gnu: python-liana-py: Update to 1.6.0.

* gnu/packages/bioinformatics.scm (python-liana-py): Update to 1.6.0.
  [arguments] <test-flags>: Skip more problematic tests. Adjust pathe
  for "--ignore" option.
  <phases>: Remove 'relax-requirements.
  [propagated-inputs]: Remove python-decoupler-py; add python-decoupler.
  [native-inputs]: Remove python-black, python-poetry-core, and
  python-pytest-cov; add python-hatchling.

Change-Id: Icfec6a217f828b5e68cccde88fc889b2ee3e32f3

gnu: Add python-decoupler.

This package is a successor of python-decoupler-py with reworked tests
and inputs. Project has changed the license from GPL3+ to BSD-3.

See: <https://github.com/scverse/decoupler/blob/main/CHANGELOG.md#200>

* gnu/packages/bioinformatics.scm (python-decoupler): New variable based
  on python-decoupler-py.
  [source] <url>: Fix permanent redirect.
  [arguments] <test-flags>: Rework skipped tests.
  <phases>: Remove 'relax-requirements.
  [propagated-inputs]: Remove python-ipython, python-matplotlib,
  python-nbsphinx, python-numpy, python-numpydoc, python-omnipath,
  python-scanpy, python-scikit-learn, python-skranger, and
  python-typing-extensions; add python-dcor, python-docrep,
  python-igraph, python-ipywidgets, python-marsilea, python-requests,
  python-session-info2, and python-xgboost.
  [native-inputs]: Remove python-poetry-core; add nss-certs-for-test,
  python-hatchling, python-gseapy, python-memory-profiler, and
  python-scanpy.
  [home-page]: Fix permanent redirect.
  [licenses]: Switch to bsd-3.

(python-decoupler-py): Deprecate package.

Change-Id: Ia517db074c7ac405408731c9a8cfe00e56b8107b

gnu: Add python-marsilea.

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

Change-Id: I2f02691e45c57783edbd3c4654fdf4f8bafafb17

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