gnu: python-ipywidgets: Update to 8.1.4.

* gnu/packages/python-xyz.scm (python-ipywidgets): Update to 8.1.4.
[build-system]: Switch pyproject-build-system.
[native-inputs]: Remove python-pytest-cov and python-setuptools-67; add
python-setuptools.

Change-Id: I09799c7cbcc5c59a04a792411977974c95d1688e
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-jupyterlab-widgets: Update to 3.0.12.

* gnu/packages/jupyter.scm (python-jupyterlab-widgets): Update to 3.0.12.

Change-Id: I934b1f4d3a9458821fbdcffb96ec663c7d315131
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-vaex-core: Update to 4.19.0.

* gnu/packages/python-science.scm (python-vaex-core): Update to 4.19.0.
[inputs]: Remove pybind11.
[propagated-inputs]: Remove python-click, python-progressbar2, python-pydantic-settings,
and python-requests; add python-diskcache, python-fsspec,
python-graphviz, python-h5py, python-httpx, python-psutil, and
python-s3fs.
[native-inputs]: Remove python-pytest and python-wheel; add pybind11.

Change-Id: Id9f65420d6be54e27ba850528c3fc3599696f320
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: htseq: Update to 2.0.9.

* gnu/packages/bioinformatics.scm (htseq): Update to 2.0.9.
[propagated-inputs]: Remove python-matplotlib.
[native-inputs]: Remove python-wheel; add python-matplotlib.

Change-Id: I026cd0ecf01418b4c112b8d0f2f6c0ab709c38d7
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-coolbox: Update to 0.3.9.

* gnu/packages/bioinformatics.scm (python-coolbox): Update to 0.3.9.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments] <tests?, test-flags>: Enable them.
<phases>: Delete 'sanity-check.
[inputs]: Remove pybind11.
[propagated-inputs]: Remove python-pybbi, python-pytest, and
python-termcolor.
[native-inputs]: Add pybind11, python-pytest, python-pypairix,
python-pybbi, python-setuptools, and samtools.

Change-Id: I356fa043a18e7901e50b15f2815f84178cf4e969
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-cooler: Update to 0.10.4.

* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.10.4.
[arguments] <phases>: Add 'fix-pytest-config.
[propagated-inputs]: Remove python-pypairix; add python-ipywidgets,
python-matplotlib, and python-psutil.
[native-inputs]: Remove python-coverage, python-isort, and
python-pytest-cov.

Change-Id: I61157064630416c599f05639ddcd21c6ace8cefb
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-circe: Update to 0.3.9.

* gnu/packages/bioinformatics.scm (python-circe): Update to 0.3.9.
[source] <uri>: Use direct URL string.
[arguments] <tests?, test-flags>: Enable them.
[inputs]: Add python-numpy-1.
[propagated-inputs]: Remove python-numpy; add python-attrs.
[native-inputs]: Add python-pytest.
[home-page]: Move above synopsis.

Change-Id: Ia4e7a18c3225b1134b71ba33c369429bc4c01305
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-scanpy: Update to 1.11.5.

* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.11.5.
[arguments] <test-flags>: Rework skipped tests.
<phases>: Remove 'patch-version-check and 'add-anndata-source.
[propagated-inputs]: Remove python-pytoml, python-sinfo,
and python-tables; add python-numpy, python-pynndescent, and
python-typing-extensions.
[native-inputs]: Remove (package-source python-anndata), python-flaky,
python-flit, python-leidenalg, python-pytest-nunit, and
python-scanorama; add python-dependency-groups, python-pytest-randomly,
and python-pytest-rerunfailures.

Change-Id: I7a9a18434ddf3cca4d34a7909cce22ef86ffa054
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-statsmodels: Update to 0.14.5.

* gnu/packages/statistics.scm (python-statsmodels): Update to 0.14.5.

Change-Id: I071c163f68f0171d16c1fe9be85783c4d00bfca3
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-biopython: Update to 1.86.

* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.86,
use G-Expressions.
[arguments] <phases>: Remove 'numpy-compatibility.
[native-inputs]: Remove python-wheel.

Change-Id: I060455d474934b6b09c5adbbdec213b89496d9a5
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-fbpca: Fix tests.

* gnu/packages/python-science.scm (python-fbpca)[arguments]
<test-flags>: Skip one test.

Change-Id: I98ea94a1986e465ad41e6d0099ad4a1f45506c8e
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pandera: Update to 0.27.1.

* gnu/packages/python-science.scm (python-pandera): Update to 0.27.1.
[arguments] <test-flags>: Rework skipped tests.

Change-Id: I7a21aa0e343cdf726e9d2c677bfccb0041dac39a
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: pyscenic: Add missing python-diptest.

* gnu/packages/bioinformatics.scm (pyscenic):
[propagated-inputs]: Add python-diptest.

Change-Id: I4871895c22e08bcdc442b7edc99c07fd796bc245
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-diptest.

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

Change-Id: I7104617dfb182b85494febe2a483c7681cdb5929
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-scikit-bio: Update to 0.7.1.post1.

* gnu/packages/bioinformatics.scm (python-scikit-bio): Update to 0.7.1.post1.
[arguments] <test-backend, test-flags>: Use 'custom, run all tests.
<phases>: Remove 'build-extensions; use default 'check; add
'remove-local-source.
[propagated-inputs]: Remove python-hdmedians; add
python-array-api-compat, python-patsy, and python-statsmodels.
[native-inputs]: Remove python-coverage; add python-cython and
python-setuptools.

Change-Id: I460ba8dd7362f5d4bbf16a5923403ecbf5fc2026
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: endgame-singularity: Update to 1.1.

* gnu/packages/games.scm (endgame-singularity): Update to 1.1.

Change-Id: I8ff76a4e11ab949ad9576f14f74164dd567c6347
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-biom-format: Update to 2.1.17.

* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.17.
[source] <snippet>: Remove redundant logic.
[arguments] <test-flags>: Only skip some doctest requiring Nose test
runner.
<phases>: Remove 'use-cython, 'build-extensions, and
'pandas-compatibility; add 'remove-local-source.
[propagated-inputs]: Remove python-flake8 and python-future.
[native-inputs]: Remove python-pytest-cov and python-wheel; add
python-setuptools.

Change-Id: Ib497f771e5de40b07df4964ebcddf6c40c15fc85
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-anndata-minimal.

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

Change-Id: I9503ac08d0fa630d748574bb121690144a80bfea
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-anndata: Update to 0.12.7.

* gnu/packages/python-science.scm (python-anndata): Update to 0.12.7.
[arguments] <test-flags>: Skip CUDA dependent tests.
[phases]{set-version}: Remove setting zip timestamp logic.
[propagated-inputs]: Remove python-importlib-metadata,
python-scikit-learn, and python-setuptools; add python-numpy.
[native-inputs]: Add hdf5, python-openpyxl, python-pyarrow,
python-pytest-randomly, and python-scikit-learn.

Change-Id: I8e68cf85d435a13db995ea966ed5ff9edac3d672
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-awkward: Update to 2.8.5.

* gnu/packages/python-xyz.scm (python-awkward): Update to 2.8.5.
[arguments] <test-flags>: Skip CUDA tests only.
[propagated-inputs]: Remove python-typing-extensions.
[home-page]: Refresh it as seen in project's README.

Change-Id: I5cebada2be766618633b0d082c88ae3d15490e9f
Signed-off-by: Rutherther <rutherther@ditigal.xyz>