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>
gnu: babeltrace: Fix python@3.12 build.
2026-04-28 06:34:05 +00:00 · 2026-04-27 14:56:43 +02:00 · 2026-04-27 14:56:42 +02:00 · 2026-04-27 14:56:42 +02:00 · 2026-04-27 14:56:42 +02:00 · 2026-04-27 14:56:42 +02:00
222 changed files with 11459 additions and 7165 deletions
--- a/.guix-authorizations
+++ b/.guix-authorizations
@@ -16,6 +16,8 @@
  ( ;; primary: "D0C2 EAC1 3310 822D 98DE  B57C E9C5 A2D9 0898 A02F"
   "01FD 85F4 1A7B 7F82 0583  06A5 935E BE07 36DC 857E"
   (name "avp"))
+  ("5D54 CF25 57B2 38E8 8DC1  80A2 2D22 3241 0AB7 4043"
+   (name "baleine"))
  ( ;; primary: "34FF 38BC D151 25A6 E340  A0B5 3453 2F9F AFCA 8B8E"
   "A3A4 B419 0074 087C A7DE  5698 BC45 CA67 E2F8 D007"
   (name "bavier"))
--- a/1
+++ b/1
@@ -336,6 +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
--- a/Makefile.am
+++ b/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	\
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -2658,12 +2658,13 @@ bootloaders.

 Once you are done partitioning the target hard disk drive, you have to
 create a file system on the relevant partition(s)@footnote{Currently
-Guix System supports only ext4, btrfs, bcachefs, JFS, F2FS, and XFS
-file systems.  In particular, code that reads file system UUIDs and
-labels works only for these file system types.  For bcachefs, also add
-the @code{bcachefs-linux-module} to your @code{operating-system}'s
-@code{initrd-modules}.}.  For the ESP, if you have one and assuming it is
-@file{/dev/sda1}, run:
+Guix System can mount only ext4, btrfs, JFS, F2FS, and XFS file systems
+at boot time.  In particular, code that reads file system UUIDs and
+labels works only for these file system types.  The code for bcachefs is
+in place, but support for loading out-of-tree kernel modules in the
+initrd is not.}.
+
+For the ESP, if you have one and assuming it is @file{/dev/sda1}, run:

@example
 mkfs.fat -F32 /dev/sda1
@@ -19215,7 +19216,7 @@ Partitioning}, for an example.

 When using GRUB as the bootloader, the LUKS password is only requested
 once: GRUB passes the master key to the initial RAM disk automatically.
-@xref{Bootloader Configuration, Automatic LUKS Master Key Passing}, for
+@xref{grub-luks-root-device-key, Automatic LUKS Master Key Passing}, for
 details.

@end defvar
@@ -48959,8 +48960,28 @@ This option in enabled by default.  In some cases involving the
 in RAM, it can be handy to disable the option by setting it to
@code{#f}.

-@subsubheading Automatic LUKS Master Key Passing
+@item @code{extra-initrd} (default: @code{#f})
+File name of an additional initrd to load during the boot.  It may or
+may not point to a file in the store, but the main use case is for
+out-of-store files containing secrets.

+For any use case not involving secrets, you should use regular initrd
+(@pxref{operating-system Reference, @code{initrd}}) instead.
+
+Be careful when using this option, since pointing to a file that is not
+readable by the grub while booting will cause the boot to fail and
+require a manual edit of the initrd line in the grub menu.
+
+Currently only supported by GRUB.
+@end table
+
+@end deftp
+
+@anchor{grub-luks-root-device-key}
+@unnumberedsubsec Automatic LUKS Master Key Passing
+
+@cindex LUKS, root file system encryption
+@cindex passphrase, for LUKS-encrypted root
 When booting from a LUKS-encrypted device using GRUB, the password is
 normally requested twice: once by GRUB to access @file{/boot}, and a
 second time by the initial RAM disk to mount the root file system.
@@ -49001,22 +49022,7 @@ No configuration is required: GRUB's @code{procfs} and @code{luks}
 modules are loaded automatically when encrypted devices are declared
 via @code{luks-device-mapping} (@pxref{Mapped Devices}).

-@item @code{extra-initrd} (default: @code{#f})
-File name of an additional initrd to load during the boot.  It may or
-may not point to a file in the store, but the main use case is for
-out-of-store files containing secrets.
-
-For any use case not involving secrets, you should use regular initrd
-(@pxref{operating-system Reference, @code{initrd}}) instead.
-
-Be careful when using this option, since pointing to a file that is not
-readable by the grub while booting will cause the boot to fail and
-require a manual edit of the initrd line in the grub menu.
-
-Currently only supported by GRUB.
-@end table
-
-@end deftp
+@unnumberedsubsec Additional Boot Entries

@cindex dual boot
@cindex boot menu
@@ -49145,9 +49151,13 @@ example of chainloading a different GNU/Linux system.
@end table
@end deftp

+@unnumberedsubsec Themes
+
@cindex HDPI
@cindex HiDPI
@cindex resolution
+@cindex themes, for GRUB
+@cindex bootloader themes
@c FIXME: Write documentation once it's stable.
 For now only GRUB has theme support.  GRUB themes are created using
 the @code{grub-theme} form, which is not fully documented yet.
@@ -49167,7 +49177,7 @@ Return the default GRUB theme used by the operating system if no
@code{theme} field is specified in @code{bootloader-configuration}
 record.

-It comes with a fancy background image displaying the GNU and Guix
+It comes with a fancy background image displaying the Guix
 logos.
@end deffn

--- a/etc/teams.scm
+++ b/etc/teams.scm
@@ -975,7 +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"
--- a/gnu/build/linux-container.scm
+++ b/gnu/build/linux-container.scm
@@ -445,10 +445,14 @@ load path must be adjusted as needed."
          ;; Behave like an init process: create a sub-process that calls
          ;; THUNK, and wait for child processes.  Furthermore, forward
          ;; RELAYED-SIGNALS to the child process.
-          (match (primitive-fork)
-            (0
+          ;; We presently use `safe-clone` here due to a bug in the interaction
+          ;; between Guix and `primitive-fork` in Guile 3.0.11:
+          ;; https://codeberg.org/guix/guix/issues/7690#issuecomment-12744123
+          (safe-clone
+            SIGCHLD
+            (lambda ()
             (call-with-clean-exit thunk))
-            (pid
+            (lambda (pid)
             (install-signal-handlers pid)
             (let loop ()
               (match (wait-child-process)
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1130,7 +1130,6 @@ 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-0.11.1-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    \
@@ -1187,6 +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				\
@@ -1586,7 +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 \
@@ -1699,7 +1701,6 @@ dist_patch_DATA =						\
  %D%/packages/patches/libcss-check-format.patch		\
  %D%/packages/patches/libeb-gcc-14.patch			\
  %D%/packages/patches/libextractor-tidy-support.patch		\
-  %D%/packages/patches/libfossil-skip-amalgamation.patch	\
  %D%/packages/patches/libftdi-fix-paths-when-FTDIPP-set.patch	\
  %D%/packages/patches/libgeotiff-fix-tests-with-proj-9.1.1.patch	\
  %D%/packages/patches/libgeotiff-fix-tests-with-proj-9.3.0.patch	\
@@ -1714,6 +1715,7 @@ dist_patch_DATA =						\
  %D%/packages/patches/libretro-dolphin-emu-libusb-assert.patch \
  %D%/packages/patches/libretro-dolphin-emu-vulkan-headers.patch        \
  %D%/packages/patches/libretranslate-use-flasgger.patch	\
+  %D%/packages/patches/librewolf-150.0-encoding_rs-rust-fix.patch       \
  %D%/packages/patches/librewolf-add-store-to-rdd-allowlist.patch       \
  %D%/packages/patches/librewolf-compare-paths.patch		\
  %D%/packages/patches/librewolf-neuter-locale-download.patch	\
@@ -2121,6 +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	\
@@ -2400,6 +2403,8 @@ dist_patch_DATA =						\
  %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-codex-0.124.0-code-mode-stub-toolname.patch	\
+  %D%/packages/patches/rust-codex-0.124.0-remove-patch-sections.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	\
@@ -2505,7 +2510,6 @@ 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		\
--- a/gnu/packages/acl.scm
+++ b/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
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012-2025 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2012-2026 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013 Cyril Roelandt <tipecaml@gmail.com>
 ;;; Copyright © 2014, 2015, 2016, 2018, 2019, 2020 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2014, 2015-2018, 2020-2023 Eric Bavier <bavier@posteo.net>
@@ -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)
@@ -3751,59 +3750,68 @@ summarizes network bandwidth by process and remote host.")
 (define-public munge
  (package
    (name "munge")
-    (version "0.5.14")
+    (version "0.5.18")
    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/dun/munge/releases/"
-                                  "download/munge-" version "/munge-"
-                                  version ".tar.xz"))
+              (method git-fetch)
+              (uri (git-reference
+                     (url "https://github.com/dun/munge")
+                     (commit (string-append "munge-" version))))
+              (file-name (git-file-name name version))
              (sha256
               (base32
-                "0h06sghb4rqvv1ywyd6mzsmbcgh712v6ygrff0gzm440y4ca41k6"))
+                "1b7gm680dlvmgvj9vxy7n0cqmnv1rl9n4563vasxdxx54f78j30s"))
              (modules '((guix build utils)))
              (snippet
-               '(begin
-                  ;; Don't insist on write access to /var.
-                  (substitute* "src/etc/Makefile.in"
-                    (("\\$\\(INSTALL\\)(.*)localstatedir" _ middle)
-                     (string-append "-$(INSTALL)" middle "localstatedir"))
-                    (("\\$\\(MKDIR_P\\) .*(local|run)statedir.*")
-                     ""))
-                  #t))))
+               ;; Don't insist on write access to /var.
+               #~(substitute* "src/etc/Makefile.am"
+                   (("\\$\\(MKDIR_P\\) .*(local|run)statedir.*" all)
+                    (string-append ": " all))))))
    (inputs
     (list openssl libgcrypt))
+    (native-inputs
+     (list autoconf
+           automake
+           libtool
+           procps))                               ;for tests
    (build-system gnu-build-system)
    (arguments
-     `(#:configure-flags
-       (list "--localstatedir=/var"
-             (string-append "--with-pkgconfigdir="
-                            (assoc-ref %outputs "out") "/lib/pkgconfig")
-             (string-append "--with-libgcrypt-prefix="
-                            (assoc-ref %build-inputs "libgcrypt"))
-             ,@(if (%current-target-system)
-                 ;; Assume yes on pipes when cross compiling.
-                 `("ac_cv_file__dev_spx=yes"
-                   "x_ac_cv_check_fifo_recvfd=yes")
-                 '()))
-       #:phases
-       (modify-phases %standard-phases
-         ;; XXX Many test series fail.  Some might be fixable, others do no-no
-         ;; things like invoking ‘sudo’.
-         (add-after 'unpack 'skip-failing-tests
-           (lambda _
-             (for-each (lambda (test)
-                         (substitute* "t/Makefile.in"
-                           (((string-append test "\\.t ")) "")))
-                       (list "0100-munged-lock"
-                             "0010-basic"
-                             "0011-munged-cmdline"
-                             "0012-munge-cmdline"
-                             "0013-unmunge-cmdline"
-                             "0101-munged-security-socket"
-                             "0102-munged-security-keyfile"
-                             "0103-munged-security-logfile"
-                             "0110-munged-origin-addr"))
-             #t)))))
+     (list #:configure-flags
+           #~(list "--localstatedir=/var"
+                   "--disable-static"
+                   #$@(if (%current-target-system)
+                          ;; Assume yes on pipes when cross compiling.
+                          `("ac_cv_file__dev_spx=yes"
+                            "x_ac_cv_check_fifo_recvfd=yes")
+                          '())
+
+                   ;; The '.pc' file is not installed when omitting this flag.
+                   (string-append "--with-pkgconfigdir="
+                                  #$output "/lib/pkgconfig"))
+           #:phases
+           #~(modify-phases %standard-phases
+               (add-before 'bootstrap 'pre-bootstrap
+                 (lambda _
+                   (for-each patch-shebang (find-files "build-aux"))))
+               (add-after 'unpack 'skip-failing-tests
+                 (lambda _
+                   ;; Pass '--force' to 'munged'; without it, it fails with "Socket
+                   ;; is inaccessible" due to the build directory not being
+                   ;; world-readable.
+                   (substitute* "tests/sharness.d/03-munged.sh"
+                     (("--group-update-time=-1" all)
+                      (string-append all " --force")))
+
+                   ;; The tests below invoke 'sudo' or have special expectations
+                   ;; about network interfaces.
+                   (for-each (lambda (test)
+                               (substitute* "tests/Makefile.am"
+                                 (((string-append test "\\.t "))
+                                  "")))
+                             (list "0100-munged-lock"
+                                   "0101-munged-security-socket"
+                                   "0102-munged-security-keyfile"
+                                   "0103-munged-security-logfile"
+                                   "0110-munged-origin-addr")))))))
    (home-page "https://dun.github.io/munge/")
    (synopsis "Cluster computing authentication service")
    (description
@@ -3918,6 +3926,18 @@ 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)
@@ -4047,51 +4067,59 @@ 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
--- a/gnu/packages/algebra.scm
+++ b/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)
--- a/gnu/packages/android.scm
+++ b/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)
--- a/gnu/packages/apparmor.scm
+++ b/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
--- a/gnu/packages/astronomy.scm
+++ b/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))
--- a/gnu/packages/audio.scm
+++ b/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 "'" #$(this-package-input "libsndfile")
                                "/lib/libsndfile"))))))))
    (native-inputs
-     (list python-pytest
-           python-pytest-cov
-           python-setuptools))
+     (list python-pytest python-setuptools))
    (inputs
     (list libsndfile
           portaudio))
@@ -7827,60 +7821,59 @@ Rate} 3600x2250 bit/s vocoder used in various radio systems.")
                  (delete-file-recursively "third_party")
                  (delete-file-recursively "modules")))))
    (build-system cmake-build-system)
+    (arguments
+     (list
+      #:configure-flags
+      #~(list "-DLINK_BUILD_QT_EXAMPLES=ON"
+              "-DLINK_BUILD_JACK=ON")
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'check
+            (lambda* (#:key inputs tests? #:allow-other-keys)
+              (when tests?
+                (let* ((python (search-input-file inputs "/bin/python3"))
+                       (run-tests "../source/ci/run-tests.py"))
+                  (invoke python run-tests "--target" "LinkCoreTest")
+                  (invoke python run-tests "--target" "LinkDiscoveryTest")))))
+          (add-before 'install 'patch-cmake
+            (lambda* (#:key inputs #:allow-other-keys)
+              (let* ((source "../source/"))
+                (substitute* (string-append source
+                                            "cmake_include/AsioStandaloneConfig.cmake")
+                  (((string-append "\\$\\{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
@@ -8066,7 +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
@@ -8096,8 +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.
@@ -8122,7 +8114,6 @@ Home Page}.")
     (list python-matplotlib
           python-packaging
           python-pytest
-           python-pytest-cov
           python-resampy
           python-setuptools
           python-wheel))
--- a/gnu/packages/aux-files/python/pytest_guix.py
+++ b/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="?")
--- a/gnu/packages/backup.scm
+++ b/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
--- a/gnu/packages/benchmark.scm
+++ b/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)
--- a/gnu/packages/bioinformatics.scm
+++ b/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))
--- a/gnu/packages/bittorrent.scm
+++ b/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
--- a/gnu/packages/boost.scm
+++ b/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)
--- a/gnu/packages/build-tools.scm
+++ b/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)
@@ -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)
--- a/gnu/packages/c.scm
+++ b/gnu/packages/c.scm
@@ -23,7 +23,7 @@
 ;;; Copyright © 2023, 2024 David Elsing <david.elsing@posteo.net>
 ;;; Copyright @ 2022, Kitzman <kitzman@disroot.org>
 ;;; Copyright @ 2025 Dariqq <dariqq@posteo.net>
-;;; Copyright © 2025 Ashish SHUKLA <ashish.is@lostca.se>
+;;; Copyright © 2025, 2026 Ashish SHUKLA <ashish.is@lostca.se>
 ;;; Copyright © 2026 Cayetano Santos <csantosb@inventati.org>
 ;;; Copyright © 2026 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;;
@@ -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)
@@ -1762,7 +1761,7 @@ string.h, but with a utf8* prefix instead of the str* prefix.")
 (define-public simdutf
  (package
    (name "simdutf")
-    (version "7.7.1")
+    (version "9.0.0")
    (source
     (origin
       (method git-fetch)
@@ -1771,7 +1770,7 @@ string.h, but with a utf8* prefix instead of the str* prefix.")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "0kw4j4qqcfjaii667xa745pklj50m70nqq8cj5agj714acczbk7y"))))
+        (base32 "0f5ccvqj7pfa69m9y1kxp2v1lybx6x8i9pykdqfkr7dydqbhrhx6"))))
    (build-system cmake-build-system)
    (arguments (list #:configure-flags #~(list "-DBUILD_SHARED_LIBS=ON")))
    (synopsis "SIMD Unicode validation and transcoding")
--- a/gnu/packages/calendar.scm
+++ b/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)
--- a/gnu/packages/check.scm
+++ b/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
--- a/gnu/packages/chemistry.scm
+++ b/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)
@@ -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.
--- a/gnu/packages/cinnamon.scm
+++ b/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)
--- a/gnu/packages/cmake.scm
+++ b/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)
--- a/gnu/packages/code.scm
+++ b/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)
--- a/gnu/packages/codex.scm
+++ b/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-0.120.0, transitively loads (gnu packages
+;;; defines rust-codex-0.124.0, 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-0.120.0 is defined, causing an unbound
+;;; rust-apps before rust-codex-0.124.0 is defined, causing an unbound
 ;;; variable error.

 (define-module (gnu packages codex)
@@ -54,14 +54,14 @@
 (define-public codex
  (package
    (name "codex")
-    (version (package-version rust-codex-0.120.0))
+    (version (package-version rust-codex-0.124.0))
    (source
     (origin
-       (inherit (package-source rust-codex-0.120.0))
+       (inherit (package-source rust-codex-0.124.0))
       (patches (search-patches
                 "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-0.124.0-code-mode-stub-toolname.patch"
+                 "rust-codex-0.124.0-remove-patch-sections.patch"
                 "rust-codex-0.120.0-remove-libwebrtc.patch"
                 "rust-codex-0.98.0-test-shebangs.patch"
                 "rust-codex-0.120.0-test-timeout.patch"))))
@@ -69,7 +69,12 @@
    (arguments
     (list
      #:install-source? #f
-      #:cargo-install-paths '(list "cli" "exec" "exec-server"
+      ;; exec-server is library-only in 0.124 (no [[bin]] in
+      ;; exec-server/Cargo.toml); cargo install --path exec-server fails
+      ;; with "no packages found with binaries or examples".  Drop it
+      ;; from the install paths -- the library is consumed via the
+      ;; workspace by other binaries here, not installed standalone.
+      #:cargo-install-paths '(list "cli" "exec"
                                   "linux-sandbox" "mcp-server"
                                   "app-server" "tui")
      ;; schema_fixtures_match_generated (upstream fixture is stale:
@@ -317,7 +322,164 @@
                                ;; (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")
+                                "--skip" "mcp_server_status_list_tools_and_auth_only_skips_slow_inventory_calls"
+                                ;;; BEGIN Stack overflow in 'current_thread'
+                                ;;; tokio runtime.  The sibling tests in
+                                ;;; tracing_tests.rs use the local helper
+                                ;;; run_current_thread_test_with_stack
+                                ;;; (4 MiB) but this one uses bare
+                                ;;; #[tokio::test] on the 2 MiB default
+                                ;;; test-thread stack, and TurnStart's
+                                ;;; future graph exceeds it.  With
+                                ;;; RUST_MIN_STACK raised the overflow is
+                                ;;; gone but the test then deterministically
+                                ;;; times out waiting for a span tagged
+                                ;;; codex.op = "user_input" on the remote
+                                ;;; trace that upstream never emits on that
+                                ;;; trace in our environment.
+                                "--skip" "turn_start_jsonrpc_span_parents_core_turn_spans"
+                                ;;; END tracing test stack/timeout
+                                ;;; BEGIN The upstream loader resolves the
+                                ;;; MCP OAuth credentials store mode by
+                                ;;; calling
+                                ;;; resolve_mcp_oauth_credentials_store_mode
+                                ;;; with env!("CARGO_PKG_VERSION") -- which
+                                ;;; in the released 0.124.0 tarball is
+                                ;;; "0.124.0".  These fixture tests
+                                ;;; construct the expected Config by
+                                ;;; passing the LOCAL_DEV_BUILD_VERSION
+                                ;;; constant ("0.0.0") to the same
+                                ;;; resolver, and the resolver only returns
+                                ;;; File for "0.0.0" -- Auto otherwise.
+                                ;;; Upstream CI builds from a checkout
+                                ;;; still carrying version = "0.0.0" so the
+                                ;;; tests pass there; they cannot pass
+                                ;;; against a released tag.
+                                "--skip" "test_precedence_fixture_with_gpt3_profile"
+                                "--skip" "test_precedence_fixture_with_gpt5_profile"
+                                "--skip" "test_precedence_fixture_with_o3_profile"
+                                "--skip" "test_precedence_fixture_with_zdr_profile"
+                                ;;; END LOCAL_DEV_BUILD_VERSION fixture mismatch
+                                ;;; BEGIN Verifies that Codex's user-shell
+                                ;;; spawn produces a child where
+                                ;;; CODEX_SANDBOX_NETWORK_DISABLED is unset
+                                ;;; (asserts stdout == "not-set").  We
+                                ;;; deliberately set that env var at the
+                                ;;; check phase to trigger upstream's
+                                ;;; skip_if_no_network! guards; the var then
+                                ;;; leaks into the spawned shell and the
+                                ;;; assertion fails.  The guix skip is a
+                                ;;; direct cost of the network-gate fix --
+                                ;;; trading one broken test for two that
+                                ;;; now skip cleanly.
+                                "--skip" "user_shell_command_does_not_set_network_sandbox_env_var"
+                                ;;; END CODEX_SANDBOX_NETWORK_DISABLED leak
+                                ;;; BEGIN The exec-server/tests/file_system
+                                ;;; integration tests invoke the real
+                                ;;; system bwrap, which tries to execvp the
+                                ;;; test binary at the cargo target path
+                                ;;; under the build dir.  Same root cause
+                                ;;; as the existing
+                                ;;; sandbox_reenables_writable_subpaths_under_unreadable_parents
+                                ;;; skip: guix builds live under /tmp but
+                                ;;; bwrap's mount namespace excludes /tmp,
+                                ;;; making the binary invisible inside the
+                                ;;; namespace.
+                                "--skip" "file_system_copy_preserves_symlink_source"
+                                "--skip" "file_system_copy_rejects_symlink_escape_destination"
+                                "--skip" "file_system_copy_rejects_symlink_escape_source"
+                                "--skip" "file_system_create_directory_rejects_symlink_escape"
+                                "--skip" "file_system_read_directory_rejects_symlink_escape"
+                                "--skip" "file_system_remove_rejects_symlink_escape"
+                                "--skip" "file_system_remove_removes_symlink_not_target"
+                                "--skip" "file_system_sandboxed_read_allows_readable_root"
+                                "--skip" "file_system_sandboxed_read_rejects_symlink_escape"
+                                "--skip" "file_system_sandboxed_read_rejects_symlink_parent_dotdot_escape"
+                                "--skip" "file_system_sandboxed_write_allows_additional_write_root"
+                                "--skip" "file_system_sandboxed_write_rejects_symlink_escape"
+                                "--skip" "file_system_sandboxed_write_rejects_unwritable_path"
+                                ;;; END bwrap-cant-see-/tmp file_system tests
+                                ;;; BEGIN Landlock is unavailable on Guix,
+                                ;;; so the sandbox cannot deny network
+                                ;;; syscalls.  These tests expect
+                                ;;; SandboxErr::Denied for the nc, ping,
+                                ;;; ssh, getent, and dev_tcp_redirection
+                                ;;; commands but those commands instead
+                                ;;; block on connect() until the test's 2s
+                                ;;; timeout fires (Timeout, exit 124).
+                                ;;; Same root cause as the Landlock skips
+                                ;;; at the top of this list; new test names
+                                ;;; in 0.124.
+                                "--skip" "sandbox_blocks_nc"
+                                "--skip" "sandbox_blocks_ping"
+                                "--skip" "sandbox_blocks_dev_tcp_redirection"
+                                "--skip" "sandbox_blocks_getent"
+                                "--skip" "sandbox_blocks_ssh"
+                                ;;; END Landlock network block
+                                ;;; BEGIN Requires github.com network access.
+                                ;;; With no "extraKnownMarketplaces" entry
+                                ;;; in settings.json,
+                                ;;; collect_marketplace_import_sources
+                                ;;; inserts a fallback entry for the
+                                ;;; "claude-plugins-official" marketplace
+                                ;;; pointing at the github shorthand
+                                ;;; "anthropics/claude-plugins-official".
+                                ;;; add_marketplace -> parse_marketplace_source
+                                ;;; expands that to a github.com/.git URL
+                                ;;; and clone_git_source runs 'git clone'.
+                                ;;; The Guix build sandbox has no network,
+                                ;;; so the clone fails and the marketplace
+                                ;;; lands in failed_marketplaces.  No mock
+                                ;;; cloner is injected via
+                                ;;; ExternalAgentConfigService::new_for_test,
+                                ;;; so there is no in-tree way to satisfy
+                                ;;; the test offline.
+                                "--skip" "import_plugins_infers_claude_official_marketplace_when_missing_from_settings"
+                                ;;; END github.com network access
+                                ;;; BEGIN Async race between the rollout
+                                ;;; writer task and a direct SQLite read.
+                                ;;; The test calls
+                                ;;; update_memory_settings_with_app_server,
+                                ;;; which routes through the in-memory
+                                ;;; thread path on the app-server's
+                                ;;; ThreadMemoryModeSet handler ->
+                                ;;; Session::set_thread_memory_mode ->
+                                ;;; persist_thread_memory_mode_update,
+                                ;;; which writes a RolloutItem::SessionMeta
+                                ;;; with the new mode to the rollout file
+                                ;;; via recorder.record_items + flush.  The
+                                ;;; rollout writer task then asynchronously
+                                ;;; calls sync_thread_state_after_write,
+                                ;;; which calls state_db::apply_rollout_items
+                                ;;; to mirror the SessionMeta into SQLite.
+                                ;;; flush() only awaits the rollout-file
+                                ;;; write, not the subsequent SQLite sync.
+                                ;;; The test opens a fresh StateRuntime and
+                                ;;; reads get_thread_memory_mode
+                                ;;; immediately, so it observes the creation
+                                ;;; default of "enabled" written by
+                                ;;; upsert_thread_with_creation_memory_mode
+                                ;;; instead of the new "disabled".  Upstream
+                                ;;; CI wins this race; we lose.
+                                "--skip" "update_memory_settings_updates_current_thread_memory_mode"
+                                ;;; END memory-mode rollout/sqlite race
+                                ;;; BEGIN The Stopwatch::new constructor in
+                                ;;; codex_shell_escalation anchors
+                                ;;; T0 = Instant::now() at construction;
+                                ;;; the spawned cancellation task fires at
+                                ;;; T0 + limit.  The test captures
+                                ;;; start = Instant::now() at T1 > T0 (after
+                                ;;; cancellation_token() returns) and
+                                ;;; asserts start.elapsed() >= limit,
+                                ;;; i.e. (T0 + limit) - T1 >= limit, which
+                                ;;; is always false by the offset T1 - T0.
+                                ;;; The test only passes when scheduler
+                                ;;; jitter on the sleep wakeup happens to
+                                ;;; exceed that offset.  Upstream wins the
+                                ;;; race; we don't always.
+                                "--skip" "cancellation_receiver_fires_after_limit"
+                                ;;; END Stopwatch construction/start offset race
+                                )
      #:cargo-package-crates
      ''(;;; Tier 0: No internal deps.
         "codex-ansi-escape"
@@ -358,22 +520,31 @@
         "codex-debug-client"
         "codex-analytics"
         "codex-rollout"
+         "codex-rollout-trace"
         "codex-terminal-detection"
         "codex-utils-approval-presets"
         "codex-utils-cli"
+         "codex-uds"
+         "codex-install-context"
+         "codex-device-key"
         ;;; Tier 2.
         "codex-app-server-protocol"
         "codex-rmcp-client"
         "codex-otel"
+         "codex-thread-store"
         "codex-state"
         "codex-features"
+         "codex-model-provider"
         "codex-config"
+         "codex-agent-identity"
+         "codex-aws-auth"
         "codex-hooks"
-         "codex-instructions"
         "codex-code-mode"
         "codex-feedback"
         "codex-skills"
+         "codex-test-binary-support"
         "codex-core"
+         "codex-core-plugins"
         "codex-utils-sandbox-summary"
         "codex-linux-sandbox"
         "codex-sandboxing"
@@ -425,7 +596,7 @@
              ;; Update them to match the actual package version.
              (let ((snap-files (find-files "." "\\.snap$")))
                (substitute* snap-files
-                  (("\\(v0\\.0\\.0\\)   ") "(v0.120.0) ")))))
+                  (("\\(v0\\.0\\.0\\)   ") "(v0.124.0) ")))))
          (add-after 'chdir-to-workspace 'patch-git-deps-to-vendor
            (lambda _
              ;; Replace git dependencies with version references so cargo
@@ -436,32 +607,55 @@
                (("runfiles = \\{ git = [^}]+\\}")
                 "runfiles = \"0.1.0\""))
              ;; Remove workspace members that have unbuildable deps
-              ;; (libwebrtc requires git fetch, v8-poc requires V8).
+              ;; (v8-poc requires V8).  code-mode stays a workspace member
+              ;; so its codex-protocol resolves to the same local copy as
+              ;; the rest of the build; disabling its default features
+              ;; (below) avoids pulling in 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.
+                (("\"v8-poc\",") ""))
+              ;; Disable V8 runtime in codex-code-mode by turning off
+              ;; default features.  Keep path= so code-mode is resolved
+              ;; from the local source tree and shares codex-protocol
+              ;; (and other workspace crates) with the rest of the build;
+              ;; resolving it from the vendor instead introduces a
+              ;; duplicate codex-protocol and causes E0308 type
+              ;; mismatches in codex-tools.
              (substitute* "Cargo.toml"
                (("codex-code-mode = \\{ path = \"code-mode\" \\}")
-                 "codex-code-mode = { version = \"0.120.0\", default-features = false }"))))
+                 "codex-code-mode = { path = \"code-mode\", default-features = false }"))
+              ;; cargo build at workspace root ignores per-dep
+              ;; default-features=false and builds code-mode with its
+              ;; own default features, which include v8-runtime and
+              ;; would pull in V8.  Make the default feature empty.
+              (substitute* "code-mode/Cargo.toml"
+                (("^default = \\[\"v8-runtime\"\\]") "default = []"))))
          (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 = "0.120.0" to internal path dependencies.
+              ;; Add version = "0.124.0" 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 = \"0.120.0\", path = "))
+                   (string-append name " = { version = \"0.124.0\", path = "))
                  ;; Handle inline deps with package: name = { package = "...", path = "..." }
                  (("(codex-[a-z0-9-]+) = \\{ package = " all name)
-                   (string-append name " = { version = \"0.120.0\", package = "))
+                   (string-append name " = { version = \"0.124.0\", package = "))
                  ;; Handle section deps: [dependencies.X] with path = "..."
                  (("^(path = \"\\.\\./[^\"]*\")" all path-line)
-                   (string-append path-line "\nversion = \"0.120.0\""))))))
+                   (string-append path-line "\nversion = \"0.124.0\""))))))
+          (add-after 'chdir-to-workspace 'use-gnu-store-in-sandbox
+            (lambda _
+              ;; LINUX_PLATFORM_DEFAULT_READ_ROOTS in linux-sandbox/src/
+              ;; bwrap.rs is the read-only baseline that codex's bwrap
+              ;; sandbox bind-mounts so commands can read /usr/bin/ls,
+              ;; libc, etc.  Upstream lists "/nix/store" for NixOS;
+              ;; Guix's equivalent is "/gnu/store".  Without this swap,
+              ;; the codex sandbox cannot locate any binaries on a Guix
+              ;; system because every "system" path resolves into
+              ;; /gnu/store/<hash>-pkg/bin/...
+              (substitute* "linux-sandbox/src/bwrap.rs"
+                (("\"/nix/store\"") "\"/gnu/store\""))))
          (add-after 'chdir-to-workspace 'patch-hardcoded-paths
            (lambda* (#:key inputs #:allow-other-keys)
              (let ((bash-bin (string-append
@@ -561,10 +755,12 @@
                ;; double quotes.
                (substitute*
                  (list "core/src/plugins/startup_sync_tests.rs"
+                        "core/src/tools/runtimes/shell/unix_escalation_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"
+                        "exec-server/tests/file_system.rs"
                        "login/src/auth/auth_tests.rs"
                        "models-manager/src/manager_tests.rs"
                        "sandboxing/src/bwrap_tests.rs")
@@ -613,7 +809,17 @@
              ;; ~/... and 30 snapshot tests fail.
              (setenv "HOME" "/tmp/guix-home")
              (mkdir-p "/tmp/guix-home")
-              (setenv "USER" "nixbld"))))))
+              (setenv "USER" "nixbld")
+              ;; Default libtest thread stack is 2 MiB, which is not
+              ;; enough for tokio current_thread tests that drive
+              ;; codex-core's full turn pipeline.  Upstream gates such
+              ;; tests through run_current_thread_test_with_stack (4 MiB)
+              ;; in app-server/src/message_processor/tracing_tests.rs;
+              ;; raise the global default so future additions that
+              ;; forget the wrapper still pass.
+              (setenv "RUST_MIN_STACK" "8388608")
+              ;; Disable network access.
+              (setenv "CODEX_SANDBOX_NETWORK_DISABLED" "1"))))))
    (native-inputs `(("bubblewrap" ,bubblewrap) ;tests need bwrap on PATH
                     ("clang" ,clang)
                     ("cmake-minimal" ,cmake-minimal)
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -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
@@ -3608,7 +3606,7 @@ std::wstring, etc).")
 (define-public fast-float
  (package
    (name "fast-float")
-    (version "8.0.2")
+    (version "8.2.5")
    (source (origin
              (method git-fetch)
              (uri (git-reference
@@ -3617,7 +3615,7 @@ std::wstring, etc).")
              (file-name (git-file-name name version))
              (sha256
               (base32
-                "19x1yklf641yrpad6lk4cq3jmird10d5ig8hicm3p9lxh92k78cl"))))
+                "1l13nsl4sgq71m7aifrmmmfyl14vp48vqdh7pb50hxqq6f8bq2b5"))))
    (build-system cmake-build-system)
    (arguments
     (list
@@ -3628,12 +3626,10 @@ std::wstring, etc).")
          (add-after 'unpack 'patch-cmake-tests
            (lambda* (#:key inputs native-inputs #:allow-other-keys)
              (substitute* "tests/CMakeLists.txt"
-                (("FetchContent_GetProperties\\(supplemental_test_files.*")
-                 "")
-                (("if\\(NOT supplemental_test_files_POPULATED.*")
+                (("FetchContent_MakeAvailable\\(supplemental_test_files.*")
                 (string-append
                  "set(supplemental_test_files_BINARY_DIR "
-                  #$fast-float-test-files ")\nif(0)\n"))))))))
+                  #$fast-float-test-files ")\n"))))))))
    (native-inputs (list doctest fast-float-test-files))
    (home-page "https://github.com/fastfloat/fast_float")
    (synopsis "Floating point number parser for C++")
--- a/gnu/packages/crypto.scm
+++ b/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)
--- a/gnu/packages/cups.scm
+++ b/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)
--- a/gnu/packages/cybersecurity.scm
+++ b/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)
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -204,7 +204,6 @@
  #: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 ruby)
  #:use-module (guix build-system cmake)
@@ -1256,6 +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")
@@ -4715,33 +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
@@ -5718,7 +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"))
@@ -6315,7 +6396,7 @@ mechanism of @code{dogpile}.")
 (define-public datasette
  (package
    (name "datasette")
-    (version "1.0a19")
+    (version "1.0a26")
    (source
     (origin
       (method git-fetch)
@@ -6324,23 +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
@@ -6355,7 +6433,6 @@ mechanism of @code{dogpile}.")
           python-janus
           python-jinja2
           python-mergedeep
-           python-pint
           python-pluggy
           python-pyyaml
           python-sqlite-utils
@@ -6364,9 +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
--- a/gnu/packages/dav.scm
+++ b/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
--- a/gnu/packages/debug.scm
+++ b/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
--- a/gnu/packages/dictionaries.scm
+++ b/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)
--- a/gnu/packages/diffoscope.scm
+++ b/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
--- a/gnu/packages/digest.scm
+++ b/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)
--- a/gnu/packages/disk.scm
+++ b/gnu/packages/disk.scm
@@ -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)
--- a/gnu/packages/django.scm
+++ b/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)
@@ -201,13 +200,13 @@ your project into different processes.")
 (define-public python-django
  (package
    (name "python-django")
-    (version "5.2.11")
+    (version "5.2.13")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "django" version))
       (sha256
-        (base32 "1lq2dynfw6jmvzrzgfrlij2qnxcksaxgnrfr0pj3bvmrv0m2jbbz"))))
+        (base32 "1i1vlffzhwbzp6r6y8ycvwklc45diy4c6i897z379l48a7dqj5d3"))))
    (build-system pyproject-build-system)
    (arguments
     '(#:test-flags
@@ -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))
--- a/gnu/packages/djvu.scm
+++ b/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)
--- a/gnu/packages/docbook.scm
+++ b/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
--- a/gnu/packages/docker.scm
+++ b/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)
--- a/gnu/packages/documentation.scm
+++ b/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)
--- a/gnu/packages/dotnet.scm
+++ b/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
--- a/gnu/packages/duckdb.scm
+++ b/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)
--- a/gnu/packages/ebook.scm
+++ b/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)
--- a/gnu/packages/education.scm
+++ b/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))
--- a/gnu/packages/electronics.scm
+++ b/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
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -781,6 +781,54 @@ balance windows (keeping them roughly the same size) whenever the window
 configuration changes, e.g. after splitting or deleting a window.")
      (license license:bsd-3))))

+(define-public emacs-ben
+  (package
+    (name "emacs-ben")
+    (version "0.12.11")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://codeberg.org/pastor/ben.el")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0iqrk87dl567vwpwm8rmplrpva475a04s6c34rm24xfy2m7wrwk6"))))
+    (build-system emacs-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'set-environment
+            (lambda _
+              ;; Since the testsuite uses `direnv', the build needs a home
+              ;; directory so `direnv' can allow the contents of the `.envrc`
+              ;; files generated for the different tests.
+              (setenv "HOME" "/tmp")
+              (setenv "OFFLINE" "1") ;Enable offline tests.
+              (emacs-substitute-variables "ben.el"
+                ("ben-direnv-executable"
+                 #$(file-append (this-package-input "direnv")
+                                "/bin/direnv"))))))))
+    (inputs (list direnv))
+    (propagated-inputs (list emacs-inheritenv))
+    (home-page "https://codeberg.org/pastor/ben.el")
+    (synopsis "Asynchronous buffer-local environments via @command{direnv}")
+    (description
+     "This package allows you to load environments buffer locally.  The
+package is named @command{ben}, which stands for Buffer ENvironments.
+
+The project relies on @uref{https://direnv.net, direnv} which allows setting
+per-directory environments through @file{.envrc} files.
+
+The main improvement of @command{ben} over @command{envrc} is the asynchronous
+processing of environments, which prevents Emacs from freezing.  This is
+especially useful while loading computationally heavy environments, such when
+loading @file{.envrc} files that rely on Guix.  In these cases, computations
+can take hours to complete.  This package aims to facilitate loading such
+environments in the background.")
+    (license license:gpl3+)))
+
 (define-public emacs-bookmark-plus
  (package
    (name "emacs-bookmark-plus")
@@ -13903,7 +13951,7 @@ 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
@@ -28551,7 +28599,7 @@ unstructured, meant for quick @code{JavaScript} experiments.")
 (define-public emacs-firefox-release-notes
  (package
    (name "emacs-firefox-release-notes")
-    (version "1.7")
+    (version "1.8")
    (source
     (origin
       (method git-fetch)
@@ -28562,7 +28610,7 @@ unstructured, meant for quick @code{JavaScript} experiments.")
          (commit version)))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1i9ncnn0qys0v0bqw87jwx0sa2g31n1i1gfr9zqdml3hakyz8b5f"))))
+        (base32 "13ymnx4vgiq5f3cjk3zddrq4xnv6116j5zzza67v98q7rsvzl049"))))
    (build-system emacs-build-system)
    (arguments
     (list
@@ -39862,7 +39910,7 @@ user interfaces for various built-in modes.")
 (define-public emacs-calibredb
  (package
    (name "emacs-calibredb")
-    (version "2.13.0")
+    (version "2.14.0")
    (source
     (origin
       (method git-fetch)
@@ -39871,31 +39919,40 @@ user interfaces for various built-in modes.")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1a4gyc3gcq18j29pw2i296d70nvx5fbzlw9fdmqwzncciqz5as6m"))))
+        (base32 "1g0jg6a6fgvxd5bsydckbqwf899d2d9732laz4k1k476mbws5dqy"))))
    (build-system emacs-build-system)
    (arguments
     (list
+      #:include #~(cons "\\.py$" %default-include)
+      #:tests? #f                       ;no tests
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'patch-paths
            (lambda* (#:key inputs #:allow-other-keys)
-              (make-file-writable "calibredb-core.el")
              (let ((calibredb (search-input-file inputs "/bin/calibredb"))
                    (fetch-ebook-metadata
                     (search-input-file inputs "/bin/fetch-ebook-metadata"))
                    (ebook-convert
                     (search-input-file inputs "/bin/ebook-convert"))
                    (calibre-debug
-                     (search-input-file inputs "/bin/calibre-debug")))
+                     (search-input-file inputs "/bin/calibre-debug"))
+                    (ebook-meta
+                     (search-input-file inputs "/bin/ebook-meta"))
+                    (folder-program
+                     (string-append #$output
+                                    "/share/emacs/site-lisp/calibredb-"
+                                    #$version "/calibredb-folder.py")))
                (emacs-substitute-variables "calibredb-core.el"
                  ("calibredb-fetch-metadata-program" fetch-ebook-metadata)
                  ("calibredb-program" calibredb)
                  ("calibredb-convert-program" ebook-convert)
-                  ("calibredb-debug-program" calibre-debug))))))))
+                  ("calibredb-debug-program" calibre-debug)
+                  ("calibredb-ebook-meta-program" ebook-meta)
+                  ("calibredb-folder-program" folder-program))))))))
    (inputs
     (list calibre))
    (propagated-inputs
-     (list emacs-dash emacs-esxml emacs-s))
+     (list emacs-dash emacs-esxml emacs-request emacs-s))
    (home-page "https://github.com/chenyanming/calibredb.el")
    (synopsis "Yet another calibre client for Emacs")
    (description "This package integrates calibre into Emacs.
@@ -41493,17 +41550,65 @@ time.")
    (build-system emacs-build-system)
    (arguments
     (list
-      #:tests? #f ; requires cask
-      #:phases #~(modify-phases %standard-phases
-                   ;; Move the source files to the top level, which is
-                   ;; included in the EMACSLOADPATH.
-                   (add-after 'unpack 'move-source-files
-                     (lambda _
-                       (let ((el-files (find-files "./lisp" ".*\\.el$")))
-                         (for-each (lambda (f)
-                                     (rename-file f
-                                                  (basename f)))
-                                   el-files)))))))
+      #:test-command #~(list "make" "tests")
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; Move the source files to the top level, which is
+          ;; included in the EMACSLOADPATH.
+          (add-after 'unpack 'move-source-files
+            (lambda _
+              (let ((el-files (find-files "./lisp" ".*\\.el$")))
+                (for-each (lambda (f)
+                            (rename-file f
+                                         (basename f)))
+                          el-files))))
+          (add-before 'check 'fix-tests
+            (lambda _
+              (substitute* "Makefile"
+                (("cask") ""))
+              (substitute* "test/ert-helper.el"
+                (("lisp\\/") ""))))
+          (add-before 'check 'skip-failing-tests
+            (lambda _
+              (let-syntax
+                  ((disable-tests
+                    (syntax-rules ()
+                      ((_ file ())
+                       (syntax-error "test names list must not be empty"))
+                      ((_ file (test-name ...))
+                       (substitute* file
+                         (((string-append
+                            "^\\(ert-deftest " test-name ".*") all)
+                          (string-append all "(skip-unless nil)\n")) ...)))))
+                (disable-tests
+                 "test/mastodon-profile-tests.el"
+                 ("mastodon-profile--add-author-bylines"
+                  "mastodon-profile--make-author-buffer"))
+                (disable-tests
+                 "test/mastodon-auth-tests.el"
+                 ("mastodon-auth--handle-token-response--good"
+                  "mastodon-auth-plstore-token-check"))
+                (disable-tests
+                 "test/mastodon-client-tests.el"
+                 ("mastodon-client--make-user-active"
+                  "mastodon-client--store"
+                  "mastodon-client--store-access-token"))
+                (disable-tests
+                 "test/mastodon-tl-tests.el"
+                 ("mastodon-tl--byline-timestamp-has-relative-display"
+                  "mastodon-tl--next-tab-item--no-spaces-at-ends"
+                  "mastodon-tl--next-tab-item--with-spaces-at-ends"))
+                (disable-tests
+                 "test/mastodon-media-tests.el"
+                 ("mastodon-media--get-avatar-rendering"
+                  "mastodon-media--inline-images"
+                  "mastodon-media--load-image-from-url-avatar-with-imagemagic"
+                  "mastodon-media--load-image-from-url-avatar-without-imagemagic"
+                  "mastodon-media--load-image-from-url-media-link-with-imagemagic"
+                  "mastodon-media--load-image-from-url-media-link-without-imagemagic"
+                  "mastodon-media--load-image-from-url-url-fetching-fails"
+                  "mastodon-media--process-image-response"))))))))
+    (native-inputs (list emacs-el-mock))
    (propagated-inputs
     (list emacs-persist emacs-tp))
    (home-page "https://codeberg.org/martianh/mastodon.el")
--- a/gnu/packages/embedded.scm
+++ b/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
--- a/gnu/packages/emulators.scm
+++ b/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))
--- a/gnu/packages/enchant.scm
+++ b/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))

--- a/gnu/packages/engineering.scm
+++ b/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
--- a/gnu/packages/enlightenment.scm
+++ b/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)
--- a/gnu/packages/fediverse.scm
+++ b/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
--- a/gnu/packages/file-systems.scm
+++ b/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)
--- a/gnu/packages/finance.scm
+++ b/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)
@@ -1621,10 +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
@@ -2507,10 +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")
--- a/gnu/packages/firmware.scm
+++ b/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)
--- a/gnu/packages/flashing-tools.scm
+++ b/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)
--- a/gnu/packages/fontutils.scm
+++ b/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
--- a/gnu/packages/freedesktop.scm
+++ b/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")
@@ -3417,7 +3418,7 @@ interfaces.")
 (define-public xdg-desktop-portal-wlr
  (package
    (name "xdg-desktop-portal-wlr")
-    (version "0.7.1")
+    (version "0.8.2")
    (source (origin
              (method git-fetch)
              (uri (git-reference
@@ -3426,7 +3427,7 @@ interfaces.")
              (file-name (git-file-name name version))
              (sha256
               (base32
-                "1mbq3czka9swwmfaasnaj89y2m254p3qa522ayclh688jdwh70hq"))
+                "1jj0a9s3h3i04qsxkhcpxjzbb17hs9ngdy7wkypja09233zdz10w"))
              (patches (search-patches "xdg-desktop-portal-wlr-harcoded-length.patch"))))
    (build-system meson-build-system)
    (arguments
--- a/gnu/packages/game-development.scm
+++ b/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)
--- a/gnu/packages/geo.scm
+++ b/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)))
--- a/gnu/packages/gimp.scm
+++ b/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")
--- a/gnu/packages/gkrellm.scm
+++ b/gnu/packages/gkrellm.scm
@@ -1,7 +1,4 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
-;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -19,44 +16,8 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

 (define-module (gnu packages gkrellm)
-  #:use-module (guix build-system gnu)
-  #:use-module (guix download)
-  #:use-module (guix gexp)
-  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix packages)
-  #:use-module (guix utils)
-  #:use-module (gnu packages gettext)
-  #:use-module (gnu packages gtk)
-  #:use-module (gnu packages pkg-config)
-  #:use-module (gnu packages xorg))
+  #:use-module (gnu packages monitoring)
+  #:use-module (guix deprecation))

-(define-public gkrellm
-  (package
-    (name "gkrellm")
-    (version "2.5.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "https://gkrellm.srcbox.net/releases/gkrellm-"
-                           version ".tar.bz2"))
-       (sha256
-        (base32 "0qvy2xmwmfy5f0g09yn9lr262shnx82ba04r5il2wj4qscg3r7h8"))))
-    (build-system gnu-build-system)
-    (inputs (list gtk+-2 libsm))
-    (native-inputs (list gettext-minimal pkg-config))
-    (arguments
-     (list
-      #:tests? #f ;there is no check target
-      #:phases
-      #~(modify-phases %standard-phases
-          (delete 'configure)) ;no configure script
-      #:make-flags
-      #~(list (string-append "INSTALLROOT=" #$output)
-              (string-append "CC=" #$(cc-for-target)))))
-    (home-page "https://gkrellm.srcbox.net/")
-    (synopsis "System monitors")
-    (description
-     "GKrellM is a single process stack of system monitors which supports
-applying themes to match its appearance to your window manager, Gtk, or any
-other theme.")
-    (license license:gpl3+)))
+(define-deprecated/public-alias gkrellm
+  (@ (guix packages monitoring) gkrellm))
--- a/gnu/packages/gl.scm
+++ b/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
--- a/gnu/packages/gnome-xyz.scm
+++ b/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)
--- a/gnu/packages/gnome.scm
+++ b/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
--- a/gnu/packages/gnupg.scm
+++ b/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)
--- a/gnu/packages/golang-check.scm
+++ b/gnu/packages/golang-check.scm
@@ -245,6 +245,55 @@ go-fuzz-headers.")
@end itemize")
    (license license:expat)))

+(define-public go-github-com-alexkohler-prealloc
+  (package
+    (name "go-github-com-alexkohler-prealloc")
+    (version "1.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/alexkohler/prealloc")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "011i8yqzyjgwj17k44xvvg4bxfv8z20s0416r2d3yf4s3wqqygpq"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/alexkohler/prealloc"))
+    (home-page "https://github.com/alexkohler/prealloc")
+    (synopsis "Find slice declarations that could be preallocated")
+    (description
+     "This package is a Go static analysis tool to find slice declarations
+that could potentially be preallocated.")
+    (license license:expat)))
+
+(define-public go-github-com-alingse-asasalint
+  (package
+    (name "go-github-com-alingse-asasalint")
+    (version "0.0.11")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/alingse/asasalint")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1avz33cx3gcpps26rxijv7ic0njfmsdkbcp2mqg5yxhdcpq57s0q"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/alingse/asasalint"))
+    (propagated-inputs
+     (list go-golang-org-x-tools))
+    (home-page "https://github.com/alingse/asasalint")
+    (synopsis "Lint pass any slice as any in variadic function")
+    (description
+     "Golang linter, lint that pass any slice as any in variadic function.")
+    (license license:expat)))
+
 (define-public go-github-com-andreyvit-diff
  (package
    (name "go-github-com-andreyvit-diff")
--- a/gnu/packages/golang-crypto.scm
+++ b/gnu/packages/golang-crypto.scm
@@ -1600,7 +1600,7 @@ RSA, RSA-PSS, and ECDSA, though hooks are present for adding your own.")
 (define-public go-github-com-google-go-tpm
  (package
    (name "go-github-com-google-go-tpm")
-    (version "0.9.1")
+    (version "0.9.4")
    (source
     (origin
       (method git-fetch)
@@ -1609,7 +1609,7 @@ RSA, RSA-PSS, and ECDSA, though hooks are present for adding your own.")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1c5j5cvwl45ka93nknmv454ivd7kp9n8yql19gr6z01z0s1ph7sg"))))
+        (base32 "1sp1mbr6vz36zy9w36iksirbsj5p2jslsl8zs1cdj8s4ig4lkd9d"))))
    (build-system go-build-system)
    (arguments
     (list
--- a/gnu/packages/golang-maths.scm
+++ b/gnu/packages/golang-maths.scm
@@ -456,6 +456,29 @@ penalization.")
 FFT (Schonhage-Strassen method for multiplying integers).")
    (license license:bsd-3)))

+(define-public go-github-com-robinus2-golang-moving-average
+  (package
+    (name "go-github-com-robinus2-golang-moving-average")
+    (version "1.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/RobinUS2/golang-moving-average")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "02z3ad29653fz7whxkjjpq820ig9j8m68xj4kay14jyazkr5in1f"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/RobinUS2/golang-moving-average"))
+    (home-page "https://github.com/RobinUS2/golang-moving-average")
+    (synopsis "Moving average implementation for Go")
+    (description
+     "This package provides a moving average implementation for Go.")
+    (license license:asl2.0)))
+
 (define-public go-github-com-shopspring-decimal
  (package
    (name "go-github-com-shopspring-decimal")
--- a/gnu/packages/golang-web.scm
+++ b/gnu/packages/golang-web.scm
@@ -386,19 +386,25 @@ devices.")
            ;; - cloud.google.com/go/compute/metadata
            ;; - cloud.google.com/go/iam
            ;; - cloud.google.com/go/kms
+            ;; - cloud.google.com/go/logging
            ;; - cloud.google.com/go/longrunning
            ;; - cloud.google.com/go/monitoring
            ;; - cloud.google.com/go/security
+            ;; - cloud.google.com/go/spanner
            ;; - cloud.google.com/go/storage
+            ;; - cloud.google.com/go/trace
            (for-each delete-file-recursively
                      (list "auth"
                            "compute/metadata"
                            "iam"
                            "kms"
+                            "logging"
                            "longrunning"
                            "monitoring"
                            "security"
-                            "storage"))))))
+                            "spanner"
+                            "storage"
+                            "trace"))))))
    (build-system go-build-system)
    (arguments
     (list
@@ -440,7 +446,6 @@ devices.")
              "pubsub/v2/internal/scheduler"
              "pubsub/v2/internal/testutil"
              "rpcreplay"
-              "spanner/spansql"
              "translate")))
    (propagated-inputs
     (list ;; go-cloud-google-com-go-storage
@@ -695,6 +700,65 @@ Service (KMS) API.")
 see: @url{https://cloud.google.com/iam, IAM specification} for more details.")
    (license license:asl2.0)))

+(define-public go-cloud-google-com-go-logging
+  (package
+    (name "go-cloud-google-com-go-logging")
+    (version "1.16.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/googleapis/google-cloud-go")
+              (commit (go-version->git-ref version #:subdir "logging"))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "14khzbcymknsz4p40ibc8v1zsy33b33yn7fcvkfp4rkzw69wv356"))
+       (modules '((guix build utils)
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
+       (snippet
+        #~(begin
+            (define (delete-all-but directory . preserve)
+              (with-directory-excursion directory
+                (let* ((pred (negate (cut member <>
+                                          (cons* "." ".." preserve))))
+                       (items (scandir "." pred)))
+                  (for-each (cut delete-file-recursively <>) items))))
+            (delete-all-but "." "logging")))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "cloud.google.com/go/logging"
+      #:unpack-path "cloud.google.com/go"))
+    (native-inputs
+     ;; XXX: Remove when cycle is fixed.
+     (list go-github-com-envoyproxy-go-control-plane))
+    (propagated-inputs
+     (list go-cloud-google-com-go
+           go-cloud-google-com-go-compute-metadata
+           go-cloud-google-com-go-iam
+           go-cloud-google-com-go-longrunning
+           go-cloud-google-com-go-storage
+           go-github-com-google-go-cmp
+           go-github-com-googleapis-gax-go-v2
+           go-go-opencensus-io
+           go-go-opentelemetry-io-otel-sdk
+           go-go-opentelemetry-io-otel-trace
+           go-golang-org-x-oauth2
+           go-google-golang-org-api
+           go-google-golang-org-genproto
+           go-google-golang-org-genproto-googleapis-api
+           go-google-golang-org-genproto-googleapis-rpc
+           go-google-golang-org-grpc
+           go-google-golang-org-protobuf))
+    (home-page "https://cloud.google.com/go")
+    (synopsis "Cloud Logging API")
+    (description
+     "Package logging contains a Cloud Logging client suitable for writing
+logs.  For reading logs, and working with sinks, metrics and monitored
+resources, see package cloud.google.com/go/logging/logadmin.")
+    (license license:asl2.0)))
+
 (define-public go-cloud-google-com-go-longrunning
  (package
    (name "go-cloud-google-com-go-longrunning")
@@ -832,6 +896,78 @@ its service definition.")
     "This package provides a Go Client Library for Certificate Authority API.")
    (license license:asl2.0)))

+(define-public go-cloud-google-com-go-spanner
+  (package
+    (name "go-cloud-google-com-go-spanner")
+    (version "1.91.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/googleapis/google-cloud-go")
+              (commit (go-version->git-ref version #:subdir "spanner"))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "05jgalbqb9n1whlpdkj40rvyk8lg39q5w4l463ycsj2301pmr90h"))
+       (modules '((guix build utils)
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
+       (snippet
+        #~(begin
+            (define (delete-all-but directory . preserve)
+              (with-directory-excursion directory
+                (let* ((pred (negate (cut member <>
+                                          (cons* "." ".." preserve))))
+                       (items (scandir "." pred)))
+                  (for-each (cut delete-file-recursively <>) items))))
+            (delete-all-but "." "spanner")))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "cloud.google.com/go/spanner"
+      #:unpack-path "cloud.google.com/go"
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'remove-benchmarks
+            (lambda* (#:key import-path #:allow-other-keys)
+              (with-directory-excursion (string-append "src/" import-path)
+                (delete-file-recursively "benchmarks")))))))
+    (native-inputs
+     (list go-github-com-google-go-cmp
+           ;; XXX: Remove when cycle is fixed.
+           go-github-com-envoyproxy-go-control-plane))
+    (propagated-inputs
+     (list go-cloud-google-com-go
+           go-cloud-google-com-go-iam
+           go-cloud-google-com-go-longrunning
+           go-cloud-google-com-go-monitoring
+           go-github-com-google-uuid
+           go-github-com-googleapis-gax-go-v2
+           go-github-com-googlecloudplatform-grpc-gcp-go-grpcgcp
+           go-go-opencensus-io
+           go-go-opentelemetry-io-contrib-detectors-gcp
+           go-go-opentelemetry-io-otel
+           go-go-opentelemetry-io-otel-metric
+           go-go-opentelemetry-io-otel-sdk
+           go-go-opentelemetry-io-otel-sdk-metric
+           go-go-opentelemetry-io-otel-trace
+           go-golang-org-x-oauth2
+           go-golang-org-x-sync
+           go-google-golang-org-api
+           go-google-golang-org-genproto
+           go-google-golang-org-genproto-googleapis-api
+           go-google-golang-org-genproto-googleapis-rpc
+           go-google-golang-org-grpc
+           go-google-golang-org-protobuf))
+    (home-page "https://cloud.google.com/go")
+    (synopsis "Cloud Spanner databases Go client")
+    (description
+     "Package spanner provides a client for reading and writing to Cloud
+Spanner databases.  See
+@url{https://cloud.google.com/spanner/docs/getting-started/go/} for an
+introduction to Cloud Spanner and additional help on using this API.")
+    (license license:asl2.0)))
+
 (define-public go-cloud-google-com-go-storage
  (package
    (name "go-cloud-google-com-go-storage")
@@ -897,6 +1033,59 @@ Google Cloud Storage stores data in named objects, which are grouped into
 buckets.")
    (license license:asl2.0)))

+(define-public go-cloud-google-com-go-trace
+  (package
+    (name "go-cloud-google-com-go-trace")
+    (version "1.14.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/googleapis/google-cloud-go")
+              (commit (go-version->git-ref version #:subdir "trace"))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "14khzbcymknsz4p40ibc8v1zsy33b33yn7fcvkfp4rkzw69wv356"))
+       (modules '((guix build utils)
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
+       (snippet
+        #~(begin
+            (define (delete-all-but directory . preserve)
+              (with-directory-excursion directory
+                (let* ((pred (negate (cut member <>
+                                          (cons* "." ".." preserve))))
+                       (items (scandir "." pred)))
+                  (for-each (cut delete-file-recursively <>) items))))
+            (delete-all-but "." "trace")))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:skip-build? #t
+      #:import-path "cloud.google.com/go/trace"
+      #:unpack-path "cloud.google.com/go"))
+    (propagated-inputs
+     (list go-github-com-googleapis-gax-go-v2
+           go-google-golang-org-api
+           go-google-golang-org-genproto
+           go-google-golang-org-genproto-googleapis-api
+           go-google-golang-org-genproto-googleapis-rpc
+           go-google-golang-org-grpc
+           go-google-golang-org-protobuf))
+    (home-page "https://cloud.google.com/go")
+    (synopsis "Go Client Library for Cloud Trace API")
+    (description
+     "This package implements the @url{https://cloud.google.com/stackdriver,
+Stackdriver} Trace API in Golang.  Stackdriver Trace is a distributed tracing
+system that collects latency data from your applications and displays it in
+the Google Cloud Platform Console.
+
+It sends application trace data to Stackdriver Trace for viewing.  Trace data
+is collected for all App Engine applications by default.  Trace data from
+other applications can be provided using this API.  This library is used to
+interact with the Trace API directly.")
+    (license license:asl2.0)))
+
 (define-public go-code-gitea-io-sdk-gitea
  (package
    (name "go-code-gitea-io-sdk-gitea")
@@ -1406,6 +1595,39 @@ AWS Lambda and API Gateway or ALB without changing the existing HTTP
 handlers.")
    (license license:asl2.0)))

+(define-public go-github-com-akutz-memconn
+  (package
+    (name "go-github-com-akutz-memconn")
+    (version "0.1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/akutz/memconn")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1mhghzcx2zxr4bpyf4wx3j7ph9srw38wxg78svwbjh930r2kzssq"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/akutz/memconn"
+      #:test-flags
+      #~(list "-skip" (string-join
+                       ;; Tests fail with insecure algorithm
+                       (list "TestTLS_Memu"
+                             "TestTLS_Memb"
+                             "TestTLS_TCP"
+                             "TestTLS_UNIX"
+                             "TestTLS_HTTP_Memu"
+                             "TestTLS_HTTP_Memb")
+                       "|"))))
+    (home-page "https://github.com/akutz/memconn")
+    (synopsis "In-memory network stack for Go")
+    (description
+     "This package provides named, in-memory network connections for Go.")
+    (license license:asl2.0)))
+
 (define-public go-github-com-alexliesenfeld-health
  (package
    (name "go-github-com-alexliesenfeld-health")
@@ -3595,6 +3817,33 @@ differentiate between installs of Mozilla software in @code{installs.ini} and
                             "TestStructToDateTime")
                       "|"))))))

+(define-public go-github-com-brunoscheufler-aws-ecs-metadata-go
+  (package
+    (name "go-github-com-brunoscheufler-aws-ecs-metadata-go")
+    (version "0.0.0-20221221133751-67e37ae746cd")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/BrunoScheufler/aws-ecs-metadata-go")
+              (commit (go-version->git-ref version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1x9kn49sl6793zqq4nrbsyfhqh7i3xr25syck2ybpcqkd3mmb8k6"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/brunoscheufler/aws-ecs-metadata-go"))
+    (native-inputs
+     (list go-github-com-stretchr-testify))
+    (home-page "https://github.com/brunoscheufler/aws-ecs-metadata-go")
+    (synopsis "Retrieve AWS ECS Task metadata")
+    (description
+     "This package provides a minimal wrapper library to fetch
+@acronym{Elastic Container Service, ECS} Task metadata from any Go service
+running in container provisioned by AWS Fargate.")
+    (license license:expat)))
+
 (define-public go-github-com-buger-jsonparser
  (package
    (name "go-github-com-buger-jsonparser")
@@ -6166,7 +6415,7 @@ application's http.Handlers.")
 (define-public go-github-com-files-com-files-sdk-go-v3
  (package
    (name "go-github-com-files-com-files-sdk-go-v3")
-    (version "3.3.7")
+    (version "3.3.95")
    (source
     (origin
       (method git-fetch)
@@ -6175,7 +6424,7 @@ application's http.Handlers.")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1syx75vbamwrx5x5glf4542ml8myj9kqqkig8hmy97lhzq4d4n7a"))))
+        (base32 "19mxsybv9lyq57nf5xvll41g7f6z90lq9hrdx1p4w20mj0f51wyj"))))
    (build-system go-build-system)
    (arguments
     (list
@@ -6191,7 +6440,6 @@ application's http.Handlers.")
           go-github-com-stretchr-testify))
    (propagated-inputs
     (list go-github-com-appscode-go-querystring
-           go-github-com-bradfitz-iter
           go-github-com-chilts-sid
           go-github-com-dustin-go-humanize
           go-github-com-hashicorp-go-retryablehttp
@@ -6201,6 +6449,7 @@ application's http.Handlers.")
           go-github-com-sabhiram-go-gitignore
           go-github-com-samber-lo
           go-github-com-winfsp-cgofuse
+           go-golang-org-x-sync
           go-golang-org-x-sys
           go-golang-org-x-text
           go-moul-io-http2curl-v2))
@@ -8245,6 +8494,51 @@ Terraform by using the enterprise certificates feature.")
 for clients and servers based on @code{gRPC} and Google API conventions.")
    (license license:bsd-3)))

+(define-public go-github-com-googlecloudplatform-grpc-gcp-go-grpcgcp
+  (package
+    (name "go-github-com-googlecloudplatform-grpc-gcp-go-grpcgcp")
+    (version "1.6.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/GoogleCloudPlatform/grpc-gcp-go")
+              (commit (go-version->git-ref version #:subdir "grpcgcp"))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0p7zwbi6gg99mzi7albscf7jn63qxs714h6vars735an13bbvl12"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:go go-1.25
+      #:import-path "github.com/GoogleCloudPlatform/grpc-gcp-go/grpcgcp"
+      #:unpack-path "github.com/GoogleCloudPlatform/grpc-gcp-go"
+      ;; gcp_multiendpoint_test.go:441: endpoint wanted "localhost:50051", got
+      ;; "127.0.0.3:50051"
+      #:test-flags #~(list "-skip" "TestGCPMultiEndpoint")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'pre-check
+            (lambda _
+              ;; See: <https://go.dev/blog/synctest>.
+              (setenv "GOEXPERIMENT" "synctest")
+              (setenv "GODEBUG" "asynctimerchan=0"))))))
+    (native-inputs
+     (list go-github-com-golang-mock
+           go-github-com-google-go-cmp))
+    (propagated-inputs
+     (list go-go-opentelemetry-io-otel
+           go-go-opentelemetry-io-otel-metric
+           go-go-opentelemetry-io-otel-sdk-metric
+           go-google-golang-org-grpc
+           go-google-golang-org-protobuf))
+    (home-page "https://github.com/GoogleCloudPlatform/grpc-gcp-go")
+    (synopsis "Grpc supports for Google Cloud APIs")
+    (description
+     "Package grpcgcp provides gRPC supports for Google Cloud APIs.  For now
+it provides connection management with affinity support.")
+    (license license:asl2.0)))
+
 (define-public go-github-com-googlecloudplatform-opentelemetry-operations-go-detectors-gcp
  (package
    (name
@@ -8334,6 +8628,110 @@ testing of the detection functions in real GCP environments.")
 send collected metrics to Google Cloud.")
    (license license:asl2.0)))

+(define-public go-github-com-googlecloudplatform-opentelemetry-operations-go-exporter-trace
+  (package
+    (name "go-github-com-googlecloudplatform-opentelemetry-operations-go-exporter-trace")
+    (version "1.32.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/GoogleCloudPlatform/opentelemetry-operations-go")
+              (commit (go-version->git-ref version #:subdir "exporter/trace"))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0nizaaydcvvi718g5v4pgx8in6d546mmkrf7h3sxhz2yyyygvms3"))
+       (modules '((guix build utils)
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
+       (snippet
+        #~(begin
+            (define (delete-all-but directory . preserve)
+              (with-directory-excursion directory
+                (let* ((pred (negate (cut member <>
+                                          (cons* "." ".." preserve))))
+                       (items (scandir "." pred)))
+                  (for-each (cut delete-file-recursively <>) items))))
+            (delete-all-but "exporter" "trace")
+            (delete-all-but "." "exporter")))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path
+      (string-append "github.com/GoogleCloudPlatform/"
+                     "opentelemetry-operations-go/exporter/trace")
+      #:unpack-path
+      "github.com/GoogleCloudPlatform/opentelemetry-operations-go"))
+    (native-inputs
+     (list go-github-com-stretchr-testify))
+    (propagated-inputs
+     (list go-cloud-google-com-go-trace
+           go-github-com-googlecloudplatform-opentelemetry-operations-go-internal-cloudmock
+           go-github-com-googlecloudplatform-opentelemetry-operations-go-internal-resourcemapping
+           go-go-opentelemetry-io-otel
+           go-go-opentelemetry-io-otel-sdk
+           go-go-opentelemetry-io-otel-trace
+           go-golang-org-x-oauth2
+           go-google-golang-org-api
+           go-google-golang-org-genproto-googleapis-rpc
+           go-google-golang-org-grpc
+           go-google-golang-org-protobuf))
+    (home-page "https://github.com/GoogleCloudPlatform/opentelemetry-operations-go")
+    (synopsis "OpenTelemetry Google Cloud Trace Exporter")
+    (description
+     "@code{OpenTelemetry} Google Cloud Trace Exporter allows the user to send
+collected traces and spans to Google Cloud.")
+    (license license:asl2.0)))
+
+(define-public go-github-com-googlecloudplatform-opentelemetry-operations-go-internal-cloudmock
+  (package
+    (name "go-github-com-googlecloudplatform-opentelemetry-operations-go-internal-cloudmock")
+    (version "0.56.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/GoogleCloudPlatform/opentelemetry-operations-go")
+              (commit (go-version->git-ref version
+                                           #:subdir "internal/cloudmock"))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0nizaaydcvvi718g5v4pgx8in6d546mmkrf7h3sxhz2yyyygvms3"))
+       (modules '((guix build utils)
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
+       (snippet
+        #~(begin
+            (define (delete-all-but directory . preserve)
+              (with-directory-excursion directory
+                (let* ((pred (negate (cut member <>
+                                          (cons* "." ".." preserve))))
+                       (items (scandir "." pred)))
+                  (for-each (cut delete-file-recursively <>) items))))
+            (delete-all-but "internal" "cloudmock")
+            (delete-all-but "." "internal")))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path
+      (string-append "github.com/GoogleCloudPlatform/"
+                     "opentelemetry-operations-go/internal/cloudmock")
+      #:unpack-path
+      "github.com/GoogleCloudPlatform/opentelemetry-operations-go"))
+    (propagated-inputs
+     (list go-cloud-google-com-go-logging
+           go-cloud-google-com-go-monitoring
+           go-cloud-google-com-go-trace
+           go-google-golang-org-genproto-googleapis-api
+           go-google-golang-org-grpc
+           go-google-golang-org-protobuf))
+    (home-page "https://github.com/GoogleCloudPlatform/opentelemetry-operations-go")
+    (synopsis "OpenTelemetry Google Cloud mock library")
+    ;; XXX: There is not any documentation for this package upstrream.
+    (description
+     "This package provides OpenTelemetry Google Cloud mock Go library.")
+    (license license:asl2.0)))
+
 (define-public go-github-com-googlecloudplatform-opentelemetry-operations-go-internal-resourcemapping
  (package
    (name "go-github-com-googlecloudplatform-opentelemetry-operations-go-internal-resourcemapping")
@@ -9803,6 +10201,55 @@ protocol) - used to discover UPnP services on a network
 by the IBM Cloud @code{OpenAPI} SDK Generator (openapi-sdkgen).")
    (license license:asl2.0)))

+(define-public go-github-com-ibm-sarama
+  (package
+    (name "go-github-com-ibm-sarama")
+    (version "1.48.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/IBM/sarama")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0ak07aqb9hznvhbnkw34vak30pzbwvh2aff22lww8gcba4c9qdn7"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/IBM/sarama"
+      #:unpack-path "github.com/IBM/sarama"
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'remove-examples
+            (lambda* (#:key tests? unpack-path #:allow-other-keys)
+              (with-directory-excursion (string-append "src/" unpack-path)
+                (delete-file-recursively "examples")))))))
+    (native-inputs
+     (list go-github-com-stretchr-testify
+           go-github-com-davecgh-go-spew
+           go-go-uber-org-goleak))
+    (propagated-inputs
+     (list go-github-com-eapache-go-resiliency
+           go-github-com-eapache-queue
+           go-github-com-jcmturner-gofork
+           go-github-com-jcmturner-gokrb5-v8
+           go-github-com-klauspost-compress
+           go-github-com-pierrec-lz4-v4
+           go-github-com-rcrowley-go-metrics
+           go-golang-org-x-net
+           go-golang-org-x-sync
+           go-golang-org-x-sys))
+    (home-page "https://github.com/IBM/sarama")
+    (synopsis "Go library for Apache Kafka")
+    (description
+     "Package sarama is a pure Go client library for dealing with Apache Kafka
+(versions 0.8 and later).  It includes a high-level API for easily producing
+and consuming messages, and a low-level API for controlling bytes on the wire
+when the high-level API is insufficient.  Usage examples for the high-level
+APIs are provided inline with their full documentation.")
+    (license license:expat)))
+
 (define-public go-github-com-igungor-gofakes3
  (package
    (name "go-github-com-igungor-gofakes3")
@@ -13629,24 +14076,24 @@ standard library.")
    (build-system go-build-system)
    (arguments
     (list
-      ;; TODO: Enable tests and build when all missing inputs are packages, use
-      ;; as source only package for Kubo.
-      #:skip-build? #t
-      #:tests? #f
-      #:import-path "github.com/openzipkin/zipkin-go"))
+      #:import-path "github.com/openzipkin/zipkin-go"
+      ;; span_test.go:56: expected valid endpoint, got error: host lookup
+      ;; failure: lookup www.google.com on [::1]:53: read udp
+      ;; [::1]:56302->[::1]:53: read: connection refused
+      #:test-flags #~(list "-skip" "TestRemoteEndpoint|TestHTTPClient")))
    (native-inputs
     (list go-github-com-onsi-ginkgo-v2
           go-github-com-onsi-gomega))
    (propagated-inputs
-     (list ;; go-github-com-ibm-sarama
-           ;; go-github-com-rabbitmq-amqp091-go
+     (list go-github-com-ibm-sarama
+           go-github-com-rabbitmq-amqp091-go
           go-google-golang-org-grpc
           go-google-golang-org-protobuf))
    (home-page "https://github.com/openzipkin/zipkin-go")
    (synopsis "Zipkin Library for Go")
    (description
     "Package zipkin implements a native Zipkin instrumentation library for
-Go.")
+Go.  @url{https://zipkin.io/, Zipkin} is a distributed tracing system.")
    (license license:asl2.0)))

 (define-public go-github-com-oracle-oci-go-sdk-v65
@@ -15574,6 +16021,38 @@ currently implements
 of the specification.")
      (license license:expat)))

+(define-public go-github-com-rabbitmq-amqp091-go
+  (package
+    (name "go-github-com-rabbitmq-amqp091-go")
+    (version "1.11.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/rabbitmq/amqp091-go")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1xn0ykx08l8gg66qk6jhz2md4as8n9fqm0smzcbislyqp4d3gpr8"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/rabbitmq/amqp091-go"
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'remove-examples
+            (lambda* (#:key tests? import-path #:allow-other-keys)
+              (with-directory-excursion (string-append "src/" import-path)
+                (delete-file-recursively "_examples")))))))
+    (native-inputs
+     (list go-go-uber-org-goleak))
+    (home-page "https://github.com/rabbitmq/amqp091-go")
+    (synopsis "Go RabbitMQ Client Library")
+    (description
+     "Package amqp091 is an @acronym{Advanced Message Queuing Protocol, AMQP}
+0.9.1 client with @code{RabbitMQ} extensions.")
+    (license license:bsd-2)))
+
 (define-public go-github-com-rasky-go-xdr
  (package
    (name "go-github-com-rasky-go-xdr")
@@ -16233,6 +16712,7 @@ and consumers to transparently record signed metadata to a ledger.")
      #:test-subdirs
      #~(list "internal/algorithmregistry"
              "internal/safeint"
+              "pkg/client/read"
              "pkg/client/write"
              "pkg/types/dsse"
              "pkg/types/hashedrekord"
@@ -16247,7 +16727,8 @@ and consumers to transparently record signed metadata to a ledger.")
           go-github-com-stretchr-testify
           go-sigs-k8s-io-release-utils))
    (propagated-inputs
-     (list go-cloud-google-com-go-storage
+     (list go-cloud-google-com-go-spanner
+           go-cloud-google-com-go-storage
           go-github-com-aws-aws-sdk-go-v2
           go-github-com-aws-aws-sdk-go-v2-config
           go-github-com-aws-aws-sdk-go-v2-credentials
@@ -16264,12 +16745,14 @@ and consumers to transparently record signed metadata to a ledger.")
           go-github-com-sigstore-sigstore
           ;; go-github-com-sigstore-sigstore-go                 ;cycles
           go-github-com-sigstore-sigstore-pkg-signature-kms-aws
+           go-github-com-chainguard-dev-clog
           go-github-com-sigstore-sigstore-pkg-signature-kms-gcp
           go-github-com-tink-crypto-tink-go-awskms-v2
           go-github-com-tink-crypto-tink-go-gcpkms-v2
           go-github-com-tink-crypto-tink-go-v2
           go-github-com-transparency-dev-formats
           go-github-com-transparency-dev-merkle
+           go-github-com-transparency-dev-tessera
           go-go-opentelemetry-io-otel
           go-go-opentelemetry-io-otel-exporters-prometheus
           go-go-opentelemetry-io-otel-sdk-metric
@@ -16283,9 +16766,6 @@ and consumers to transparently record signed metadata to a ledger.")
           go-k8s-io-klog-v2

           ;; TODO: Complete packaging.
-           ;; go-cloud-google-com-go-spanner
-           ;; go-github-com-chainguard-dev-clog
-           ;; go-github-com-transparency-dev-tessera
           #;go-go-step-sm-crypto))
    (home-page "https://github.com/sigstore/rekor-tiles")
    (synopsis "Tile-based transparency log for Sigstore")
@@ -17917,7 +18397,95 @@ caching protocol.  It provides support to programmatically store and retrieve
 build caches, instead of relying on the standard actions/cache YAML step.")
    (license license:expat)))

+(define-public go-github-com-transparency-dev-tessera
+  (package
+    (name "go-github-com-transparency-dev-tessera")
+    (version "1.0.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/transparency-dev/tessera")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "101y83j67g7r1bqk49qj8mwxgys88wkxz5lf7pvjp4c6b10w5gck"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/transparency-dev/tessera"
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'fix-access-to-state-tree-state
+            (lambda* (#:key import-path #:allow-other-keys)
+              (with-directory-excursion (string-append "src/" import-path)
+                (make-file-writable "testdata/log/.state/treeState.lock"))))
+          (add-after 'check 'remove-testdata
+            (lambda* (#:key import-path #:allow-other-keys)
+              (with-directory-excursion (string-append "src/" import-path)
+                (delete-file-recursively "testdata")))))))
+    (native-inputs
+     (list strace
+           ;; XXX: Remove when cycle is fixed.
+           go-github-com-envoyproxy-go-control-plane))
+    (propagated-inputs
+     (list go-cloud-google-com-go-spanner
+           go-cloud-google-com-go-storage
+           go-github-com-avast-retry-go-v4
+           go-github-com-aws-aws-sdk-go-v2
+           go-github-com-aws-aws-sdk-go-v2-config
+           go-github-com-aws-aws-sdk-go-v2-credentials
+           go-github-com-aws-aws-sdk-go-v2-service-s3
+           go-github-com-aws-smithy-go
+           go-github-com-bitfield-script
+           go-github-com-cenkalti-backoff-v5
+           go-github-com-charmbracelet-bubbletea
+           go-github-com-charmbracelet-lipgloss
+           go-github-com-dgraph-io-badger-v4
+           go-github-com-dustin-go-humanize
+           go-github-com-gdamore-tcell-v2
+           go-github-com-go-sql-driver-mysql
+           go-github-com-google-go-cmp
+           go-github-com-googlecloudplatform-opentelemetry-operations-go-exporter-metric
+           go-github-com-googlecloudplatform-opentelemetry-operations-go-exporter-trace
+           go-github-com-hashicorp-golang-lru-v2
+           go-github-com-muesli-termenv
+           go-github-com-rivo-tview
+           go-github-com-robinus2-golang-moving-average
+           go-github-com-transparency-dev-formats
+           go-github-com-transparency-dev-merkle
+           go-go-opentelemetry-io-contrib-detectors-aws-ec2-v2
+           go-go-opentelemetry-io-contrib-detectors-aws-ecs
+           go-go-opentelemetry-io-contrib-detectors-gcp
+           go-go-opentelemetry-io-contrib-propagators-aws
+           go-go-opentelemetry-io-otel
+           go-go-opentelemetry-io-otel-exporters-otlp-otlpmetric-otlpmetricgrpc
+           go-go-opentelemetry-io-otel-exporters-otlp-otlptrace-otlptracegrpc
+           go-go-opentelemetry-io-otel-metric
+           go-go-opentelemetry-io-otel-sdk
+           go-go-opentelemetry-io-otel-sdk-metric
+           go-golang-org-x-crypto
+           go-golang-org-x-exp
+           go-golang-org-x-mod
+           go-golang-org-x-net
+           go-golang-org-x-sync
+           go-golang-org-x-time
+           go-google-golang-org-api
+           go-google-golang-org-grpc
+           go-k8s-io-klog-v2))
+    (home-page "https://github.com/transparency-dev/tessera")
+    (synopsis "Go library for building tile-based transparency logs (tlogs)")
+    (description
+     "Tessera is a Go library for building tile-based transparency logs (tlogs).
+ It is the logical successor to the approach
+@url{https://github.com/google/trillian, Trillian v1} takes in building and
+operating logs.  The implementation and its APIs bake-in current
+best-practices based on the lessons learned over the past decade of building
+and operating transparency logs in production environments and at scale.")
+    (license license:asl2.0)))
+
 (define-public go-github-com-tv42-httpunix
+
  (let ((commit "2ba4b9c3382c77e7b9ea89d00746e6111d142a22")
        (revision "0"))
    (package
@@ -19686,6 +20254,101 @@ lists)
     "Package sdk provides an auto-instrumentable @code{OpenTelemetry} SDK.")
    (license license:asl2.0)))

+(define-public go-go-opentelemetry-io-contrib-detectors-aws-ec2-v2
+  (package
+    (name "go-go-opentelemetry-io-contrib-detectors-aws-ec2-v2")
+    (version "2.5.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/open-telemetry/opentelemetry-go-contrib")
+              (commit (go-version->git-ref version
+                                           #:subdir "detectors/aws/ec2"))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0nh7g1zxr3drqcbhsnnkqaz2hn1rnawg8jalixng23c9hwfgqaly"))
+       (modules '((guix build utils)
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
+       (snippet
+        #~(begin
+            (define (delete-all-but directory . preserve)
+              (with-directory-excursion directory
+                (let* ((pred (negate (cut member <>
+                                          (cons* "." ".." preserve))))
+                       (items (scandir "." pred)))
+                  (for-each (cut delete-file-recursively <>) items))))
+            (delete-all-but "detectors/aws" "ec2")
+            (delete-all-but "detectors" "aws")
+            (delete-all-but "." "detectors")))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "go.opentelemetry.io/contrib/detectors/aws/ec2/v2"
+      #:unpack-path "go.opentelemetry.io/contrib"))
+    (native-inputs
+     (list go-github-com-stretchr-testify))
+    (propagated-inputs
+     (list go-github-com-aws-aws-sdk-go-v2
+           go-github-com-aws-aws-sdk-go-v2-config
+           go-github-com-aws-aws-sdk-go-v2-feature-ec2-imds
+           go-github-com-aws-smithy-go
+           go-go-opentelemetry-io-otel
+           go-go-opentelemetry-io-otel-sdk))
+    (home-page "https://github.com/open-telemetry/opentelemetry-go-contrib")
+    (synopsis "Resource detector for EC2 instances")
+    (description
+     "Package ec2 provides a resource detector for @acronym{Amazon Elastic
+Compute Cloud, EC2} instances using @code{aws-sdk-go-v2}.")
+    (license license:asl2.0)))
+
+(define-public go-go-opentelemetry-io-contrib-detectors-aws-ecs
+  (package
+    (name "go-go-opentelemetry-io-contrib-detectors-aws-ecs")
+    (version "1.43.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/open-telemetry/opentelemetry-go-contrib")
+              (commit (go-version->git-ref version
+                                           #:subdir "detectors/aws/ecs"))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0nh7g1zxr3drqcbhsnnkqaz2hn1rnawg8jalixng23c9hwfgqaly"))
+       (modules '((guix build utils)
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
+       (snippet
+        #~(begin
+            (define (delete-all-but directory . preserve)
+              (with-directory-excursion directory
+                (let* ((pred (negate (cut member <>
+                                          (cons* "." ".." preserve))))
+                       (items (scandir "." pred)))
+                  (for-each (cut delete-file-recursively <>) items))))
+            (delete-all-but "detectors/aws" "ecs")
+            (delete-all-but "detectors" "aws")
+            (delete-all-but "." "detectors")))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "go.opentelemetry.io/contrib/detectors/aws/ecs"
+      #:unpack-path "go.opentelemetry.io/contrib"))
+    (native-inputs
+     (list go-github-com-stretchr-testify))
+    (propagated-inputs
+     (list go-github-com-brunoscheufler-aws-ecs-metadata-go
+           go-go-opentelemetry-io-otel
+           go-go-opentelemetry-io-otel-sdk))
+    (home-page "https://go.opentelemetry.io/contrib")
+    (synopsis "OTLP resource detector for AWS ECS instances")
+    (description
+     "Package ecs provides a resource detector for AWS @acronym{Elastic
+Container Service, ECS} instances.")
+    (license license:asl2.0)))
+
 (define-public go-go-opentelemetry-io-contrib-detectors-gcp
  (package
    (name "go-go-opentelemetry-io-contrib-detectors-gcp")
@@ -20289,7 +20952,7 @@ protobuf payloads.")
 (define-public go-go-opentelemetry-io-otel-exporters-otlp-otlptrace-otlptracegrpc
  (package
    (name "go-go-opentelemetry-io-otel-exporters-otlp-otlptrace-otlptracegrpc")
-    (version "1.36.0")
+    (version "1.43.0")
    (source
     (origin
       (method git-fetch)
@@ -20299,15 +20962,12 @@ protobuf payloads.")
                                           #:subdir "exporters/otlp/otlptrace/otlptracegrpc"))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1kvfbqc56p1h9rh9cvgn37ya6k10613r0f2rhjiwrrkgs2mszk30"))
+        (base32 "0583dw99k25k07pnq8hhhb45kwqhsx30lbk9yxsh4m50ji65wl8h"))
       (modules '((guix build utils)
                  (ice-9 ftw)
                  (srfi srfi-26)))
       (snippet
        #~(begin
-            ;; XXX: 'delete-all-but' is copied from the turbovnc package.
-            ;; Consider implementing it as a reusable procedure in
-            ;; guix/build/utils or guix/build-system/go.
            (define (delete-all-but directory . preserve)
              (with-directory-excursion directory
                (let* ((pred (negate (cut member <>
@@ -20315,23 +20975,27 @@ protobuf payloads.")
                       (items (scandir "." pred)))
                  (for-each (cut delete-file-recursively <>) items))))
            (delete-all-but "exporters/otlp/otlptrace" "otlptracegrpc")
+            (delete-all-but "exporters/otlp" "otlptrace")
            (delete-all-but "." "exporters")))))
    (build-system go-build-system)
    (arguments
     (list
-      ;; TODO: Enable when all missing inputs are available, use as source
-      ;; only package for Boxo.
-      #:skip-build? #t
-      #:tests? #f
      #:import-path
      "go.opentelemetry.io/otel/exporters/otlp/otlptrace/otlptracegrpc"
      #:unpack-path "go.opentelemetry.io/otel"))
    (native-inputs
-     (list go-github-com-stretchr-testify))
+     (list go-github-com-stretchr-testify
+           go-go-uber-org-goleak))
    (propagated-inputs
     (list go-github-com-cenkalti-backoff-v5
+           go-go-opentelemetry-io-otel
+           go-go-opentelemetry-io-otel-exporters-otlp-otlptrace
+           go-go-opentelemetry-io-otel-metric
+           go-go-opentelemetry-io-otel-metric-x
+           go-go-opentelemetry-io-otel-sdk
+           go-go-opentelemetry-io-otel-sdk-metric
+           go-go-opentelemetry-io-otel-trace
           go-go-opentelemetry-io-proto-otlp
-           go-go-uber-org-goleak
           go-google-golang-org-genproto-googleapis-rpc
           go-google-golang-org-grpc
           go-google-golang-org-protobuf))
@@ -20646,6 +21310,50 @@ logging library.  Instead, install one of the bridges listed in the
     "Package metric provides an implementation of the metric part of the
 OpenTelemetry API.")))

+(define-public go-go-opentelemetry-io-otel-metric-x
+  (package
+    (name "go-go-opentelemetry-io-otel-metric-x")
+    (version "0.0.0-20260424084752-468c62dac625")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/open-telemetry/opentelemetry-go")
+              (commit (go-version->git-ref version #:subdir "metric/x"))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "16x0aw116dadi73vzh8bcwasy79sblvh6k1q7yfx8n841x48ry8r"))
+       (modules '((guix build utils)
+                  (ice-9 ftw)
+                  (srfi srfi-26)))
+       (snippet
+        #~(begin
+            (define (delete-all-but directory . preserve)
+              (with-directory-excursion directory
+                (let* ((pred (negate (cut member <>
+                                          (cons* "." ".." preserve))))
+                       (items (scandir "." pred)))
+                  (for-each (cut delete-file-recursively <>) items))))
+            (delete-all-but "metric" "x")
+            (delete-all-but "." "metric")))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "go.opentelemetry.io/otel/metric/x"
+      #:unpack-path "go.opentelemetry.io/otel"))
+    (propagated-inputs
+     (list go-go-opentelemetry-io-otel
+           go-go-opentelemetry-io-otel-metric
+           go-go-opentelemetry-io-otel-trace))
+    (home-page "https://github.com/open-telemetry/opentelemetry-go")
+    (synopsis "Experimental Metric Options")
+    (description
+     "This package contains experimental options for the OpenTelemetry metric
+package.  These options are currently under development and not part of the
+stable API. They may be changed in backwards-incompatible ways, or removed
+entirely.")
+    (license license:asl2.0)))
+
 (define-public go-go-opentelemetry-io-otel-sdk
  (package
    (name "go-go-opentelemetry-io-otel-sdk")
@@ -22770,6 +23478,34 @@ carries no encryption keys and cannot decode the traffic that it proxies.")))
    (propagated-inputs '())
    (inputs '())))

+(define-public sarama-tools
+  (package/inherit go-github-com-ibm-sarama
+    (name "sarama-tools")
+    (arguments
+     (substitute-keyword-arguments arguments
+       ((#:install-source? _ #t) #f)
+       ((#:skip-build? _ #t) #f)
+       ((#:tests? _ #t) #f)
+       ((#:import-path _) "github.com/IBM/sarama/tools/...")))
+    (native-inputs (package-propagated-inputs go-github-com-ibm-sarama))
+    (propagated-inputs '())
+    (inputs '())
+    (description
+     "This package contains applications that are useful for exploration of
+Kafka cluster, or instrumentation.  Some of these tools mirror tools that ship
+with Kafka, but these tools won't require installing the JVM to function.
+
+@itemize
+@item @command{kafka-console-producer}: a command line tool to produce a
+single message to your Kafka custer.
+@item @command{kafka-console-partitionconsumer}: a command line
+tool to consume a single partition of a topic on your Kafka cluster.
+@item @command{kafka-console-consumer}: a command line tool to consume
+arbitrary partitions of a topic on your Kafka cluster.
+@item @command{kafka-producer-performance}: a command line tool to performance
+test producers (sync and async) on your Kafka cluster.
+@end itemize")))
+
 (define-public snowflake-proxy
  (package/inherit
      go-gitlab-torproject-org-tpo-anti-censorship-pluggable-transports-snowflake-v2
--- a/gnu/packages/golang-xyz.scm
+++ b/gnu/packages/golang-xyz.scm
@@ -525,6 +525,35 @@ file along with an index.html file.")
     "Package tcell provides a gruid Driver for making terminal apps.")
    (license license:isc)))

+(define-public go-codeberg-org-chavacava-garif
+  (package
+    (name "go-codeberg-org-chavacava-garif")
+    (version "0.2.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://codeberg.org/chavacava/garif.git")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0cz037yb9gnk9fd61pni6m0n9cbrwmlxxija5vm91mplyxlih05h"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "codeberg.org/chavacava/garif"))
+    (native-inputs
+     (list go-github-com-stretchr-testify))
+    (home-page "https://codeberg.org/chavacava/garif")
+    (synopsis "Create and manipulate SARIF logs")
+    (description
+     "This package defines all the Go structures required to model a log file.
+
+SARIF, from Static Analysis Results Interchange Format, is a standard
+JSON-based format for the output of static analysis tools defined and promoted
+by @url{https://www.oasis-open.org/, OASIS}.")
+    (license license:expat)))
+
 (define-public go-codeberg-org-emersion-go-scfg
  (package
    (name "go-codeberg-org-emersion-go-scfg")
@@ -613,6 +642,33 @@ recursively any exported one.  It also won't merge structs inside
 maps (because they are not addressable using Go reflection).")
    (license license:bsd-3)))

+(define-public go-fyne-io-systray
+  (package
+    (name "go-fyne-io-systray")
+    (version "1.11.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/fyne-io/systray")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0yrd4f3n8wrqcqradmqq9w0b31hd5hali876xkynfhm3nhaz4j1i"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "fyne.io/systray"))
+    (propagated-inputs
+     (list go-github-com-godbus-dbus-v5
+           go-golang-org-x-sys))
+    (home-page "https://fyne.io/systray/")
+    (synopsis "Place an icon and menu in the notification area")
+    (description
+     "This package is a cross-platform Go library to place an icon and menu in
+the notification area.")
+    (license license:asl2.0)))
+
 (define-public go-git-sr-ht-rjarry-go-opt
  (package
    (name "go-git-sr-ht-rjarry-go-opt")
@@ -2981,6 +3037,38 @@ input from the terminal while not echoing the input back (similar to
 and is therefore compatible with cross-compiling.")
    (license license:expat)))

+(define-public go-github-com-bitfield-script
+  (package
+    (name "go-github-com-bitfield-script")
+    (version "0.24.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/bitfield/script")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1pzmz7n39sh9sprclzd0m0l0flf626286fh51m065yjhkqzrjw89"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/bitfield/script"
+      #:test-flags #~(list "-vet=off")))
+    (native-inputs
+     (list go-github-com-google-go-cmp))
+    (propagated-inputs
+     (list go-github-com-itchyny-gojq
+           go-github-com-rogpeppe-go-internal
+           go-mvdan-cc-sh-v3))
+    (home-page "https://github.com/bitfield/script")
+    (synopsis "Making it easy to write shell-like scripts in Go")
+    (description
+     "Package script aims to make it easy to write shell-type scripts in Go,
+for general system administration purposes: reading files, counting lines,
+matching strings, and so on.")
+    (license license:expat)))
+
 (define-public go-github-com-bitly-go-hostpool
  (package
    (name "go-github-com-bitly-go-hostpool")
@@ -4433,6 +4521,34 @@ over strings.")
@code{https://en.wikipedia.org/wiki/WebP, WebP} images.")
    (license license:bsd-3)))

+(define-public go-github-com-chainguard-dev-clog
+  (package
+    (name "go-github-com-chainguard-dev-clog")
+    (version "1.8.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/chainguard-dev/clog")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0b95vw8czs2r9lscyi85vppbyqj672zm6z2n9siy1s9yv6fkys62"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/chainguard-dev/clog"))
+    (home-page "https://github.com/chainguard-dev/clog")
+    (synopsis "Context aware slog")
+    (description
+     "This package provides a context-aware Go std lib
+@url{https://pkg.go.dev/log/slog, @code{slog}}.  The context Logger can be
+used to use Loggers from the context.  This is sometimes preferred over the
+@url{https://github.com/chainguard-dev/clog#context-handler, Context Handler},
+since this can make it easier to use different loggers in different
+contexts (e.g. testing).")
+    (license license:asl2.0)))
+
 (define-public go-github-com-charlievieth-fastwalk
  (package
    (name "go-github-com-charlievieth-fastwalk")
@@ -8967,6 +9083,41 @@ sub-interfaces are also provided for cases where the full Channel interface
 cannot be met (for example, @code{InChannel} for write-only channels).")
    (license license:expat)))

+(define-public go-github-com-eapache-go-resiliency
+  (package
+    (name "go-github-com-eapache-go-resiliency")
+    (version "1.7.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/eapache/go-resiliency")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "07a1r3c2spd37k3riy4fxz8v8ibxiprf8a3vw788whz4mlp6gm40"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:skip-build? #t
+      #:import-path "github.com/eapache/go-resiliency"))
+    (home-page "https://github.com/eapache/go-resiliency")
+    (synopsis "Resiliency patterns for golang")
+    (description
+     "Resiliency patterns for golang.  Based in part on
+@url{https://github.com/Netflix/Hystrix, Hystrix},
+@@url{https://github.com/Shopify/semian, Semian}, and others.
+
+Currently implemented patterns include:
+@itemize
+@item circuit-breaker
+@item semaphore
+@item deadline/timeout
+@item batching
+@item retriable
+@end itemize")
+    (license license:expat)))
+
 (define-public go-github-com-eapache-queue
  (package
    (name "go-github-com-eapache-queue")
@@ -30438,8 +30589,8 @@ The yaml package supports most of YAML 1.2, but preserves some behavior from
 ;; to build NNCP and remove vendor) dependency for Golang.  Full build depends
 ;; on Bazel <https://bazel.build/>.
 (define-public go-gvisor-dev-gvisor
-  (let ((commit "634ce95eed8d5b8e6b3e2ea30542c34cb30af148")
-        (revision "0"))
+  (let ((commit "9414b50a5633100fd7299a5a7998742575dcb669")
+        (revision "1"))
    (package
      (name "go-gvisor-dev-gvisor")
      (version (git-version "0.0.0" revision commit))
@@ -30451,7 +30602,7 @@ The yaml package supports most of YAML 1.2, but preserves some behavior from
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
-          (base32 "1l3si6qlchwgsvaq6lxyvj8iq8n8pqxlayb1hbdf3pynxi52hfkw"))))
+          (base32 "0vqaclb2ignkcs7n463bj349m0xybdsv71i6afhzh8r05hdywzax"))))
      (build-system go-build-system)
      (arguments
       (list
--- a/gnu/packages/gpodder.scm
+++ b/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)
--- a/gnu/packages/graph.scm
+++ b/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)
--- a/gnu/packages/graphics.scm
+++ b/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")
--- a/gnu/packages/graphviz.scm
+++ b/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
--- a/gnu/packages/gtk.scm
+++ b/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
--- a/gnu/packages/guile-xyz.scm
+++ b/gnu/packages/guile-xyz.scm
@@ -6442,7 +6442,8 @@ external dependencies and can be a good base for other packages, like e.g.
     (list
      #:make-flags
      #~'("GUILE_AUTO_COMPILE=0")))
-    (inputs (list guile-3.0 guile-compose))
+    (inputs (list guile-3.0))
+    (propagated-inputs (list guile-compose))
    (native-inputs (list autoconf-2.72 automake pkg-config guile-3.0 texinfo))
    (synopsis "Web application middleware composition for Guile Scheme")
    (description
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -653,7 +653,10 @@ GNU@tie{}Guile.  Use the @code{(ice-9 readline)} module and call its
 (define (guile-variant-package-name prefix)
  (lambda (name)
    "Return NAME with PREFIX instead of \"guile-\", when applicable."
-    (if (string-prefix? "guile-" name)
+    (if (and (string-prefix? "guile-" name)
+
+             ;; Don't rename guile-bootstrap@2.0.
+             (not (string=? "guile-bootstrap" name)))
        (string-append prefix "-"
                       (string-drop name
                                    (string-length "guile-")))
@@ -900,8 +903,8 @@ type system, elevating types to first-class status.")
 (define-public guile-git
  (package
    (name "guile-git")
-    (version "0.11.0")
-    (home-page "https://gitlab.com/guile-git/guile-git.git")
+    (version "0.11.1")
+    (home-page "https://codeberg.org/guile-git/guile-git.git")
    (source (origin
              (method git-fetch)
              (uri (git-reference
@@ -910,11 +913,11 @@ type system, elevating types to first-class status.")
              (file-name (git-file-name name version))
              (sha256
               (base32
-                "1yjyil6z4k80pjdps8v6h6lxikwxmjxvrslf2jrmq2rrfnajschz"))))
+                "0xpzchnglddphi3chv53xqaz2x6rpq3l4s023w7r4mmndb6lgz0b"))))
    (build-system gnu-build-system)
    (arguments
     `(#:make-flags '("GUILE_AUTO_COMPILE=0")       ; to prevent guild warnings
-       ;; https://gitlab.com/guile-git/guile-git/-/issues/20
+       ;; https://codeberg.org/guile-git/guile-git/issues/20
       ,@(if (target-ppc32?)
           `(#:phases
             (modify-phases %standard-phases
@@ -922,20 +925,7 @@ type system, elevating types to first-class status.")
                 (lambda _
                   (substitute* "Makefile.am"
                     ((".*tests/blob\\.scm.*") ""))))))
-           '())
-       ,@(if (system-hurd?)
-             (list
-              #:phases
-              #~(modify-phases %standard-phases
-                  (add-after 'unpack 'skip-tests/hurd
-                    (lambda _
-                      (substitute* "tests/proxy.scm"
-                        (("\\(test-begin.*" all)
-                         (string-append
-                          all
-                          "(when (string-ci= \"GNU\" (vector-ref (uname) 0))\n"
-                          "  (test-skip 1))\n")))))))
-             '())))
+           '())))
    (native-inputs
     (list pkg-config autoconf automake texinfo guile-3.0 guile-bytestructures))
    (inputs
--- a/gnu/packages/hardware.scm
+++ b/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)
--- a/gnu/packages/ibus.scm
+++ b/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)
--- a/gnu/packages/image-processing.scm
+++ b/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)
--- a/gnu/packages/image-viewers.scm
+++ b/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)
--- a/gnu/packages/image.scm
+++ b/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
--- a/gnu/packages/instrumentation.scm
+++ b/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))
@@ -489,7 +489,7 @@ ftrace.")
 (define-public systemtap
  (package
    (name "systemtap")
-    (version "4.9")
+    (version "5.4")
    (source (origin
              (method url-fetch)
              (uri (string-append
@@ -497,20 +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/")
--- a/gnu/packages/irc.scm
+++ b/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)
--- a/gnu/packages/iso-codes.scm
+++ b/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))
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -8941,6 +8941,12 @@ generated sources by ANTLR.")))
          (add-after 'unpack 'chdir
            (lambda _
              (chdir "runtime/Python3")))
+          ;; TODO: Remove when updating ANTLR4:
+          ;; https://github.com/antlr/antlr4/pull/4593
+          (add-after 'chdir 'fix-python-3.12-compatibility
+            (lambda _
+              (substitute* "tests/TestIntervalSet.py"
+                (("assertEquals") "assertEqual"))))
          (add-after 'chdir 'regenerate-parsers
            (lambda _
              (invoke "antlr4" "-no-listener" "-Dlanguage=Python3"
--- a/gnu/packages/jupyter.scm
+++ b/gnu/packages/jupyter.scm
@@ -47,7 +47,6 @@
  #:use-module (guix git-download)
  #:use-module (guix build-system cmake)
  #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
  #:use-module (guix utils)
  #:use-module (gnu packages algebra)
  #:use-module (gnu packages bash)
@@ -177,8 +176,7 @@ simulation, statistical modeling, machine learning and much more.")
           python-hatchling
           python-ipyparallel-bootstrap
           python-pytest
-           python-pytest-asyncio-0.26  ;some tests fail with v1
-           python-pytest-cov
+           python-pytest-asyncio-0.26
           python-pytest-timeout))
    (home-page "https://ipython.org")
    (synopsis "IPython Kernel for Jupyter")
@@ -380,7 +378,7 @@ the namespace @code{/nbclassic/}.")
    (build-system pyproject-build-system)
    (arguments
     (list
-      ;; tests: 307 passed, 7 skipped, 16 deselected, 9 warnings
+      ;; tests: 305 passed, 7 skipped, 18 deselected, 2696 warning
      #:test-flags
      '(list "-k" (string-append
                   ;; TODO: This tests fails because nbconvert does not
@@ -396,6 +394,12 @@ the namespace @code{/nbclassic/}.")
                   ;; tornado.simple_httpclient.HTTPTimeoutError: Timeout
                   ;; during request
                   " and not test_connections")
+        ;; AttributeError: 'TestContentsManager' object has no attribute
+        ;; 'assertDictContainsSubset'
+        (string-append "--deselect=notebook/services/contents/tests/"
+                       "test_manager.py::TestContentsManager::test_get")
+        (string-append "--deselect=notebook/services/contents/tests/"
+                       "test_manager.py::TestContentsManagerNoAtomic::test_get")
        ;; These tests require a browser.
        "--ignore=notebook/tests/selenium")
      #:phases
@@ -440,15 +444,12 @@ the namespace @code{/nbclassic/}.")
           python-tornado
           python-traitlets))
    (native-inputs
-     (list python-coverage
-           python-jupyter-server
+     (list python-jupyter-server
           python-nbval
           python-pytest
-           python-pytest-cov
           python-requests
           python-requests-unixsocket2
-           python-setuptools
-           python-wheel))
+           python-setuptools))
    (home-page "https://jupyter.org/")
    (synopsis "Web-based notebook environment for interactive computing")
    (description
@@ -987,7 +988,6 @@ the JupyterLab CSS variables.")
           python-openapi-spec-validator
           python-pytest
           python-pytest-console-scripts
-           python-pytest-cov
           python-pytest-jupyter
           python-pytest-timeout
           python-requests-mock
@@ -1239,7 +1239,6 @@ are interactive HTML widgets for Jupyter notebooks and the IPython kernel.")
    (native-inputs (list python-ansi2html
                         python-hatchling
                         python-pytest-console-scripts
-                         python-pytest-cov
                         python-pytest-xdist
                         python-tornado))
    (home-page "https://github.com/jupyterlite/jupyterlite")
@@ -1345,7 +1344,6 @@ and a default CommManager that can be used.")
           python-flaky
           python-pytest
           python-pytest-asyncio
-           python-pytest-cov
           python-testpath
           python-xmltodict))
    (home-page "https://jupyter.org")
@@ -1648,7 +1646,6 @@ Docker registry.")
     (list python-jupyter-packaging
           python-nbval
           python-pytest
-           python-pytest-cov
           python-setuptools))
    (home-page "https://github.com/vidartf/ipydatawidgets")
    (synopsis "Widgets to help facilitate reuse of large datasets across widgets")
@@ -1660,7 +1657,7 @@ datasets across widgets.")
 (define-public python-papermill
  (package
    (name "python-papermill")
-    (version "2.6.0")
+    (version "2.7.0")
    (source
     (origin
       (method git-fetch)
@@ -1669,26 +1666,25 @@ datasets across widgets.")
              (commit version)))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1i5zikvl9inficryqfz0v885v24pcs78cj5nzyjw0x232kxbj41p"))))
+        (base32 "0lafh4lazx4rc3ly746bjflmihkzf9rhp788bni1l4vq12ks6a49"))))
    (build-system pyproject-build-system)
    (arguments
     (list
-      ;; tests: 500 passed, 3 skipped, 2 deselected, 29 warnings
+      ;; tests: 503 passed, 2 deselected, 226 warnings
      #:test-flags
      ;; Do not bother testing Azure, AWS, and Google Cloud features.
      #~(list "--ignore=papermill/tests/test_abs.py"
              "--ignore=papermill/tests/test_adl.py"
              "--ignore=papermill/tests/test_gcs.py"
              "--ignore=papermill/tests/test_s3.py"
-              ;; AssertionError
-              #$@(map (lambda (test) (string-append "--deselect="
-                                                    "papermill/tests/"
-                                                    "test_execute.py::"
-                                                    test))
-                      (list "TestBrokenNotebook2::test"
-                            "TestOutputFormatting::test_output_formatting")))))
+              #$@(map (lambda (ls)
+                        (string-append "--deselect=papermill/tests/"
+                                       (string-join ls "::")))
+                      ;; AssertionError: 'error' != 'display_data'
+                      '(("test_execute.py" "TestBrokenNotebook2" "test")
+                        ;; NameError: name 'FileSelector' is not defined
+                        ("test_hdfs.py" "HDFSTest" "test_hdfs_listdir"))))))
    (propagated-inputs (list python-aiohttp
-                             python-ansicolors
                             python-click
                             python-entrypoints
                             python-nbclient
--- a/gnu/packages/libffi.scm
+++ b/gnu/packages/libffi.scm
@@ -45,7 +45,6 @@
  #:use-module (gnu packages sphinx)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system pyproject)
-  #:use-module ((guix build-system python) #:select (pypi-uri))
  #:use-module (guix build-system ruby))

 (define-public libffi
--- a/gnu/packages/libreoffice.scm
+++ b/gnu/packages/libreoffice.scm
@@ -35,7 +35,6 @@
  #:use-module (guix build-system cmake)
  #:use-module (guix build-system glib-or-gtk)
  #:use-module (guix build-system gnu)
-  #:use-module (guix build-system python)
  #:use-module (guix build-system pyproject)
  #:use-module (guix gexp)
  #:use-module (guix download)
--- a/gnu/packages/librewolf.scm
+++ b/gnu/packages/librewolf.scm
@@ -125,14 +125,14 @@
  ;; ex:
  ;; tar xf /gnu/store/...-firefox-123.4.source.tar.xz -O \
  ;;     firefox-123.4/browser/locales/l10n-changesets.json | grep revision
-  (let ((commit "0245ffb160688061f0e0c67ea488bcdfdacbeca4"))
+  (let ((commit "fefe280d909d0eee8d60edd2a6db7d969df56c5b"))
    (origin
      (method git-fetch)
      (uri (git-reference
            (url "https://github.com/mozilla-l10n/firefox-l10n.git")
            (commit commit)))
      (file-name (git-file-name "firefox-l10n" commit))
-      (sha256 (base32 "0y8xdxql04yys0wj685v4yp3kmx1ivnndg6z11vam8vszh0j7ak6")))))
+      (sha256 (base32 "0z1ksvspbn4bbzxdl2w4x7bg36j4rwhaby8g37apg4393frh558i")))))

 (define* (make-librewolf-source #:key version firefox-hash librewolf-hash l10n)
  (let* ((ff-src (firefox-source-origin
@@ -205,7 +205,8 @@
       (search-patches
        "librewolf-compare-paths.patch"
        "librewolf-use-system-wide-dir.patch"
-        "librewolf-add-store-to-rdd-allowlist.patch"))
+        "librewolf-add-store-to-rdd-allowlist.patch"
+        "librewolf-150.0-encoding_rs-rust-fix.patch"))
      ;; Slim down the tarball by removing unbundled libraries and 75 Mo (800+
      ;; Mo uncompressed) of unused tests.
      ;; TODO: Unbundle security/nss and media/libpng.
@@ -244,17 +245,17 @@
 ;; It's used for cache validation and therefore can lead to strange bugs.
 ;; ex: date '+%Y%m%d%H%M%S'
 ;; or: (format-time-string "%Y%m%d%H%M%S")
-(define %librewolf-build-id "20260409162101")
+(define %librewolf-build-id "20260421153818")

 (define-public librewolf
  (package
    (name "librewolf")
-    (version "149.0.2-2")
+    (version "150.0-1")
    (source
     (make-librewolf-source
      #:version version
-      #:firefox-hash "1kkhg3lgyakinn5ankxrlxbf39wi61mqbhwrj1l4q5l7y0n1m4va"
-      #:librewolf-hash "1bai8g2kc9snck2f724al29q6r57vkj3d7v58rf0mgzpqzvwnw5f"
+      #:firefox-hash "151rxzl80dm8jsxl6fwzgbirwq4zpms5adwwnbjcwdd1r3s3vr7v"
+      #:librewolf-hash "0iw9v3zc1fxc93yyhldqarxaypgmbndh2ylsy330kcbpb6p1gnmr"
      #:l10n firefox-l10n))
    (build-system gnu-build-system)
    (arguments
@@ -352,18 +353,18 @@
                             (cdr pref)))
                   `(("extensions.getAddons.search.browseURL"
                      ,(string-append
-                        "https://gnuzilla.gnu.org/mozzarella/"
+                        "https://gnuzilla.gnu.org/"
                        "search.php?q=%TERMS%"))
                     ("extensions.getAddons.get.url" .
-                      "https://gnuzilla.gnu.org/mozzarella")
+                      "https://gnuzilla.gnu.org")
                     ("extensions.getAddons.link.url" .
-                      "https://gnuzilla.gnu.org/mozzarella")
+                      "https://gnuzilla.gnu.org")
                     ("extensions.getAddons.discovery.api_url" .
-                      "https://gnuzilla.gnu.org/mozzarella")
+                      "https://gnuzilla.gnu.org")
                     ("extensions.getAddons.langpacks.url" .
-                      "https://gnuzilla.gnu.org/mozzarella")
+                      "https://gnuzilla.gnu.org")
                     ("lightweightThemes.getMoreURL" .
-                      "https://gnuzilla.gnu.org/mozzarella")))))))
+                      "https://gnuzilla.gnu.org")))))))
          (add-after 'patch-source-shebangs 'patch-cargo-checksums
            (lambda _
              (use-modules (guix build cargo-utils))
--- a/gnu/packages/libusb.scm
+++ b/gnu/packages/libusb.scm
@@ -43,7 +43,6 @@
  #: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 download)
  #:use-module (guix gexp)
  #:use-module (guix git-download)
@@ -532,7 +531,8 @@ broken iOS devices.")
    (inputs
     (list python))
    (native-inputs
-     (list autoconf automake libtool pkg-config python-cython-0)) ; to build Python bindings
+     (list autoconf automake libtool pkg-config
+           python-cython-0 python-setuptools)) ; to build Python bindings
    (home-page "https://libimobiledevice.org/")
    (synopsis "C library to handle Apple Property List files")
    (description "This package provides a small portable C library to handle
@@ -585,7 +585,7 @@ connections from and to iOS devices by connecting to a socket provided by a
    (inputs
     (list python))
    (native-inputs
-     (list pkg-config python-cython-0))
+     (list pkg-config python-cython-0 python-setuptools))
    (home-page "https://libimobiledevice.org/")
    (synopsis "Protocol library and tools to communicate with Apple devices")
    (description "libimobiledevice is a software library that talks the
--- a/gnu/packages/license.scm
+++ b/gnu/packages/license.scm
@@ -37,7 +37,6 @@
  #:use-module (gnu packages version-control)
  #:use-module (gnu packages web)
  #:use-module (guix build-system perl)
-  #:use-module (guix build-system python)
  #:use-module (guix build-system pyproject)
  #:use-module (guix download)
  #:use-module (guix gexp)
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -218,7 +218,6 @@
  #:use-module (guix build-system linux-module)
  #: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 trivial)
  #:use-module (guix deprecation)    ;for libcap/next
@@ -6652,10 +6651,7 @@ isolation or root privileges.")
    (inputs
     (list singularity))
    (native-inputs
-     (list python-pytest
-           python-pytest-runner
-           python-setuptools
-           python-wheel))
+     (list python-pytest python-setuptools python-wheel))
    (home-page "https://github.com/singularityhub/singularity-cli")
    (synopsis "Singularity Python client")
    (description "@code{python-spython} is a Python library to interact with
--- a/gnu/packages/lirc.scm
+++ b/gnu/packages/lirc.scm
@@ -24,7 +24,6 @@
  #:use-module (guix download)
  #:use-module (guix git-download)
  #:use-module (guix build-system gnu)
-  #:use-module (guix build-system python)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (gnu packages)
  #:use-module (gnu packages pkg-config)
--- a/Show More
+++ b/Show More