gnu: python-numpoly: Update to 1.3.4. * gnu/packages/python-science.scm (python-numpoly): Update to 1.3.4. [arguments] <test-flags>: Skip one test. [native-inputs]: Remove python-wheel; add python-cython. Change-Id: I62142fd288ccfbc6506ed44d054b25af801a6b16 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-pyudev: Update to 0.24.4. * gnu/packages/admin.scm (python-pyudev): Update to 0.24.4. [source]: Switch to git-fetch for tests. [build-system]: Switch to pyproject-build-system. [arguments]: Use gexps. <#:tests?>: Enable tests. <#:test-flags>: Disable tests that need /sys/devices. <#:phases>: Update 'patch-ctypes-udev phase. [propagated-inputs]: Remove python-six. [native-inputs]: Remove python-docutils, python-hypothesis, python-mock, and python-sphinx; add python-setuptools. Change-Id: I70834b09e280ef52c621b2a98455a8b7897f4367 Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com> Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-plotly: Update to 5.24.1. * gnu/packages/python-science.scm (python-plotly): Update to 5.24.1. [arguments] <test-flags>: Rework skipped tests. [propagated-inputs]: Remove python-ipython, python-pandas, python-pillow, python-requests, python-retrying, python-scikit-image, python-statsmodels, and python-vaex-core; add python-packaging. [native-inputs]: Add python-geopandas, python-ipykernel, python-ipython-minimal, python-matplotlib, python-numpy-1, python-orjson, python-pandas, python-pillow, python-psutil, python-pyshp, python-pytz, python-requests, python-retrying, python-scikit-image, python-scipy, python-shapely, python-statsmodels, python-tenacity, and python-vaex-core. Change-Id: Ib9c80494d708627f4c0b30a18b4ddf53a33484ce Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: Add python-array-api-strict. * gnu/packages/python-xyz.scm (python-array-api-strict): New variable. Change-Id: Iab9649b967da898521316481ac466342afff2631 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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>