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2024-05-05gnu: snakemake-5: Make compatible with tabulate 0.9.0.Ricardo Wurmus
* gnu/packages/python-xyz.scm (snakemake-5)[arguments]: Add phase 'tabulate-compatibility. Change-Id: I0b0ddafe9c2da91dbe10a584eb6fa0a3d5d62e87
2024-05-05gnu: snakemake: Fetch from git repository.Ricardo Wurmus
* gnu/packages/python-xyz.scm (snakemake)[source]: Fetch from git repository to include tests. [arguments]: Enable tests; add 'pre-check phase. [build-system]: Use pyproject-build-system. [native-inputs]: Add git-minimal, python-wrapper, python-pytest, python-pandas, and python-requests-mock. Change-Id: I32e9d36752cc91eacb8f05138d969834dbbce817
2024-05-05gnu: snakemake-7: Make compatible with tabulate 0.9.0.Ricardo Wurmus
* gnu/packages/python-xyz.scm (snakemake-7)[arguments]: Add phase 'tabulate-compatibility. Change-Id: Ie6b2a7d65bc76e3df7c3946ba4533b301f5a3610
2024-05-05gnu: snakemake-6: Make compatible with tabulate 0.9.0.Ricardo Wurmus
* gnu/packages/python-xyz.scm (snakemake-6)[arguments]: Add phase 'tabulate-compatibility. Change-Id: I0471726e2000af76871e2542ed347cd1727bf0c9
2024-05-05gnu: python-jsonpickle: Update to 3.0.4.Ricardo Wurmus
* gnu/packages/python-web.scm (python-jsonpickle): Update to 3.0.4. [build-system]: Use pyproject-build-system. [arguments]: Use test-flags; add 'pre-check phase. [propagated-inputs]: Add python-importlib-metadata. [native-inputs]: Add python-bson, python-ecdsa, python-feedparser, python-pymongo, python-pytest, python-pytest-benchmark, python-pytest-cov, python-pytest-enabler, python-setuptools, python-setuptools-scm, python-simplejson, python-sqlalchemy, python-ujson, and tzdata-for-tests. Change-Id: I99e41ae2652ce02b090ee2b99a7b850a19b5f353
2024-05-05gnu: python-imbalanced-learn: Update to 0.12.2.Ricardo Wurmus
* gnu/packages/machine-learning.scm (python-imbalanced-learn): Update to 0.12.2. [native-inputs]: Remove python-numpydoc. Change-Id: I8af0017f76d5ab3a2d55a96c0ace6be22d57fb66
2024-05-05gnu: tadbit: Add R to inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (tadbit)[inputs]: Add r-minimal. Change-Id: I4929dd89ddd27b4fcbd8b3a00b8ab8f3586945d2
2024-05-05gnu: tadbit: Patch for compatibility with latest scipy.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (tadbit)[arguments]: Add phase 'scipy-compatibility. Change-Id: Ib25b9cde75f0505c347c4ff470e61f06fb162839
2024-05-05gnu: tadbit: Update to 1.0.1-2.2838129.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (tadbit): Update to 1.0.1-2.2838129. Change-Id: I2c220ae37cd196ca508d30aefc24938cce985527
2024-05-05gnu: python-cooler: Update to 0.9.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.9.3. Change-Id: I4b89d552a424e74f76cda0c527dc7b712b8c9f31
2024-05-05gnu: python-dask: Do not reference pyarrow_hotfix.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-dask)[arguments]: Add 'patch-pyproject phase. Change-Id: Idd173b72b1467540c295224072f3740c7f42b0a8
2024-05-05gnu: python-dask: Disable some tests.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-dask)[arguments]: Disable ORC tests and those that fail due to differences in job id. Change-Id: I272a77c8291b121b57b02750916f520b52185bbe
2024-05-05gnu: python-dask: Propagate python-dask-expr.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-dask/bootstrap): New variable. (python-dask)[propagated-inputs]: Add python-dask-expr. * gnu/packages/python-science.scm (python-dask-expr)[propagated-inputs]: Remove python-dask. [native-inputs]: Add python-dask/bootstrap. Change-Id: I1196641425421c7dde94c6fea8d573e78db9c402
2024-05-05gnu: python-umap-learn: Disable failing test.Ricardo Wurmus
* gnu/packages/machine-learning.scm (python-umap-learn)[arguments]: Disable one failing test. Change-Id: Ic8f5f60f7d7bea0c24b417932daab3d54813d5fd
2024-05-05gnu: python-umap-learn: Update to 0.5.6.Ricardo Wurmus
* gnu/packages/machine-learning.scm (python-umap-learn): Update to 0.5.6. Change-Id: If05cf1a9c7ad1d9fd0439bc888983608d70aea75
2024-05-05gnu: python-pandas-stubs: Accept numpy 1.23.Ricardo Wurmus
* gnu/packages/python-science.scm (python-pandas-stubs)[arguments]: Add phase 'relax-requirements. Change-Id: I62e04574d53abd7d67068d08475522dd8989dcca
2024-05-05gnu: python-dask: Disable all tokenize tests.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-dask)[arguments]: Ignore the test file. Change-Id: Icbd4845361aa57c493f473ab87a15ade8a20a65f
2024-05-05Revert "gnu: python-numpy: Update to 1.26.0."Ricardo Wurmus
numba cannot use numpy > 1.24. This reverts commit 6b8efd211fbd619e80628d2a78f99c6afc18723e.
2024-05-05gnu: python-numpy: Update to 1.26.0.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-numpy): Update to 1.26.0. [build-system]: Use pyproject-build-system. [arguments]: Move test flags to #:test-flags; add phase 'use-setuptools-backend. [native-inputs]: Remove gfortran; add replace python-cython with python-cython-3; add meson/newer and ninja. Change-Id: I783bbca58624bf6f047056ba21d838f5ecb09ac2
2024-05-05gnu: python-tabulate: Enable tests and fix version string.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-tabulate)[arguments]: Enable tests. [native-inputs]: Add python-pytest and python-setuptools-scm. Change-Id: I14073151916fd637d83905c03e76b96c390db917
2024-05-05gnu: python-pandas-stubs: Update tests.Ricardo Wurmus
This is a follow-up to adding ORC support to pyarrow. * gnu/packages/python-science.scm (python-pandas-stubs)[arguments]: Disable more tests that are due to enabling ORC support to pyarrow. Change-Id: I8c3ca6afff8128792738251c85a1dba3dc3b0569
2024-05-05gnu: python-scikit-bio: Update to 0.6.0.Ricardo Wurmus
* gnu/packages/patches/python-scikit-bio-1887.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove patch. * gnu/packages/bioinformatics.scm (python-scikit-bio): Update to 0.6.0. [source]: Remove patch. [arguments]: Disable skbio.diversity doctest; remove 'compatibility phase. [propagated-inputs]: Add python-biom-format; remove python-ipython and python-matplotlib. Change-Id: I9bd9e0fd72f5f1b80ef6ff61c52da5fd56a715ed
2024-05-05gnu: python-biom-format: Untangle from python-scikit-bio.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-biom-format)[arguments]: Add phase 'pandas-compatibility; disable tests that need sciki-bio. [propagated-inputs]: Remove python-scikit-bio. Change-Id: Ifd528d256a1c75962fb05aef5602edbf67a5af26
2024-05-05gnu: python-anndata: Update to 0.10.7.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-anndata): Update to 0.10.7. [arguments]: Patch conftest.py; adjust tests; remove old patch for version string; add phase 'set-numba-cache-dir. [native-inputs]: Add python-awkward, python-dask, python-distributed, python-hatchling, python-hatch-vcs, python-loompy, python-matplotlib, python-pytest-doctestplus, and python-pytest-xdist. [propagated-inputs]: Add python-array-api-compat and python-exceptiongroup. Change-Id: I3099cbfbb1865743c75d32243be9e5a59df1507d
2024-05-05gnu: Add python-array-api-compat.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-array-api-compat): New variable. Change-Id: Ibfd701630b41f860c7ad4df57fd3624d9c5b7752
2024-05-05gnu: Add python-awkward.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-awkward): New variable. Change-Id: Ie4f9b12d3662b9029f6e042f9c3a4d547073a6e7
2024-05-05gnu: Add python-awkward-cpp.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-awkward-cpp): New variable. Change-Id: I68f7e314aa6b575eb7135aa5308c327d5f6bf3ea
2024-05-05gnu: Add python-scikit-build-core.Ricardo Wurmus
* gnu/packages/python-science.scm (python-scikit-build-core): New variable. Change-Id: If234d19d720afe88f6893bdd36fcc4955a45c5d3
2024-05-05gnu: python-distributed: Update to 2024.4.2.Ricardo Wurmus
* gnu/packages/python-science.scm (python-distributed): Update to 2024.4.2. [propagated-inputs]: Add python-dask-expr. [arguments]: Adjust tests. Change-Id: I9d3b45d14ae052f3a5a5dec3587bc01d13e4b71f
2024-05-05gnu: Add python-dask-expr.Ricardo Wurmus
* gnu/packages/python-science.scm (python-dask-expr): New variable. Change-Id: I691593ab713fe865c771aa68b5521c4c10cc58f6
2024-05-05gnu: python-partd: Update to 1.4.1.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-partd): Update to 1.4.1. [propagated-inputs]: Remove python-blosc. Change-Id: I3aff28899339f9ffaa47b6f5c81e0e68ce660963
2024-05-05gnu: python-dask: Update to 2024.4.2.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-dask): Update to 2024.4.2. [arguments]: Disable a few tests. Change-Id: I759ddee2ec49fbf74f368c3313f7215906b0e5a2
2024-05-05gnu: python-tables: Update to 3.7.0.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-tables): Update to 3.7.0. [propagated-inputs]: Add python-packaging and python-py-cpuinfo. Change-Id: I8653bef9a07bb898933b249aad92ddb2b79b8d85
2024-05-05gnu: python-pyarrow: Build with ORC support.Ricardo Wurmus
* gnu/packages/databases.scm (python-pyarrow)[propagated-inputs]: Add apache-orc. [arguments]: Set PYARROW_WITH_ORC variable. Change-Id: Ic35cd1db75349ecb51d35815d710d8ca3a303b00
2024-05-05gnu: apache-arrow: Build with ORC.Ricardo Wurmus
* gnu/packages/databases.scm (apache-arrow)[arguments]: Set options needed to build with ORC support; remove unused options -DBENCHMARK_ENABLE_GTEST_TESTS=OFF and -DARROW_GLOG=ON. [inputs]: Add apache-orc. Change-Id: Icabe6e3a73478c8464ea1e8efc103899da8e5a86
2024-05-05gnu: Add apache-orc.Ricardo Wurmus
* gnu/packages/databases.scm (apache-orc): New variable. Change-Id: I9e7df4a03a5d2f258ff44d9705f539f9fc925a99
2024-05-05gnu: python-pandas-stub: Update to 2.1.1.230928.Ricardo Wurmus
This is a follow-up to commit ff2d0ecfca87450c82df8d74666261b1c19cbe66. * gnu/packages/python-science.scm (python-pandas-stub): Update to 2.1.1.230928. Change-Id: I2e8ce18bd25399b467a6ff2a6fb846f8bb969e4c
2024-05-05gnu: python-tabulate: Update to 0.9.0.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-tabulate): Update to 0.9.0. [build-system]: Use pyproject-build-system. Change-Id: If360e5be6433b35308b76bd1284bb6ddb74008e8
2024-05-05gnu: python-pandas-2: Fix version.Ricardo Wurmus
* gnu/packages/python-science.scm (python-pandas-2)[arguments]: Write version string to "_version.py", not "_version_meson.py" to avoid reporting the version as "0+unknown". Change-Id: I1a18814e37c023102714326bc8bd505705234205
2024-05-05gnu: python-scikit-learn: Update to 1.4.2.Ricardo Wurmus
* gnu/packages/machine-learning.scm (python-scikit-learn): Update to 1.4.2. [native-inputs]: Replace python-cython-0.29.35 with python-cython-3. Change-Id: Id8be08f931bf250a8ecb8bc46b44d7148b4c4a2f
2024-05-05gnu: python-cython-3: Update to 3.0.8.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-cython-3): Update to 3.0.8. Change-Id: I9129a7837cefea0b95b0a3c3cdf73997d91f7484
2024-05-05gnu: python-pyjanitor: Update to 0.27.0.Ricardo Wurmus
* gnu/packages/python-science.scm (python-pyjanitor): Update to 0.27.0. [arguments]: Disable a few more tests; add phase 'pandas-compat. Change-Id: Ia8891971a687342166f30ded11f9e341a208d95e
2024-05-05gnu: tadbit: Use G-expression.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (tadbit)[arguments]: Use G-expression. Change-Id: I4fe4afc41eb3442f243b0e415ddcb363be36ce7f
2024-05-05gnu: r-reticulate: Update to 1.36.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-reticulate): Update to 1.36.1. Change-Id: I7119ca05b8411209c617be318806b3ff4bc3b530
2024-05-05gnu: python-xarray: Disable tests that are known to fail.Ricardo Wurmus
* gnu/packages/python-science.scm (python-xarray)[arguments]: Disable two tests. Change-Id: I70954173e0aca5a377cf19476e9390a97febadc7
2024-05-05gnu: python-pandas: Default to version 2.x.Ricardo Wurmus
* gnu/packages/python-science.scm (python-pandas): Define as alias for python-pandas-2; rename existing definition to... (python-pandas-1): ...this new variable. Change-Id: If359e3b2d42c683d7d0152b1757bbc5a979c999b
2024-05-05gnu: python-scikit-opt: Add missing input.Ricardo Wurmus
* gnu/packages/python-science.scm (python-scikit-opt)[propagated-inputs]: Add python-pytorch. Change-Id: I037cc43bedeaebb05bf038c0bca72919f8c27c40
2024-05-05gnu: python-plastid: Replace nose with pytest.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-plastid)[native-inputs]: Replace python-nose with python-pytest. Change-Id: Ie0e5362d2304d3af0bcb1405fa0c1ad36fb2ace6
2024-05-05gnu: Add python-metacells.Marco Baggio
* gnu/packages/bioinformatics.scm (python-metacells): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net> Change-Id: I4fc760dc4317bde79c815f441ad0cc453248990a
2024-05-05gnu: Add python-cvxpy.Marco Baggio
* gnu/packages/python-science.scm (python-cvxpy): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net> Change-Id: I440ab3768cbc4e78364dc31cf9484effd9670f49
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