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>

gnu: python-pyte: Update to 0.8.2.

* gnu/packages/terminals.scm (python-pyte): Update to 0.8.2.

Change-Id: I6255a5598d86cb02f74c36c393e58d09f6a9b9a9
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-rchitect: Update to 0.4.8.

* gnu/packages/statistics.scm (python-rchitect): Update to 0.4.8.

Change-Id: If96584dc8ebec144ddb2ea9c0743b5ec36105abf
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-py2bit: Update to 0.3.3.

* gnu/packages/bioinformatics.scm (python-py2bit): Update to 0.3.3.
[native-inputs]: Add python-setuptools-scm.

Change-Id: Ib7e9d701595501e5da76288e5a8cae32e1dc6739
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-radian: Update to 0.6.15.

* gnu/packages/statistics.scm (python-radian): Update to 0.6.15.

Change-Id: Ic0b3227884ff7fef0b9b9a3b166da14ddc90dcb3
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-pyro-api: Switch to pyproject.

* gnu/packages/machine-learning.scm (python-pyro-api):
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-setuptools, python-wheel.

Change-Id: Iab866450e9ab7104ecba8ff21bf34e8a4226e1b2
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-pytest-isort: Switch to pyproject.

* gnu/packages/python-check.scm (python-pytest-isort):
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]: Remove them.
[native-inputs]: Add python-poetry-core.
[home-page]: Refresh.

Change-Id: I712fcdd2bb659b5f9d2a8fbfca2d8cd0d2cdb127
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-pyte: Switch to pyproject.

* gnu/packages/terminals.scm (python-pyte):
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]: Remove them.
[native-inputs]: Add python-setuptools, python-wheel.  Remove
python-pytest-runner.

Change-Id: I6467cc03b9d71de5a5b70f39def7f409a64bdfce
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-asyncmy: Update to 0.2.10.

* gnu/packages/databases.scm (python-asyncmy): Update to 0.2.10.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:tests?>: Disable them for now.
<#:phases>: Replace 'check phase. Add a 'cleanup phase.
[native-inputs]: Add mysql, python-poetry-core, python-pytest,
python-pytest-asyncio, python-setuptools, python-wheel.

Change-Id: I759a85d29372b0d50c2d8992ee303724b7462958
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>