gnu: python-scikit-learn-1.6: Skip 3 more tests.

* gnu/packages/machine-learning.scm (python-scikit-learn-1.6)[arguments]
<test-flags>: Skip 3 more tests.

Change-Id: I1c7e2eb7c18ddc5479cf45b84a6cf07d374842fe
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-vector: Update to 1.7.0.

* 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>

gnu: python-papermill: Reduce closure size; skip 2 tests.

The most of the native inputs were there to tests ignored tests, they
are removed now to reduce closure size.

* gnu/packages/jupyter.scm (python-papermill):
[arguments] <test-flags>: Skip 2 failing tests.
[native-inputs]: Remove python-boto3, python-botocore, python-ipython,
python-ipywidgets, python-moto, and python-requests.

Change-Id: I4c07a024a9514a44b5819196754e44ee86d47883
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-glue-qt: Relax requirements for ipython version.

* gnu/packages/astronomy.scm (python-glue-qt):
[phases]{relax-requirements}: New phase.

Change-Id: I25ede5ae073ff7e5d568e99b29b15a95008a696f
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Remove python-xarray-datatree.

* gnu/packages/python-science.scm (python-xarray-datatree): Delete variable.

Fixes: guix/guix#5348
Change-Id: I7150cbe534f900286fb575f5883d9fe0980aa975
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-multiscale-spatial-image: Update to 2.0.3.

* 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>

gnu: Add python-xarray-dataclass.

* gnu/packages/python-science.scm (python-xarray-dataclass): New variable.

Change-Id: Id4293a97741704c434b6847b7b1ede8d35dd1edd
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-fenics-ffc: Use python-numpy@1.

* gnu/packages/simulation.scm (python-fenics-ffc):
[propagated-inputs]: Add python-numpy-1.

Change-Id: I57a991c70947babc1734660c1d6723789ef77466
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-fenics-ufl-2019: Use python-numpy@1.

* gnu/packages/simulation.scm (python-fenics-ufl-2019):
[inputs]: Remove python-numpy.
[propagated-inputs]: Add python-numpy-1

Change-Id: I3171b24924f08a6210504ee03b3726a18609b186
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-episcanpy: Use python-numpy@1.

* gnu/packages/bioinformatics.scm (python-episcanpy):
[propagated-inputs]: Remove python-numpy; add python-numpy-1.
[native-inputs]: Remove python-pytest and python-wheel; add
python-setuptools.

Change-Id: I896e2e9c44383d71ad4cea3ca7e4f445999f5842
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-utilities-awetzel: Remove relax-requirements phase.

* gnu/packages/astronomy.scm (python-utilities-awetzel):
[phases]{relax-requirements}: Remove phase.

Change-Id: I00ac6703449056eefd27e3b0ceb60499c5a9fdcb
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-specreduce: Remove relax-requirements phase.

* gnu/packages/astronomy.scm (python-specreduce):
[phases]{relax-requirements}: Remove phase.

Change-Id: Ibf28ad731ffcffda538b6ab0499774be36b666ea
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-sncosmo: Adjust phases.

* gnu/packages/astronomy.scm (python-sncosmo):
[phases]{relax-requirements, prepare-test-environment}: Remove phases.
{pre-check}: New phase, do not re-build extension just remove local
source to reduce compute time.
[native-inputs]: Remove python-wheel; add python-iminuit and
python-pytest-xdist.

Change-Id: I3b8642b1a55a1563640b1a5306614f2cb9ec5c2a
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-sep: Remove relax-requirements phase.

* gnu/packages/astronomy.scm (python-sep):
[phases]{relax-requirements}: Remove phase.
[native-inputs]: Remove python-wheel.

Change-Id: Ifb16d132624f1fb3c9b578e6644fda5ee524745b
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-gizmo-analysis: Remove relax-requirements phase.

* gnu/packages/astronomy.scm (python-gizmo-analysis):
[phases]{relax-requirements}: Remove phase.

Change-Id: Id35c2554efe5dcdf84fd0bcbc947e3017e345646
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-drizzlepac: Update to 3.10.0-0.e01563c.

* gnu/packages/astronomy.scm (python-drizzlepac): Update to
e01563c48206f02f4cd4c525732764b9b827b3c4 commit.
[source]: Switch to git-fetch.
[phases]{set-version}: New phase.
[propagated-inputs]: Remove python-markupsafe, python-pypdf2,
python-regions, and python-tables; add python-pypdf and python-stregion.
[native-inputs]: Remove python-astropy and python-wheel; add
python-markupsafe.

Change-Id: I623f369b763d741405a6f25ed455466d009cb3d5
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-stregion.

* gnu/packages/astronomy.scm (python-stregion): New variable.

Change-Id: Ic3854a54498e628ead422eba5b223773c700c98b
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-drep: Update to 3.6.2-0.7b4b8fb.

* gnu/packages/bioinformatics.scm (python-drep): Update to
7b4b8fbf9dfdfef61caf949f1aa1d4fc3be61d5a commit.
[source]: Switch to git-fetch providing tests.
[arguments] <test-flags>: Skip some tests requiring not available
optional packages.
[build-system]: Switch to pyproject-build-system.
[propagated-inputs]: Remove python-pytest; add python-networkx.
[native-inputs]: Add mash, python-pytest, and python-setuptools.

Change-Id: I5e22f7c142e267592b2ed74cf1c1d37a02472992
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-mygene: Switch to pyproject.

* gnu/packages/bioinformatics.scm (python-mygene):
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-setuptools.

Change-Id: Ieb062c8dc8f8e2a8cede4b5d1bb816ec9d9d10db
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-funsor: Update to 0.4.6.

* gnu/packages/machine-learning.scm (python-funsor): Update to 0.4.6.
[source]: Switch to git-fetch providing a fresh version.
[arguments] <test-flags>: Run tests in parallel, supported upstream;
skip more problematic tests.
[propagated-inputs]: Remove python-numpy; add python-numpy-1,
python-pyro-ppl, and python-pytorch.
[native-inputs]: Add python-pytest-xdist.

Change-Id: I6a82951485324e465c93aec07b4f98ef632ebae3
Signed-off-by: Rutherther <rutherther@ditigal.xyz>