gnu: python-pytensor: Update to 2.36.3. * gnu/packages/python-science.scm (python-pytensor): Update to 2.36.3. [arguments] <test-flags>: Add option to skip/disable benchmark tests and rework skipped tests. [native-inputs]: Add python-pytest-benchmark and python-pytest-xdist. Change-Id: I9c3c42c21091524741ccef55e4698b59e818512d Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-fastparquet: Update to 2025.12.0. * gnu/packages/databases.scm (python-fastparquet): Update to 2025.12.0. [arguments] <phases>: Remove 'relax-requirements,'pretend-version, and 'build-cython-extensions; add 'remove-dependencies-on-git, 'set-version and 'remove-local-source. [native-inputs]: Remove python-wheel. Change-Id: I808357310fbd78c1465d638788a3040ba2b8a452 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-pygam: Update to 0.12.0. * gnu/packages/bioinformatics.scm (python-pygam): Update to 0.12.0. [arguments] <test-flags>: Skip one test. <phases>: Remove 'patch-pyproject. [propagated-inputs]: Remove python-black, python-flake8, python-ipython, and python-poetry-core. [native-inputs]: Remove python-pytest-cov; add python-matplotlib and python-setuptools. Change-Id: I5b3b95deb2bbe455582d4c74fe672c62b9aa8ff4 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-pyemd: Use python-numpy@1. * gnu/packages/python-xyz.scm (python-pyemd): [propagated-inputs]: Remove python-numpy; add python-numpy-1. [native-inputs]: Remove python-wheel. Change-Id: I7cad3d609f1eec432d3e77945ffd2b2dc30b4900 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-pot: Update to 0.9.6.post1. * gnu/packages/machine-learning.scm (python-pot): Update to 0.9.6.post1. [arguments]: Drop all. [propagated-inputs]: Add python-cvxopt and python-matplotlib. [native-inputs]: Remove python-pytest-cov. Change-Id: I763bf521a30f1bd4067089133421239af160173c Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-pingouin: Fix tests. * gnu/packages/python-science.scm (python-pingouin): [arguments] <test-flags>: Rework skipped tests. <phases>: Add 'relax-requirements. [native-inputs]: Remove python-pytest-cov; add python-setuptools. Change-Id: If45e91fabbd479819731041c09dd6e1e561774d6 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-phenograph: Fix tests. * gnu/packages/bioinformatics.scm (python-phenograph): [arguments] <test-flags>: Skip 3 more tests. <phases>: Remove 'disable-leiden-test, and move logic to <#:test-flags>. [propagated-inputs]: Remove python-numpy; add python-numpy-1. [native-inputs]: Remove python-wheel. Change-Id: Id7a7cb67adb13749bde59ad93d5c1125f2903065 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-scikit-survival: Fix indentation. * gnu/packages/python-science.scm (python-scikit-survival): Fix indentation. Change-Id: Iff0ab38a0b484938613df08ffb0fbd83da489289 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-scikit-survival: Update to 0.26.0. * gnu/packages/python-science.scm (python-scikit-survival): Update to 0.26.0. [native-inputs]: Add python-pytest-xdist. Change-Id: If92ba627c894cb65976b7687062e738656b06e96 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: Remove python-dask-expr. * gnu/packages/python-science.scm (python-dask/bootstrap) (python-dask-expr): Delete variables. Fixes: guix/guix#4766 Change-Id: I8243329353fe41b0ffff35fd4383a9a09047cd52 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: openmm: Update to 8.4.0. * gnu/packages/machine-learning.scm (openmm): Update to 8.4.0. Change-Id: If91f5557966b7982b3504800d7761cc9b79b3af2 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: Remove fanc. * gnu/packages/bioinformatics.scm (fanc): Delete variable. Change-Id: I6ecb68155c021a67ff548bb2bd3bb6052676dc3a Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: Remove ginga-qt5. * gnu/packages/astronomy.scm (ginga-qt5): Delete variable. Change-Id: I86a926bd8af1a999780c64e4bd435238d7dd3c85 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: Remove python-webbpsf. * gnu/packages/astronomy.scm (python-webbpsf): Delete variable. Change-Id: I87374a9f04ad87eb940a9ad2751a217f779e5ea3 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: Remove python-watchgod. * gnu/packages/python-xyz.scm (python-watchgod): Delete variable. Change-Id: I52cbd0577de38bb21094ed8f6ee5ef14741634e0 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: Remove python-statannot. A message from upstream: "This repository is not maintained anymore. I recommend using the forked package trevismd/statannotations, which has a cleaner API and further extends the functionalities of statannot." * gnu/packages/python-science.scm (python-statannot): Delete variable. Fixes: guix/guix#5355 Change-Id: Ib3347ff2077f62d4e97c0f9dc437b419d260c4b5 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-perfplot: Use python-numpy@1. * gnu/packages/python-xyz.scm (python-perfplot): [propagated-inputs]: Remove python-numpy; add python-numpy-1. Change-Id: Ib7ea70587df75876a01e44899b7aebdd121f19fb Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-peaks2utr: Use python-numpy@1. * gnu/packages/bioinformatics.scm (python-peaks2utr): [propagated-inputs]: Remove python-numpy; add python-numpy-1. Change-Id: I9aacc181e7fd2330c7ed46f14902701aba843fe8 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-pandapower: Update to 3.3.0. * gnu/packages/engineering.scm (python-pandapower): Update to 3.3.0. [source]: Switch to git-fetch. [arguments] <test-flags>: Run tests in parallel, supported by upstream. <phases>: Add 'relax-requirements. [propagated-inputs]: Add python-pandera, python-geopandas, python-lxml, python-matplotlib, python-openpyxl, python-pyproj, and python-shapely. [native-inputs]: Remove python-pyproj, python-wheel, and unzip; add python-nbmake and python-pytest-xdist. Change-Id: I26e0f5ab3efa299beb1acf6ced4dfa3d15f7df3f Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-deepdiff: Update to 8.6.1. * gnu/packages/python-xyz.scm (python-deepdiff): Update to 8.6.1. [native-inputs]: Add python-uuid6. Change-Id: Ife7367c5772c8bba067e698f01b974cf2bfb4bfb Signed-off-by: Rutherther <rutherther@ditigal.xyz>