| Age | Commit message (Expand) | Author |
|---|
| 2024-01-16 | gnu: abjad-ext-ipython: Fix build....* gnu/packages/music.scm (abjad-ext-ipython): Fix build.
[propagated-inputs]: Add python-sphinx-autodoc-typehints.
Change-Id: Id20c0527e61b8be194c5387c6c43fdf82ab5ff09
| Sharlatan Hellseher |
| 2024-01-16 | gnu: python-deepdish: Fix build....* gnu/packages/python-science.scm (python-deepdish): Fix build.
[build-system]: Swap to pyproject-build-system.
[arguments]<#:test-flags>: Silent failing tests.
Change-Id: I4c4df66fc80434aaf5b95a7a62b83e0c1c02a4c6
| Sharlatan Hellseher |
| 2024-01-16 | gnu: Add samtools-1.14....* gnu/packages/bioinformatics.scm (samtools-1.14): New variable.
Change-Id: I0bd35b3865d7a417f55f1f768f7eb0c78a795e0f
| Ricardo Wurmus |
| 2024-01-16 | gnu: samtools: Update to 1.19....* gnu/packages/bioinformatics.scm (samtools): Update to 1.19.
[source]: Simplify snippet.
Change-Id: If0e02bbbc8e0443eb418c078dc47525f432d7ebe
| Ricardo Wurmus |
| 2024-01-16 | gnu: htslib: Update to 1.19....* gnu/packages/bioinformatics.scm (htslib): Update to 1.19.
Change-Id: I4d66d8ce37bfd335411a2acc6060f9a8c20c9e4a
| Ricardo Wurmus |
| 2024-01-16 | gnu: htscodecs: Update to 1.6.0....* gnu/packages/bioinformatics.scm (htscodecs): Update to 1.6.0.
Change-Id: Ibd5be30e8fbe7fe5d0ef494c1b1e0cd9ec3333cc
| Ricardo Wurmus |
| 2024-01-16 | gnu: Add python-prisma....* gnu/packages/databases.scm (python-prisma): New variable.
Change-Id: I7df9b5600fb49ef46a73678323bc29993f35fae2
| Ricardo Wurmus |
| 2024-01-16 | gnu: Add python-strenum....* gnu/packages/python-xyz.scm (python-strenum): New variable.
Change-Id: I6b6d64024db9358ea0a65cfd6c7cd6f94747de42
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-readpaf: Explicitly disable tests....* gnu/packages/bioinformatics.scm (python-readpaf)[arguments]: Disable tests.
Change-Id: I28ddfa46675b74bd5073c12e5d33bcbf9dee8252
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-pyls-black: Fix build....* gnu/packages/patches/python-pyls-black-41.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/python-xyz.scm (python-pyls-black)[source]: Add patch.
[build-system]: Use pyproject-build-system.
[arguments]: Disable one failing test.
Change-Id: I14b2982644e58c0b43d76838febc6dfceb220b15
| Ricardo Wurmus |
| 2024-01-16 | gnu: debian-ports-archive-keyring: Update to 2024.01.05....* gnu/packages/debian.scm (debian-ports-archive-keyring): Update to 2024.01.05.
Change-Id: Ibaa279a91d9e39804eb5cc1bf759ca3afd69e962
| Efraim Flashner |
| 2024-01-16 | gnu: debootstrap: Update to 1.0.134....* gnu/packages/debian.scm (debootstrap): Update to 1.0.134.
[arguments]: Remove obsolete substitution in 'patch-source phase.
Change-Id: I2a50ae75a43c0970e3ef866e02c49d87094e14eb
| Efraim Flashner |
| 2024-01-16 | gnu: gourmet: Add missing input....* gnu/packages/nutrition.scm (gourmet)[inputs]: Add python-toml.
Change-Id: I53bc9b0247c6dc32c5ec6e3cc518dbc982362bd2
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-pyrdfa3: Update to 3.6.2....* gnu/packages/rdf.scm (python-pyrdfa3): Update to 3.6.2.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom build phases.
[propagated-inputs]: Add python-requests.
Change-Id: Ie8a1a369a569d29c8f43248d03f024e6cc19c004
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-clingraph: Update to 1.1.2....* gnu/packages/potassco.scm (python-clingraph): Update to 1.1.2.
Change-Id: I5910853d39389ff9ad981543204fd8ef1445e495
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-astroml: Make compatible with recent Matplot and Scipy....* gnu/packages/astronomy.scm (python-astroml)[arguments]: Add phases
'matplotlib-compatibility and 'scipy-compatibility.
Change-Id: Id88cf769f705f9326f41f951403583155bcee58f
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-bbknn: Update to 1.6.0....* gnu/packages/bioinformatics.scm (python-bbknn): Update to 1.6.0.
[arguments]: Remove phase 'do-not-fail-to-find-sklearn.
[propagated-inputs]: Add python-pynndescent.
[native-inputs]: Add python-flit-core.
Change-Id: I5fca2d6ca52e54eb7650b3bb24a34a0aa47b1782
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-geopandas: Update to 0.14.2....* gnu/packages/geo.scm (python-geopandas): Update to 0.14.2.
[arguments]: Disable test_pandas_kind tests.
Change-Id: I2a49d6ef73a79b84751ce0225757a2b83019cd42
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-dask: Propagate click....* gnu/packages/python-xyz.scm (python-dask)[native-inputs]: Move python-click
from here...
[propagated-inputs]: ...to here.
Change-Id: I1a1617d9cb00268d9fc26f4fe6c9ecc6d0a2e375
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-xarray: Update to 2023.12.0....* gnu/packages/python-science.scm (python-xarray): Update to 2023.12.0.
[arguments]: Ignore one test file.
[propagated-inputs]: Add python-packaging.
Change-Id: I6b70f59670f7bc8b56787fe3436579db8ac113bb
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-telomerecat: Disable tests....* gnu/packages/bioinformatics.scm (python-telomerecat)[arguments]: Disable tests.
Change-Id: I0422ae1e563374a8cc408fc9584cfb7b0e880e95
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-mysql-connector-python: Defuse time bomb....Additional tests fail due to expired certificates. Disable them.
* gnu/packages/python-xyz.scm (python-mysql-connector-python)[arguments]:
Disable six additional tests.
Change-Id: I99b5f15736af89c0281ab7aca56c1bd3958d1a46
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-adjusttext: Disable tests....* gnu/packages/python-xyz.scm (python-adjusttext)[arguments]: Disable tests.
Change-Id: Ib1002de20a6e301f43bb34f64f7299d4316d8a67
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-scikit-bio: Update to 0.5.9....* gnu/packages/bioinformatics.scm (python-scikit-bio): Update to 0.5.9.
[source]: Add patch.
[arguments]: Disable one test via #:test-flags; adjust 'compatibility phase;
update 'check phase.
[propagated-inputs]: Remove python-cachecontrol, python-lockfile, and
python-scikit-learn; add python-requests.
* gnu/packages/patches/python-scikit-bio-1887.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
Change-Id: Ie57b0256cf695e5ea088545cd2102335303a93e7
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-pandas: Update to 1.5.3....* gnu/packages/python-science.scm (python-pandas): Update to 1.5.3.
[build-system]: Use pyproject-build-system.
[arguments]: Use G-expression; move test flags to #:test-flags; add phase
'patch-build-system; fix substitution of "which" executable; remove
'enable-parallel-build; remove custom 'check phase; add 'pre-check phase.
[propagated-inputs]: Add python-matplotlib.
[native-inputs]: Replace python-cython with python-cython-0.29.35.
Change-Id: I9d09971f707b925f469e29be67fe040c181314ff
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-click-default-group: Update to 1.2.4....* gnu/packages/python-xyz.scm (python-click-default-group): Update to 1.2.4.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-flit-core and python-pytest.
Change-Id: I7e617ee57499542b7e832bb5ea24417b70e8cf85
| Ricardo Wurmus |
| 2024-01-16 | gnu: datasette: Update to 1.0a7....* gnu/packages/databases.scm (datasette): Update to 1.0a7.
[propagated-inputs]: Add python-asyncinject and python-sqlite-utils.
Change-Id: If713cd0f115c8092f9cc200daa850f9a78a20f6b
| Ricardo Wurmus |
| 2024-01-16 | gnu: Add python-asyncinject....* gnu/packages/python-xyz.scm (python-asyncinject): New variable.
Change-Id: I2647e8340bca2efabc222d19155d330b1a5ff16f
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-metpy: Update to 1.6.0....* gnu/packages/geo.scm (python-metpy): Update to 1.6.0.
[arguments]: Add phases 'fix-version-check and 'hide-imp-deprecation-warnings.
[native-inputs]: Add python-packaging; remove python-shapely and
python-cartopy.
Change-Id: I4a46a5e60b1904699475608146f2a09aefc07624
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-pint: Add missing input....This is a follow-up to commit 23b8601cd2cf90ed11a51ca6db133083433e74d8.
Without this input the version string will be 0.0.0.
* gnu/packages/python-xyz.scm (python-pint)[native-inputs]: Add
python-setuptools-scm.
Change-Id: Id621e459f119d7268cdcc41ef93bcae135e842d1
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-hicexplorer: Make compatible with latest scipy....* gnu/packages/bioinformatics.scm (python-hicexplorer)[arguments]: Add
'scipy-compatibility phase.
Change-Id: I31e9058b7fd4ff9245837d5f1cd145b569ec35ad
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-hicmatrix: Update to 17.1....* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 17.1.
[arguments]: Remove.
Change-Id: I6b1230d703d0dc1a88ee61a84cc6cd95f7eeb6f9
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-scikit-optimize: Make compatible with latest sklearn....* gnu/packages/python-science.scm (python-scikit-optimize)[source]: Add
snippet to fix outdated use of "max_features" option.
Change-Id: I4272ffc82b4951315b74b4adee27527e8d513fca
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-fit-nbinom: Disable tests....* gnu/packages/python-xyz.scm (python-fit-nbinom)[arguments]: Disable tests.
Change-Id: I980480a3326dccc67930d34474832712005d1bb2
| Ricardo Wurmus |
| 2024-01-16 | gnu: scvelo: Make compatible with latest matplotlib....* gnu/packages/bioinformatics.scm (scvelo)[arguments]: Add phase
'matplotlib-compatibility.
Change-Id: Ia761821c8aa1e516525cff7c680db471a5908e5f
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-cartopy: Update to 0.22.0....* gnu/packages/geo.scm (python-cartopy): Update to 0.22.0.
[build-system]: Use pyproject-build-system.
[arguments]: Use G-expression; use #:test-flags; update list of disabled
tests; add phase 'remove-endpoint.
[propagated-inputs]: Add python-packaging; remove python-pykdtree.
[native-inputs]: Add python-coveralls and python-pytest-xdist; remove
python-flufl-lock.
Change-Id: I353fff0ceade648286ef552effdc35671032c62c
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-demuxem: Disable tests....* gnu/packages/bioinformatics.scm (python-demuxem)[arguments]: Disable tests,
because there aren't any.
Change-Id: I50364ca6744cf9d2704d4b75a8c79c4fdc4ada6e
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-pint: Update to 0.23....* gnu/packages/python-xyz.scm (python-pint): Update to 0.23.
[arguments]: Disable "test_load_definitions_stage_2" test.
[native-inputs]: Remove python-dask, python-distributed,
python-importlib-metadata, python-setuptools-scm, python-sparse,
python-uncertainties, and python-xarray; add python-pytest-benchmark.
[propagated-inputs]: Add python-uncertainties.
Change-Id: I98baae3369e5ffeea96355d9509296771c33dc50
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-cooler: Update to 0.9.1....* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.9.1.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom build phases; disable tests via #:test-flags.
[propagated-inputs]: Remove python-six and python-sparse.
[native-inputs]: Remove python-codecov, python-mock, and python-pytest-flake8;
add python-coverage, python-hatchling, and python-isort.
Change-Id: I48b6a9c07a2bc1c213971585d7191573fd5d5aca
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-plastid: Update to 0.6.1....* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.6.1.
[arguments]: Disable four tests.
Change-Id: If0225f226e702e89d451e2955d0f76691a8816c0
| Ricardo Wurmus |
| 2024-01-16 | gnu: cnvkit: Update to 0.9.10....* gnu/packages/bioinformatics.scm (cnvkit): Update to 0.9.10.
[arguments]: Remove.
[inputs]: Add r-minimal.
Change-Id: Iaa27fd3dddc507c7a955441f066d4b0e3b8f1757
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-reportlab: Update to 4.0.8....* gnu/packages/pdf.scm (python-reportlab): Update to 4.0.8.
[arguments]: Update configure flags and 'find-libraries phase.
[inputs]: Remove freetype and libart-lgpl.
[propagated-inputs]: Add python-chardet.
Change-Id: I626ef4c71a0b867ec4e1c74a71e45843349f46ef
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-pegasusio: Disable tests....* gnu/packages/bioinformatics.scm (python-pegasusio)[arguments]: Disable
tests.
Change-Id: I6b32ed416b562b47088dbc34eb7bcb0b8e2cc414
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-pyani: Disable tests....There are none.
* gnu/packages/bioinformatics.scm (python-pyani)[arguments]: Disable tests.
Change-Id: I6862082c8335e5d487da6d1705ed094922f14e47
| Ricardo Wurmus |
| 2024-01-16 | gnu: tadbit: Add missing input....* gnu/packages/bioinformatics.scm (tadbit)[native-inputs]: Add glib.
Change-Id: Ia1f79e2a30f5b57616cf3d1f7b6438f07451fbbf
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-captum: Update to 0.7.0....* gnu/packages/machine-learning.scm (python-captum): Update to 0.7.0.
[propagated-inputs]: Add python-tqdm.
Change-Id: I8917b6e294fe08077a3af4423deefa9769ba9384
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-poliastro: Make compatible with latest matplotlib....* gnu/packages/astronomy.scm (python-poliastro)[arguments]: Add phase
'matplotlib-compatibility; disable test_porkchop_plotting.
Change-Id: Ie70673c69d4bdfa424e324d2848e9567360b03ef
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-cleanlab: Disable test_aux_inputs, enable other tests....* gnu/packages/machine-learning.scm (python-cleanlab)[arguments]: Remove
'disable-bad-tests phase and ignore test files in #:test-flags instead;
disable test_aux_inputs test, but re-enable tests from
test_multilabel_classification.py.
[native-inputs]: Add python-pytest-lazy-fixture.
Change-Id: I77a16768ff61215e918c98bccd3efa216fb30d7f
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-scanpy: Update to 1.9.6....* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.9.6.
[arguments]: Update test flags.
[native-inputs]: Add python-hatchling, python-hatch-vcs, and
python-pytest-nunit.
Change-Id: I6d4dcd267a076c5697ed103650841f520dc9917f
| Ricardo Wurmus |
| 2024-01-16 | gnu: Add python-pytest-nunit....* gnu/packages/check.scm (python-pytest-nunit): New variable.
Change-Id: Ic67c973460f09b15bf683f70040a3f5e4381108d
| Ricardo Wurmus |
