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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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* gnu/packages/python-science.scm (python-pythran): Adjust style and
remove unused parts.
[source] <url>: Use a direct URL string.
[arguments] <test-flags, phase:pre-check>: Drop them as not used.
[native-inputs]: Remove openblas, python-pytest, python-pytest-xdist,
and python-wheel.
[home-page]: Move above [synopsis].
Change-Id: I7708981548ce68351c00fbf4e8f8e806a18f798a
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-asap3): Update to 3.13.10.
[arguments] <tests?>: Enable.
[native-inputs]: Add python-pytest.
Change-Id: I166dfaf5f07f23d2d835d70f460cfa5f3f31ddb9
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-ase): Update to 3.26.0.
[arguments] <test-flags>: Run tests in parallel up to 8 threads.
[native-inputs]: Remove python-wheel.
Change-Id: Ib2e5c9751f6c3358bb35084076f79586473da88f
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-numdifftools): Update to 0.9.42.
[arguments] <test-flags>: Keep only exclusion markers.
<phases>: Remove 'relax-requirements; add 'fix-pytest-config.
[propagated-inputs]: Add python-matplotlib.
[native-inputs]: Remove python-setuptools, python-setuptools-scm, and
python-wheel; add python-pdm-backend.
Change-Id: I87bdd34812df8771f53dd2ab8cfc4634ffb0b07d
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-modin): Update to 0.37.1.
[arguments] <test-flags>: Rework options.
<phases>: Remove 'loosen-requirements; add 'versioneer, and
'fix-pytest-config; rework {check} phase to include some API tests
scenarios.
[propagated-inputs]: Remove python-cloudpickle and python-s3fs; add
python-fsspec, python-psutil, and python-typing-extensions.
[native-inputs]: Remove python-jinja2, python-lxml, python-matplotlib,
python-msgpack, python-openpyxl, python-psutil, python-pyarrow,
python-pytest-benchmark, python-pytest-cov, python-scipy,
python-sqlalchemy, python-tables, python-tqdm, python-xarray,
python-xlrd, and python-wheel; add python-s3fs, python-setuptools, and
python-versioneer.
Change-Id: I86feaa9f1cd110ed2c430e9816d34da165bccb74
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-xarray-einstats): Update to 0.9.1.
[propagated-inputs]: Add python-einops and python-numba.
[native-inputs]: Remove python-einops and python-numba.
Change-Id: Ic3e05114dc3d6343523aec222f527ef9653ed2d6
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-dask-image): Update to 2025.11.0.
[arguments] <test-flags>: All tests passed.
<phases>: Add 'fix-pytest-config; rework 'set-version to read from envar.
[propagated-inputs]: Remove python-tifffile-for-dask-image; add
python-tifffile.
[native-inputs]: Remove python-setuptools-scm; add
python-setuptools-scm-next.
* gnu/packages/python-xyz.scm (python-tifffile-for-dask-image): Delete variable.
Change-Id: I928c39c848f3a20d5eb51d10e4c8374891b8f0b0
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-xarray): Update to 2025.12.0.
[arguments] <test-flags> Rework skipped tests, do not depend on MyPy
type checker.
[native-inputs]: Remove python-wheel; add python-pytest-asyncio.
Change-Id: I49e33b614926cde8bd5fad09ac278bc79e9d3cb1
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-jacobi)[arguments]<phases>:
Add 'fix-pytest-config.
Change-Id: Ia8b4c30d2d8d6cfe9bae79342614747c90ae6735
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-scikit-image-next): Deprecate
in favor of python-scikit-image.
Change-Id: I006f4a302eabab82abd9c853f1b6a3d352f546ef
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-scikit-image): Update to 0.25.2.
[arguments] <test-flags>: Ignore benchmark tests.
<phases>: Remove 'change-home-dir, 'pre-check, 'post-check; add
'remove-local-source.
[propagated-inputs]: Remove python-cloudpickle, python-dask,
python-matplotlib, python-pythran, and python-pywavelets; add
python-packaging.
[native-inputs]: Remove python-numpydoc, python-packaging, and
python-wheel; add python-pythran.
Change-Id: Ifbfbb3e2d28dc8784f600a4cd1a0f0c7129fddb5
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-fgivenx): Update
towcf51dbf8b7efdd8d84f055740a069a5b882dcf77.
[source]: Switch to git-fetch providing comparability with recent
matblotlib version.
[arguments]: Drop all.
[home-page]: Fix URL https://github.com/fgivenx/fgivenx responding with
404, new one is taken from PyPI page.
Change-Id: Ia255f4b44967ee32e9b4a18cc15b80aa4cf0b09e
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-algopy): Update to 0.7.2.
[native-inputs]: Remove python-wheel.
Change-Id: Ifac98dffd209bea3d50ef3ded0a0aee0a24faa8c
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-ndindex): Update to 1.10.1.
[arguments] <test-flags>: Provide option to run tests again installed
module.
<phases>: Add 'remove-local-source.
[native-inputs]: Remove python-wheel; add python-sympy.
Change-Id: I2c7129b540c5fc4e25dac8945c38359cc6c71eac
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-distributed): Update to 2025.11.0.
[arguments] <tests?, test-flags>: Disable for now.
<phases>: Remove 'versioneer, 'fix-references, and 'pre-check.
[propagated-inputs]: Remove python-cryptography, python-dask-expr, and
python-setuptools; add python-jinja2, python-locket, and
python-packaging.
[native-inputs]: Remove python-flaky, python-importlib-metadata,
python-pytest, python-pytest-timeout, python-versioneer, and
python-wheel; add python-setuptools and python-setuptools-scm-next.
Change-Id: I1c368ee626d4bc5dc206df06431d164cd8df3428
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-xyz.scm (python-pydantic-2): Deprecate variable.
* gnu/packages/astronomy.scm (python-czml3, python-edps, python-hvpy):
[propagated-inputs]: Remove python-pydantic-2; add python-pydantic.
* gnu/packages/cybersecurity.scm (gallia):
[inputs]: Remove python-pydantic-2; add python-pydantic.
* gnu/packages/databases.scm (python-prisma)[propagated-inputs]:
Remove python-pydantic-2; add python-pydantic.
(python-tortoise-orm, aerich)[native-inputs]: Remove python-pydantic-2;
add python-pydantic.
* gnu/packages/django.scm (python-django-ninja)[propagated-inputs]:
Remove python-pydantic-2; add python-pydantic.
* gnu/packages/finance.scm (python-schwifty)[native-inputs]: Remove
python-pydantic-2; add python-pydantic.
* gnu/packages/games.scm (tuxemon)[propagated-inputs]: Remove
python-pydantic-2; add python-pydantic.
* gnu/packages/machine-learning.scm (python-spacy, python-thinc):
[propagated-inputs]: Remove python-pydantic-2; add python-pydantic.
* gnu/packages/maths.scm (python-libensemble)[propagated-inputs]: Remove
python-pydantic-2; add python-pydantic.
* gnu/packages/protobuf.scm (python-pure-protobuf)[native-inputs]:
Remove python-pydantic-2; add python-pydantic.
* gnu/packages/python-check.scm (python-inline-snapshot)[native-inputs]:
Remove python-pydantic-2; add python-pydantic.
* gnu/packages/python-science.scm (python-iminuit):[native-inputs]:
Remove python-pydantic-2; add python-pydantic.
(python-pandera, python-vaex-core)[propagated-inputs]: Remove
python-pydantic-2; add python-pydantic.
* gnu/packages/python-web.scm: (python-cloudpathlib, python-huggingface-hub):
[native-inputs]: Remove python-pydantic-2; add python-pydantic.
(python-aws-sam-translator, python-weasel, python-openai,
python-fastapi, python-fastapi-csrf-protect,
python-fastapi-pagination-minimal, python-fastapi-pagination):
[propagated-inputs]: Remove python-pydantic-2; add python-pydantic.
* gnu/packages/python-xyz.scm: (python-safety-schemas,
python-pytoolconfig, python-pydantic-cli, python-pydantic-settings,
python-confection, python-safety)[propagated-inputs]: Remove
python-pydantic-2; add python-pydantic.
(python-deepdiff, python-lief)[native-inputs]: Remove
python-pydantic-2; add python-pydantic.
Change-Id: I20842162ae8a6c0abd54e4ef1fc676f928541184
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-dask): Update to 2025.11.0.
[arguments] <test-flags>: Do not max out availalbe thread, keep them on
4 for stability; rework skipped/ignored tests.
<phases>: Remove 'versioneer, and 'patch-pyproject.
[propagated-inputs]: Remove python-dask-expr; add python-lz4 and
python-pyarrow.
[native-inputs]: Remove python-importlib-metadata and python-versioneer;
add python-pytest-asyncio, python-pytest-mock, python-pytest-timeout,
python-setuptools-scm-next, and tzdata-for-tests.
Change-Id: I8234ad1923a2a228c9c240bb34c9e1c9dfcbbd55
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-scipy): Update to 1.16.3.
[arguments] <test-flags>: Use Pytest directly, as seen in project's
GitHub Actions.
<phases>: Remove 'apply-i686-patch; add 'relax-requirements,
'hide-gfortran; rework custom 'check to run Pytest directly.
[native-inputs]: Remove gcc, python-cython-0; add python-cython, and
python-hypothesis.
[inputs]: Remove pybind11-2.10; add boost, pybind11, qhull, and xsimd.
* gnu/packages/patches/python-scipy-i686.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Deregister patch.
Change-Id: Ibc38577b9b0c915e54ca3b3096727c9c2f82e19c
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-pandas-2): Update to 2.3.3 and
rename to python-pandas.
[arguments] <test-flags>: Rework skipped tests.
<phases>: Remove 'pre-check, and 'patch-which; use custom 'check.
[inputs]: Remove which, it's implemanted with Python's `shutil.which()'.
[propagated-inputs]: Remove python-jinja2, python-matplotlib,
python-openpyxl, python-xlrd, and python-xlsxwriter.
[native-inputs]: Remove python-beautifulsoup4, python-cython,
python-html5lib, python-matplotlib, python-openpyxl,
python-pytest-localserver, and python-pytest-mock; add meson and
tzdata-for-tests.
(python-pandas-2): Deprecate variable in favor of python-pandas.
Change-Id: Ib4aefbbc33f46f793430ac396cbe5e6c4107ec2f
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
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* gnu/packages/python-science.scm (python-climin): Delete variable.
Fixes: guix/guix#4556
Change-Id: I8e26118c854a6ece21a5d8946a30812b626dc52e
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* gnu/packages/python-science.scm (python-osfclient): New variable.
Change-Id: I236ee7e8f56758fbd75b8b83f67161f37d812e6e
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* gnu/packages/python-science.scm (python-pylems): Update to v0.6.9.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]: Execute project tests.
[native-inputs]: Add python-pytest and python-setuptools.
[propagated-inputs]: Add python-matplotlib.
[description]: Update with acronym.
Closes guix/guix#5024
Change-Id: Id3e454e5ae6f4ca49fad29cd4e0238aeb75e7653
Signed-off-by: Cayetano Santos <csantosb@inventati.org>
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* gnu/packages/python-science.scm (python-pytensor):
[arguments] <test-flags>: Let pytest discover tests.
[phases]{pre-check}: Replace re-build extensions by deleting local
source.
[propagated-inputs]: Remove python-typing-extensions.
[native-inputs]: Remove python-wheel.
Change-Id: I42f97a93e1704856d29691f99414d4f2497723b9
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* gnu/packages/python-science.scm (python-pytensor)
[arguments]<#:test-flags>: Ignore more failing tests.
Change-Id: I542ba0025bf43ebef08b2ab67c19e618b3b32621
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
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* gnu/packages/python-science.scm (python-tspex): Update to
d393ff497b7c14d673e792bd6c84ddd734be1239 commit.
[source]: Switch to git-fetch for tests.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:phases>: Add 'remove-coverage and 'fix-seaborn phases.
[propagated-inputs]: Add python-seaborn.
[native-inputs]: Add python-pytest and python-setuptools.
Change-Id: I367198165d5d78e1f1e04708272136711e5b22b5
Reviewed-by: Nicolas Graves <ngraves@ngraves.fr>
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
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* gnu/packages/python-science.scm (python-pynrrd): Update to 1.1.3.
[build-system]: Switch to pyproject-build-system.
[propagated-inputs]: Remove python-nptyping and python-typing-extensions.
[native-inputs]: Add python-pytest and python-setuptools.
Change-Id: Id98a3424f35fc791324010deae357f89e2d93362
Reviewed-by: Nicolas Graves <ngraves@ngraves.fr>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
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* gnu/packages/python-science.scm (python-simplespectral): Switch to
pyproject-build-system.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:tests>: Set to #f, as there are no tests.
[native-inputs]: Add python-setuptools.
Change-Id: Ifabd9561978fec3a7380d8cdb7641732baad01d8
Reviewed-by: Nicolas Graves <ngraves@ngraves.fr>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
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* .mailmap: New entry.
Change-Id: I839ba6c7be463c5b59c7e68247ae5e46d2ceeeaf
Reviewed-by: Maxim Cournoyer <maxim@guixotic.coop>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
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* gnu/packages/python-science.scm (python-numpy-groupies): Update to 0.11.3.
[build-system]: Switch to pyproject-build-system.
[propagated-inputs]: Add python-numpy.
[native-inputs]: Remove python-pytest-runner and python-numpy; add python-pandas,
python-setuptools, and python-setuptools-scm.
Change-Id: Iffe9007c357ac5f299a07cfb1d3fcd20da862c81
Signed-off-by: Andreas Enge <andreas@enge.fr>
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* gnu/packages/python-science.scm (python-msgpack-numpy): Switch to
pyproject-build-system.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:test-backend>: Select unittest.
[native-inputs]: Add python-setuptools.
Change-Id: I47958f2fe83411cefd91b664197a5b08e33205b4
Signed-off-by: Andreas Enge <andreas@enge.fr>
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* gnu/packages/python-science.scm (python-traittypes)[native-inputs]:
Replace python-nose by python-pynose. Remove python-wheel.
Change-Id: Ia90b2d1311026af1bfee295cc5db3c0cac392932
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
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The change was automated via:
git grep -l goodoldpaul@autistici.org |
xargs sed -i 's/goodoldpaul@autistici.org/therewasa@fishinthecalculator.me/g'
* .mailmap: New entry.
Change-Id: I1629388334695d221647afe6a14faf61af5fe0d6
Signed-off-by: Maxim Cournoyer <maxim@guixotic.coop>
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* gnu/packages/python-science.scm (python-unyt): Update to 3.0.4.
[arguments]: Drop all.
[propagated-inputs]: Remove python-h5py and python-matplotlib; add
python-packaging.
[native-inputs]: Remove python-pint and python-wheel.
Change-Id: I3759ce1befbb804d1c2508df042c19082f9a7833
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* gnu/packages/python-science.scm (python-nestcheck): New variable.
Change-Id: Ieb2d6942e0f8f802853f821bc13c3b86aee74a6f
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* gnu/packages/python-science.scm (python-fgivenx): New variable.
Change-Id: I2f3d49e5340b803616618628439df6889c86fc61
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* gnu/packages/python-science.scm (python-pynetdicom):
[propagated-inputs]: Remove python-mypy.
[native-inputs]: Remove python-codespell, python-coverage,
python-pytest-cov, pythonb-pytest-xdist, python-sphinx, and
python-sphinx-rtd-theme.
Change-Id: Ie0fc078cec3473e061ebc4dc87de59ca309a6194
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* gnu/packages/python-xyz.scm (python-clarabel)[arguments]
<#:phases>: Extend with (pyproject-guile-json).
Change-Id: I258bc867cc4269779ccf886601a00323b8f80083
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
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