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* gnu/packages/python-science.scm (python-scikit-build-core)
[propagated-inputs]: Drop python-exceptiongroup.
Change-Id: Id6e5491f3bab5bfbe4719f5313ff21d72e44d232
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
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* gnu/packages/astronomy.scm (python-asdf-compression)
(python-asdf-fits-schemas, python-cdflib, python-sunkit-spex):
* gnu/packages/bioinformatics.scm (python-whatshap, python-mudata)
(python-pyfaidx, python-ctxcore, scvelo):
* gnu/packages/bootloaders.scm (dtc):
* gnu/packages/check.scm (python-pytest-xdist, python-pytest-forked):
* gnu/packages/databases.scm (python-fastparquet):
* gnu/packages/disk.scm (greaseweazle-host-tools):
* gnu/packages/docker.scm (python-docker):
* gnu/packages/finance.scm (python-ledgerblue):
* gnu/packages/fontutils.scm (python-compreffor)
(python-defcon-bootstrap, nototools):
* gnu/packages/games.scm (sc-controller):
* gnu/packages/machine-learning.scm (python-botorch):
* gnu/packages/music.scm (python-pylast):
* gnu/packages/package-management.scm (conda):
* gnu/packages/python-build.scm (python-exceptiongroup):
* gnu/packages/python-science.scm (python-dask-image)
(python-distributed, python-osqp):
* gnu/packages/python-web.scm (python-branca, python-smart-open):
* gnu/packages/python-xyz.scm (python-conda-content-trust)
(python-menuinst, python-isort, python-pyclibrary)
(python-pyclipper, python-csb43-0.10, python-orgparse)
(python-deepmerge, python-scooby, python-uuid6):
* gnu/packages/radio.scm (nanovna-saver):
* gnu/packages/sphinx.scm (python-sphinx-autodoc-typehints):
[arguments]: Remove phases setting SETUPTOOLS_SCM_PRETEND_VERSION.
* gnu/packages/python-xyz.scm (python-bagit)
[arguments]: Refactor manual 'check phase into #:test-flags.
Change-Id: I0713d6603f982a7f956d02fc3b85a384f4dd6ce4
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
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Remove python-pip from [native-inputs] in the following packages as not
required for build/tests/install:
* gnu/packages/python-science.scm: (python-scikit-build-core)
* gnu/packages/python-xyz.scm: (python-pypandoc)
* gnu/packages/shells.scm: (xonsh)
Change-Id: I26579cf868b1e56d075b5c8d8ef7914feee44bcb
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
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Remove python-coveralls from [native-inputs] in the following packages
as not required for build/tests/install:
* gnu/packages/python-science.scm (python-trimesh)
* gnu/packages/python-xyz.scm (python-affine)
Change-Id: Ia2beeec4ebc4e651f0a079efb644afa8026d53de
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
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* gnu/packages/python-science.scm (python-scikit-image-next): Delete variable.
Change-Id: Ieecd9370c75ba24ea1740615fc950d9b1ffcb216
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* gnu/packages/python-science.scm (python-pandas-2): Delete variable.
Change-Id: Ia08c92f284f3bdb5849967376d5cfc38c61c7703
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* gnu/packages/bioinformatics.scm (python-bed-reader, python-gseapy)
* gnu/packages/chemistry.scm (gemmi, ringdecomposerlib, rdkit)
* gnu/packages/cinnamon.scm (libxapp)
* gnu/packages/cups.scm (hplip)
* gnu/packages/djvu.scm (ocrodjvu)
* gnu/packages/finance.scm (electron-cash)
* gnu/packages/gnome.scm (terminator)
* gnu/packages/image-processing.scm (insight-toolkit)
* gnu/packages/machine-learning.scm (onnxruntime, tensorflow-lite,
koboldcpp, python-tokenizers)
* gnu/packages/maths.scm (gmsh, z3, fp16)
* gnu/packages/music.scm (quodlibet)
* gnu/packages/photo.scm (lensfun)
* gnu/packages/python-science.scm (python-clarabel)
* gnu/packages/python-xyz.scm (python-orjson, python-libcst,
python-rpds-py, python-streamtracer, python-tiktoken)
* gnu/packages/rpm.scm (createrepo-c)
* gnu/packages/rust-apps.scm (maturin)
* gnu/packages/sugar.scm (sugar, sugar-datastore)
* gnu/packages/version-control.scm (mercurial, hg-commitsigs)
* gnu/packages/vpn.scm (python-proton-vpn-local-agent)
[arguments]<#:phases>: Remove uneeded use of pyproject-guile-json
extension.
* gnu/packages/python-xyz.scm (python-streamtracer)[arguments]
<#:phases>: Also rewrite 'check phase replacement.
Change-Id: I779c354120ada3d94f07a127b9ec5011e73254c2
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
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* gnu/packages/python-science.scm (python-cmasher): New variable.
Change-Id: I74c8ad6f9170b34b8c4fd1760c2ca3ba90d2a1f5
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* gnu/packages/python-science.scm (python-pyjanitor): Update to 0.32.5.
[arguments] <test-flags>: Rework ignored/skipped tests.
[propagated-inputs]: Remove python-requests.
[native-inputs]: Add python-openpyxl and python-requests.
[synopsys]: pandas->Pandas.
Change-Id: I12f3f1f6ab84d63882325103e8c729d44656c97c
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-pandas-flavor): Update to 0.8.1.
[phases]{fix-pytest-config}: New phase.
[propagated-inputs]: Remove python-lazy-loader and python-packaging.
[native-inputs]: Add python-setuptools and python-setuptools-scm.
Change-Id: I1f1325350f77ed61146f32da5bdc81aad1daec27
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-scikit-misc)
[propagated-inputs]: Remove python-numpydoc.
[native-inputs]: Add python-numpydoc.
Change-Id: I9f3d3550789dd2943f496d90f59a063ac7df5e97
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-pynetdicom)
[propagated-inputs]: Remove python-numpydoc.
[native-inputs]: Add python-numpydoc.
Change-Id: Ib0bc20a289972af1d346f38213413c6930218ef0
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-ruffus):
[build-system]: Switch to pyproject-build-system.
[arguments]<#:phases>: Improve style. Improve 'check phase.
[native-inputs]: Add python-setuptools.
Change-Id: If6607ce5db313c97d5aaff062ac8bfa4b55d5dee
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-geosketch): Update to 1.3.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:tests>: Ignore them.
[native-inputs]: Add python-setuptools.
Change-Id: Ib86bb1a690585d925f3cd7ba801e89e04273d8e1
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-pyvista)[arguments]
<#:test-flags>: Ignore failing test.
Change-Id: I0dba730e92c7fd7e9d7d6273bba3b5e7646278c2
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-pyts): Update to 0.13.0-0.4f3d97b.
[source]: Switch to git-fetch.
[native-inputs]: Remove python-wheel.
[description]: Improve it.
Change-Id: I64947107888826ad3db8cf1e2e4d3790c6a3e070
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-qutip): Update to 5.2.2.
[arguments] <test-flags>: Rework skipped/ignored tests.
<phases>: Use default 'check; add 'remove-local-source.
[propagated-inputs]: Add python-cvxopt, python-cvxpy, python-mpi4py,
python-mpmath, and python-tqdm.
[native-inputs]: Remove python-numpy, python-packaging, python-scipy,
and python-wheel; add python-pytest-rerunfailures.
Change-Id: I1ee08658e6a7c6ef2c6b42b9d121113dedad04f7
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* 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>
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* 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>
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* gnu/packages/python-science.scm (python-scikit-survival): Fix indentation.
Change-Id: Iff0ab38a0b484938613df08ffb0fbd83da489289
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* 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>
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* 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>
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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>
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* gnu/packages/python-science.scm (python-pandas-stubs): Update to 2.3.3.251219.
[arguments]: Drop all but 2 skipped tests.
[propagated-inputs]: Add python-numpy.
[native-inputs]: Remove python-tables, which, xclip,
xorg-server-for-tests, and xsel; add python-beautifulsoup4,
python-fsspec, python-html5lib, python-jinja2, python-loguru,
python-mypy, python-numexpr, python-openpyxl, python-typing-extensions,
python-xlrd, python-xlsxwriter, and tzdata-for-tests.
Change-Id: I7b7b85c1ce9b1e575069a79321db4ff515372942
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-narwhals): Update to 2.15.0.
[propagated-inputs]: Add python-duckdb, python-packaging, and python-rich.
[native-inputs]: Remove python-duckdb.
Change-Id: I0af82e4cbe2b3c2b3ae3803b77cde5f6c921a1a6
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-narwhals-minimal): New variable.
Change-Id: I972010ea88c649d41227c51256b739a022a350df
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-libneuroml): Update to 0.6.7.
[native-inputs]: Remove python-wheel.
Change-Id: I7ef49953a922116bd2c1aeb12ea548d0dd8afb18
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-pyfma):
[propagated-inputs]: Remove python-numpy; add python-numpy-1.
[native-inputs]: Remove python-wheel.
Change-Id: I8236576e39b7e6f8b981126cbf67fc55f35db83c
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-salib): Update to 1.5.2.
[phases]{set-version}: New phase.
[native-inputs]: Remove python-pytest-cov; add python-hatch-vcs.
Change-Id: Ibff2633efa0f7657a40b580a3028cb71f57b923d
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-pyamg): Update to 5.3.0.
[arguments] <test-flags>: Remove local source instead in phase..
<phases>: Add 'pre-check.
[native-inputs]: Remove python-wheel.
Change-Id: I3f231c1201013b4cbc7a8fbda14937aa0685827e
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-scikit-surprise):
[propagated-inputs]: Remove python-numpy; add python-numpy-1.
[native-inputs]: Remove python-wheel.
Change-Id: I4ae8d087b602a04ff94ad1ef72c6ef0589938054
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-paramz): Move from here ...
* gnu/packages/machine-learning.scm: ... to here.
Change-Id: I128d863626a9b70bf31c37e200d40ad6ccd48ad2
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-paramz):
[propagated-inputs]: Remove python-numpy; add python-numpy-1.
Change-Id: Ibc355d9a6e1ab635f63c21fe5e068a0ddfcc906a
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-vector): Update to 1.7.0.
[propagated-inputs]: Add python-awkward, python-numba, and python-sympy.
[native-inputs]: Remove python-awkward and python-sympy; add python-notebook,
python-optree, and python-papermill.
Change-Id: I760c26d69b5a5e4530e80d8e57af65db2fdf319f
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-xarray-datatree): Delete variable.
Fixes: guix/guix#5348
Change-Id: I7150cbe534f900286fb575f5883d9fe0980aa975
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-multiscale-spatial-image): Update to 2.0.3.
[propagated-inputs]: Remove quasiquote and ((unquote insight-toolkit) "python"); add
python-dask, python-numpy, python-dateutil, python-spatial-image,
python-xarray, python-xarray-dataclass, and python-zarr.
[native-inputs]: Remove python-fsspec, python-ipfsspec, python-jsonschema,
python-nbmake, python-pooch, python-pytest, python-pytest-mypy,
python-urllib3, and python-zarr.
Change-Id: I22f93379f92da785f851c17d149745ea9124a999
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-xarray-dataclass): New variable.
Change-Id: Id4293a97741704c434b6847b7b1ede8d35dd1edd
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-deepdish):
[propagated-inputs]: Remove python-numpy; add python-numpy-1.
[native-inputs]: Remove python-wheel.
Change-Id: I8c4e2bd6538411df0f33d05b80fe178690fcc4d8
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-tdda):
[arguments] <test-flags>: Skip one more test.
[native-inputs]: Remove python-wheel.
Change-Id: I1bcb5223627945d580d64e911cd73cf2da06287a
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-fastcluster): Update to 1.3.0.
[arguments]: Drop all.
[native-inputs]: Remove python-wheel; add python-pytest.
Change-Id: Ib57e7067d7eff527f5d84f297d668cc0c7997a9c
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-cvxpy): Update to 1.7.5.
[arguments] <test-flags>: Skip some tests.
[propagated-inputs]: Remove pybind11; add python-cvxopt.
[native-inputs]: Remove python-wheel; add pybind11.
Change-Id: I83974c14d6422284c1f31fe8922cd9e7bc5a9253
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-scs): Update to 3.2.10.
[source]: Do not pull git submodules.
[phases]{substitute-git-submodules}: New phase.
[inputs]: Add lapack.
[native-inputs]: Add pythoncapi-compat and scs.
Change-Id: I44778c1969f074c80ca4ddf8350b6db5c2db136a
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-osqp): Update to 1.0.5.
[arguments] <test-flags>: Rework skipped tests.
[phases]{relax-requirements}: Remove phase.
{fix-osqp-source-location}: New phase.
[propagated-inputs]: Remove python-qdldl; add python-jinja2,
python-joblib, and python-setuptools.
[native-inputs]: Remove python-setuptools and python-wheel; add osqp,
pybind11, python-pytorch, python-scikit-build-core, and qdldl.
Change-Id: Ic6180f814a215d5bd772e4134f7ca291f1120081
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* 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>
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* 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>
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* 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>
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* gnu/packages/python-science.scm (python-fbpca)[arguments]
<test-flags>: Skip one test.
Change-Id: I98ea94a1986e465ad41e6d0099ad4a1f45506c8e
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* 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>
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* gnu/packages/python-science.scm (python-anndata-minimal): New variable.
Change-Id: I9503ac08d0fa630d748574bb121690144a80bfea
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-anndata): Update to 0.12.7.
[arguments] <test-flags>: Skip CUDA dependent tests.
[phases]{set-version}: Remove setting zip timestamp logic.
[propagated-inputs]: Remove python-importlib-metadata,
python-scikit-learn, and python-setuptools; add python-numpy.
[native-inputs]: Add hdf5, python-openpyxl, python-pyarrow,
python-pytest-randomly, and python-scikit-learn.
Change-Id: I8e68cf85d435a13db995ea966ed5ff9edac3d672
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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