83l1ffhlyfl0s4jf7ii2i1j3s1m9sz7y0"))))
+                "0185hxbwqxhjiyym0s7bmrm50f3p4bnvx92qqmgvg3zd7r1x8m8s"))))
     (build-system cmake-build-system)
     (arguments
      (list #:tests? #f))                ; no tests

gnu/packages/aux-files/renpy/renpy.in

@@ -37,7 +37,27 @@ def path_to_saves(gamedir, save_directory=None):
     if not save_directory:
         return gamedir + "/saves"
 
-    return os.path.join(os.path.expanduser("~/.renpy"), save_directory)
+    prefix = os.environ.get("RENPY_PATH_TO_SAVES",
+                            os.path.expanduser("~/.renpy"))
+
+    return os.path.join(prefix, save_directory)
+
+def path_to_logdir(basedir):
+    return basedir
+
+def predefined_searchpath(commondir):
+    import renpy
+
+    # The default gamedir, in private.
+    searchpath = [ renpy.config.gamedir ]
+
+    if env_searchpath := os.environ.get("RENPY_SEARCHPATH"):
+        searchpath.extend(env_searchpath.split("::"))
+
+    if commondir and os.path.isdir(commondir):
+        searchpath.append(commondir)
+
+    return searchpath
 
 def main():
     try:

gnu/packages/axoloti.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2016, 2017, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2016, 2017, 2019, 2020, 2021, 2024 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -18,6 +18,7 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages axoloti)
+  #:use-module (guix gexp)
   #:use-module (guix utils)
   #:use-module (guix packages)
   #:use-module (guix download)
@@ -218,8 +219,9 @@ runtime.")
     (name "axoloti-patcher")
     (version (package-version axoloti-runtime))
     (arguments
-     `(#:tests? #f ; no check target
+     (list
-       #:modules ((guix build gnu-build-system)
+      #:tests? #f ; no check target
+      #:modules '((guix build gnu-build-system)
                   ((guix build ant-build-system) #:prefix ant:)
                   (guix build utils)
                   (srfi srfi-1)
@@ -229,14 +231,10 @@ runtime.")
                   (sxml simple)
                   (sxml xpath)
                   (sxml transform))
-       #:imported-modules ((guix build ant-build-system)
+      #:imported-modules `((guix build ant-build-system)
                            ,@%gnu-build-system-modules)
        #:phases
-       (modify-phases %standard-phases
+       #~(modify-phases %standard-phases
-         (add-after 'unpack 'make-git-checkout-writable
-           (lambda _
-             (for-each make-file-writable (find-files "."))
-             #t))
            (delete 'configure)
            (replace 'build
              (lambda* (#:key inputs #:allow-other-keys)
@@ -263,7 +261,7 @@ runtime.")
                      (sxml->xml
                       (pre-post-order
                        build.xml
-                     `(;; Remove all zipfileset tags from the "jar" tree and
+                       `( ;; Remove all zipfileset tags from the "jar" tree and
                          ;; inject our own tags.
                          (jar . ,(lambda (tag . kids)
                                    `(jar ,@(append-map
@@ -297,11 +295,10 @@ runtime.")
                          "-Djavac.source=1.7"
                          "-Djavac.target=1.7"
                          (string-append "-Dtag.short.version="
-                                      ,version)))))
+                                        #$version)))))
            (replace 'install
-           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (lambda* (#:key inputs #:allow-other-keys)
-             (let* ((out   (assoc-ref outputs "out"))
+               (let ((share (string-append #$output "/share/axoloti/")))
-                    (share (string-append out "/share/axoloti/")))
                  (install-file "dist/Axoloti.jar" share)
 
                  ;; We do this to ensure that this package retains references to
@@ -309,16 +306,17 @@ runtime.")
                  (install-file "build.xml" share)
 
                  ;; Create a launcher script
-               (mkdir (string-append out "/bin"))
+                 (mkdir (string-append #$output "/bin"))
-               (let ((target (string-append out "/bin/Axoloti")))
+                 (let ((target (string-append #$output "/bin/Axoloti")))
                    (with-output-to-file target
                      (lambda ()
-                     (let* ((dir       (string-append (assoc-ref outputs "out")
+                       (let* ((dir       (string-append #$output "/share/axoloti"))
-                                                      "/share/axoloti"))
                               (runtime   (search-input-directory inputs
                                                                  "share/axoloti"))
                               (toolchain (assoc-ref inputs "cross-toolchain"))
                               (includes  (string-append
+                                          toolchain
+                                          "/arm-none-eabi/include/:"
                                           toolchain
                                           "/arm-none-eabi/include/c++:"
                                           toolchain

gnu/packages/backup.scm

@@ -71,7 +71,10 @@
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
+  #:use-module (gnu packages golang-crypto)
   #:use-module (gnu packages golang-web)
+  #:use-module (gnu packages golang-xyz)
   #:use-module (gnu packages gperf)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages guile)
@@ -1270,27 +1273,28 @@ backup.")
 (define-public disarchive
   (package
     (name "disarchive")
-    (version "0.5.0")
+    (version "0.6.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://files.ngyro.com/disarchive/"
                                   "disarchive-" version ".tar.gz"))
               (sha256
                (base32
-                "16sjplkn9nr7zhfrqll7l1m2b2j4hg8k29p6bqjap9fkj6zpn2q2"))))
+                "1s4lyhhh1zsaxgn11hy2b1kdvnvpipii68wba0hwr471rd43m08k"))))
     (build-system gnu-build-system)
     (native-inputs
      (list autoconf
            automake
            pkg-config
            guile-3.0 ;for cross-compilation
+           guile-bzip2
            guile-gcrypt
            guile-lzma
            guile-quickcheck))
     (inputs
      (list guile-3.0 zlib))
     (propagated-inputs
-     (list guile-gcrypt guile-lzma))
+     (list guile-bzip2 guile-gcrypt guile-lzma))
     (home-page "https://ngyro.com/software/disarchive.html")
     (synopsis "Software archive disassembler")
     (description "Disarchive can disassemble software archives into data
@@ -1337,7 +1341,7 @@ compression parameters used by Gzip.")
                      (invoke "pytest")))))))
     (inputs
      (list borg python-colorama python-jsonschema python-requests
-           python-ruamel.yaml))
+           python-ruamel.yaml-0.16))
     (native-inputs
      (list python-flexmock python-pytest python-pytest-cov))
     (home-page "https://torsion.org/borgmatic/")

gnu/packages/base.scm

@@ -1551,8 +1551,8 @@ command.")
 (define-public tzdata
   (package
     (name "tzdata")
-    ;; This package should be kept in sync with python-pytz in (gnu packages
+    ;; This package should be kept in sync with python-pytz and python-tzdata
-    ;; time).
+    ;; in (gnu packages time).
     (version "2022a")
     (source (origin
              (method url-fetch)

gnu/packages/bioinformatics.scm

@@ -4,7 +4,7 @@
 ;;; Copyright © 2015, 2016, 2018, 2019, 2020 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2016, 2020, 2021 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2016-2023 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016-2024 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2020, 2022 Marius Bakke <marius@gnu.org>
 ;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com>
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -93,7 +93,9 @@
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gd)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
   #:use-module (gnu packages golang-check)
+  #:use-module (gnu packages golang-compression)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages graph)
   #:use-module (gnu packages graphics)
@@ -1100,6 +1102,43 @@ high-throughput sequence analysis.  The package is primarily useful to
 developers of other R packages who wish to make use of HTSlib.")
       (license license:lgpl2.0+))))
 
+(define-public r-scenic
+  (let ((commit "cedf8490a634da550cea2c831544e5f7f14467d2")
+        (revision "1"))
+    (package
+      (name "r-scenic")
+      (version (git-version "1.3.1" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/aertslab/SCENIC")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "17ai0q260hdqbvm1km1s5dw93pgz4f546ycfii57jyy9m9jka7r0"))))
+      (properties `((upstream-name . "SCENIC")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-aucell
+                               r-data-table
+                               r-dynamictreecut
+                               r-genie3
+                               r-ggrepel
+                               r-mixtools
+                               r-nmf
+                               r-rcistarget
+                               r-rtsne))
+      (native-inputs (list r-knitr))
+      (home-page "https://github.com/aertslab/SCENIC")
+      (synopsis
+       "SCENIC (Single Cell rEgulatory Network Inference and Clustering)")
+      (description "SCENIC (Single-cell regulatory network inference and
+clustering) is an R package to infer Gene Regulatory Networks and cell types
+from single-cell RNA-seq data.")
+      ;; As of commit cedf8490a634da550cea2c831544e5f7f14467d2 the license is
+      ;; GPLv3.
+      (license license:gpl3))))
+
 (define-public r-singlet
   (let ((commit "765a6c45081807a1522f0e8983e2417822a36f36")
         (revision "1"))
@@ -1470,6 +1509,39 @@ cpp.find_library('hdf5_cpp', dirs : '~a'), "
      "Blasr is a genomic sequence aligner for processing PacBio long reads.")
     (license license:bsd-3)))
 
+(define-public randfold
+  (package
+    (name "randfold")
+    (version "2.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://bioinformatics.psb.ugent.be/"
+                           "supplementary_data/erbon/nov2003/downloads/"
+                           "randfold-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0gqixl4ncaibrxmn25d6lm2hrw4ml2fj13nrc9q1kilsxdfi91mj"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:tests? #f                       ;no tests provided
+      #:phases
+      #~(modify-phases %standard-phases
+          (delete 'configure)
+          (replace 'install
+            (lambda _
+              (install-file "randfold"
+                            (string-append #$output "/bin")))))))
+    (inputs (list eddylab-squid))
+    (home-page
+     "http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/")
+    (synopsis "Minimum free energy of folding randomization test software")
+    (description "randfold computes the probability that, for a given
+sequence, the @dfn{Minimum Free Energy} (MFE) of the secondary structure is
+different from MFE computed with random sequences.")
+    (license license:gpl2)))
+
 (define-public ribotaper
   (package
     (name "ribotaper")
@@ -2112,6 +2184,45 @@ matplotlib Axes objects, making them easy to style and incorporate into
 multi-panel figures.")
     (license license:expat)))
 
+(define-public python-magic-impute
+  (package
+    (name "python-magic-impute")
+    (version "1.2.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/KrishnaswamyLab/MAGIC")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "1yjs16vg87lcg9g16bnblg1v9sk73j6dm229lkcz0bfjlzxjhv8w"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:tests? #false ;there are none
+      #:phases
+      '(modify-phases %standard-phases
+         (add-after 'unpack 'chdir
+           (lambda _ (chdir "python"))))))
+    (propagated-inputs
+     (list python-future
+           python-graphtools
+           python-matplotlib
+           python-numpy
+           python-pandas
+           python-scikit-learn
+           python-scipy
+           python-tasklogger))
+    (home-page "https://github.com/KrishnaswamyLab/MAGIC")
+    (synopsis "Markov affinity-based graph imputation of cells")
+    (description "MAGIC is an interactive tool to impute missing values in
+single-cell sequencing data and to restore the structure of the data.  It also
+provides data pre-processing functionality such as dimensionality reduction
+and gene expression visualization.")
+    (license license:gpl2+)))
+
 (define-public python-parabam
   (package
     (name "python-parabam")
@@ -2135,6 +2246,38 @@ parallel.  It uses Python's native multiprocessing framework to apply a user
 defined rule on an input file.")
     (license license:gpl3)))
 
+(define-public python-pdbfixer
+  (package
+    (name "python-pdbfixer")
+    (version "1.9")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/openmm/pdbfixer")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1zjhb19q5dclkwvzh8n29p31n1vzkhlmmzwqllimi89jsis1cx35"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      '(list "-k"
+             ;; These tests fail because they require internet access.
+             (string-append "not test_build_and_simulate.py"
+                            " and not test_cli.py"
+                            " and not test_mutate.py"))))
+    (propagated-inputs (list openmm python-numpy))
+    (native-inputs (list python-pytest))
+    (home-page "https://github.com/openmm/pdbfixer")
+    (synopsis "Application for fixing problems in Protein Data Bank")
+    (description
+     "PDBFixer is designed to rectify issues in Protein Data Bank files.
+Its intuitive interface simplifies the process of resolving problems
+encountered in PDB files prior to simulation tasks.")
+    (license license:expat)))
+
 (define-public python-peaks2utr
   (package
     (name "python-peaks2utr")
@@ -2382,6 +2525,70 @@ Python.")
     ;; licensed lgpl2.1+
     (license (list license:expat license:lgpl2.1+))))
 
+(define-public python-ega-download-client
+  (package
+    (name "python-ega-download-client")
+    (version "5.1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/EGA-archive/ega-download-client")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0k9rfq2yyvfxs5sq9lsm8krp9ddx4s18hv85ikf3b37zv24kpwjk"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      '(list
+        ;; These tests fail because they require internet access.
+        "--ignore=tests/functional/test_download.py"
+        "--ignore=tests/functional/test_htsget.py"
+        "-k"
+        (string-append "not test_error_5xx"
+                       " and not test_error_too_many_requests"
+                       ;; Something's wrong here.  On some powerful machines
+                       ;; (but not on my laptop) these fail, and tests like
+                       ;; test_file_is_saved_into_an_existing_directory_which_was_specified_by_the_user
+                       ;; take a *very* long time to complete.
+                       ;;
+                       ;; It looks like "dataset_in_fire.download" takes an
+                       ;; unusually long time on those machines.  We disable
+                       ;; tests that fail under these conditions.
+                       " and not test_download_file"
+                       " and not test_output_file_is_removed_if_md5_was_invalid"
+                       " and not test_post_stats_if_download_succeeded"))
+      #:phases
+      '(modify-phases %standard-phases
+         (add-after 'unpack 'relax-requirements
+           (lambda _
+             (substitute* "setup.py"
+               (("==") ">=")))))))
+    (propagated-inputs (list python-htsget python-psutil python-requests
+                             python-tqdm python-urllib3))
+    (native-inputs (list python-coverage python-pytest python-pyfakefs
+                         python-responses python-mock))
+    (home-page "https://github.com/EGA-archive/ega-download-client")
+    (synopsis "EGA download client")
+    (description "PyEGA3 is a tool for viewing and downloading files from
+authorized EGA datasets.  It uses the EGA data API and has several key
+features:
+
+@itemize
+@item Files are transferred over secure https connections and received
+  unencrypted, so no need for decryption after download.
+@item Downloads resume from where they left off in the event that the
+  connection is interrupted.
+@item Supports file segmenting and parallelized download of segments,
+  improving overall performance.
+@item After download completes, file integrity is verified using checksums.
+@item Implements the GA4GH-compliant htsget protocol for download of genomic
+  ranges for data files with accompanying index files.
+@end itemize\n")
+    (license license:asl2.0)))
+
 (define-public python-scdamandtools
   (package
     (name "python-scdamandtools")
@@ -3549,14 +3756,14 @@ gapped, local, and paired-end alignment modes.")
 (define-public bowtie1
   (package
     (name "bowtie1")
-    (version "1.3.0")
+    (version "1.3.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/bowtie-bio/bowtie/"
                                   version "/bowtie-" version "-src.zip"))
               (sha256
                (base32
-                "11dbihdnrizc6qhx9xsw77w3q5ssx642alaqzvhxx32ak9glvq04"))
+                "0q87nhgj9wrnbazcpvqp4594hmyh1isi3s9b2wlghvl4afm1fdg2"))
               (modules '((guix build utils)))
               (snippet
                '(substitute* "Makefile"
@@ -3565,16 +3772,22 @@ gapped, local, and paired-end alignment modes.")
                   (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))))
     (build-system gnu-build-system)
     (arguments
-     `(#:tests? #f                      ; no "check" target
+     `(#:tests? #f                      ; Tests need various perl modules
+       #:test-target "simple-test"
        #:make-flags
-       ,#~(list "CC=gcc" "all"
+       ,#~(append #$(if (not (target-x86?))
-                (string-append "prefix=" #$output))
+                        #~'("POPCNT_CAPABILITY=0")
+                        #~'())
+                  (list (string-append "CC=" #$(cc-for-target))
+                        (string-append "CXX=" #$(cxx-for-target))
+                        "all"
+                        (string-append "prefix=" #$output)))
        #:phases
        (modify-phases %standard-phases
          (delete 'configure))))
     (inputs
-     (list python-wrapper tbb-2020 zlib))
+     (list python-wrapper tbb zlib))
-    (supported-systems '("x86_64-linux"))
+    (supported-systems %64bit-supported-systems)
     (home-page "https://bowtie-bio.sourceforge.net/index.shtml")
     (synopsis "Fast aligner for short nucleotide sequence reads")
     (description
@@ -3898,39 +4111,7 @@ omics data.")
     (license license:bsd-3)))
 
 (define-public python-pyega3
-  (package
+  (deprecated-package "python-pyega3" python-ega-download-client))
-    (name "python-pyega3")
-    (version "3.4.1")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "pyega3" version))
-              (sha256
-               (base32
-                "1k736in8g27rarx65ym9xk50x53zjg75h37bb8ljynxv04rypx2q"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:tests? #f)) ; The tests require network access.
-    (native-inputs
-     (list python-psutil python-htsget))
-    (propagated-inputs
-     (list python-requests python-tqdm python-urllib3 python-responses))
-    (home-page "https://github.com/EGA-archive/ega-download-client")
-    (synopsis "Python client for EGA")
-    (description "This package is a python-based tool for viewing and
-downloading files from authorized EGA datasets.  It uses the EGA data API and
-has several key features:
-@itemize
-@item Files are transferred over secure https connections and received
-  unencrypted, so no need for decryption after download.
-@item Downloads resume from where they left off in the event that the
-  connection is interrupted.
-@item Supports file segmenting and parallelized download of segments,
-  improving overall performance.
-@item After download completes, file integrity is verified using checksums.
-@item Implements the GA4GH-compliant htsget protocol for download of genomic
-  ranges for data files with accompanying index files.
-@end itemize\n")
-    (license license:asl2.0)))
 
 (define-public python-pysam
   (package
@@ -4652,6 +4833,64 @@ meso, or continuum scale.")
 files.")
     (license license:expat)))
 
+(define-public lsgkm
+  (package
+    (name "lsgkm")
+    (version "0.1.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/Dongwon-Lee/lsgkm.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0b3m94kndvimdfjaf1q2yhmsn7lm5s9v81c5xgfjcp6ig7mh3sa5"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:make-flags '(list "-C" "src")
+      #:tests? #false                   ;there are no executable tests
+      #:phases
+      #~(modify-phases %standard-phases
+          (delete 'configure)
+          (replace 'install
+            (lambda _
+              (let ((bin (string-append #$output "/bin")))
+                (for-each (lambda (file)
+                            (install-file file bin))
+                          '("src/gkmtrain"
+                            "src/gkmpredict"))))))))
+    (home-page "https://github.com/Dongwon-Lee/lsgkm")
+    (synopsis "Predict regulatory DNA elements in large-scale data")
+    (description "gkm-SVM, a sequence-based method for predicting regulatory
+DNA elements, is a useful tool for studying gene regulatory mechanisms.
+LS-GKM is an effort to improve the method.  It offers much better scalability
+and provides further advanced gapped k-mer based kernel functions.  As a
+result, LS-GKM achieves considerably higher accuracy than the original
+gkm-SVM.")
+    (license license:gpl3+)))
+
+(define-public python-fcsparser
+  (package
+    (name "python-fcsparser")
+    (version "0.2.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "fcsparser" version))
+       (sha256
+        (base32 "1skk1k8phq9sj4ar0cnq8px89y3kcyh5zrbl6anz9wcdcyzkc16z"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-numpy python-pandas))
+    (native-inputs (list python-poetry-core python-pytest))
+    (home-page "https://github.com/eyurtsev/fcsparser")
+    (synopsis "Package for reading raw fcs files")
+    (description
+     "This package provides a Python package for reading raw fcs files")
+    (license license:expat)))
+
 (define-public python-pybigwig
   (package
     (name "python-pybigwig")
@@ -4686,40 +4925,127 @@ files.")
 accessing bigWig files.")
     (license license:expat)))
 
+(define-public python-pyfasta
+  ;; The release on pypi does not contain the test data files.
+  (let ((commit "c2f0611c5311f1b1466f2d56560447898b4a8b03")
+        (revision "1"))
+    (package
+      (name "python-pyfasta")
+      (version (git-version "0.5.2" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/brentp/pyfasta")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "0a189id3fbv88gssyk6adbmz2ll1mqpmyw8vxmx3fi955gvaq9j7"))))
+      (build-system pyproject-build-system)
+      (arguments
+       (list
+        #:phases
+        '(modify-phases %standard-phases
+           (add-after 'unpack 'python3.10-compat
+             (lambda _
+               (substitute* "pyfasta/__init__.py"
+                 (("from fasta import")
+                  "from pyfasta.fasta import")
+                 (("from records import")
+                  "from pyfasta.records import")
+                 (("from split_fasta import")
+                  "from pyfasta.split_fasta import")
+                 (("in f.iteritems")
+                  "in f.items"))
+               (substitute* "pyfasta/fasta.py"
+                 (("from collections import Mapping")
+                  "from collections.abc import Mapping")
+                 (("from records import")
+                  "from pyfasta.records import"))
+               (substitute* "pyfasta/records.py"
+                 (("cPickle") "pickle")
+                 (("\\(int, long\\)")
+                  "(int, int)")
+                 ;; XXX: it's not clear if this is really correct.
+                 (("buffer\\(self\\)")
+                  "memoryview(bytes(str(self), encoding='utf-8'))")
+                 (("sys.maxint") "sys.maxsize"))
+               (substitute* "pyfasta/split_fasta.py"
+                 (("from cStringIO import")
+                  "from io import")
+                 (("in lens.iteritems") "in lens.items"))
+               (substitute* "tests/test_all.py"
+                 (("f.keys\\(\\)\\) == \\['a-extra'")
+                  "list(f.keys())) == ['a-extra'")
+                 (("f.iterkeys\\(\\)") "iter(f.keys())")
+                 (("tests/data/" m)
+                  (string-append (getcwd) "/" m))))))))
+      (propagated-inputs (list python-numpy))
+      (native-inputs (list python-nose))
+      (home-page "https://github.com/brentp/pyfasta/")
+      (synopsis "Pythonic access to fasta sequence files")
+      (description
+       "This library provides fast, memory-efficient, pythonic (and
+command-line) access to fasta sequence files.  It stores a flattened version
+of a fasta sequence file without spaces or headers and uses either a
+@code{mmap} in numpy binary format or @code{fseek}/@code{fread} so the
+sequence data is never read into memory.  It saves a pickle (@code{.gdx}) of
+the start and stop (for @code{fseek}/@code{mmap}) locations of each header in
+the fasta file for internal use.
+
+Note that this package has been deprecated in favor of @code{pyfaidx}.")
+      (license license:expat))))
+
 (define-public python-schema-salad
   (package
     (name "python-schema-salad")
-    (version "8.2.20211116214159")
+    (version "8.5.20240102191335")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "schema-salad" version))
         (sha256
          (base32
-          "005dh2y45x92zl8sf2sqjmfvcqr4hrz8dfckgkckv87003v7lwqc"))))
+          "035202p696i3jylb8b3nm9qcxsqby15hhqn1dl4nrz73a17p0ckx"))))
     (build-system pyproject-build-system)
     (arguments
-     `(#:phases
+     (list
-       (modify-phases %standard-phases
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'set-version
+            (lambda _
+              ;; Set exact version.
+              (substitute* "setup.py"
+                (("use_scm_version=True")
+                 (string-append "version=\"" #$version "\"")))))
           (add-before 'check 'skip-failing-tests
             (lambda _
               ;; Skip tests that require network access.
-             (substitute* "schema_salad/tests/test_cwl11.py"
+              (let ((skip-test
-               (("^def test_(secondaryFiles|outputBinding)" all)
+                     (lambda (test-pattern)
                        (string-append "@pytest.mark.skip(reason="
                                       "\"test requires network access\")\n"
-                               all))))))))
+                                      test-pattern))))
+                (substitute* "schema_salad/tests/test_cg.py"
+                  (("^def test_(load(_by_yaml_metaschema|_metaschema|_cwlschema|)|include|idmap|idmap2)\\(" all)
+                   (skip-test all)))
+                (substitute* "schema_salad/tests/test_cwl11.py"
+                  (("^def test_(secondaryFiles|outputBinding|yaml_tab_error)\\(" all)
+                   (skip-test all)))
+                (substitute* "schema_salad/tests/test_examples.py"
+                  (("^def test_bad_schemas\\(" all)
+                   (skip-test all)))))))))
     (propagated-inputs
      (list python-cachecontrol
-           python-lockfile
+           python-importlib-resources
-           python-mistune
+           python-mistune-next
+           python-mypy-extensions
            python-rdflib
-           python-rdflib-jsonld
            python-requests
-           python-ruamel.yaml
+           python-ruamel.yaml))
-           python-typing-extensions))
     (native-inputs
-     (list python-black python-pytest python-pytest-runner))
+     (list python-black python-pytest python-pytest-runner python-pytest-xdist))
     (home-page "https://github.com/common-workflow-language/schema_salad")
     (synopsis "Schema Annotations for Linked Avro Data (SALAD)")
     (description
@@ -4811,10 +5137,104 @@ resources for bioinformatics.")
 doublets in single-cell RNA-seq data.")
     (license license:expat)))
 
+(define-public python-cwlformat
+  (package
+    (name "python-cwlformat")
+    (version "2022.02.18")
+    (source
+     ;; The PyPI tarball is missing Readme.md. Readme.md is required for the
+     ;; build.
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/rabix/cwl-format")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0agkz2w86k91rc9m5vx5hsqi5nm6fcmzkng6j99hjapz0r9233ql"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs
+     (list python-importlib-resources
+           python-ruamel.yaml))
+    (home-page "https://github.com/rabix/cwl-format")
+    (synopsis "Prettifier for CWL code")
+    (description "@code{python-cwlformat} is a specification and a reference
+implementation for a very opinionated @acronym{CWL, Common Workflow Language}
+code formatter.  It outputs CWL in a standardized YAML format.")
+    (license license:asl2.0)))
+
+(define-public python-cwl-upgrader
+  (package
+    (name "python-cwl-upgrader")
+    (version "1.2.11")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "cwl-upgrader" version))
+       (sha256
+        (base32
+         "12j6z8nvwnzjjyypz59hwj5hmrcri2r6aknw52n9dbj6lbzbdd2p"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list python-pytest))
+    (propagated-inputs
+     (list python-ruamel.yaml
+           python-schema-salad))
+    (home-page "https://github.com/common-workflow-language/cwl-upgrader")
+    (synopsis "CWL document upgrader")
+    (description "@code{python-cwl-upgrader} is a standalone upgrader for
+@acronym{CWL, Common Workflow Language} documents from version draft-3, v1.0,
+and v1.1 to v1.2.")
+    (license license:asl2.0)))
+
+(define-public python-cwl-utils
+  (package
+    (name "python-cwl-utils")
+    (version "0.32")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "cwl-utils" version))
+       (sha256
+        (base32
+         "06wkw8d8cqm3hnz8xwnysz874gwaym36c358cr7frw5iglhvsj98"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      #~(list "-k"
+              (string-append "not test_graph_split"
+                             " and not test_load_document_with_remote_uri"
+                             " and not test_remote_packing"
+                             " and not test_remote_packing_github_soft_links"
+                             " and not test_value_from_two_concatenated_expressions"))))
+    (inputs
+     (list node))
+    (native-inputs
+     (list python-mypy-extensions
+           python-pytest
+           python-pytest-mock
+           python-pytest-runner))
+    (propagated-inputs
+     (list python-cwl-upgrader
+           python-cwlformat
+           python-packaging
+           python-rdflib
+           python-requests
+           python-ruamel.yaml
+           python-schema-salad))
+    (home-page "https://github.com/common-workflow-language/cwl-utils")
+    (synopsis "Python utilities for CWL")
+    (description "@code{python-cwl-utils} provides python utilities and
+autogenerated classes for loading and parsing CWL v1.0, CWL v1.1, and CWL v1.2
+documents.")
+    (license license:asl2.0)))
+
 (define-public cwltool
   (package
     (name "cwltool")
-    (version "3.1.20220119140128")
+    (version "3.1.20240112164112")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -4823,21 +5243,22 @@ doublets in single-cell RNA-seq data.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1jmrm0qrqgka79avc1kq63fgh20gx6g07fc8p3iih4k85vhdyl3f"))))
+                "1fpc5kqgpbn48g5vlvy64p297x2wm3gfz8casgpk15ap593wwh33"))))
     (build-system pyproject-build-system)
     (arguments
-     `(#:phases
+     (list
-       (modify-phases %standard-phases
+      #:phases
+      #~(modify-phases %standard-phases
           (add-after 'unpack 'loosen-version-restrictions
             (lambda _
               (substitute* "setup.py"
-               (("== 1.5.1") ">=1.5.1")))) ; prov
+                (("== 1.5.1") "> 1.5.1")))) ; prov
-         (add-after 'unpack 'dont-use-git
+          (add-after 'unpack 'set-version
             (lambda _
-             (substitute* "gittaggers.py"
+              ;; Set exact version.
-               (("self.git_timestamp_tag\\(\\)")
+              (substitute* "setup.py"
-                (string-append "time.strftime('.%Y%m%d%H%M%S', time.gmtime(int("
+                (("use_scm_version=True")
-                               (string-drop ,version 4) ")))")))))
+                 (string-append "version=\"" #$version "\"")))))
           (add-after 'unpack 'modify-tests
             (lambda _
               ;; Tries to connect to the internet.
@@ -4857,22 +5278,16 @@ doublets in single-cell RNA-seq data.")
                 (("def test_v1_0_arg_empty_prefix_separate_false")
                  (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
                                 "def test_v1_0_arg_empty_prefix_separate_false")))
-
+              (substitute* '("tests/subgraph/env-tool2.cwl"
-             (substitute* '("cwltool/schemas/v1.1/tests/env-tool1.cwl"
-                            "cwltool/schemas/v1.1/tests/env-tool2.cwl"
-                            "cwltool/schemas/v1.1/tests/imported-hint.cwl"
-                            "tests/subgraph/env-tool2.cwl"
                              "tests/subgraph/env-tool2_req.cwl"
                              "tests/subgraph/env-wf2_subwf-packed.cwl"
                              "tests/subgraph/env-tool2_no_env.cwl")
-               (("\"/bin/sh\"") (string-append "\"" (which "sh") "\"")))
+                (("\"/bin/sh\"") (string-append "\"" (which "sh") "\""))))))))
-             ;; Pytest doesn't know what to do with "-n auto"
-             (substitute* "tox.ini"
-               (("-n auto") "")))))))
     (inputs
      (list python-argcomplete
            python-bagit
            python-coloredlogs
+           python-cwl-utils
            python-mypy-extensions
            python-prov
            python-pydot
@@ -4882,6 +5297,7 @@ doublets in single-cell RNA-seq data.")
            python-ruamel.yaml
            python-schema-salad
            python-shellescape
+           python-spython
            python-typing-extensions
            ;; Not listed as needed but still necessary:
            node))
@@ -4892,7 +5308,8 @@ doublets in single-cell RNA-seq data.")
            python-pytest
            python-pytest-cov
            python-pytest-mock
-           python-pytest-runner))
+           python-pytest-runner
+           python-pytest-xdist))
     (home-page
      "https://github.com/common-workflow-language/common-workflow-language")
     (synopsis "Common Workflow Language reference implementation")
@@ -5432,6 +5849,35 @@ quantitative phenotypes.")
     ;; license is the GPL.
     (license license:gpl3+)))
 
+(define-public eddylab-squid
+  (package
+    (name "eddylab-squid")
+    (version "1.9g")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://eddylab.org/software/squid/squid-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "19ywv1h581a84yyjnp64gwww99vhgbxi8v4rl37xp92ag7l44brh"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'set-perl-search-path
+           (lambda _
+             ;; Work around "dotless @INC" build failure.
+             (setenv "PERL5LIB"
+                     (string-append (getcwd) "/Testsuite:"
+                                    (getenv "PERL5LIB"))))))))
+    (inputs (list perl))
+    (home-page "http://eddylab.org/software.html")
+    (synopsis "C function library for sequence analysis")
+    (description "SQUID is Sean Eddy's personal library of C functions
+and utility programs for sequence analysis.")
+    (license license:gpl2)))
+
 (define-public edirect
   (package
     (name "edirect")
@@ -6075,6 +6521,43 @@ sequences to the genome---manipulating the sequences to produce better mapping
 results.  The FASTX-Toolkit tools perform some of these preprocessing tasks.")
     (license license:agpl3+)))
 
+(define-public flash
+  (package
+    (name "flash")
+    (version "1.2.11")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://sourceforge/flashpage/FLASH-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "1b1ns9ghbcxy92xwa2a53ikqacvnyhvca0zfv0s7986xzvvscp38"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:make-flags #~(list (string-append "CC=" #$(cc-for-target)))
+      #:tests? #f                       ;no tests
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; No configure script
+          (delete 'configure)
+          ;; No install target
+          (replace 'install
+            (lambda _
+              (install-file "flash"
+                            (string-append #$output "/bin")))))))
+    (inputs (list zlib))
+    (home-page "http://ccb.jhu.edu/software/FLASH/")
+    (synopsis "Merge paired-end nucleotide reads from NGS experiments")
+    (description "FLASH (Fast Length Adjustment of SHort reads) is a tool to
+merge paired-end reads from next-generation sequencing experiments.  FLASH is
+designed to merge pairs of reads when the original DNA fragments are shorter
+than twice the length of reads.  The resulting longer reads can significantly
+improve genome assemblies.  They can also improve transcriptome assembly when
+FLASH is used to merge RNA-seq data.")
+    (license license:gpl3+)))
+
 (define-public flexbar
   (package
     (name "flexbar")
@@ -7367,6 +7850,49 @@ to measure the reproducibility of findings identified from replicate
 experiments and provide highly stable thresholds based on reproducibility.")
     (license license:gpl2+)))
 
+(define-public isolator
+  (let ((commit "24bafc0a102dce213bfc2b5b9744136ceadaba03")
+        (revision "1"))
+    (package
+      (name "isolator")
+      (version (git-version "0.0.2" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/dcjones/isolator.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "12mbcfqhiggcjvzizf2ff7b05z31i47njcyzcivpw5j74pfbr3dv"))))
+      (build-system cmake-build-system)
+      (arguments
+       (list
+        #:tests? #f                     ;no check target
+        #:phases
+        '(modify-phases %standard-phases
+           (add-after 'unpack 'fix-std
+             (lambda _
+               (substitute* '("src/summarize.cpp"
+                              "src/shredder.cpp")
+                 (("isnan") "std::isnan")
+                 (("isinf") "std::isinf")))))))
+      (inputs
+       (list boost hdf5 zlib))
+      (home-page "https://github.com/dcjones/isolator")
+      (synopsis "Tools for the analysis of RNA-Seq experiments")
+      (description "Isolator analyzes RNA-Seq experiments.  Isolator has a
+particular focus on producing stable, consistent estimates.  It implements a
+full hierarchical Bayesian model of an entire RNA-Seq experiment.  It saves
+all the samples generated by the sampler, which can be processed to compute
+posterior probabilities for arbitrarily complex questions, far beyond the
+confines of pairwise tests.  It aggressively corrects for technical effects,
+such as random priming bias, GC-bias, 3' bias, and fragmentation effects.
+Compared to other MCMC approaches, it is exceedingly efficient, though
+generally slower than modern maximum likelihood approaches.")
+      (license license:expat))))
+
 (define-public jellyfish
   (package
     (name "jellyfish")
@@ -7840,6 +8366,45 @@ probabilistic distances of genome abundance and tetranucleotide frequency.")
     (license (license:non-copyleft "file://license.txt"
                                    "See license.txt in the distribution."))))
 
+(define-public metal
+  (package
+    (name "metal")
+    (version "2011-03-25")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://csg.sph.umich.edu/abecasis/Metal/"
+                           "download/generic-metal-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1bk00hc0xagmq0mabmbb8bykl75qd4kfyirba869h4x6hmn4a0f3"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:tests? #f
+      #:make-flags
+      #~(list (string-append "INSTALLDIR=" #$output "/bin") "all")
+      #:phases
+      '(modify-phases %standard-phases
+         (replace 'configure
+           (lambda _
+             (substitute* "Makefile"
+               (("^CFLAGS=") "CFLAGS=-std=c++11 ")))))))
+    (inputs (list zlib `(,zlib "static")))
+    (home-page "http://csg.sph.umich.edu/abecasis/Metal/")
+    (synopsis "Facilitate meta-analysis of large datasets")
+    (description "METAL is a tool for meta-analysis genomewide association
+scans.  METAL can combine either test statistics and standard errors or
+p-values across studies (taking sample size and direction of effect into
+account).  METAL analysis is a convenient alternative to a direct analysis of
+merged data from multiple studies.  It is especially appropriate when data
+from the individual studies cannot be analyzed together because of differences
+in ethnicity, phenotype distribution, gender or constraints in sharing of
+individual level data imposed.  Meta-analysis results in little or no loss of
+efficiency compared to analysis of a combined dataset including data from all
+individual studies.")
+    (license license:bsd-3)))
+
 (define-public minced
   (package
     (name "minced")
@@ -7932,6 +8497,41 @@ program for nucleotide and protein sequences.")
     ;; License information found in 'muscle -h' and usage.cpp.
     (license license:public-domain)))
 
+(define-public music
+  (let ((commit "b1caecdb164b1ab80acccb9463abe2526a56f69f")
+        (revision "1"))
+    (package
+      (name "music")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/gersteinlab/MUSIC.git")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0arj300h8cpbya7y98g066xsxcg2a65h3y0qs250rlj072f1b4ia"))))
+      (build-system gnu-build-system)
+      (arguments
+       (list
+        #:tests? #f                     ; no "check" target
+        #:phases
+        #~(modify-phases %standard-phases
+            (delete 'configure)
+            ;; There is no "install" target.
+            (replace 'install
+              (lambda _
+                (let ((bin (string-append #$output "/bin")))
+                  (install-file "bin/MUSIC" bin)))))))
+      (home-page "https://github.com/gersteinlab/MUSIC/")
+      (synopsis "Multiscale enrichment calling for ChIP-Seq datasets")
+      (description
+       "MUSIC is an algorithm for identification of enriched regions at
+multiple scales in the read depth signals from ChIP-Seq experiments.")
+      ;; See https://github.com/gersteinlab/MUSIC/issues/6
+      (license license:gpl2+))))
+
 (define-public newick-utils
   ;; There are no recent releases so we package from git.
   (let ((commit "da121155a977197cab9fbb15953ca1b40b11eb87"))
@@ -11146,11 +11746,11 @@ single-cell data.")
       (license license:gpl3))))
 
 (define-public r-archr
-  (let ((commit "92ab814f86be0cea75c661f9827a9549c2cf47f5")
+  (let ((commit "c61b0645d1482f80dcc24e25fbd915128c1b2500")
         (revision "1"))
     (package
       (name "r-archr")
-      (version (git-version "1.0.1" revision commit))
+      (version (git-version "1.0.2" revision commit))
       (source
        (origin
          (method git-fetch)
@@ -11159,7 +11759,7 @@ single-cell data.")
                (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-          (base32 "1m1vp3kkpvd0fcviv5vb3gcbm3w91ih6gm9ivg48swnbqny44kqb"))))
+          (base32 "0sgdfd8iwgj8cssj2zr3gmshg8nv54q6dd8asjf99i39qkni7p9i"))))
       (properties `((upstream-name . "ArchR")))
       (build-system r-build-system)
       (propagated-inputs
@@ -21320,7 +21920,7 @@ single-cell data named @url{https://github.com/PMBio/cardelino, cardelino}.")
 (define-public ccwl
   (package
     (name "ccwl")
-    (version "0.2.0")
+    (version "0.3.0")
     (source
      (origin
        (method url-fetch)
@@ -21328,7 +21928,7 @@ single-cell data named @url{https://github.com/PMBio/cardelino, cardelino}.")
                            version ".tar.lz"))
        (sha256
         (base32
-         "1ar8rfz3zrksgygrv67zv77y8gfvvz54zcs546jn6j28y20basla"))))
+         "0za710mcn9di1njli3dk3660n3836ip8b4msb8f958498va95y7j"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags '("GUILE_AUTO_COMPILE=0") ; to prevent guild warnings
@@ -21339,6 +21939,12 @@ single-cell data named @url{https://github.com/PMBio/cardelino, cardelino}.")
                            ,@%gnu-build-system-modules)
        #:phases
        (modify-phases %standard-phases
+         (add-after 'patch-source-shebangs 'patch-more-source-shebangs
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "scripts/ccwl"
+               (("^exec guile")
+                (string-append "exec "
+                               (search-input-file inputs "/bin/guile"))))))
          (add-after 'install 'wrap
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (let ((out (assoc-ref outputs "out"))

gnu/packages/bittorrent.scm

@@ -529,7 +529,7 @@ desktops.")
 (define-public qbittorrent
   (package
     (name "qbittorrent")
-    (version "4.6.2")
+    (version "4.6.3")
     (source
      (origin
        (method git-fetch)
@@ -538,7 +538,7 @@ desktops.")
              (commit (string-append "release-" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1wps17iv4gj7y751fibvcxk51v09wyniv6xm2yx429dj7z8rfmzs"))))
+        (base32 "01d393v0v4c9rp909l3ddif984pp1z6sym74yc0kgxqq2kplj5g1"))))
     (build-system qt-build-system)
     (arguments
      (list #:configure-flags #~(list "-DTESTING=ON")
@@ -547,7 +547,7 @@ desktops.")
      (list qttools-5))
     (inputs
      (list boost
-           libtorrent-rasterbar-1.2
+           libtorrent-rasterbar
            openssl
            python-wrapper
            qtsvg-5

gnu/packages/books.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2023 Artyom V. Poptsov <poptsov.artyom@gmail.com>
+;;; Copyright © 2023, 2024 Artyom V. Poptsov <poptsov.artyom@gmail.com>
 ;;; Copyright © 2023 Adam Faiz <adam.faiz@disroot.org>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -19,30 +19,30 @@
 
 (define-module (gnu packages books)
   #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix utils)
+  #:use-module (guix build-system gnu)
-  #:use-module (guix gexp)
   #:use-module (guix download)
+  #:use-module (guix gexp)
   #:use-module (guix git-download)
   #:use-module (guix packages)
-  #:use-module (guix build-system gnu)
+  #:use-module (guix utils)
   #:use-module (gnu packages)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages base)
   #:use-module (gnu packages bash)
-  #:use-module (gnu packages music)
+  #:use-module (gnu packages fonts)
+  #:use-module (gnu packages fontutils)
   #:use-module (gnu packages inkscape)
+  #:use-module (gnu packages music)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages tex)
   #:use-module (gnu packages texlive)
-  #:use-module (gnu packages version-control)
+  #:use-module (gnu packages version-control))
-  #:use-module (gnu packages fonts)
-  #:use-module (gnu packages fontutils))
 
 (define-public book-sparc
   (package
     (name "book-sparc")
-    (version "1.1.0")
+    (version "2.0.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -50,7 +50,7 @@
                     (commit (string-append "v" version))))
               (sha256
                (base32
-                "0k1miyrnh5362qy50jzp5j3ww0c8hr7wk3y5kg6xlqgk9f8msvag"))
+                "0bn3a3m0kcjybyaz1a7pj8n48jh1cg4szwi9px3zjhhm5818wi7z"))
               (file-name (git-file-name name version))
               (modules '((guix build utils)))
               (snippet
@@ -81,6 +81,7 @@
            texlive-bibtex
            texlive-bibtexperllibs
            texlive-bigfoot
+           texlive-chngcntr
            texlive-circuitikz
            texlive-collection-langcyrillic
            texlive-fontspec

gnu/packages/browser-extensions.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2020, 2021 Marius Bakke <marius@gnu.org>
 ;;; Copyright © 2023 Nicolas Graves <ngraves@ngraves.fr>
-;;; Copyright © 2023 Clément Lassieur <clement@lassieur.org>
+;;; Copyright © 2023, 2024 Clément Lassieur <clement@lassieur.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -58,8 +58,8 @@ supported content to the Kodi media center.")
   ;; Arbitrary commit of branch master,
   ;; Update when updating uBlockOrigin.
   (let* ((name "ublock-main-assets")
-         (commit "76bd7cb53036a36f7e7df5ee9173f588ba8aa966")
+         (commit "b15998fae22b2b9593794b6b46647385b9c101d4")
-         (revision "1")
+         (revision "2")
          (version (git-version "0" revision commit)))
     (origin
       (method git-fetch)
@@ -68,14 +68,14 @@ supported content to the Kodi media center.")
             (commit commit)))
       (file-name (git-file-name name version))
       (sha256
-       (base32 "1kdzvflr1yxykyva5vsjqr0p2ik1200xbhxwpl3cx2jsiv8l95sk")))))
+       (base32 "1jnj3qhsqd7k28f6l2cibkpipnf7y7j97fsrwwfz4zqd8p69c3fx")))))
 
 (define ublock-prod-assets
   ;; Arbitrary commit of branch gh-pages,
   ;; Update when updating uBlockOrigin.
   (let* ((name "ublock-prod-assets")
-         (commit "a379a168fc149ffbd6d10cd0700d4ab4801e57f2")
+         (commit "60fa7b4b33d5d257d9d0f1ee8db65c1e663f2d31")
-         (revision "1")
+         (revision "2")
          (version (git-version "0" revision commit)))
     (origin
       (method git-fetch)
@@ -84,12 +84,12 @@ supported content to the Kodi media center.")
             (commit commit)))
       (file-name (git-file-name name version))
       (sha256
-       (base32 "0syf3kbhvsbn5xka5knpclxby2kp92my1w7ixvf5fs9n08ylcip1")))))
+       (base32 "092llpcv24xn8p3h73r0q582vwxia9rh9ss6xxbra2xmy70hg24k")))))
 
 (define ublock-origin
   (package
     (name "ublock-origin")
-    (version "1.54.0")
+    (version "1.56.0")
     (home-page "https://github.com/gorhill/uBlock")
     (source (origin
               (method git-fetch)
@@ -99,7 +99,7 @@ supported content to the Kodi media center.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1yacqpf9z8lprwsj194bhlp2ba9ywzbagd6lwxj3h6g405s7zp2k"))))
+                "150n3g42wx8bp1dgmf360gd87g8pk6zzgkyd8k698mj6r5anfwpa"))))
     (build-system gnu-build-system)
     (outputs '("xpi" "firefox" "chromium"))
     (properties '((addon-id . "uBlock0@raymondhill.net")))

gnu/packages/c.scm

@@ -20,7 +20,7 @@
 ;;; Copyright © 2022 Antero Mejr <antero@mailbox.org>
 ;;; Copyright © 2023 zamfofex <zamfofex@twdb.moe>
 ;;; Copyright © 2023 Foundation Devices, Inc. <hello@foundationdevices.com>
-;;; Copyright © 2023 David Elsing <david.elsing@posteo.net>
+;;; Copyright © 2023, 2024 David Elsing <david.elsing@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1349,7 +1349,7 @@ performance concurrent systems developed in C99+.")
 (define-public tinydir
   (package
     (name "tinydir")
-    (version "1.2.5")
+    (version "1.2.6")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1358,7 +1358,7 @@ performance concurrent systems developed in C99+.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1nprgdfx4i8wzc1idw6chan4fjfa75b5ll8kghdc0q2278pny259"))
+                "143n6yabznxk032gv5g2k8glf0kzicarg9cx0714zsbfmzj8lr07"))
               (patches (search-patches "tinydir-fix-cbehave-test.patch"))
               (modules '((guix build utils)))
               (snippet '(delete-file-recursively "tests/cbehave"))))
@@ -1390,7 +1390,7 @@ directory contents.")
 (define-public libdispatch
   (package
     (name "libdispatch")
-    (version "5.7")
+    (version "5.9.2")
     (source
      (origin
        (method git-fetch)
@@ -1400,7 +1400,7 @@ directory contents.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0skg1azbhbg7y0ql2a5sx6lmfip8l1rajqm95zzf9xv45n4dg9nn"))))
+         "02k90asz0yxrcmy67mmqqc68n8f16jf445l0n7jryb7nk30bgmm6"))))
     (build-system cmake-build-system)
     (arguments
      (list #:phases

gnu/packages/calendar.scm

@@ -2,7 +2,7 @@
 ;;; Copyright © 2015 David Thompson <davet@gnu.org>
 ;;; Copyright © 2015, 2016, 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016 Kei Kebreau <kkebreau@posteo.net>
-;;; Copyright © 2016, 2017, 2020, 2022, 2023 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2020, 2022-2024 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Troy Sankey <sankeytms@gmail.com>
 ;;; Copyright © 2016, 2021 Stefan Reichoer <stefan@xsteve.at>
 ;;; Copyright © 2018, 2019, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -292,7 +292,11 @@ proper handling of holidays.")
                             version "/" name "-" version ".tar.bz2"))
         (sha256
          (base32
-          "0qkpq412p78znw8gckwcx3l0wcss9s0dgw1pvjb1ih2pxf6hm4rw"))))
+          "0qkpq412p78znw8gckwcx3l0wcss9s0dgw1pvjb1ih2pxf6hm4rw"))
+        (snippet
+         #~(begin (use-modules (guix build utils))
+                  (substitute* "libhdate.pc.in"
+                    (("prefix=/usr") "prefix=@prefix@"))))))
     (build-system gnu-build-system)
     (home-page "http://libhdate.sourceforge.net/")
     (synopsis "Library to use Hebrew dates")

gnu/packages/check.scm

@@ -48,6 +48,7 @@
 ;;; Copyright © 2023 Reza Housseini <reza@housseini.me>
 ;;; Copyright © 2023 Hilton Chain <hako@ultrarare.space>
 ;;; Copyright © 2023 Troy Figiel <troy@troyfigiel.com>
+;;; Copyright © 2024 Giacomo Leidi <goodoldpaul@autistici.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -77,6 +78,7 @@
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages guile-xyz)
@@ -898,94 +900,6 @@ prevent common NGINX misconfigurations.  It provides the @command{gixy}
 command.")
       (license license:mpl2.0))))
 
-(define-public go-github.com-smartystreets-gunit
-  (package
-    (name "go-github.com-smartystreets-gunit")
-    (version "1.0.0")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/smartystreets/gunit")
-                    (commit version)))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "00m4zg0kdj49mnpmf9klb44ba71p966xsk6zknrzqgfc8119f35z"))))
-    (build-system go-build-system)
-    (arguments
-     '(;; TODO: This package depends on go-github.com-smartystreets-assertions
-       ;; for running the tests, but go-github.com-smartystreets-assertions
-       ;; depends on this package, so break this loop by not running the tests
-       ;; for this package.
-       #:tests? #f
-       #:import-path "github.com/smartystreets/gunit"))
-    (synopsis "Testing tool for Go, in the style of xUnit")
-    (description
-     "@code{gunit} allows the test author to use a struct as the scope for a
-group of related test cases, in the style of xUnit fixtures.  This makes
-extraction of setup/teardown behavior (as well as invoking the system under
-test) much simpler.")
-    (home-page "https://github.com/smartystreets/gunit")
-    (license license:expat)))
-
-(define-public go-github.com-smartystreets-assertions
-  (package
-    (name "go-github.com-smartystreets-assertions")
-    (version "1.13.0")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/smartystreets/assertions")
-                    (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32 "0flf3fb6fsw3bk1viva0fzrzw87djaj1mqvrx2gzg1ssn7xzfrzr"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-       #:import-path "github.com/smartystreets/assertions"
-       #:phases
-       #~(modify-phases %standard-phases
-           (replace 'check
-             (lambda* (#:key inputs #:allow-other-keys #:rest args)
-               (unless
-                 ;; The tests fail when run with gccgo.
-                 (false-if-exception (search-input-file inputs "/bin/gccgo"))
-                 (apply (assoc-ref %standard-phases 'check) args)))))))
-    (native-inputs
-     (list go-github.com-smartystreets-gunit))
-    (synopsis "Assertions for testing with Go")
-    (description
-     "The @code{assertions} package provides convenient assertion functions
-for writing tests in Go.")
-    (home-page "https://github.com/smartystreets/assertions")
-    (license license:expat)))
-
-(define-public go-github.com-smartystreets-goconvey
-  (package
-    (name "go-github.com-smartystreets-goconvey")
-    (version "1.6.3")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/smartystreets/goconvey")
-                    (commit version)))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "1ph18rkl3ns3fgin5i4j54w5a69grrmf3apcsmnpdn1wlrbs3dxh"))))
-    (build-system go-build-system)
-    (arguments
-     '(#:import-path "github.com/smartystreets/goconvey"))
-    (propagated-inputs
-     (list go-github.com-jtolds-gls go-github.com-smartystreets-assertions))
-    (synopsis "Go testing tool with both a web and terminal user interface")
-    (description
-     "GoConvey is a testing tool for Go. It integrates with go test, can show
-test coverage and has a web user interface that will refresh automatically.")
-    (home-page "https://github.com/smartystreets/goconvey")
-    (license license:expat)))
-
 (define-public googletest
   (package
     (name "googletest")
@@ -1028,7 +942,7 @@ generation.")
 (define-public googlebenchmark
   (package
     (name "googlebenchmark")
-    (version "1.8.2")
+    (version "1.8.3")
     (home-page "https://github.com/google/benchmark")
     (source (origin
               (method git-fetch)
@@ -1037,7 +951,7 @@ generation.")
               (file-name (git-file-name "google-benchmark" version))
               (sha256
                (base32
-                "1p72bw7xcd88d8268fmmzji59408f552fbiv37jmsixml5dmq9wv"))))
+                "1hf8xrdd9k57kw3mpdi68a78fd96vzdqv3179v2yy5dxx336ffw3"))))
     (build-system cmake-build-system)
     (arguments
      '(#:configure-flags (list "-DBUILD_SHARED_LIBS=ON"
@@ -1052,6 +966,29 @@ generation.")
 similar to unit tests.")
     (license license:asl2.0)))
 
+(define-public greatest
+  (package
+   (name "greatest")
+   (version "1.5.0")
+   (source (origin
+            (method git-fetch)
+            (uri (git-reference
+                  (url "https://github.com/silentbicycle/greatest")
+                  (commit (string-append "v" version))))
+            (file-name (git-file-name name version))
+            (sha256
+             (base32
+              "11rajkb5m7mlzi3i3v0i27k6rrjw3x8a7bl6fkc29igzpwfbxndy"))))
+   (build-system copy-build-system)
+   (arguments (list #:install-plan
+                    #~'(("greatest.h" "include/"))))
+   (home-page "https://github.com/silentbicycle/greatest")
+   (synopsis "Single-header test system")
+   (description "Greatest is a single-header test system for C, including
+macros for defining tests, grouping them into suites, and providing a test
+runner.  It is quite unopinionated with most of its features being optional.")
+   (license license:isc)))
+
 (define-public cpputest
   (package
     (name "cpputest")
@@ -1227,14 +1164,14 @@ available via the @code{unittest.mock} module.")
 (define-public python-nose2
   (package
     (name "python-nose2")
-    (version "0.11.0")
+    (version "0.14.0")
       (source
         (origin
           (method url-fetch)
           (uri (pypi-uri "nose2" version))
           (sha256
            (base32
-            "1scxwvwbgfdj41acma41xzdhcfdwjj9irj6sfifdbyf9dryqs83d"))))
+            "1936fkrxg672bhp9i32ivna7jbydl9dpbhyn5f3059xrl1qdfa2w"))))
     (build-system python-build-system)
     (arguments
      (list #:phases
@@ -1245,10 +1182,6 @@ available via the @code{unittest.mock} module.")
                      ;; Tests require nose2 itself.
                      (setenv "PYTHONPATH" (getcwd))
                      (invoke (string-append #$output "/bin/nose2") "-v")))))))
-    (native-inputs
-     (list python-coverage))
-    (propagated-inputs
-     (list python-six))
     (home-page "https://github.com/nose-devs/nose2")
     (synopsis "Next generation of nicer testing for Python")
     (description
@@ -3194,6 +3127,36 @@ retried.")
 allowing you to declaratively define \"match\" rules.")
     (license license:bsd-3)))
 
+(define-public theft
+  (package
+   (name "theft")
+   (version "0.4.5")
+   (source (origin
+            (method git-fetch)
+            (uri (git-reference
+                  (url "https://github.com/silentbicycle/theft")
+                  (commit (string-append "v" version))))
+            (file-name (git-file-name name version))
+            (sha256
+             (base32
+              "1n2mkawfl2bpd4pwy3mdzxwlqjjvb5bdrr2x2gldlyqdwbk7qjhd"))
+            (snippet #~(begin
+                         (delete-file "vendor/greatest.h")))))
+   (build-system gnu-build-system)
+   (arguments (list #:make-flags #~(list "VENDOR="
+                                         (string-append "CC=" #$(cc-for-target))
+                                         (string-append "PREFIX=" #$output))
+                    #:test-target "test"
+                    #:phases
+                    #~(modify-phases %standard-phases
+                        (delete 'bootstrap)
+                        (delete 'configure))))
+   (native-inputs (list greatest))
+   (home-page "https://github.com/silentbicycle/theft")
+   (synopsis "Property-based testing for C")
+   (description "Theft is a library for property-based testing.")
+   (license license:isc)))
+
 (define-public unittest-cpp
   (package
     (name "unittest-cpp")
@@ -3594,6 +3557,29 @@ tables by saving expected data in a data directory (courtesy of pytest-datadir)
 that can be used to verify that future runs produce the same data.")
     (license license:expat)))
 
+(define-public python-pytest-tornado5
+  (package
+    (name "python-pytest-tornado5")
+    (version "2.0.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "pytest-tornado5" version))
+              (sha256
+               (base32
+                "0qb62jw2w0xr6y942yp0qxiy755bismjfpnxaxjjm05gy2pymr8d"))))
+    (build-system pyproject-build-system)
+    (arguments
+     ;; Tests require pytest < 6
+     (list #:tests? #f))
+    (propagated-inputs (list python-pytest python-tornado))
+    (home-page "https://github.com/vidartf/pytest-tornado")
+    (synopsis
+     "Fixtures and markers to simplify testing of Tornado applications")
+    (description
+     "This package provides a @code{py.test} plugin supplying fixtures and
+markers to simplify testing of asynchronous tornado applications.")
+    (license license:asl2.0)))
+
 (define-public guile-proba
   (package
     (name "guile-proba")

gnu/packages/chemistry.scm

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

gnu/packages/ci.scm

@@ -5,7 +5,7 @@
 ;;; Copyright © 2017, 2020, 2021 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2017, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
-;;; Copyright © 2022 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2022, 2024 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2023 David Pflug <david@pflug.io>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -209,14 +209,15 @@ intended as a replacement for Hydra.")
              (use-modules (ice-9 popen))
 
              (mkdir-p "../build/js")
-             (for-each (lambda (name)
+             (invoke "tar" "-xf" (assoc-ref inputs "chart.js.tgz")
-                         (let* ((file
+                     "--strip-components" "2"
-                                 (assoc-ref inputs (string-append name ".js")))
+                     "package/dist/chart.js")
-                                (port
+             (for-each (lambda (file minified-file)
+                         (let* ((port
                                  (open-pipe* OPEN_READ "uglifyjs" file))
                                 (destination
                                  (string-append
-                                  "../build/js/" name ".min.js")))
+                                  "../build/js/" minified-file)))
 
                            (call-with-output-file destination
                              (lambda (output-port)
@@ -226,9 +227,12 @@ intended as a replacement for Hydra.")
                              (unless (zero? exit)
                                (error "uglifyjs failed" exit)))))
 
-                       '("vue"
+                       (list (assoc-ref inputs "vue.js")
-                         "vue-router"
+                             (assoc-ref inputs "vue-router.js")
-                         "Chart"))
+                             "chart.js")
+                       (list "vue.min.js"
+                             "vue-router.min.js"
+                             "Chart.min.js"))
 
              ;; ansi_up.js isn't minified
              (copy-file (assoc-ref inputs "ansi_up.js")
@@ -260,13 +264,13 @@ intended as a replacement for Hydra.")
                  (sha256
                   (base32
                    "1dx8wn38ds8d01kkih26fx1yrisg3kpz61qynjr4zil03ap0hrlr"))))
-       ("Chart.js"
+       ("chart.js.tgz"
         ,(origin (method url-fetch)
                  (uri (string-append "https://github.com/chartjs/Chart.js/"
-                                     "releases/download/v2.7.2/Chart.js"))
+                                     "releases/download/v3.9.1/chart.js-3.9.1.tgz"))
                  (sha256
                   (base32
-                   "05m3gk6hqjx92j20drnk7q075qpjraywqaf25lnglmsgsgpiqsr7"))))))
+                   "1ikjgspaknqlhpjad17563yph4pvrh8dkzjdx58pl23gg58hf7hi"))))))
     (synopsis "Lightweight continuous integration service")
     (description
      "Laminar is a lightweight and modular continuous integration service.  It

gnu/packages/clifm.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2023 Rodion Goritskov <rodion.goritskov@gmail.com>
+;;; Copyright © 2023, 2024 Rodion Goritskov <rodion.goritskov@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -30,7 +30,7 @@
 (define-public clifm
   (package
     (name "clifm")
-    (version "1.15")
+    (version "1.17")
     (source
      (origin
        (method git-fetch)
@@ -39,7 +39,7 @@
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1r9pxlyn8jg0wmzbmbc71l42098lz5k32k6yid09yz6d0gaax7g1"))))
+        (base32 "00f5x0352dsf8f9ixkcwma7wr5pg78maavmd950nni38m647clm6"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags (list (string-append "CC="
@@ -53,8 +53,8 @@
     (inputs (list readline acl libcap))
     (home-page "https://github.com/leo-arch/clifm")
     (synopsis "Command-line file manager")
-    (description "Clifm a shell-like, text-based terminal file manager that
+    (description "Clifm is a shell-like, text-based terminal file manager
-sits on the command line.
+that sits on the command line.
 
 It is built with command line principles in mind: instead of navigating
 through a big menu of files, it lets you type, exactly as you do in your

gnu/packages/clojure.scm

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

gnu/packages/cmake.scm

@@ -4,7 +4,7 @@
 ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2014 Ian Denhardt <ian@zenhack.net>
 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
-;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2024 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017, 2018, 2020, 2021 Marius Bakke <marius@gnu.org>
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -380,6 +380,8 @@ and workspaces that can be used in the compiler environment of your choice.")
                         (string-append "-DCMAKE_DOC_DIR=share/doc/cmake-"
                                        #$(version-major+minor (package-version
                                                                cmake-minimal)))
+                        (string-append "-DCMake_INSTALL_VIMFILES_DIR=" #$output
+                                       "/share/vim/vimfiles/pack/guix/start/cmake")
                         "-DCMAKE_INFO_DIR=share/info"
                         "-DCMAKE_MAN_DIR=share/man")
                   #$flags))

gnu/packages/cobol.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2017, 2018, 2021-2023 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2017, 2018, 2021-2024 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -23,7 +23,9 @@
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix gexp)
+  #:use-module (gnu packages bison)
   #:use-module (gnu packages dbm)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages perl)
@@ -42,7 +44,17 @@
                version ".tar.xz"))
         (sha256
          (base32
-          "1qifkkrmscc5csri1l4rm9pbik74c3pc5za1rzx7jizddks8md1v"))))
+          "1qifkkrmscc5csri1l4rm9pbik74c3pc5za1rzx7jizddks8md1v"))
+        (snippet
+         #~(begin (use-modules (guix build utils))
+                  ;; Remove some files generated by bison and flex.
+                  (for-each delete-file
+                            '("cobc/parser.c"
+                              "cobc/parser.h"
+                              "cobc/ppparse.c"
+                              "cobc/ppparse.h"
+                              "cobc/pplex.c"
+                              "cobc/scanner.c"))))))
     (arguments
      (list
        #:configure-flags
@@ -62,7 +74,9 @@
              (lambda _ (setenv "TERM" "xterm-256color"))))
        #:test-target "checkall"))
     (native-inputs
-     `(("perl" ,perl)
+     `(("bison" ,bison)
+       ("flex" ,flex)
+       ("perl" ,perl)
        ("newcob" ,(origin
                     (method url-fetch)
                     (uri "https://www.itl.nist.gov/div897/ctg/suites/newcob.val.Z")

gnu/packages/code.scm

@@ -2,7 +2,7 @@
 ;;; 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>
+;;; Copyright © 2016, 2017, 2019-2024 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017, 2018 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2017 Andy Wingo <wingo@igalia.com>
@@ -436,7 +436,7 @@ features that are not supported by the standard @code{stdio} implementation.")
 (define-public universal-ctags
   (package
     (name "universal-ctags")
-    (version "6.0.20231001.0")
+    (version "6.1.20240218.0")
     (source
      (origin
        (method git-fetch)
@@ -446,7 +446,7 @@ features that are not supported by the standard @code{stdio} implementation.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0qik6rsai254prydfx8k2bq7wpim3a272jiw1y37r734k4s9xbrb"))
+         "09cjlj7mq3s98x9zsg4slq86h1myixjxxqfnc0kglf2hnr9nrkf5"))
        (modules '((guix build utils)))
        (snippet
         '(begin

gnu/packages/compression.scm

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

gnu/packages/compton.scm

@@ -4,7 +4,7 @@
 ;;; Copyright © 2019 Alexandru-Sergiu Marton <brown121407@member.fsf.org>
 ;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
 ;;; Copyright © 2022 Jai Vetrivelan <jaivetrivelan@gmail.com>
-;;; Copyright © 2023 John Kehayias <john.kehayias@protonmail.com>
+;;; Copyright © 2023, 2024 John Kehayias <john.kehayias@protonmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -113,7 +113,7 @@ performance).
 (define-public picom
   (package
     (name "picom")
-    (version "10.2")
+    (version "11.2")
     (source
      (origin
        (method git-fetch)
@@ -122,23 +122,25 @@ performance).
              (commit (string-append "v" version))))
        (sha256
         (base32
-         "1vd4nhvfykwdhpyhb0jmcj333zxhm6dyikafd76fa4z4fhjrrs0b"))
+         "0swmpw6lj0aiwypdfkzsy38jwsm9wfcn7i5klrqfn2klrwinv27f"))
        (file-name (string-append "picom-" version))))
     (build-system meson-build-system)
     (inputs
      (list dbus
            libconfig
+           libepoxy
+           libev
            libx11
            libxext
-           libev
+           libxdg-basedir
            mesa
-           xprop
+           pcre2
-           xcb-util-renderutil
-           xcb-util-image
            pixman
            uthash
-           libxdg-basedir
+           xcb-util
-           pcre))
+           xcb-util-renderutil
+           xcb-util-image
+           xprop))
     (native-inputs
      (list asciidoc pkg-config xorgproto))
     (arguments

gnu/packages/configuration-management.scm

@@ -21,7 +21,9 @@
   #:use-module (guix build-system go)
   #:use-module (guix git-download)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
   #:use-module (gnu packages golang-web)
+  #:use-module (gnu packages golang-xyz)
   #:use-module (gnu packages version-control)
   #:use-module (gnu packages textutils)
   #:use-module ((guix licenses) #:prefix license:)
@@ -31,9 +33,7 @@
 (define-public chezmoi
   (package
     (name "chezmoi")
-    ;; XXX: Make sure 7f238faa61e46d79b54d4d0ea8f0b5fc27db84b2 applied before
+    (version "1.8.10")
-    ;; version update, which should fix @code{password-store} integration.
-    (version "1.8.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -42,47 +42,78 @@
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1b8y0wq3myhvjdnwl0i4x85iil7i7kmsjajvbw1a47afm83jkbaw"))))
+                "0ildvlq7v8vnw74y4fgnv3hpq49bpl6zh1wmakfh46crwg7ffmjb"))))
     (build-system go-build-system)
     (arguments
      `(#:import-path "github.com/twpayne/chezmoi"
-       ;; We don't need to install the source code for end-user applications.
+       #:install-source? #f
-       #:install-source? #f))
+       #:phases
+       (modify-phases %standard-phases
+       ;; Remove test script which expect additional user's programs available
+       ;; in the PATH. The testdata directory is removed in the latest version
+       ;; (2.46.1) of the program.
+         (add-after 'unpack 'remove-failing-test-scripts
+           (lambda* (#:key import-path #:allow-other-keys)
+             (for-each (lambda (f)
+                         (delete-file (string-append "src/" import-path "/testdata/scripts/" f)))
+                       '("bitwarden.txt"
+                         "cd.txt"
+                         "cd_unix.txt"
+                         "completion.txt"
+                         "diff.txt"
+                         "edit.txt"
+                         "editconfig.txt"
+                         "git.txt"
+                         "gopass.txt"
+                         "keepassxc.txt"
+                         "lastpass.txt"
+                         "onepassword.txt"
+                         "pass.txt"
+                         "runscriptdir_unix.txt"
+                         "script_unix.txt"
+                         "secretgeneric.txt"
+                         "secretgopass.txt"
+                         "secretkeepassxc.txt"
+                         "secretlastpass.txt"
+                         "secretonepassword.txt"
+                         "secretpass.txt")))))))
     (native-inputs
-     (list go-github-com-masterminds-sprig
+     (list go-etcd-io-bbolt
-           go-github-com-masterminds-goutils
-           go-github-com-masterminds-semver
-           go-github-com-google-uuid
-           go-github-com-huandu-xstrings
-           go-github-com-imdario-mergo
-           go-github-com-mitchellh-reflectwalk
-           go-github-com-mitchellh-copystructure
-           go-github-com-bmatcuk-doublestar
-           go-github-com-charmbracelet-glamour
            go-github-com-alecthomas-chroma
+           go-github-com-aymerick-douceur
+           go-github-com-bmatcuk-doublestar-v2
+           go-github-com-charmbracelet-glamour
+           go-github-com-chris-ramon-douceur
            go-github-com-coreos-go-semver
            go-github-com-danwakefield-fnmatch
            go-github-com-dlclark-regexp2
-           go-github-go-git
+           go-github-com-godbus-dbus
-           go-github-com-google-go-github
+           go-github-com-google-go-github-v33
            go-github-com-google-go-querystring
-           go-github-com-google-renameio
-           go-github-com-microcosm-cc-bluemonday
-           go-github-com-aymerick-douceur
-           go-github-com-chris-ramon-douceur
-           go-github-com-gorilla-css
-           go-github-com-muesli-reflow-ansi
-           go-github-com-muesli-reflow-wordwrap
-           go-github-com-muesli-reflow-indent
-           go-github-com-muesli-reflow-padding
-           go-github-com-muesli-termenv
            go-github-com-google-goterm
+           go-github-com-google-renameio
+           go-github-com-google-uuid
+           go-github-com-gorilla-css
+           go-github-com-huandu-xstrings
+           go-github-com-imdario-mergo
            go-github-com-lucasb-eyer-go-colorful
+           go-github-com-masterminds-goutils
+           go-github-com-masterminds-semver
+           go-github-com-masterminds-sprig
            go-github-com-mattn-go-isatty
            go-github-com-mattn-go-runewidth
+           go-github-com-microcosm-cc-bluemonday
+           go-github-com-mitchellh-copystructure
+           go-github-com-mitchellh-reflectwalk
+           go-github-com-muesli-reflow-ansi
+           go-github-com-muesli-reflow-indent
+           go-github-com-muesli-reflow-padding
+           go-github-com-muesli-reflow-wordwrap
+           go-github-com-muesli-termenv
            go-github-com-olekukonko-tablewriter
            go-github-com-pelletier-go-toml
            go-github-com-pkg-diff
+           go-github-com-rogpeppe-go-internal
            go-github-com-sergi-go-diff
            go-github-com-spf13-cobra
            go-github-com-spf13-viper
@@ -92,12 +123,11 @@
            go-github-com-twpayne-go-xdg
            go-github-com-yuin-goldmark
            go-github-com-zalando-go-keyring
-           go-github-com-godbus-dbus
+           go-github-go-git
-           go-etcd-io-bbolt
            go-golang-org-x-crypto
            go-golang-org-x-net
            go-golang-org-x-oauth2
-           go-github-com-rogpeppe-go-internal
+           go-golang-org-x-term
            go-gopkg-in-errgo-fmt-errors))
     (home-page "https://www.chezmoi.io/")
     (synopsis "Personal configuration files manager")

gnu/packages/containers.scm

@@ -5,6 +5,7 @@
 ;;; Copyright © 2022 Michael Rohleder <mike@rohleder.de>
 ;;; Copyright © 2023 Zongyuan Li <zongyuan.li@c0x0o.me>
 ;;; Copyright © 2023 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2024 Tomas Volf <~@wolfsden.cz>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -53,37 +54,25 @@
   #:use-module (gnu packages wget))
 
 (define-public crun
-  (let ((commit "c381048530aa750495cf502ddb7181f2ded5b400"))
   (package
     (name "crun")
-      (version "1.4.5")
+    (version "1.14.1")
     (source
      (origin
-         (method git-fetch)
+       (method url-fetch)
-         (uri (git-reference
+       (uri (string-append
-               (url "https://github.com/containers/crun")
+             "https://github.com/containers/crun/releases/download/"
-               (commit commit)
+             version
-               (recursive? #t)))
+             "/crun-" version ".tar.gz"))
        (sha256
-          (base32 "0x2xmr5sv9ivvcv5fl5jjk4kq9b3n97s5hsqiqfwl4rz8qcz4xk1"))
+        (base32
-         (file-name (git-file-name name version))))
+         "02lplc2asyllb58mvy7l8b9gsk7fxs95g928xk28yzmf592ay33x"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags '("--disable-systemd")
        #:tests? #f ; XXX: needs /sys/fs/cgroup mounted
        #:phases
        (modify-phases %standard-phases
-           (add-after 'unpack 'do-not-depend-on-git
-             (lambda _
-               (substitute* "autogen.sh"
-                 (("^git submodule update.*")
-                  ""))
-               (with-output-to-file "git-version.h"
-                 (lambda ()
-                   (display (string-append
-                             "/* autogenerated.  */\n#ifndef GIT_VERSION\n# define GIT_VERSION \""
-                             ,commit
-                             "\"\n#endif\n"))))))
          (add-after 'unpack 'fix-tests
            (lambda _
              (substitute* (find-files "tests" "\\.(c|py)")
@@ -108,7 +97,7 @@
     (description
      "crun is a fast and low-memory footprint Open Container Initiative (OCI)
 Container Runtime fully written in C.")
-      (license license:gpl2+))))
+    (license license:gpl2+)))
 
 (define-public conmon
   (package
@@ -221,7 +210,7 @@ containers or various tools.")
 (define-public slirp4netns
   (package
     (name "slirp4netns")
-    (version "1.2.0")
+    (version "1.2.3")
     (source
      (origin
        (method git-fetch)
@@ -229,7 +218,7 @@ containers or various tools.")
              (url "https://github.com/rootless-containers/slirp4netns")
              (commit (string-append "v" version))))
        (sha256
-        (base32 "1rlzwp5fx1x3q179j9s2jp02imjag5pgj333z110nrvi7azl22l8"))
+        (base32 "0czvdsdv821fz4jd9rgrlkdhhjna6frawr8klvx3k2cfh444fbii"))
        (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (arguments

gnu/packages/coq.scm

@@ -31,6 +31,7 @@
   #:use-module (gnu packages base)
   #:use-module (gnu packages bison)
   #:use-module (gnu packages boost)
+  #:use-module (gnu packages compression)
   #:use-module (gnu packages emacs)
   #:use-module (gnu packages flex)
   #:use-module (gnu packages gawk)
@@ -51,10 +52,10 @@
   #:use-module (guix utils)
   #:use-module ((srfi srfi-1) #:hide (zip)))
 
-(define-public coq-core
+(define-public coq
   (package
-    (name "coq-core")
+    (name "coq")
-    (version "8.16.1")
+    (version "8.17.1")
     (source
      (origin
        (method git-fetch)
@@ -64,28 +65,35 @@
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0ljpqhh5lfsim29fcfp2xfcvm3j84pf1mb0gnpdr8vcqqw7mqwpf"))
+         "0gg6hizq0i08lk741b579cbswhy6qvkh6inc3d3i5a2af98psq63"))))
-       (patches (search-patches "coq-fix-envvars.patch"))))
     (native-search-paths
      (list (search-path-specification
             (variable "COQPATH")
-            (files (list "lib/ocaml/site-lib/coq/user-contrib"
+            (files (list "lib/coq/user-contrib")))))
-                         "lib/coq/user-contrib")))
-           (search-path-specification
-            (variable "COQLIBPATH")
-            (files (list "lib/ocaml/site-lib/coq")))
-           (search-path-specification
-            (variable "COQCORELIB")
-            (files (list "lib/ocaml/site-lib/coq-core"))
-            (separator #f))))
     (build-system dune-build-system)
+    (arguments
+     (list
+      #:package "coq-core,coq-stdlib,coq"
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'build 'configure
+            (lambda* (#:key outputs #:allow-other-keys)
+              (let* ((out (assoc-ref outputs "out"))
+                     (coqlib (string-append out "/lib/ocaml/site-lib/coq/")))
+                (invoke "./configure" "-prefix" out
+                        "-libdir" coqlib))))
+          (add-before 'build 'make-dunestrap
+            (lambda _ (invoke "make" "dunestrap")))
+          (replace 'install
+            (lambda* (#:key outputs #:allow-other-keys)
+              (let* ((out (assoc-ref outputs "out"))
+                     (libdir (string-append out "/lib/ocaml/site-lib")))
+                (invoke "dune" "install" "--prefix" out
+                        "--libdir" libdir "coq" "coq-core" "coq-stdlib")))))))
     (inputs
      (list gmp ocaml-zarith))
     (native-inputs
      (list ocaml-ounit2 which))
-    (arguments
-     `(#:package "coq-core"
-       #:test-target "."))
     (properties '((upstream-name . "coq"))) ; also for inherited packages
     (home-page "https://coq.inria.fr")
     (synopsis "Proof assistant for higher-order logic")
@@ -97,39 +105,6 @@ It is developed using Objective Caml and Camlp5.")
     ;; Some of the documentation is distributed under opl1.0+.
     (license (list license:lgpl2.1 license:opl1.0+))))
 
-(define-public coq-stdlib
-  (package
-    (inherit coq-core)
-    (name "coq-stdlib")
-    (arguments
-     `(#:package "coq-stdlib"
-       #:test-target "."
-       #:phases
-       (modify-phases %standard-phases
-         (add-before 'build 'fix-dune
-           (lambda _
-             (substitute* "user-contrib/Ltac2/dune"
-               (("coq-core.plugins.ltac2")
-                (string-join
-                  (map (lambda (plugin) (string-append "coq-core.plugins." plugin))
-                       '("ltac2" "number_string_notation" "tauto" "cc"
-                         "firstorder"))
-                  " "))))))))
-    (inputs
-     (list coq-core gmp ocaml-zarith))
-    (native-inputs '())))
-
-(define-public coq
-  (package
-    (inherit coq-core)
-    (name "coq")
-    (arguments
-     `(#:package "coq"
-       #:test-target "."))
-    (propagated-inputs
-     (list coq-core coq-stdlib))
-    (native-inputs '())))
-
 (define-public coq-ide-server
   (package
     (inherit coq)
@@ -148,7 +123,7 @@ It is developed using Objective Caml and Camlp5.")
      `(#:tests? #f
        #:package "coqide"))
     (propagated-inputs
-     (list coq coq-ide-server))
+     (list coq coq-ide-server zlib))
     (inputs
      (list lablgtk3 ocaml-lablgtk3-sourceview3))))
 
@@ -242,7 +217,7 @@ provers.")
 (define-public coq-flocq
   (package
     (name "coq-flocq")
-    (version "4.1.0")
+    (version "4.1.1")
     (source
      (origin
        (method git-fetch)
@@ -252,7 +227,7 @@ provers.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1yscj1120wch6myakaia03j11qji416v78ylx842d23hrbaqwmw5"))))
+         "01x38w58j95ba9679vpb5wv4bvfnrapd5dzjqlyz8k7i8a9sfqn0"))))
     (build-system gnu-build-system)
     (native-inputs
      (list autoconf automake ocaml which coq))
@@ -315,7 +290,7 @@ inside Coq.")
 (define-public coq-gappa
   (package
     (name "coq-gappa")
-    (version "1.5.2")
+    (version "1.5.3")
     (source
      (origin
        (method git-fetch)
@@ -325,7 +300,7 @@ inside Coq.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0l65ah81yj9vabgkwqh47c02qvscvl8nl60gqn1qrs47dx1pi80q"))))
+         "1dzkb2sfglhik2ymw8p65khl163xxjsaqji9agnnkvlk5r6589v6"))))
     (build-system gnu-build-system)
     (native-inputs
      (list autoconf
@@ -375,7 +350,7 @@ assistant.")
 (define-public coq-mathcomp
   (package
     (name "coq-mathcomp")
-    (version "1.15.0")
+    (version "1.17.0")
     (source
      (origin
        (method git-fetch)
@@ -384,7 +359,7 @@ assistant.")
              (commit (string-append "mathcomp-" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "158zl36zbvi5qx2nqbfnrg00jpgp6hjr5hmls7d8d0421ar6b67i"))))
+        (base32 "06i6kw5p2024n6h9mf8bvwn54il1a4z2h4qrgc8y0iq8hkvx4fnd"))))
     (build-system gnu-build-system)
     (native-inputs
      (list ocaml which coq))
@@ -412,7 +387,7 @@ part of the distribution.")
 (define-public coq-coquelicot
   (package
     (name "coq-coquelicot")
-    (version "3.2.0")
+    (version "3.4.0")
     (source
      (origin
        (method git-fetch)
@@ -422,7 +397,7 @@ part of the distribution.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "146s5y2xsc7wb43m1pq1n4p14hw99gqbzx0ic3a4naxq16v7cv4w"))))
+         "1f6zim6hnm6zrij964vas6rfbxh5p147qsxxmmbxm7gyb85hhy45"))))
     (build-system gnu-build-system)
     (native-inputs
      (list autoconf automake ocaml which coq))
@@ -495,7 +470,7 @@ provides BigN, BigZ, BigQ that used to be part of Coq standard library.")
 (define-public coq-interval
   (package
     (name "coq-interval")
-    (version "4.5.2")
+    (version "4.8.0")
     (source
      (origin
        (method git-fetch)
@@ -505,7 +480,7 @@ provides BigN, BigZ, BigQ that used to be part of Coq standard library.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "138vgb0bq6wkygrhkahjgb9spwpzc6x6kkycj2qnf5naxx1z412w"))))
+         "0m3icx77p99ld9qfl3xjq62q572pyi4m77i1kc3whvipvg7834rh"))))
     (build-system gnu-build-system)
     (native-inputs
      (list autoconf automake ocaml which coq))
@@ -542,21 +517,17 @@ Coq proof assistant.")
     (license license:cecill-c)))
 
 (define-public coq-autosubst
-  ;; Latest commit on that branch, where work on supporting coq 8.6 and
-  ;; more recent versions of coq happen.
-  (let ((branch "coq86-devel")
-        (commit "fa6ef30664511ffa659cbcf3c962715cbee03572"))
   (package
     (name "coq-autosubst")
-      (version (git-version "1" branch commit))
+    (version "1.8")
     (source (origin
               (method git-fetch)
               (uri (git-reference
-                      (url "git://github.com/uds-psl/autosubst")
+                    (url "https://github.com/coq-community/autosubst")
-                      (commit commit)))
+                    (commit (string-append "v" version))))
               (file-name (git-file-name name version))
               (sha256
-                 (base32 "1cl0bp96bk6lplbl7n5c703vd3gvbs5mvf2qrf8q333kkqd7jqq4"))))
+               (base32 "0qk72r6cqxwhqqkl2kmryhw365w3l2016qii1q1sk3md7zq46jcz"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f
@@ -581,21 +552,21 @@ usage of substitution lemmas unnecessary.  The tactic is based on our current
 work on a decision procedure for the equational theory of an extension of the
 sigma-calculus by Abadi et al.  The library is completely written in Coq and
 uses Ltac to synthesize the substitution operation.")
-      (license license:bsd-3))))
+    (license license:bsd-3)))
 
 (define-public coq-equations
   (package
     (name "coq-equations")
-    (version "1.3")
+    (version "1.3-8.17")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/mattam82/Coq-Equations")
-                    (commit (string-append "v" version "-8.16"))))
+                    (commit (string-append "v" version))))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "08f756vgdd1wklkarg0b93j4n5mhkqm5ixxrhyb23dcv2dwhc8yg"))))
+                "0g68h4c1ijpphixvl9wkd7sibds38v4236dpvvh194j5ii42vnn8"))))
     (build-system gnu-build-system)
     (native-inputs
      (list ocaml coq camlp5))
@@ -673,7 +644,7 @@ also provided in Coq, without associated proofs.")
 (define-public coq-stdpp
   (package
     (name "coq-stdpp")
-    (version "1.7.0")
+    (version "1.8.0")
     (synopsis "Alternative Coq standard library std++")
     (source (origin
               (method git-fetch)
@@ -683,7 +654,7 @@ also provided in Coq, without associated proofs.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0447wbzm23f9rl8byqf6vglasfn6c1wy6cxrrwagqjwsh3i5lx8y"))))
+                "0xawh3xkh76yhs689zw52k55cbzga2gyzl4g1a3pgg6yy420chjn"))))
     (build-system gnu-build-system)
     (inputs
      (list coq))
@@ -747,7 +718,7 @@ for goals involving set operations.
                                          "/lib/coq/user-contrib"))
        #:phases (modify-phases %standard-phases
                   (delete 'configure))))
-    (inputs (list coq coq-stdlib coq-mathcomp which))
+    (inputs (list coq coq coq-mathcomp which))
     (synopsis "Finite sets and finite types for coq-mathcomp")
     (description
      "This library is an extension of coq-mathcomp which supports finite sets
@@ -778,7 +749,7 @@ subsume notations for finite sets.")
        ;; by the packaged project in the future.
        #:tests? #f
        #:make-flags ,#~(list (string-append "COQBIN="
-                                            #$(this-package-input "coq-core")
+                                            #$(this-package-input "coq")
                                             "/bin/")
                              (string-append "COQMF_COQLIB="
                                             (assoc-ref %outputs "out")
@@ -788,7 +759,7 @@ subsume notations for finite sets.")
                                             "/lib/coq/user-contrib"))
        #:phases (modify-phases %standard-phases
                   (delete 'configure))))
-    (propagated-inputs (list coq coq-core coq-mathcomp which))
+    (propagated-inputs (list coq coq-mathcomp which))
     (home-page "https://math-comp.github.io/")
     (synopsis "Small library to do epsilon - N reasoning")
     (description

gnu/packages/cpp.scm

@@ -8,7 +8,7 @@
 ;;; Copyright © 2019 Jan Wielkiewicz <tona_kosmicznego_smiecia@interia.pl>
 ;;; Copyright © 2020, 2021 Nicolò Balzarotti <nicolo@nixo.xyz>
 ;;; Copyright © 2020 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2020, 2021, 2023 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2020, 2021, 2023, 2024 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2020 Brice Waegeneire <brice@waegenei.re>
 ;;; Copyright © 2020, 2021, 2022 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2020, 2022 Marius Bakke <marius@gnu.org>
@@ -25,11 +25,11 @@
 ;;; Copyright © 2021 jgart <jgart@dismail.de>
 ;;; Copyright © 2021 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2021 Disseminate Dissent <disseminatedissent@protonmail.com>
-;;; Copyright © 2022, 2023 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2022-2024 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2022 muradm <mail@muradm.net>
 ;;; Copyright © 2022 Attila Lendvai <attila@lendvai.name>
 ;;; Copyright © 2022 Arun Isaac <arunisaac@systemreboot.net>
-;;; Copyright © 2022, 2023 David Elsing <david.elsing@posteo.net>
+;;; Copyright © 2022, 2023, 2024 David Elsing <david.elsing@posteo.net>
 ;;; Copyright © 2022, 2023 Zheng Junjie <873216071@qq.com>
 ;;; Copyright © 2022, 2023, 2024 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2022 Antero Mejr <antero@mailbox.org>
@@ -187,41 +187,35 @@ development effort.")
 (define-public range-v3
   (package
     (name "range-v3")
-    (version "0.11.0")
+    (version "0.12.0")
     (source
      (origin
        (method git-fetch)
-       (uri
+       (uri (git-reference
-        (git-reference
              (url "https://github.com/ericniebler/range-v3.git")
              (commit version)))
-       (file-name
+       (file-name (git-file-name name version))
-        (git-file-name name version))
-       (patches (search-patches "range-v3-build-with-gcc10.patch"))
        (sha256
-        (base32 "18230bg4rq9pmm5f8f65j444jpq56rld4fhmpham8q3vr1c1bdjh"))))
+        (base32 "0r85s5rmp5ixmik2y5y4w760pa38j1sg9hbr1fss2flibzvrf53d"))))
     (build-system cmake-build-system)
     (arguments
      (list
-       #:configure-flags
+      #:configure-flags #~(list "-DRANGES_NATIVE=OFF")))
-       #~(list "-DRANGES_NATIVE=OFF")))
+    (native-inputs (list doxygen perl))
-    (native-inputs
+    (inputs (list boost))
-     (list doxygen gcc-9 perl))
-    (inputs
-     (list boost))
     (synopsis "Range library for C++14/17/20")
-    (description "Range-v3 is an extension of the Standard Template Library that
+    (description
+     "Range-v3 is an extension of the Standard Template Library that
 makes its iterators and algorithms more powerful by making them composable.
 Unlike other range-like solutions which, seek to do away with iterators, in
 range-v3 ranges are an abstraction layer on top of iterators.")
     (home-page "https://github.com/ericniebler/range-v3/")
-    (license
+    (license (list
-     (list
               ;; Elements of Programming
               (license:x11-style "file:///LICENSE.txt")
               ;; SGI STL
               license:sgifreeb2.0
-;;; LibC++ (dual-licensed)
+              ;; LibC++ (dual-licensed)
               license:expat
               license:ncsa
               ;; Others
@@ -285,16 +279,18 @@ use by the C++ Core Guidelines maintained by the Standard C++ Foundation.")
     (name "c2ffi")
     ;; As per the c2ffi README: the first three elements are encoding the
     ;; required Clang/LLVM version, and the last one is the c2ffi revision.
-    (version "12.0.0.0")
+    (version "16.0.0.0")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/rpav/c2ffi")
-             (commit (string-append "v" version))))
+             ;; Upstream is not tagging releases consistently.
+             ;; (commit (string-append "v" version))
+             (commit "097cbe61ca02dc79ea60859aa056975131a9d985")))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1qq8dfismd20d9kfxpfvwz07v9mfvd0y7p5r3c92mk2pm4xnmzfy"))
+        (base32 "1mqhw4838chl495gaj9z0731ahkmqb4f3wlc1qalk82fdsaniyd5"))
        (modules '((guix build utils)))
        (snippet
         '(substitute* "CMakeLists.txt"
@@ -315,9 +311,9 @@ LLVMOption LLVMBitReader LLVMProfileData")))))
              (when tests?
                (invoke "./bin/c2ffi" "--help")))))))
     (native-inputs
-     (list clang-12)) ; CMakeLists.txt invokes `clang -print-resource-dir`
+     (list clang-16)) ; CMakeLists.txt invokes `clang -print-resource-dir`
     (inputs
-     (list clang-12)) ; Compiled with gcc, but links against libclang-cpp.so
+     (list clang-16)) ; Compiled with gcc, but links against libclang-cpp.so
     (home-page "https://github.com/rpav/c2ffi")
     (synopsis "Clang-based FFI wrapper generator")
     (description
@@ -519,7 +515,17 @@ operating on batches.")
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags (list "-DHWY_SYSTEM_GTEST=on"
-                               "-DBUILD_SHARED_LIBS=ON")))
+                               "-DBUILD_SHARED_LIBS=ON")
+       ,@(if (string-prefix? "i686-linux" (or (%current-system)
+                                              (%current-target-system)))
+             '(#:phases
+               (modify-phases %standard-phases
+                 (add-after 'unpack 'really-skip-precision-tests
+                   (lambda _
+                     (substitute* "hwy/contrib/math/math_test.cc"
+                       (("Skipping math_test due to GCC issue with excess precision.*" m)
+                        (string-append m "return;\n")))))))
+             '())))
     (native-inputs
      (list googletest))
     (home-page "https://github.com/google/highway")
@@ -1061,10 +1067,9 @@ and make @code{cpplint} usable in wider contexts.")
           (base32 "09xnf8hmld1fk8j33zwlz1qcxnjdx1ncbg62csic9va4m1wc2v1d"))))
    (build-system cmake-build-system)
    (arguments
-      ;; No tests.
+    (list #:tests? #f     ; No tests.
-    `(#:tests? #f
+          #:configure-flags #~(list "-DBUILD_SHARED_LIBS=ON"
-      ;; Build the shared library instead of a static one.
+                                    "-DREPROC++=ON")))
-      #:configure-flags `("-DBUILD_SHARED_LIBS=1")))
    (native-inputs
     (list pkg-config))
    (synopsis "Process IO library")
@@ -1628,7 +1633,7 @@ provides a number of utilities to make coding with expected cleaner.")
 (define-public immer
   (package
    (name "immer")
-   (version "0.8.0")
+   (version "0.8.1")
    (source (origin
             (method git-fetch)
             (uri (git-reference
@@ -1636,19 +1641,12 @@ provides a number of utilities to make coding with expected cleaner.")
                   (commit (string-append "v" version))))
             (file-name (git-file-name name version))
             (sha256
-             (base32 "11km3l5h3rgsbj8yfyzk3fnx9na55l6zs2sxpx922yvlvs2blh27"))
+             (base32 "03qkr42h0g6rivj3kq207gzgnv7hq88y69q16l2vg1lbvjcgca2g"))))
-            (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"))
+   (arguments (list #:test-target "check"
+                    ;; -Werror appears to report false positives.
+                    ;; See <https://github.com/arximboldi/immer/issues/223>.
+                    #:configure-flags #~(list "-DDISABLE_WERROR=ON")))
    (inputs (list boost libgc c-rrb))
    (native-inputs (list catch2 doctest fmt pkg-config))
    (home-page "https://sinusoid.es/immer")
@@ -2455,7 +2453,7 @@ CRC32C algorithm, which is specified in RFC 3720, section 12.1.")
 (define-public fast-float
   (package
     (name "fast-float")
-    (version "3.5.1")
+    (version "6.0.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -2464,7 +2462,7 @@ CRC32C algorithm, which is specified in RFC 3720, section 12.1.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0z3rxxd0pwvw70dbnv63rm67biw829vdqf50y16isxm6g3sbrz8g"))))
+                "1xf4gbllha760cr0ri53zsja46dypj45lj070ijb5f78xavfd8f8"))))
     (build-system cmake-build-system)
     (arguments
      (list
@@ -2480,9 +2478,7 @@ CRC32C algorithm, which is specified in RFC 3720, section 12.1.")
                 (("if\\(NOT supplemental_test_files_POPULATED.*")
                  (string-append
                   "set(supplemental_test_files_BINARY_DIR "
-                  (search-input-directory (or native-inputs inputs)
+                  #$fast-float-test-files ")\nif(0)\n"))))))))
-                                          "data")
-                  ")\nif(0)\n"))))))))
     (native-inputs (list doctest fast-float-test-files))
     (home-page "https://github.com/fastfloat/fast_float")
     (synopsis "Floating point number parser for C++")
@@ -2708,6 +2704,37 @@ addition and subtraction for all combinations of signed and unsigned 32-bit and
 64-bit integers.")
     (license license:expat)))
 
+(define-public wide-integer
+  (let ((commit "22b8428746248e682d5276f8e8b7fb52af73ea47")
+        (revision "1314"))              ; commit count
+   (package
+    (name "wide-integer")
+    (version (git-version "0" revision commit))
+    (source (origin
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/ckormanyos/wide-integer")
+                   (commit commit)))
+             (file-name (git-file-name name version))
+             (sha256
+              (base32 "0bhjnbdcphv5kddddh8kpwjpjix23m12vmfsz0r6wjc5d27md33z"))
+             (modules '((guix build utils)))
+             (snippet #~(substitute* "CMakeLists.txt"
+                          (("WideIntegerTargets") "wide-integer-targets")
+                          (("WideIntegerConfig") "wide-integer-config")
+                          (("WideInteger") "wide-integer")))))
+    (build-system cmake-build-system)
+    (native-inputs (list boost))
+    (home-page "https://github.com/ckormanyos/wide-integer")
+    (synopsis "C++ template for arbitrary-precision integers")
+    (description "This package implements a generic template for extended
+width signed and unsigned integral types.  Up to 63 limbs of any built-in
+integer type are supported, and can be used to build powers of two like
+int128_t, uint256_t, but also somewhat esoteric types such as int24_t,
+uint80_t, or uint1536_t.  The provided types can be used in much the same
+way as basic integer types.")
+    (license license:boost1.0))))
+
 (define-public wdl
   ;; No tag is available.
   (let ((commit "da86a62d11e46e4ecd8b16f9775cb5188340a0e2")

gnu/packages/cross-base.scm

@@ -745,7 +745,9 @@ returned."
   "Returns PACKAGE that contains a cross-compilation tool chain for TARGET
 with XBINUTILS, XGCC and LIBC (if exists for TARGET)."
   (package
-    (name (string-append (package-name xgcc) "-toolchain"))
+    ;; Using PACKAGE-NAME of XGCC is avoided here as there are platforms that
+    ;; still need a toolchain but don't have a libc (e.g. or1k-elf).
+    (name (string-append "gcc-cross-" target "-toolchain"))
     (version (package-version xgcc))
     (source #f)
     (build-system trivial-build-system)

gnu/packages/cross-toolchain.scm

@@ -38,5 +38,8 @@
 (define-public gcc-cross-i686-w64-mingw32-toolchain
   (cross-gcc-toolchain "i686-w64-mingw32"))
 
+(define-public gcc-cross-or1k-elf-toolchain
+  (cross-gcc-toolchain "or1k-elf"))
+
 (define-public gcc-cross-x86_64-w64-mingw32-toolchain
   (cross-gcc-toolchain "x86_64-w64-mingw32"))

gnu/packages/crypto.scm

@@ -53,6 +53,7 @@
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cpp)
+  #:use-module (gnu packages crates-crypto)
   #:use-module (gnu packages crates-io)
   #:use-module (gnu packages cryptsetup)
   #:use-module (gnu packages curl)
@@ -60,6 +61,7 @@
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages image)
   #:use-module (gnu packages kerberos)

gnu/packages/curl.scm

@@ -49,6 +49,7 @@
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages kerberos)
   #:use-module (gnu packages logging)
@@ -421,7 +422,7 @@ sugar and output formatting inspired from @code{httpie}.")
 (define-public trurl
   (package
     (name "trurl")
-    (version "0.8")
+    (version "0.9")
     (source
      (origin
        (method git-fetch)
@@ -430,7 +431,7 @@ sugar and output formatting inspired from @code{httpie}.")
              (commit (string-append name "-" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "19zdpjp01n7s7zgixq3irqfnx66dmqf8zyp0dlb6y7ga673lqwi8"))))
+        (base32 "10gsl0fdpybfcffmgf3qww7cpw3ifczl601042a2mqmwwrlx5zj7"))))
     (build-system gnu-build-system)
     (arguments
      (list

gnu/packages/databases.scm

@@ -46,7 +46,7 @@
 ;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
 ;;; Copyright © 2021 Sharlatan Hellseher <sharlatanus@gmail.com>
-;;; Copyright © 2021 Greg Hogan <code@greghogan.com>
+;;; Copyright © 2021, 2024 Greg Hogan <code@greghogan.com>
 ;;; Copyright © 2021 David Larsson <david.larsson@selfhosted.xyz>
 ;;; Copyright © 2021 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2021 Bonface Munyoki Kilyungi <me@bonfacemunyoki.com>
@@ -107,6 +107,7 @@
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
   #:use-module (gnu packages golang-check)
   #:use-module (gnu packages golang-web)
   #:use-module (gnu packages gperf)
@@ -189,6 +190,39 @@
   #:use-module (srfi srfi-26)
   #:use-module (ice-9 match))
 
+(define-public duckdb
+  (package
+    (name "duckdb")
+    (version "0.9.2")
+    (source
+      (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/duckdb/duckdb")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0dbsxyiz7c8sxflbfj87qv0b2s69zk802vsk5h00ra8w8fcbqlj0"))
+       (modules '((guix build utils)))
+       (snippet
+        #~(begin
+            ;; There is no git checkout from which to read the version tag.
+            (substitute* "CMakeLists.txt"
+              (("set\\(DUCKDB_VERSION \"[^\"]*\"")
+               (string-append "set(DUCKDB_VERSION \"v" #$version "-dev0\"")))))))
+    (build-system cmake-build-system)
+    (home-page "https://duckdb.org")
+    (synopsis "In-process SQL OLAP database management system")
+    (description "CLI and C/C++ source libraries for DuckDB, a relational
+(table-oriented) @acronym{DBMS, Database Management System} that supports
+@acronym{SQL, Structured Query Language}, contains a columnar-vectorized query
+execution engine, and provides transactional @acronym{ACID, Atomicity
+Consistency Isolation and Durability} guarantees via bulk-optimized
+@acronym{MVCC, Multi-Version Concurrency Control}.  Data can be stored in
+persistent, single-file databases with support for secondary indexes.")
+    (license license:expat)))
+
 (define-public ephemeralpg
   (package
     (name "ephemeralpg")
@@ -1446,6 +1480,56 @@ PostgreSQL extension, providing automatic partitioning across time and space
 (partitioning key), as well as full SQL support.")
     (license license:asl2.0)))
 
+(define-public pgvector
+  (package
+    (name "pgvector")
+    (version "0.6.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/pgvector/pgvector")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "19zcjrlmyj7gfbn8prh014yq50iy4dg97pirsm7idxsr829vwyc5"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      ;; Do not use -march=native
+      #:make-flags
+      '(list "OPTFLAGS=")
+      #:phases
+      #~(modify-phases %standard-phases
+          (delete 'configure)
+          (replace 'install
+            (lambda _
+              (let ((extension (string-append #$output "/share/extension"))
+                    (lib (string-append #$output "/lib"))
+                    (headers (string-append #$output "/include/server/extension/vector")))
+                (for-each mkdir-p (list extension lib headers))
+                (install-file "vector.so" lib)
+                (chmod (string-append lib "/vector.so") #o755)
+                (install-file "vector.control" extension)
+                (for-each (lambda (file)
+                            (install-file file extension))
+                          (find-files "sql" "\\.sql$"))
+                (install-file "src/vector.h" headers)))))))
+    (inputs (list postgresql))
+    (home-page "https://github.com/pgvector/pgvector")
+    (synopsis "Vector similarity search for Postgres")
+    (description
+     "This package provides a vector similarity search extension for Postgres.
+Store your vectors with the rest of your data.  It supports:
+
+@itemize
+@item exact and approximate nearest neighbor search;
+@item L2 distance, inner product, and cosine distance;
+@item any language with a Postgres client.
+@end itemize
+")
+    (license (license:x11-style "file://COPYRIGHT"))))
+
 (define-public pgloader
   (package
     (name "pgloader")
@@ -3348,6 +3432,10 @@ etc., and an SQL engine for performing simple SQL queries.")
     (arguments
      '(#:tests? #f      ; Tests try to use a running mongodb server.
        #:import-path "gopkg.in/mgo.v2"))
+    (propagated-inputs
+     (list go-gopkg.in-tomb.v2))
+    (inputs
+     (list cyrus-sasl))
     (native-inputs
      (list go-gopkg-in-check-v1))
     (home-page "https://gopkg.in/mgo.v2")
@@ -3792,7 +3880,7 @@ PickleShare.")
 (define-public python-apsw
   (package
     (name "python-apsw")
-    (version "3.42.0.1")
+    (version "3.45.1.0")
     ;; The compressed release has fetching functionality disabled.
     (source
      (origin
@@ -3802,11 +3890,11 @@ PickleShare.")
              version "/apsw-" version ".zip"))
        (sha256
         (base32
-         "0dr7zymn45x2793cilr709rnwn9g1c4n4vzln57y2lhj7420ykic"))))
+         "1vfrzb414pbh5k0cgcqkp039jvla2galapn4a551zgh8xi70bnrp"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-cython unzip))
+     (list unzip))
-    (inputs (list sqlite-next))         ;SQLite 3.42 required.
+    (inputs (list sqlite-next))         ;SQLite 3.45.1 required.
     (arguments
      (list
       #:phases
@@ -4423,7 +4511,7 @@ the SQL language using a syntax that reflects the resulting query.")
 (define-public apache-arrow
   (package
     (name "apache-arrow")
-    (version "14.0.0")
+    (version "14.0.2")
     (source
      (origin
        (method git-fetch)
@@ -4433,7 +4521,7 @@ the SQL language using a syntax that reflects the resulting query.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "08x01jcibmx03g9p0sjikp3dyynw6is6gyn0m3cy1gwkpkwk2ad2"))))
+         "1idw58vs8r6g6xy2qkhccgc79hwx4r5rr4bhd6ilxx56fwq9hkn2"))))
     (build-system cmake-build-system)
     (arguments
      (list

gnu/packages/debian.scm

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

gnu/packages/debug.scm

@@ -50,6 +50,7 @@
   #:use-module (gnu packages code)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages flex)
+  #:use-module (gnu packages gcc)
   #:use-module (gnu packages gdb)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gtk)
@@ -59,6 +60,7 @@
   #:use-module (gnu packages libusb)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages llvm)
+  #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages ninja)
   #:use-module (gnu packages perl)
@@ -459,6 +461,59 @@ server and embedded PowerPC, and S390 guests.")
     ;; Several tests fail on MIPS.
     (supported-systems (delete "mips64el-linux" %supported-systems))))))
 
+(define-public aflplusplus
+  (package
+    (inherit american-fuzzy-lop)
+    (name "aflplusplus")
+    (version "4.09c")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/AFLplusplus/AFLplusplus")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "12bplpd8cifla6m9l130fd22ggzkhd1w5s1aifw1idpy3njhj129"))))
+    (arguments
+     (substitute-keyword-arguments (package-arguments american-fuzzy-lop)
+       ((#:make-flags _ ''())
+        #~(list (string-append "PREFIX=" #$output)
+                (string-append "DOC_PATH=" #$output "/share/doc/"
+                               #$(package-name this-package) "-"
+                               #$(package-version this-package))
+                (string-append "CC=" #$(cc-for-target))))
+       ((#:phases phases '%standard-phases)
+        #~(modify-phases #$phases
+            ;; For GCC plugins.
+            (add-after 'unpack 'patch-gcc-path
+              (lambda* (#:key inputs #:allow-other-keys)
+                (substitute* "src/afl-cc.c"
+                  (("alt_cc = \"gcc\";")
+                   (format #f "alt_cc = \"~a\";"
+                           (search-input-file inputs "bin/gcc")))
+                  (("alt_cxx = \"g\\+\\+\";")
+                   (format #f "alt_cxx = \"~a\";"
+                           (search-input-file inputs "bin/g++"))))))))))
+    ;; According to the Dockerfile, GCC 12 is producing compile errors for some
+    ;; targets, so explicitly use GCC 11 here.
+    (inputs (list gcc-11 gmp python qemu))
+    (native-inputs (list gcc-11))
+    (home-page "https://aflplus.plus/")
+    (description
+     "AFLplusplus is a security-oriented fuzzer that employs a novel type of
+compile-time instrumentation and genetic algorithms to automatically discover
+clean, interesting test cases that trigger new internal states in the targeted
+binary.  This substantially improves the functional coverage for the fuzzed
+code.  The compact synthesized corpora produced by the tool are also useful for
+seeding other, more labor- or resource-intensive testing regimes down the road.
+It is a fork of American Fuzzy Lop fuzzer and features:
+@itemize
+@item A more recent qemu version.
+@item More algorithms like collision-free coverage, enhanced laf-intel &
+redqueen, AFLfast++ power schedules, MOpt mutators, unicorn_mode, etc.
+@end itemize")))
+
 (define-public stress-make
   (let ((commit "97815bed8060de33952475b3498767c91f59ffd9")
         (revision "2"))                 ;No official source distribution

gnu/packages/diffoscope.scm

@@ -74,7 +74,7 @@
 (define-public diffoscope
   (package
     (name "diffoscope")
-    (version "253")
+    (version "258")
     (source
      (origin
        (method git-fetch)
@@ -83,7 +83,7 @@
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1nvq0lv246rah0ryb2qd20yf3gfy0iwfi3335rg9c3gpz0ha4wnb"))))
+        (base32 "1wppshi18lyrgxxi8j06ij0qi31zdgqwjj6bycsyvipkc1cj6xhp"))))
     (build-system python-build-system)
     (arguments
      (list
@@ -305,7 +305,7 @@ them in detail for later analysis.")
 (define-public trydiffoscope
  (package
    (name "trydiffoscope")
-   (version "67.0.1")
+   (version "67.0.6")
    (source
     (origin
       (method git-fetch)
@@ -315,7 +315,7 @@ them in detail for later analysis.")
       (file-name (git-file-name name version))
       (sha256
        (base32
-        "03b66cjii7l2yiwffj6ym6mycd5drx7prfp4j2550281pias6mjh"))))
+        "0jzxgqraf727fvjcc9bgwz8zymjiix07x54xzqpvm52cv681nd9j"))))
     (arguments
      `(#:phases
        (modify-phases %standard-phases

gnu/packages/disk.scm

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

gnu/packages/dlang.scm

@@ -5,8 +5,8 @@
 ;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017, 2019, 2022 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2020 Guy Fleury Iteriteka <gfleury@disroot.org>
-;;; Copyright © 2021-2023 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2021-2024 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2021, 2024 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2022 ( <paren@disroot.org>
 ;;; Copyright © 2022 Esther Flashner <esther@flashner.co.il>
 ;;;
@@ -136,8 +136,7 @@ to a minimal test case.")
                     (string-append "my $gdc_dir = \""
                                    (dirname (search-input-file inputs "/bin/gdc"))
                                    "\";\n"))))))))
-      (inputs
+      (inputs (list gdc perl))
-       (list gdc-11 perl))
       (home-page "https://github.com/D-Programming-GDC/gdmd")
       (synopsis "DMD-like wrapper for GDC")
       (description "This package provides a DMD-like wrapper for the
@@ -192,8 +191,8 @@ to a minimal test case.")
        ("libedit" ,libedit)
        ("zlib" ,zlib)))
     (native-inputs
-     `(("lld-wrapper" ,(make-lld-wrapper lld-14 #:lld-as-ld? #t))
+     `(("lld-wrapper" ,(make-lld-wrapper lld-15 #:lld-as-ld? #t))
-       ("llvm" ,llvm-14)
+       ("llvm" ,llvm-15)
        ("ldc" ,gdmd)
        ("ninja" ,ninja)
        ("python-wrapper" ,python-wrapper)
@@ -356,9 +355,177 @@ integration tests...\n")
      (append (delete "llvm"
                      (alist-replace "ldc" (list ldc-bootstrap)
                                     (package-native-inputs ldc-bootstrap)))
-         `(("clang" ,clang-14)          ;propagates llvm and clang-runtime
+         `(("clang" ,clang-15)          ;propagates llvm and clang-runtime
            ("python-lit" ,python-lit))))))
 
+;;; Bootstrap version of phobos that is built with GDC, using GDC's standard
+;;; library.
+(define dmd-bootstrap
+  (package
+    ;; This package is purposefully named just "dmd" and not "dmd-bootstrap",
+    ;; as the final dmd package rewrites references from this one to itself,
+    ;; and their names must have the same length to avoid corrupting the
+    ;; binary.
+    (name "dmd")
+    (version "2.106.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/dlang/dmd")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name "dmd" version))
+              (sha256
+               (base32
+                "1bq4jws1vns2jjzfz7biyngrx9y5pvvgklymhrvb5kvbzky1ldmy"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:disallowed-references (list (gexp-input (canonical-package gcc)
+                                                "lib"))
+      ;; Disable tests, as gdmd cannot cope with some arguments used such as
+      ;; '-conf'.
+      #:tests? #f
+      #:test-target "test"
+      #:make-flags
+      #~(list (string-append "CC=" #$(cc-for-target))
+              ;; XXX: Proceed despite conflicts from symbols provided by both
+              ;; the source built and GDC.
+              "DFLAGS=-L--allow-multiple-definition"
+              "ENABLE_RELEASE=1"
+              (string-append "HOST_CXX=" #$(cxx-for-target))
+              "HOST_DMD=gdmd"
+              (string-append "INSTALL_DIR=" #$output)
+              ;; Do not build the shared libphobos2.so library, to avoid
+              ;; retaining a reference to gcc:lib.
+              "SHARED=0"
+              (string-append "SYSCONFDIR=" #$output "/etc")
+              "VERBOSE=1"
+              "-f" "posix.mak")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'copy-phobos-source-and-chdir
+            ;; Start with building phobos, which in turns will automatically
+            ;; build druntime and dmd.  A minimal dmd command is still
+            ;; required to do so, which is why we need dmd-bootstrap-0.
+            (lambda _
+              (symlink "." "dmd")  ;to please the build system expected layout
+              (copy-recursively
+               #$(origin
+                   (method git-fetch)
+                   (uri (git-reference
+                         (url "https://github.com/dlang/phobos")
+                         (commit (string-append "v" version))))
+                   (file-name (git-file-name "phobos" version))
+                   (sha256
+                    (base32
+                     "1yw7nb5d78cx9m7sfibv7rfc7wj3w0dw9mfk3d269qpfpnwzs4n9")))
+               "phobos")
+              (chdir "phobos")))
+          (add-after 'copy-phobos-source-and-chdir 'adjust-phobos-install-dirs
+            (lambda _
+              (substitute* "posix.mak"
+                ;; Install to lib directory, not to e.g. 'linux/lib64'.
+                (("\\$\\(INSTALL_DIR)/\\$\\(OS)/\\$\\(lib_dir)")
+                 (string-append #$output "/lib"))
+                ;; Do not install license file, already done by the gnu build
+                ;; system.
+                ((".*\\$\\(INSTALL_DIR)/phobos-LICENSE.txt.*") ""))))
+          (delete 'configure)
+          (add-after 'install 'install-druntime
+            (lambda args
+              (chdir "../druntime")
+              (apply (assoc-ref %standard-phases 'install) args)
+              (chdir "..")))
+          (add-after 'install-druntime 'install-includes
+            (lambda _
+              ;; Normalize the include files prefix to include/dmd.
+              (let ((include-dir (string-append #$output "/include/dmd")))
+                (mkdir-p include-dir)
+                (rename-file (string-append #$output "/src/phobos")
+                             (string-append include-dir))
+                (copy-recursively "druntime/import" include-dir))
+              (delete-file-recursively (string-append #$output "/src"))))
+          (add-after 'install-druntime 'install-dmd
+            (assoc-ref %standard-phases 'install))
+          (add-after 'install-license-files 'refine-install-layout
+            (lambda _
+              (let* ((docdir (string-append #$output "/share/doc/"
+                                            (strip-store-file-name #$output)))
+                     ;; The dmd binary gets installed to
+                     ;; e.g. /linux/bin64/dmd.
+                     (dmd (car (find-files #$output "^dmd$")))
+                     (dmd.conf (car (find-files #$output "^dmd.conf$")))
+                     (os-dir (dirname (dirname dmd))))
+                ;; Move samples from root to the doc directory.
+                (rename-file (string-append #$output "/samples")
+                             (string-append docdir "/samples"))
+                ;; Remove duplicate license file.
+                (delete-file (string-append #$output
+                                            "/dmd-boostlicense.txt"))
+                ;; Move dmd binary and dmd.conf.
+                (install-file dmd (string-append #$output "/bin"))
+                (install-file dmd.conf (string-append #$output "/etc"))
+                (delete-file-recursively os-dir))))
+          (add-after 'refine-install-layout 'patch-dmd.conf
+            (lambda* (#:key outputs #:allow-other-keys)
+              (substitute* (search-input-file outputs "etc/dmd.conf")
+                (("lib(32|64)")
+                 "lib")
+                (("\\.\\./src/(phobos|druntime/import)")
+                 "include/dmd")))))))
+    (native-inputs (list gdmd which))
+    (home-page "https://github.com/dlang/dmd")
+    (synopsis "Reference D Programming Language compiler")
+    (description "@acronym{DMD, Digital Mars D compiler} is the reference
+compiler for the D programming language.")
+    ;; As reported by upstream:
+    ;; https://wiki.dlang.org/Compilers#Comparison
+    (supported-systems '("i686-linux" "x86_64-linux"))
+    (license license:boost1.0)))
+
+;;; Second bootstrap of DMD, built using dmd-bootstrap, with its shared
+;;; libraries preserved.
+(define-public dmd
+  (package
+    (inherit dmd-bootstrap)
+    (arguments
+     (substitute-keyword-arguments
+         (strip-keyword-arguments
+          '(#:tests?)                   ;reinstate tests
+          (package-arguments dmd-bootstrap))
+       ((#:disallowed-references  _ ''())
+        (list dmd-bootstrap))
+       ((#:modules _ ''())
+        '((guix build gnu-build-system)
+          (guix build utils)
+          (srfi srfi-1)))               ;for fold
+       ((#:make-flags flags ''())
+        #~(fold delete #$flags '("DFLAGS=-L--allow-multiple-definition"
+                                 "HOST_DMD=gdmd"
+                                 "SHARED=0")))
+       ((#:phases phases '%standard-phases)
+        #~(modify-phases #$phases
+            (add-after 'patch-dmd.conf 'rewrite-references-to-bootstrap
+              ;; DMD keeps references to include files used to build a
+              ;; binary.  Rewrite those of dmd-bootstrap to itself, to reduce
+              ;; its closure size.
+              (lambda* (#:key native-inputs inputs outputs
+                        #:allow-other-keys)
+                (let ((dmd (search-input-file outputs "bin/dmd"))
+                      (dmd-bootstrap (dirname
+                                      (dirname
+                                       (search-input-file
+                                        (or native-inputs inputs)
+                                        "bin/dmd")))))
+                  ;; XXX: Use sed, as replace-store-references wouldn't
+                  ;; replace the references, while substitute* throws an
+                  ;; error.
+                  (invoke "sed" "-i"
+                          (format #f "s,~a,~a,g" dmd-bootstrap #$output)
+                          dmd))))))))
+    (native-inputs (modify-inputs (package-native-inputs dmd-bootstrap)
+                     (replace "gdmd" dmd-bootstrap)))))
+
 (define-public dub
   (package
     (name "dub")
@@ -453,3 +620,35 @@ needed.")
     (synopsis "D binding and OO wrapper of GTK+")
     (description "This package provides bindings to GTK+ for D.")
     (license license:lgpl2.1)))
+
+(define-public d-demangler
+  (package
+    (name "d-demangler")
+    (version "0.0.2")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/lievenhey/d_demangler")
+                    (commit (string-append "version-" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "13lbbxlaa1mffjs57xchl1g6kyr5lxi0z5x7snyvym0knslxwx2g"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:tests? #f                       ;no test suite
+      #:make-flags #~(list (string-append "CC=" #$(cc-for-target))
+                           "d_demangle")
+      #:phases #~(modify-phases %standard-phases
+                   (delete 'configure)
+                   (replace 'install
+                     (lambda _
+                       (install-file "libd_demangle.so"
+                                     (string-append #$output "/lib")))))))
+    (native-inputs (list dmd))
+    (home-page "https://github.com/lievenhey/d_demangler")
+    (synopsis "Utility to demangle D symbols")
+    (description "@command{d_demangle} is a small utility that can be used to
+demangle D symbols.  A shared library is also provided.")
+    (license license:gpl3+)))

gnu/packages/dns.scm

@@ -21,6 +21,7 @@
 ;;; Copyright © 2021 Zheng Junjie <873216071@qq.com>
 ;;; Copyright © 2023 Bruno Victal <mirai@makinata.eu>
 ;;; Copyright © 2023 Hilton Chain <hako@ultrarare.space>
+;;; Copyright © 2024 John Kehayias <john.kehayias@protonmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -293,7 +294,7 @@ prompt the user with the option to go with insecure DNS only.")
 (define-public dnsmasq
   (package
     (name "dnsmasq")
-    (version "2.89")
+    (version "2.90")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -301,7 +302,7 @@ prompt the user with the option to go with insecure DNS only.")
                     version ".tar.xz"))
               (sha256
                (base32
-                "02dnxfnman38armn3sw56w80f9wb2vgm3qgm15crs2yg8q1j7g82"))))
+                "1r09l537vi867hlpv6vl7nvqhscvq1kf04m896bfrgrpv2dk0l4f"))))
     (build-system gnu-build-system)
     (native-inputs
      (list pkg-config))
@@ -336,23 +337,23 @@ and BOOTP/TFTP for network booting of diskless machines.")
     ;; When updating, check whether isc-dhcp's bundled copy should be as well.
     ;; The BIND release notes are available here:
     ;; https://www.isc.org/bind/
-    (version "9.16.38")
+    (version "9.19.21")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://ftp.isc.org/isc/bind9/" version
                            "/bind-" version ".tar.xz"))
        (sha256
-        (base32 "03y52iyc2g63lkk9x2vaizpr0jv27g1z6mcxnjw8m8l4kaflrx4d"))
+        (base32 "133f1aq8acaz9z03cl0gcrj4pq0hqm6c3sm4hz67d37phndsjs1b"))))
-       (patches
-        (search-patches "bind-re-add-attr-constructor-priority.patch"))))
     (build-system gnu-build-system)
     (outputs `("out" "utils"))
     (inputs
      ;; It would be nice to add GeoIP and gssapi once there are packages.
      (list libcap
+           liburcu
            libuv
            libxml2
+           `(,nghttp2 "lib")
            openssl
            p11-kit
            python
@@ -635,14 +636,14 @@ BIND and djbdns---whilst using relatively little memory.")
 (define-public unbound
   (package
     (name "unbound")
-    (version "1.17.1")
+    (version "1.19.1")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://www.unbound.net/downloads/unbound-"
                            version ".tar.gz"))
        (sha256
-        (base32 "1x55f5aqlzynpy24ryf1rsmdy8m8iyi19n7k03k889g1rk78ah7f"))))
+        (base32 "1ad34jxprygjp7g84q1bgmvcc114f2mgyhfwk9rs0inq7mpmf7dw"))))
     (build-system gnu-build-system)
     (outputs '("out" "python"))
     (native-inputs
@@ -844,7 +845,7 @@ Extensions} (DNSSEC).")
 (define-public knot
   (package
     (name "knot")
-    (version "3.3.2")
+    (version "3.3.4")
     (source
      (origin
        (method git-fetch)
@@ -853,7 +854,7 @@ Extensions} (DNSSEC).")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "17zdpk6wf0cf90dp4cls35si8ywjsqjrmgssw2gmb1y0zfyp19vq"))
+        (base32 "0w7drq0pj94d43qn9wmzxab34mjhxj9x84rixbswc270ywh6d9pr"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -983,14 +984,14 @@ synthesis, and on-the-fly re-configuration.")
 (define-public knot-resolver
   (package
     (name "knot-resolver")
-    (version "5.5.3")
+    (version "5.7.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://secure.nic.cz/files/knot-resolver/"
                                   "knot-resolver-" version ".tar.xz"))
               (sha256
                (base32
-                "0bgdbx66dsfik3sdqi4g2imddalqc1p41n444xk7s8vxig35g3x3"))))
+                "18n3jh17d22xmzpg8syw2dm85vv7jchdc4hzk5x78lqxqqav856s"))))
     (build-system meson-build-system)
     (outputs '("out" "doc"))
     (arguments

gnu/packages/docker.scm

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

gnu/packages/education.scm

@@ -47,7 +47,9 @@
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
   #:use-module (gnu packages golang-check)
+  #:use-module (gnu packages golang-xyz)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages gstreamer)
   #:use-module (gnu packages image)
@@ -1161,3 +1163,37 @@ mentored learning for programming languages.")
     (description "Mazo is a learning application that helps you memorize
 simple concepts using multimedia flash cards and spaced reviews.")
     (license license:public-domain)))
+
+(define-public tagainijisho
+  (package
+    (name "tagainijisho")
+    (version "1.2.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://github.com/Gnurou/tagainijisho/releases/download/"
+             version
+             "/tagainijisho-" version ".tar.gz"))
+       (sha256
+        (base32
+         "00whfcnpn42asxmafcfbcmpwfwyv40qaqdk28psa1vp0lainmyhh"))))
+    (build-system qt-build-system)
+    (arguments
+     (list #:tests? #f))                ;no test target
+    (native-inputs
+     (list qttools-5))
+    (synopsis "Japanese dictionary and learning assistant")
+    (description
+     "Tagaini Jisho is a Japanese dictionary and kanji lookup tool.  It aims
+at becoming your Japanese study assistant.  It allows you to quickly search
+for entries and mark those that you wish to study, along with tags and
+personal notes.  It also let you train entries you are studying and follows
+your progression in remembering them.  Finally, it makes it easy to review
+entries you did not remember by listing them on screen or printing them on
+a small booklet.
+
+Tagaini Jisho also features complete stroke order animations for more than
+6000 kanji.")
+    (home-page "https://www.tagaini.net")
+    (license license:gpl3+)))

gnu/packages/elixir.scm

@@ -7,6 +7,8 @@
 ;;; Copyright © 2018 Nikita <nikita@n0.is>
 ;;; Copyright © 2021 Oskar Köök <oskar@maatriks.ee>
 ;;; Copyright © 2021 Cees de Groot <cg@evrl.com>
+;;; Copyright © 2024 Andrew Tropin <andrew@trop.in>
+;;; Copyright © 2024 Ivan Sokolov <ivan-p-sokolov@ya.ru>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -101,12 +103,26 @@
           (add-after 'install 'wrap-programs
             (lambda* (#:key inputs outputs #:allow-other-keys)
               (let* ((out (assoc-ref outputs "out"))
-                     (programs '("elixir" "elixirc" "iex" "mix")))
+                     (programs '("elixir" "elixirc" "iex")))
+                ;; mix can be sourced as an elixir script by other elixir
+                ;; program, for example `iex -S mix`, so we should not wrap
+                ;; mix into shell script.
+                (substitute* (string-append out "/bin/mix")
+                  (("Mix.start\\(\\)")
+                   (format #f "\
+~~w[GUIX_ELIXIR_LIBS ERL_LIBS]
+|> Enum.map(&System.get_env/1)
+|> Enum.reject(&is_nil/1)
+|> Enum.join(\":\")
+|> case do \"\" -> :ok; erl_libs -> System.put_env(\"ERL_LIBS\", erl_libs) end
+System.put_env(\"MIX_REBAR3\", System.get_env(\"MIX_REBAR3\", \"~a\"))
+Mix.start()"
+                           (search-input-file inputs "/bin/rebar3"))))
                 (for-each (lambda (program)
                             (wrap-program (string-append out "/bin/" program)
                               '("ERL_LIBS" prefix ("${GUIX_ELIXIR_LIBS}"))))
                           programs)))))))
-    (inputs (list erlang git))
+    (inputs (list erlang rebar3 git))
     (native-search-paths
      (list (search-path-specification
             (variable "GUIX_ELIXIR_LIBS")

gnu/packages/embedded.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2016, 2017, 2018, 2019, 2023 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2016, 2017, 2018, 2019, 2023, 2024 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017 Theodoros Foradis <theodoros@foradis.org>
 ;;; Copyright © 2016 David Craven <david@craven.ch>
 ;;; Copyright © 2017, 2020 Efraim Flashner <efraim@flashner.co.il>
@@ -983,14 +983,16 @@ code.")
                   "0w0dff3s7wv2d9m78a4jhckiik58q38wx6wpbba5hzbs4yxz35ck"))))
       (build-system gnu-build-system)
       (arguments
-       `(#:tests? #f ; no tests
+       (list
+        #:tests? #false                 ;no tests
+        #:parallel-build? #false        ;not supported
         #:make-flags
-         (list "OS=linux"
+        #~(list "OS=linux"
-               (string-append "TARGET=" (assoc-ref %outputs "out")))
+                (string-append "TARGET=" #$output))
         #:phases
-         (modify-phases %standard-phases
+        '(modify-phases %standard-phases
            (add-after 'unpack 'chdir
-             (lambda _ (chdir "loader") #t))
+             (lambda _ (chdir "loader")))
            (delete 'configure))))
       (native-inputs
        (list openspin (make-propeller-toolchain)))
@@ -1637,7 +1639,7 @@ PicoBlaze; and Zilog Z80 families, plus many of their variants.")
 (define-public sdcc
   (package
     (name "sdcc")
-    (version "4.3.0")
+    (version "4.4.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1645,7 +1647,7 @@ PicoBlaze; and Zilog Z80 families, plus many of their variants.")
                     "/" version "/sdcc-src-" version ".tar.bz2"))
               (sha256
                (base32
-                "1kckr20jqa4rp4qcw38lwagmw3yfm3z0xb4kygd0608847qc0vra"))
+                "0xbaj3vx5cp3na1kmyhy4jvhcqwrg648scjbykgq0xmibqb1535f"))
               (modules '((guix build utils)))
               (snippet
                #~(begin

gnu/packages/emulators.scm

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

gnu/packages/engineering.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015-2023 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
-;;; Copyright © 2016, 2018, 2020-2023 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2018, 2020-2024 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 David Thompson <davet@gnu.org>
 ;;; Copyright © 2016-2019, 2021, 2023 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016, 2017, 2018 Theodoros Foradis <theodoros@foradis.org>
@@ -1098,7 +1098,7 @@ Emacs).")
 (define-public kicad
   (package
     (name "kicad")
-    (version "7.0.10")
+    (version "7.0.11")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1106,7 +1106,7 @@ Emacs).")
                     (commit version)))
               (sha256
                (base32
-                "0rmlkgzgvpd70jzspyrrb2f618fimw52qrhpsp777flmpyh91wly"))
+                "1qn7w6pb1n5gx73z1zqbv140chh4307y8764z7xkdvric9i48qj4"))
               (file-name (git-file-name name version))))
     (build-system cmake-build-system)
     (arguments
@@ -1206,7 +1206,7 @@ electrical diagrams), gerbview (viewing Gerber files) and others.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0lc7d6hn8ya8m51kjnf59v41pbp03l5ncxir75s21pb92l26xgnv"))))
+                "10iwp35xywdz15a83vialzfd46rjw6mlz174dxawm2rw4ws2n7j4"))))
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags (list "-DBUILD_FORMATS=html")
@@ -1240,7 +1240,7 @@ electrical diagrams), gerbview (viewing Gerber files) and others.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0nlgmxf9z1vf4g350dfkxql1dawgmw275wqxkgszsfxmhdfpmi9v"))))
+                "057zmhf4h3p3p4y6jqxch9cj1wqf129k6kmvx2gshb9lgda0kjr8"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f))                    ; no tests exist
@@ -1269,7 +1269,7 @@ libraries.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1az6fzh1lma71mj12bc4bblnmzjayrxhkb8w9rjvlhvvgv33cdmy"))))
+                "1r9v8v41n0yrgwsqaksskmdgb9vyw1sb92xh81bwrv2ag3p5vdg7"))))
     (synopsis "Official KiCad footprint libraries")
     (description "This package contains the official KiCad footprint libraries.")))
 
@@ -1286,7 +1286,7 @@ libraries.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0xzyi4mgyifwc6dppdzh6jq294mkj0a71cwkqw2ymz1kfbksw626"))))
+                "0lcy1av7ixg1f7arflk50jllpc1749sfvf3h62hkxsz97wkr97xj"))))
     (synopsis "Official KiCad 3D model libraries")
     (description "This package contains the official KiCad 3D model libraries.")))
 
@@ -2681,7 +2681,7 @@ measurement devices and test equipment via GPIB, RS232, Ethernet or USB.")
 (define-public python-scikit-rf
   (package
     (name "python-scikit-rf")
-    (version "0.30.0")
+    (version "0.31.0")
     (source (origin
               (method git-fetch) ;PyPI misses some files required for tests
               (uri (git-reference
@@ -2689,7 +2689,7 @@ measurement devices and test equipment via GPIB, RS232, Ethernet or USB.")
                     (commit (string-append "v" version))))
               (sha256
                (base32
-                "1fbws80glrakd08xzhifna831yk0bd8b0cizhfcjkg4km2nyx65c"))
+                "1cidv2373lwxy26kbzg4slaqvn2gpq67mvijgp0rydfx6mm6a89i"))
               (file-name (git-file-name name version))))
     (build-system pyproject-build-system)
     (propagated-inputs (list python-matplotlib
@@ -3272,6 +3272,8 @@ program that can perform mesh processing tasks in batch mode, without a GUI.")
                   (guix build utils))
       #:configure-flags
       #~(list "--disable-static"
+              (string-append "--with-vimdir=" #$output
+                             "/share/vim/vimfiles/pack/guix/start/poke")
               (string-append "--with-lispdir="
                              (emacs:elpa-directory #$output)))))
     (home-page "https://www.gnu.org/software/poke/#documentation")

gnu/packages/file-systems.scm

@@ -12,7 +12,8 @@
 ;;; Copyright © 2021, 2023 Kaelyn Takata <kaelyn.alexi@protonmail.com>
 ;;; Copyright © 2022 Brian Cully <bjc@spork.org>
 ;;; Copyright © 2023 Aaron Covrig <aaron.covrig.us@ieee.org>
-;;;
+;;; Copyright © 2024 Ahmad Draidi <a.r.draidi@redscript.org>
+;;
 ;;; This file is part of GNU Guix.
 ;;;
 ;;; GNU Guix is free software; you can redistribute it and/or modify it
@@ -67,11 +68,14 @@
   #:use-module (gnu packages flex)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gawk)
+  #:use-module (gnu packages gettext)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
   #:use-module (gnu packages golang-check)
+  #:use-module (gnu packages golang-crypto)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages jemalloc)
   #:use-module (gnu packages kerberos)
@@ -81,6 +85,8 @@
   #:use-module (gnu packages linux)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages man)
+  #:use-module (gnu packages m4)
+  #:use-module (gnu packages ncurses)
   #:use-module (gnu packages nfs)
   #:use-module (gnu packages onc-rpc)
   #:use-module (gnu packages openldap)
@@ -105,6 +111,7 @@
   #:use-module (gnu packages tls)
   #:use-module (gnu packages valgrind)
   #:use-module (gnu packages version-control)
+  #:use-module (gnu packages web)
   #:use-module (gnu packages xml))
 
 (define-public autofs
@@ -581,26 +588,25 @@ from a mounted file system.")
     (license license:gpl2+)))
 
 (define-public bcachefs-tools
-  (let ((commit "1e358401ecdf1963e5799de19ab69111e82e5ebc")
-        (revision "0"))
   (package
     (name "bcachefs-tools")
-      (version (git-version "1.2" revision commit))
+    (version "1.4.1")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://evilpiepirate.org/git/bcachefs-tools.git")
-               (commit commit)))
+             (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-          (base32 "0bflgqb3q9jikyyrv6hywv6m1fapzzn874hlhf86pn6abxrlf5fa"))))
+        (base32 "0axwbckqrw1v3v50nzhpkvpyjbjwy3rq5bv23db84x3xia497apq"))))
     (build-system gnu-build-system)
     (arguments
      (list #:make-flags
            #~(list (string-append "VERSION=" #$version) ; ‘v…-nogit’ otherwise
                    (string-append "PREFIX=" #$output)
                    "INITRAMFS_DIR=$(PREFIX)/share/initramfs-tools"
+                   "PKGCONFIG_UDEVRULESDIR=$(PREFIX)/lib/udev/rules.d"
                    (string-append "CC=" #$(cc-for-target))
                    (string-append "PKG_CONFIG=" #$(pkg-config-for-target))
                    ;; ‘This will be less of an option in the future, as more
@@ -666,6 +672,7 @@ from a mounted file system.")
            `(,zstd "lib")
 
            ;; Only for mount.bcachefs.sh.
+           bash-minimal
            coreutils-minimal
            gawk
            util-linux))
@@ -682,7 +689,7 @@ multiple block devices for replication and/or performance, similar to RAID.
 In addition, bcachefs provides all the functionality of bcache, a block-layer
 caching system, and lets you assign different roles to each device based on its
 performance and other characteristics.")
-      (license license:gpl2+))))
+    (license license:gpl2+)))
 
 (define-public bcachefs-tools/static
   (package
@@ -1218,6 +1225,70 @@ APFS.")
       (home-page "https://github.com/sgan81/apfs-fuse")
       (license license:gpl2+))))
 
+(define-public snapper
+  (package
+    (name "snapper")
+    (version "0.10.7")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/openSUSE/snapper")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0nwmyzjwid1lf29dsr6w72dr781c81xyrjpk5y3scn4r55b5df0h"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           (delete-file-recursively "dists")
+           (delete-file-recursively "zypp-plugin")
+           (substitute* '("configure.ac" "doc/Makefile.am")
+             ((".*dists.*") "")
+             ((".*zypp-plugin.*") ""))
+           (substitute* "Makefile.am"
+             (("zypp-plugin") ""))))))
+    (build-system gnu-build-system)
+    (arguments
+     (list #:phases #~(modify-phases %standard-phases
+                        (add-after 'unpack 'relative-file-locations
+                          (lambda* (#:key outputs #:allow-other-keys)
+                            (let* ((out (assoc-ref outputs "out")))
+                              (substitute* (list "scripts/Makefile.am"
+                                                 "data/Makefile.am")
+                                (("/usr/share")
+                                 (string-append out "/share"))
+                                (("/usr/lib")
+                                 (string-append out "/lib"))
+                                (("/etc/")
+                                 (string-append out "/etc/"))))
+                            (substitute* "client/Makefile.am"
+                              (("/usr/lib")
+                               "@libdir@")))))))
+    (home-page "https://snapper.io")
+    (native-inputs
+     (list glibc-locales autoconf automake libtool pkg-config))
+    (inputs
+     (list btrfs-progs
+           e2fsprogs
+           `(,util-linux "lib")
+           linux-pam
+           dbus
+           libxml2
+           json-c
+           acl
+           boost
+           ncurses/tinfo
+           libxslt
+           docbook-xsl
+           gettext-minimal))
+    (synopsis "Manage Btrfs file system snapshots and allow roll-backs")
+    (description "This package provides Snapper, a tool that helps with
+managing snapshots of Btrfs subvolumes and thin-provisioned LVM volumes.  It
+can create and compare snapshots, revert differences between them, and
+supports automatic snapshots timelines.")
+    (license license:gpl2)))
+
 (define-public xfstests
   ;; The last release (1.1.0) is from 2011.
   (let ((revision "3")

gnu/packages/finance.scm

@@ -36,6 +36,7 @@
 ;;; Copyright © 2023 Skylar Hill <stellarskylark@posteo.net>
 ;;; Copyright © 2023 Foundation Devices, Inc. <hello@foundationdevices.com>
 ;;; Copyright © 2023 Attila Lendvai <attila@lendvai.name>
+;;; Copyright © 2024 Saku Laesvuori <saku@laesvuori.fi>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1308,7 +1309,7 @@ agent.")
 (define-public kitsas
   (package
     (name "kitsas")
-    (version "4.0.3")
+    (version "5.4.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1317,17 +1318,24 @@ agent.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0hrbsqqm6v2pmjq17s7i4akjgclz3d051mg02vcykq80xgxvbkgf"))))
+                "16zkfpl5d9ia202fqg5vrhjqdw0g6wp044ih6n7nz2hbxj9y3m1z"))))
     (build-system qt-build-system)
-    (inputs (list qtbase-5 libzip poppler-qt5 qtsvg-5))
+    (inputs (list libzip qtsvg qtwebengine qt5compat))
     (arguments
-     (list #:tests? #f               ;XXX: some tests fail and others segfault
+     (list #:tests? #f           ; tests do not even build with Qt6 anymore
            #:test-target "check"
+           #:qtbase qtbase       ; use Qt6
            #:phases
            #~(modify-phases %standard-phases
                (replace 'configure
                  (lambda* _
                    (invoke "qmake" "kitsasproject.pro" "CONFIG+=release")))
+               ;; The tests are not maintained and some don't even build
+               (add-before 'configure 'disable-broken-tests
+                 (lambda _
+                   (substitute* "kitsasproject.pro"
+                     ((" *(unittest|testit).*") "")
+                     (("\\\\") ""))))
                (replace 'install
                  (lambda* _
                    (install-file "kitsas/kitsas"
@@ -2243,7 +2251,7 @@ and manipulation.")
 (define-public xmrig
   (package
     (name "xmrig")
-    (version "6.20.0")
+    (version "6.21.0")
     (source
      (origin
        (method git-fetch)
@@ -2251,7 +2259,7 @@ and manipulation.")
              (url "https://github.com/xmrig/xmrig")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
-       (sha256 (base32 "02clipcixn0g4sm3b5r1cxx56ddhjkm8sqnq40jy1zm66ad5zhkj"))
+       (sha256 (base32 "1nmzgwd2r7ra7g4p0s5b77bgh099hf1kisbv4d946c9yiwbdzqgc"))
        (modules '((guix build utils)))
        (snippet
         ;; TODO: Try to use system libraries instead of bundled ones in

gnu/packages/firmware.scm

@@ -1197,11 +1197,13 @@ such as:
           ;; Adding debug symbols causes the size to exceed limits.
           #~(delete "DEBUG=1" #$flags)))))))
 
-(define (make-crust-package platform)
+(define make-crust-firmware
+  (mlambda (platform)
     (package
       (name (string-append "crust-"
-                         (string-replace-substring platform "_" "-")))
+                           (string-replace-substring platform "_" "-")
-    (version "0.5")
+                           "-firmware"))
+      (version "0.6")
       (source
        (origin
          (method git-fetch)
@@ -1212,43 +1214,19 @@ such as:
          (file-name (git-file-name "crust" version))
          (sha256
           (base32
-         "0xgbbhifg3miwd3yp6jq9kp7nqgz5gzy00w95vba45j8jk5vjvvz"))))
+           "1blq6bi2rmg4qqwwr07pamv28b50mwcsybhpn9bws8vbzxa43afd"))))
       (build-system gnu-build-system)
       (arguments
        (list
+        #:target "or1k-elf"
         #:tests? #f                       ;no test suite
-      #:make-flags
+        #:make-flags #~'("CROSS_COMPILE=or1k-elf-"
-      (let ((triplet-without-vendor
-             (and (%current-target-system)
-                  ;; TODO: Is there a use case for allowing this?
-                  (not (target-avr?))
-                  (match (string-split (nix-system->gnu-triplet
-                                        (%current-target-system)) #\-)
-                    ((arch vendor os ..1)
-                     (string-join `(,arch ,@os) "-"))))))
-        #~(list "CROSS_COMPILE=or1k-elf-"
                          "V=1"
-                #$@(if triplet-without-vendor
+                         "HOSTAR=ar"
-                       ;; We are cross-compiling the tools, intended to be
+                         "HOSTCC=gcc"
-                       ;; executable for the target system.
+                         "LEX=flex")
-                       (list (string-append "HOSTAR=" triplet-without-vendor
-                                            "-ar")
-                             (string-append "HOSTCC=" triplet-without-vendor
-                                            "-gcc"))
-                       ;; Not cross-compiling.
-                       (list "HOSTAR=ar"
-                             "HOSTCC=gcc"))
-                "LEX=flex"))
         #:phases
         #~(modify-phases %standard-phases
-          (add-after 'unpack 'do-not-build-tests
-            (lambda _
-              ;; Attempting to build the tools test binary on a non-aarch64
-              ;; architecture fails with: "No cache cleaning implementation
-              ;; available for this architecture".  Avoid building it (see:
-              ;; https://github.com/crust-firmware/crust/issues/182).
-              (substitute* "tools/Makefile"
-                (("tools-y \\+= test") ""))))
             (delete 'configure)
             (add-before 'build 'defconfig
               (lambda* (#:key make-flags #:allow-other-keys)
@@ -1259,18 +1237,10 @@ such as:
                 (for-each (lambda (file)
                             (install-file file (string-append #$output
                                                               "/libexec")))
-                        (find-files "." "(scp\\.bin|\\.config)$"))
+                          (find-files "." "(scp\\.bin|\\.config)$")))))))
-              (install-file "build/tools/load"
+      (native-inputs (list bison flex))
-                            (string-append #$output "/bin")))))))
-    ;; The firmware is cross-compiled using a "bare bones" compiler (no libc).
-    ;; Use our own tool chain for that.
-    (native-inputs
-     (list bison
-           (cross-gcc "or1k-elf")
-           (cross-binutils "or1k-elf")
-           flex))
       (home-page "https://github.com/crust-firmware/crust")
-    (synopsis "System control processor firmware for Allwinner sunxi boards")
+      (synopsis "Firmware for Allwinner sunxi SoCs")
       (description "Crust improves battery life and thermal performance by
 implementing a deep sleep state.  During deep sleep, the CPU cores, the DRAM
 controller, and most onboard peripherals are powered down, reducing power
@@ -1281,7 +1251,74 @@ dedicated always-on microprocessor called a System Control Processor (SCP).
 Crust is designed to run on a specific SCP implementation, Allwinner's
 AR100.")
       ;; Most files are dual-licensed "BSD-3 OR GPL2", a few are GPL2 only.
-    (license (list license:bsd-3 license:gpl2))))
+      (license (list license:bsd-3 license:gpl2)))))
+
+(define make-crust-tools
+  (mlambda (platform firmware)
+    (package
+      (inherit firmware)
+      (name (string-append "crust-"
+                           (string-replace-substring platform "_" "-")
+                           "-tools"))
+      (arguments
+       (list #:make-flags
+             #~(list "V=1"
+                     "LEX=flex"
+                     (string-append "HOSTAR=" #$(ar-for-target))
+                     (string-append "HOSTCC=" #$(cc-for-target)))
+             #:phases
+             #~(modify-phases %standard-phases
+                 (add-after 'unpack 'do-not-build-tests
+                   (lambda _
+                     ;; Attempting to build the tools test binary on a
+                     ;; non-aarch64 architecture fails with: "No cache
+                     ;; cleaning implementation available for this
+                     ;; architecture".  Avoid building it (see:
+                     ;; https://github.com/crust-firmware/crust/issues/182).
+                     (substitute* "tools/Makefile"
+                       (("tools-y \\+= test") ""))))
+                 (replace 'configure
+                   (lambda* (#:key inputs native-inputs #:allow-other-keys)
+                     (copy-file (search-input-file inputs "/libexec/.config")
+                                ".config")))
+                 (replace 'build
+                   (lambda* (#:key make-flags parallel-build?
+                             #:allow-other-keys)
+                     (apply invoke "make" "tools"
+                            `(,@(if parallel-build?
+                                    `("-j"
+                                      ,(number->string (parallel-job-count)))
+                                     '())
+                              ,@make-flags))))
+                 (replace 'install
+                   (lambda _
+                     (install-file "build/tools/load"
+                                   (string-append #$output "/bin")))))))
+      (synopsis "Firmware for Allwinner sunxi SoCs (tools)")
+      (inputs (list firmware)))))
+
+(define make-crust-package
+  (mlambda (platform)
+    (let* ((firmware (make-crust-firmware platform))
+           (tools (make-crust-tools platform firmware)))
+      (package
+        (inherit firmware)
+        (name (string-append "crust-"
+                             (string-replace-substring platform "_" "-")))
+        (source #f)
+        (build-system trivial-build-system)
+        (arguments
+         (list #:modules '((guix build union))
+               #:builder
+               #~(begin
+                   (use-modules (ice-9 match)
+                                (guix build union))
+
+                   (match %build-inputs
+                     (((names . directory) ...)
+                      (union-build #$output directory))))))
+        (native-inputs '())
+        (inputs (list firmware tools))))))
 
 (define-public crust-pinebook
   (make-crust-package "pinebook"))

gnu/packages/fonts.scm

@@ -58,7 +58,8 @@
 ;;; Copyright © 2023 gemmaro <gemmaro.dev@gmail.com>
 ;;; Copyright © 2023 Denis 'GNUtoo' Carikli <GNUtoo@cyberdimension.org>
 ;;; Copyright © 2023 chris <chris@bumblehead.com>
-;;; Copyright © 2023 Luis Felipe López Acevedo <sirgazil@zoho.com>
+;;; Copyright © 2023, 2024 Luis Felipe López Acevedo <sirgazil@zoho.com>
+;;; Copyright © 2024 Christina O'Donnell <cdo@mutix.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -216,7 +217,7 @@ in print.  With attention to detail for high resolution rendering.")
 (define-public font-intel-one-mono
   (package
     (name "font-intel-one-mono")
-    (version "1.2.1")
+    (version "1.3.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -225,8 +226,26 @@ in print.  With attention to detail for high resolution rendering.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1md57997nzkz75ambsahawzy1x71qvkp6f87zcqibksm66yvcjdc"))))
+                "0w9isn8az1k3a3q4m2llwnryy79i5v30dx1hfaf90x0zkj98ky5h"))))
+    (outputs '("out" "ttf" "woff"))
     (build-system font-build-system)
+    (arguments
+     (list #:phases
+           #~(modify-phases %standard-phases
+               (add-after 'install 'split-outputs
+                 (lambda* (#:key outputs #:allow-other-keys)
+                   (let ((out-fonts (string-append (assoc-ref outputs "out")
+                                                   "/share/fonts"))
+                         (ttf-fonts (string-append (assoc-ref outputs "ttf")
+                                                   "/share/fonts"))
+                         (woff-fonts (string-append (assoc-ref outputs "woff")
+                                                    "/share/fonts")))
+                     (mkdir-p ttf-fonts)
+                     (mkdir-p woff-fonts)
+                     (rename-file (string-append out-fonts "/truetype")
+                                  (string-append ttf-fonts "/truetype"))
+                     (rename-file (string-append out-fonts "/web")
+                                  (string-append woff-fonts "/web"))))))))
     (home-page "https://github.com/intel/intel-one-mono")
     (synopsis "Expressive monospaced font family")
     (description
@@ -587,6 +606,30 @@ The unified Libertinus family consists of:
 @end enumerate\n")
     (license license:silofl1.1)))
 
+(define-public font-libre-franklin
+  (let ((commit "bfc61d6e403771c2e90aa6e0bd54975633974fb2")
+        (revision "0"))
+    (package
+      (name "font-libre-franklin")
+      (version (git-version "1.015" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/impallari/Libre-Franklin")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "07rm9fkhm8ckxpaj0zixl4vgzmj6bj4xzbaqm5hngdjds1bjv1ls"))))
+      (build-system font-build-system)
+      (home-page "https://fonts.google.com/specimen/Libre+Franklin")
+      (synopsis "Font family based on Franklin Gothic")
+      (description
+       "The Libre Franklin font family is an open source interpretation and
+expansion of Franklin Gothic, a classic font.  It covers 105 Latin Languages.")
+      (license license:silofl1.1))))
+
 (define-public font-terminus
   (package
     (name "font-terminus")
@@ -1975,7 +2018,7 @@ weights and five widths in both Roman and Italic, plus variable fonts.")
 (define-public font-sarasa-gothic
   (package
     (name "font-sarasa-gothic")
-    (version "1.0.3")
+    (version "1.0.5")
     (source
      (origin
        (method url-fetch)
@@ -1983,7 +2026,7 @@ weights and five widths in both Roman and Italic, plus variable fonts.")
                            "/releases/download/v" version
                            "/Sarasa-TTC-" version ".7z"))
        (sha256
-        (base32 "1cgqf15fhg567s2bwjpal3xfcdnbgyy0iav5181zkn6b4k56dgl4"))))
+        (base32 "0sfmqrjfzjy2zxd26kjrdbp59ahxj7p2qr1z5qy512j2cgl1gyiq"))))
     (build-system font-build-system)
     (arguments
      `(#:phases (modify-phases %standard-phases
@@ -2638,6 +2681,61 @@ It comes in seven weights and Roman, Italic and Oblique styles.")
    (home-page "https://rubjo.github.io/victor-mono/")
    (license license:expat)))
 
+(define-public font-dongle
+  (let ((commit "f7127c4d2450e1cad20254ec692591347e2fc260")
+        (revision "1"))
+    (package
+      (name "font-dongle")
+      (version (git-version "0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/yangheeryu/Dongle")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1gwrjv468bqfa3nxh01vprk7rp24cnhk3zlkrv5mzqcbcdf96nqp"))))
+      (build-system font-build-system)
+      (arguments
+       `(#:phases
+         (modify-phases %standard-phases
+           (add-before 'install 'build
+             (lambda _
+               (begin
+                 (chdir "sources")
+                 (invoke "unzip" "Dongle.zip")
+                 (chdir "..")
+                 (invoke "python3" "build.py")))))))
+      (native-inputs
+       (list python
+             python-glyphslib
+             python-fonttools
+             python-ufolib2
+             python-ufo2ft
+             zip))
+      (synopsis
+       "Rounded sans-serif typeface, supporting Hangeul and Latin glyphs")
+      (description
+       "Dongle(동글) is a rounded sans-serif typeface for display.  It is a
+modular Hangeul with the de-square frame, creating a playful and rhythmic
+movement.  The name, Dongle comes from a Korean onomatopoeia, meaning 'rounded
+or curved shape (with adorable impression)’.
+
+Dongle was originally designed as a 'Jamo (consonant and vowel in Hangeul)
+typing module' for the author's student project.  Later it revised into
+‘syllabic module’ to be released to the public.  As the character size varies
+according to the syllable structure, Dongle typeface is much smaller compared
+to other square frame Korean typefaces.  Therefore, it is better to adjust the
+font size visually to your liking, rather than relying on the point size of
+the editing program.
+
+It is designed especially for Hangeul typography, but it also includes Latin
+alphabet as a part of KS X 1001.  This typeface has a light, regular, and bold
+weight.")
+      (home-page "https://github.com/yangheeryu/Dongle")
+      (license license:silofl1.1))))
+
 (define-public font-meera-inimai
   (package
     (name "font-meera-inimai")
@@ -3521,3 +3619,31 @@ for display purposes.  It features four weights (light, medium, bold,
 and black), a stylistic alternative, small caps, and many alternate
 glyphs.")
       (license license:silofl1.1))))
+
+(define-public font-oswald
+  (let ((version "0")
+        (commit "6e65651c229e897dc55fb8d17097ee7f75b2769b")
+        (revision "0"))
+    (package
+      (name "font-oswald")
+      (version (git-version version revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/googlefonts/OswaldFont")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "0m5c98crw6df6hbhxv4smh6ldzk5fx434fyri8xgnsjjcrkqxy0h"))))
+      (build-system font-build-system)
+      (home-page "https://github.com/googlefonts/OswaldFont")
+      (synopsis "Gothic typeface")
+      (description "Oswald is a reworking of the classic gothic typeface
+style historically represented by designs such as 'Alternate Gothic'.
+The characters of Oswald have been re-drawn and reformed to better fit
+the pixel grid of standard digital screens.  Oswald is designed to be
+used freely across the internet by web browsers on desktop computers,
+laptops and mobile devices.")
+      (license license:silofl1.1))))

gnu/packages/fontutils.scm

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

gnu/packages/fpga.scm

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

gnu/packages/freedesktop.scm

@@ -5,7 +5,7 @@
 ;;; Copyright © 2015-2017, 2019, 2021-2022 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015, 2017, 2018, 2019, 2021, 2022, 2023 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 David Hashe <david.hashe@dhashe.com>
-;;; Copyright © 2016, 2017, 2019, 2021-2023 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2019, 2021-2024 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Kei Kebreau <kkebreau@posteo.net>
 ;;; Copyright © 2017 Nikita <nikita@n0.is>
 ;;; Copyright © 2017, 2018 Mark H Weaver <mhw@netris.org>
@@ -3002,7 +3002,7 @@ for xdg-desktop-portal that is using Qt/KF5.")
                            (string-append (assoc-ref outputs "out")
                                           "/share/doc/" ,name)))))))
     (native-inputs
-     (list cmake pkg-config))
+     (list cmake-minimal pkg-config))
     (inputs (list elogind
                   bash-minimal
                   grim

gnu/packages/game-development.scm

@@ -6,7 +6,7 @@
 ;;; Copyright © 2015, 2016, 2017 David Thompson <davet@gnu.org>
 ;;; Copyright © 2016-2021, 2023 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2017, 2020 Kei Kebreau <kkebreau@posteo.net>
-;;; Copyright © 2016, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2016, 2018, 2019, 2024 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017, 2018 Julian Graham <joolean@gmail.com>
 ;;; Copyright © 2017–2021 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Manolis Fragkiskos Ragkousis <manolis837@gmail.com>
@@ -58,6 +58,7 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system copy)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system pyproject)
   #:use-module (guix build-system python)
   #:use-module (guix build-system scons)
   #:use-module (gnu packages)
@@ -115,6 +116,7 @@
   #:use-module (gnu packages sphinx)
   #:use-module (gnu packages sqlite)
   #:use-module (gnu packages stb)
+  #:use-module (gnu packages swig)
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages textutils)
   #:use-module (gnu packages tls)
@@ -453,6 +455,40 @@ compiling NML files (along with their associated language, sound and graphic
 files) into @file{.grf} and/or @file{.nfo} files.")
     (license license:gpl2+)))
 
+(define-public python-pybox2d
+  (package
+    (name "python-pybox2d")
+    (version "2.3.10")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/pybox2d/pybox2d")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0dha28yscr1lpyzy9ygqc01a8pyf7n9vavyxikqh469wr2zcacna"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; It is not clear how to run the tests
+      #:tests? #false
+      #:phases
+      '(modify-phases %standard-phases
+         (add-before 'build 'build-ext
+           (lambda _
+             (invoke "python" "setup.py" "build_ext" "--inplace"))))))
+    (native-inputs (list swig))
+    (home-page "https://github.com/pybox2d/pybox2d")
+    (synopsis "2D game physics for Python")
+    (description
+     "Pybox2d is a 2D physics library for your games and simple simulations.
+It's based on the Box2D library, written in C++.  It supports several shape
+types (circle, polygon, thin line segments), and quite a few joint
+types (revolute, prismatic, wheel, etc.).")
+    (license license:zlib)))
+
 (define-public python-sge
   (package
     (name "python-sge")
@@ -1275,13 +1311,13 @@ interface (API).")
 (define-public python-pygame
   (package
     (name "python-pygame")
-    (version "2.1.2")
+    (version "2.5.2")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "pygame" version))
               (sha256
                (base32
-                "0g6j79naab7583kymf1bgxc5l5c9h5laq887rmvh8vw8iyifrl6n"))))
+                "0jn2n70hmgr33yc6xzdi33cs5w7jnmgi44smyxfarrrrsnsrxf61"))))
     (build-system python-build-system)
     (arguments
      (list
@@ -1344,7 +1380,7 @@ and multimedia programs in the Python language.")
 
 (define-public python-pygame-sdl2
   (let ((real-version "2.1.0")
-        (renpy-version "8.1.3"))
+        (renpy-version "8.2.0"))
     (package
       (inherit python-pygame)
       (name "python-pygame-sdl2")
@@ -1354,7 +1390,7 @@ and multimedia programs in the Python language.")
          (method url-fetch)
          (uri (string-append "https://www.renpy.org/dl/" renpy-version
                              "/pygame_sdl2-" version ".tar.gz"))
-         (sha256 (base32 "0qlprs9n3w254ilizqzvr6s01zx72gh7an0bgwxsq4hm22qypdws"))
+         (sha256 (base32 "17mc39c7ha83kzv2wmq61a15mn6p8wh2y33ixhf5sb4bvyr48mhy"))
          (modules '((guix build utils)))
          (snippet
           '(begin
@@ -1395,7 +1431,7 @@ developed mainly for Ren'py.")
 (define-public python-renpy
   (package
     (name "python-renpy")
-    (version "8.1.3")
+    (version "8.2.0")
     (source
      (origin
        (method url-fetch)
@@ -1403,7 +1439,7 @@ developed mainly for Ren'py.")
                            "/renpy-" version "-source.tar.bz2"))
        (sha256
         (base32
-         "1g6fz5dxp7yxhgv6q4brzf5hpfqq3l1g3dfv3fsiwwn6mj0b01z2"))
+         "02v54qqjjigfqhdr50kzhkdvplk56bvprq65jl57kcs1qhvlf5s9"))
        (modules '((guix build utils)))
        (snippet
         #~(begin
@@ -2038,7 +2074,7 @@ games.")
            libxi
            libxinerama
            libxrandr
-           mbedtls-apache
+           mbedtls-lts
            mesa
            opusfile
            pcre2
@@ -2280,7 +2316,7 @@ scripted in a Python-like language.")
            libxinerama
            libxkbcommon
            libxrandr
-           mbedtls-apache
+           mbedtls-lts
            mesa
            openxr
            opusfile
@@ -3228,7 +3264,7 @@ progresses the level, or you may regenerate tiles as the world changes.")
 (define-public raylib
   (package
     (name "raylib")
-    (version "4.5.0")
+    (version "5.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -3238,7 +3274,7 @@ progresses the level, or you may regenerate tiles as the world changes.")
               ;; TODO: Unbundle src/external
               (sha256
                (base32
-                "00y8fsa4g9fk93s3wihbxl929m84hw3fflr0h409s3i1kfmv7ajj"))))
+                "0327licmylwlh5iyzw35pq7ci2d15rp3jms5i9p0vfg1rlv2sjw0"))))
     (build-system cmake-build-system)
     (arguments
      (list #:tests? #f  ;no test

gnu/packages/games.scm

@@ -37,7 +37,7 @@
 ;;; Copyright © 2018 Benjamin Slade <slade@jnanam.net>
 ;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
 ;;; Copyright © 2019, 2020 Pierre Neidhardt <mail@ambrevar.xyz>
-;;; Copyright © 2019, 2020 Oleg Pykhalov <go.wigust@gmail.com>
+;;; Copyright © 2019, 2020, 2024 Oleg Pykhalov <go.wigust@gmail.com>
 ;;; Copyright © 2019 Pierre Langlois <pierre.langlois@gmx.com>
 ;;; Copyright © 2019 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2019, 2020 Jesse Gibbons <jgibbons2357+guix@gmail.com>
@@ -60,7 +60,7 @@
 ;;; Copyright © 2021 Olivier Rojon <o.rojon@posteo.net>
 ;;; Copyright © 2021 Stefan Reichör <stefan@xsteve.at>
 ;;; Copyright © 2021, 2022 Greg Hogan <code@greghogan.com>
-;;; Copyright © 2021 David Pflug <david@pflug.io>
+;;; Copyright © 2021, 2024 David Pflug <david@pflug.io>
 ;;; Copyright © 2021, 2022 Felix Gruber <felgru@posteo.net>
 ;;; Copyright © 2021 Solene Rapenne <solene@perso.pw>
 ;;; Copyright © 2021, 2022 Noisytoot <ron@noisytoot.org>
@@ -72,7 +72,7 @@
 ;;; Copyright © 2022 Roman Riabenko <roman@riabenko.com>
 ;;; Copyright © 2022, 2023 zamfofex <zamfofex@twdb.moe>
 ;;; Copyright © 2022 Gabriel Arazas <foo.dogsquared@gmail.com>
-;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2022, 2024 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2022 Hendursaga <hendursaga@aol.com>
 ;;; Copyright © 2022 Parnikkapore <poomklao@yahoo.com>
 ;;; Copyright © 2023 Zheng Junjie <873216071@qq.com>
@@ -80,6 +80,7 @@
 ;;; Copyright © 2023 Ivana Drazovic <iv.dra@hotmail.com>
 ;;; Copyright © 2023, 2024 gemmaro <gemmaro.dev@gmail.com>
 ;;; Copyright © 2023 Wilko Meyer <w@wmeyer.eu>
+;;; Copyright © 2024 Vagrant Cascadian <vagrant@debian.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -149,6 +150,7 @@
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages gnuzilla)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages golang-build)
   #:use-module (gnu packages gperf)
   #:use-module (gnu packages graphics)
   #:use-module (gnu packages graphviz)
@@ -6230,6 +6232,106 @@ application that locks the keyboard and mouse and instead displays bright
 colors, pictures, and sounds.")
     (license license:gpl3+)))
 
+(define-public moonlight-qt
+  (package
+    (name "moonlight-qt")
+    (version "5.0.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/moonlight-stream/moonlight-qt")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1g1y736vw36lmh2bjymsf4b4ypr76x9lqz7frzpj7sn0vb9y5315"))))
+    (build-system qt-build-system)
+    (arguments
+     (list
+      #:tests? #f ;no test suite
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'configure
+            (lambda* _
+              (symlink (string-append
+                        #$(this-package-input "sdl2-gamecontrollerdb")
+                        "/share/sdl2/gamecontrollerdb.txt")
+                       "app/SDL_GameControllerDB/gamecontrollerdb.txt")
+              ;; Unbundle libraries.
+              (substitute* "moonlight-qt.pro"
+                (("    moonlight-common-c.*\n") "")
+                (("    qmdnsengine.*\n") "")
+                (("    h264bitstream.*\n") "")
+                (("    app \\\\") "    app")
+                (("app.depends") "INCLUDEPATH +="))
+              (invoke "qmake" (string-append "PREFIX=" #$output)))))))
+    (native-inputs (list pkg-config qttools-5))
+    (inputs (list ffmpeg
+                  h264bitstream
+                  libva
+                  libvdpau
+                  moonlight-common
+                  openssl
+                  opus
+                  qmdnsengine
+                  qtbase-5
+                  qtdeclarative-5
+                  qtquickcontrols2-5
+                  qtsvg-5
+                  sdl2
+                  sdl2-ttf
+                  sdl2-gamecontrollerdb))
+    (synopsis "GameStream client")
+    (description
+     "Moonlight is an implementation of NVIDIA's GameStream, as used by the
+NVIDIA Shield.")
+    (home-page "https://moonlight-stream.org")
+    (license license:gpl3+)))
+
+(define-public moonlight-common
+  ;; Used as submodule in https://github.com/moonlight-stream/moonlight
+  (let ((commit "5de4a5b85a28d8d639482a1a105c3a06eb67a2fd")
+        (revision "1"))
+    (package
+      (name "moonlight-common")
+      (version (git-version "5.0.1" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url
+                       "https://github.com/moonlight-stream/moonlight-common-c")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "05jm0vhyb6pizd8yj89rp6ak7bf5j9w06rrmbxh8jccxwqjgll92"))))
+      (build-system cmake-build-system)
+      (arguments
+       (list #:tests? #f
+             #:phases #~(modify-phases %standard-phases
+                          (add-after 'unpack 'use-system-enet-package
+                            (lambda _
+                              (substitute* "CMakeLists.txt"
+                                (("add_subdirectory\\(enet\\)")
+                                 ""))))
+                          (replace 'install
+                            (lambda* (#:key outputs source #:allow-other-keys)
+                              (let* ((include (string-append #$output
+                                                             "/include"))
+                                     (lib (string-append #$output "/lib")))
+                                (mkdir-p include)
+                                (mkdir-p lib)
+                                (install-file (string-append source
+                                               "/src/Limelight.h") include)
+                                (install-file "libmoonlight-common-c.so" lib)))))))
+      (native-inputs (list pkg-config))
+      (inputs (list enet-moonlight openssl qtbase-5))
+      (synopsis "GameStream protocol core implementation")
+      (description
+       "This package provides the GameStream core code for the protocol.")
+      (home-page "https://github.com/moonlight-stream/moonlight-common-c")
+      (license license:gpl3+))))
+
 (define-public mrrescue
   (package
     (name "mrrescue")
@@ -7099,27 +7201,26 @@ monsters in a quest to find the mystifyingly fabulous Orb of Zot.")
     (version "1.2")
     (source (origin
               (method url-fetch)
-              (uri (string-append "https://bitbucket.org/osslugaru/lugaru/downloads/"
+              (uri (string-append "https://github.com/osslugaru/lugaru/releases"
-                                  "lugaru-" version ".tar.xz"))
+                                  "/download/" version
+                                  "/lugaru-" version ".tar.xz"))
               (sha256
-               (base32
+               (base32 "15zgcshy22q51rm72zi6y9z7qlgnz5iw3gczjdlir4bqmxy4gspk"))
-                "15zgcshy22q51rm72zi6y9z7qlgnz5iw3gczjdlir4bqmxy4gspk"))))
+              (patches
+               (search-patches "lugaru-fix-sound.patch"))))
     (build-system cmake-build-system)
     (arguments
-     `(#:configure-flags
+     (list #:configure-flags #~(list "-DSYSTEM_INSTALL=ON")
-       (list "-DSYSTEM_INSTALL=ON")
+           #:tests? #f))                ;no test suite
-       ;; no test target
+    (native-inputs (list pkg-config))
-       #:tests? #f))
-    (native-inputs
-     (list pkg-config))
     (inputs
-     `(("sdl2" ,sdl2)
+     (list glu
-       ("glu" ,glu)
+           libjpeg-turbo
-       ("libjpeg" ,libjpeg-turbo)
+           libpng
-       ("libpng" ,libpng)
+           libvorbis
-       ("openal" ,openal)
+           openal
-       ("vorbis" ,libvorbis)
+           sdl2
-       ("zlib" ,zlib)))
+           zlib))
     (home-page "https://osslugaru.gitlab.io")
     (synopsis "Cross-platform third-person action game")
     (description "Lugaru is a third-person action game.  The main character,
@@ -7169,6 +7270,7 @@ fight against their plot and save his fellow rabbits from slavery.")
     (synopsis "Data files for 0ad")
     (description "0ad-data provides the data files required by the game 0ad.")
     (home-page "https://play0ad.com")
+    (properties '((hidden? . #t)))
     (license (list (license:fsdg-compatible
                     "http://tavmjong.free.fr/FONTS/ArevCopyright.txt"
                     "Similar to the license of the Bitstream Vera fonts.")
@@ -7996,26 +8098,49 @@ Strife, Chex Quest, and fan-created games like Harmony, Hacx and Freedoom.")
 (define-public odamex
   (package
     (name "odamex")
-    (version "0.9.5")
+    (version "10.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (string-append
              "mirror://sourceforge/odamex/Odamex/" version "/"
-             "odamex-src-" version ".tar.bz2"))
+             "odamex-src-" version ".tar.xz"))
        (sha256
-        (base32 "1x0c9vnwn336inkfamh4na8xjyfjmzfxfn49j4snqymkypjqw6jq"))))
+        (base32 "1isrmki18471yry48mmm7lxzp1kiqma9cc7fx38cvpm2mpgfyvzk"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           ;; XXX: Unbundle more, they are not replaced by the ones provided
+           ;; in inputs: fltk, jsoncpp, miniupnp, protobuf.
+           ;;
+           ;; Remove some bundled libraries.
+           (with-directory-excursion "libraries"
+             (for-each delete-file-recursively
+                       '("curl" "libpng" "portmidi" "zlib")))))))
     (build-system cmake-build-system)
-    (arguments `(#:tests? #f))          ; no tests
+    (arguments
+     (list
+      #:tests? #f ; no tests
+      #:configure-flags
+      #~(list "-DBUILD_CLIENT=1"
+              "-DBUILD_MASTER=1"
+              "-DBUILD_SERVER=1"
+              "-DUSE_INTERNAL_LIBS=0"
+              "-DUSE_INTERNAL_MINIUPNP=0")))
     (native-inputs
-     (list deutex))
+     (list deutex pkg-config))
     (inputs
-     `(("sdl" ,sdl2)
+     (list alsa-lib
-       ("sdl-mixer" ,sdl2-mixer)
+           curl
-       ("zlib" ,zlib)
+           fltk
-       ("libpng" ,libpng)
+           jsoncpp
-       ("curl" ,curl)
+           libpng
-       ("alsa-lib" ,alsa-lib)))
+           miniupnpc
+           portmidi
+           protobuf
+           sdl2
+           sdl2-mixer
+           zlib))
     (home-page "https://odamex.net/")
     (synopsis "Multiplayer Doom port")
     (description "Odamex is a modification of the Doom engine that
@@ -11223,7 +11348,7 @@ disassembly of the DOS version, extended with new features.")
 (define-public fheroes2
   (package
     (name "fheroes2")
-    (version "1.0.5")
+    (version "1.0.11")
     (source
      (origin
        (method git-fetch)
@@ -11232,7 +11357,7 @@ disassembly of the DOS version, extended with new features.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0v7dxzb5cfjb55jydd8f61zzlvxq9mrgdy51hq19b06dmrx1dnc7"))))
+        (base32 "1i1a4dynlb5kl55rmfmib2jha1b2igw5jyiiyla1fxgkbkjnbf27"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f                      ; no tests
@@ -11254,7 +11379,7 @@ play; it will look for them at @file{~/.local/share/fheroes2} folder.")
 (define-public vcmi
   (package
     (name "vcmi")
-    (version "1.3.2")
+    (version "1.4.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -11263,7 +11388,7 @@ play; it will look for them at @file{~/.local/share/fheroes2} folder.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1x1bzd89h0j4xci91d2v5aj5vgkx6vm12iml805wkia4hy1jp4ff"))
+                "039d9dvb2i4y1fj6q5py34r17fwb5jqxkjcg7j57asjk4w9b7i8b"))
               (patches (search-patches "vcmi-disable-privacy-breach.patch"))))
     (build-system cmake-build-system)
     (arguments

gnu/packages/gcc.scm

@@ -192,13 +192,16 @@ where the OS part is overloaded to denote a specific ABI---into GCC
         `(#:out-of-source? #t
           #:configure-flags ,(let ((flags (configure-flags))
                                    (version (package-version this-package)))
-                               ;; GCC 4.9 and 5.0 requires C++11 but GCC
+                               ;; GCC 11.3.0 defaults to C++17 which is partly
-                               ;; 11.3.0 defaults to C++17, which is partly
+                               ;; incompatible with some earlier versions.
-                               ;; incompatible.  Force C++11.
+                               ;; Force an earlier C++ standard while building.
-                               (if (or (version-prefix? "4.9" version)
+                               (cond
+                                 ((version-prefix? "4.8" version)
+                                  `(cons "CXX=g++ -std=c++03" ,flags))
+                                 ((or (version-prefix? "4.9" version)
                                       (version-prefix? "5" version))
-                                   `(cons "CXX=g++ -std=c++11" ,flags)
+                                  `(cons "CXX=g++ -std=c++11" ,flags))
-                                   flags))
+                                 (else flags)))
 
           #:make-flags
           ;; None of the flags below are needed when doing a Canadian cross.
@@ -419,6 +422,37 @@ Go.  It also includes runtime support libraries for these languages.")
                      (("struct ucontext") "ucontext_t")))
                  '("aarch64" "alpha" "bfin" "i386" "m68k"
                    "pa" "sh" "tilepro" "xtensa")))))
+    (arguments
+     ;; Since 'arguments' is a function of the package's version, define
+     ;; 'parent' such that the 'arguments' thunk gets to see the right
+     ;; version.
+     (let ((parent (package
+                     (inherit gcc-4.7)
+                     (version (package-version this-package)))))
+       (if (%current-target-system)
+           (package-arguments parent)
+           ;; For native builds of some GCC versions the C++ include path needs to
+           ;; be adjusted so it does not interfere with GCC's own build processes.
+           (substitute-keyword-arguments (package-arguments parent)
+             ((#:modules modules %gnu-build-system-modules)
+              `((srfi srfi-1)
+                ,@modules))
+             ((#:phases phases)
+              `(modify-phases ,phases
+                 (add-after 'set-paths 'adjust-CPLUS_INCLUDE_PATH
+                   (lambda* (#:key inputs #:allow-other-keys)
+                     (let ((libc (assoc-ref inputs "libc"))
+                           (gcc (assoc-ref inputs  "gcc")))
+                       (setenv "CPLUS_INCLUDE_PATH"
+                               (string-join (fold delete
+                                                  (string-split (getenv "CPLUS_INCLUDE_PATH")
+                                                                #\:)
+                                                  (list (string-append libc "/include")
+                                                        (string-append gcc "/include/c++")))
+                                            ":"))
+                       (format #t
+                               "environment variable `CPLUS_INCLUDE_PATH' changed to ~a~%"
+                               (getenv "CPLUS_INCLUDE_PATH")))))))))))
     (supported-systems %supported-systems)
     (inputs
      (modify-inputs (package-inputs gcc-4.7)
@@ -454,38 +488,7 @@ Go.  It also includes runtime support libraries for these languages.")
                    "pa" "sh" "tilepro" "xtensa")))))
     ;; Override inherited texinfo-5 with latest version.
     (native-inputs (list perl ;for manpages
-                         texinfo))
+                         texinfo))))
-    (arguments
-     ;; Since 'arguments' is a function of the package's version, define
-     ;; 'parent' such that the 'arguments' thunk gets to see the right
-     ;; version.
-     (let ((parent (package
-                     (inherit gcc-4.8)
-                     (version (package-version this-package)))))
-       (if (%current-target-system)
-           (package-arguments parent)
-           ;; For native builds of GCC 4.9 and GCC 5, the C++ include path needs
-           ;; to be adjusted so it does not interfere with GCC's own build processes.
-           (substitute-keyword-arguments (package-arguments parent)
-             ((#:modules modules %gnu-build-system-modules)
-              `((srfi srfi-1)
-                ,@modules))
-             ((#:phases phases)
-              `(modify-phases ,phases
-                 (add-after 'set-paths 'adjust-CPLUS_INCLUDE_PATH
-                   (lambda* (#:key inputs #:allow-other-keys)
-                     (let ((libc (assoc-ref inputs "libc"))
-                           (gcc (assoc-ref inputs  "gcc")))
-                       (setenv "CPLUS_INCLUDE_PATH"
-                               (string-join (fold delete
-                                                  (string-split (getenv "CPLUS_INCLUDE_PATH")
-                                                                #\:)
-                                                  (list (string-append libc "/include")
-                                                        (string-append gcc "/include/c++")))
-                                            ":"))
-                       (format #t
-                               "environment variable `CPLUS_INCLUDE_PATH' changed to ~a~%"
-                               (getenv "CPLUS_INCLUDE_PATH")))))))))))))
 
 (define gcc-canadian-cross-objdump-snippet
   ;; Fix 'libcc1/configure' error when cross-compiling GCC.  Without that,
@@ -546,7 +549,7 @@ Go.  It also includes runtime support libraries for these languages.")
                                        "gcc-5.0-libvtv-runpath.patch"))))
 
     ;; GCC 4.9 and 5 has a workaround that is not needed for GCC 6 and later.
-    (arguments (package-arguments gcc-4.8))
+    (arguments (package-arguments gcc-4.7))
 
     (inputs
      `(("isl" ,isl)
@@ -1124,6 +1127,12 @@ as the 'native-search-paths' field."
    (custom-gcc gcc-11 "gdc" '("d")
                %generic-search-paths)))
 
+;;; Alias tracking the latest GDC version.
+(define-public gdc
+  (hidden-package
+   (custom-gcc gcc "gdc" '("d")
+               %generic-search-paths)))
+
 (define-public (make-libgccjit gcc)
   (package
     (inherit gcc)

gnu/packages/gdb.scm

@@ -145,25 +145,25 @@ written in C, C++, Ada, Objective-C, Pascal and more.")
     (properties `((hidden? . #t)))
     (license gpl3+)))
 
-(define-public gdb-12
+(define-public gdb-14
   (package
     (inherit gdb/pinned)
-    (version "12.1")
+    (version "14.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnu/gdb/gdb-"
                                   version ".tar.xz"))
               (sha256
                (base32
-                "1vczsqcbh5y0gx7qrclpna0qzx26sk7lra6y8qzxam1biyzr65qf"))))
+                "106v7rj72km56mb2ssjsyjfix3yn4f3wqr7lpzy52d0lfq9gavfn"))))
     (properties '())))
 
 (define-public gdb
   ;; The "default" version.
-  gdb-12)
+  gdb-14)
 
 (define-public gdb-multiarch
-  (package/inherit gdb-12
+  (package/inherit gdb-14
     (name "gdb-multiarch")
     (arguments
      `(#:configure-flags
@@ -172,17 +172,17 @@ written in C, C++, Ada, Objective-C, Pascal and more.")
              "--enable-interwork"
              "--enable-languages=c,c++"
              "--disable-nls")
-       ,@(package-arguments gdb-12)))
+       ,@(package-arguments gdb-14)))
     (synopsis "The GNU debugger (with all architectures enabled)")))
 
 (define-public gdb-minimal
-  (package/inherit gdb-12
+  (package/inherit gdb-14
     (name "gdb-minimal")
     (inputs (fold alist-delete (package-inputs gdb)
                   '("libxml2" "ncurses" "python-wrapper" "source-highlight")))))
 
 (define-public avr-gdb
-  (package/inherit gdb-12
+  (package/inherit gdb-14
     (name "avr-gdb")
     (arguments
      `(#:configure-flags
@@ -191,7 +191,7 @@ written in C, C++, Ada, Objective-C, Pascal and more.")
              "--enable-languages=c,c++"
              "--with-system-readline"
              "--enable-source-highlight")
-       ,@(package-arguments gdb-12)))
+       ,@(package-arguments gdb-14)))
     (synopsis "The GNU Debugger for AVR")
     (description
      "GDB is the GNU debugger.  With it, you can monitor what a program is

gnu/packages/geo.scm

@@ -13,11 +13,12 @@
 ;;; Copyright © 2019, 2020 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2020, 2022 Marius Bakke <marius@gnu.org>
 ;;; Copyright © 2020 Christopher Baines <mail@cbaines.net>
-;;; Copyright © 2020, 2021, 2022, 2023 Felix Gruber <felgru@posteo.net>
+;;; Copyright © 2020–2024 Felix Gruber <felgru@posteo.net>
-;;; Copyright © 2021, 2023 Sharlatan Hellseher <sharlatanus@gmail.com>
+;;; Copyright © 2021, 2023, 2024 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;; Copyright © 2021, 2023, 2024 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2021 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2021, 2022 Nikolay Korotkiy <sikmir@disroot.org>
+;;; Copyright © 2022 Patrick Noll <patrick@patricknoll.com>
 ;;; Copyright © 2022 Roman Scherer <roman.scherer@burningswell.com>
 ;;; Copyright © 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2022 Denis 'GNUtoo' Carikli <GNUtoo@cyberdimension.org>
@@ -61,6 +62,7 @@
   #:use-module (gnu packages audio)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages backup)
+  #:use-module (gnu packages base)
   #:use-module (gnu packages bash)
   #:use-module (gnu packages bison)
   #:use-module (gnu packages boost)
@@ -432,7 +434,7 @@ OpenStreetMap written in C using eXpat, Cairo and GLib.")
 (define-public geos
   (package
     (name "geos")
-    (version "3.11.2")
+    (version "3.12.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://download.osgeo.org/geos/geos-"
@@ -440,7 +442,7 @@ OpenStreetMap written in C using eXpat, Cairo and GLib.")
                                   ".tar.bz2"))
               (sha256
                (base32
-                "1k744nwfa5sj4amzsdjxgac83wh6xfb9xi7z5bka7ic1jik7gw5i"))))
+                "00qdk9a4048pzfj2rhzkfw3lvm642znf6kr4x29i3d94494pxsnn"))))
     (build-system cmake-build-system)
     (arguments `(#:phases
                  (modify-phases %standard-phases
@@ -448,7 +450,7 @@ OpenStreetMap written in C using eXpat, Cairo and GLib.")
                     'unpack 'patch-test-shebangs
                     (lambda _
                       (substitute* '("tests/xmltester/testrunner.sh"
-                                     "tests/geostest/testrunner.sh")
+                                     "tests/xmltester/safe_to_xml.sh")
                         (("/bin/sh") (which "sh"))))))))
     (inputs
      (list glib))
@@ -546,7 +548,11 @@ and driving.")
        (method url-fetch)
        (uri (string-append "http://download.osgeo.org/geotiff/libgeotiff/libgeotiff-"
                            version ".tar.gz"))
-       (patches (search-patches "libgeotiff-fix-tests-with-proj-9.1.1.patch"))
+       (patches
+         (search-patches "libgeotiff-fix-tests-with-proj-9.1.1.patch"
+                         "libgeotiff-fix-tests-with-proj-9.3.0.patch"
+                         "libgeotiff-fix-tests-with-proj-9.3.1.patch"
+                         "libgeotiff-fix-tests-on-i386.patch"))
        (sha256
         (base32 "1mjmgv48x51ppax5dnb6lq7z600czxll53bx6jbzqwd4m93i7aq5"))
        (modules '((guix build utils)))
@@ -738,7 +744,7 @@ fully fledged Spatial SQL capabilities.")
 (define-public proj
   (package
     (name "proj")
-    (version "9.2.0")
+    (version "9.3.1")
     (source
      (origin
        (method url-fetch)
@@ -746,7 +752,7 @@ fully fledged Spatial SQL capabilities.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "03nm1sgvh237my7ss6kayn6887cbnayvjxrrxsrfcakkmbsida6y"))))
+         "1g0hkpiablvhsmw0kn5frwgdir3q7avc45p6lc1zhhhzkv5ikydh"))))
     (build-system cmake-build-system)
     (native-inputs (list googletest pkg-config))
     (propagated-inputs (list curl libtiff sqlite)) ;required by proj.pc
@@ -842,31 +848,36 @@ projections.")
 (define-public python-pyproj
   (package
     (name "python-pyproj")
-    (version "3.5.0")
+    (version "3.6.1")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "pyproj" version))
         (sha256
           (base32
-            "1xhvr0n5gb7v6x0wd7cqmc0zrky2fag7bq2shx6l2qqq3icx2ncq"))))
+            "1gq1spm5zdq9k8kl9cb31b9m08ybyrdggfw3sjrqyz9b9iq7raj4"))))
     (build-system python-build-system)
     (arguments
-     `(#:phases
+     (list
-       (modify-phases %standard-phases
+      #:phases
+      #~(modify-phases %standard-phases
           (add-after 'unpack 'set-proj-path
-           (lambda* (#:key inputs #:allow-other-keys)
+            (lambda* (#:key #:allow-other-keys)
-             (let ((proj (assoc-ref inputs "proj")))
+              (let ((proj #$(this-package-input "proj")))
                 (setenv "PROJ_DIR" proj)
                 (substitute* "pyproj/datadir.py"
                   (("(internal_datadir = ).*$" all var)
-                  (string-append var "Path(\"" proj "/share/proj\")\n")))))))))
+                   (string-append var "Path(\"" proj
+                                  "/share/proj\")\n")))))))))
     (inputs
       (list proj))
     (propagated-inputs
       (list python-certifi))
     (native-inputs
-      (list python-cython python-numpy python-pandas python-pytest
+      (list python-cython
+            python-numpy
+            python-pandas
+            python-pytest
             python-xarray))
     (home-page "https://github.com/pyproj4/pyproj")
     (synopsis
@@ -974,29 +985,83 @@ enables you to easily do operations in Python that would otherwise
 require a spatial database such as PostGIS.")
     (license license:bsd-3)))
 
+(define-public python-ogr2osm
+  (package
+    (name "python-ogr2osm")
+    (version "1.2.0")
+    (source
+     (origin
+       (method git-fetch) ; no tests data in PyPi package
+       (uri
+        (git-reference
+         (url "https://github.com/roelderickx/ogr2osm/")
+         (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0hwqnx3cdqxmniydpj1v31kglq1xjsx41d8p10c9j4hg8kb43j80"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; There are tests in git checkout but non of the examples taken from
+      ;; GitHub Actions worked for me. Disabling them to be checked later
+      ;; <https://github.com/roelderickx/ogr2osm/blob/main/.github/workflows/test.yml>.
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                ;; TODO: Fix provided tests.
+                ;; (invoke "cram" "test/basic_usage.t")
+                ;; (invoke "cram" "test/osm_output.t")
+                ;; (invoke "cram" "test/pbf_output.t")
+
+                ;; Run simple tests to ensure that the command is working.
+                (invoke "ogr2osm" "--help")
+                (invoke
+                 "ogr2osm" "-f" "test/shapefiles/basic_geometries.kml")))))))
+    (inputs
+     (list gdal))
+    (native-inputs
+     (list coreutils
+           diffutils
+           libxml2
+           python-cram
+           which))
+    (propagated-inputs
+     (list python-lxml
+           python-protobuf))
+    (home-page "https://github.com/roelderickx/ogr2osm")
+    (synopsis "Convert ogr-readable files like shapefiles into OSM or PDF formats")
+    (description
+     "@code{ogr2osm} is a tool for converting ogr-readable files into
+@acronym{OSM, OpenStreetMap} format.  It supports reading from OGR files like
+shapefiles or PostgresSQL database and converts data into @code{osm} or
+@code{osm.pbf} formats.  A translation file can be used to manipulate the data
+during conversion.")
+    (license license:expat)))
+
 (define-public python-osmnx
   (package
     (name "python-osmnx")
-    (version "1.1.2")
+    (version "1.8.1")
     (source
      (origin
-       ; Fetch from github as the pypi package is missing the tests dir.
+       ;; Fetch from github as the pypi package is missing the tests dir.
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/gboeing/osmnx")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1n8qjn184p5a2s3j6x6iyc1i7p3l3xnbqqxm6ajwgwv6j5fw1d5a"))))
+        (base32 "0n238n07pp5jw9cg8nqw9qhpkw8plzb5imz1gxbliw2l1idqyjcl"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:test-flags
+      #:test-flags '(list "-k"
-      '(list "-k"
                           (string-append
                            ;; The following tests require network access.
-               "not test_geocode_to_gdf"
+                           "not test_stats"
-               " and not test_stats"
+                           " and not test_geocoder"
                            " and not test_osm_xml"
                            " and not test_elevation"
                            " and not test_routing"
@@ -1005,20 +1070,16 @@ require a spatial database such as PostGIS.")
                            " and not test_api_endpoints"
                            " and not test_graph_save_load"
                            " and not test_graph_from_functions"
-               " and not test_geometries"))))
+                           " and not test_features"))))
-    (propagated-inputs
+    (propagated-inputs (list python-folium
-      (list python-folium
                              python-geopandas
                              python-matplotlib
                              python-networkx
                              python-numpy
                              python-pandas
-            python-pyproj
                              python-requests
-            python-rtree
                              python-shapely))
-    (native-inputs
+    (native-inputs (list python-hatchling python-pytest))
-      (list python-numpy python-pytest))
     (home-page "https://github.com/gboeing/osmnx")
     (synopsis
      "Retrieve, model, analyze, and visualize OpenStreetMap street networks")
@@ -1262,7 +1323,7 @@ utilities for data translation and processing.")
 (define-public python-pyshp
   (package
     (name "python-pyshp")
-    (version "2.1.3")
+    (version "2.3.1")
     (source
      (origin
        (method git-fetch)
@@ -1271,16 +1332,13 @@ utilities for data translation and processing.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0jsraqzq82pw19wvx84x7w5cs8agr44a9b5y0jjw540wim4xa73r"))))
+        (base32 "02pbr091p8v4kfv1p6p2aa4asgm9r74dc12r35lvgmhs9y163z69"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
+     (list
-       (modify-phases %standard-phases
+      #:test-flags
-         (replace 'check
+      ;; This test requires internet access.
-           (lambda* (#:key tests? #:allow-other-keys)
+      '(list "--deselect" "test_shapefile.py::test_reader_url")))
-             (when tests?
-               ;; This is the only test file.
-               (invoke "python" "-m" "pytest" "test_shapefile.py")))))))
     (native-inputs
      (list python-pytest python-pytest-runner))
     (home-page "https://github.com/GeospatialPython/pyshp")
@@ -1619,7 +1677,7 @@ based on the Osmium library.")
 (define-public osm2pgsql
   (package
     (name "osm2pgsql")
-    (version "1.9.2")
+    (version "1.11.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1628,7 +1686,7 @@ based on the Osmium library.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "198qcgl42pb8lk1bn41ncp8hc9gcg9k2p0ny42vak019w5l6jcj7"))
+                "135vqahlcrhwa3b9hfgbiqkzbbsjd4i79fp41cd0rp4zarcpi47p"))
               (modules '((guix build utils)))
               (snippet
                ;; Remove bundled libraries.
@@ -1636,20 +1694,21 @@ based on the Osmium library.")
     (build-system cmake-build-system)
     (arguments
      (list #:tests? #f ;tests fail because we need to setup a database
-           #:configure-flags #~(list "-DUSE_PROJ_LIB=4" ;use API version 4
+           #:configure-flags #~(list "-DUSE_PROJ_LIB=6" ;use API version 6
                                      "-DWITH_LUAJIT=ON"
                                      "-DEXTERNAL_LIBOSMIUM=ON"
                                      "-DEXTERNAL_PROTOZERO=ON"
                                      "-DEXTERNAL_FMT=ON")))
     (inputs (list boost
                   bzip2
+                  cli11
                   expat
                   fmt-8
                   libosmium
                   luajit
                   nlohmann-json
                   postgresql
-                  proj-7
+                  proj
                   protozero
                   zlib))
     (native-inputs (list pandoc python python-argparse-manpage))
@@ -2508,19 +2567,19 @@ track your position right from your laptop.")
         "-DLICENSING_PROVIDER:BOOL=OFF"
         "-DMapper_MANUAL_QTHELP:BOOL=OFF")))
     (inputs
-     `(("clipper" ,clipper)
+     (list clipper
-       ("cups" ,cups)
+           cups
-       ("curl" ,curl)
+           curl
-       ("gdal" ,gdal)
+           gdal
-       ("proj" ,proj)
+           proj
-       ("qtbase" ,qtbase-5)
+           qtbase-5
-       ("qtimageformats" ,qtimageformats-5)
+           qtimageformats-5
-       ("qtlocation" ,qtlocation)
+           qtlocation
-       ("qtsensors" ,qtsensors)
+           qtsensors
-       ("zlib" ,zlib)))
+           zlib))
     (native-inputs
-     `(("doxygen" ,doxygen)
+     (list doxygen
-       ("qttools-5" ,qttools-5)))
+           qttools-5))
     (home-page "https://www.openorienteering.org/apps/mapper/")
     (synopsis "OpenOrienteering Mapper (OOM)")
     (description
@@ -2529,7 +2588,7 @@ orienteering sport.")
     (license license:gpl3+)))
 
 (define-public grass
-  (let* ((version "7.8.7")
+  (let* ((version "7.8.8")
          (majorminor (string-join (list-head (string-split version #\.) 2) ""))
          (grassxx (string-append "grass" majorminor)))
     (package
@@ -2541,7 +2600,7 @@ orienteering sport.")
          (uri (string-append "https://grass.osgeo.org/" grassxx
                              "/source/grass-" version ".tar.gz"))
          (sha256
-          (base32 "0sbz0ba9p963phvd0gmvfqq1fg4ixpipzcjbf20ys86qavjppzsg"))))
+          (base32 "1gpfbppfajc8d6b9alw9fdzgaa83w26kl6fff1395bc9gal215ms"))))
       (build-system gnu-build-system)
       (inputs
        `(("bzip2" ,bzip2)
@@ -2815,6 +2874,7 @@ growing set of geoscientific methods.")
                              "test_core_pointcloudlayerexporter"
                              "test_core_projectstorage"
                              "test_core_coordinatereferencesystem"
+                             "test_core_overlayexpression"
                              "test_gui_queryresultwidget"
                              "test_provider_copcprovider"
                              "test_provider_eptprovider"
@@ -2838,6 +2898,7 @@ growing set of geoscientific methods.")
                              "PyQgsOGRProviderGpkg"
                              "PyQgsProcessExecutablePt1"
                              "PyQgsProcessExecutablePt2"
+                             "PyQgsProjectionSelectionWidgets"
                              "PyQgsProviderConnectionGpkg"
                              "PyQgsProviderConnectionSpatialite"
                              "PyQgsOGRProvider"
@@ -3046,6 +3107,30 @@ path loss.")
      "This is a python implementation of the geodesic routines in GeographicLib.")
     (license license:expat)))
 
+(define-public python-geoip2fast
+  (package
+    (name "python-geoip2fast")
+    (version "1.2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "geoip2fast" version))
+       (sha256
+        (base32 "1cmdjlwjd4pg3qvsb8d4vghqj1im58npxb6dmrd5q90wjga4rfvm"))))
+    (build-system pyproject-build-system)
+    ;; The tests are speed tests or development tests to compare results with
+    ;; a different library.
+    (arguments (list #:tests? #false))
+    (home-page "https://github.com/rabuchaim/geoip2fast")
+    (synopsis
+     "Fast GeoIP2 country/city/asn lookup library")
+    (description
+     "@code{GeoIP2Fast} is a fast @code{GeoIP2} country/city/asn lookup
+library that supports IPv4 and IPv6.  A search takes less than 0.00003
+seconds.  It has its own data file updated twice a week with
+Maxmind-Geolite2-CSV, supports IPv4/IPv6 and is pure Python.")
+    (license license:expat)))
+
 (define-public python-geopy
   (package
     (name "python-geopy")
@@ -3091,15 +3176,8 @@ using third-party geocoders and other data sources.")
               (sha256
                (base32
                 "0inxyj5n4jzgg5xiadqx9sk83gdx5ff989l9s04smdzbd3b8c0c8"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (native-inputs (list python-pytest python-numpy))
-    (arguments
-      (list #:phases
-            #~(modify-phases %standard-phases
-                (replace 'check
-                  (lambda* (#:key tests? inputs #:allow-other-keys)
-                    (when tests?
-                      (invoke "pytest")))))))
     (home-page "https://github.com/mapado/haversine")
     (synopsis "Calculate the distance between 2 points on Earth")
     (description "This package provides functions to calculate the

gnu/packages/gl.scm

@@ -19,6 +19,7 @@
 ;;; Copyright © 2022 Petr Hodina <phodina@protonmail.com>
 ;;; Copyright © 2023 Kaelyn Takata <kaelyn.alexi@protonmail.com>
 ;;; Copyright © 2023, 2024 Zheng Junjie <873216071@qq.com>
+;;; Copyright © 2024 Liliana Marie Prikler <liliana.prikler@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -39,6 +40,7 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages bison)
+  #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages elf)
@@ -1217,3 +1219,84 @@ the glProgramViewportFlip before it was replaced with glProgramViewportInfo.")
      "glmark2 is an OpenGL 2.0 and OpenGL ES 2.0 benchmark based on the
 original glmark benchmark by Ben Smith.")
     (license license:gpl3+)))
+
+(define-public waffle
+  (package
+    (name "waffle")
+    (version "1.8.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                     (url "https://gitlab.freedesktop.org/mesa/waffle")
+                     (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32 "1mrw0arlrpm83cwaz7rnimkkjv3a134rcmi1h512y2g4yjzhnm8r"))
+              (modules '((ice-9 ftw)
+                         (guix build utils)))
+              (snippet #~(with-directory-excursion "third_party"
+                           (let ((keep '("." ".." "meson.build" "threads")))
+                             (for-each (lambda (f)
+                                         (unless (member f keep)
+                                           (delete-file-recursively f)))
+                                       (scandir ".")))))))
+    (build-system meson-build-system)
+    (propagated-inputs (list mesa wayland))
+    (native-inputs (list cmocka pkg-config))
+    (home-page "https://waffle.freedesktop.org/")
+    (synopsis "Choose OpenGL API at runtime")
+    (description "Waffle is a library that allows one to defer selection of an
+ OpenGL API and a window system until runtime.")
+    (license license:bsd-2)))
+
+(define-public piglit
+  (let ((revision "1")
+        (commit "814046fe6942eac660ee4a6cc5fcc54011a49945"))
+    (package
+     (name "piglit")
+     (version (git-version "0.0.0" revision commit))
+     (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://gitlab.freedesktop.org/mesa/piglit")
+                    (commit commit)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32 "1bzaalcxskckfnwprw77sbbmfqi59by2j8imaq8ghnlzhlxv7mk7"))))
+     (build-system cmake-build-system)
+     (arguments
+      (list #:configure-flags #~(list "-DPIGLIT_SSE2=OFF")
+            ;; Tests are not invoked through cmake.  Instead, there are
+            ;; pytest/tox-based tests for the framework, but they require
+            ;; unpackaged plugins.
+            #:tests? #f
+            #:phases
+            #~(modify-phases %standard-phases
+                (add-after 'unpack 'patch-source
+                  (lambda* (#:key inputs #:allow-other-keys)
+                    (substitute* (find-files "framework/" "\\.py$")
+                      (("'wflinfo'")
+                       (string-append "'"
+                                      (search-input-file inputs "/bin/wflinfo")
+                                      "'")))))
+                (add-after 'install 'wrap
+                  (lambda* (#:key outputs #:allow-other-keys)
+                    (wrap-script (string-append (assoc-ref outputs "out")
+                                                "/bin/piglit")
+                      `("GUIX_PYTHONPATH" prefix
+                        (,(getenv "GUIX_PYTHONPATH")))))))))
+     (inputs (list guile-3.0            ; for wrap-script
+                   libxkbcommon
+                   python python-lxml python-mako python-numpy
+                   glslang vulkan-headers vulkan-loader
+                   waffle))
+     (native-inputs (list pkg-config))
+     (home-page "https://piglit.freedesktop.org/")
+     (synopsis "Test OpenGL implementations")
+     (description "Piglit is a collection of automated tests for OpenGL and
+OpenCL implementations.")
+     ;; A mix of licenses for various tests
+     (license (list license:expat
+                    license:bsd-3
+                    license:gpl2+
+                    license:gpl3+)))))

gnu/packages/gnome-xyz.scm

@@ -13,7 +13,7 @@
 ;;; Copyright © 2021, 2022 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net>
 ;;; Copyright © 2021 Songlin Jiang <hollowman@hollowman.ml>
-;;; Copyright © 2021, 2022 Justin Veilleux <terramorpha@cock.li>
+;;; Copyright © 2021, 2022, 2024 Justin Veilleux <terramorpha@cock.li>
 ;;; Copyright © 2021 Attila Lendvai <attila@lendvai.name>
 ;;; Copyright © 2021 Charles Jackson <charles.b.jackson@protonmail.com>
 ;;; Copyright © 2022 Eric Bavier <bavier@posteo.net>
@@ -1016,33 +1016,33 @@ It uses ES6 syntax and claims to be more actively maintained than others.")
 (define-public gnome-shell-extension-paperwm
   (package
     (name "gnome-shell-extension-paperwm")
-    (version "36.0")
+    (version "44.17.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/paperwm/PaperWM")
-                    (commit version)))
+                    (commit (string-append "v" version))))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1ssnabwxrns36c61ppspjkr9i3qifv08pf2jpwl7cjv3pvyn4kly"))
+                "1d91k9qih81wckqf6554kf8grv6q61rkk4g776g0ijpmf35ljdin"))
               (snippet
                '(begin (delete-file "schemas/gschemas.compiled")))))
     (build-system copy-build-system)
     (arguments
-     '(#:install-plan
+     (list
-       '(("." "share/gnome-shell/extensions/paperwm@hedning:matrix.org"
+      #:install-plan
+      #~'(("." "share/gnome-shell/extensions/paperwm@paperwm.github.com"
            #:include-regexp ("\\.js(on)?$" "\\.css$" "\\.ui$" "\\.png$"
-                            "\\.xml$" "\\.compiled$")))
+                             "\\.xml$" "\\.compiled$" "\\.svg$")))
       #:phases
-       (modify-phases %standard-phases
+      #~(modify-phases %standard-phases
           (add-before 'install 'compile-schemas
             (lambda _
               (with-directory-excursion "schemas"
-               (invoke "make"))
+                (invoke "make")))))))
-             #t)))))
     (native-inputs
-     `(("glib:bin" ,glib "bin"))) ; for glib-compile-schemas
+     (list `(,glib "bin"))) ; for glib-compile-schemas
     (home-page "https://github.com/paperwm/PaperWM")
     (synopsis "Tiled scrollable window management for GNOME Shell")
     (description "PaperWM is an experimental GNOME Shell extension providing

gnu/packages/gnome.scm

@@ -8,7 +8,7 @@
 ;;; Copyright © 2015 Mathieu Lirzin <mthl@openmailbox.org>
 ;;; Copyright © 2015, 2017 Andy Wingo <wingo@igalia.com>
 ;;; Copyright © 2015 David Hashe <david.hashe@dhashe.com>
-;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2023 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015-2020, 2023, 2024 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015, 2016, 2017, 2018, 2021 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 David Thompson <davet@gnu.org>
 ;;; Copyright © 2015-2024 Efraim Flashner <efraim@flashner.co.il>
@@ -238,6 +238,7 @@
   #:use-module (guix git-download)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
+  #:use-module (guix platform)
   #:use-module (guix utils)
   #:use-module (guix gexp)
   #:use-module (ice-9 match)
@@ -3397,7 +3398,7 @@ compiles to GTKBuilder XML.")
            python-pycairo
            python-pygobject
            python-lxml
-           webkitgtk
+           webkitgtk-for-gtk3
            webkitgtk))
     (native-inputs
      (list `(,glib "bin")
@@ -3593,12 +3594,12 @@ for dealing with different structured file formats.")
               ;; In lieu of #:make-flags
               (setenv "CC" #$(cc-for-target))
               (setenv "PKG_CONFIG" #$(pkg-config-for-target))
-              (when #$(%current-target-system)
+              #$@(if (%current-target-system)
-                (setenv "RUST_TARGET"
+                     #~((setenv "RUST_TARGET"
-                        (string-replace
+                                #$(platform-rust-target
-                          #$(%current-target-system)
+                                    (lookup-platform-by-target
-                          "-unknown-linux-gnu"
+                                      (%current-target-system)))))
-                          (string-index #$(%current-target-system) #\-))))
+                     #~())
               ;; Something about the build environment resists building
               ;; successfully with the '--locked' flag.
               (substitute* '("Makefile.am" "Makefile.in")
@@ -7911,7 +7912,17 @@ to display dialog boxes from the commandline and shell scripts.")
               ;; let's disable them as well.
               ;; See <https://gitlab.gnome.org/GNOME/mutter/-/issues/2125>
               (substitute* "src/tests/clutter/conform/meson.build"
-                (("'timeline.*',") ""))))
+                (("'timeline.*',") ""))
+
+              ;; On i686-linux this test fails with a dbus error.  This seems
+              ;; to be fine in later versions, so this workaround can probably
+              ;; be removed soon.
+              #$@(if (string=? "i686-linux" (or (%current-target-system)
+                                                (%current-system)))
+                     #~((substitute* "src/tests/wayland-unit-tests.c"
+                          (("g_test_add_func \\(\"/wayland/toplevel/activation\",") "")
+                          (("^                   toplevel_activation\\);") "")))
+                     #~())))
           (replace 'check
             (lambda* (#:key tests? test-options parallel-tests?
                       #:allow-other-keys)

gnu/packages/gnucash.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015, 2016, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 Eric Bavier <bavier@member.fsf.org>
-;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2024 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Chris Marusich <cmmarusich@gmail.com>
 ;;; Copyright © 2017, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019, 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
@@ -66,14 +66,14 @@
   ;; directory.
   (package
     (name "gnucash")
-    (version "5.3")
+    (version "5.5")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "mirror://sourceforge/gnucash/gnucash%20%28stable%29/"
                            version "/gnucash-" version ".tar.bz2"))
        (sha256
-        (base32 "0npilq0spalpg1ma956j7vlbn0yc5f0z5imy4kbyksl5ql4cnn0l"))))
+        (base32 "0fzds1yq298c3rvi07if1bfxff904jbzmsb27wr0ddwjp1xzdnml"))))
     (outputs '("out" "doc" "debug" "python"))
     (build-system cmake-build-system)
     (arguments
@@ -214,13 +214,11 @@ installed as well as Yelp, the Gnome help browser.")
       (source
        (origin
          (method url-fetch)
-         ;; The filename for version 5.3 is gnucash-docs-5.2.tar.gz, not
-         ;; gnucash-docs-5.3.tar.gz.
          (uri (string-append
                "mirror://sourceforge/gnucash/gnucash%20%28stable%29/"
-               version "/gnucash-docs-5.2" revision ".tar.gz"))
+               version "/gnucash-docs-" version revision ".tar.gz"))
          (sha256
-          (base32 "16xlxwdgc0w4cg9kxg4w2f1y974cb16wq2c9icq5qrh3nj0nbsxr"))))
+          (base32 "1ay8jzxrsb9qmbx0v12kqdjk6l3j7cafgxswa92yynihv5ahymlk"))))
       (build-system cmake-build-system)
       ;; These are native-inputs because they are only required for building the
       ;; documentation.

gnu/packages/gnupg.scm

@@ -71,6 +71,7 @@
   #:use-module (gnu packages swig)
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages tls)
+  #:use-module (gnu packages tor)
   #:use-module (gnu packages web)
   #:use-module (gnu packages xorg)
   #:use-module (gnu packages xdisorg)
@@ -345,11 +346,33 @@ compatible to GNU Pth.")
            zlib))
     (arguments
      (list
-      #:configure-flags #~'(;; Otherwise, the test suite looks for the `gpg`
+      #:configure-flags
+      ;; Always use quasiquote on the next core-updates cycle.
+      #~(#$(if (%current-target-system)
+               #~quasiquote
+               #~quote)
+         (#$@(if (%current-target-system)
+                 #~(,(string-append
+                      "--with-libgpg-error-prefix="
+                      #$(this-package-input "libgpg-error"))
+                    ,(string-append
+                      "--with-libgcrypt-prefix="
+                      #$(this-package-input "libgcrypt"))
+                    ,(string-append
+                      "--with-libassuan-prefix="
+                      #$(this-package-input "libassuan"))
+                    ,(string-append
+                      "--with-ksba-prefix="
+                      #$(this-package-input "libksba"))
+                    ,(string-append
+                      "--with-npth-prefix="
+                      #$(this-package-input "npth")))
+                 #~())
+          ;; Otherwise, the test suite looks for the `gpg`
           ;; executable in its installation directory in
           ;; /gnu/store before it has been installed.
           "--enable-gnupg-builddir-envvar"
-                            "--enable-all-tests")
+          "--enable-all-tests"))
       #:phases
       #~(modify-phases %standard-phases
           (add-before 'configure 'patch-paths
@@ -1129,7 +1152,7 @@ files, to verify signatures, and to manage the private and public keys.")
            perl-try-tiny
            perl-type-tiny
            perl-types-path-tiny
-           (@ (gnu packages tor) torsocks))) ;avoid dependency loop
+           torsocks))
     (native-inputs
      (list perl-file-which
            perl-gnupg-interface