gnu: bonnie++: Fix build.

* gnu/packages/benchmark.scm (bonnie++): Fix build by switching to GCC 10.
[native-inputs]: Add gcc-10.

Change-Id: I222a8c14abab16481a9873432738eead9ae49d5d

gnu: trealla: Update to 2.84.12.

* gnu/packages/prolog.scm (trealla): Update to 2.84.12.

Change-Id: I38fabf1237e323fd7864062110b76ba5a4b75ba3

daemon: Fix compilation error while using Zig (LLVM)

* nix/libstore/build.cc (guestUID, guestGID): Rename to 'defaultGuestUID' and
'defaultGuestGID' respectively.
(initializeUserNamespace, DerivationGoal::startBuilder): Rename references to
variables accordingly.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: supertuxkart: Remove gcc@14 compatibility build phase.

gnu/packages/games.scm (supertuxkart)[arguments]{#:phases}:
remove 'gcc14 phase.

Change-Id: I4fddc2ebfa5a34f8589840874b410cb62bc01247
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: supertuxkart: Update to 1.5.

* gnu/packages/games.scm (%supertuxkart-version): Update to 1.5.
(supertuxkart-data)[version]: Update "commit" to 18621.
(supertuxkart)[native-inputs]: Add shaderc.

Change-Id: Ief59d2b31f0464d31cd1e958ee2c97d9df36687b
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

installer: Add Sway as an option in the Desktop environment page.

* gnu/installer/services.scm (%system-services): desktop-environment for sway
and its minimal companion packages.
* gnu/tests/install.scm (installation-target-desktop-os-for-gui-tests): Add
sway and its companion packages to operating-system packages.

Change-Id: I22f4cb67752ce1a15009680a1ba081fae129d45a
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

inferior: Fix cached-channel-instance utime call and return value.

This fixes a bug introduced in 529dce6e98c22f00052df231414bca4f86e02094 where
the utime procedure would just get a procedure rather than the actual file.

* inferior.scm (cached-channel-instance):
  Use (cached commit) let-bound to cached-directory instead as value
  to utime and return-value.

Fixes: guix/guix#4042
Change-Id: Ibe7fb78fa68292d70e3bbe4ab9234757510cc539
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: python-av: Re-enable deselected tests.

* gnu/packages/python-xyz.scm (python-av): Drop the deselection of
  Chapter and Packet side-data tests now that python-av-testdata provides
  the required samples; keep the dash IO exclusion.
  [arguments] <test-flags>: Update comment accordingly.
* gnu/packages/python-xyz.scm (python-av-testdata): Add the required FATE
  samples.

Change-Id: I0c3c35ffd37403dcbe3e698c1d9fe9f3c3b44f5c
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-torchmetrics: Update to 1.8.2.

* gnu/packages/machine-learning.scm (python-torchmetrics): Update to 1.8.2.
  [source]: Update hash.

Change-Id: I95df5598ae30528cae7c2c10d6695decb06647e7
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-botorch: Update to 0.16.0.

* gnu/packages/machine-learning.scm (python-botorch): Update to 0.16.0.
  [source]: Switch upstream URL to meta-pytorch; update hash.
  [arguments]: In #:test-flags, skip tests that mock
  fmin_l_bfgs_b_batched (not imported with SciPy<1.13):
  test_emsemble_map_saas, test_negative_fixed_features.  Also ignore
  test_community/ (requires optional 'pfns').
  [native-inputs]: Drop python-wheel.

Change-Id: I8249ef0730bd6f6849dc515fbafa8068bf0bfe9a
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-gpytorch: Update to 1.14.2.

* gnu/packages/machine-learning.scm (python-gpytorch): Update to 1.14.2.
  [source]: Update hash.
  [native-inputs]: Drop python-wheel.

Change-Id: Icd6ef2b964e17b918bbe92179e0803d4e001ec13
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-pgmpy: Skip flaky test_get_edges.

* gnu/packages/statistics.scm (python-pgmpy): Skip flaky test_get_edges.
  [arguments]: In #:test-flags, add "test_get_edges" to the pytest -k skip
  list.  Add a brief comment about the FileNotFoundError in tearDown removing
  missing 'dog_problem.xml'.
  [native-inputs]: Drop python-wheel.

Change-Id: I48609db063adb7d99c0813013fb95c049e874964
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-pot: Update to 0.9.6.

* gnu/packages/machine-learning.scm (python-pot): Update to 0.9.6.
  [source]: Switch to git-fetch (upstream tag).  Update hash.  Remove
  snippet for deleting 'ot/lp/emd_wrap.cpp'—not present in VCS source.
  [arguments]: Add test-flags to skip 'test_entropic_semirelaxed_gromov'
  (TypeError).
  [native-inputs]: Drop python-wheel; add python-pytest and
  python-pytest-cov.

Change-Id: I8932a58ad9b83fd9c82c21fbb7db23fb06336a64
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: onnxruntime: Skip exporter-dependent tests needing onnxscript.

* gnu/packages/machine-learning.scm (onnxruntime): Skip exporter-dependent
  tests needing onnxscript.
  [arguments]: Extend pytest ignore list to exclude exporter tests that
  require python-onnxscript (test_pytorch_export_contrib_ops.py and
  transformers parity/phi_vision tests).

Change-Id: I7fe48815fcbd53121049a3b61d43af636df2bffe
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-torchaudio: Skip additional TorchScript consistency tests.

* gnu/packages/machine-learning.scm (python-torchaudio): Extend pytest -k
  filter to exclude FrequencyMasking/TimeMasking/deemphasis/RNNTLoss
  TorchScript tests that fail with PyTorch 2.9.0.
  [native-inputs]: Drop python-wheel.

Change-Id: I87e4360cd3ebe433f5e5e508028872b8fdc294b7
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-pytorch: Update to 2.9.0.

* gnu/packages/machine-learning.scm (python-pytorch): Update to 2.9.0.
  [source]: Update hash.
  [arguments]: Add 'skip-pip-redirect' phase to avoid pip redirect in
  setup.py.  Extend concurrentqueue include fix to cover nativert.
  [native-inputs]: Add python-setuptools.

* gnu/packages/patches/python-pytorch-system-libraries.patch: Update for 2.9.0.

Change-Id: I26606949da3c36fe8d7b6933ec54cb2c347a1bb9
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: gloo: Update to 0.0.0-4.54cbae0.

* gnu/packages/machine-learning.scm (gloo): Update to commit
54cbae0d3a67fa890b4c3d9ee162b7860315e341.
[source]: Switch upstream URL to https://github.com/pytorch/gloo and update hash.

Change-Id: Ibbea0a6739dc658f9ae147641fe128650f1370b9
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: conda: Update to 25.9.1.

* gnu/packages/package-management.scm (conda): Update to 25.9.1. Use
G-Expressions, move all propagated-inputs to inputs, as it's a final
command.
[arguments] <test-flags>: Ignored test files are reworked to keep just
bare minimal of unit tests, more attention is required to resolve the
rest, rework skipped tests. Run test in parallel.
<phases>: Remove 'use-older-pytest, 'fix-ruamel-yaml-dependency, and
'create-version-file'; add 'fix-pytest-config,
'set-default-solver-to-classic, 'set-version, 'pre-check, and
'wrap-executable.
[inputs]: Add python-archspec, python-boltons, python-boto3,
python-charset-normalizer, python-conda-package-handling,
python-conda-content-trust, python-distro, python-frozendict,
python-jsonpatch, python-menuinst, python-packaging,
python-platformdirs, python-pluggy, python-pycosat, python-requests,
python-ruamel.yaml, python-setuptools, python-tqdm,
python-truststore, and python-zstandard.
[propagated-inputs]: Remove python-anaconda-client, python-boto3,
python-conda-package-handling, python-cytoolz, python-mock,
python-pluggy, python-pycosat, python-pytest, python-pyyaml,
python-requests, python-responses, python-ruamel.yaml-0.16,
python-tqdm, and zstd.
[native-inputs]: Remove python-coverage, python-pytest-cov, and
python-wheel; add nss-certs-for-test, patchelf, python-hatch-vcs,
python-anaconda-client, python-flask, python-hatchling,
python-importlib-resources, python-pexpect, python-pytest,
python-pytest-mock, python-pytest-rerunfailures, python-pytest-split,
python-pytest-xdist, python-responses, and python-werkzeug.

Fixes: guix/guix#3928
Change-Id: Ie8b463e1614d1477b169cf1cf4f94328f49fc4f2

gnu: Add python-pytest-split.

* gnu/packages/python-check.scm (python-pytest-split): New variable.

Change-Id: If5137abe8d1dd5f9cb6a8f93bd7e740cf5fcec94

gnu: Add python-conda-content-trust.

* gnu/packages/python-xyz.scm (python-conda-content-trust): New variable.

Change-Id: Icaca13dccb6cf161e2cf9ea1ed785c616f4dc22d