gnu: Add python-diptest.
* gnu/packages/statistics.scm (python-diptest): New variable.
Change-Id: I7104617dfb182b85494febe2a483c7681cdb5929
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-scikit-bio: Update to 0.7.1.post1.
* gnu/packages/bioinformatics.scm (python-scikit-bio): Update to 0.7.1.post1.
[arguments] <test-backend, test-flags>: Use 'custom, run all tests.
<phases>: Remove 'build-extensions; use default 'check; add
'remove-local-source.
[propagated-inputs]: Remove python-hdmedians; add
python-array-api-compat, python-patsy, and python-statsmodels.
[native-inputs]: Remove python-coverage; add python-cython and
python-setuptools.
Change-Id: I460ba8dd7362f5d4bbf16a5923403ecbf5fc2026
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: endgame-singularity: Update to 1.1.
* gnu/packages/games.scm (endgame-singularity): Update to 1.1.
Change-Id: I8ff76a4e11ab949ad9576f14f74164dd567c6347
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-biom-format: Update to 2.1.17.
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.17.
[source] <snippet>: Remove redundant logic.
[arguments] <test-flags>: Only skip some doctest requiring Nose test
runner.
<phases>: Remove 'use-cython, 'build-extensions, and
'pandas-compatibility; add 'remove-local-source.
[propagated-inputs]: Remove python-flake8 and python-future.
[native-inputs]: Remove python-pytest-cov and python-wheel; add
python-setuptools.
Change-Id: Ib497f771e5de40b07df4964ebcddf6c40c15fc85
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: Add python-anndata-minimal.
* gnu/packages/python-science.scm (python-anndata-minimal): New variable.
Change-Id: I9503ac08d0fa630d748574bb121690144a80bfea
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-anndata: Update to 0.12.7.
* 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>
gnu: python-awkward: Update to 2.8.5.
* gnu/packages/python-xyz.scm (python-awkward): Update to 2.8.5.
[arguments] <test-flags>: Skip CUDA tests only.
[propagated-inputs]: Remove python-typing-extensions.
[home-page]: Refresh it as seen in project's README.
Change-Id: I5cebada2be766618633b0d082c88ae3d15490e9f
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-awkward-cpp: Update to 47.
* gnu/packages/python-xyz.scm (python-awkward-cpp): Update to 47.
[arguments]: Drop all.
[home-page]: Refresh it as seen in project's README.
Change-Id: I27be188fc95447a17c10b09f653bb28325367998
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: crossmap: Update to 0.7.3.
* gnu/packages/bioinformatics.scm (crossmap): Update to 0.7.3.
[source] <snippet>: Adjust it for a new location of egg info directory.
Change-Id: Ic826c4c42c2386dc9d1b301667be1dbb5d2db3eb
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-pynbody: Use python-ipython-minimal for tests.
* gnu/packages/astronomy.scm (python-pynbody)[native-inputs]: Remove
python-ipython; add python-ipython-minimal.
Change-Id: I2a87ff21b94cff7b3b3b2eb5c150b362fadede60
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-pycollada: Update to 0.9.2.
* gnu/packages/python-xyz.scm (python-pycollada): Update to 0.9.2.
[native-inputs]: Remove python-wheel.
Change-Id: I3cc70c7eeda9e4c54a0457ba430e4c6cbe1697f3
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-notebook: Fix build.
* gnu/packages/jupyter.scm (python-notebook)[arguments] <test-flags>:
Skip one test.
[propagated-inputs]: Swap python-jupyter-client@8 with
python-jupyter-client@7.
Change-Id: I37b420120395924c524f1936723e2a2c6228761d
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: Add python-jupyter-client-7.
* gnu/packages/jupyter.scm (python-jupyter-client-7): New variable.
Change-Id: I6164464161b0725d97c8eaf6ac1b46b03b1f13e3
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-jupyter-console: Move to jupyter.
* gnu/packages/python-xyz.scm (python-jupyter-console): Move from here ...
* gnu/packages/jupyter.scm: ... to here.
Change-Id: I687d44df58fab4d62a3eac92f2dab1eebdc89921
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-jupyter-console: Update to 6.6.3.
* gnu/packages/python-xyz.scm (python-jupyter-console): Update to 6.6.3.
[arguments] <test-flags>: Skip one test.
<phases>: Add 'pre-check.
[propagated-inputs]: Add python-ipython, python-jupyter-core,
python-pyzmq, and python-traitlets.
[native-inputs]: Remove python-setuptools; add python-flaky and
python-hatchling.
Change-Id: Ia7d12b313cfcc890a5173813b92d97872ece742b
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-ipykernel: Update to 7.1.0.
* gnu/packages/jupyter.scm (python-ipykernel): Update to 7.1.0.
Remove artifacts.
[arguments] <modules>: Drop them as not required.
<test-flags>: Skip just one shaky test.
<phases>: Remove 'relax-a-bit, and 'hide-deprecation-warnings; add
'fix-pytest-config.
Change-Id: I49512675b1d2f4ab1e74ec02aab92ae6673016b2
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-jupyter-client: Update to 8.7.0.
* gnu/packages/jupyter.scm (python-jupyter-client): Update to 8.7.0.
[inputs]: Add net-tools and openssh.
[propagated-inputs]: Remove python-entrypoints and python-nest-asyncio.
[native-inputs]: Remove python-pytest-asyncio, python-async-generator, and
python-ipython; add python-anyio and python-pytest-jupyter-minimal.
Change-Id: I0c058aa67c6fcb71c5fcfaca34c72a15d132b0ee
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: Add python-pytest-jupyter-minimal.
* gnu/packages/jupyter.scm (python-pytest-jupyter-minimal): New variable.
Change-Id: I0192ea6c58702664651fe838c5f38a82a5fad6d2
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: Remove python-jupyter-console-minimal.
Variable is not public and not in use by any other packages.
* gnu/packages/python-xyz.scm (python-jupyter-console-minimal): Delete variable.
Fixes: guix/guix#4881
Change-Id: I3b13ec6522f8c7c61a39e8f2262b652fbcb4210b
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-jupyter-client: Move to jupyter.
* gnu/packages/python-xyz.scm (python-jupyter-client,
python-jupyter-client-bootstrap): Move from here ...
* gnu/packages/jupyter.scm: ... to here.
Change-Id: I036632e68c808877de14da7f91863be50cdafd61
Signed-off-by: Rutherther <rutherther@ditigal.xyz>