gnu: Add python-legendkit.

* gnu/packages/python-science.scm (python-legendkit): New variable.

Change-Id: I98f9eb01b9162dec907b7b4a7423d718e2437fdd

gnu: Add python-dcor.

* gnu/packages/statistics.scm (python-dcor): New variable.

Change-Id: I87d8562b9e0cc3a6d2faf28f38c8d9b3f757c618

gnu: python-scanpy: Update to 1.11.2.

* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.11.2.
  [arguments] <test-flags>: Run tests in parallel, supported
  upstream. Skipp some more problematic tests.
  <phases>: Remove 'set-numba-cache-dir; add combined 'pre-check.
  [propagated-inputs]: Remove python-session-info; add python-session-info2.
  [native-inputs]: Add python-flaky, python-pytest-xdist, and python-scanorama.

Change-Id: I6a13a7c3449b0d60801daf49e40e6f1fcc48f0c0

gnu: python-seaborn: Update to 0.13.2.

* gnu/packages/python-xyz.scm (python-seaborn): Update to 0.13.2.
  [arguments] <test-flags>: Run tests in parallel, supported upstream.
  [native-inputs]: Remove python-flake8, python-ipykernel,
  python-nbconvert, python-numpydoc, python-mypy, python-pytest-cov, and
  python-pyyaml.

Change-Id: Ie8df114f7b617a8c5ce0999242b47e84f8255fa6

gnu: python-statsmodels: Update to 0.14.4.

* gnu/packages/statistics.scm (python-statsmodels): Update to 0.14.4.
  [native-inputs]: Remove python-colorama, python-cython, python-flake8,
  python-isort, python-joblib, python-pytest, python-pytest-randomly,
  python-pytest-xdist, python-setuptools, and python-wheel; add
  python-cython-3 and python-setuptools-next.

Change-Id: I59164ed861224bfb8230686b2133639a7d1c649e

gnu: Add python-session-info2.

* gnu/packages/python-xyz.scm (python-session-info2): New variable.

Change-Id: I8773329702f7ef7c6c9a929317cc3d5295b8b507

gnu: Add python-hatch-docstring-description.

* gnu/packages/python-build.scm (python-hatch-docstring-description): New variable.

Change-Id: I859fbd0beb3a31c812c818caf0eabc75e55df9b8

gnu: blast+: Update to 2.17.0.

* gnu/packages/bioinformatics.scm (blast+): Update to 2.17.0.

Change-Id: I37b460e057b392a88934a03f9a41d2b445e08f20

gnu: java-cisd-jhdf5: Fix build with gcc@14.

* gnu/packages/java.scm (java-cisd-jhdf5): [phases]
{build-native-library}: Add "-Wno-error=implicit-function-declaration"
option to relax GCC strictness.

Change-Id: Icee8001a4908e9124b76bf1ffb27d2659868e32d

gnu: salmon: Update to 1.10.3, fix build.

* gnu/packages/bioinformatics.scm (salmon): Update to 1.10.3.
[inputs]: Update pufferfish sources.

Change-Id: Iba95cc2bc61bbd8bddd1c9b679c9705e260a1364

gnu: lmms: Fix build.

Fixes guix/guix#1802

* gnu/packages/music.scm (lmms) [arguments] <phases>: Add
'fix-carla-export.

Change-Id: I763418c78068388c76066a62b7bf9277afe3a355

gnu: r-voltron: Fix tests.

* gnu/packages/bioinformatics.scm (r-voltron): [inputs]: Add which.

Change-Id: Id16ef6a5810f592a349249f1327dc747db9a66b1

gnu: r-stringfish: Update to 0.17.0, fix build with gcc@14.

* gnu/packages/cran.scm (r-stringfish): Update to 0.17.0.
  [arguments] <phases>: Add 'use-system-tbb, and
  'relax-gcc-14-strictness.
  [inputs]: Add tbb-2020.

Change-Id: Ibb7b7fface988727b185763b47cf7074119088f0

gnu: r-hdf5dataframe: Update to 0.0.0-2.1e30e6b.

* gnu/packages/bioinformatics.scm (r-hdf5dataframe): Update to 0.0.0-2.1e30e6b.
[native-inputs]: Add r-testthat.

Change-Id: I4b7b933dd8fe668d03f3e04ccd78336b4efa7e5f

gnu: python-mudata: Update to 0.3.2.

* gnu/packages/bioinformatics.scm (python-mudata): Update to 0.3.2.

Change-Id: I60c2b5d16dd1afddafc5f06231d6c5bf28a4b20c

gnu: python-anndata: Update to 0.12.1.

* gnu/packages/python-science.scm (python-anndata): Update to 0.12.1.
  [arguments] <test-flags>: Rework ignored and skipped tests.
  [propagated-inputs]: Remove python-exceptiongroup and
  python-numcodecs; add python-legacy-api-wrap.
  [native-inputs]: Remove python-pytest-doctestplus, python-toml, and
  python-flit.

Change-Id: I46c46c73f3a232345cc029d79b1018290505f5af

gnu: python-zarr: Update to 2.18.7.

* gnu/packages/python-xyz.scm (python-zarr): Update to 2.18.7.
[native-inputs]: Remove python-pytest-doctestplus, python-sphinx,
python-sphinx-copybutton, python-sphinx-design, and
python-sphinx-issues.

Change-Id: I9db3ffe51bb9daba53b0759a4c6a5814ff285b83

gnu: python-case: Deprecate package.

* gnu/packages/python-check.scm (python-case): Deprecate variable.
* gnu/packages/python-xyz.scm (python-kombu, python-billiard,
python-celery)[native-inputs]: Remove python-case.

Change-Id: I98d19e88aa5b8fa2b47f347a4d0c958d71096e4e
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-case: Move to (gnu packages python-check).

* /gnu/packages/python-xyz.scm (python-case): Move from here…
* gnu/packages/python-check.scm (python-case): …to here.

Change-Id: I59379226031edbd4dc63c70f15725b488668d05c
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-curtsies: Update to 0.4.3.

* gnu/packages/terminals.scm (python-curtsies): Update to 0.4.3.

Change-Id: I516134ed9a3a02be805498f76b552a8ab1e4411d
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>