| Age | Commit message (Expand) | Author |
|---|
| 2024-05-05 | gnu: Add python-termcolor-1....* gnu/packages/python-xyz.scm (python-termcolor-1): New variable.
Change-Id: I1aca97b6b7976cb698131c3a0be73e4798bef6d6
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-pytest-shutil: Disable a test....* gnu/packages/python-check.scm (python-pytest-shutil)[build-system]: Use
pyproject-build-system.
[arguments]: Disable test_pretty_formatter.
Change-Id: I862320feab5b3c6e375bf652deced6a631dfc575
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-cleanlab: Update to 2.6.3....* gnu/packages/machine-learning.scm (python-cleanlab): Update to 2.6.3.
[arguments]: Disable tests that require "datasets" package; add phase
'remove-datasets.
Change-Id: I6af99e3e749a10515328db4874974a3504658352
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-termcolor: Update to 2.4.0....* gnu/packages/python-xyz.scm (python-termcolor): Update to 2.4.0.
[build-system]: Use pyproject-build-system.
[arguments]: Add 'fix-pyproject build phase.
[native-inputs]: Add python-hatch-vcs, python-hatchling, python-pytest, and
python-pytest-cov.
Change-Id: I1b824ca6f125305169c3f64f00dbacbeb77d0ed0
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-hicexplorer: Update to 3.7.4....* gnu/packages/bioinformatics.scm (python-hicexplorer): Update to 3.7.4.
[source]: Remove obsolete snippet.
[arguments]: Remove obsolete phase 'scipy-compatibility.
[propagated-inputs]: Replace python-cleanlab-1 with python-cleanlab.
Change-Id: Iac9a24cc4551b7d7e1d41d1f07a6db6d620b119e
| Ricardo Wurmus |
| 2024-05-05 | gnu: snakemake-5: Patch version string....* gnu/packages/python-xyz.scm (snakemake-5)[arguments]: Add phase
'patch-version.
Change-Id: I647625e9d26b2ee06274a0c5bb844ccb87035537
| Ricardo Wurmus |
| 2024-05-05 | gnu: snakemake-5: Make compatible with tabulate 0.9.0....* gnu/packages/python-xyz.scm (snakemake-5)[arguments]: Add phase
'tabulate-compatibility.
Change-Id: I0b0ddafe9c2da91dbe10a584eb6fa0a3d5d62e87
| Ricardo Wurmus |
| 2024-05-05 | gnu: snakemake: Fetch from git repository....* 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
| Ricardo Wurmus |
| 2024-05-05 | gnu: snakemake-7: Make compatible with tabulate 0.9.0....* gnu/packages/python-xyz.scm (snakemake-7)[arguments]: Add phase
'tabulate-compatibility.
Change-Id: Ie6b2a7d65bc76e3df7c3946ba4533b301f5a3610
| Ricardo Wurmus |
| 2024-05-05 | gnu: snakemake-6: Make compatible with tabulate 0.9.0....* gnu/packages/python-xyz.scm (snakemake-6)[arguments]: Add phase
'tabulate-compatibility.
Change-Id: I0471726e2000af76871e2542ed347cd1727bf0c9
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-jsonpickle: Update to 3.0.4....* 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
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-imbalanced-learn: Update to 0.12.2....* gnu/packages/machine-learning.scm (python-imbalanced-learn): Update to
0.12.2.
[native-inputs]: Remove python-numpydoc.
Change-Id: I8af0017f76d5ab3a2d55a96c0ace6be22d57fb66
| Ricardo Wurmus |
| 2024-05-05 | gnu: tadbit: Add R to inputs....* gnu/packages/bioinformatics.scm (tadbit)[inputs]: Add r-minimal.
Change-Id: I4929dd89ddd27b4fcbd8b3a00b8ab8f3586945d2
| Ricardo Wurmus |
| 2024-05-05 | gnu: tadbit: Patch for compatibility with latest scipy....* gnu/packages/bioinformatics.scm (tadbit)[arguments]: Add phase
'scipy-compatibility.
Change-Id: Ib25b9cde75f0505c347c4ff470e61f06fb162839
| Ricardo Wurmus |
| 2024-05-05 | gnu: tadbit: Update to 1.0.1-2.2838129....* gnu/packages/bioinformatics.scm (tadbit): Update to 1.0.1-2.2838129.
Change-Id: I2c220ae37cd196ca508d30aefc24938cce985527
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-cooler: Update to 0.9.3....* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.9.3.
Change-Id: I4b89d552a424e74f76cda0c527dc7b712b8c9f31
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-dask: Do not reference pyarrow_hotfix....* gnu/packages/python-xyz.scm (python-dask)[arguments]: Add 'patch-pyproject
phase.
Change-Id: Idd173b72b1467540c295224072f3740c7f42b0a8
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-dask: Disable some tests....* gnu/packages/python-xyz.scm (python-dask)[arguments]: Disable ORC tests and
those that fail due to differences in job id.
Change-Id: I272a77c8291b121b57b02750916f520b52185bbe
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-dask: Propagate python-dask-expr....* 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
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-umap-learn: Disable failing test....* gnu/packages/machine-learning.scm (python-umap-learn)[arguments]: Disable
one failing test.
Change-Id: Ic8f5f60f7d7bea0c24b417932daab3d54813d5fd
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-umap-learn: Update to 0.5.6....* gnu/packages/machine-learning.scm (python-umap-learn): Update to 0.5.6.
Change-Id: If05cf1a9c7ad1d9fd0439bc888983608d70aea75
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-pandas-stubs: Accept numpy 1.23....* gnu/packages/python-science.scm (python-pandas-stubs)[arguments]: Add phase
'relax-requirements.
Change-Id: I62e04574d53abd7d67068d08475522dd8989dcca
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-dask: Disable all tokenize tests....* gnu/packages/python-xyz.scm (python-dask)[arguments]: Ignore the test file.
Change-Id: Icbd4845361aa57c493f473ab87a15ade8a20a65f
| Ricardo Wurmus |
| 2024-05-05 | Revert "gnu: python-numpy: Update to 1.26.0."...numba cannot use numpy > 1.24.
This reverts commit 6b8efd211fbd619e80628d2a78f99c6afc18723e.
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-numpy: Update to 1.26.0....* 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
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-tabulate: Enable tests and fix version string....* gnu/packages/python-xyz.scm (python-tabulate)[arguments]: Enable tests.
[native-inputs]: Add python-pytest and python-setuptools-scm.
Change-Id: I14073151916fd637d83905c03e76b96c390db917
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-pandas-stubs: Update tests....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
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-scikit-bio: Update to 0.6.0....* 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
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-biom-format: Untangle from python-scikit-bio....* 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
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-anndata: Update to 0.10.7....* 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
| Ricardo Wurmus |
| 2024-05-05 | gnu: Add python-array-api-compat....* gnu/packages/python-xyz.scm (python-array-api-compat): New variable.
Change-Id: Ibfd701630b41f860c7ad4df57fd3624d9c5b7752
| Ricardo Wurmus |
| 2024-05-05 | gnu: Add python-awkward....* gnu/packages/python-xyz.scm (python-awkward): New variable.
Change-Id: Ie4f9b12d3662b9029f6e042f9c3a4d547073a6e7
| Ricardo Wurmus |
| 2024-05-05 | gnu: Add python-awkward-cpp....* gnu/packages/python-xyz.scm (python-awkward-cpp): New variable.
Change-Id: I68f7e314aa6b575eb7135aa5308c327d5f6bf3ea
| Ricardo Wurmus |
| 2024-05-05 | gnu: Add python-scikit-build-core....* gnu/packages/python-science.scm (python-scikit-build-core): New variable.
Change-Id: If234d19d720afe88f6893bdd36fcc4955a45c5d3
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-distributed: Update to 2024.4.2....* gnu/packages/python-science.scm (python-distributed): Update to 2024.4.2.
[propagated-inputs]: Add python-dask-expr.
[arguments]: Adjust tests.
Change-Id: I9d3b45d14ae052f3a5a5dec3587bc01d13e4b71f
| Ricardo Wurmus |
| 2024-05-05 | gnu: Add python-dask-expr....* gnu/packages/python-science.scm (python-dask-expr): New variable.
Change-Id: I691593ab713fe865c771aa68b5521c4c10cc58f6
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-partd: Update to 1.4.1....* gnu/packages/python-xyz.scm (python-partd): Update to 1.4.1.
[propagated-inputs]: Remove python-blosc.
Change-Id: I3aff28899339f9ffaa47b6f5c81e0e68ce660963
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-dask: Update to 2024.4.2....* gnu/packages/python-xyz.scm (python-dask): Update to 2024.4.2.
[arguments]: Disable a few tests.
Change-Id: I759ddee2ec49fbf74f368c3313f7215906b0e5a2
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-tables: Update to 3.7.0....* gnu/packages/python-xyz.scm (python-tables): Update to 3.7.0.
[propagated-inputs]: Add python-packaging and python-py-cpuinfo.
Change-Id: I8653bef9a07bb898933b249aad92ddb2b79b8d85
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-pyarrow: Build with ORC support....* gnu/packages/databases.scm (python-pyarrow)[propagated-inputs]: Add
apache-orc.
[arguments]: Set PYARROW_WITH_ORC variable.
Change-Id: Ic35cd1db75349ecb51d35815d710d8ca3a303b00
| Ricardo Wurmus |
| 2024-05-05 | gnu: apache-arrow: Build with ORC....* 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
| Ricardo Wurmus |
| 2024-05-05 | gnu: Add apache-orc....* gnu/packages/databases.scm (apache-orc): New variable.
Change-Id: I9e7df4a03a5d2f258ff44d9705f539f9fc925a99
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-pandas-stub: Update to 2.1.1.230928....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
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-tabulate: Update to 0.9.0....* gnu/packages/python-xyz.scm (python-tabulate): Update to 0.9.0.
[build-system]: Use pyproject-build-system.
Change-Id: If360e5be6433b35308b76bd1284bb6ddb74008e8
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-pandas-2: Fix version....* 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
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-scikit-learn: Update to 1.4.2....* 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
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-cython-3: Update to 3.0.8....* gnu/packages/python-xyz.scm (python-cython-3): Update to 3.0.8.
Change-Id: I9129a7837cefea0b95b0a3c3cdf73997d91f7484
| Ricardo Wurmus |
| 2024-05-05 | gnu: python-pyjanitor: Update to 0.27.0....* 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
| Ricardo Wurmus |
| 2024-05-05 | gnu: tadbit: Use G-expression....* gnu/packages/bioinformatics.scm (tadbit)[arguments]: Use G-expression.
Change-Id: I4fe4afc41eb3442f243b0e415ddcb363be36ce7f
| Ricardo Wurmus |
| 2024-05-05 | gnu: r-reticulate: Update to 1.36.1....* gnu/packages/cran.scm (r-reticulate): Update to 1.36.1.
Change-Id: I7119ca05b8411209c617be318806b3ff4bc3b530
| Ricardo Wurmus |
