gnu: python-ldaptor: Fix build on python@3.12.

* gnu/packages/python-web.scm (python-ldaptor)[arguments]<#:phases>:
Add phase python-3.12-patch.

Change-Id: I10157ab41a5a5f78c4166a5c0a76ab9028ffd54d
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

CODEOWNERS

@@ -179,6 +179,7 @@ guix/scripts/import/elpa\.scm                      @guix/emacs
 tests/import/elpa\.scm                             @guix/emacs
 
 gnu/packages/bootloaders\.scm                      @guix/embedded
+gnu/packages/coreboot\.scm                         @guix/embedded
 gnu/packages/firmware\.scm                         @guix/embedded
 
 gnu/packages/emulators\.scm                        @guix/games
@@ -318,6 +319,7 @@ gnu/packages/tor-browsers\.scm                     @guix/mozilla
 
 gnu/packages/ocaml\.scm                            @guix/ocaml
 gnu/packages/coq\.scm                              @guix/ocaml
+gnu/packages/rocq\.scm                             @guix/ocaml
 guix/build/ocaml-build-system\.scm                 @guix/ocaml
 guix/build/dune-build-system\.scm                  @guix/ocaml
 guix/build-system/ocaml\.scm                       @guix/ocaml
@@ -334,6 +336,7 @@ guix/build-system/rakudo\.scm                      @guix/perl
 guix/import/cpan\.scm                              @guix/perl
 guix/scripts/import/cpan\.scm                      @guix/perl
 
+gnu/packages/aux-files/python/.*\.py$              @guix/python
 gnu/packages/django\.scm                           @guix/python
 gnu/packages/jupyter\.scm                          @guix/python
 gnu/packages/python(-.+|)\.scm$                    @guix/python

Makefile.am

@@ -486,6 +486,7 @@ AUX_FILES =						\
   gnu/packages/aux-files/linux-libre/5.10-x86_64.conf	\
   gnu/packages/aux-files/ovmf/51-edk2-ovmf-2m-raw-x64-nosb.json	\
   gnu/packages/aux-files/pack-audit.c			\
+  gnu/packages/aux-files/python/pytest_guix.py		\
   gnu/packages/aux-files/python/sanity-check.py		\
   gnu/packages/aux-files/python/sitecustomize.py	\
   gnu/packages/aux-files/renpy/renpy.in	\

doc/contributing.texi

@@ -1667,6 +1667,9 @@ can be turned into a version string via @code{git-version}, for example
 @code{rust-pipewire-0.8.0.fd3d8f7} and @code{rust-pubgrub-0.3.0.b70cf70}.
 @end table
 
+When contributing Rust packages, we should have all modifications to these
+two modules, in the same commit as the package we are contributing.
+
 To avoid merge conflicts with changes from multiple branches, these two modules
 are maintained by the Rust team (@pxref{Teams}).
 
@@ -1696,6 +1699,68 @@ tree.
 @xref{Packaging Rust Crates,,, guix-cookbook, GNU Guix Cookbook}, for
 packaging workflow.
 
+@subsubsection Commit messages
+
+The commit message must have a general brief mention to entry changes
+in @code{(gnu packages rust-crates)}. For changes in @code{(gnu packages
+rust-sources)}, the commit message must explicitly mention all changes to the
+packages.
+
+Here are some examples for different situations:
+
+@itemize
+
+@item
+Adding a new Rust package:
+
+@example
+gnu: Add catppuccin-whiskers.
+
+* gnu/packages/rust-apps.scm (catppuccin-whiskers): New variable.
+* gnu/packages/rust-crates.scm (lookup-cargo-inputs)
+[catppuccin-whiskers]: New entry.
+@end example
+
+@item
+Updating a simple package:
+
+@example
+gnu: watchexec: Update to 2.3.2.
+
+* gnu/packages/rust-apps.scm (watchexec): Update to 2.3.2.
+* gnu/packages/rust-crates.scm (lookup-cargo-inputs)[watchexec]:
+Update entry.
+@end example
+
+@item
+Updating a package with sources:
+
+@example
+gnu: typst: Update to 0.14.0.
+
+* gnu/packages/rust-apps.scm (typst): Update to 0.14.0.
+[arguments]<#:rust>: Use rust-1.88.
+* gnu/packages/rust-crates.scm (lookup-cargo-inputs)[typst]: Update
+entry.
+[rust-syntect-5]: Rename to rust-syntect-5.2.
+[rust-syntect-5.3]: New entry.
+* gnu/packages/rust-sources.scm (rust-hypher-0.1): Update to 0.1.6.
+(rust-syntect-5): Rename to rust-syntect-5.2.
+[inputs]: Rename cargo-inputs rust-syntect-5 to rust-syntect-5.2.
+(rust-syntect-5.3): New variable.
+@end example
+
+@end itemize
+
+@subsubsection Resolving merge conflicts in Pull Requests
+
+For Rust crates, the recommended way to solve merge conflicts is to drop all
+changes to @code{gnu/packages/rust-crates.scm}, rebase onto the desired branch
+and run the lockfile importer again, manually adding back all relevant snippets
+(if any).
+
+@xref{Common Workflow for Resolving Merge Conflicts on Existing Pull Requests,,, guix-cookbook, GNU Guix Cookbook} for
+a suggested workflow on resolving merge conflicts.
 
 @node Elm Packages
 @subsection Elm Packages
@@ -2650,6 +2715,7 @@ applications settings page}, granting read/write access to the
 
 @cindex decision making
 @cindex consensus seeking
+Every contribution to the project involves a form of decision making.
 It is expected from all contributors, and even more so from committers,
 to help build consensus and make decisions based on consensus.  By using
 consensus, we are committed to finding solutions that everyone can live
@@ -2664,6 +2730,26 @@ 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}.
 
+Day-to-day decision making, for instance discussions about pull requests
+(@pxref{Reviewing the Work of Others}), happens informally among
+interested parties such as contributors and members of the relevant
+teams (@pxref{Teams}).
+
+@cindex GCD, Guix Consensus Documents
+@cindex Guix Consensus Documents (GCD)
+Decisions that are expected to have an impact on most contributors
+and/or on the broader user community---e.g., changes to project-wide
+policies, to core functionality, and so on---are made following the
+@acronym{GCD, Guix Consensus Document} process.  The process provides a
+framework to formalize proposals and draw attention to them, to leave
+time for interested parties to discuss them, and to collectively accept
+or withdraw them based on input from participating team members.  It is
+defined in
+@uref{https://consensus.guix.gnu.org/gcd/001-gcd-process.html,
+GCD@tie{}001}.  Past GCDs can be seen at
+@uref{https://consensus.guix.gnu.org}, and discussions take place at
+@uref{https://codeberg.org/guix/guix-consensus-documents}.
+
 @node Commit Access
 @section Commit Access
 

doc/guix-cookbook.texi

@@ -146,6 +146,8 @@ Packaging Rust Crates
 * Common Workflow for Rust Packaging::
 * Cargo Workspaces and Development Snapshots::
 * Using Rust Libraries in Other Build Systems::
+* Common Workflow for Updating Existing Rust Packages::
+* Common Workflow for Resolving Merge Conflicts on Existing Pull Requests::
 
 System Configuration
 
@@ -1647,6 +1649,8 @@ $ guix shell rust rust:cargo cargo-audit cargo-license
 * Common Workflow for Rust Packaging::
 * Cargo Workspaces and Development Snapshots::
 * Using Rust Libraries in Other Build Systems::
+* Common Workflow for Updating Existing Rust Packages::
+* Common Workflow for Resolving Merge Conflicts on Existing Pull Requests::
 @end menu
 
 @node Common Workflow for Rust Packaging
@@ -1705,6 +1709,15 @@ $ cargo audit
 $ cargo license
 @end example
 
+@quotation Note
+Before running @command{cargo generate-lockfile}, make sure you have checked
+out the correct tag for the version you are packaging. This ensures that
+@code{Cargo.toml} matches the file used in the packages's @code{source} field.
+To make sure, you can obtain the exact source with @command{./pre-inst-env guix
+build --source <package>} and only then run @command{cargo generate-lockfile} on
+that source tree.
+@end quotation
+
 @command{cargo generate-lockfile} updates dependencies to compatible versions.
 Applying it to all Rust applications helps reduce a great number of Rust
 libraries we need to check later.  Although sometimes libraries may fail to
@@ -1987,6 +2000,316 @@ method, one of the most popular choices for Traditional Chinese users.")
     (license license:lgpl2.1+)))
 @end lisp
 
+@node Common Workflow for Updating Existing Rust Packages
+@subsubsection Common Workflow for Updating Existing Rust Packages
+
+For this example, we'll update @code{niri}. The package definition looks like
+this initially:
+
+@lisp
+(define-public niri
+  (package
+   (name "niri")
+   (version "25.08")
+   (source (origin
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/YaLTeR/niri")
+                   (commit (string-append "v" version))))
+             (file-name (git-file-name name version))
+             (sha256
+              (base32
+               "09nsxd211mly8r1ys2lq6ia4jxgb980h1axrbgw748r0knfbbj7n"))))
+   (build-system cargo-build-system)
+...
+@end lisp
+
+We start by running the usual @command{guix refresh -u niri}.
+
+The @command{-u} flag will update in place the version and hash for the
+@code{niri} package.
+
+The package definition will then look like this:
+
+@lisp
+(define-public niri
+  (package
+   (name "niri")
+   (version "25.11")
+   (source (origin
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/YaLTeR/niri")
+                   (commit (string-append "v" version))))
+             (file-name (git-file-name name version))
+             (sha256
+              (base32
+               "0752qm245wc2gak0jhp0fnr0rdj3z54m2h97k3cxbjym9pcn658n"))))
+   (build-system cargo-build-system)
+...
+@end lisp
+
+This means the source field was updated successfully, thus we can now proceed to
+get the updated source with @command{guix build --source niri} as follows:
+
+@example shell
+$ cp -r $(./pre-inst-env guix build --source niri) /tmp
+$ cd /tmp/<hash>-niri-25.11-checkout/
+@end example
+
+@quotation Note
+In this specific example, the source is a git checkout, thus a directory. If the
+package source is a compressed archive, you would at this point extract it to a
+directory to proceed.
+@end quotation
+
+Now, given that we have access to the @code{Cargo.toml} file, we can now run
+the following inside the checkout:
+
+@example shell
+$ guix shell rust rust:cargo -- cargo generate-lockfile
+$ guix shell rust rust:cargo -- cargo audit
+$ guix shell rust rust:cargo -- cargo license
+@end example
+
+@quotation Note
+Sometimes the package will require a more up-to-date version of rust, that is
+not yet the default rust on guix. For these cases you can use:
+@example shell
+$ guix shell -e "(@ (gnu packages rust) rust-1.90)" \
+     -e '`(,(@ (gnu packages rust) rust-1.90) "cargo")'
+@end example
+@end quotation
+
+The first command will ensure that all cargo dependencies are up to date
+and semver compatible, while also providing some other benefits, as further
+explained in @ref{Common Workflow for Rust Packaging}.
+
+The following command will warn if there are any known vulnerabilities in the
+crates being imported. The last one will output the license information of all
+the dependent crates.
+
+If everything looks good, we can now replace the contents of the @code{niri}
+indentifier, located inside the @code{lookup-cargo-inputs} variable on the
+bottom of the @file{gnu/packages/rust-crates.scm} module, with the newer updated
+crates by running the importer on the lockfile as follows:
+
+@example shell
+$ guix import -i /path/to/gnu/packages/rust-crates.scm \
+     crate -f Cargo.lock niri
+@end example
+
+@quotation Note
+For the purpose of contributing a package to Guix (@pxref{Contributing,,,
+guix, GNU Guix Reference Manual}), there is no need to cleanup the leftover
+crates as a result of the package update.  This is tasked to the rust-team
+(@pxref{Teams,,, guix, GNU Guix Reference Manual}) to periodically run a
+convenient script in @code{etc/teams/rust} to cleanup unused crates from
+@file{gnu/packages/rust-crates.scm}.
+@end quotation
+
+We then need to check whether the importer has placed some TODOs for us,
+inside @file{gnu/packages/rust-crates.scm} (you can use @command{git diff --
+gnu/packages/rust-crates.scm} for this purpose).
+
+There are a few types of TODO messages that you might encounter during this
+step, each type requiring you to perform a different action.
+
+The first one we encounter in our example is:
+
+@lisp
+(define rust-libdisplay-info-sys-0.3.0
+  ;; TODO REVIEW: Check bundled sources.
+  (crate-source "libdisplay-info-sys" "0.3.0"
+                "07xmkc2aqcdn6d58321y87rd3gzdr4nx3ncm1mmrr7w1p1ahsn96"))
+@end lisp
+
+This specific TODO message tells us that there is a high probability of
+encountering bundled sources within a crate definition generated by the
+importer.
+
+We then check if there are any bundled sources within the
+@code{rust-libdisplay-info-sys-0.3.0} crate. Since there are none (in our
+example), we can simply remove the TODO line, and continue to the next TODO.
+
+If there were any bundled sources inside the crate, we would have to patch
+it with a snippet, in order to unbundle it. You can see some examples on
+how to unbundle inside @file{gnu/packages/rust-crates.scm} (search for the
+@code{#:snippet} keyword).
+
+@quotation Note
+If the unbundle is considered too difficult to be executed (e.g. the effort
+needed to unbundle is unreasonable), the @code{TODO REVIEW} line should be
+converted to a regular TODO comment explicitly stating the unbundle was not done
+(e.g. @code{TODO: Unbundle rust-libdisplay-info-sys.}).
+@end quotation
+
+Continuing, another TODO message we encounter in this example is the following:
+
+@lisp
+(define rust-smithay-0.7.0.d743e1a
+  ;; TODO REVIEW: Define standalone package if this is a workspace.
+  (origin
+    (method git-fetch)
+    (uri (git-reference (url "https://github.com/Smithay/smithay.git")
+                        (commit "d743e1a317fa0f01d1c4cadd96d277a1ec7b59d9")))
+    (file-name (git-file-name "rust-smithay" "0.7.0.d743e1a"))
+    (sha256 (base32 "11327mhxxf844bs0v5bw1g9bzjssnzhidsissywy6kwng16x727v"))))
+@end lisp
+
+This specific TODO message tells us that there is a high probability of the
+@code{rust-smithay-0.7.0.d743e1a} crate being a workspace.
+
+After verifying that it is indeed a workspace, we now need to make it an
+actual package in @file{gnu/packages/rust-sources.scm}, referencing it in the
+crate-source definition (see @ref{Common Workflow for Rust Packaging} for more
+details).
+
+@quotation Note
+You can verify if a crate is a workspace by cloning the crate repository (in
+this case @code{https://github.com/Smithay/smithay.git}), checking out the
+specific revision (in this case @command{git checkout d743e1a}), and looking
+for @code{[workspace]} in its main @file{Cargo.toml} file. If it does not have a
+TOML @code{[workspace]} section, then it is not a workspace.
+@end quotation
+
+After defining the separate source package for the workspace in
+@file{gnu/packages/rust-sources.scm} (see @ref{Common Workflow for Rust
+Packaging} for more details on how to do this), the crate definition for
+@code{rust-smithay-0.7.0.d743e1a} would then become the following (notice we
+also remove the TODO line):
+
+@lisp
+(define rust-smithay-0.7.0.d743e1a package:rust-smithay-0.7.0.d743e1a)
+@end lisp
+
+If @code{rust-smithay-0.7.0.d743e1a} was not a workspace, we would simply remove
+the TODO line and move on.
+
+We then try to build the package with @command{guix build niri}, and make sure
+whether it builds successfully, which it does.
+
+As a good practice, we can further check the output of the
+@code{check-for-pregenerated-files} phase to ensure there are no extraneous
+pregenerated files inside the crates. If there are any, it is important to
+snippet them out, like these:
+
+@lisp
+(define rust-winapi-x86-64-pc-windows-gnu-0.4.0
+  (crate-source "winapi-x86_64-pc-windows-gnu" "0.4.0"
+                "0gqq64czqb64kskjryj8isp62m2sgvx25yyj3kpc2myh85w24bki"
+                #:snippet '(delete-file-recursively "lib")))
+
+(define rust-flate2-1.1.4
+  (crate-source "flate2" "1.1.4"
+                "1a8a3pk2r2dxays4ikc47ygydhpd1dcxlgqdi3r9kiiq9rb4wnnw"
+                #:snippet '(for-each delete-file-recursively '("examples" "tests"))))
+
+(define rust-flo-curves-0.3.1
+  (crate-source "flo_curves" "0.3.1"
+                "16x293dp8825jh465kgms4yyvl4960j26gh37h3skflq9zxpy8hw"
+                #:snippet '(for-each delete-file '("logo-small.png" "logo.png"))))
+
+(define rust-interception-sys-0.1.3
+  (crate-source "interception-sys" "0.1.3"
+                "1lgwbml7gzq5a5rriy708w68gx6yiw9cdg7xy2c5vsrrck7pbs5b"
+                #:snippet '(for-each delete-file (find-files "." "\\.(dll|lib)$"))))
+@end lisp
+
+@node Common Workflow for Resolving Merge Conflicts on Existing Pull Requests
+@subsubsection Common Workflow for Resolving Merge Conflicts on Existing Pull Requests
+
+Whenever a Rust package change is merged into our target branch from a different
+Pull Request, we often encounter many merge conflicts in @code{(gnu packages
+rust-crates)} when rebasing the Pull Request on top of the target branch. Since
+we should avoid modifying the rust-crates file manually (e.g. using the git
+interface to solve merge conflicts), it is recommended (and often much faster)
+to drop all changes to @code{(gnu packages rust-crates)} and run the lockfile
+importer once again, manually adding back all the manual changes.
+
+This workflow describes one of many ways to do the described procedure.
+
+In this example we'll update the @code{codeberg-cli} package, which has produced
+some merge conflicts in @file{gnu/packages/rust-crates.scm} when we tried a git
+pull rebase.
+
+Before starting, make sure we're not in a rebase environment, by aborting the
+rebase we tried previously (the one which created the merge conflicts by git
+pulling):
+
+@example
+$ git rebase --abort
+@end example
+
+@cindex git rebase --interactive
+@cindex interactive rebase
+To begin, we interactively rebase our PR branch by marking as
+@code{edit} the commit we want to edit, which is the one containing the
+@file{gnu/packages/rust-crates.scm} changes:
+
+@example
+# Change 1 to the number of relevant commits
+$ git rebase -i HEAD~1
+@end example
+
+In our example, we would mark the @code{codeberg-cli} commit like so:
+
+@example
+edit 6ef4f1ad043 # gnu: codeberg-cli: Update to 0.5.4.
+@end example
+
+After that, we'll be in rebase mode, where we can restore the changes made to
+@file{gnu/packages/rust-crates.scm}:
+
+@quotation Note
+Notice that we will lose all manual changes we have previously made to
+@file{gnu/packages/rust-crates.scm} (e.g. snippets, deleting TODO comments,
+if there were any). We'll need to manually add them back after we run the guix
+lockfile importer once again, so make sure you have them saved somewhere, for
+example in your PR link under the @code{Files changed} tab.
+@end quotation
+
+@example
+$ git restore --source=HEAD~ gnu/packages/rust-crates.scm
+@end example
+
+Having restored the file, we can stage the changes, commit, finish the rebase
+and pull rebase from the target branch:
+
+@example
+$ git add gnu/packages/rust-crates.scm
+$ git commit --amend --no-edit
+$ git rebase --continue
+$ git pull <remote> <target branch>
+@end example
+
+We then proceed to run the guix lockfile importer:
+
+@quotation Note
+Remember to checkout the correct tag you're packaging in the package repository
+checkout. Don't forget to run @code{cargo generate-lockfile} before running
+the lockfile importer, see @ref{Common Workflow for Rust Packaging} for more
+detailed steps on what to do before running the guix lockfile importer.
+@end quotation
+
+@example
+$ guix import --insert=gnu/packages/rust-crates.scm \
+      crate --lockfile=/path/to/Cargo.lock codeberg-cli
+@end example
+
+Now is the time we manually add back the snippets and remove the relevant TODOs
+we have already checked (if there are any).
+
+After running the lockfile importer and checking if there are any changes to
+manually add back, we can finally:
+
+@example
+$ git add gnu/packages/rust-crates.scm
+# Our target commit is the last one:
+$ git commit --amend --no-edit
+@end example
+
+We now have a non-conflicting tree, from which we can now update our PR with.
 
 @c *********************************************************************
 @node System Configuration

doc/guix.texi

@@ -8843,12 +8843,12 @@ dependencies than the original package.  For example, the default
 optional dependency, you can define a variant that removes that
 dependency like so:
 
+@findex package/inherit
 @lisp
 (use-modules (gnu packages gdb))   ;for 'gdb'
 
 (define gdb-sans-guile
-  (package
-    (inherit gdb)
+  (package/inherit gdb
     (inputs (modify-inputs inputs
               (delete "guile")))))
 @end lisp
@@ -8856,6 +8856,23 @@ dependency like so:
 In the body of the @code{inputs} field above, @code{inputs} is bound to
 the inherited value.  Thus, the @code{modify-inputs} form above removes
 the @code{"guile"} package from the @code{inputs} field of @code{gdb}.
+
+@quotation Note
+The example above uses @code{(package/inherit gdb @dots{})} instead of
+the usual @code{(package (inherit gdb) @dots{})}.  While the latter
+would work, @code{package/inherit} does extra work: if @code{gdb} has a
+@code{replacement} field (@pxref{Security Updates}),
+@code{package/inherit} propagates the @code{inputs} changes of this
+variant to the replacement.
+
+In other words, @code{package/inherit} ensures the variant gets a
+consistent @code{replacement} when the original package has one.  Thus,
+one should generally use @code{package/inherit} when creating a variant
+for the same version, but not when targeting a different version, as in
+the @code{hello} example we saw earlier, where the replacement may be
+incorrect.
+@end quotation
+
 The @code{modify-inputs} macro is a helper that can prove useful anytime
 you want to remove, add, or replace package inputs.
 
@@ -15534,7 +15551,7 @@ gnu/packages/qt.scm:452:13: qtbase would be upgraded from 5.15.8 to 5.15.10
 @end example
 
 @cindex partial version specification, guix refresh
-A per-package equivalent to --target-version is made available by
+A per-package equivalent to @option{--target-version} is made available by
 prefixing the version specification with the @samp{~} (tilde) character.
 For example:
 
@@ -16095,7 +16112,7 @@ it unchanged.
 @item git-source
 If the @code{home-page} is a Git repository (as per
 @code{git-repository-url?}), and the actual Git repository is tagged
-with @code{version} or @code{(string-append ``v'' version)}, change the
+with a version string, possibly prefixed by ``v'', change the
 package origin to the @code{git-fetch} method
 (@pxref{origin Reference}).  Consider this example:
 
@@ -16124,14 +16141,16 @@ its @code{source} field like to:
     (inherit guile-json-3)
     (name "guile-json")
     (version "4.7.3")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference (url
-                                   "https://github.com/aconchillo/guile-json")
-                                  (commit version)))
-              (file-name (git-file-name name version))
-              (sha256 (base32
-                       "0akhm8xjv8fl55fyq0w6c9c6hi5j7mifjx01w07np7qg1cjl9f06"))))))
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/aconchillo/guile-json")
+               (commit version)))
+        (file-name (git-file-name name version))
+        (sha256
+          (base32
+            "0akhm8xjv8fl55fyq0w6c9c6hi5j7mifjx01w07np7qg1cjl9f06"))))))
 @end lisp
 
 @end table
@@ -27248,6 +27267,28 @@ Package object for GVfs.
 @end table
 @end deftp
 
+@defvar kmonad-service-type
+This is the type of the service that runs
+@uref{https://github.com/kmonad/kmonad, KMonad}.  Its value is a
+@code{kmonad-configuration} object.  This service allows spawning
+@command{kmonad} configurations to manage keyboards.
+
+@deftp {Data Type} kmonad-configuration
+Configuration record for the KMonad service.
+
+@table @asis
+@item @code{kmonad} (default: @code{kmonad})
+The KMonad package to use.
+
+@item @code{keymaps}
+A list of files with KMonad configurations. One shepherd service will be
+created to control each configuration. Each configuration should target
+a distinct input device as KMonad operates on a per-input basis.
+
+@end table
+@end deftp
+@end defvar
+
 @defvar colord-service-type
 This is the type of the service that runs @command{colord}, a system
 service with a D-Bus

etc/teams.scm

@@ -16,6 +16,7 @@ exec $pre_inst_env_maybe guix repl -- "$0" "$@"
 ;;; Copyright © 2025 Cayetano Santos <csantosb@inventati.org>
 ;;; Copyright © 2025-2026 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2025 jgart <jgart@dismail.de>
+;;; Copyright © 2026 Denis 'GNUtoo' Carikli <GNUtoo@cyberdimension.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -690,6 +691,7 @@ ecosystem."
   (team 'embedded
         #:name "Embedded"
         #:scope (list "gnu/packages/bootloaders.scm"
+                      "gnu/packages/coreboot.scm"
                       "gnu/packages/firmware.scm")))
 
 (define-team games
@@ -943,6 +945,7 @@ importer, and the ocaml-build-system."
         #:scope
         (list "gnu/packages/ocaml.scm"
               "gnu/packages/coq.scm"
+              "gnu/packages/rocq.scm"
               "guix/build/ocaml-build-system.scm"
               "guix/build/dune-build-system.scm"
               "guix/build-system/ocaml.scm"
@@ -972,7 +975,8 @@ perl-build-system as well as the rakudo-build-system."
         #:description
         "Python, Python packages, the \"pypi\" importer, and the python-build-system."
         #:scope
-        (list "gnu/packages/django.scm"
+        (list (make-regexp* "^gnu/packages/aux-files/python/.*\\.py$")
+              "gnu/packages/django.scm"
               "gnu/packages/jupyter.scm"
               (make-regexp* "^gnu/packages/python(-.+|)\\.scm$")
               "gnu/packages/sphinx.scm"
@@ -1246,6 +1250,11 @@ the \"texlive\" importer."
                        "jonsger")
   mozilla)
 
+(define-member (person "Denis Carikli"
+                       "GNUtoo@cyberdimension.org"
+                       "GNUtoo")
+  embedded)
+
 (define-member (person "Ludovic Courtès"
                        "ludo@gnu.org"
                        "civodul")

etc/teams/rust/audit-rust-crates

@@ -1,6 +1,6 @@
 #!/usr/bin/env -S gawk -f
 # GNU Guix --- Functional package management for GNU
-# Copyright © 2025 Efraim Flashner <efraim@flashner.co.il>
+# Copyright © 2025, 2026 Efraim Flashner <efraim@flashner.co.il>
 #
 # This file is part of GNU Guix.
 #
@@ -21,20 +21,22 @@
 # ./etc/teams/rust/audit-rust-crates ./path/to/file.scm
 # Prints the output of cargo-audit to the shell.
 
-# Make sure we have cargo-audit in our PATH
 BEGIN {
-    if (system("which cargo-audit 1> /dev/null"))
-        exit 1;
+    "which cargo-audit" | getline cargoAudit
+    close("which cargo-audit")
+    cargoAudit = cargoAudit " audit --file -"
+
     # Parse a record at a time.
     RS = "\n\n"
-    cargoAudit = "cargo-audit audit --file -"
 }
 
-# Check the crate-source origin-only inputs
+# Check the crate-source origin-only inputs, like in rust-crates.scm
 /crate-source/ {
     for(i=3; i <= NF-2; i++) {
         if($i == "(crate-source") {
-            cargoLock = cargoLock "[[package]]\nname = " $(i+1) "\nversion = " $(i+2) "\n"
+            crateName = $(i+1)
+            crateVersion = $(i+2)
+            cargoLock = cargoLock "[[package]]\nname = " crateName "\nversion = " crateVersion "\n"
             next
         }
     }
@@ -44,27 +46,64 @@ BEGIN {
 /crate-uri/ {
     for(i=3; i <= NF; i++) {
         if($i == "(version")
-           crateVersion = $(i+1)
+            crateVersion = $(i+1)
         if($i == "(crate-uri")
-           crateName = $(i+1)
+            crateName = $(i+1)
     }
     gsub(/)/, "", crateVersion)
     cargoLock = cargoLock "[[package]]\nname = " crateName "\nversion = " crateVersion "\n"
+    next
 }
 
-# The xxxx-cargo-input variables have a set style
-# TODO: Replace the last dash between the name and the version with a space!
-# This doesn't take into account swapping between "-" and "_" so we skip it.
-#( $2 ~ /-cargo-inputs/ ) {
-#    sub(/-cargo-inputs/, "", $2)
-#    gsub(/)/, "", $0)
-#    gsub(/rust-/, "", $0)
-#    #gensub(/([[:alpha:]])-([[:digit:]]+)/, "\\1 \\2", "g", $i)
-#    print "[[package]]\nname = \"" $2 "\"\nversion = \"1.0.0\"\ndependencies = ["
-#    for (i = 4; i <= NF; i++) {
-#        print "\"" $i "\","
-#    }
-#    print "]"
-#}
+# Parse the crates created from packages using 'cargo package'
+/package:rust/ {
+    pkg = $2
+    split(pkg, name_version, "-")
+    crateVersion = name_version[length(name_version)]
+    crateName = substr(pkg, 6, (length(pkg) - length(crateVersion) - 6))
+    split(crateVersion, versionDots, ".")
+    if(crateVersion && (crateVersion != "(git-version") && (length(versionDots) == 3) && crateName) {
+        cargoLock = cargoLock "[[package]]\nname = \"" crateName "\"\nversion = \"" crateVersion "\"\n"
+    } else {
+        untested++
+        #print("Unable to test " $0)
+    }
+    next
+}
 
-END { print cargoLock | cargoAudit }
+# We make an attempt to create the crate name from the package name otherwise
+/git-reference/ {
+    for(i=3; i <= NF; i++) {
+        if($i == "(version")
+            crateVersion = $(i+1)
+        if($i == "(name")
+            crateName = $(i+1)
+        if($i == "(git-file-name") {
+            crateName = $(i+1)
+            crateVersion = $(i+2)
+        }
+    }
+    gsub(/)/, "", crateVersion)
+    gsub(/)/, "", crateName)
+    sub(/rust-/, "", crateName)
+    # The crate version MUST be major.minor.patch
+    split(crateVersion, versionParts, ".")
+    if(crateVersion && (crateVersion != "(git-version") && (length(versionParts) == 3) && crateName) {
+        cargoLock = cargoLock "[[package]]\nname = " crateName "\nversion = " crateVersion "\n"
+    } else {
+        untested++
+        #print("Unable to test " $0)
+    }
+    next
+}
+
+# Note those which we were unable to parse
+/define rust/ {
+    if($3 == "#f)")
+        next
+    print("Unable to parse " $0)
+    }
+
+{ untested++ }
+
+END { print("Number of crates untested: " untested); print cargoLock | cargoAudit }

gnu/local.mk

@@ -610,6 +610,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/rocm-apps.scm			\
   %D%/packages/rocm-libs.scm			\
   %D%/packages/rocm-tools.scm			\
+  %D%/packages/rocq.scm				\
   %D%/packages/rpc.scm				\
   %D%/packages/rpm.scm				\
   %D%/packages/rrdtool.scm			\
@@ -1129,10 +1130,10 @@ dist_patch_DATA =						\
   %D%/packages/patches/clog-fix-shared-build.patch		\
   %D%/packages/patches/clucene-gcc-14.patch			\
   %D%/packages/patches/clucene-pkgconfig.patch			\
-  %D%/packages/patches/coda-use-system-libs.patch		\
-  %D%/packages/patches/codex-acp-0.9.2-remove-patch-sections.patch \
-  %D%/packages/patches/codex-acp-0.9.2-replace-result-flatten.patch    \
+  %D%/packages/patches/codex-acp-0.11.1-disable-code-mode.patch \
+  %D%/packages/patches/codex-acp-0.11.1-remove-patch-sections.patch \
   %D%/packages/patches/codex-0.98.0-remove-patch-sections.patch    \
+  %D%/packages/patches/rust-codex-0.117.0-remove-patch-sections.patch    \
   %D%/packages/patches/cogl-fix-double-free.patch		\
   %D%/packages/patches/collada-dom-boost.patch			\
   %D%/packages/patches/collectd-5.11.0-noinstallvar.patch	\
@@ -1185,6 +1186,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/date-output-pkg-config-files.patch	\
   %D%/packages/patches/dbacl-include-locale.h.patch		\
   %D%/packages/patches/dbacl-icheck-multiple-definitions.patch	\
+  %D%/packages/patches/dblatex-importlib.patch		\
   %D%/packages/patches/dblatex-inkscape-1.0.patch		\
   %D%/packages/patches/dbus-helper-search-path.patch		\
   %D%/packages/patches/ddd-build.patch				\
@@ -1466,7 +1468,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/ghostscript-no-header-creationdate.patch \
   %D%/packages/patches/gimp-fix-metadata-editor.patch		\
   %D%/packages/patches/gimp-fix-tiff-load.patch			\
-  %D%/packages/patches/git-clar-path-max.patch			\
   %D%/packages/patches/git-filter-repo-generate-doc.patch	\
   %D%/packages/patches/gklib-suitesparse.patch			\
   %D%/packages/patches/glib-appinfo-watch.patch			\
@@ -1585,7 +1586,9 @@ dist_patch_DATA =						\
   %D%/packages/patches/gtk3-respect-GUIX_GTK3_PATH.patch	\
   %D%/packages/patches/gtk3-respect-GUIX_GTK3_IM_MODULE_FILE.patch \
   %D%/packages/patches/gtk-doc-respect-xml-catalog.patch	\
-  %D%/packages/patches/gtk-doc-mkhtml-test-fix.patch	\
+  %D%/packages/patches/gtk-doc-mkhtml-test-fix.patch	        \
+  %D%/packages/patches/gtk4-demo-reproducible.patch             \
+  %D%/packages/patches/gtk4-needs-udmabuf.patch                 \
   %D%/packages/patches/gtk4-respect-GUIX_GTK4_PATH.patch    	\
   %D%/packages/patches/gtkglext-disable-disable-deprecated.patch \
   %D%/packages/patches/gtksourceview-2-add-default-directory.patch \
@@ -1616,7 +1619,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/hurd-refcounts-assert.patch		\
   %D%/packages/patches/hurd-rumpdisk-no-hd.patch		\
   %D%/packages/patches/hurd-startup.patch			\
-  %D%/packages/patches/hwloc-1-test-btrfs.patch			\
   %D%/packages/patches/hwloc-add-with-opencl.patch		\
   %D%/packages/patches/i3lock-blur-fix-build-on-gcc-10.patch	\
   %D%/packages/patches/i7z-gcc-10.patch				\
@@ -1652,6 +1654,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/id3lib-CVE-2007-4460.patch			\
   %D%/packages/patches/id3lib-UTF16-writing-bug.patch			\
   %D%/packages/patches/ilmbase-fix-tests.patch			\
+  %D%/packages/patches/inetutils-drop-test.patch                \
   %D%/packages/patches/inferno-fix-crash.patch		\
   %D%/packages/patches/iniparser-remove-fetchcontent-usage.patch		\
   %D%/packages/patches/inkscape-libxml2.patch		\
@@ -2120,6 +2123,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-pyreadstat-link-libiconv.patch	\
   %D%/packages/patches/python-sip-include-dirs.patch	\
   %D%/packages/patches/python-scikit-build-setuptools-compat.patch	\
+  %D%/packages/patches/python-scikit-image-fix-python-pillow.patch	\
   %D%/packages/patches/python-sgmllib3k-assertions.patch	\
   %D%/packages/patches/python-sphobjinv-defer-ssl-import.patch	\
   %D%/packages/patches/python-sphinx-prompt-docutils-0.19.patch	\
@@ -2394,6 +2398,11 @@ dist_patch_DATA =						\
   %D%/packages/patches/rust-codex-0.98.0-test-shebangs.patch	\
   %D%/packages/patches/rust-codex-0.98.0-test-timeout.patch	\
   %D%/packages/patches/rust-codex-0.98.0-windows-sandbox-protocol-version.patch	\
+  %D%/packages/patches/rust-codex-0.117.0-core-remove-self-dep.patch	\
+  %D%/packages/patches/rust-codex-0.120.0-core-remove-self-dep.patch	\
+  %D%/packages/patches/rust-codex-0.120.0-connectors-cache-test-race.patch	\
+  %D%/packages/patches/rust-codex-0.120.0-remove-libwebrtc.patch	\
+  %D%/packages/patches/rust-codex-0.120.0-test-timeout.patch	\
   %D%/packages/patches/rust-ring-0.17-ring-core.patch		\
   %D%/packages/patches/rw-igraph-0.10.patch			\
   %D%/packages/patches/rxvt-unicode-fix-cursor-position.patch	\
@@ -2499,7 +2508,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/texmacs-wayland-hidpi.patch	\
   %D%/packages/patches/tflite-micro_disable_download.patch 	\
   %D%/packages/patches/thefuck-test-environ.patch		\
-  %D%/packages/patches/thefuck-remove-broken-tests.patch	\
   %D%/packages/patches/tidy-CVE-2015-5522+5523.patch		\
   %D%/packages/patches/timewarrior-time-sensitive-tests.patch	\
   %D%/packages/patches/tinydir-fix-cbehave-test.patch		\

gnu/packages/acl.scm

@@ -37,7 +37,6 @@
   #:use-module (gnu packages)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix utils))
 
 (define-public acl

gnu/packages/admin.scm

@@ -109,7 +109,6 @@
   #:use-module (guix build-system go)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system ruby)
@@ -1158,7 +1157,7 @@ on memory usage on GNU/Linux systems.")
 (define-public htop
   (package
     (name "htop")
-    (version "3.4.1")
+    (version "3.5.0")
     (source
      (origin
        (method git-fetch)
@@ -1166,7 +1165,7 @@ on memory usage on GNU/Linux systems.")
              (url "https://github.com/htop-dev/htop")
              (commit version)))
        (sha256
-        (base32 "058y4a4mvx9m179dyr4wi8mlm6i4ybywshadaj4cvfn9fv0r0nkx"))
+        (base32 "1r07ri0dl9xz0jn1hc2g8q3l0q4clvnxs05yagpzsz0zigp4flj5"))
        (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (arguments
@@ -1309,7 +1308,8 @@ re-executing them as necessary.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "11n01vsd51r7qraaaylhhx04hq4s6vcq0896zkz0yp1wvqfbwmm1"))))
+                "11n01vsd51r7qraaaylhhx04hq4s6vcq0896zkz0yp1wvqfbwmm1"))
+              (patches (search-patches "inetutils-drop-test.patch"))))
     (build-system gnu-build-system)
     (arguments
      (list
@@ -3441,7 +3441,7 @@ modules and plugins that extend Ansible.")
      (list ansible
            bash-minimal
            encfs
-           fuse-2
+           fuse
            util-linux ;; for umount
            findutils
            git
@@ -3917,6 +3917,18 @@ rules is done with the @code{auditctl} utility.")
                 (wrap-program (string-append ndiff "/bin/ndiff")
                   `("GUIX_PYTHONPATH" prefix
                     (,(python-path ndiff)))))))
+          (add-before 'check 'fix-tests-for-python-3.12
+            (lambda _
+              (substitute* "ndiff/ndifftest.py"
+                (("import imp")
+                 "import importlib.util")
+                (("ndiff = imp\\.load_source\\(\"ndiff\", \"ndiff\\.py\"\\)")
+                 (string-join
+                  '("spec = \
+importlib.util.spec_from_file_location(\"ndiff\", \"ndiff.py\")"
+                    "ndiff = importlib.util.module_from_spec(spec)"
+                    "spec.loader.exec_module(ndiff)")
+                  "\n")))))
           ;; These are the tests that do not require network access.
           (replace 'check
             (lambda* (#:key tests? #:allow-other-keys)
@@ -4046,51 +4058,59 @@ plug-in architecture to allow monitoring other system metrics.")
     (license license:gpl2+)))
 
 (define-public thefuck
-  (package
-    (name "thefuck")
-    (version "3.32")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/nvbn/thefuck")
-             (commit version)))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "18ipa1bm6q1n5drbi8i65726hhqhl1g41390lfqrc11hkbvv443d"))
-       (patches (search-patches "thefuck-test-environ.patch"
-                                "thefuck-remove-broken-tests.patch"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-before 'check 'pre-check
-            (lambda _
-              ;; Tests look for installed package
-              ;; Some tests need write access to $HOME.
-              (setenv "HOME" "/tmp")
-              ;; Even with that, this function tries to mkdir /.config.
-              (substitute* "tests/test_utils.py"
-                (("settings\\.init\\(\\)") "")))))))
-    (native-inputs
-     (list go
-           python-mock
-           python-pytest-8
-           python-pytest-mock
-           python-setuptools
-           python-wheel))
-    (inputs
-     (list python-colorama
-           python-decorator
-           python-psutil
-           python-pyte))
-    (home-page "https://github.com/nvbn/thefuck")
-    (synopsis "Correct mistyped console command")
-    (description
-     "The Fuck tries to match a rule for a previous, mistyped command, creates
+  ;; Latest release, 3.32, is not compatible with Python 3.12.
+  (let ((revision "0")
+        (commit "c7e7e1d884d3bb241ea6448f72a989434c2a35ec"))
+    (package
+      (name "thefuck")
+      (version (git-version "3.32" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+                (url "https://github.com/nvbn/thefuck")
+                (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1l3i2cpdf3vznpbzqw7b18l23xikqs7andx6yzqvm5415snaqg06"))
+         (patches (search-patches "thefuck-test-environ.patch"))))
+      (build-system pyproject-build-system)
+      (arguments
+       (list
+        #:test-flags
+        #~(list
+           "--deselect=tests/test_utils.py::TestGetValidHistoryWithoutCurrent"
+           "--ignore=tests/functional/conftest.py")
+        #:phases
+        #~(modify-phases %standard-phases
+            (add-before 'check 'pre-check
+              (lambda _
+                ;; ModuleNotFoundError: No module named 'pytest_docker_pexpect'
+                (delete-file "tests/functional/conftest.py")
+                ;; Tests look for installed package
+                ;; Some tests need write access to $HOME.
+                (setenv "HOME" "/tmp")
+                ;; Even with that, this function tries to mkdir /.config.
+                (substitute* "tests/test_utils.py"
+                  (("settings\\.init\\(\\)") "")))))))
+      (native-inputs
+       (list go
+             python-mock
+             ;; Uses test markers that are incompatible with pytest 9.
+             python-pytest-8
+             python-pytest-mock
+             python-setuptools))
+      (inputs
+       (list python-colorama
+             python-decorator
+             python-psutil
+             python-pyte))
+      (home-page "https://github.com/nvbn/thefuck")
+      (synopsis "Correct mistyped console command")
+      (description
+       "The Fuck tries to match a rule for a previous, mistyped command, creates
 a new command using the matched rule, and runs it.")
-    (license license:x11)))
+      (license license:x11))))
 
 (define-public di
   (package
@@ -7169,6 +7189,35 @@ stored in an SQL database.")
 (connects via USB OTG).")
     (license license:expat)))
 
+(define-public yoctofetch
+  (package
+    (name "yoctofetch")
+    (version "2.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://codeberg.org/Phosphenius/yoctofetch.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0smkaydv74p2231gafibvqbwsy469w56hya8gz8wq0gw7m2l7zh3"))))
+    ; Support for other platforms not available per upstream:
+    ; https://codeberg.org/Phosphenius/yoctofetch#supported-platforms
+    (supported-systems '("x86_64-linux" "aarch64-linux"))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:tests? #f)) ; No tests available.
+    (home-page "https://codeberg.org/Phosphenius/yoctofetch")
+    (synopsis "Fast and low footprint system fetch tool for the Linux UAPI")
+    (description
+     "This package provides a system fetch tool, similar to
+@command{neofetch}, @command{fastfetch}, etc.  It is lightweight and
+has a focus on performance.  It can be used as a greeter by starting
+it from @file{~/.bashrc} for example.")
+    (license license:agpl3+)))
+
 (define-public zzz
   (package
     (name "zzz")

gnu/packages/algebra.scm

@@ -88,7 +88,6 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system pyproject)
-  #:use-module ((guix build-system python) #:select (pypi-uri))
   #:use-module (guix build-system r)
   #:use-module (guix download)
   #:use-module (guix gexp)

gnu/packages/android.scm

@@ -41,7 +41,6 @@
   #:use-module (guix build-system emacs)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system trivial)

gnu/packages/apparmor.scm

@@ -180,7 +180,7 @@ supported by Canonical since 2009.")
        (list libapparmor))
       ;; Python module `readline' needed
       (native-inputs
-       (list bison flex gettext-minimal perl python which))
+       (list bison flex gettext-minimal perl python python-setuptools which))
       (license license:gpl2))))
 
 (define-public pam-apparmor

gnu/packages/astronomy.scm

@@ -37,7 +37,6 @@
 
 (define-module (gnu packages astronomy)
   #:use-module ((guix licenses) #:prefix license:)
-  #:use-module ((guix build-system python) #:select (pypi-uri)) ;to be removed soon
   #:use-module (guix build-system ant)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system copy)
@@ -3790,10 +3789,6 @@ bad pixel tracking throughout the reduction process.")
       #~(list "-m" "not remote_data")
       #:phases
       #~(modify-phases %standard-phases
-          (add-after 'unpack 'fix-pytest-config
-            (lambda _
-              (substitute* "pyproject.toml"
-                ((" --cov=cdflib --cov-report=xml") ""))))
           (add-before 'check 'set-home-env
             (lambda _
               (setenv "HOME" (getcwd)))))))
@@ -4425,7 +4420,6 @@ Cesium.")
     (native-inputs
      (list python-pydot
            python-pytest
-           python-pytest-cov
            python-pytest-asdf-plugin
            python-pytest-doctestplus
            python-pytest-filter-subpackage
@@ -4950,7 +4944,6 @@ files.")
     (build-system pyproject-build-system)
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-setuptools
            python-setuptools-scm
            python-wheel))
@@ -5512,7 +5505,6 @@ across many files.")
      (list python-mock
            python-objgraph
            python-pytest
-           python-pytest-cov
            ;; python-pytest-faulthandler
            python-setuptools
            python-wheel
@@ -6326,19 +6318,6 @@ files.")
                  (string-append
                   "from astropy.units.core import Unit, UnitBase\n"
                   "from astropy.units.errors import UnitTypeError\n")))))
-          (add-after 'unpack 'relax-requirements
-            (lambda _
-              (substitute* "pyproject.toml"
-                ;; RuntimeError: Unable to detect version control
-                ;; system. Checked: Git. Not installed: Mercurial, Darcs,
-                ;; Subversion, Bazaar, Fossil, Pijul.  See
-                ;; <https://github.com/blacklanternsecurity/bbot/issues/1257>.
-                (("enable = true") "enable = false"))))
-          (add-before 'build 'set-version
-            (lambda _
-              ;; TODO: Include in pyproject-build-system.
-              (setenv "POETRY_DYNAMIC_VERSIONING_BYPASS"
-                      #$(version-major+minor+point version))))
           (add-before 'check 'prepare-test-environment
             (lambda _
               (setenv "HOME" "/tmp"))))))
@@ -9923,13 +9902,7 @@ implemented in the @acronym{JWST, James Webb Space Telescope} and
                             "test_step.py::test_build_config_pipe_kwarg"
                             "test_step.py::test_build_config_step_config_file"
                             "test_step.py::test_build_config_step_kwarg"
-                            "test_step.py::test_step_list_args")))
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'set-version
-            (lambda _
-              (setenv "SETUPTOOLS_SCM_PRETEND_VERSION"
-                      #$(version-major+minor+point version)))))))
+                            "test_step.py::test_step_list_args")))))
     (native-inputs
      (list python-pytest
            python-pytest-doctestplus
@@ -10937,7 +10910,6 @@ cosmological simulations.")
     (build-system pyproject-build-system)
     (propagated-inputs (list python-numpy python-scipy))
     (native-inputs (list python-pytest
-                         python-pytest-cov
                          python-pytest-doctestplus
                          python-setuptools-scm
                          python-wheel))

gnu/packages/audio.scm

@@ -179,7 +179,6 @@
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system trivial)
@@ -3238,30 +3237,27 @@ synchronous execution of all clients, and low latency operation.")
   (package
     (inherit jack-1)
     (name "jack2")
-    (version "1.9.21")
+    ;; 1.9.22 does not compile with Python 3.12, use the latest commit instead.
+    (properties '((commit . "17959465a722225a36a8b612aed26764036f258e")
+                  (revision . "0")))
+    (version (git-version "1.9.22"
+                          (assoc-ref properties 'revision)
+                          (assoc-ref properties 'commit)))
     (source (origin
               (method git-fetch)
               (uri (git-reference
-                    (url "https://github.com/jackaudio/jack2")
-                    (commit (string-append "v" version))))
+                     (url "https://github.com/jackaudio/jack2")
+                     (commit (assoc-ref properties 'commit))))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0sbrffmdbajvrk7iqvsvrnwnpvmicvbjyq3f52r6ashdsznsz03b"))))
+                "18dbjq9y8mcp27j9aaqdlg4976hrisr7b88lk84ck09gmzlwqalp"))))
     (build-system waf-build-system)
     (arguments
      `(#:tests? #f                      ; no check target
        #:configure-flags '("--dbus" "--alsa")
        #:phases
        (modify-phases %standard-phases
-         ;; Python 3.11 has removed the 'U' (universal newline) mode.  It has
-         ;; been the default since Python 3.3.
-         (add-after 'unpack 'python-compatibility
-           (lambda _
-             (substitute* '("waflib/Context.py"
-                            "waflib/ConfigSet.py")
-               (("m='rU'") "m='r'")
-               (("read\\('rU'") "read('r'"))))
          (add-before 'configure 'set-linkflags
            (lambda _
              ;; Ensure -lstdc++ is the tail of LDFLAGS or the simdtests.cpp
@@ -3287,7 +3283,7 @@ synchronous execution of all clients, and low latency operation.")
            expat
            libsamplerate
            opus
-           python-dbus-1.2
+           python-dbus
            readline))
     (native-inputs
      (list pkg-config))
@@ -4090,9 +4086,7 @@ one-dimensional sample-rate conversion library.")
                  (string-append "'" #$(this-package-input "libsndfile")
                                 "/lib/libsndfile"))))))))
     (native-inputs
-     (list python-pytest
-           python-pytest-cov
-           python-setuptools))
+     (list python-pytest python-setuptools))
     (inputs
      (list libsndfile
            portaudio))
@@ -6529,22 +6523,23 @@ on the ALSA software PCM plugin.")
 (define-public snd
   (package
     (name "snd")
-    (version "25.2")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "ftp://ccrma-ftp.stanford.edu/pub/Lisp/"
-                                  "snd-" version ".tar.gz"))
-              (sha256
-               (base32
-                "0fgxqk0byxdj6059mb9d5qic2dqjabz49j0szsrn2y3c9nz6iyq4"))))
+    (version "26.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://ccrma.stanford.edu/software/snd/snd-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "1d573mjlrn9rhl9g0a3d1rkar34q60ln8mwlbibfalpn8lsz59a0"))))
     (build-system gnu-build-system)
     (arguments
      (list
-      #:tests? #f                       ; no tests
-      #:out-of-source? #f               ; for the 'install-doc' phase
+      #:tests? #f                       ; No tests.
+      #:out-of-source? #f               ; Required by 'install-doc'.
       #:configure-flags
-      #~(let ((docdir (string-append #$output "/share/doc/"
-                                     #$name "-" #$version)))
+      #~(let
+            ((docdir (string-append #$output "/share/doc/snd-" #$version)))
           (list "--with-alsa"
                 "--with-jack"
                 "--with-gmp"
@@ -6552,18 +6547,20 @@ on the ALSA software PCM plugin.")
                 (string-append "--with-doc-dir=" docdir)))
       #:phases
       #~(modify-phases %standard-phases
-          (add-after 'install 'install-s7
+          (add-after 'install 'install-s7-h
             (lambda _
-              (install-file "s7.h" (string-append #$output "/include"))))
+              (install-file "s7.h" (string-append #$output
+                                                  "/include"))))
           (add-after 'install 'install-doc
             (lambda _
-              (let ((doc (string-append #$output "/share/doc/"
-                                        #$name "-" #$version)))
+              (let
+                  ((docdir (string-append #$output "/share/doc/snd-"
+                                          #$version)))
                 (for-each
                  (lambda (f)
-                   (install-file f doc))
+                   (install-file f docdir))
                  (find-files "." "\\.html$"))
-                (copy-recursively "pix" (string-append doc "/pix"))))))))
+                (copy-recursively "pix" (string-append docdir "/pix"))))))))
     (native-inputs
      (list pkg-config))
     (inputs
@@ -6582,13 +6579,16 @@ on the ALSA software PCM plugin.")
            timidity++
            vorbis-tools
            wavpack))
+    (home-page "https://ccrma.stanford.edu/software/snd/snd/snd.html")
     (synopsis "Sound editor")
-    (home-page "https://ccrma.stanford.edu/software/snd/")
     (description
      "Snd is a sound editor modelled loosely after Emacs.  It can be
 customized and extended using either the s7 Scheme implementation (included in
 the Snd sources), Ruby, or Forth.")
-    (license (license:non-copyleft "file://COPYING"))))
+    (license
+     ;; INFO: pkgsrc classifies this as `esdl-license', a license not included
+     ;; in OSI or FSF lists, despite being similar to ISC.
+     (license:non-copyleft "file://COPYING"))))
 
 (define-public libspecbleach
   (package
@@ -7821,60 +7821,59 @@ Rate} 3600x2250 bit/s vocoder used in various radio systems.")
                   (delete-file-recursively "third_party")
                   (delete-file-recursively "modules")))))
     (build-system cmake-build-system)
+    (arguments
+     (list
+      #:configure-flags
+      #~(list "-DLINK_BUILD_QT_EXAMPLES=ON"
+              "-DLINK_BUILD_JACK=ON")
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'check
+            (lambda* (#:key inputs tests? #:allow-other-keys)
+              (when tests?
+                (let* ((python (search-input-file inputs "/bin/python3"))
+                       (run-tests "../source/ci/run-tests.py"))
+                  (invoke python run-tests "--target" "LinkCoreTest")
+                  (invoke python run-tests "--target" "LinkDiscoveryTest")))))
+          (add-before 'install 'patch-cmake
+            (lambda* (#:key inputs #:allow-other-keys)
+              (let* ((source "../source/"))
+                (substitute* (string-append source
+                                            "cmake_include/AsioStandaloneConfig.cmake")
+                  (((string-append "\\$\\{CMAKE_CURRENT_LIST_DIR\\}/\\.\\./"
+                                   "modules/asio-standalone/asio/include"))
+                   (dirname (search-input-file inputs "include/asio.hpp"))))
+                (substitute* (string-append source "AbletonLinkConfig.cmake")
+                  (("\\$\\{CMAKE_CURRENT_LIST_DIR\\}/include")
+                   "${CMAKE_CURRENT_LIST_DIR}/../../../include")
+                  (("\\$\\{CMAKE_CURRENT_LIST_DIR\\}/include/ableton/Link\\.hpp")
+                   "${CMAKE_CURRENT_LIST_DIR}/../../../include/ableton/Link.hpp")))))
+          (replace 'install
+            (lambda _
+              (let* ((out #$output)
+                     (lib-cmake (string-append out "/lib/cmake/ableton-link"))
+                     (source "../source"))
+                (for-each delete-file
+                          '("bin/LinkDiscoveryTest" "bin/LinkCoreTest"))
+                (copy-recursively "bin" (string-append out "/bin"))
+                (copy-recursively (string-append source "/include/ableton")
+                                  (string-append out "/include/ableton"))
+                (install-file (string-append source "/AbletonLinkConfig.cmake")
+                              lib-cmake)
+                (install-file (string-append source
+                                             "/cmake_include/AsioStandaloneConfig.cmake")
+                              (string-append lib-cmake "/cmake_include"))))))))
     (native-inputs
      (list catch-framework
-           python ;for running tests
-           portaudio)) ;for portaudio examples
+           portaudio                    ;for portaudio examples
+           python                       ;for running tests
+           python-setuptools))          ;for running tests
     (inputs
      (list jack-1)) ;for JACK examples
     (propagated-inputs
      ;; This is because include/ableton/platforms/asio/AsioWrapper.hpp
      ;; contains '#include <asio.hpp>'.
      (list asio-1.28))
-    (arguments
-     `(#:configure-flags
-       '("-DLINK_BUILD_QT_EXAMPLES=ON"
-         "-DLINK_BUILD_JACK=ON")
-       #:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key inputs tests? #:allow-other-keys)
-             (when tests?
-               (let* ((python (search-input-file inputs "/bin/python3"))
-                      (run-tests "../source/ci/run-tests.py"))
-                 (invoke python run-tests "--target" "LinkCoreTest")
-                 (invoke python run-tests "--target" "LinkDiscoveryTest")))))
-         (add-before 'install 'patch-cmake
-           (lambda* (#:key inputs #:allow-other-keys)
-             (let* ((source "../source/"))
-               (substitute* (string-append source
-                                           "cmake_include/AsioStandaloneConfig.cmake")
-                 (((string-append "\\$\\{CMAKE_CURRENT_LIST_DIR\\}/\\.\\./"
-                                  "modules/asio-standalone/asio/include"))
-                  (string-append (assoc-ref inputs "asio")
-                                 "/include")))
-               (substitute* (string-append source "AbletonLinkConfig.cmake")
-                 (("\\$\\{CMAKE_CURRENT_LIST_DIR\\}/include")
-                  "${CMAKE_CURRENT_LIST_DIR}/../../../include")
-                 (("\\$\\{CMAKE_CURRENT_LIST_DIR\\}/include/ableton/Link\\.hpp")
-                  "${CMAKE_CURRENT_LIST_DIR}/../../../include/ableton/Link.hpp")))))
-         (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (bin (string-append out "/bin"))
-                    (lib-cmake (string-append out "/lib/cmake/ableton-link"))
-                    (source "../source"))
-               (for-each (lambda (test-file)
-                           (delete-file test-file))
-                         '("bin/LinkDiscoveryTest" "bin/LinkCoreTest"))
-               (copy-recursively "bin" bin)
-               (copy-recursively (string-append source "/include/ableton")
-                                 (string-append out "/include/ableton"))
-               (install-file (string-append source "/AbletonLinkConfig.cmake")
-                             lib-cmake)
-               (install-file (string-append source
-                                            "/cmake_include/AsioStandaloneConfig.cmake")
-                             (string-append lib-cmake "/cmake_include"))))))))
     (home-page "https://github.com/Ableton/link")
     (synopsis "Synchronize musical beat, tempo, and phase across multiple applications")
     (description
@@ -8060,7 +8059,7 @@ as sample rate, determining whether an audio file is silent, and much more.")
     (propagated-inputs
      (list python-numba python-numpy python-scipy python-six))
     (native-inputs
-     (list python-pytest python-pytest-cov python-setuptools python-wheel))
+     (list python-pytest python-setuptools python-wheel))
     (home-page "https://github.com/bmcfee/resampy")
     (synopsis "Efficient signal resampling")
     (description
@@ -8090,8 +8089,7 @@ Home Page}.")
      (list
       #:test-flags
       ;; Ignore --mpl flag.
-      '(list "-c" "/dev/null"
-             "-k" (string-append
+      '(list "-k" (string-append
                    ;; Resampling tests require python-samplerate.
                    "not resample"
                    ;; These tests use Pooch and download data files.
@@ -8116,7 +8114,6 @@ Home Page}.")
      (list python-matplotlib
            python-packaging
            python-pytest
-           python-pytest-cov
            python-resampy
            python-setuptools
            python-wheel))

gnu/packages/aux-files/python/pytest_guix.py

@@ -0,0 +1,58 @@
+# GNU Guix --- Functional package management for GNU
+# Copyright © 2025 Nicolas Graves <ngraves@ngraves.fr>
+#
+# 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/>.
+
+import importlib.util
+import json
+
+
+def pytest_addoption(parser):
+    """Add stub options to be ignored by pytest.
+
+    More precisely, inject all options provided in .pytest_guix_options.json,
+    except options whose plugin is indeed installed.
+
+    For example, if the json file records --cov:
+      if the pytest_cov module is installed, its --cov will be used.
+      otherwise, --cov is ignored (read by this parser, but nothing is done
+      with it).
+
+    Flags can be given with additional keyword arguments in a json object.
+    If the json object is not given, fallback to the default
+    {"action": "append", "nargs": "?"}.  In practice, these arguments are only
+    mandatory for the store_true and store_const actions to avoid eating other
+    arguments.
+
+    This allows to remove development packages, which are not required at build
+    time while at the same time avoiding the need to adjust test options in
+    pyproject.toml or other configuration files.
+    """
+    with open(".pytest_guix_options.json", "r") as options_file:
+        plugin_options = json.load(options_file)
+        group = parser.getgroup(
+            "guix", "Options ignored by the Guix pyproject-build-system"
+        )
+
+        # Only add options for plugins that are not present.
+        for key, options in plugin_options.items():
+            if importlib.util.find_spec(f"pytest_{key}") is None:
+                # Plugin not found, add stub options
+                for option, kwargs in options.items():
+                    if kwargs:
+                        group.addoption(option, **kwargs)
+                    else:
+                        group.addoption(option, action="append", nargs="?")

gnu/packages/backup.scm

@@ -50,7 +50,6 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix download)
   #:use-module (guix gexp)
@@ -107,6 +106,7 @@
   #:use-module (gnu packages rsync)
   #:use-module (gnu packages ruby-xyz)
   #:use-module (gnu packages serialization)
+  #:use-module (gnu packages sphinx)
   #:use-module (gnu packages ssh)
   #:use-module (gnu packages time)
   #:use-module (gnu packages tls)
@@ -137,7 +137,6 @@
            python-paramiko
            python-pexpect
            python-pytest
-           python-pytest-runner
            python-setuptools-scm
            tzdata-for-tests
            python-mock))
@@ -632,41 +631,26 @@ rsnapshot uses hard links to deduplicate identical files.")
 (define-public borg
   (package
     (name "borg")
-    (version "1.4.3")
+    (version "1.4.4")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "borgbackup" version))
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/borgbackup/borg")
+              (commit version)))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "07s4jqcv03s98hi6lvqpvmnnhl532qnvv11mjy2xc08rbmsgmfvr"))
-       (snippet
-        #~(begin
-            ;; Delete files generated by Cython.  We used to have a regex that
-            ;; created the list of generated files but Borg has added new
-            ;; non-generated C files that cause the regex to generate the
-            ;; wrong list.
-            (for-each delete-file
-                      '("src/borg/algorithms/checksums.c"
-                        "src/borg/chunker.c"
-                        "src/borg/compress.c"
-                        "src/borg/crypto/low_level.c"
-                        "src/borg/hashindex.c"
-                        "src/borg/item.c"
-                        "src/borg/platform/darwin.c"
-                        "src/borg/platform/freebsd.c"
-                        "src/borg/platform/linux.c"
-                        "src/borg/platform/posix.c"
-                        "src/borg/platform/syncfilerange.c"
-                        "src/borg/platform/windows.c"))))))
+        (base32 "0bk302lbjjz1y8dg78wqqys80bm7mzkj5yf6wgyqdwvbqpsnpim4"))))
     (build-system pyproject-build-system)
     (arguments
      (list
       #:modules '((srfi srfi-26)        ; for cut
                   (guix build utils)
                   (guix build pyproject-build-system))
+      ;; tests: 1318 passed, 293 skipped
       #:test-flags
       #~(list "--benchmark-skip"
-              "--numprocesses" (number->string (parallel-job-count))
+              "--numprocesses" (number->string (min 8 (parallel-job-count)))
               "--pyargs" "borg.testsuite"
               "-k" (string-join
                     ;; These tests need to write to '/var'.
@@ -687,7 +671,15 @@ rsnapshot uses hard links to deduplicate identical files.")
                           "test_mount_hardlinks "
                           "test_readonly_mount "
                           "test_fuse_versions_view "
-                          "test_migrate_lock_alive")
+                          "test_migrate_lock_alive"
+                          ;; Test files are not in /gnu/store
+                          "test_convert_all[False]"
+                          "test_convert_all[True]"
+                          "test_convert_segments[False]"
+                          "test_convert_segments[True]"
+                          "test_detect_attic_repo"
+                          "test_key_export_qr"
+                          "test_keys")
                     " and not "))
       #:phases
       #~(modify-phases %standard-phases
@@ -703,46 +695,58 @@ rsnapshot uses hard links to deduplicate identical files.")
                 (setenv "BORG_LIBLZ4_PREFIX" lz4)
                 (setenv "BORG_LIBXXHASH_PREFIX" xxhash)
                 (setenv "BORG_LIBZSTD_PREFIX" zstd))))
-          (add-after 'install 'install-doc
+          (add-before 'build 'fix-testsuite-setuid-mode
             (lambda _
-              (let ((man (string-append #$output "/share/man/man1"))
-                    (misc (string-append #$output "/share/doc/borg-"
-                                         #$(package-version this-package))))
+              (substitute* "src/borg/testsuite/archiver.py"
+                (("0o4755") "0o0755"))))
+          (add-after 'install 'build-and-install-docs
+            (lambda _
+              (let* ((doc (string-append #$output "/share/doc/borg-" #$version))
+                     (html (string-append doc "/html"))
+                     (txt (string-append doc "/txt"))
+                     (misc (string-append doc "/misc"))
+                     (man (string-append #$output "/share/man/man1")))
+                (with-directory-excursion "docs"
+                  (invoke "make" "text" "man" "singlehtml"))
                 (for-each (cut install-file <> misc)
                           '("docs/misc/create_chunker-params.txt"
                             "docs/misc/borg-data-flow.png"
                             "docs/misc/internals-picture.txt"
                             "docs/misc/prune-example.txt"))
-                (copy-recursively "docs/man" man))))
-          (add-after 'install-doc 'install-shell-completions
+                (copy-recursively "docs/_build/man" man)
+                (copy-recursively "docs/_build/singlehtml" html)
+                (copy-recursively "docs/_build/text" txt))))
+          (add-after 'build-and-install-docs 'install-shell-completions
             (lambda _
-              (let ((etc (string-append #$output "/etc"))
-                    (share (string-append #$output "/share")))
+              (let* ((etc (string-append #$output "/etc"))
+                     (share (string-append #$output "/share"))
+                     (bash (string-append etc "/bash_completion.d"))
+                     (zsh (string-append share "/zsh/site-functions"))
+                     (fish (string-append share "/fish/vendor_completions.d")))
                 (with-directory-excursion "scripts/shell_completions"
-                  (install-file "bash/borg"
-                                (string-append etc "/bash_completion.d"))
-                  (install-file "zsh/_borg"
-                                (string-append share "/zsh/site-functions"))
-                  (install-file "fish/borg.fish"
-                                (string-append share "/fish/vendor_completions.d")))))))))
+                  (install-file "bash/borg" bash)
+                  (install-file "zsh/_borg" zsh)
+                  (install-file "fish/borg.fish" fish))))))))
     (native-inputs
      (list python-cython
-           python-dateutil
+           python-guzzle-sphinx-theme
+           python-pkgconfig
            python-pytest
            python-pytest-benchmark
            python-pytest-xdist
            python-setuptools
            python-setuptools-scm
-           python-wheel))
+           python-sphinx
+           python-sphinxcontrib-jquery))
     (inputs
      (list acl
            lz4
            openssl
-           ;; This is the latest version of msgpack accepted by 'setup.py'.
-           python-msgpack-for-borg
+           python-msgpack
            ;; FUSE 3 isn't working well, so we stick with FUSE 2 for now:
            ;; <https://issues.guix.gnu.org/53407>
            python-llfuse
+           python-packaging
            xxhash
            `(,zstd "lib")))
     (synopsis "Deduplicated, encrypted, authenticated and compressed backups")
@@ -1299,7 +1303,6 @@ compression parameters used by Gzip.")
     (native-inputs
      (list python-flexmock
            python-pytest
-           python-pytest-cov
            python-setuptools
            python-wheel))
     (inputs
@@ -1363,9 +1366,9 @@ borgmatic is powered by borg.")
             (assoc-ref qt:%standard-phases 'qt-wrap)))))
     (native-inputs
      (list python-platformdirs
+           python-pytest
            python-pytest-mock
            python-pytest-qt
-           python-pytest-runner
            python-setuptools
            python-setuptools-git))
     (inputs

gnu/packages/benchmark.scm

@@ -42,7 +42,6 @@
   #:use-module (guix search-paths)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system meson)
   #:use-module (gnu packages)

gnu/packages/bioinformatics.scm

@@ -65,7 +65,6 @@
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system r)
   #:use-module (guix build-system ruby)
@@ -2288,7 +2287,6 @@ version = ~s
                   (delete-file-recursively
                    (string-append #$output "/.pytest_cache")))))))))
     (native-inputs (list python-pytest
-                         python-pytest-cov
                          python-pytest-datadir
                          python-pytest-doctestplus
                          python-recommonmark
@@ -3379,35 +3377,36 @@ encountered in PDB files prior to simulation tasks.")
 (define-public python-peaks2utr
   (package
     (name "python-peaks2utr")
-    (version "1.4.1")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "peaks2utr" version))
-              (sha256
-               (base32
-                "104il0kk61q07b58g9xrss7xflwlbx4kzsmw9iih99lhfsii0wzg"))))
+    (version "1.5.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/haessar/peaks2utr")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1b4qiccp5j394pzqd1d4ss3k90zv3kdr84lykl6p8izn3k85b2bl"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:test-flags
-      ;; These tests fail because file names are not URLs.
-      '(list "-k" (string-join
-                   (list "not test_forward_strand_annotations"
-                         "test_matching_chr"
-                         "test_reverse_strand_annotations")
-                   " and not "))
       #:phases
-      '(modify-phases %standard-phases
-         (add-after 'unpack 'relax-requirements
-           (lambda _
-             (substitute* "setup.cfg"
-               (("==") ">=")))))))
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'relax-requirements
+            (lambda _
+              (substitute* "setup.cfg"
+                (("==") ">=")
+                ;; See: <https://github.com/haessar/peaks2utr/issues/47>.
+                (("numpy >= 1.21.4, <= 1.26.4") "numpy >= 1.21.4")))))))
+    (native-inputs
+     (list python-pytest
+           python-setuptools))
     (propagated-inputs
      (list python-asgiref
            python-gffutils
            python-importlib-resources
-           macs
-           python-numpy-1
+           macs-3
+           python-numpy
            python-psutil
            python-pybedtools
            python-pysam
@@ -3415,7 +3414,6 @@ encountered in PDB files prior to simulation tasks.")
            python-tqdm
            python-typing-extensions
            python-zipp))
-    (native-inputs (list python-setuptools python-wheel))
     (home-page "https://github.com/haessar/peaks2utr")
     (synopsis "Python CLI for annotating three prime UTR")
     (description
@@ -3864,7 +3862,6 @@ raw/ed14e050b2b75e7f4ddb73d512fbe928bbdb2b85")
            python-scipy))
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-pytest-datadir
            python-pytest-doctestplus
            python-setuptools
@@ -4290,7 +4287,6 @@ e.g. microbiome samples, genomes, metagenomes.")
     (native-inputs
      (list python-cython
            python-pytest
-           python-pytest-cov
            python-setuptools
            python-wheel))
     (propagated-inputs
@@ -6966,7 +6962,6 @@ and v1.1 to v1.2.")
      (list python-mypy-extensions
            python-pytest
            python-pytest-mock
-           python-pytest-runner
            python-setuptools
            python-wheel))
     (propagated-inputs
@@ -8846,7 +8841,8 @@ high-throughput sequencing (HTS) assays")
          ;; Needed by tests
          (add-after 'unpack 'set-HOME
            (lambda _ (setenv "HOME" "/tmp"))))))
-    (propagated-inputs (list python-appdirs
+    (propagated-inputs (list mysql-connector-python
+                             python-appdirs
                              python-biopython
                              python-click
                              python-colorama
@@ -8854,7 +8850,6 @@ high-throughput sequencing (HTS) assays")
                              python-filelock
                              python-loguru
                              python-mygene
-                             python-mysql-connector-python
                              python-norns
                              python-numpy
                              python-pandas
@@ -9810,29 +9805,39 @@ sequencing tag position and orientation.")
 (define-public macs-3
   (package
     (name "macs")
-    (version "3.0.3")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/macs3-project/MACS")
-                    (commit (string-append "v" version))
-                    (recursive? #true)))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "08hi0a2a0md9gfg7jc75wxv69rggv2yqfd1hyrg4mi5bhi712m0v"))))
+    (version "3.0.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/macs3-project/MACS")
+              (commit (string-append "v" version))
+              (recursive? #true)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "16cv6bvvppi0z69r5l357ai8x4jg61rx8xrvcapk1wz6mh9naf5s"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      ;; AssertionError: np.float32(1.0) != np.float64(-1.0)
+      ;; calculated step by step:
+      ;;  6.559423e-18
+      ;; expected:
+      ;;  -2.98155597e-18
+      #~(list (string-append "--deselect=test/test_SignalProcessing.py::"
+                             "Test_maxima::test_implement_smooth_here"))))
+    (native-inputs
+     (list python-cython
+           python-pytest
+           python-setuptools
+           zlib))
     (propagated-inputs
      (list python-cykhash
            python-hmmlearn
            python-numpy
            python-scikit-learn
            python-scipy))
-    (native-inputs
-     (list python-cython
-           python-pytest
-           python-setuptools
-           zlib))
     (home-page "https://github.com/macs3-project/MACS")
     (synopsis "Model based analysis for ChIP-Seq data")
     (description
@@ -14305,11 +14310,7 @@ quality control are provided.")
             (lambda _
               (substitute* "setup.cfg"
                 (("intervaltree~=3.0.2") "intervaltree")
-                (("termcolor~=1.1.0") "termcolor"))))
-          (add-after 'unpack 'fix-pytest-config
-            (lambda _
-              (substitute* "pyproject.toml"
-                ((" --cov=gdc_client --cov-report term") "")))))))
+                (("termcolor~=1.1.0") "termcolor")))))))
     (native-inputs
      (list python-flask
            python-httmock
@@ -20230,13 +20231,7 @@ fasta subsequences.")
               " and not test_roundtrip"
               ;; This test depends on ipytree, which contains a lot of
               ;; minified JavaScript.
-              " and not test_print_trees"))
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'fix-pytest-config
-            (lambda _
-              (substitute* "pyproject.toml"
-                ((".*--cov.*") "")))))))
+              " and not test_print_trees"))))
     (native-inputs
      (list python-hatchling
            python-pytest))
@@ -22349,37 +22344,6 @@ combinatorial configurations.\", G. Ehrlich - Journal of the ACM (JACM),
 1973. (Algorithm 7.)")
     (license license:expat)))
 
-(define-public fsom
-  (let ((commit "a6ef318fbd347c53189384aef7f670c0e6ce89a3"))
-    (package
-      (name "fsom")
-      (version (git-version "0.0.0" "1" commit))
-      (source (origin
-        (method git-fetch)
-        (uri (git-reference
-              (url "https://github.com/ekg/fsom/")
-              (commit commit)))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32 "0gw1lpvr812pywg9y546x0h1hhj261xwls41r6kqhddjlrcjc0pi"))))
-      (build-system gnu-build-system)
-      (arguments
-       `(#:tests? #f ; There are no tests to run.
-         #:phases
-         (modify-phases %standard-phases
-           (delete 'configure) ; There is no configure phase.
-           (replace 'install
-             (lambda* (#:key outputs #:allow-other-keys)
-               (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
-                 (install-file "fsom" bin)))))))
-      (native-inputs
-       (list gcc-6))
-      (home-page "https://github.com/ekg/fsom")
-      (synopsis "Manage SOM (Self-Organizing Maps) neural networks")
-      (description "A tiny C library for managing SOM (Self-Organizing Maps)
-neural networks.")
-      (license license:gpl3))))
-
 (define-public fastahack
   (package
     (name "fastahack")

gnu/packages/bittorrent.scm

@@ -86,7 +86,6 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix download)
   #:use-module (guix gexp)
@@ -533,8 +532,9 @@ and will take advantage of multiple processor cores where possible.")
     (inputs (list boost-1.83 openssl))
     (native-inputs
      (list libfaketime
-           python-wrapper
-           pkg-config))
+           pkg-config
+           python-setuptools
+           python-wrapper))
     (home-page "https://www.libtorrent.org/")
     (synopsis "Feature-complete BitTorrent implementation")
     (description

gnu/packages/boost.scm

@@ -83,9 +83,6 @@
     (build-system gnu-build-system)
     (arguments
      (list
-      #:imported-modules %pyproject-build-system-modules
-      #:modules `(((guix build pyproject-build-system) #:select (python-version))
-                  ,@%default-gnu-modules)
       #:tests? #f
       #:configure-flags
       #~(let ((icu (dirname (dirname (search-input-file
@@ -94,17 +91,26 @@
            ;; Auto-detection looks for ICU only in traditional
            ;; install locations.
            (string-append "--with-icu=" icu)
-           ;; Ditto for Python.
-           #$@(if (%current-target-system)
-                  #~()
-                  #~((let ((python (dirname (dirname (search-input-file
-                                                      %build-inputs
-                                                      "bin/python")))))
-                       (string-append "--with-python-root=" python)
-                       (string-append "--with-python=" python
-                                      "/bin/python")
-                       (string-append "--with-python-version="
-                                      (python-version python)))))
+           ;; Ditto for Python.  The Gexp can't be evaluated if python is not
+           ;; in the inputs (e.g. boost-for-mysql), so delay its evaluation
+           ;; after checking for python, rather than concurrently.
+           #$@(force
+               (if (or (%current-target-system)
+                       (not (this-package-input "python-minimal-wrapper")))
+                   (delay
+                     #~())
+                   (delay
+                     #~((let ((python (dirname (dirname (search-input-file
+                                                         %build-inputs
+                                                         "bin/python")))))
+                          (string-append "--with-python-root=" python)
+                          (string-append "--with-python=" python
+                                         "/bin/python")
+                          (string-append "--with-python-version="
+                                         #$(version-major+minor
+                                            (package-version
+                                             (this-package-input
+                                              "python-minimal-wrapper")))))))))
            "--with-toolset=gcc"))
       #:make-flags
       #~(list "threading=multi" "link=shared"
@@ -200,29 +206,39 @@
           (replace 'install
             (lambda* (#:key make-flags #:allow-other-keys)
               (apply invoke "./b2" "install" make-flags)))
-          #$@(if (%current-target-system)
-                 #~()
-                 #~((add-after 'install 'provide-libboost_python
-                      (lambda* (#:key make-flags inputs outputs #:allow-other-keys)
-                        (let* ((static? (member "link=static" make-flags))
-                               (libext (if static? ".a" ".so"))
-                               (python (dirname (dirname (search-input-file
-                                                          inputs "bin/python"))))
-                               (python-version (python-version python))
-                               (libboost_pythonNN
-                                (string-append "libboost_python"
-                                               (string-join (string-split
-                                                             python-version #\.)
-                                                            "")
-                                               libext)))
-                          (with-directory-excursion (string-append #$output "/lib")
-                            (symlink libboost_pythonNN
-                                     (string-append "libboost_python" libext))
-                            ;; Some packages only look for the major version.
-                            (symlink libboost_pythonNN
-                                     (string-append "libboost_python"
-                                                    (string-take python-version 1)
-                                                    libext)))))))))))
+          #$@(force  ; See above for why the force is necessary.
+              (if (or (%current-target-system)
+                      (not (this-package-input "python-minimal-wrapper")))
+                  (delay
+                    #~())
+                  (delay
+                    #~((add-after 'install 'provide-libboost_python
+                         (lambda* (#:key make-flags inputs outputs
+                                   #:allow-other-keys)
+                           (let* ((static? (member "link=static" make-flags))
+                                  (ext (if static? ".a" ".so"))
+                                  (python (dirname
+                                           (dirname (search-input-file
+                                                     inputs "bin/python"))))
+                                  (python-version
+                                   #$(version-major+minor
+                                      (package-version
+                                       (this-package-input
+                                        "python-minimal-wrapper"))))
+                                  (NN (string-join (string-split
+                                                    python-version #\.)
+                                                   ""))
+                                  (libboost_pythonNN
+                                   (string-append "libboost_python" NN ext))
+                                  (major (string-take python-version 1)))
+                             (with-directory-excursion
+                                 (string-append #$output "/lib")
+                               (symlink libboost_pythonNN
+                                        (string-append "libboost_python" ext))
+                               ;; Some packages only look for the major version.
+                               (symlink libboost_pythonNN
+                                        (string-append "libboost_python"
+                                                       major ext)))))))))))))
     (inputs
      (append
       (list icu4c zlib)

gnu/packages/build-tools.scm

@@ -94,7 +94,6 @@
   #:use-module (guix build-system hare)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system trivial)
   #:use-module (guix deprecation)
   #:use-module (guix download)
@@ -275,14 +274,14 @@ generate such a compilation database.")
 (define-public bmake
   (package
     (name "bmake")
-    (version "20260313")
+    (version "20260406")
     (source
      (origin
        (method url-fetch)
        (uri (string-append
              "http://www.crufty.net/ftp/pub/sjg/bmake-" version ".tar.gz"))
        (sha256
-        (base32 "0xgryknmv625idw37rq89mpl5rymwdb15j5w8zxwy1gf8b6z7j3n"))
+        (base32 "09nzd9v12n2pwxmf67056kzjnvxcpk5q2x1fs5qkrsk1ssh5yvpd"))
        (patches (search-patches "bmake-run-check-separately.patch"))))
     (build-system gnu-build-system)
     (inputs
@@ -432,9 +431,8 @@ files and generates build instructions for the Ninja build system.")
     (arguments
      (list
       #:tests? #f                       ;disabled to avoid extra dependencies
-      ;; Essentially a lighter copy of the former python-build-system.
-      ;; Using it rather than pyproject-build-system allows to edit the latter
-      ;; without a C++ world rebuild.
+      ;; Custom build steps to prevent using pyproject-build-system which
+      ;; allows to edit the latter without a C++ world rebuild.
       #:phases
       #~(modify-phases %standard-phases
           (delete 'bootstrap)

gnu/packages/c.scm

@@ -54,7 +54,6 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix store)
   #:use-module (gnu packages)
   #:use-module (gnu packages bash)

gnu/packages/calendar.scm

@@ -45,7 +45,6 @@
   #:use-module (guix build-system go)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system pyproject)
-  #:use-module ((guix build-system python) #:select (pypi-uri))
   #:use-module (gnu packages admin)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages base)

gnu/packages/check.scm

@@ -131,7 +131,6 @@
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system trivial)
   #:use-module (ice-9 match)
   #:use-module (srfi srfi-1))
@@ -1882,7 +1881,6 @@ http server.")
     (arguments (list #:tests? #false)) ;no tests included
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-setuptools
            python-wheel
            python-xmlschema))
@@ -1915,42 +1913,6 @@ XML output")
 decorators from external files.")
     (license license:expat)))
 
-(define-public python-pytest-random-order
-  (package
-    (name "python-pytest-random-order")
-    (version "1.1.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "pytest-random-order" version))
-       (sha256
-        (base32 "104hww3b86jchk41kjhyycr541pd2dfgqkww6lx5y70z9z9xfwj4"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:test-flags
-      ;; AttributeError: module 'py' has no attribute 'code'.
-      #~(list "-k" (string-append "not test_it_works_with_actual_tests"
-                                  " and not test_failed_first"
-                                  " and not test_doctests"))))
-    (native-inputs
-     (list python-pytest-xdist
-           python-setuptools
-           python-py
-           python-wheel))
-    (propagated-inputs
-     (list python-pytest))
-    (home-page "https://github.com/jbasko/pytest-random-order")
-    (synopsis "Pytest plugin to randomize the order of tests")
-    (description "@code{pytest-random-order} is a Pytest plugin that
-randomizes the order of tests.  This can be useful to detect a test that
-passes just because it happens to run after an unrelated test that leaves the
-system in a favourable state.  The plugin allows user to control the level of
-randomness they want to introduce and to disable reordering on subsets of
-tests.  Tests can be rerun in a specific order by passing a seed value
-reported in a previous test run.")
-    (license license:expat)))
-
 (define-public python-pytest-runner
   (package
     (name "python-pytest-runner")
@@ -2956,12 +2918,8 @@ mypy plugins.")
                            "and not upstream_url"))))
     (native-inputs
      (list python-pytest
-           python-pytest-black
            python-pytest-checkdocs
-           python-pytest-cov
            python-pytest-enabler
-           python-pytest-flake8
-           python-pytest-mypy
            python-setuptools
            python-wheel))
     (propagated-inputs
@@ -3086,7 +3044,6 @@ possible to write plugins to add your own checks.")
            python-path
            python-pyhamcrest
            python-pytest
-           python-pytest-html
            python-setuptools))
     (propagated-inputs
      (list python-colorama
@@ -3131,7 +3088,7 @@ time by mocking the datetime module.")
 (define-public python-flaky
   (package
     (name "python-flaky")
-    (version "3.8.1")
+    (version "3.8.1")  ; On bump, remove some skipped tests in python-cherrypy.
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "flaky" version))
@@ -3719,30 +3676,6 @@ system.  The code under test requires no modification to work with pyfakefs.")
 directories and files.")
     (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))
-    (native-inputs (list python-setuptools python-wheel))
-    (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

@@ -28,7 +28,6 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix download)
   #:use-module (guix gexp)
   #:use-module (guix git-download)
@@ -580,7 +579,7 @@ stored with user-specified precision.")
            python-sphinx))
     (inputs
      (list fftwf
-           `(,hwloc-2 "lib")
+           `(,hwloc "lib")
            libtirpc
            lmfit
            muparser
@@ -826,7 +825,7 @@ colleagues, or to generate pre-rendered animations.")
 (define-public python-pyscf
   (package
     (name "python-pyscf")
-    (version "2.9.0")
+    (version "2.12.1")
     (source
      (origin
        (method git-fetch)
@@ -835,14 +834,10 @@ colleagues, or to generate pre-rendered animations.")
               (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1lj48c749aqf9zd5xbshjsfr0y972r2nsm8lf3760jbfadg9jdsi"))))
+        (base32 "00q5c0r5yzp05m65679164s7jzm9678b63msm8g7953vh8v9g25y"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:modules
-      '((guix build pyproject-build-system)
-        (guix build utils)
-        (ice-9 textual-ports))
       ;; Some tests take a very long time and libxc support is not enabled.
       #:tests? #f
       #:phases
@@ -868,16 +863,8 @@ colleagues, or to generate pre-rendered animations.")
                          "-DBUILD_XCFUN=OFF"
                          "-DBUILD_LIBCINT=OFF"))))))))
     (native-inputs
-     (list
-      cmake-minimal
-      ;; HACK: Add gcc, make tune work.
-      ;; build-system-with-tuning-compiler on guix/transformations.scm
-      ;; want to find compiler on the build-inputs, but gcc is on the
-      ;; python-build-system's host-inputs, so when tune it , will report:
-      ;; "failed to determine which compiler is used"
-      (canonical-package gcc)
-      python-setuptools
-      python-wheel))
+     (list cmake-minimal
+           python-setuptools))
     (inputs
      (list
       ;; Use qcint when tuning for x86_64.

gnu/packages/cinnamon.scm

@@ -30,7 +30,6 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (gnu packages)
   #:use-module (gnu packages admin)
   #:use-module (gnu packages autotools)

gnu/packages/cmake.scm

@@ -47,7 +47,6 @@
   #:use-module (guix build-system copy)
   #:use-module (guix build-system emacs)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module ((guix search-paths) #:select ($SSL_CERT_DIR $SSL_CERT_FILE))
   #:use-module (gnu packages)
   #:use-module (gnu packages backup)

gnu/packages/code.scm

@@ -49,7 +49,6 @@
   #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system cmake)
-  #:use-module ((guix build-system python) #:select (pypi-uri))
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system trivial)
   #:use-module (guix build-system go)

gnu/packages/codex.scm

@@ -18,10 +18,10 @@
 
 ;;; This module is separate from (gnu packages rust-apps) to avoid a
 ;;; circular module dependency: (gnu packages rust-sources), which
-;;; defines rust-codex-0.98.0, transitively loads (gnu packages
+;;; defines rust-codex-0.120.0, transitively loads (gnu packages
 ;;; rust-apps) through its #:use-module chain.  If the codex package
 ;;; lived in rust-apps.scm, loading rust-sources would trigger loading
-;;; rust-apps before rust-codex-0.98.0 is defined, causing an unbound
+;;; rust-apps before rust-codex-0.120.0 is defined, causing an unbound
 ;;; variable error.
 
 (define-module (gnu packages codex)
@@ -36,33 +36,41 @@
   #:use-module (gnu packages base)
   #:use-module (gnu packages cmake)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages linux)
   #:use-module (gnu packages libunwind)
   #:use-module (gnu packages llvm)
+  #:use-module (gnu packages lsof)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
   #:use-module (gnu packages rust-sources)
   #:use-module (gnu packages sqlite)
+  #:use-module (gnu packages textutils)
+  #:use-module (gnu packages nss)
   #:use-module (gnu packages tls)
-  #:use-module (gnu packages version-control))
+  #:use-module (gnu packages version-control)
+  #:use-module (gnu packages virtualization))
 
 (define-public codex
   (package
     (name "codex")
-    (version (package-version rust-codex-0.98.0))
+    (version (package-version rust-codex-0.120.0))
     (source
      (origin
-       (inherit (package-source rust-codex-0.98.0))
+       (inherit (package-source rust-codex-0.120.0))
        (patches (search-patches
-                 "codex-0.98.0-remove-patch-sections.patch"
+                 "codex-acp-0.11.1-disable-code-mode.patch"
+                 "rust-codex-0.117.0-remove-patch-sections.patch"
+                 "rust-codex-0.120.0-connectors-cache-test-race.patch"
+                 "rust-codex-0.120.0-remove-libwebrtc.patch"
                  "rust-codex-0.98.0-test-shebangs.patch"
-                 "rust-codex-0.98.0-test-timeout.patch"))))
+                 "rust-codex-0.120.0-test-timeout.patch"))))
     (build-system cargo-build-system)
     (arguments
      (list
       #:install-source? #f
       #:cargo-install-paths '(list "cli" "exec" "exec-server"
-                                   "linux-sandbox" "mcp-server" "network-proxy"
+                                   "linux-sandbox" "mcp-server"
                                    "app-server" "tui")
       ;; schema_fixtures_match_generated (upstream fixture is stale:
       ;; FileChange::Update in codex-protocol gained old_content,
@@ -71,72 +79,55 @@
       #:cargo-test-flags '(list "--workspace"
                                 "--exclude" "codex-app-server-protocol"
                                 "--"
-                                ;; These tests exercise sandbox denial and
-                                ;; escalation, which requires Landlock to
-                                ;; cleanly deny filesystem access.  Inside the
-                                ;; build container Landlock returns NotEnforced
-                                ;; and the sandbox binary panics instead.
-                                ;; Disabling Landlock would not help either,
-                                ;; since these tests need a working sandbox to
-                                ;; have anything to deny and escalate.
+                                ;;; BEGIN Landlock returns NotEnforced
+                                ;;; in the build container; the sandbox
+                                ;;; binary panics instead of cleanly
+                                ;;; denying filesystem access.
+                                ;; Sandbox denial and escalation tests.
                                 "--skip" "sandbox_denied_shell_returns_original_output"
+                                ;; Sandbox denial and escalation tests.
                                 "--skip" "shell_escalated_permissions_rejected_then_ok"
+                                ;; Sandbox denial and escalation tests.
                                 "--skip" "unified_exec_runs_under_sandbox"
-                                ;; These tests (in codex-exec) directly call
-                                ;; spawn_command_under_linux_sandbox to verify
-                                ;; that python and bash work correctly inside
-                                ;; the Landlock sandbox.  The sandbox binary
-                                ;; (codex-exec) panics with LandlockRestrict
-                                ;; (exit code 101) before the inner command
-                                ;; even starts.
+                                ;; codex-exec: spawn_command_under_linux_sandbox
+                                ;; panics with LandlockRestrict (exit 101).
                                 "--skip" "python_getpwuid_works_under_sandbox"
+                                ;; Same as above.
                                 "--skip" "python_multiprocessing_lock_works_under_sandbox"
+                                ;; Same as above.
                                 "--skip" "sandbox_distinguishes_command_and_policy_cwds"
-                                ;; These linux-sandbox tests directly invoke
-                                ;; the Landlock sandbox via
-                                ;; process_exec_tool_call; same root cause.
+                                ;; linux-sandbox: process_exec_tool_call
+                                ;; invokes Landlock; same panic.
                                 "--skip" "test_writable_root"
+                                ;; Same as above.
                                 "--skip" "test_timeout"
+                                ;; Same as above.
                                 "--skip" "test_root_read"
+                                ;; Same as above.
                                 "--skip" "test_dev_null_write"
+                                ;; Same as above.
                                 "--skip" "test_no_new_privs_is_enabled"
-                                ;; This test iterates many approval scenarios;
-                                ;; one of them
-                                ;; (danger_full_access_on_request_allows_network)
-                                ;; runs a command through the Landlock sandbox
-                                ;; binary, which panics with LandlockRestrict
-                                ;; inside the build container.  Cargo --skip
-                                ;; cannot target individual scenarios, so we
-                                ;; skip the entire matrix.
+                                ;; One scenario runs through Landlock
+                                ;; which panics; cargo --skip cannot
+                                ;; target individual scenarios.
                                 "--skip" "approval_matrix_covers_all_modes"
-                                ;; This test verifies session-level patch
-                                ;; approval caching: approve once, skip
-                                ;; future prompts for the same file.  When
-                                ;; Landlock is unavailable (as in the Guix
-                                ;; build container) the sandbox binary panics,
-                                ;; triggering the escalation-retry path, which
-                                ;; interferes with the approval cache and
-                                ;; causes a spurious re-prompt on the second
-                                ;; patch.
+                                ;; Landlock panic triggers escalation-retry
+                                ;; which interferes with the approval cache.
                                 "--skip" "approving_apply_patch_for_session_skips_future_prompts_for_same_file"
                                 ;; These tests expect to interrupt a
                                 ;; long-running 'sleep 60' and receive
-                                ;; TurnAborted.  Default test config is
-                                ;; OnRequest + ReadOnly.  What happens:
+                                ;; TurnAborted.  What happens:
                                 ;;
                                 ;; 1. ReadOnly wraps the command with
                                 ;;    codex-linux-sandbox (Landlock-based).
-                                ;; 2. Landlock is unavailable in the Guix
-                                ;;    build container, so the sandbox
-                                ;;    binary exits instantly (~1 ms).
+                                ;; 2. Landlock is unavailable, so the
+                                ;;    sandbox binary exits instantly.
                                 ;; 3. Orchestrator gets SandboxErr::Denied.
                                 ;;    wants_no_sandbox_approval(OnRequest)
-                                ;;    returns false (sandboxing.rs:222),
-                                ;;    so no escalation -- denial returned
-                                ;;    directly.
+                                ;;    returns false, so no escalation --
+                                ;;    denial returned directly.
                                 ;; 4. ToolEmitter::finish sends the error
-                                ;;    to the mock model as
-                                ;;    function_call_output.
+                                ;;    to the mock model.
                                 ;; 5. Second mock SSE response fires,
                                 ;;    turn finishes with TurnComplete.
                                 ;; 6. Op::Interrupt arrives 100 ms later,
@@ -150,74 +141,213 @@
                                 ;; has only one mock response (so the turn
                                 ;; cannot complete first).
                                 "--skip" "interrupt_persists_turn_aborted_marker_in_next_request"
+                                ;; Same causal chain as above.
                                 "--skip" "interrupt_tool_records_history_entries"
-                                ;; Upstream bug: test hardcodes "0.0.0" in the
-                                ;; expected user-agent string but the workspace
-                                ;; version is "0.98.0".
-                                "--skip" "get_user_agent_returns_current_codex_user_agent"
-                                ;; Same upstream bug: mcp-server tests
-                                ;; check the initialize response which
-                                ;; includes "version": "0.0.0" but the
-                                ;; server returns "0.98.0".
+                                ;; WorkspaceWrite sandbox policy wraps
+                                ;; commands with codex-linux-sandbox;
+                                ;; Landlock panics, command never runs,
+                                ;; exit_code is None instead of Some(0).
+                                "--skip" "request_permissions_grants_apply_to_later_exec_command_calls"
+                                ;; Same root cause.
+                                "--skip" "request_permissions_grants_apply_to_later_shell_command_calls"
+                                ;; Same root cause.
+                                "--skip" "partial_request_permissions_grants_do_not_preapprove_new_permissions"
+                                ;;; END Landlock
+                                ;;; BEGIN mcp_process.rs initialize
+                                ;;; assertion expects "version":"0.0.0"
+                                ;;; but the server returns "0.120.0".
                                 "--skip" "test_codex_tool_passes_base_instructions"
                                 "--skip" "test_shell_command_approval_triggers_elicitation"
                                 "--skip" "test_patch_approval_triggers_elicitation"
-                                ;; These codex-exec-server tests need
-                                ;; "dotslash", a Meta tool that lazily
-                                ;; downloads pre-built binaries from a
-                                ;; JSON manifest.  The test helper
-                                ;; create_transport runs
-                                ;; `dotslash -- fetch <path>` to obtain a
-                                ;; custom bash binary described in
-                                ;; exec-server/tests/suite/bash.
-                                ;; dotslash is not available in the build
-                                ;; container.
-                                "--skip" "list_tools"
-                                "--skip" "accept_elicitation_for_prompt_rule"
-                                ;;; Test isolation bug: each test in
-                                ;;; state/src/runtime.rs calls
-                                ;;; unique_temp_dir() to get its own
-                                ;;; temporary directory (and thus its
-                                ;;; own SQLite database).  That function
-                                ;;; names directories using the current
-                                ;;; nanosecond timestamp, so when tests
-                                ;;; run in parallel several can receive
-                                ;;; the same name and open the same
-                                ;;; database.  The initial SQLite
-                                ;;; migration runs CREATE TABLE threads
-                                ;;; (without IF NOT EXISTS), so any init
-                                ;;; after the first panics with "table
-                                ;;; threads already exists".  Any of
-                                ;;; these tests
-                                ;;; can be the victim.
+                                ;;; END version mismatch
+                                ;;; BEGIN Test isolation bug:
+                                ;;; unique_temp_dir() in
+                                ;;; state/src/runtime.rs names dirs
+                                ;;; using nanosecond timestamps, so
+                                ;;; parallel tests can collide.  The
+                                ;;; SQLite migration runs CREATE TABLE
+                                ;;; threads (without IF NOT EXISTS),
+                                ;;; so the second init panics with
+                                ;;; "table threads already exists".
                                 "--skip" "init_removes_legacy_state_db_files"
                                 "--skip" "upsert_and_get_thread_memory"
                                 "--skip" "get_last_n_thread_memories_for_cwd_matches_exactly"
                                 "--skip" "upsert_thread_memory_errors_for_unknown_thread"
                                 "--skip" "get_last_n_thread_memories_for_cwd_zero_returns_empty"
                                 "--skip" "get_last_n_thread_memories_for_cwd_does_not_prefix_match"
-                                "--skip" "deleting_thread_cascades_thread_memory")
+                                "--skip" "deleting_thread_cascades_thread_memory"
+                                ;;; END SQLite test isolation
+                                ;; The test spawns 'sh' after
+                                ;; env_clear() with an empty env map;
+                                ;; glibc execvp uses confstr(_CS_PATH)
+                                ;; ("/bin:/usr/bin") when PATH is
+                                ;; unset, but /bin/sh does not exist
+                                ;; in the build container.
+                                "--skip" "cancellation_expiration_keeps_process_alive_until_terminated"
+                                ;; Proxy baseline_policy returns 403
+                                ;; "not_allowed_local" for example.com;
+                                ;; test expects 200.
+                                "--skip" "managed_network_proxy_decider_survives_full_access_start"
+                                ;;; BEGIN bash_snapshot_script() uses
+                                ;;; "compgen -e" to list exports but
+                                ;;; bash-minimal lacks programmable
+                                ;;; completion; export section is empty.
+                                ;; stdout.contains("VALID_NAME") fails.
+                                "--skip" "bash_snapshot_filters_invalid_exports"
+                                ;; stdout.contains("MULTILINE_CERT") fails.
+                                "--skip" "bash_snapshot_preserves_multiline_exports"
+                                ;; snapshot.contains("PATH") fails.
+                                "--skip" "linux_bash_snapshot_includes_sections"
+                                ;;; END compgen
+                                ;; substitute* patches PAGER to store
+                                ;; path of cat; test expects bare "cat".
+                                "--skip" "unified_exec_env_injects_defaults"
+                                ;;; BEGIN V8 disabled (codex-code-mode
+                                ;;; default-features = false).
+                                "--skip" "suite::code_mode::"
+                                "--skip" "suite::js_repl::"
+                                "--skip" "suite::view_image::js_repl_"
+                                ;;; END V8 disabled
+                                ;;; BEGIN same compgen root cause:
+                                ;;; assert_posix_snapshot_sections
+                                ;;; asserts snapshot.contains("PATH").
+                                "--skip" "linux_shell_command_uses_shell_snapshot"
+                                "--skip" "linux_unified_exec_uses_shell_snapshot"
+                                "--skip" "shell_command_snapshot_still_intercepts_apply_patch"
+                                ;;; END compgen / shell snapshot
+                                ;;; BEGIN These sandbox tests set
+                                ;;; exclude_slash_tmp: true which makes
+                                ;;; bwrap exclude /tmp from its mount
+                                ;;; namespace.  Since Guix builds under
+                                ;;; /tmp, the codex-linux-sandbox binary
+                                ;;; becomes invisible to bwrap even though
+                                ;;; the test adds the helper dir as a
+                                ;;; filesystem carve-out -- the parent /tmp
+                                ;;; bind-mount is absent so the carve-out
+                                ;;; has nothing to carve out of.
+                                "--skip" "sandbox_reenables_writable_subpaths_under_unreadable_parents"
+                                "--skip" "managed_proxy_mode_routes_through_bridge_and_blocks_direct_egress"
+                                ;;; END exclude_slash_tmp
+                                ;; Expects 3 TerminalInteraction events
+                                ;; across timed poll windows; under CPU
+                                ;; contention events merge into 2.
+                                "--skip" "unified_exec_terminal_interaction_captures_delayed_output"
+                                ;;; BEGIN assert_parallel_duration
+                                ;;; requires < 1600 ms for parallel ops.
+                                ;; Two 300 ms test_sync_tool calls.
+                                "--skip" "read_file_tools_run_in_parallel"
+                                ;; Two "sleep 0.25" shell commands.
+                                "--skip" "shell_tools_run_in_parallel"
+                                ;; One test_sync_tool + one shell sleep.
+                                "--skip" "mixed_parallel_tools_run_in_parallel"
+                                ;;; END assert_parallel_duration
+                                ;; Asserts elapsed >= 4500 ms and
+                                ;; < 5800 ms for a 5 s timeout; under
+                                ;; contention elapsed drifts past 5800.
+                                "--skip" "remote_models_request_times_out_after_5s"
+                                ;; Queued inter-agent mail must be
+                                ;; injected between the reasoning/
+                                ;; commentary item and the gate release;
+                                ;; under contention the gate fires before
+                                ;; the mail is processed, so the snapshot
+                                ;; shows the stale function_call instead
+                                ;; of the expected mail message.
+                                "--skip" "queued_inter_agent_mail_triggers_follow_up_after_commentary_message_item"
+                                ;; Same root cause: snapshot mismatch at
+                                ;; pending_input.rs assert_two_responses_
+                                ;; input_snapshot; expects mail at position
+                                ;; 04 but gets function_call/shell instead.
+                                "--skip" "queued_inter_agent_mail_triggers_follow_up_after_reasoning_item"
+                                ;;; BEGIN DNS for hostnames like
+                                ;;; example.com fails in the build
+                                ;;; sandbox.  host_resolves_to_non_
+                                ;;; public_ip() in runtime.rs treats
+                                ;;; failed DNS as non-public and
+                                ;;; returns NotAllowedLocal, so tests
+                                ;;; expecting Allowed or Decider get
+                                ;;; Deny/BaselinePolicy instead.
+                                "--skip" "host_blocked_requires_allowlist_match"
+                                "--skip" "add_allowed_domain_removes_matching_deny_entry"
+                                "--skip" "host_blocked_subdomain_wildcards_exclude_apex"
+                                "--skip" "host_blocked_global_wildcard_allowlist_allows_public_hosts_except_denylist"
+                                "--skip" "evaluate_host_policy_emits_domain_event_for_decider_ask"
+                                "--skip" "evaluate_host_policy_emits_domain_event_for_decider_allow_override"
+                                "--skip" "http_connect_accept_blocks_in_limited_mode"
+                                "--skip" "http_connect_accept_allows_allowlisted_host_in_full_mode"
+                                "--skip" "mitm_policy_blocks_disallowed_method_and_records_telemetry"
+                                ;;; END DNS failure / NotAllowedLocal
+                                ;;; BEGIN Flaky: wiremock mock expects
+                                ;;; 1 POST to /codex/safety/arc but
+                                ;;; receives 0.  Passes in some builds,
+                                ;;; fails in others with identical code
+                                ;;; and env.  The identical custom_
+                                ;;; variant always passes; only the
+                                ;;; CODEX_APPS_MCP_SERVER_NAME variant
+                                ;;; flakes, suggesting a timing race
+                                ;;; in the async POST under contention.
+                                "--skip" "approve_mode_blocks_when_arc_returns_interrupt_for_model"
+                                "--skip" "approve_mode_blocks_when_arc_returns_interrupt_without_annotations"
+                                ;;; END ARC monitor flake
+                                ;;; BEGIN nss-certs sets SSL_CERT_FILE
+                                ;;; which makes build_reqwest_client load
+                                ;;; 171 CA certs via add_root_certificate.
+                                ;;; This changes the reqwest TLS backend
+                                ;;; configuration; the ARC safety POST to
+                                ;;; the localhost mock server never arrives
+                                ;;; (wiremock expects 1 request, gets 0).
+                                "--skip" "approve_mode_blocks_when_arc_returns_interrupt_for_model"
+                                "--skip" "approve_mode_blocks_when_arc_returns_interrupt_without_annotations"
+                                ;;; END nss-certs / ARC monitor
+                                ;; Upstream bug: JsonRpcConnection has
+                                ;; no websocket keepalive or read timeout.
+                                ;; When the exec-server is killed, the
+                                ;; client's reader task blocks on
+                                ;; websocket_reader.next() forever because
+                                ;; TCP doesn't detect the dead peer without
+                                ;; a write or keepalive probe.  Previously
+                                ;; masked because empty env made "sleep 10"
+                                ;; fail instantly; with PATH the process
+                                ;; lives long enough to hit the deadlock.
+                                "--skip" "remote_exec_process_reports_transport_disconnect"
+                                ;; 500 ms timeout on MCP list response
+                                ;; (mcp_server_status.rs timeout at
+                                ;; Duration::from_millis(500)).  With
+                                ;; nss-certs TLS now works, so the
+                                ;; startup plugin sync HTTP requests
+                                ;; (chatgpt.com, api.github.com) wait
+                                ;; for TCP timeout instead of failing
+                                ;; instantly at TLS, eating the budget.
+                                "--skip" "mcp_server_status_list_tools_and_auth_only_skips_slow_inventory_calls")
       #:cargo-package-crates
       ''(;;; Tier 0: No internal deps.
+         "codex-ansi-escape"
          "codex-async-utils"
+         "codex-backend-openapi-models"
          "codex-client"
          "codex-execpolicy"
          "codex-file-search"
-         "codex-git"
+         "codex-git-utils"
          "codex-keyring-store"
+         "codex-process-hardening"
          "codex-utils-absolute-path"
          "codex-utils-cache"
          "codex-utils-cargo-bin"
+         "codex-utils-elapsed"
+         "codex-utils-fuzzy-match"
          "codex-utils-home-dir"
          "codex-utils-json-to-toml"
+         "codex-utils-path"
+         "codex-utils-plugins"
          "codex-utils-pty"
          "codex-utils-readiness"
+         "codex-utils-rustls-provider"
+         "codex-utils-sleep-inhibitor"
+         "codex-utils-stream-parser"
          "codex-utils-string"
-         "codex-backend-openapi-models"
-         "codex-process-hardening"
-         "codex-ansi-escape"
-         ;;; Tier 1: Depends on tier 0.
+         "codex-utils-template"
+         ;;; Tier 1.
          "codex-utils-image"
+         "codex-utils-output-truncation"
          "codex-apply-patch"
          "codex-protocol"
          "codex-windows-sandbox"
@@ -226,35 +356,60 @@
          "codex-secrets"
          "codex-execpolicy-legacy"
          "codex-debug-client"
+         "codex-analytics"
+         "codex-rollout"
+         "codex-terminal-detection"
+         "codex-utils-approval-presets"
+         "codex-utils-cli"
          ;;; Tier 2.
          "codex-app-server-protocol"
          "codex-rmcp-client"
          "codex-otel"
          "codex-state"
-         "codex-core"
-         "codex-linux-sandbox"
+         "codex-features"
+         "codex-config"
+         "codex-hooks"
+         "codex-instructions"
+         "codex-code-mode"
          "codex-feedback"
+         "codex-skills"
+         "codex-core"
+         "codex-utils-sandbox-summary"
+         "codex-linux-sandbox"
+         "codex-sandboxing"
+         "codex-connectors"
+         "codex-core-skills"
          ;;; Tier 3.
          "codex-arg0"
          "codex-lmstudio"
          "codex-login"
          "codex-ollama"
-         "codex-common"
+         "codex-utils-oss"
          "codex-mcp-server"
          "codex-backend-client"
          "codex-responses-api-proxy"
+         "codex-shell-command"
+         "codex-shell-escalation"
+         "codex-plugin"
+         "codex-model-provider-info"
+         "codex-models-manager"
          ;;; Tier 4.
          "codex-cloud-requirements"
          "codex-exec"
          "codex-exec-server"
-         "codex-stdio-to-uds"
          "codex-network-proxy"
+         "codex-stdio-to-uds"
          "codex-chatgpt"
          "codex-cloud-tasks-client"
+         "codex-cloud-tasks-mock-client"
+         "codex-tools"
+         "codex-mcp"
+         "codex-collaboration-mode-templates"
          ;;; Tier 5.
          "codex-app-server"
          "codex-app-server-test-client"
          "codex-tui"
+         "codex-response-debug-context"
          ;;; Tier 6.
          "codex-cloud-tasks"
          ;; The main executable.
@@ -270,7 +425,7 @@
               ;; Update them to match the actual package version.
               (let ((snap-files (find-files "." "\\.snap$")))
                 (substitute* snap-files
-                  (("\\(v0\\.0\\.0\\) ") "(v0.98.0)")))))
+                  (("\\(v0\\.0\\.0\\)   ") "(v0.120.0) ")))))
           (add-after 'chdir-to-workspace 'patch-git-deps-to-vendor
             (lambda _
               ;; Replace git dependencies with version references so cargo
@@ -279,23 +434,34 @@
                 (("nucleo = \\{ git = [^}]+\\}")
                  "nucleo = \"0.5.0\"")
                 (("runfiles = \\{ git = [^}]+\\}")
-                 "runfiles = \"0.1.0\""))))
-          (add-after 'chdir-to-workspace 'add-version-to-workspace-deps
+                 "runfiles = \"0.1.0\""))
+              ;; Remove workspace members that have unbuildable deps
+              ;; (libwebrtc requires git fetch, v8-poc requires V8).
+              (substitute* "Cargo.toml"
+                (("\"v8-poc\",") "")
+                (("\"code-mode\",") ""))
+              ;; Disable V8 runtime in codex-code-mode: remove path
+              ;; so cargo resolves it from the vendor (where it has
+              ;; optional = true on v8) and disable default features.
+              (substitute* "Cargo.toml"
+                (("codex-code-mode = \\{ path = \"code-mode\" \\}")
+                 "codex-code-mode = { version = \"0.120.0\", default-features = false }"))))
+          (add-after 'patch-git-deps-to-vendor 'add-version-to-workspace-deps
             (lambda _
               ;; cargo package requires all dependencies to have versions.
               ;; cargo package requires all dependencies to have versions.
-              ;; Add version = "0.98.0" to internal path dependencies.
+              ;; Add version = "0.120.0" to internal path dependencies.
               (let ((cargo-files (find-files "." "^Cargo\\.toml$")))
                 (substitute* cargo-files
                   ;; Handle inline deps: name = { path = "..." }
                   (("(codex-[a-z0-9-]+) = \\{ path = " all name)
-                   (string-append name " = { version = \"0.98.0\", path = "))
+                   (string-append name " = { version = \"0.120.0\", path = "))
                   ;; Handle inline deps with package: name = { package = "...", path = "..." }
                   (("(codex-[a-z0-9-]+) = \\{ package = " all name)
-                   (string-append name " = { version = \"0.98.0\", package = "))
+                   (string-append name " = { version = \"0.120.0\", package = "))
                   ;; Handle section deps: [dependencies.X] with path = "..."
                   (("^(path = \"\\.\\./[^\"]*\")" all path-line)
-                   (string-append path-line "\nversion = \"0.98.0\""))))))
+                   (string-append path-line "\nversion = \"0.120.0\""))))))
           (add-after 'chdir-to-workspace 'patch-hardcoded-paths
             (lambda* (#:key inputs #:allow-other-keys)
               (let ((bash-bin (string-append
@@ -325,6 +491,14 @@
                    (string-append "\"" bash-bin "/bash "))
                   (("\"/bin/sh ")
                    (string-append "\"" bash-bin "/sh "))
+                  ;; Single-quoted paths in test assertion strings,
+                  ;; e.g. "exec '/bin/bash' -c ...".  Must match the
+                  ;; double-quoted substitutions above so both sides
+                  ;; of assert_eq!/contains use the store path.
+                  (("'/bin/bash'")
+                   (string-append "'" bash-bin "/bash'"))
+                  (("'/bin/sh'")
+                   (string-append "'" bash-bin "/sh'"))
                   ;; coreutils.
                   (("\"/bin/(cat|cp|date|echo|head|ls|rm|sleep|true|touch)\"" all cmd)
                    (string-append "\"" coreutils-bin "/" cmd "\""))
@@ -339,28 +513,120 @@
                    (string-append "\"" git-bin "/git\""))
                   (("\"/usr/bin/sed\"")
                    (string-append "\"" sed-bin "/sed\"")))
+                ;; Bare Command::new("git") and Command::new("ls")
+                ;; in codex source files that exec internally.
+                (substitute* (find-files "git-utils" "\\.rs$")
+                  (("Command::new\\(\"git\"\\)")
+                   (string-append "Command::new(\"" git-bin "/git\")")))
+                (substitute* "tui/src/get_git_diff.rs"
+                  (("Command::new\\(\"git\"\\)")
+                   (string-append "Command::new(\"" git-bin "/git\")")))
+                (substitute* "core/src/turn_diff_tracker.rs"
+                  (("Command::new\\(\"git\"\\)")
+                   (string-append "Command::new(\"" git-bin "/git\")")))
+                (substitute* "cloud-tasks/src/env_detect.rs"
+                  (("Command::new\\(\"git\"\\)")
+                   (string-append "Command::new(\"" git-bin "/git\")")))
+                (substitute* "core/src/plugins/startup_sync.rs"
+                  (("\"git\",")
+                   (string-append "\"" git-bin "/git\",")))
+                (substitute* "file-search/src/lib.rs"
+                  (("Command::new\\(\"ls\"\\)")
+                   (string-append "Command::new(\"" coreutils-bin "/ls\")")))
+                ;; Neutralize pager with absolute path to cat.
+                (substitute* "core/src/unified_exec/process_manager.rs"
+                  (("\"PAGER\", \"cat\"")
+                   (string-append "\"PAGER\", \"" coreutils-bin "/cat\""))
+                  (("\"GIT_PAGER\", \"cat\"")
+                   (string-append "\"GIT_PAGER\", \"" coreutils-bin "/cat\""))
+                  (("\"GH_PAGER\", \"cat\"")
+                   (string-append "\"GH_PAGER\", \"" coreutils-bin "/cat\"")))
+                ;; Bare /bin/sleep inside a format! string
+                ;; (no surrounding double quotes, so the main
+                ;; pattern does not match).
+                (substitute*
+                  "shell-escalation/src/unix/escalate_server.rs"
+                  (("/bin/sleep")
+                   (string-append coreutils-bin "/sleep")))
                 ;; @SHELL@ placeholder from test-shebangs patch
                 (substitute*
                   (list "rmcp-client/src/program_resolver.rs"
                         "tui/src/external_editor.rs")
                   (("@SHELL@")
                    (string-append bash-bin "/sh")))
-                ;; shebang in test-only file
+                ;; Shebangs inside raw string literals (r#"..."#)
+                ;; that are written to scripts at runtime.  The
+                ;; main "/bin/sh" patterns only match double-quoted
+                ;; occurrences; these shebangs have no surrounding
+                ;; double quotes.
                 (substitute*
-                  "core/tests/suite/user_notification.rs"
+                  (list "core/src/plugins/startup_sync_tests.rs"
+                        "core/tests/suite/client.rs"
+                        "core/tests/suite/js_repl.rs"
+                        "core/tests/suite/skill_approval.rs"
+                        "core/tests/suite/user_notification.rs"
+                        "login/src/auth/auth_tests.rs"
+                        "models-manager/src/manager_tests.rs"
+                        "sandboxing/src/bwrap_tests.rs")
                   (("#!/bin/bash")
-                   (string-append "#!" bash-bin "/bash"))))))
+                   (string-append "#!" bash-bin "/bash"))
+                  (("#!/bin/sh")
+                   (string-append "#!" bash-bin "/sh")))
+                ;; Test helpers pass env: Default::default() to the
+                ;; spawn code which calls env_clear(), leaving
+                ;; processes with no PATH.  Inject the build-time
+                ;; PATH so tests find coreutils, bash, etc.
+                (substitute* (find-files "." "\\.rs$")
+                  (("env: Default::default\\(\\)")
+                   (string-append
+                    "env: std::env::var(\"PATH\")"
+                    ".into_iter()"
+                    ".map(|p| (\"PATH\".to_string(), p))"
+                    ".collect()")))
+                ;; Test-only absolute path; bare name works via PATH.
+                (substitute* "exec-server/tests/exec_process.rs"
+                  (("\"/usr/bin/python3\"")
+                   "\"python3\""))
+                ;; Same empty-env issue but in JSON literals
+                ;; (serde_json::json! macro).
+                (substitute* "exec-server/tests/process.rs"
+                  (("\"env\": \\{\\}")
+                   (string-append
+                    "\"env\": {\"PATH\": \""
+                    (getenv "PATH")
+                    "\"}"))))))
+          (add-before 'build 'set-bubblewrap-source
+            (lambda* (#:key inputs #:allow-other-keys)
+              (setenv "CODEX_BWRAP_SOURCE_DIR"
+                      (string-append
+                       (assoc-ref inputs "bubblewrap-source")
+                       "/"))))
+          (add-before 'build 'create-node-version-file
+            (lambda _
+              (call-with-output-file "guix-vendor/node-version.txt"
+                (lambda (port)
+                  (display "22.22.0" port)))))
           (add-before 'check 'set-home
             (lambda _
-              (setenv "HOME" "/tmp")
+              ;; HOME must not be a prefix of /tmp, otherwise
+              ;; the TUI's path shortener replaces /tmp/... with
+              ;; ~/... and 30 snapshot tests fail.
+              (setenv "HOME" "/tmp/guix-home")
+              (mkdir-p "/tmp/guix-home")
               (setenv "USER" "nixbld"))))))
-    (native-inputs (list clang              ;bindgen uses libclang to parse BoringSSL's C headers
-                         cmake-minimal    ;BoringSSL is compiled from C source
-                         libunwind        ;BoringSSL tests verify stack unwinding in assembly
-                         perl python-minimal ;for tests
-                         pkg-config))
+    (native-inputs `(("bubblewrap" ,bubblewrap) ;tests need bwrap on PATH
+                     ("clang" ,clang)
+                     ("cmake-minimal" ,cmake-minimal)
+                     ("libunwind" ,libunwind)
+                     ("lsof" ,lsof)            ;app-server tests
+                     ("nss-certs-for-test" ,nss-certs-for-test) ;OTLP gRPC TLS
+                     ("perl" ,perl)
+                     ("procps" ,procps)         ;tests use ps
+                     ("python-minimal" ,python-minimal)
+                     ("pkg-config" ,pkg-config)
+                     ("bubblewrap-source" ,(package-source bubblewrap))))
     (inputs (cons* bash-minimal coreutils git-minimal sed
-                   openssl sqlite `(,zstd "lib")
+                   libcap oniguruma openssl sqlite zlib `(,zstd "lib")
                    (cargo-inputs 'codex)))
     (home-page "https://github.com/openai/codex")
     (synopsis "AI-assisted coding CLI and TUI")
@@ -368,13 +634,15 @@
      "Codex is an AI-powered coding assistant that runs in the terminal.
 It provides an interactive TUI for conversations with AI models, with
 support for shell command execution, file editing, and code generation.
-Configure providers via @file{~/.codex/config.toml}.")
+Configure providers via @file{~/.codex/config.toml}.
+
+codex-code-mode's V8 Javascript executor is disabled.")
     (license license:asl2.0)))
 
 (define-public codex-acp
   (package
     (name "codex-acp")
-    (version "0.9.2")
+    (version "0.11.1")
     (source
      (origin
        (method git-fetch)
@@ -383,9 +651,8 @@ Configure providers via @file{~/.codex/config.toml}.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "190sq6s6jfz8dkj1y8305r7x6ln86qqr2j1bnfjci7f1x2wyzmsj"))
-       (patches (search-patches "codex-acp-0.9.2-remove-patch-sections.patch"
-                                "codex-acp-0.9.2-replace-result-flatten.patch"))))
+        (base32 "1rlgkbvrbdl5jhf49sjn2mifn2rq6z0vwf0gard23y1bz6sr3wmr"))
+       (patches (search-patches "codex-acp-0.11.1-remove-patch-sections.patch"))))
     (build-system cargo-build-system)
     (arguments
      (list
@@ -393,13 +660,43 @@ Configure providers via @file{~/.codex/config.toml}.")
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'patch-codex-deps
-            (lambda _
+            (lambda* (#:key inputs #:allow-other-keys)
               ;; Rewrite git dependencies to use vendored sources from rust-codex
               (substitute* "Cargo.toml"
-                (("git = \"https://github.com/zed-industries/codex\", branch = \"acp\"")
-                 "version = \"0.0.0\"")))))))
-    (native-inputs (list pkg-config))
-    (inputs (cons* openssl sqlite `(,zstd "lib") (cargo-inputs 'codex-acp)))
+                (("git = \"https://github.com/openai/codex\", tag = \"rust-v0.117.0\"")
+                 "version = \"0.117.0\""))
+              ;; Disable V8 runtime in codex-code-mode (transitive dep).
+              (let ((port (open-file "Cargo.toml" "a")))
+                (display "
+[dependencies.codex-code-mode]
+version = \"0.117.0\"
+default-features = false
+" port)
+                (close-port port))
+              ;; Point codex-linux-sandbox at system bubblewrap source.
+              (setenv "CODEX_BWRAP_SOURCE_DIR"
+                      (string-append
+                       (assoc-ref inputs "bubblewrap-source")
+                       "/"))))
+          (add-before 'check 'set-home
+            (lambda _
+              (setenv "HOME" "/tmp")
+              (setenv "USER" "nixbld")))
+          (add-before 'build 'create-node-version-file
+            (lambda _
+              ;; codex-core's js_repl uses include_str! to read
+              ;; node-version.txt four directories up from its source;
+              ;; create it where the vendored crate expects it.
+              (call-with-output-file "guix-vendor/node-version.txt"
+                (lambda (port)
+                  (display "22.22.0" port))))))))
+    (native-inputs
+     `(("cmake-minimal" ,cmake-minimal)
+       ("clang" ,clang)
+       ("pkg-config" ,pkg-config)
+       ("bubblewrap-source" ,(package-source bubblewrap))))
+    (inputs (cons* libcap openssl sqlite zlib `(,zstd "lib")
+                   (cargo-inputs 'codex-acp)))
     (home-page "https://github.com/zed-industries/codex-acp")
     (synopsis "ACP-compatible agent bridging Zed Codex with ACP clients")
     (description

gnu/packages/containers.scm

@@ -150,7 +150,7 @@ as created by Podman, CRI-O and containerd.")))
 (define-public crun
   (package
     (name "crun")
-    (version "1.25.1")
+    (version "1.26")
     (source
      (origin
        (method url-fetch)
@@ -160,7 +160,7 @@ as created by Podman, CRI-O and containerd.")))
              "/crun-" version ".tar.gz"))
        (sha256
         (base32
-         "02kksvnja234k8mpq5j7yms8npbpvh8iz3k03h21lwcqzqsb88rx"))))
+         "1hdwk5dpsz9danxiyfli07b7sqid6hr34qmhs5qjl2dcc00is89j"))))
     (build-system gnu-build-system)
     (arguments
      (list

gnu/packages/cpp.scm

@@ -44,7 +44,7 @@
 ;;; Copyright © 2024 Jakob Kirsch <jakob.kirsch@web.de>
 ;;; Copyright © 2025 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;; Copyright © 2025 Sergio Pastor Pérez <sergio.pastorperez@gmail.com>
-;;; Copyright © 2025 Ashish SHUKLA <ashish.is@lostca.se>
+;;; Copyright © 2025, 2026 Ashish SHUKLA <ashish.is@lostca.se>
 ;;; Copyright © 2025 Nicolas Graves <ngraves@ngraves.fr>
 ;;; Copyright © 2025 Romain Garbage <romain.garbage@inria.fr>
 ;;; Copyright © 2024, 2025 Janneke Nieuwenhuizen <janneke@gnu.org>
@@ -78,7 +78,6 @@
   #:use-module (guix build-system copy)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system scons)
   #:use-module (guix modules)
@@ -1904,8 +1903,7 @@ using the string similarity calculations from FuzzyWuzzy.")
           (add-after 'unpack 'fix-pytest-config
             (lambda _
               (substitute* "pyproject.toml"
-                ((" \"pytest-cov\", ") "")
-                ((" --cov-fail-under=90 --cov=cpplint") "")))))))
+                (("\"pytest-cov\", ") "")))))))
     (native-inputs
      (list python-pytest
            python-pytest-timeout
@@ -3360,7 +3358,7 @@ which can evaluate Jsonnet files and expressions.")))
 (define-public simdjson
   (package
     (name "simdjson")
-    (version "3.13.0")
+    (version "4.6.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -3369,7 +3367,7 @@ which can evaluate Jsonnet files and expressions.")))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "005yli56nrkvlyx9g9cq8dczk42r9a18l162i2s5k81lj3y7mcrp"))))
+                "0729mxnc2wjb94gr4znwlzfmgw5w2v9kd8glvn3vnjhkdnd87zry"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f                      ; tests require downloading dependencies

gnu/packages/crypto.scm

@@ -105,7 +105,6 @@
   #:use-module (guix build-system copy)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system perl)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix utils)
   #:use-module (srfi srfi-1)
@@ -276,18 +275,17 @@ Ed448-Goldilocks and Curve448, using the Decaf encoding.")
 (define-public libsodium
   (package
     (name "libsodium")
-    (version "1.0.18")
-    (source (origin
-            (method url-fetch)
-            (uri (list (string-append
-                        "https://download.libsodium.org/libsodium/"
-                        "releases/libsodium-" version ".tar.gz")
-                       (string-append
-                        "https://download.libsodium.org/libsodium/"
-                        "releases/old/libsodium-" version ".tar.gz")))
-            (sha256
-             (base32
-              "1h9ncvj23qbbni958knzsli8dvybcswcjbx0qjjgi922nf848l3g"))))
+    (version "1.0.22")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/jedisct1/libsodium")
+              (commit (string-append version "-RELEASE"))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "05lqdn6nzldsia5mv5a9xfvc5k0kybh9snwv7qsb135gva4bpjwk"))))
     (build-system gnu-build-system)
     (synopsis "Portable NaCl-based crypto library")
     (description

gnu/packages/cups.scm

@@ -62,7 +62,6 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix download)
   #:use-module (guix git-download)

gnu/packages/cybersecurity.scm

@@ -31,7 +31,6 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages check)
   #:use-module (gnu packages cpp)

gnu/packages/databases.scm

@@ -70,6 +70,7 @@
 ;;; Copyright © 2025 bdunahu <bdunahu@operationnull.com>
 ;;; Copyright © 2026 Spencer King <spencer.king@wustl.edu>
 ;;; Copyright © 2026 Peter Polidoro <peter@polidoro.io>
+;;; Copyright © 2026 Josep Bigorra <jjbigorra@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -126,6 +127,7 @@
   #:use-module (gnu packages gperf)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages guile)
+  #:use-module (gnu packages guile-xyz)
   #:use-module (gnu packages icu4c)
   #:use-module (gnu packages jemalloc)
   #:use-module (gnu packages language)
@@ -198,10 +200,10 @@
   #:use-module (guix build-system emacs)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
+  #:use-module (guix build-system guile)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system ruby)
   #:use-module (guix build-system cmake)
@@ -1253,6 +1255,98 @@ management system that supports the standardized Structured Query
 Language.")
     (license license:gpl2)))
 
+(define-public mysql-connector-python
+  (package
+    (name "mysql-connector-python")
+    (version "8.3.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/mysql/mysql-connector-python")
+              (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "18jvpnnwmfrn961rvqmsygp7dw3spf3swhxhal4hhj5hqddckj5f"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; tests: 1371 passed
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'compatibility
+            (lambda _
+              (substitute* "src/mysql_capi.c"
+                (("res = mysql_options\\(&self->session, MYSQL_OPT_LOAD_DATA_LOCAL_DIR.*")
+                 "res = 0;")
+                (("mysql_options\\(&self->session, MYSQL_OPT_LOAD_DATA_LOCAL_DIR.*")
+                 "")
+                (("mysql_options\\(&self->session, MYSQL_OPT_TLS_CIPHERSUITES.*")
+                 "")
+                ;; The C API does not have mysql_bind_param, so we produce an
+                ;; error here.
+                (("status = mysql_bind_param.*") "status = 1;")
+                (("#include \"mysql_capi_conversion\\.h\"" all)
+                 (string-append all "\n" "#include <stdbool.h>")))))
+          (add-after 'unpack 'chdir
+            (lambda _
+              (chdir "mysql-connector-python")))
+          (add-before 'build 'prepare-build
+            (lambda _
+              (setenv "MYSQL_CAPI" #$(this-package-input "mysql"))))
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                ;; Some of these tests might be failing due to the build
+                ;; container's restrictions, others are due to the version
+                ;; mismatch.
+                (substitute* "tests/cext/test_cext_api.py"
+                  (("def test_change_user") "def _do_not_test_change_user")
+                  (("def test_get_character_set_info")
+                   "def _do_not_test_get_character_set_info"))
+                (substitute* "tests/test_bugs.py"
+                  (("def test_change_user") "def _do_not_test_change_user")
+                  (("def test_lost_connection") "def _do_not_test_lost_connection")
+                  (("def test_kill_query") "def _do_not_test_kill_query")
+                  ;; These all fail because of expired certificates.
+                  (("def test_cext_verify_server_certificate")
+                   "def _do_not_test_cext_verify_server_certificate")
+                  (("def test_pure_verify_server_certificate")
+                   "def _do_not_test_pure_verify_server_certificate")
+                  (("def test_verify_server_name_cext_cnx")
+                   "def _do_not_test_verify_server_name_cext_cnx")
+                  (("def test_verify_server_name_pure_cnx")
+                   "def _do_not_test_verify_server_name_pure_cnx"))
+                (substitute* '("tests/test_connection.py"
+                               "tests/test_aio_connection.py")
+                  (("def test_allow_local_infile_in_path")
+                   "def _do_not_test_allow_local_infile_in_path")
+                  ;; This fails because of expired certificates.
+                  (("def test_connect_with_unix_socket")
+                   "def _do_not_test_connect_with_unix_socket"))
+                (substitute* "tests/test_constants.py"
+                  (("def test_deprecated")
+                   "def _do_not_test_deprecated"))
+                (mkdir-p "/tmp/datadir")
+                (invoke "python3" "unittests.py"
+                        "--verbosity=3"
+                        (string-append "--with-mysql=" #$(this-package-input "mysql"))
+                        "--keep"
+                        "--mysql-topdir=/tmp/datadir"
+                        "--unix-socket=/tmp/datadir")))))))
+    (propagated-inputs (list python-protobuf))
+    (inputs (list mysql protobuf-3.20 openssl-1.1 zlib))
+    (native-inputs (list python-setuptools))
+    (home-page "https://dev.mysql.com/doc/connector-python/en/index.html")
+    (synopsis "MySQL driver written in Python")
+    (description "MySQL Connector/Python enables Python programs to access
+MySQL databases, using an API that is compliant with the Python Database API
+Specification v2.0 (PEP 249).")
+    (license license:gpl2)))
+
+(define-deprecated-package python-mysql-connector-python
+  mysql-connector-python)
+
 (define-public mariadb
   (package
     (name "mariadb")
@@ -4712,33 +4806,24 @@ PickleShare.")
 (define-public python-apsw
   (package
     (name "python-apsw")
-    (version "3.46.0.0")
-    ;; The compressed release has fetching functionality disabled.
+    (version "3.50.4.0")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append
-             "https://github.com/rogerbinns/apsw/releases/download/"
-             version "/apsw-" version ".zip"))
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/rogerbinns/apsw")
+              (commit version)))
+       (file-name (git-file-name name version))
        (sha256
-        (base32
-         "10yfbasi4mq63g0svyl1h49ylwn9znjylq78id16dzxzk9q9ipdx"))))
+        (base32 "0r9awjgpl9cmqz5xd4zbqrpiv0rv5c36a18jkqnsfky6n6sgr424"))))
     (build-system pyproject-build-system)
-    (native-inputs
-     (list unzip python-setuptools python-wheel))
-    (inputs (list sqlite-next))         ;SQLite 3.45.1 required.
     (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-before 'build 'build-extensions
-            (lambda _
-              (invoke "python" "setup.py" "build" "--enable-all-extensions"
-                      "--enable=load_extension")))
-          (add-after 'build 'build-test-helper
-            (lambda _
-              (invoke "gcc" "-fPIC" "-shared" "-o" "./testextension.sqlext"
-                      "-I." "-Isqlite3" "src/testextension.c"))))))
+     (list #:test-backend #~'custom
+           #:test-flags #~(list "-m" "apsw.tests")))
+    (native-inputs
+     (list python-setuptools))
+    (inputs
+     (list sqlite-next))         ;SQLite 3.45.1 required.
     (home-page "https://github.com/rogerbinns/apsw/")
     (synopsis "Another Python SQLite Wrapper")
     (description
@@ -5046,6 +5131,54 @@ postgresql = postgresql://nixbld@/yoyo_test~%")))
 files or Python scripts that define a list of migration steps.")
     (license license:asl2.0)))
 
+(define-public mutastructura
+  (package
+    (name "mutastructura")
+    (version "0.6.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://codeberg.org/jjba23/mutastructura")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "08vzlc5imavqf3bdzgbh70c7z44xjhf05gr7i2g5ksl49lv39gzh"))))
+    (build-system guile-build-system)
+    (arguments
+     (list
+      #:source-directory "src"
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'build 'install-program-files
+            (lambda _
+              (let* ((bin (string-append #$output "/bin"))
+                     (share (string-append #$output "/share")))
+                (copy-recursively "resources"
+                                  (string-append share "/resources"))
+                (install-file "scripts/mutastructura" bin)
+                (install-file "scripts/log.bash"
+                              (string-append share "/scripts/"))
+                (chmod (string-append bin "/mutastructura") #o755)))))))
+    (native-inputs (list guile-3.0))
+    (propagated-inputs (list guile-dbi
+                             guile-dbd-mysql
+                             guile-dbd-sqlite3
+                             guile-dbd-postgresql
+                             guile-gcrypt))
+    (inputs (list guile-3.0 bash-minimal))
+    (home-page "https://codeberg.org/jjba23/mutastructura")
+    (synopsis "Relational database schema migrations powered by Guile Scheme")
+    (description
+     "Mutastructura provides a familiar, declarative and transactional
+approach to managing database states. It exposes a user-friendly 
+@acronym{CLI, command-line interface} and has support for PostgreSQL, MySQL, and SQLite.
+It also exposes library functions and can be imported and used directly from other Guile code.
+
+Features include executing migrations transactionally and computing SHA256
+checksums to track schema evolution in a @code{migrations_history} table.")
+    (license license:agpl3+)))
+
 (define-public python-mysqlclient
   (package
     (name "python-mysqlclient")
@@ -5667,7 +5800,6 @@ __version_tuple__ = version_tuple = (~a)~%" version version-tuple))))))
            pkg-config
            python-cython
            python-pytest
-           python-pytest-runner
            python-setuptools-scm
            python-setuptools))
     (outputs '("out"))
@@ -6264,7 +6396,7 @@ mechanism of @code{dogpile}.")
 (define-public datasette
   (package
     (name "datasette")
-    (version "1.0a19")
+    (version "1.0a26")
     (source
      (origin
        (method git-fetch)
@@ -6273,23 +6405,20 @@ mechanism of @code{dogpile}.")
               (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0wb73iksrc5vg2lnq3q4vr7yhlzxwr711jfmjdndd0s77996zsfh"))))
+        (base32 "1ra0yfrz9w3jx7ix3dmcsg0g8hjxkz37586g7ijmqshxpzczxfm7"))))
     (build-system pyproject-build-system)
     (arguments
      (list
+      ;; tests: 1720 passed, 9 skipped, 8 xfailed, 13 xpassed, 3 warnings, 120
+      ;; subtests passed
       #:test-flags
-      ;; See https://github.com/simonw/datasette/issues/2048
-      #~(list "-k" (string-append
-                    ;; These contain two unexpected extra items.
-                    "not test_searchable"
-                    " and not test_searchmode")
-              "--ignore=tests/test_black.py"
-              "-n" (number->string (parallel-job-count)))
+      #~(list "--numprocesses" (number->string (min 8 (parallel-job-count)))
+              "--ignore=tests/test_black.py")
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'relax-requirements
             (lambda _
-              (substitute* "setup.py"
+              (substitute* "pyproject.toml"
                 (("\"pip\",") "")))))))
     (propagated-inputs
      (list python-aiofiles
@@ -6304,7 +6433,6 @@ mechanism of @code{dogpile}.")
            python-janus
            python-jinja2
            python-mergedeep
-           python-pint
            python-pluggy
            python-pyyaml
            python-sqlite-utils
@@ -6313,9 +6441,9 @@ mechanism of @code{dogpile}.")
      (list nss-certs-for-test
            python-beautifulsoup4
            python-cogapp
+           python-multipart-form-data-conformance
            python-pytest
-           python-pytest-asyncio-0.26
-           python-pytest-runner
+           python-pytest-asyncio
            python-pytest-timeout
            python-pytest-xdist
            python-setuptools

gnu/packages/dav.scm

@@ -27,7 +27,6 @@
 (define-module (gnu packages dav)
   #:use-module (guix build-system cargo)
   #:use-module (guix build-system gnu)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix download)
   #:use-module (guix gexp)
@@ -143,9 +142,6 @@ CardDAV server with a local folder or file.")
     (build-system pyproject-build-system)
     (native-inputs
      (list python-pytest
-           python-pytest-cov
-           python-pytest-flake8
-           python-pytest-isort
            python-setuptools
            python-waitress
            python-wheel))
@@ -244,7 +240,6 @@ efficient syncing
      (list python-aioresponses
            python-pytest
            python-pytest-asyncio
-           python-pytest-cov
            python-pytest-httpserver
            python-setuptools
            python-setuptools-scm

gnu/packages/debug.scm

@@ -275,7 +275,7 @@ simple way to add custom protocol messages.")
        (file-name (git-file-name name version))))
     (build-system cmake-build-system)
     (native-inputs
-     (list flex python-pytest python-pytest-flake8))
+     (list flex python-pytest))
     (inputs
      (list bash-minimal clang llvm unifdef
            python python-pebble python-psutil python-chardet))
@@ -1213,7 +1213,7 @@ and input distributions can also be expressed in Fandango.")
                           ;; Shorten paths to sockets in tests.
                           (lambda _ (setenv "TMPDIR" "/tmp"))))
            #:test-target "test"))
-    (native-inputs (list python))      ; for tests
+    (native-inputs (list python python-setuptools)) ; for tests
     (synopsis "Fault injector in userspace")
     (description "Fiu provides CLI utilities and a C library
 to mark points of failure inside your code

gnu/packages/dictionaries.scm

@@ -41,7 +41,6 @@
   #: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 qt)
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages)

gnu/packages/diffoscope.scm

@@ -67,7 +67,6 @@
   #:use-module (gnu packages vim)
   #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix gexp)
   #:use-module (guix git-download)
@@ -290,14 +289,6 @@ install.")
               (for-each (lambda (file)
                           (chmod file #o755))
                         (find-files #$output "autopkgtest-virt-.*"))))
-          ;; Adjust use of importlib.resources to use python 3.10 compatible
-          ;; syntax, which requires an argument.
-          ;; Drop when switching to python 3.12+.
-          (add-after 'unpack 'adjust-importlib-resources-for-old-python
-            (lambda _
-              (substitute* "reprotest/__init__.py"
-                (("importlib.resources.files\\(\\)")
-                  "importlib.resources.files(package='reprotest')"))))
           (add-after 'unpack 'skip-most-tests
             ;; These tests require functionality not available in the guix
             ;; build environment

gnu/packages/digest.scm

@@ -27,7 +27,6 @@
   #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system trivial)
   #:use-module (guix utils)
   #:use-module (gnu packages check)

gnu/packages/disk.scm

@@ -31,7 +31,7 @@
 ;;; Copyright © 2023 Zheng Junjie <873216071@qq.com>
 ;;; Copyright © 2024-2025 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;; Copyright © 2025 Ashish SHUKLA <ashish.is@lostca.se>
-;;; Copyright © 2025 Vinicius Monego <monego@posteo.net>
+;;; Copyright © 2025, 2026 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2025 Grigory Shepelev <shegeley@gmail.com>
 ;;; Copyright © 2026 Luis Guilherme Coelho <lgcoelho@disroot.org>
 
@@ -59,7 +59,6 @@
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system scons)
   #:use-module (guix build-system trivial)
@@ -94,6 +93,8 @@
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages golang-build)
+  #:use-module (gnu packages golang-check)
+  #:use-module (gnu packages golang-compression)
   #:use-module (gnu packages golang-xyz)
   #:use-module (gnu packages graphics)
   #:use-module (gnu packages gtk)
@@ -420,6 +421,49 @@ tables, and it understands a variety of different formats.")
 similarity.")
     (license license:gpl3+)))
 
+(define-public gdu
+  (package
+    (name "gdu")
+    (version "5.35.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/dundee/gdu")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "051xf3wncdiavjwyl9djmni5vd2dqjgn6drkw2nm21c9l0rjfv6d"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:install-source? #f
+      #:import-path "github.com/dundee/gdu/v5/cmd/gdu"
+      #:unpack-path "github.com/dundee/gdu/v5"))
+    (native-inputs
+     (list go-github-com-dgraph-io-badger-v4
+           go-github-com-fatih-color
+           go-github-com-gdamore-tcell-v2
+           go-github-com-h2non-filetype
+           go-github-com-maruel-natural
+           go-github-com-mattn-go-isatty
+           go-github-com-pkg-errors
+           go-github-com-rivo-tview
+           go-github-com-sirupsen-logrus
+           go-github-com-spf13-cobra
+           go-github-com-stretchr-testify
+           go-github-com-ulikunitz-xz
+           go-golang-org-x-sys
+           go-golang-org-x-text
+           go-gopkg-in-yaml-v3
+           go-modernc-org-sqlite))
+    (home-page "https://github.com/dundee/gdu")
+    (synopsis "Disk usage analyzer")
+    (description "Gdu is a disk usage analyzer written in Go.  It is intended
+primarily for SSD disks where it can fully utilize parallel processing, but it
+also works on HDDs.")
+    (license license:expat)))
+
 (define-public gpart
   ;; The latest (0.3) release is from 2015 and is missing a crash fix.
   (let ((commit "ec03350a01ad69708b5a3e2d47b8e002b0eba6c9")

gnu/packages/django.scm

@@ -37,7 +37,6 @@
   #:use-module (guix git-download)
   #:use-module (guix gexp)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix deprecation)
   #:use-module (guix search-paths)
   #:use-module (guix utils)
@@ -329,7 +328,7 @@ to the @dfn{don't repeat yourself} (DRY) principle.")
         (base32 "1a5vd07wrnfbclvf6pz9p8ag9kdd1453lsl9q0bkyc45hq2xqd2a"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-django python-pytest python-pytest-cov python-setuptools))
+     (list python-django python-pytest python-setuptools))
     (home-page "https://github.com/epicserve/django-cache-url")
     (synopsis "Configure Django cache settings from URLs")
     (description
@@ -420,7 +419,6 @@ and adapters that are useful for non-trivial configuration scenarios.")
            python-factory-boy
            python-pygments
            python-pytest
-           python-pytest-cov ; runs by default
            python-pytest-django
            python-setuptools
            python-shortuuid
@@ -1329,7 +1327,6 @@ server headers required for Cross-Origin Resource Sharing (CORS).")
            python-mock
            python-msgpack
            python-pytest
-           python-pytest-cov
            python-pytest-django
            python-pytest-mock
            python-setuptools
@@ -2186,7 +2183,6 @@ templates and not in python-level form definitions.")
     (build-system pyproject-build-system)
     (native-inputs
      (list python-pytest
-           python-pytest-cov ; runs by default
            python-pytest-django
            python-setuptools
            python-wheel))

gnu/packages/djvu.scm

@@ -29,7 +29,6 @@
   #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages base)
   #:use-module (gnu packages bash)

gnu/packages/docbook.scm

@@ -53,7 +53,6 @@
   #: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 (srfi srfi-26))
 
 ;; The fetch-plan, install-plan and phases for docbook-xml tend to vary
@@ -666,7 +665,8 @@ the in DocBook SGML DTDs.")
                (base32
                 "0yd09nypswy3q4scri1dg7dr99d7gd6r2dwx0xm81l9f4y32gs0n"))
               (patches
-               (search-patches "dblatex-inkscape-1.0.patch"))))
+               (search-patches "dblatex-importlib.patch"
+                               "dblatex-inkscape-1.0.patch"))))
     (outputs '("out" "doc"))
     (build-system pyproject-build-system)
     (arguments

gnu/packages/docker.scm

@@ -39,7 +39,6 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix utils)
   #:use-module (gnu packages autotools)

gnu/packages/documentation.scm

@@ -41,7 +41,6 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system copy)
   #:use-module (guix build-system perl)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system qt)
   #:use-module (guix deprecation)
@@ -472,9 +471,8 @@ inspired by Dash.")
     (build-system gnu-build-system)
     (arguments
      (list
-      ;; Essentially a lighter copy of the former python-build-system.
-      ;; Using it rather than pyproject-build-system allows to edit the latter
-      ;; without a texlive + haskell world rebuild.
+      ;; Custom build steps to prevent using pyproject-build-system which
+      ;; allows to edit the latter without a texlive + haskell world rebuild.
       #:phases
       #~(modify-phases %standard-phases
           (delete 'bootstrap)

gnu/packages/dotnet.scm

@@ -62,7 +62,6 @@
   #:use-module (guix utils)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
-  #:use-module (guix build-system python)
   #:use-module (ice-9 match))
 
 (define-public treecc

gnu/packages/duckdb.scm

@@ -25,7 +25,6 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system pyproject)
-  #:use-module ((guix build-system python) #:select (pypi-uri))
   #:use-module (guix build-system r)
   #:use-module (guix download)
   #:use-module (guix gexp)

gnu/packages/ebook.scm

@@ -40,7 +40,6 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (gnu packages)
   #:use-module (gnu packages autotools)

gnu/packages/education.scm

@@ -91,7 +91,6 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system trivial)
   #:use-module (srfi srfi-1))

gnu/packages/electronics.scm

@@ -64,7 +64,6 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix deprecation)
   #:use-module (guix download)
@@ -480,8 +479,10 @@ individual low-level driver modules.")
     (build-system gnu-build-system)
     (arguments
      (list
-      #:imported-modules (append %default-gnu-imported-modules
-                                 %python-build-system-modules)
+      #:imported-modules %pyproject-build-system-modules
+      #:modules '((guix build gnu-build-system)
+                  ((guix build pyproject-build-system) #:prefix py:)
+                  (guix build utils))
       #:make-flags
       #~(list (string-append "PREFIX=" #$output))
       #:phases
@@ -507,8 +508,7 @@ individual low-level driver modules.")
                 ;; https://github.com/YosysHQ/eqy/actions/runs/18767539188/job/53545383858
                 (invoke "make" "-C" "examples/spm")
                 (invoke "make" "-C" "examples/simple"))))
-          (add-after 'install 'python:wrap
-            (@@ (guix build python-build-system) wrap)))))
+          (add-after 'install 'python:wrap py:wrap))))
     (native-inputs
      (list clang python-minimal-wrapper python-sphinx texinfo yosys))
     (inputs
@@ -2074,7 +2074,10 @@ versus schematic} tests and can assist with automatic routing.")
      (list
       #:tests? #f                       ;there are no tests
       #:imported-modules (append %qt-build-system-modules
-                                 %python-build-system-modules)
+                                 %pyproject-build-system-modules)
+      #:modules '((guix build qt-build-system)
+                  ((guix build pyproject-build-system) #:prefix py:)
+                  (guix build utils))
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'build-info-documentation
@@ -2102,8 +2105,7 @@ versus schematic} tests and can assist with automatic routing.")
                   (chmod bin_ #o755)))
               (install-it "mcy")
               (install-it "mcy-dash")))
-          (add-after 'make-install 'python:wrap
-            (@@ (guix build python-build-system) wrap)))))
+          (add-after 'make-install 'python:wrap py:wrap))))
     (native-inputs
      (list pkg-config
            python-sphinx
@@ -3010,7 +3012,6 @@ Numpy arrays for convenience.")
               (setenv "PDM_BUILD_SCM_VERSION" #$version))))))
     (native-inputs
      (list python-pdm-backend
-           python-pytest-cov
            python-setuptools
            python-setuptools-scm
            sby
@@ -3323,9 +3324,7 @@ Standard} data mode.")
         (base32 "15nnydvr1a4ykh8cagi484sfgvdg0dnjxaw6c0ivhjbrbblpaqnw"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-pytest-cov
-           python-setuptools
-           python-setuptools-scm))
+     (list python-setuptools python-setuptools-scm))
     (home-page "http://pyvcd.readthedocs.io/")
     (synopsis "Library to manipulate digital wave files")
     (description
@@ -3602,10 +3601,7 @@ Automation}.")
                          #$output "/share/info/hdlmake-figures")))))
       #:test-flags #~(list "test_all.py")))
     (native-inputs
-     (list python-pytest-cov
-           python-setuptools
-           python-sphinx
-           texinfo))
+     (list python-setuptools python-sphinx texinfo))
     (propagated-inputs (list python-networkx))
     (home-page "https://ohwr.gitlab.io/project/hdl-make/")
     (synopsis "Generate multi-purpose makefiles for HDL projects")
@@ -3768,18 +3764,9 @@ design.")
       ;; Tests are expensive and may introduce race condition on systems with
       ;; high (more than 16) threads count; limit parallel jobs to 8x.
       #~(list
-         "--numprocesses" (number->string (min 8 (parallel-job-count))))
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'pathch-pytest-options
-            (lambda _
-              (substitute* "pyproject.toml"
-                ((".*--cov=.*") "")
-                ((".*--self-contained-html.*") "")
-                ((".*-n.*auto.*") "")))))))
+         "--numprocesses" (number->string (min 8 (parallel-job-count))))))
     (native-inputs
-     (list python-pytest-cov
-           python-pytest-html
+     (list python-pytest
            python-pytest-xdist
            python-setuptools))
     (propagated-inputs
@@ -4248,11 +4235,10 @@ them usable as simple logic analyzer and/or oscilloscope hardware.")
      (list
       #:parallel-tests? #f
       #:test-target "test"
+      #:imported-modules %pyproject-build-system-modules
       #:modules `((guix build gnu-build-system)
-                  ((guix build python-build-system) #:prefix python:)
+                  ((guix build pyproject-build-system) #:prefix python:)
                   (guix build utils))
-      #:imported-modules `(,@%default-gnu-imported-modules
-                           (guix build python-build-system))
       #:make-flags #~(list (string-append "PREFIX=" #$output))
       #:phases
       #~(modify-phases %standard-phases

gnu/packages/elixir-i18n.scm

@@ -290,7 +290,7 @@ based upon the Common Locale Data Repository (CLDR).")
   (package
     (inherit elixir-ex-cldr-minimal)
     (name "elixir-ex-cldr")
-    (version "2.43.2")
+    (version "2.47.2")
     (source
      (origin
        ;; The hex.pm package ships only the en locale.
@@ -300,7 +300,7 @@ based upon the Common Locale Data Repository (CLDR).")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1wgwp74ya0gkvd5pk4qv9s38p85r5yw370y4wv7jywy3hrbrj9f5"))))
+        (base32 "1rivy61aq0c9zfklm4bpvvkj7lzjgy316rwxl8qz92xqp6xa292y"))))
     (arguments
      (list
       #:phases

gnu/packages/elixir-web.scm

@@ -303,7 +303,17 @@ purposes.  Its goal is to be as close as possible to
      (list
       #:test-flags
       ;; These tests require network access to badssl.com.
-      #~(list "--exclude" "network")))
+      #~(list "--exclude" "network")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'make-reproducible
+            (lambda _
+              ;; Buffer size has been increased in OTP 28+. For more info see:
+              ;; https://github.com/erlang/otp/issues/9722#issuecomment-2808683303
+              (substitute* "test/httpoison_test.exs"
+                (("stream/20") "stream/100")
+                (("<= expected_length") "<= expected_length * 1.1")
+                ((">= max_length") ">= max_length * 0.9")))))))
     (native-inputs
      (list erlang-cowboy
            elixir-earmark

gnu/packages/emacs-xyz.scm

@@ -56,7 +56,7 @@
 ;;; Copyright © 2019 Jelle Licht <jlicht@fsfe.org>
 ;;; Copyright © 2019 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
 ;;; Copyright © 2019 Stephen Webber <montokapro@gmail.com>
-;;; Copyright © 2019, 2021 Liliana Marie Prikler <liliana.prikler@gmail.com>
+;;; Copyright © 2019, 2021—2026 Liliana Marie Prikler <liliana.prikler@gmail.com>
 ;;; Copyright © 2019 David Wilson <david@daviwil.com>
 ;;; Copyright © 2020 Paul Garlick <pgarlick@tourbillion-technology.com>
 ;;; Copyright © 2020 Robert Smith <robertsmith@posteo.net>
@@ -147,7 +147,7 @@
 ;;; Copyright © 2024 Artyom V. Poptsov <poptsov.artyom@gmail.com>
 ;;; Copyright © 2024, 2025 Spencer King <spencer.king@wustl.edu>
 ;;; Copyright © 2024 emma thompson <bigbookofbug@proton.me>
-;;; Copyright © 2024-2025 Liam Hupfer <liam@hpfr.net>
+;;; Copyright © 2024-2026 Liam Hupfer <liam@hpfr.net>
 ;;; Copyright © 2024-2025 Alvin Hsu <aurtzy@gmail.com>
 ;;; Copyright © 2024 Olivier Rojon <o.rojon@posteo.net>
 ;;; Copyright © 2024 Divya Ranjan Pattanaik <divya@subvertising.org>
@@ -656,6 +656,30 @@ supported algorithm is chosen to ensure interoperability with
 Emacs Lisp.")
     (license license:gpl3)))
 
+(define-public emacs-org-arbeitszeit
+  (package
+    (name "emacs-org-arbeitszeit")
+    (version "0.0.5")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/bkaestner/org-arbeitszeit")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0krxainwpn7bnnvbrrhivmh302i9dyfixs6l5wb7xw7qpjgwqzc8"))))
+    (build-system emacs-build-system)
+    (arguments (list #:tests? #f))      ; no tests
+    (home-page "https://github.com/bkaestner/org-arbeitszeit")
+    (synopsis "Calculate your worktime")
+    (description
+     "This package provides a new dynamic block for Org called \"arbeitszeit\"
+(German for \"working hours\").  The dynamic block collects all clocked hours and
+provides a weekly table to quickly see your accumulated overtime.  To insert a
+new block, use @samp{M-x org-dynamic-block-insert-dblock}.")
+    (license license:gpl3+)))
+
 (define-public emacs-perl-doc
   (package
     (name "emacs-perl-doc")
@@ -834,7 +858,7 @@ input via a small child-frame spawned at the position of the cursor.")
 (define-public emacs-arei
   (package
     (name "emacs-arei")
-    (version "0.9.6")
+    (version "0.9.7")
     (source
      (origin
        (method git-fetch)
@@ -844,10 +868,13 @@ input via a small child-frame spawned at the position of the cursor.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1m8ic5pcshz2y2maxvbgg70n4k2kgxvj98zisqal15j7djz0hzji"))))
+         "1fp4l8rzfd7cds80p8c9jgwwlb7rsw35djh0hs50g89h937w5s02"))))
     (build-system emacs-build-system)
-    (arguments (list #:tests? #f))      ; no tests
-    (propagated-inputs (list emacs-eros emacs-sesman emacs-queue))
+    (arguments
+     (list #:lisp-directory "lisp"
+           #:tests? #f))                ; no tests
+    (propagated-inputs
+     (list emacs-consult emacs-eros emacs-sesman emacs-queue))
     (home-page "https://git.sr.ht/~abcdw/emacs-arei")
     (synopsis "Asynchronous Reliable Extensible IDE")
     (description "Sleek Guile IDE for Emacs.")
@@ -13518,8 +13545,8 @@ for compilation, debugging, documentation lookup, and so on.")
     (license (list license:gpl2+ license:public-domain))))
 
 (define-public emacs-sliver
-  (let ((commit "d08d41947bb943f25ee2de9573459a6c720e027f")
-        (revision "0"))
+  (let ((commit "b4cb9cd2a810ba59c946e2592c4a4d56060a8d22")
+        (revision "1"))
     (package
       (name "emacs-sliver")
       ;; No tagged releases. Version comes from source code.
@@ -13532,7 +13559,7 @@ for compilation, debugging, documentation lookup, and so on.")
                 (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-          (base32 "08qycim0mxyiqbik9hjlmzpdggl506bcsv1q1icxzd05bm73sh6n"))))
+          (base32 "1wddivmp5f4m6fdib96vfylqp4kgcw3ipdsi4b9w50dqzvrqrfjh"))))
       (build-system emacs-build-system)
       (arguments
        (list
@@ -13876,7 +13903,7 @@ libraries from Swagger specs.")
       #:imported-modules (append %emacs-build-system-modules
                                  %pyproject-build-system-modules)
       #:modules '((guix build emacs-build-system)
-                  ((guix build python-build-system) #:prefix py:)
+                  ((guix build pyproject-build-system) #:prefix py:)
                   (guix build emacs-utils)
                   (guix build utils))
       #:phases
@@ -15797,8 +15824,16 @@ versions utilizing Consult's internal API.")
     (arguments
      (list
       #:tests? #f                       ;no tests
-      #:include #~(cons "^extensions\\/consult-eglot-embark"
-                        %default-include)))
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; Move the extensions source files to the top level, which is
+          ;; included in the EMACSLOADPATH.
+          (add-after 'unpack 'move-source-files
+            (lambda _
+              (let ((el-files (find-files "./extensions" ".*\\.el$")))
+                (for-each (lambda (f)
+                            (rename-file f (basename f)))
+                          el-files)))))))
     (propagated-inputs (list emacs-consult emacs-eglot emacs-embark))
     (home-page "https://github.com/mohkale/consult-eglot")
     (synopsis "Consulting-read interface for eglot")
@@ -25071,7 +25106,7 @@ lines, and @code{gc} to comment out the target of a motion.")
 (define-public emacs-eglot
   (package
     (name "emacs-eglot")
-    (version "1.21")
+    (version "1.23")
     (source
      (origin
        (method url-fetch)
@@ -25079,7 +25114,7 @@ lines, and @code{gc} to comment out the target of a motion.")
                            ".tar"))
        (sha256
         (base32
-         "03fx22rv8ijxq0jnn7xlfqhkpk2b109ygpjbcchp41sa4q7d6nbl"))))
+         "1l83c90rdamlk576bd859jkg6406hgxi7w4c6ixlw509c66qr3s6"))))
     (build-system emacs-build-system)
     (propagated-inputs
      (list emacs-eldoc
@@ -32038,6 +32073,31 @@ leverages the Parinfer Rust Emacs library to do most of the heavy lifting.")
 bookmarks and history.")
     (license license:gpl3+)))
 
+(define-public emacs-shr-syntax-highlight
+  (package
+    (name "emacs-shr-syntax-highlight")
+    (version "0.1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://codeberg.org/coopi/emacs-shr-syntax-highlight")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "04ax8svpw2s0085pp93dsz5xhhbqr58ghkr1ab2g38pczlsbz18s"))))
+    (build-system emacs-build-system)
+    (home-page "https://codeberg.org/coopi/emacs-shr-syntax-highlight")
+    (synopsis "Syntax highlighting for code blocks rendered by shr")
+    (description
+     "This package adds syntax highlighting to @code{<pre>} code blocks
+rendered by @acronym{@code{shr}, Simple @acronym{HTML, HyperText Markup
+Language} Renderer}, used by @acronym{EWW, Emacs Web Wowser} and similar
+interfaces.  It reads @acronym{CSS, Cascading Style Sheets} class annotations
+such as @code{language-python} and fontifies block contents using the
+corresponding Emacs major mode.")
+    (license license:agpl3+)))
+
 (define-public emacs-stumpwm-mode
     (let ((commit "920f8fc1488f7953f205e1dda4c2ecbbbda56d6")
         (revision "3"))

gnu/packages/embedded.scm

@@ -45,7 +45,6 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system trivial)
   #:use-module ((guix build utils) #:select (alist-replace delete-file-recursively))
   #:use-module (gnu packages)
@@ -2033,13 +2032,7 @@ whereas kdmx creates pseudo-ttys.")
       ;; tests: 631 passed, 27 skipped, 1 warning
       #:test-flags
       ;; E   ModuleNotFoundError: No module named 'mbed_tools_ci_scripts'
-      #~(list "--ignore=tests/ci_scripts/test_sync_board_db.py")
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'fix-pytest-config
-            (lambda _
-              (substitute* "pytest.ini"
-                (("addopts = .*") "")))))))
+      #~(list "--ignore=tests/ci_scripts/test_sync_board_db.py")))
     (native-inputs
      (list python-factory-boy
            python-pytest

gnu/packages/emulators.scm

@@ -140,7 +140,6 @@
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system trivial))
@@ -3452,7 +3451,7 @@ This is a part of the TiLP project.")
 (define-public mame
   (package
     (name "mame")
-    (version "0.252")
+    (version "0.287")
     (source
      (origin
        (method git-fetch)
@@ -3461,16 +3460,16 @@ This is a part of the TiLP project.")
              (commit (apply string-append "mame" (string-split version #\.)))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "07qhcm1v47sy2wj30nx3cbhvcbgki0cl83gabr0miiw60fhgyn6j"))
+        (base32 "1p9v71gvaqiyj6sa1b0wkdksa9wnr6yr2a43ckycljjfas5s36kq"))
        (modules '((guix build utils)))
        (snippet
         ;; Remove bundled libraries.
         '(begin
            (with-directory-excursion "3rdparty"
              (for-each delete-file-recursively
-                       '("asio" "expat" "glm" "libflac" "libjpeg" "lua"
-                         "portaudio" "portmidi" "pugixml" "rapidjson" "SDL2"
-                         "SDL2-override" "sqlite3" "utf8proc" "zlib")))))))
+                       '("asio" "expat" "glm" "flac" "libjpeg" "lua"
+                         "portaudio" "portmidi" "pugixml" "rapidjson"
+                         "sqlite3" "utf8proc" "zlib")))))))
     (build-system gnu-build-system)
     (arguments
      (list
@@ -3604,7 +3603,9 @@ This is a part of the TiLP project.")
            libjpeg-turbo
            libxi
            libxinerama
-           lua
+           ;; MAME requires Lua compiled as C++ to work correctly.
+           ;; See https://www.mamedev.org/?p=523
+           lua-5.4-for-c++
            portaudio
            portmidi
            pugixml

gnu/packages/enchant.scm

@@ -41,7 +41,6 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix licenses)
   #:use-module (srfi srfi-1))
 

gnu/packages/engineering.scm

@@ -77,7 +77,6 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix download)
   #:use-module (guix gexp)
@@ -1828,7 +1827,6 @@ it suitable for security research and analysis.")
     (native-inputs (list python-gitpython
                          python-pytest
                          python-pytest-asyncio
-                         python-pytest-cov
                          python-pytest-mock
                          python-setuptools))
     (inputs (list bash-minimal
@@ -2367,7 +2365,6 @@ Newton-Raphson power flow solvers in the C++ library lightsim2grid, and the
                          python-networkx
                          python-openpyxl
                          python-pytest
-                         python-pytest-cov ; --cov runs by default on skrf
                          python-pytest-mock
                          python-pyvisa
                          python-setuptools
@@ -2901,20 +2898,22 @@ interpolation toolkit.")
 (define-public python-motulator
   (package
     (name "python-motulator")
-    (version "0.5.0")
+    (version "0.6.2")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "motulator" version))
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/Aalto-Electric-Drives/motulator/")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "1kh13zfa4w73q04pny2w2zgym47fp8xy7glwfx82fdx4fihk7dv7"))))
+        (base32 "1di2r1i19jl751v0hj426zkwk48w5yf8zpw2bl6qzk0vq4z2vpbw"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:tests? #f)) ; there are no tests
-    (propagated-inputs (list python-matplotlib python-numpy python-scipy))
-    (native-inputs (list python-hatchling
-                         python-ipykernel
-                         python-toml))
+    (propagated-inputs
+     (list python-numpy python-matplotlib python-scipy python-tqdm))
+    (native-inputs (list python-hatchling))
     (home-page "https://aalto-electric-drives.github.io/motulator/")
     (synopsis "Motor Drive Simulator in Python")
     (description "This package includes simulation models for an induction

gnu/packages/enlightenment.scm

@@ -30,7 +30,6 @@
   #:use-module (guix gexp)
   #:use-module (guix utils)
   #:use-module (guix build-system meson)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (gnu packages)
   #:use-module (gnu packages algebra)

gnu/packages/erlang.scm

@@ -50,7 +50,7 @@
 (define-public erlang
   (package
     (name "erlang")
-    (version "27.3.4.6")
+    (version "28.4.3")
     (source (origin
               (method git-fetch)
               ;; The tarball from http://erlang.org/download contains many
@@ -62,7 +62,7 @@
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0dhz2c7w28ss0ypj7jh88pfs3kc8hbwiiq91in1j2miy5sn4cp3x"))
+                "1dsdmp2rccc0rhzy2w8r4amxmc6nr9hbi053j2s0bg9db30b48rc"))
               (patches (search-patches "erlang-man-path.patch"))))
     (build-system gnu-build-system)
     (native-inputs
@@ -75,7 +75,7 @@
                                "/OTP-" version "/otp_doc_man_" version ".tar.gz"))
            (sha256
             (base32
-             "1j1fcli7ma9vi4qyv67lq7yiznhpnfvcmh57bn8qxvha6ky2pngm"))))))
+             "1g17wzv8j12g9272yvv55nj4wqs09hxkv3i0vnp7d6gcs24bmphi"))))))
     (inputs
      (list ncurses openssl wxwidgets))
     (propagated-inputs

gnu/packages/fabric-management.scm

@@ -220,6 +220,7 @@ testing InfiniBand networks.")
                            "--disable-assertions"
                            "--disable-params-check"
 
+                           "--enable-mt"
                            (string-append "--with-verbs="
                                           #$(this-package-input "rdma-core"))
 

gnu/packages/fediverse.scm

@@ -29,7 +29,6 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix utils)
   #:use-module (gnu packages)
@@ -245,7 +244,6 @@ seamlessly with your desktop environment.")
     (native-inputs
      (list nss-certs-for-test
            python-pytest
-           python-pytest-cov
            python-pytest-mock
            python-pytest-recording
            python-pytest-retry

gnu/packages/file-systems.scm

@@ -50,7 +50,6 @@
   #:use-module (guix build-system go)
   #:use-module (guix build-system linux-module)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system trivial)
   #:use-module (guix utils)

gnu/packages/finance.scm

@@ -70,7 +70,6 @@
   #:use-module (guix build-system copy)
   #:use-module (guix build-system emacs)
   #:use-module (guix build-system haskell)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system go)
@@ -165,7 +164,7 @@
   ;; <https://bitcoincore.org/en/lifecycle/#schedule>.
   (package
     (name "bitcoin-core")
-    (version "30.2")
+    (version "31.0")
     (source (origin
               (method url-fetch)
               (uri
@@ -173,7 +172,7 @@
                               version "/bitcoin-" version ".tar.gz"))
               (sha256
                (base32
-                "1jw4djh22v0nih0n7irdbknfbqavlc4l3b8176b5qgc88a60pl3g"))))
+                "1qxkcyq8nwq6sw4qi660z8n8356mqdsf4jvpq5ndkvrsx9gfz80b"))))
     (build-system qt-build-system)
     (arguments
      (list #:qtbase qtbase
@@ -197,9 +196,7 @@
                     "python3" "./test/functional/test_runner.py" "--timeout-factor=2"
                     (string-append "--jobs=" (number->string (parallel-job-count)))))))))
     (native-inputs
-     (list bash ; provides the sh command for system_tests
-           coreutils ; provides the cat, echo and false commands for system_tests
-           pkg-config
+     (list pkg-config
            python ; for the tests
            python-pyzmq ; for the tests
            qttools))
@@ -1623,10 +1620,7 @@ features:
        (sha256
         (base32 "0yir8hka3vmpk0qhiaffagkdjg3mjgai808s0razsggbd5cn80bb"))))
     (build-system pyproject-build-system)
-    (native-inputs
-     (list python-pytest
-           python-pytest-cov
-           python-setuptools))
+    (native-inputs (list python-pytest python-setuptools))
     (home-page "https://arthurdejong.org/python-stdnum/")
     (synopsis "Python module to handle standardized number and code formats")
     (description
@@ -2509,10 +2503,6 @@ analysis of financial market data.")
         (base32 "13g5338aa8vgkx8g94vz5d8ynfq3jndvyh1nz6dlhw4axwr4x8dp"))))
     (properties '(("upstream-name" #{.}# "mt-940")))
     (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:test-flags
-      #~(list "-c" "/dev/null")))       ; Remove custom --cov flags.
     (native-inputs (list python-pytest python-pyyaml python-setuptools))
     (home-page "https://mt940.readthedocs.io/")
     (synopsis "Python parser for MT940-encoded SWIFT data")

gnu/packages/firmware.scm

@@ -47,7 +47,6 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages)

gnu/packages/flashing-tools.scm

@@ -49,7 +49,6 @@
   #:use-module (guix build-system go)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix download)
   #:use-module (guix gexp)

gnu/packages/fonts.scm

@@ -4658,46 +4658,6 @@ is a stylish type with a polished yet relaxed feel.  Its versatility makes it
 suitable for a wide range of uses.")
       (license license:silofl1.1))))
 
-(define-public font-cozette
-  (package
-    (name "font-cozette")
-    (version "1.13.0")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                     (url "https://github.com/slavfox/Cozette")
-                     (commit (string-append "v." version))))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "178i812n4sfsvid7jhnm683jlxqmrv4ck6qbb4nwyllhwg3gyq60"))))
-    (build-system font-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'dont-depend-on-git
-           (lambda _
-             (substitute* "build.py"
-               ;; Merely importing this module requires a git repository.
-               ;; We don't use get_changelog, so just disable the import.
-               (("from cozette_builder\\.changeloggen import get_changelog")
-                ""))))
-         (add-before 'install 'build
-           (lambda _
-             (invoke "python3" "build.py" "fonts"))))))
-    (native-inputs
-     (list fontforge
-           python
-           python-crayons
-           python-fonttools
-           python-numpy
-           python-pillow))
-    (home-page "https://github.com/slavfox/Cozette")
-    (synopsis "Bitmap programming font")
-    (description "Cozette is a 6x13px (bounding box) bitmap font based on Dina
-and heavily inspired by Creep.")
-    (license license:expat)))
-
 (define-public font-montserrat
   (package
     (name "font-montserrat")

gnu/packages/fontutils.scm

@@ -96,7 +96,6 @@
   #:use-module (guix build-system go)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix utils)
   #:use-module (srfi srfi-1))
 
@@ -473,6 +472,53 @@ font design software, it allows you to join, split, offset, and perform many
 other operations on paths.")
     (license license:expat)))
 
+(define-public python-booleanoperations
+  (package
+    (name "python-booleanoperations")
+    (version "0.9.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/typemytype/booleanOperations")
+              (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0ahfgamyq1ndwbr9n8sdx8qhqc2195xnbahylgjpk877hbr2gxav"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; Some tests fail due to small differences in the expected result (see:
+      ;; <https://github.com/typemytype/booleanOperations/issues/69>).
+      #:test-flags
+      #~(list "-k"
+              (string-join
+               (list "not test_QTail_reversed_difference"
+                     "test_QTail_reversed_intersection"
+                     "test_QTail_reversed_union"
+                     "test_QTail_reversed_xor"
+                     "test_Q_difference"
+                     "test_Q_intersection"
+                     "test_Q_union"
+                     "test_Q_xor")
+               " and not "))))
+    (native-inputs
+     (list python-defcon-bootstrap
+           python-fontpens-bootstrap
+           python-pytest
+           python-setuptools
+           python-setuptools-scm))
+    (propagated-inputs
+     (list python-fonttools-minimal
+           python-pyclipper))
+    (home-page "https://github.com/typemytype/booleanOperations")
+    (synopsis "Boolean operations on paths")
+    (description
+     "Boolean operations on paths which uses a super fast
+@url{http://www.angusj.com/delphi/clipper.php, polygon clipper library by
+Angus Johnson}.")
+    (license license:expat)))
+
 (define-public python-cffsubr
   (package
     (name "python-cffsubr")
@@ -574,7 +620,6 @@ for fontTools.")
      (list python-cython
            python-defcon
            python-pytest
-           python-pytest-runner
            python-setuptools
            python-setuptools-scm
            python-wheel
@@ -701,8 +746,7 @@ implementing the pen protocol for manipulating glyphs.")
       (modify-inputs native-inputs
         (append python-fontparts-bootstrap
                 python-fontpens-bootstrap
-                python-pytest
-                python-pytest-runner))))))
+                python-pytest))))))
 
 ;;; A variant used to break a cycle with python-fontpens.
 (define-public python-fontparts-bootstrap
@@ -983,7 +1027,6 @@ suite of the @code{psautohint} package.")
     (native-inputs
      (list psautohint-font-data
            python-pytest
-           python-pytest-cov
            python-pytest-xdist
            python-setuptools-scm
            python-setuptools
@@ -1827,6 +1870,10 @@ definitions.")
            pango
            potrace
            python
+           ;; XXX: Python 3.12 lacks distutils:
+           ;; ModuleNotFoundError: No module named 'distutils'
+           ;; Remove when package is updated.
+           python-setuptools-bootstrap
            zlib))
     (arguments
      (append

gnu/packages/freedesktop.scm

@@ -73,7 +73,6 @@
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system qt)
   #:use-module (guix search-paths)
@@ -1378,41 +1377,43 @@ For information about libevdev, see:
     (license license:expat)))
 
 (define-public python-pyxdg
-  (package
-    (name "python-pyxdg")
-    (version "0.28")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "pyxdg" version))
-       (sha256
-        (base32
-         "1d48bqwkbnpid80cpwz6h62i112laxl0ivpj58hdyd79fhqbnrrj"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:test-flags
-      ;; Tests failing with error: AssertionError: 'image' != 'inode'
-      #~(list "--deselect=test/test_mime.py::MimeTest::test_get_type"
-              "--deselect=test/test_mime.py::MimeTest::test_get_type2")
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-before 'check 'pre-check
-            (lambda _
-              (setenv "XDG_DATA_DIRS"
-                      (string-append #$(this-package-native-input "shared-mime-info")
-                                     "/share/")))))))
-    (native-inputs
-     (list shared-mime-info
-           hicolor-icon-theme
-           python-pytest
-           python-setuptools))
-    (home-page "https://www.freedesktop.org/wiki/Software/pyxdg")
-    (synopsis "Implementations of freedesktop.org standards in Python")
-    (description
-     "PyXDG is a collection of implementations of freedesktop.org standards in
+  ;; Latest unreleased commits add Python 3.12, 3.14 and 3.15 support.
+  (let ((commit "63033ac306aa26d32e1439417e59ae8f8a4c9820")
+        (revision "0"))
+    (package
+      (name "python-pyxdg")
+      (version "0.28")
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+                (url "https://gitlab.freedesktop.org/xdg/pyxdg")
+                (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "10wk95rmcr2fglmvmv1a6ad9hkw9587r0rlww0gq6kbfz85whgmd"))))
+      (build-system pyproject-build-system)
+      (arguments
+       (list
+        #:phases
+        #~(modify-phases %standard-phases
+            (add-before 'check 'pre-check
+              (lambda _
+                (setenv "XDG_DATA_DIRS"
+                        (string-append #$(this-package-native-input "shared-mime-info")
+                                       "/share/")))))))
+      (native-inputs
+       (list shared-mime-info
+             hicolor-icon-theme
+             python-pytest
+             python-setuptools))
+      (home-page "https://www.freedesktop.org/wiki/Software/pyxdg")
+      (synopsis "Implementations of freedesktop.org standards in Python")
+      (description
+       "PyXDG is a collection of implementations of freedesktop.org standards in
 Python.")
-    (license license:lgpl2.0)))
+      (license license:lgpl2.0))))
 
 (define-public hyprland-protocols
   (package
@@ -2177,7 +2178,7 @@ which speak the Qualcomm MSM Interface (QMI) protocol.")
            libxslt                      ;for xsltproc
            pkg-config
            python-minimal
-           python-dbus-1.2              ;for test
+           python-dbus                  ;for test
            python-pygobject             ;for test
            vala))
     (propagated-inputs
@@ -2371,7 +2372,7 @@ different sorts of messages in different formats.")
           (base32 "02wb61h2k3hhis5y2xi5rhc6pmikd13x722hk620sqb9b3m5pn3s"))))
       (build-system gnu-build-system)
       (native-inputs (list autoconf automake libtool pkg-config))
-      (inputs (list libxslt python-wrapper python-dbus-1.2))
+      (inputs (list libxslt python-wrapper python-dbus))
       (propagated-inputs (list telepathy-glib))
       (home-page "https://telepathy.freedesktop.org/")
       (synopsis "Telepathy IRC connection manager")
@@ -3454,7 +3455,7 @@ interfaces.")
                            (string-append (assoc-ref outputs "out")
                                           "/share/doc/" ,name)))))))
     (native-inputs
-     (list cmake-minimal pkg-config))
+     (list cmake-minimal pkg-config scdoc))
     (inputs (list elogind
                   bash-minimal
                   grim

gnu/packages/game-development.scm

@@ -70,7 +70,6 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system renpy)
   #:use-module (guix build-system scons)
   #:use-module (gnu packages)

gnu/packages/games.scm

@@ -5534,23 +5534,13 @@ falling, themeable graphics and sounds, and replays.")
     (build-system cmake-build-system)
     (arguments
      (list #:tests? #f                  ;no test target
-           #:configure-flags #~'("-DENABLE_SYSTEM_LUA=ON")
-           #:phases
-           #~(modify-phases %standard-phases
-               (add-before 'configure 'pre-configure
-                 (lambda _
-                   ;; XXX: Our Lua doesn't have a C++ library, force C linkage.
-                   (substitute* '("src/lua/wrapper_lua.h"
-                                  "src/lua/wrapper_lualib.h"
-                                  "src/lua/wrapper_lauxlib.h")
-                     (("#include \"(lua|lualib|lauxlib)\\.h\"")
-                      "#include \"lua.hpp\"")))))))
+           #:configure-flags #~'("-DENABLE_SYSTEM_LUA=ON")))
     (inputs
      (list boost-1.83
            curl
            dbus
            libvorbis
-           lua-5.4
+           lua-5.4-for-c++
            openssl
            pango
            sdl2
@@ -5937,7 +5927,7 @@ Transport Tycoon Deluxe.")
           (add-after 'unpack 'patch-sources
             (lambda* (#:key inputs #:allow-other-keys)
               (substitute* "src/music/fluidsynth.cpp"
-                (("default_sf\\[\\] = \\{" all)
+                (("_default_soundfonts\\[\\] = \\{" all)
                  (string-append all "
 \t/* Guix hardcoded :P */
 \t\"" (search-input-file inputs "/share/soundfonts/FreePatsGM.sf2") "\",
@@ -5964,7 +5954,7 @@ Transport Tycoon Deluxe.")
   (package
     (inherit openttd)
     (name "openttd-jgrpp")
-    (version "0.70.2")
+    (version "0.71.1")
     (source
      (origin
        (method git-fetch)
@@ -5973,7 +5963,7 @@ Transport Tycoon Deluxe.")
              (commit (string-append "jgrpp-" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1jzzvribf2cqvjl9cympyx9qpplljvmhqrrlw7aq4ckzl92d87z3"))))
+        (base32 "1cy1ghc1mc61hdz8lykx2ggs5nld30jdgj8y4vdli2v1ffhy7xy9"))))
     (inputs (modify-inputs inputs
               (append zstd harfbuzz)))
     (arguments

gnu/packages/geo.scm

@@ -55,7 +55,6 @@
   #:use-module (guix build-system go)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system r)
   #:use-module (guix build-system zig)
@@ -298,7 +297,7 @@ than 600 operators available.")
 (define-public h3
   (package
     (name "h3")
-    (version "4.1.0")
+    (version "4.4.1")
     (source
      (origin
        (method git-fetch)
@@ -307,7 +306,7 @@ than 600 operators available.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0x764xzna8ka6yhgv2y4hb158a61y3g9a6835qckqp7wfkpqvb7f"))))
+        (base32 "1ijnbr4a54ph7bkn8waqwgnxmxlylv9yly9mwjdj69lkmdfjgaml"))))
     (build-system cmake-build-system)
     (arguments
      (list #:configure-flags #~(list "-DBUILD_SHARED_LIBS=ON")))
@@ -319,48 +318,25 @@ combining the benefits of a hexagonal grid with S2's hierarchical
 subdivisions.")
     (license license:asl2.0)))
 
-;; For python-timezonefinder, remove it when it starts supporting newer
-;; version.
-(define-public h3-3
-  (package
-    (inherit h3)
-    (name "h3")
-    (version "3.7.2")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/uber/h3")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0bvsljfxmjvl23v9gxykc4aynjzh5xfy3wg02bxad7cknr1amx9j"))))))
-
 (define-public python-h3
   (package
     (name "python-h3")
-    (version "4.0.0b2")
+    (version "4.4.2")
     (source
      (origin
-       (method git-fetch) ; no tests data in PyPi package
+       (method git-fetch)
        (uri (git-reference
              (url "https://github.com/uber/h3-py")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1k1n256hhlh05gjcj64pqh08zlaz6962jkb6nk1aazsgg8p41zs0"))
+        (base32 "02gry51hn8x2bl80y1ipcyrg0ghcif4vjch26qil215wdzz1yrzv"))
        (modules '((guix build utils)))
        ;; Remove bundled H3 lib.
        (snippet #~(begin (delete-file-recursively "src/h3lib")))))
     (build-system pyproject-build-system)
     (arguments
      (list
-      ;; FIXME: Check why these tests are failing.
-      ;; test_versions - assert (4, 1) == (4, 0)
-      ;; test_resolution - h3._cy.error_system.H3Failed
-      #:test-flags #~(list "-k" (string-append
-                                 "not test_versions"
-                                 " and not test_resolution"))
       #:phases
       #~(modify-phases %standard-phases
           ;; Use packaged in Guix h3 source.
@@ -381,10 +357,7 @@ subdivisions.")
            python-cython
            python-numpy
            python-pytest
-           python-scikit-build
-           python-setuptools
-           python-setuptools-scm
-           python-wheel))
+           python-scikit-build-core))
     (inputs (list h3))
     (home-page "https://uber.github.io/h3-py")
     (synopsis "Python bindings for H3")
@@ -392,26 +365,6 @@ subdivisions.")
 hierarchical hexagonal geospatial indexing system")
     (license license:asl2.0)))
 
-;; For python-timezonefinder, remove it when it starts supporting newer
-;; version.
-(define-public python-h3-3
-  (package
-    (inherit python-h3)
-    (name "python-h3")
-    (version "3.7.6")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/uber/h3-py")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "16gxa1sivghxw179rik87r918mjasars2qkzidlwq83qfa4axn20"))))
-    (inputs
-     (modify-inputs inputs
-       (replace "h3" h3-3)))))
-
 (define-public geos
   (package
     (name "geos")
@@ -1059,7 +1012,6 @@ for seismology.")
     (inputs (list gdal))
     (native-inputs (list python-cython
                          python-pytest
-                         python-pytest-cov
                          python-setuptools
                          python-tomli
                          python-versioneer
@@ -1159,7 +1111,7 @@ projections and coordinate transformations library.")
 (define-public python-fiona
   (package
     (name "python-fiona")
-    (version "1.9.6")
+    (version "1.10.1")
     (source
      (origin
        (method git-fetch)
@@ -1168,24 +1120,38 @@ projections and coordinate transformations library.")
               (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "08whhjrspp194qasjhr9kf70fl342ms47k78rwpcf5q6ikf0rfii"))))
+        (base32 "0xribbcy5wvrm5y3bq281dry86vhjcnphg9772yp9s3y30y7mlz4"))))
     (build-system pyproject-build-system)
     (arguments
      (list
+      ;; tests: 757 passed, 161 skipped, 24 deselected, 1 xfailed, 6 xpassed
       #:test-flags
       #~(list "-m" "not network and not wheel"
-              ;; FIXME: Find why the
-              ;; test_no_append_driver_cannot_append[PCIDSK] test is failing.
-              "-k" "not test_no_append_driver_cannot_append")
+              #$@(map (lambda (test) (string-append "--deselect=tests/" test))
+                      ;; UserWarning: The parameter --where is used more than
+                      ;; once. Remove its duplicate as parameters should be
+                      ;; unique.
+                      (list "test_fio_cat.py::test_bbox_json_yes"
+                            "test_fio_cat.py::test_bbox_no"
+                            "test_fio_cat.py::test_bbox_where"
+                            "test_fio_cat.py::test_bbox_yes"
+                            "test_fio_cat.py::test_bbox_yes_two_files"
+                            "test_fio_cat.py::test_dst_crs_epsg3857"
+                            "test_fio_cat.py::test_multi_layer"
+                            "test_fio_cat.py::test_one"
+                            "test_fio_cat.py::test_two"
+                            "test_fio_cat.py::test_vfs"
+                            "test_fio_cat.py::test_where_no"
+                            "test_fio_cat.py::test_where_yes"
+                            "test_fio_cat.py::test_where_yes_two_files"
+                            ;; FileNotFoundError:
+                            ;; https://github.com/Toblerity/Fiona/files/\
+                            ;; 11151652/coutwildrnp.zip
+                            "test_pyopener.py::test_opener_fsspec_zip_http_fs")))
       #:phases
       #~(modify-phases %standard-phases
-          (add-before 'build 'set-configure-flags
+          (add-before 'check 'remove-local-source
             (lambda _
-              (setenv "CFLAGS" "-Wno-error=incompatible-pointer-types")))
-          (add-before 'check 'remove-local-fiona
-            (lambda _
-              ;; This would otherwise interfere with finding the installed
-              ;; fiona when running tests.
               (delete-file-recursively "fiona"))))))
     (inputs
      (list gdal))
@@ -1193,19 +1159,19 @@ projections and coordinate transformations library.")
      (list python-attrs
            python-certifi
            python-click
-           python-click-plugins-1
+           python-click-plugins
            python-cligj))
     (native-inputs
      (list gdal ; for gdal-config
            python-boto3
            python-cython
+           python-fsspec
            python-pytest
-           python-pytest-cov
            python-pytz
-           python-setuptools))
+           python-setuptools
+           python-shapely))
     (home-page "https://github.com/Toblerity/Fiona")
-    (synopsis
-     "Fiona reads and writes spatial data files")
+    (synopsis "Fiona reads and writes spatial data files")
     (description
      "Fiona is GDAL’s neat and nimble vector API for Python programmers. Fiona
 is designed to be simple and dependable.  It focuses on reading and writing
@@ -1465,7 +1431,6 @@ street bearings/orientations, and speed/travel time.")
            python-pyproj
            python-pyyaml
            python-pytest
-           python-pytest-cov
            python-pytest-httpserver
            python-pytz
            python-requests
@@ -1797,10 +1762,7 @@ utilities for data translation and processing.")
       ;; This test requires internet access.
       '(list "--deselect" "test_shapefile.py::test_reader_url")))
     (native-inputs
-     (list python-pytest
-           python-pytest-runner
-           python-setuptools
-           python-wheel))
+     (list python-pytest python-setuptools python-wheel))
     (home-page "https://github.com/GeospatialPython/pyshp")
     (synopsis "Read/write support for ESRI Shapefile format")
     (description
@@ -3530,10 +3492,9 @@ orienteering sport.")
        (list
         #:tests? #f                    ; No tests
         #:modules `((guix build gnu-build-system)
-                    ((guix build python-build-system) #:prefix python:)
+                    ((guix build pyproject-build-system) #:prefix python:)
                     (guix build utils))
-        #:imported-modules `(,@%default-gnu-imported-modules
-                             (guix build python-build-system))
+        #:imported-modules %pyproject-build-system-modules
         #:configure-flags
         #~(list "--with-blas"
                 "--with-bzlib"
@@ -3705,13 +3666,13 @@ growing set of geoscientific methods.")
     (build-system cmake-build-system)
     (arguments
      (list
+      #:imported-modules (append %cmake-build-system-modules
+                                 %pyproject-build-system-modules
+                                 '((guix build qt-utils)))
       #:modules '((guix build cmake-build-system)
-                  ((guix build python-build-system) #:prefix python:)
+                  ((guix build pyproject-build-system) #:prefix py:)
                   (guix build qt-utils)
                   (guix build utils))
-      #:imported-modules `(,@%cmake-build-system-modules
-                           (guix build python-build-system)
-                           (guix build qt-utils))
       #:configure-flags
       #~(list "-DWITH_QTWEBKIT=NO")
       #:phases
@@ -3872,11 +3833,10 @@ growing set of geoscientific methods.")
             ;; Configure correct path to PyQt5 SIP directory
             (add-after 'unpack 'configure-pyqt5-sip-path
               (lambda* (#:key inputs #:allow-other-keys)
-                (let ((sip-dir (string-append
-                                (assoc-ref inputs "python-pyqt+qscintilla")
-                                "/lib/python"
-                                (python:python-version (assoc-ref inputs "python"))
-                                "/site-packages/PyQt5/bindings")))
+                (let* ((pyqt (assoc-ref inputs "python-pyqt+qscintilla"))
+                       (sip-dir (string-append
+                                 (py:site-packages inputs `(("out" . ,pyqt)))
+                                 "/PyQt5/bindings")))
                   (substitute* "cmake/FindPyQt5.py"
                     (("sip_dir = cfg.default_sip_dir")
                      (string-append "sip_dir = \"" sip-dir "\"")))
@@ -3906,7 +3866,7 @@ SET\\(PYQT5_SIP_DIR \"\\$\\{Python_SITEARCH\\}/PyQt5/bindings\"\\)")
                               "-E" (string-join ignored-tests "|")))
                     (format #t "test suite not run~%"))))
             (add-after 'install 'wrap-python
-              (assoc-ref python:%standard-phases 'wrap))
+              (assoc-ref py:%standard-phases 'wrap))
             (add-after 'wrap-python 'wrap-qt
               (lambda* (#:key inputs #:allow-other-keys)
                 (wrap-qt-program "qgis" #:output #$output #:inputs inputs)))

gnu/packages/gimp.scm

@@ -476,17 +476,31 @@ inverse fourier transform.")
   (package
     (name "libmypaint")
     (version "1.6.1")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/mypaint/libmypaint/"
-                                  "releases/download/v" version "/libmypaint-"
-                                  version ".tar.xz"))
-              (sha256
-               (base32
-                "0priwpmc7dizccqvn21ig6d649bprl3xl1hmjj7nddznjgr585vl"))))
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/mypaint/libmypaint")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1ppgpmnhph9h8ayx9776f79a0bxbdszfw9c6bw7c3ffy2yk40178"))))
     (build-system gnu-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'bootstrap 'overwrite-automake-and-aclocal-versions
+            (lambda _
+              (setenv "AUTOMAKE" "automake")
+              (setenv "ACLOCAL" "aclocal"))))))
     (native-inputs
-     (list intltool pkg-config))
+     (list autoconf
+           automake
+           intltool
+           libtool
+           pkg-config
+           python))
     ;; As needed by 'libmypaint.pc'.
     (propagated-inputs
      (list json-c gobject-introspection))
@@ -498,6 +512,26 @@ brushstrokes which is used by MyPaint and GIMP.")
     (home-page "http://mypaint.org")
     (license license:isc)))
 
+;; To update mypaint, remove when a fresh version is released.
+(define-public libmypaint-next
+  (package
+    (inherit libmypaint)
+    (name "libmypaint")
+    (properties '((commit . "551dfb9ca5d2b82f2361a5a8a9e7f386f35fd320")
+                  (revision . "0")))
+    (version (git-version "1.6.1"
+                          (assoc-ref properties 'revision)
+                          (assoc-ref properties 'commit)))
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/mypaint/libmypaint")
+              (commit (assoc-ref properties 'commit))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0pl8cma6gfkrqx364fs1xw7f491f7y6pzxqjq1cdqlrf9r8gg0sk"))))))
+
 (define-public mypaint-brushes
   (package
     (name "mypaint-brushes")

gnu/packages/gl.scm

@@ -79,7 +79,6 @@
   #:use-module (guix build-system cargo)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system meson)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
@@ -1420,8 +1419,8 @@ original glmark benchmark by Ben Smith.")
     (license license:bsd-2)))
 
 (define-public piglit
-  (let ((revision "1")
-        (commit "814046fe6942eac660ee4a6cc5fcc54011a49945"))
+  (let ((revision "2")
+        (commit "040ed91f234abb6a502d3a6910f1b0e54bd239a7"))
     (package
      (name "piglit")
      (version (git-version "0.0.0" revision commit))
@@ -1432,7 +1431,7 @@ original glmark benchmark by Ben Smith.")
                     (commit commit)))
               (file-name (git-file-name name version))
               (sha256
-               (base32 "1bzaalcxskckfnwprw77sbbmfqi59by2j8imaq8ghnlzhlxv7mk7"))))
+               (base32 "1j5dmkym1mmz410xgwygimnjk2aswsqmcpjwz4s98pgmymh1yjvf"))))
      (build-system cmake-build-system)
      (arguments
       (list #:configure-flags #~(list "-DPIGLIT_SSE2=OFF")
@@ -1451,16 +1450,21 @@ original glmark benchmark by Ben Smith.")
                                       "'")))))
                 (add-after 'install 'wrap
                   (lambda* (#:key outputs #:allow-other-keys)
-                    (wrap-script (string-append (assoc-ref outputs "out")
-                                                "/bin/piglit")
+                    (wrap-script (string-append #$output "/bin/piglit")
                       `("GUIX_PYTHONPATH" prefix
                         (,(getenv "GUIX_PYTHONPATH")))))))))
-     (inputs (list guile-3.0            ; for wrap-script
+     (inputs (list glslang
+                   guile-3.0            ; for wrap-script
                    libxkbcommon
-                   python python-lxml python-mako python-numpy-1
-                   glslang vulkan-headers vulkan-loader
+                   python
+                   wayland-protocols
+                   vulkan-headers
+                   vulkan-loader
                    waffle))
-     (native-inputs (list pkg-config))
+     (native-inputs (list pkg-config
+                          python-lxml
+                          python-mako
+                          python-numpy))
      (home-page "https://piglit.freedesktop.org/")
      (synopsis "Test OpenGL implementations")
      (description "Piglit is a collection of automated tests for OpenGL and

gnu/packages/gnome-xyz.scm

@@ -51,7 +51,6 @@
   #:use-module (guix build-system copy)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix gexp)
   #:use-module (guix git-download)
   #:use-module (guix packages)

gnu/packages/gnome.scm

@@ -250,7 +250,6 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system trivial)
   #:use-module ((guix config) #:select (%storedir))
   #:use-module (guix deprecation)
@@ -2759,7 +2758,7 @@ schemas for settings shared by various components of the GNOME desktop.")
                 (invoke "./run-tests")))))))
     (native-inputs (list python-pytest python-setuptools xorg-server-for-tests))
     (inputs (list gtk+))
-    (propagated-inputs (list python-pygobject))
+    (propagated-inputs (list python-pygobject-3.50))
     (home-page "https://getting-things-gnome.github.io/liblarch")
     (synopsis "Library to easily handle complex data structures")
     (description
@@ -2818,7 +2817,7 @@ and how they are displayed (View).")
            gtksourceview-4
            pango
            python
-           python-dbus-1.2
+           python-dbus
            python-liblarch
            python-lxml
            python-pycairo
@@ -2986,7 +2985,7 @@ guidelines.")
            python
            cups
            gtk+
-           python-dbus-1.2
+           python-dbus
            python-pygobject
            python-pycups
            python-requests
@@ -5000,6 +4999,7 @@ as OpenStreetMap, OpenCycleMap, OpenAerialMap and Maps.")
     (arguments
      (list
       #:configure-flags #~(list "-Ddocs=disabled")
+      #:parallel-tests? #f              ;hsts-db-test might hang otherwise.
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'adjust-tests
@@ -5041,7 +5041,7 @@ as OpenStreetMap, OpenCycleMap, OpenAerialMap and Maps.")
            zlib))
     (inputs
      (list samba/pinned))               ; For ntlm_auth support
-    (home-page "https://wiki.gnome.org/Projects/libsoup")
+    (home-page "https://libsoup.gnome.org")
     (synopsis "GLib-based HTTP Library")
     (description
      "LibSoup is an HTTP client/server library for GNOME.  It uses GObjects
@@ -5157,7 +5157,7 @@ and the GLib main loop, to integrate well with GNOME applications.")
            libxslt
            pkg-config
            python
-           python-dbus-1.2
+           python-dbus
            python-pygobject-3.50
            vala))
     (propagated-inputs
@@ -8158,12 +8158,6 @@ to display dialog boxes from the commandline and shell scripts.")
     (build-system meson-build-system)
     (arguments
      (list
-      #:modules '((guix build meson-build-system)
-                  ((guix build python-build-system) #:prefix python:)
-                  (guix build utils)
-                  (ice-9 match))
-      #:imported-modules `(,@%meson-build-system-modules
-                           (guix build python-build-system))
       #:glib-or-gtk? #t
       #:configure-flags
       #~(list
@@ -8686,7 +8680,7 @@ users.")
            libxslt
            perl
            pkg-config
-           python-dbus-1.2
+           python-dbus
            python-pygobject-3.50
            python-wrapper
            vala))
@@ -12337,7 +12331,6 @@ advanced image management tool")
            intltool
            pkg-config
            python-psutil
-           python-pytest-runner
            python-pytest))
     (inputs
      (list bash-minimal ;for wrap-program
@@ -12346,7 +12339,7 @@ advanced image management tool")
            gsettings-desktop-schemas
            gtk+
            python-wrapper
-           python-dbus-1.2
+           python-dbus
            python-notify2
            python-pycairo
            python-pygobject

gnu/packages/gnupg.scm

@@ -86,7 +86,6 @@
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix download)
   #:use-module (guix gexp)

gnu/packages/gnuzilla.scm

@@ -605,9 +605,9 @@ in the case of Firefox, it is browser/locales/all-locales."
     "zh-TW"))
 
 ;;; Please keep these versions in sync with icedove.
-(define %icecat-base-version "140.9.1")
+(define %icecat-base-version "140.10.0")
 (define %icecat-version (string-append %icecat-base-version "-gnu1"))
-(define %icecat-build-id "20260414000000") ;must be of the form YYYYMMDDhhmmss
+(define %icecat-build-id "20260421000000") ;must be of the form YYYYMMDDhhmmss
 
 ;; 'icecat-source' is a "computed" origin that generates an IceCat tarball
 ;; from the corresponding upstream Firefox ESR tarball, using the 'makeicecat'
@@ -627,9 +627,9 @@ in the case of Firefox, it is browser/locales/all-locales."
                   "firefox-" upstream-firefox-version ".source.tar.xz"))
             (sha256
              (base32
-              "1hld2kbzvrmr7pqq0r5hw639xl8kw29lm2hsbn0m4kxang1fdlj5"))))
+              "06996548nfmn4r4mfw3wvgb1mp35majc5hjyhs1krgp33ck2m1f0"))))
 
-         (gnuzilla-commit "f3595923458a5255f61a3853bd83bb5f004dc3bc")
+         (gnuzilla-commit "02125f31250c0240ee2ab1aa629ce66d4ffb9f30")
          (gnuzilla-source
           (origin
             (method git-fetch)
@@ -640,7 +640,7 @@ in the case of Firefox, it is browser/locales/all-locales."
                                       (string-take gnuzilla-commit 8)))
             (sha256
              (base32
-              "03kc08cvmdv3sxihf5hfhw2k91mg1y6f46b3x47p7q98phgk03cv"))))
+              "1hgx286gp0j46pklzzh5kvsnari1j3s0bff384m505m942k6l4hf"))))
 
          ;; 'search-patch' returns either a valid file name or #f, so wrap it
          ;; in 'assume-valid-file-name' to avoid 'local-file' warnings.
@@ -1249,6 +1249,166 @@ testing.")
        (cpe-name . "firefox_esr")
        (cpe-version . ,(first (string-split version #\-)))))))
 
+;;; TEMPORARY old version of icecat-source for use by icedove until it is updated.
+(define %icecat-140.9.1-base-version "140.9.1")
+(define %icecat-140.9.1-version (string-append %icecat-140.9.1-base-version "-gnu1"))
+(define icecat-140.9.1-source
+  (let* ((major-version (first  (string-split %icecat-140.9.1-base-version #\.)))
+         (minor-version (second (string-split %icecat-140.9.1-base-version #\.)))
+         (sub-version   (third  (string-split %icecat-140.9.1-base-version #\.)))
+
+         (upstream-firefox-version (string-append %icecat-140.9.1-base-version "esr"))
+         (upstream-firefox-source
+          (origin
+            (method url-fetch)
+            (uri (string-append
+                  "https://ftp.mozilla.org/pub/firefox/releases/"
+                  upstream-firefox-version "/source/"
+                  "firefox-" upstream-firefox-version ".source.tar.xz"))
+            (sha256
+             (base32
+              "1hld2kbzvrmr7pqq0r5hw639xl8kw29lm2hsbn0m4kxang1fdlj5"))))
+
+         (gnuzilla-commit "f3595923458a5255f61a3853bd83bb5f004dc3bc")
+         (gnuzilla-source
+          (origin
+            (method git-fetch)
+            (uri (git-reference
+                  (url "git://git.savannah.gnu.org/gnuzilla.git")
+                  (commit gnuzilla-commit)))
+            (file-name (git-file-name "gnuzilla"
+                                      (string-take gnuzilla-commit 8)))
+            (sha256
+             (base32
+              "03kc08cvmdv3sxihf5hfhw2k91mg1y6f46b3x47p7q98phgk03cv"))))
+
+         ;; 'search-patch' returns either a valid file name or #f, so wrap it
+         ;; in 'assume-valid-file-name' to avoid 'local-file' warnings.
+         (makeicecat-patch
+          (local-file (assume-valid-file-name
+                       (search-patch "icecat-makeicecat.patch")))))
+
+    (origin
+      (method computed-origin-method)
+      (file-name (string-append "icecat-" %icecat-140.9.1-version ".tar.zst"))
+      (sha256 #f)
+      (uri
+       (delay
+        (with-imported-modules '((guix build utils))
+          #~(begin
+              (use-modules (guix build utils))
+              (let ((firefox-dir
+                     (string-append "firefox-" #$%icecat-140.9.1-base-version))
+                    (icecat-dir
+                     (string-append "icecat-" #$%icecat-140.9.1-version)))
+
+                (set-path-environment-variable
+                 "PATH" '("bin")
+                 (list #+python
+                       #+(canonical-package bash)
+                       #+(canonical-package coreutils)
+                       #+(canonical-package findutils)
+                       #+(canonical-package patch)
+                       #+(canonical-package xz)
+                       #+(canonical-package zstd)
+                       #+(canonical-package sed)
+                       #+(canonical-package grep)
+                       #+(canonical-package bzip2)
+                       #+(canonical-package gzip)
+                       #+(canonical-package tar)))
+
+                (set-path-environment-variable
+                 "PYTHONPATH"
+                 (list #+(format #f "lib/python~a/site-packages"
+                                 (version-major+minor
+                                  (package-version python))))
+                 '#+(cons python-jsonschema
+                          (map second
+                               (package-transitive-propagated-inputs
+                                python-jsonschema))))
+
+                ;; We copy the gnuzilla source directory because it is
+                ;; read-only in 'gnuzilla-source', and the makeicecat script
+                ;; uses "cp -a" to copy parts of it and assumes that the
+                ;; copies will be writable.
+                (copy-recursively #+gnuzilla-source "/tmp/gnuzilla"
+                                  #:log (%make-void-port "w"))
+
+                (with-directory-excursion "/tmp/gnuzilla"
+                  (make-file-writable "makeicecat")
+                  (invoke "patch" "--force" "--no-backup-if-mismatch"
+                          "-p1" "--input" #+makeicecat-patch)
+                  (patch-shebang "makeicecat")
+                  (substitute* "makeicecat"
+                    (("^readonly FFMAJOR=(.*)" all ffmajor)
+                     (unless (string=? #$major-version
+                                       (string-trim-both ffmajor))
+                       ;; The makeicecat script cannot be expected to work
+                       ;; properly on a different version of Firefox, even if
+                       ;; no errors occur during execution.
+                       (error "makeicecat major version mismatch"))
+                     (string-append "readonly FFMAJOR=" #$major-version "\n"))
+                    (("^readonly FFMINOR=.*")
+                     (string-append "readonly FFMINOR=" #$minor-version "\n"))
+                    (("^readonly FFSUB=.*")
+                     (string-append "readonly FFSUB=" #$sub-version "\n"))
+                    (("^readonly DATADIR=.*")
+                     "readonly DATADIR=/tmp/gnuzilla/data\n")
+                    (("^readonly SOURCEDIR=.*")
+                     (string-append "readonly SOURCEDIR=" icecat-dir "\n"))
+                    (("/bin/sed")
+                     #+(file-append (canonical-package sed) "/bin/sed"))))
+
+                (format #t "Unpacking upstream firefox tarball...~%")
+                (force-output)
+                (invoke "tar" "xf" #+upstream-firefox-source)
+                (rename-file firefox-dir icecat-dir)
+
+                (with-directory-excursion icecat-dir
+                  (format #t "Populating l10n directory...~%")
+                  (force-output)
+                  (mkdir "l10n")
+                  (with-directory-excursion "l10n"
+                    (for-each
+                     (lambda (locale)
+                       (let ((locale-dir (string-append #+mozilla-l10n "/"
+                                                        locale)))
+                         (format #t "  ~a~%" locale)
+                         (force-output)
+                         (copy-recursively locale-dir locale
+                                           #:log (%make-void-port "w"))
+                         (for-each make-file-writable (find-files locale))
+                         (with-directory-excursion locale
+                           (mkdir-p "browser/chrome/browser/preferences")
+                           (call-with-output-file "browser/chrome/browser/\
+preferences/advanced-scripts.dtd"
+                             (lambda (port) #f)))))
+                     '#+%icecat-locales)
+                    (copy-recursively #+mozilla-compare-locales
+                                      "compare-locales"
+                                      #:log (%make-void-port "w"))
+                    (delete-file "compare-locales/.gitignore")))
+
+                (format #t "Running makeicecat script...~%")
+                (force-output)
+                (invoke "bash" "/tmp/gnuzilla/makeicecat")
+
+                (format #t "Packing IceCat source tarball...~%")
+                (force-output)
+                (setenv "ZSTD_NBTHREADS" (number->string (parallel-job-count)))
+                (invoke "tar" "cfa" #$output
+                        ;; Avoid non-determinism in the archive.  We set the
+                        ;; mtime of files in the archive to early 1980 because
+                        ;; the build process fails if the mtime of source
+                        ;; files is pre-1980, due to the creation of zip
+                        ;; archives.
+                        "--mtime=@315619200" ; 1980-01-02 UTC
+                        "--owner=root:0"
+                        "--group=root:0"
+                        "--sort=name"
+                        icecat-dir)))))))))
+
+
 (define %icedove-build-id "20260403000000") ;must be of the form YYYYMMDDhhmmss
 ;;; See <https://product-details.mozilla.org/1.0/thunderbird_versions.json>
 ;;; for the source of truth regarding Thunderbird releases.
@@ -1383,7 +1543,7 @@ testing.")
                ;; Extract the base Icecat tarball, renaming its top-level
                ;; directory.
                (invoke "tar" "--transform" (string-append "s,[^/]*," #$name ",")
-                       "-xf" #$icecat-source)
+                       "-xf" #$icecat-140.9.1-source)
                (chdir #$name)
 
                ;; Merge the Thunderdbird localization data.

gnu/packages/golang-crypto.scm

@@ -31,6 +31,7 @@
 ;;; Copyright © 2025 Arthur Rodrigues <arthurhdrodrigues@proton.me>
 ;;; Copyright © 2025 Patrick Norton <patrick.147.norton@gmail.com>
 ;;; Copyright © 2025 Giacomo Leidi <therewasa@fishinthecalculator.me>
+;;; Copyright © 2026 Evgeny Pisemsky <mail@pisemsky.site>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -2873,7 +2874,7 @@ package.")
 (define-public go-github-com-refraction-networking-utls
   (package
     (name "go-github-com-refraction-networking-utls")
-    (version "1.6.0")
+    (version "1.8.2")
     (source
      (origin
        (method git-fetch)
@@ -2882,7 +2883,7 @@ package.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1iywar5vqsml4b177k2nkcxmjm8mw92g3p112yjsrpmikiwpwpyw"))))
+        (base32 "03kgwxdm2lg28fn2w5q7ql2szsiwj2xjdf477h1g3a4a9y9j6zk0"))))
     (build-system go-build-system)
     (arguments
      `(#:import-path "github.com/refraction-networking/utls"
@@ -3640,6 +3641,39 @@ algorithm described in @url{https://rfc-editor.org/rfc/rfc2898.html,RFC 2898}
 and @url{https://rfc-editor.org/rfc/rfc8018.html,RFC 8018}.")
     (license license:asl2.0)))
 
+(define-public go-github-com-xtls-reality
+  (package
+    (name "go-github-com-xtls-reality")
+    (version "0.0.0-20260322125925-9234c772ba8f")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/xtls/reality")
+              (commit (go-version->git-ref version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1wncy5aph6nmq4814xjhj6b5p1wm2fyrqn83dw0xlyxvq2z6iqfs"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/xtls/reality"))
+    (propagated-inputs
+     (list go-github-com-cloudflare-circl
+           go-github-com-juju-ratelimit
+           go-github-com-pires-go-proxyproto
+           go-github-com-refraction-networking-utls
+           go-golang-org-x-crypto
+           go-golang-org-x-sys))
+    (home-page "https://github.com/xtls/reality")
+    (synopsis "Implementation of REALITY protocol")
+    (description
+     "This package provides an implementation of REALITY protocol, which is
+intented to eliminate the detectable TLS fingerprint on the server side, while
+still maintain the secrecy.  It achieves full real TLS that is
+undistingwishable with the specified SNI to the middleman.")
+    (license (list license:bsd-3 license:mpl2.0))))
+
 (define-public go-github-com-youmark-pkcs8
   (package
     (name "go-github-com-youmark-pkcs8")

gnu/packages/golang-web.scm

@@ -50,6 +50,7 @@
 ;;; Copyright © 2026 Carlos Durán Domínguez <wurt@wurt.eu>
 ;;; Copyright © 2026 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2026 Evgeny Pisemsky <mail@pisemsky.site>
+;;; Copyright © 2026 Vinicius Monego <monego@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -20005,6 +20006,36 @@ at
 Tracer implementation from the @code{OpenTracing} project.")
     (license license:asl2.0)))
 
+(define-public go-go-opentelemetry-io-contrib-zpages
+  (package
+    (name "go-go-opentelemetry-io-contrib-zpages")
+    (version "0.68.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/open-telemetry/opentelemetry-go-contrib")
+             (commit (go-version->git-ref version
+                                          #:subdir "zpages"))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0nh7g1zxr3drqcbhsnnkqaz2hn1rnawg8jalixng23c9hwfgqaly"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:go go-1.25
+      #:import-path "go.opentelemetry.io/contrib/zpages"
+      #:unpack-path "go.opentelemetry.io/contrib"))
+    (native-inputs (list go-github-com-stretchr-testify))
+    (propagated-inputs (list go-go-opentelemetry-io-otel
+                             go-go-opentelemetry-io-otel-sdk
+                             go-go-opentelemetry-io-otel-trace))
+    (home-page "https://opentelemetry.io/")
+    (synopsis "Display telemetry stats")
+    (description "Package zPages implements a collection of HTML pages that
+display telemetry stats.")
+    (license license:asl2.0)))
+
 (define-public go-go-opentelemetry-io-otel
   (package
     (name "go-go-opentelemetry-io-otel")

gnu/packages/golang-xyz.scm

@@ -75,6 +75,7 @@
 ;;; Copyright © 2026 Carlos Durán Domínguez <wurt@wurt.eu>
 ;;; Copyright © 2026 Giacomo Leidi <therewasa@fishinthecalculator.me>
 ;;; Copyright © 2026 Evgeny Pisemsky <mail@pisemsky.site>
+;;; Copyright © 2026 Vinicius Monego <monego@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -8036,7 +8037,7 @@ supports concurrent serializable transactions.")
   (package
     (inherit go-github-com-dgraph-io-badger)
     (name "go-github-com-dgraph-io-badger-v4")
-    (version "4.5.2")
+    (version "4.9.1")
     (source
      (origin
        (method git-fetch)
@@ -8045,7 +8046,7 @@ supports concurrent serializable transactions.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0v4c69whypm3k40hrx8bw9rjrcb0swz43v056s0fadqr04j0ncwj"))))
+        (base32 "0a9lk7fw06yb89wy9rp4q50ircw5imm1cqzhyhs92d0cia5qbhh6"))))
     (arguments
      (list
       #:tests? #f ; TODO: tests hang, find out why.
@@ -8058,7 +8059,8 @@ supports concurrent serializable transactions.")
            go-github-com-klauspost-compress
            go-github-com-pkg-errors
            go-github-com-spf13-cobra
-           go-go-opencensus-io
+           go-go-opentelemetry-io-contrib-zpages
+           go-go-opentelemetry-io-otel
            go-golang-org-x-net
            go-golang-org-x-sys
            go-google-golang-org-protobuf))))
@@ -17604,7 +17606,7 @@ implementing features like:
 (define-public go-github-com-maruel-natural
   (package
     (name "go-github-com-maruel-natural")
-    (version "1.1.1")
+    (version "1.3.0")
     (source
      (origin
        (method git-fetch)
@@ -17613,7 +17615,7 @@ implementing features like:
               (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "040aikizdd7c4zm8xindb2ps16s60i0fkf8gkll2rir7lwv6q7ks"))))
+        (base32 "1nr1ai3b7yvz4wz4k0jqvjq3978hpk9yxarn7g7i3d2sxbdc0g4q"))))
     (build-system go-build-system)
     (arguments
      (list
@@ -22786,16 +22788,16 @@ it is capable of logging at some or all levels.")
 (define-public go-github-com-rivo-tview
   (package
     (name "go-github-com-rivo-tview")
-    (version "0.0.0-20241227133733-17b7edb88c57")
+    (version "0.42.0")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/rivo/tview")
-             (commit (go-version->git-ref version))))
+             (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1w59vyvs8k5mzl7k39zpwcwwdgam2pbz0rnrfnnjgvkld1rh81dc"))))
+        (base32 "0jw47h92l0vp1lg6s5kng4hjv81hi8qxx9h5yilc7rzrr8l9ksd2"))))
     (build-system go-build-system)
     (arguments
      (list #:import-path "github.com/rivo/tview"))

gnu/packages/gpodder.scm

@@ -29,7 +29,6 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (gnu packages)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages base)

gnu/packages/graph.scm

@@ -36,7 +36,6 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system r)
   #:use-module (guix download)
   #:use-module (guix gexp)

gnu/packages/graphics.scm

@@ -146,7 +146,6 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system qt)
   #:use-module (guix download)
@@ -1265,51 +1264,6 @@ basic geometries.")
     ;; https://gitlab.com/inkscape/inkscape/issues/784).
     (license license:gpl3+)))
 
-(define-public python-booleanoperations
-  (package
-    (name "python-booleanoperations")
-    (version "0.9.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/typemytype/booleanOperations")
-              (commit version)))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0ahfgamyq1ndwbr9n8sdx8qhqc2195xnbahylgjpk877hbr2gxav"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list
-      ;; Some tests fail due to small differences in the expected result (see:
-      ;; <https://github.com/typemytype/booleanOperations/issues/69>).
-      #:test-flags
-      #~(list "-k"
-              (string-join
-               (list "not test_QTail_reversed_difference"
-                     "test_QTail_reversed_intersection"
-                     "test_QTail_reversed_union"
-                     "test_QTail_reversed_xor"
-                     "test_Q_difference"
-                     "test_Q_intersection"
-                     "test_Q_union"
-                     "test_Q_xor")
-               " and not "))))
-    (propagated-inputs (list python-fonttools-minimal python-pyclipper))
-    (native-inputs
-     (list python-defcon-bootstrap
-           python-fontpens-bootstrap
-           python-pytest
-           python-setuptools
-           python-setuptools-scm))
-    (home-page "https://github.com/typemytype/booleanOperations")
-    (synopsis "Boolean operations on paths")
-    (description
-     "Boolean operations on paths which uses a super fast
-@url{http://www.angusj.com/delphi/clipper.php, polygon clipper library by
-Angus Johnson}.")
-    (license license:expat)))
-
 (define-public pstoedit
   (package
     (name "pstoedit")

gnu/packages/graphviz.scm

@@ -35,7 +35,6 @@
   #:use-module (guix packages)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix download)
   #:use-module (guix git-download)
   #:use-module (guix utils)
@@ -152,32 +151,46 @@ interfaces for other technical domains.")
 (define-public python-graphviz
   (package
     (name "python-graphviz")
-    (version "0.20.3")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "graphviz" version ".zip"))
-              (sha256
-               (base32
-                "0pcjnnhprs1hb4r9jr7r4qjxc7lzsjlka8d5gcp3kym9ws0vrmh9"))))
+    (version "0.21")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/xflr6/graphviz")
+              (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "00hgh1ab54h2jhqnwn5vrggg0hqbwmjn0cx2a9nw4vi1wmijib53"))))
     (build-system pyproject-build-system)
     (arguments
      (list
+      #:test-flags
+      #~(list "--ignore=tests/backend/")
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'patch-pytest-options
             (lambda _
-              (substitute* "setup.cfg"
-                ((".*doctest.*") "")
-                (("--cov.*") ""))))
-          (replace 'check
-            (lambda* (#:key tests? test-flags #:allow-other-keys)
+              (substitute* "pyproject.toml"
+                ((".*--cov-report=term.*") ""))))
+          (add-before 'check 'pre-check
+            (lambda _
+              (setenv "HOME" "/tmp")))
+          (add-after 'check 'test-backend
+            (lambda* (#:key tests? #:allow-other-keys)
+              ;; Running tests together fails with error:
+              ;;
+              ;; import file mismatch:
+              ;; imported module 'conftest' has this __file__ attribute:
+              ;;   /<...>/source/tests/backend/conftest.py
+              ;; which is not the same as the test file we want to collect:
+              ;;   /<...>/source/tests/conftest.py
+              ;;
+              ;; HINT: remove __pycache__ / .pyc files and/or use a unique
+              ;; basename for your test file modules
               (when tests?
-                (setenv "HOME" "/tmp")
-                  (apply invoke "python" "run-tests.py" test-flags)))))))
+                (invoke "pytest" "-v" "tests/backend/")))))))
     (native-inputs
-     (list unzip
-           ;; For tests.
-           graphviz
+     (list graphviz
            python-mock
            python-pytest
            python-pytest-mock
@@ -246,7 +259,6 @@ layout algorithms.")
      (list graphviz
            python-defusedxml
            python-pytest
-           python-pytest-cov
            python-setuptools
            python-typing-extensions))
     (propagated-inputs

gnu/packages/gtk.scm

@@ -71,7 +71,6 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system waf)
   #:use-module (gnu packages)
@@ -1120,7 +1119,7 @@ application suites.")
 (define-public gtk
   (package
     (name "gtk")
-    (version "4.20.3")
+    (version "4.22.1")
     (source
      (origin
        (method url-fetch)
@@ -1128,9 +1127,11 @@ application suites.")
                            (version-major+minor version)  "/"
                            name "-" version ".tar.xz"))
        (sha256
-        (base32 "0ly1gqc6ybxv5f2a9hvjp5k6l9mfzy2yv8iy2xqnr9l8628g4wr8"))
+        (base32 "1z2mkmazc2d51jbg3qwwdycycqiwswm88nhw6bxscz8j86f5lyyd"))
        (patches
-        (search-patches "gtk4-respect-GUIX_GTK4_PATH.patch"))
+        (search-patches "gtk4-demo-reproducible.patch"
+                        "gtk4-needs-udmabuf.patch"
+                        "gtk4-respect-GUIX_GTK4_PATH.patch"))
        (modules '((guix build utils)))))
     (build-system meson-build-system)
     (outputs '("out" "bin" "doc"))
@@ -1254,8 +1255,10 @@ application suites.")
               (setenv "XDG_CACHE_HOME" (getcwd))))
           (add-before 'check 'pre-check
             (lambda* (#:key inputs #:allow-other-keys)
-              ;; Tests require a running X server.
-              (system "Xvfb :1 +extension GLX &")
+              ;; Tests require a running X server.  The '-noreset' option is
+              ;; necessary to avoid spurious "Failed to open display" test
+              ;; errors.
+              (system "Xvfb :1 +extension GLX -screen 0 1024x768x24 -noreset &")
               (setenv "DISPLAY" ":1")
               ;; Tests write to $HOME.
               (setenv "HOME" (getcwd))
@@ -1298,6 +1301,7 @@ application suites.")
            docbook-xsl
            gettext-minimal
            `(,glib "bin")
+           glibc-utf8-locales           ;some tests require en_US.UTF-8
            gobject-introspection        ;for building introspection data
            graphene
            gtk-doc/stable               ;for building documentation
@@ -1365,8 +1369,8 @@ application suites.")
     (native-search-paths
      (list
       (search-path-specification
-       (variable "GUIX_GTK4_PATH")
-       (files '("lib/gtk-4.0")))))
+        (variable "GUIX_GTK4_PATH")
+        (files '("lib/gtk-4.0")))))
     (search-paths native-search-paths)
     (home-page "https://www.gtk.org/")
     (synopsis "Cross-platform widget toolkit")
@@ -2766,7 +2770,7 @@ popovers.")
 (define-public goocanvas
   (package
     (name "goocanvas")
-    (version "2.0.4")
+    (version "3.0.0")
     (source
      (origin
        (method url-fetch)
@@ -2774,7 +2778,7 @@ popovers.")
                            (version-major+minor version)
                            "/goocanvas-" version ".tar.xz"))
        (sha256
-        (base32 "141fm7mbqib0011zmkv3g8vxcjwa7hypmq71ahdyhnj2sjvy4a67"))))
+        (base32 "06j05g2lmwvklmv51xsb7gm7rszcarhm01sal41jfp0qzrbpa2k7"))))
     (build-system gnu-build-system)
     (native-inputs
      (list gettext-minimal

gnu/packages/guile-xyz.scm

@@ -60,6 +60,7 @@
 ;;; Copyright © 2025 Andy Tai <atai@atai.org>
 ;;; Copyright © 2025 Ekaitz Zarraga <ekaitz@elenq.tech>
 ;;; Copyright © 2026 Matt Wette <matt.wette@gmail.com>
+;;; Copyright © 2026 Dzianis Jackievič <mail@miesta.by>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1167,7 +1168,7 @@ is not available for Guile 2.0.")
   (package
     (inherit guile-fibers-1.3)
     (name "guile-fibers")
-    (version "1.4.2")
+    (version "1.4.3")
     (source
      (origin (inherit (package-source guile-fibers-1.3))
              (file-name (git-file-name name version))
@@ -1176,7 +1177,7 @@ is not available for Guile 2.0.")
                     (commit (string-append "v" version))))
              (sha256
               (base32
-               "0qh0czz5qvk5mmrc8x2gmvl5psdfd22q2rhzj4jrpan6k3d55bl8"))
+               "1q0a9y0cc8rld1z7mcj61fkldhd0kn9n4yq25izxslbgg4g5h9j6"))
              (patches '())))
     (arguments
      (if (target-aarch64?)
@@ -1256,30 +1257,8 @@ is not available for Guile 2.0.")
      (modify-inputs native-inputs
        (replace "guile" guile-2.2)))))
 
-(define-public guile-fibers-next
-  (let ((commit "297359f0ad655378bcc3ff0d4e96101965ef39b4")
-        (revision "0"))
-    (package
-      (inherit guile-fibers)
-      (name "guile-fibers-next")
-      (version (git-version "1.4.2"
-                            revision
-                            commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "https://codeberg.org/guile/fibers.git")
-                      (commit commit)))
-                (file-name (git-file-name name version))
-                (sha256
-                 (base32
-                  "0qh0czz5qvk5mmrc8x2gmvl5psdfd22q2rhzj4jrpan6k3d55bl8"))))
-      (inputs
-       (modify-inputs inputs
-         (replace "guile" guile-next)))
-      (native-inputs
-       (modify-inputs native-inputs
-         (replace "guile" guile-next))))))
+;; Deprecated on 2026-04-23
+(define-deprecated-package guile-fibers-next guile-fibers)
 
 (define-public guile-kracht
   (package
@@ -1537,7 +1516,7 @@ order to provide IDE functionality for Guile Scheme.")
 (define-public guile-ares-rs
   (package
     (name "guile-ares-rs")
-    (version "0.9.6")
+    (version "0.9.7")
     (source
      (origin
        (method git-fetch)
@@ -1547,35 +1526,42 @@ order to provide IDE functionality for Guile Scheme.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1vkww3vc0lsh5f8yh6fnh402rx3rsm0ss69rdkmplhzp4c7c4z1d"))))
+         "1xbznh5zjswfydgqg53g50ya7zm0hidin74g2glk849l9j45szw3"))))
     (build-system guile-build-system)
     (arguments
      (list
       #:source-directory "src/guile"
       #:phases
       #~(modify-phases %standard-phases
-          (add-after 'build 'install-script
+          (add-after 'build 'install-scripts
             (lambda _
-              (let* ((bin (string-append #$output "/bin"))
-                     (oldpath (string-append
-                               #$output
-                               ;; This file will be named ares-nrepl.scm for
-                               ;; the next version.
-                               "/share/guile/site/3.0/ares/scripts/ares.scm"))
-                     (newpath (string-append bin "/ares-nrepl")))
-                (mkdir bin)
-                (symlink oldpath newpath)
-                (wrap-program newpath
-                  `("GUILE_LOAD_PATH" ":" =
-                    ,(list (string-append #$output "/share/guile/site/3.0")
-                           (getenv "GUILE_LOAD_PATH")))
-                  `("GUILE_LOAD_COMPILED_PATH" ":" =
-                    ,(list (string-append #$output "/lib/guile/3.0/site-ccache")
-                           (getenv "GUILE_LOAD_COMPILED_PATH"))))
-                ;; Not needed since the wrapper followed the symlink.
-                (delete-file (string-append bin "/.ares-nrepl-real"))))))))
-    (inputs (list bash-minimal guile-3.0))
-    (propagated-inputs (list guile-fibers guile-custom-ports))
+              (define bin (string-append #$output "/bin"))
+              (define site (string-append #$output "/share/guile/site/3.0"))
+              (define ccache
+                (string-append #$output "/lib/guile/3.0/site-ccache"))
+
+              (define (install-script name)
+                (let ((oldpath
+                       (string-append site "/ares/scripts/" name ".scm"))
+                      (newpath
+                       (string-append bin "/" name)))
+                  (symlink oldpath newpath)
+                  (wrap-program newpath
+                    `("GUILE_LOAD_PATH" ":" =
+                      ,(list "$GUILE_LOAD_PATH"
+                             site
+                             (getenv "GUILE_LOAD_PATH")))
+                    `("GUILE_LOAD_COMPILED_PATH" ":" =
+                      ,(list "$GUILE_LOAD_COMPILED_PATH"
+                             ccache
+                             (getenv "GUILE_LOAD_COMPILED_PATH"))))
+                  ;; Not needed since the wrapper followed the symlink.
+                  (delete-file (string-append bin "/." name "-real"))))
+
+              (mkdir bin)
+              (for-each install-script '("ares-nrepl" "ares-suitbl")))))))
+    (inputs (list bash-minimal guile-3.0-latest))
+    (propagated-inputs (list guile-fibers))
     (home-page "https://git.sr.ht/~abcdw/guile-ares-rs")
     (synopsis "Asynchronous Reliable Extensible Sleek RPC Server for Guile")
     (description "Asynchronous Reliable Extensible Sleek RPC Server for
@@ -5707,27 +5693,32 @@ perform geometrical transforms on JPEG images.")
       (license license:gpl3+))))
 
 (define-public guile-jtd
-  (package
-    (name "guile-jtd")
-    (version "220323a")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/mwette/guile-jtd")
-                    (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "1l8fyqhvksarvpbr903i3ss3432jzvyvhgcqa15j922ngqh4ds6f"))))
-    (build-system guile-build-system)
-    (native-inputs (list guile-3.0))
-    (home-page "https://github.com/mwette/guile-jtd")
-    (synopsis "Python's @code{pdb.set_trace()} but for Guile")
-    (description
-     "The @code{(jtd)} module for Guile provides a procedure
+  ;; There are a few unreleased commits that include niceties such as warning
+  ;; that the debug VM must be used; use the latest commit until the next
+  ;; release comes.
+  (let ((commit "425f86ae954d6445aaedacfd4ecd50aa0022e59d")
+        (revision "0"))
+    (package
+      (name "guile-jtd")
+      (version (git-version "220323a" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/mwette/guile-jtd")
+                       (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1l8fyqhvksarvpbr903i3ss3432jzvyvhgcqa15j922ngqh4ds6f"))))
+      (build-system guile-build-system)
+      (native-inputs (list guile-3.0))
+      (home-page "https://github.com/mwette/guile-jtd")
+      (synopsis "Python's @code{pdb.set_trace()} but for Guile")
+      (description
+       "The @code{(jtd)} module for Guile provides a procedure
 @code{jump-to-debugger} for escaping to the Guile REPL for the purpose of
 debugging code.")
-    (license license:lgpl2.1+)))
+      (license license:lgpl2.1+))))
 
 (define-public guile-png
   (package
@@ -6399,6 +6390,87 @@ as signed sessions, multipart message support, etc.")
     (propagated-inputs
      (list guile2.2-irregex guile2.2-gcrypt))))
 
+(define-public guile-compose
+  (package
+    (name "guile-compose")
+    (version "0.1.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://codeberg.org/jadzi/guile-compose.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1g68gczs96nrb0vf1hv4n07zsp2516gpiwq1wwlhcq4rzynhf12h"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:make-flags
+      #~'("GUILE_AUTO_COMPILE=0")))
+    (inputs (list guile-3.0))
+    (native-inputs (list autoconf-2.72 automake pkg-config guile-3.0 texinfo))
+    (synopsis "Procedure composition utilities for Guile Scheme")
+    (description
+     "This tiny package provides some procedures and macros to extend
+Guile Scheme procedure composition facilities.  For example, there is
+a @code{compose-top}, a reverse-order analog to native @code{compose}
+procedure.  The @code{compose-cont} is a macro, utilizing some power of
+continuations to build really flexible flows.
+
+This library is intended to stay basic and small, so it has no any
+external dependencies and can be a good base for other packages, like e.g.
+@code{guile-web-middleware}.")
+    (license (list license:lgpl3+))
+    (home-page "https://jadzi.codeberg.page/guile-compose")))
+
+(define-public guile-web-middleware
+  (package
+    (name "guile-web-middleware")
+    (version "0.11.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://codeberg.org/jadzi/guile-web-middleware.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "01wb8v0lszphdv08ly4aqv59qm5h8yw2fgm025vkn61djspsq4j9"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:make-flags
+      #~'("GUILE_AUTO_COMPILE=0")))
+    (inputs (list guile-3.0 guile-compose))
+    (native-inputs (list autoconf-2.72 automake pkg-config guile-3.0 texinfo))
+    (synopsis "Web application middleware composition for Guile Scheme")
+    (description
+     "This package provides means to compose a web application by
+chaining procedures, a.k.a. middlewares.  By those means, composed
+procedures form a standard request handler for any Guile's web server
+implementation.
+
+Each middleware has its own limited responsibility in request
+processing.  Also, middlewares are simple Scheme procedures, so they
+can be easily tested and shared among web applications.
+
+Out of the box, this package provides several procedures for commonly
+required tasks.  Among them:
+
+@itemize
+@item Error handling with customizable page contents.
+@item Request filtering.
+@item Request logging.
+@item Serving static files, file URL generation.
+@item Request routing, handling parameters, route URL generation.
+@item Middleware nesting, composing whole apps.
+@end itemize
+
+This package relies on @code{guile-compose} package as its only dependency.")
+    (license (list license:lgpl3+))
+    (home-page "https://jadzi.codeberg.page/guile-web-middleware")))
+
 (define-public guile-web-driver-ng
   (package
     (name "guile-web-driver-ng")
@@ -7716,13 +7788,13 @@ is an attempt to combine both into something useful.")
      (list pkg-config
            autoconf
            automake
-           guile-next
+           guile-3.0-latest
            guile-lib
-           guile-fibers-next))
+           guile-fibers))
     (inputs
-     (list guile-next))
+     (list guile-3.0-latest))
     (propagated-inputs
-     (list guile-fibers-next))
+     (list guile-fibers))
     (home-page "https://cbaines.codeberg.page/guile-knots/")
     (synopsis "Patterns and functionality to use with Guile Fibers")
     (description
@@ -8018,14 +8090,14 @@ application to open a given file or URL based on given configurations.")
 (define-public guile-goblins
   (package
     (name "guile-goblins")
-    (version "0.17.0")
+    (version "0.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://files.spritely.institute/releases"
                            "/guile-goblins/guile-goblins-" version ".tar.gz"))
        (sha256
-        (base32 "16jkmfspsnza2fdk5jr05a5pfh7x856gpg031i21s1yvy43l8mi0"))))
+        (base32 "0gj5018wmq97ln1z7x03a13z3p35xc8762id9bl9fgkxwm01df1a"))))
     (build-system gnu-build-system)
     (arguments
      (list

gnu/packages/guile.scm

@@ -1004,7 +1004,7 @@ Guile's foreign function interface.")
        (file-name (string-append "guile-lzlib-" version ".tar.gz"))
        (sha256
         (base32
-         "1whgmwkr1v8m63p4aaqn8blwl9vcrswwhbfv4bm0aghl5a6rryd7"))
+         "1v1pfqp6hwl0rivs7swhqnfgznxlfnws9ldmn6avnhd10filfa3a"))
        (patches (search-patches "guile-lzlib-gcc-14.patch"
                                 "guile-lzlib-hurd64.patch"))))
     (build-system gnu-build-system)

gnu/packages/hardware.scm

@@ -117,7 +117,6 @@
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix download)
   #:use-module (guix gexp)

gnu/packages/haskell-crypto.scm

@@ -914,7 +914,7 @@ regular) Diffie Hellman key exchanges, and many extensions.")
      (list #:extra-directories (list "openssl")
            #:configure-flags
            #~(list "--ghc-options=-optc=-Wno-incompatible-pointer-types")))
-    (inputs (list ghc-network openssl))
+    (inputs (list ghc-network openssl-3.0))
     (home-page "https://github.com/haskell-cryptography/HsOpenSSL")
     (synopsis "Partial OpenSSL binding for Haskell")
     (description

gnu/packages/high-availability.scm

@@ -489,11 +489,22 @@ lost.
                 "0b9d2i22ghyjarwi1c596q5mf7gj1k04k784hnmrd2d4x9hgv9ax"))))
     (build-system gnu-build-system)
     (arguments
-     (list #:configure-flags #~(list "--with-corosync" "--disable-static"
+     (list #:configure-flags #~(list "--with-corosync"
+                                     "--disable-static"
+                                     "--localstatedir=/var"
                                      (string-append "--with-initdir="
                                                     #$output "/etc/init.d")
                                      (string-append "--with-ocfdir="
-                                                    #$output "/lib"))))
+                                                    #$output "/lib"))
+           #:phases
+           #~(modify-phases %standard-phases
+               (add-before 'configure 'pre-configure
+                 (lambda _
+                   ;; Do not attempt to install /var.
+                   (substitute* '("Makefile.am"
+                                  "daemons/schedulerd/Makefile.am")
+                     (("install-exec-local:")
+                      "install-exec-local-disabled:")))))))
     (native-inputs (list autoconf
                          automake
                          cmocka

gnu/packages/ibus.scm

@@ -43,7 +43,6 @@
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix utils)
   #:use-module (gnu packages)
   #:use-module (gnu packages anthy)

gnu/packages/image-processing.scm

@@ -58,7 +58,6 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (gnu packages)
   #:use-module (gnu packages algebra)

gnu/packages/image-viewers.scm

@@ -66,7 +66,6 @@
   #:use-module (guix build-system copy)
   #:use-module (guix build-system go)
   #:use-module (guix build-system meson)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system qt)
   #:use-module (gnu packages autotools)

gnu/packages/image.scm

@@ -29,7 +29,7 @@
 ;;; Copyright © 2020, 2025 Janneke Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2020 Zhu Zihao <all_but_last@163.com>
 ;;; Copyright © 2020, 2021, 2022, 2023, 2024 Vinicius Monego <monego@posteo.net>
-;;; Copyright © 2021 Sharlatan Hellseher <sharlatanus@gmail.com>
+;;; Copyright © 2021, 2026 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;; Copyright © 2021 Nicolò Balzarotti <nicolo@nixo.xyz>
 ;;; Copyright © 2021 Alexandr Vityazev <avityazev@posteo.org>
 ;;; Copyright © 2022 Jai Vetrivelan <jaivetrivelan@gmail.com>
@@ -42,8 +42,9 @@
 ;;; Copyright © 2025 Josep Bigorra <jjbigorra@gmail.com>
 ;;; Copyright © 2025 Jake Forster <jakecameron.forster@gmail.com>
 ;;; Copyright © 2025 Ghislain Vaillant <ghislain.vaillant@inria.fr>
-;;; Copyright © 2026 Carlos Durán Domínguez <wurt@wurt.eu>
 ;;; Copyright © 2025 Junker <dk@junkeria.club>
+;;; Copyright © 2025 Hugo Buddelmeijer <hugo@buddelmeijer.nl>
+;;; Copyright © 2026 Carlos Durán Domínguez <wurt@wurt.eu>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -128,7 +129,6 @@
   #:use-module (guix build-system guile)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system scons)
   #:use-module (guix deprecation)
@@ -2967,77 +2967,89 @@ GIF, TIFF, WEBP, BMP, PNG, XPM formats.")
 (define-public mypaint
   (package
     (name "mypaint")
-    (version "2.0.1")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/mypaint/mypaint/"
-                                  "releases/download/v" version "/mypaint-"
-                                  version ".tar.xz"))
-              (sha256
-               (base32
-                "05mvay73vb9d2sh1ckv4vny45n059dmsps1jcppjizfmrpbkgr7k"))))
-    (build-system python-build-system)
+    ;; The latest changes contains support for Python 3.12+.
+    (properties '((commit . "35aa9d33cd3deba6cafea6d8fc901b5a1d161ceb")
+                  (revision . "0")))
+    (version (git-version "2.0.1"
+                          (assoc-ref properties 'revision)
+                          (assoc-ref properties 'commit)))
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/mypaint/mypaint")
+              (commit (assoc-ref properties 'commit))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1p1i799dzpx0zr7chkz0pjdq9l32ahckgyagbiw82c27mwxqabfh"))))
+    (build-system pyproject-build-system)
     (arguments
-     `(#:imported-modules ((guix build glib-or-gtk-build-system)
-                           ,@%python-build-system-modules)
-       #:modules ((guix build python-build-system)
+     (list
+      #:imported-modules `(,@%pyproject-build-system-modules
+                           (guix build glib-or-gtk-build-system))
+      #:modules '((guix build pyproject-build-system)
                   ((guix build glib-or-gtk-build-system) #:prefix glib-or-gtk:)
                   (guix build utils))
-       ;; XXX: Tests are not discovered.
-       #:tests? #false
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'python3.11-compatibility
-           (lambda _
-             (substitute* "setup.py"
-               (("\"rU\"") "\"r\"")
-               (("test_suite='tests'.*") ""))
-             (substitute* "setup.cfg"
-               (("install-") "install_"))
-             ;; This file makes Python confuse it for a module, so we rename
-             ;; it.
-             (rename-file "lib/xml.py" "lib/xmlo.py")
-             (substitute* (find-files "." "\\.py$")
-               (("lib.xml") "lib.xmlo"))
-             ;; This procedure has been removed.
-             (substitute* "lib/gettext_setup.py"
-               (("c = gettext.bind_textdomain_codeset.*") "c = True\n"))))
-         (add-after 'install 'glib-or-gtk-wrap
-           (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap))
-         (add-after 'install 'wrap-program
-           (lambda* (#:key outputs inputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (gdk-pixbuf (assoc-ref inputs "gdk-pixbuf"))
-                    (gtk+ (assoc-ref inputs "gtk+")))
-               ;; This is replaced with an invalid shebang.
-               (substitute* (string-append out "/bin/mypaint")
-                 (("#!python")
-                  (string-append "#!" (which "python3"))))
-               (wrap-program (string-append out "/bin/mypaint")
-                 `("GI_TYPELIB_PATH" ":" prefix
-                   (,(getenv "GI_TYPELIB_PATH")))))))
-         (add-before 'check 'pre-check
-           (lambda _
-             ;; Tests need writing access
-             (setenv "HOME" "/tmp"))))))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'install 'move-assets-to-data
+            ;; XXX: Check why.
+            ;;
+            ;; ERROR: gui.application: Missing icon 'org.mypaint.MyPaint':
+            ;; check that mypaint icons have been installed into
+            ;; /gnu/store/<...>/data/icons
+            ;;
+            ;; gi.repository.GLib.GError: g-file-error-quark: Failed to open
+            ;; file
+            ;; “/gnu/store/<...>/data/mypaint/pixmaps/cursor_color_picker.png”:
+            ;; No such file or directory (4)
+            (lambda _
+              (let* ((data (string-append #$output "/data"))
+                     (data-icons (string-append data "/icons"))
+                     (data-mypaint (string-append data "/mypaint"))
+                     (icons (string-append #$output "/icons"))
+                     (mypaint (string-append #$output "/mypaint")))
+                (mkdir-p data-icons)
+                (mkdir-p data-mypaint)
+                (copy-recursively icons data-icons)
+                (copy-recursively mypaint data-mypaint)
+                (delete-file-recursively icons)
+                (delete-file-recursively mypaint))))
+          (add-after 'install 'glib-or-gtk-wrap
+            (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap))
+          (add-after 'install 'wrap-program
+            (lambda* (#:key outputs inputs #:allow-other-keys)
+              (wrap-program (string-append #$output "/bin/mypaint")
+                `("GI_TYPELIB_PATH" ":" prefix
+                  (,(getenv "GI_TYPELIB_PATH"))))))
+          (add-before 'check 'pre-check
+            (lambda _
+              ;; Need to get the 'lib' in 'build/'.
+              (delete-file-recursively "lib")
+              ;; Tests need writing access
+              (setenv "HOME" "/tmp"))))))
     (native-inputs
-     (list pkg-config
+     (list gettext-minimal
            gobject-introspection
-           swig-4.0
-           gettext-minimal))
+           pkg-config
+           python-pytest
+           python-setuptools
+           swig))
     (inputs
      (list bash-minimal
+           gdk-pixbuf
            gtk+
-           (librsvg-for-system)
            hicolor-icon-theme
-           libmypaint
-           mypaint-brushes
            json-c
            lcms
+           libmypaint-next
+           libpng
+           (librsvg-for-system)
+           mypaint-brushes
            python-numpy
            python-pycairo
            python-pygobject))
-    (home-page "http://mypaint.org/")
+    (home-page "https://mypaint.org/")
     (synopsis "Fast and simple painting app for artists")
     (description
      "MyPaint is a simple drawing and painting program that works well with

gnu/packages/instrumentation.scm

@@ -63,7 +63,6 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system linux-module)
   #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
   #:use-module (guix download)
   #:use-module (guix gexp)
   #:use-module (guix git-download)
@@ -109,6 +108,7 @@
            flex
            pkg-config
            python-3
+           python-setuptools
            python-sphinx
            swig-4.0
            xmltoman))
@@ -339,30 +339,6 @@ coverage.")
     ;; that list in further version.
     (supported-systems (list "x86_64-linux"))))
 
-(define-public lttng-modules
-  (package
-    (name "lttng-modules")
-    (version "2.13.14")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://lttng.org/files/lttng-modules/"
-                                  "lttng-modules-" version ".tar.bz2"))
-              (sha256
-               (base32
-                "19jx1yz1hsbr4vwfp2nr6z52a5g50iimaak962k49diay5zryi66"))))
-    (build-system linux-module-build-system)
-    (arguments
-     `(#:tests? #f ; no tests
-       #:make-flags (list "CONFIG_LTTNG=m"
-                          "CONFIG_LTTNG_CLOCK_PLUGIN_TEST=m")))
-    (home-page "https://lttng.org/")
-    (synopsis "LTTng kernel modules for the LTTng tracer toolset")
-    (description
-     "LTTng kernel modules are Linux kernel modules which make
-LTTng kernel tracing possible.  They include essential control modules and
-many probes which instrument numerous interesting parts of Linux.")
-    (license (list license:lgpl2.1 license:gpl2 license:expat))))
-
 (define-public lttng-ust
   (package
     (name "lttng-ust")
@@ -513,7 +489,7 @@ ftrace.")
 (define-public systemtap
   (package
     (name "systemtap")
-    (version "4.9")
+    (version "5.4")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -521,20 +497,9 @@ ftrace.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "161smpv4ajqfncmgylvs89bbix1id60nf0g7clmga2lxxax3646h"))))
+                "0vibrp5chf3q0n7byg6bdv3bl6z4354dqavhywjv0xbpf5rk5yfa"))))
     (build-system gnu-build-system)
-    (arguments
-     (list
-      #:configure-flags
-      #~(list "CXXFLAGS=-g -O2 -Wno-error=calloc-transposed-args"
-              "CFLAGS=-g -O2 -Wno-error=calloc-transposed-args")
-      #:phases #~(modify-phases %standard-phases
-                   (add-after 'unpack 'patch-source
-                     (lambda _
-                         (substitute* "language-server/jsonrpc.h"
-                           (("#include <unistd.h>")
-                            "#include <unistd.h>\n#include<stdint.h>")))))))
-    (native-inputs (list cpio python))
+    (native-inputs (list boost cpio python python-setuptools))
     (inputs (list elfutils))
 
     (home-page "https://sourceware.org/systemtap/")

gnu/packages/irc.scm

@@ -47,7 +47,6 @@
   #:use-module (guix build-system guile)
   #:use-module (guix build-system haskell)
   #:use-module (guix build-system meson)
-  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system qt)
   #:use-module (gnu packages)

gnu/packages/iso-codes.scm

@@ -231,8 +231,6 @@ concerned with representation of names for languages and language groups.")
           (add-after 'unpack 'fix-pytest-config
             (lambda _  ; Removes the need for python-pytest-cov.
               (substitute* "pyproject.toml"
-                (("--cov --cov-report=html --cov-report=term-missing")
-                 "")
                 (("^required_plugins =.*")
                  "")))))))
     (native-inputs (list python-poetry-core python-pytest))

gnu/packages/java-compression.scm

@@ -55,13 +55,12 @@
        (modify-phases %standard-phases
          (add-after 'unpack 'make-git-checkout-writable
            (lambda _
-             (for-each make-file-writable (find-files "."))
-             #t))
+             (for-each make-file-writable (find-files "."))))
          (add-before 'build 'remove-binaries
            (lambda _
              (delete-file "lib/org/xerial/snappy/OSInfo.class")
-             (delete-file-recursively "src/main/resources/org/xerial/snappy/native")
-             #t))
+             (delete-file-recursively
+              "src/main/resources/org/xerial/snappy/native")))
          (add-before 'build 'build-jni
            (lambda _
              ;; Rebuild one of the binaries we removed earlier
@@ -98,36 +97,33 @@
          (add-after 'build-jni 'copy-jni
            (lambda _
              (copy-recursively "src/main/resources/org/xerial/snappy/native"
-                               "build/classes/org/xerial/snappy/native")
-             #t))
+                               "build/classes/org/xerial/snappy/native")))
          (add-before 'build 'set-test-memory-size
            (lambda _
              (substitute* "build.xml"
-               (("<junit printsummary=") "<junit maxmemory=\"2G\" printsummary="))
-             #t))
+               (("<junit printsummary=")
+                "<junit maxmemory=\"2G\" printsummary="))))
          (add-before 'check 'fix-failing
            (lambda _
              (with-directory-excursion "src/test/java/org/xerial/snappy"
-               ;; This package assumes maven build, which puts results in "target".
-               ;; We put them in "build" instead, so fix that.
+               ;; This package assumes maven build, which puts results in
+               ;; "target". We put them in "build" instead, so fix that.
                (substitute* "SnappyLoaderTest.java"
                  (("target/classes") "build/classes"))
                ;; This requires Hadoop, which is not in Guix yet.
-               (delete-file "SnappyHadoopCompatibleOutputStreamTest.java"))
-             #t)))))
+               (delete-file "SnappyHadoopCompatibleOutputStreamTest.java")))))))
     (inputs
-     `(("osgi-framework" ,java-osgi-framework)))
+     (list java-osgi-framework))
     (propagated-inputs
-     `(("bitshuffle" ,bitshuffle-for-snappy)
-       ("snappy" ,snappy)))
+     (list bitshuffle-for-snappy snappy))
     (native-inputs
-     `(("junit" ,java-junit)
-       ("hamcrest" ,java-hamcrest-core)
-       ("xerial-core" ,java-xerial-core)
-       ("classworlds" ,java-plexus-classworlds)
-       ("commons-lang" ,java-commons-lang)
-       ("commons-io" ,java-commons-io)
-       ("perl" ,perl)))
+     (list java-junit
+           java-hamcrest-core
+           java-xerial-core
+           java-plexus-classworlds
+           java-commons-lang
+           java-commons-io
+           perl))
     (home-page "https://github.com/xerial/snappy-java")
     (synopsis "Compression/decompression algorithm in Java")
     (description "Snappy-java is a Java port of snappy, a fast C++
@@ -156,13 +152,13 @@ compressor/decompressor.")
          (add-before 'build 'remove-binaries
            (lambda _
              (delete-file "lib/org/xerial/snappy/OSInfo.class")
-             (delete-file-recursively "src/main/resources/org/xerial/snappy/native")
-             #t))
+             (delete-file-recursively
+              "src/main/resources/org/xerial/snappy/native")))
          (add-before 'build 'build-jni
            (lambda _
              ;; Rebuild one of the binaries we removed earlier
              (invoke "javac" "src/main/java/org/xerial/snappy/OSInfo.java"
-                      "-d" "lib")
+                     "-d" "lib")
              ;; Link to the dynamic snappy, not the static ones
              (substitute* "Makefile.common"
                (("-shared") "-shared -lsnappy"))
@@ -184,16 +180,14 @@ compressor/decompressor.")
          (add-after 'build-jni 'copy-jni
            (lambda _
              (copy-recursively "src/main/resources/org/xerial/snappy/native"
-                               "build/classes/org/xerial/snappy/native")
-             #t))
+                               "build/classes/org/xerial/snappy/native")))
          (add-before 'check 'fix-tests
            (lambda _
              (mkdir-p "src/test/resources/org/xerial/snappy/")
              (copy-recursively "src/test/java/org/xerial/snappy/testdata"
                                "src/test/resources/org/xerial/snappy/testdata")
              (install-file "src/test/java/org/xerial/snappy/alice29.txt"
-                           "src/test/resources/org/xerial/snappy/")
-             #t)))))))
+                           "src/test/resources/org/xerial/snappy/"))))))))
 
 (define-public java-iq80-snappy
   (package