gnu: mageck: Use python-numpy@1.

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

Change-Id: If26cf31016b769b01d502c33b97c5579873337b6
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: idr: Fix build.

* gnu/packages/bioinformatics.scm (idr):
[propagated-inputs]: Use python-numpy-1.
[native-inputs]: Use python-cython-0.

Change-Id: Ic1fabb53311a74db3872f50c2f67f8e1310be204
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-cnmf: Update to 1.7.0.

* gnu/packages/bioinformatics.scm (python-cnmf): Update to 1.7.0.
[arguments] <tests?, test-flags>: Enable them.
[native-inputs]: Remove python-wheel; add python-pytest.

Change-Id: I927b10045e563cc81bcb077f3af9ba3312869280
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-cooltools: Update to 0.7.1.

* gnu/packages/bioinformatics.scm (python-cooltools): Update to 0.7.1.
[arguments] <phases>: Add 'fix-pytest-config.
[native-inputs]: Add python-setuptools.

Change-Id: I1a5c03cc626c1401f1a6b34f7af13d2a259e74a3
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-magic-impute: Update to 3.0.0.

* gnu/packages/bioinformatics.scm (python-magic-impute): Update to 3.0.0.
[arguments] <tests?, test-flags>: Enable them.
[native-inputs]: Add python-pytest and python-setuptools.
[propagated-inputs]: Add python-scprep.

Change-Id: I4e1567fc6b5b32ee77f13d801042ea321f33dfa8
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-scprep.

* gnu/packages/bioinformatics.scm (python-scprep): New variable.

Change-Id: I61674e690bf798c17e84806b606673f84bd07636
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

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

* gnu/packages/bioinformatics.scm (python-fcsparser):
[propagated-inputs]: Remove python-numpy; add python-numpy-1.

Change-Id: I2a069293821b769aa981c15ccbc5c96cde5a497a
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-graphtools: Update to 2.1.0.

* gnu/packages/graph.scm (python-graphtools): Update to 2.1.0.
[arguments]<phases>: Remove 'patch-tets; use default 'check; add
'fix-pytest-config.
[native-inputs]: Remove util-linux, python-pynose, and python-nose2; add
python-pytest and python-setuptools.

Change-Id: If5561d5c4de1a9c78e7d4baa7011bd0ad622c4ef
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pygsp: Update to 0.6.0.

* gnu/packages/graph.scm (python-pygsp): Update to 0.6.0.
[source] <pypi-uri>: Fix name.
[arguments] <test-flags>: Rework skipped tests.
<phases>: Remove 'disable-doctets.
[propagated-inputs]: Remove python-scikit-image.
[native-inputs]: Remove python-coverage, python-coveralls, and
python-flake8; add python-matplotlib, python-pyunlocbox,
python-scikit-image, and python-setuptools.

Change-Id: Ic2ef43e47967897e2d7df7e628a8d02ff7684360
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-pyunlocbox.

* gnu/packages/graph.scm (python-pyunlocbox): New variable.

Change-Id: I0281d2e1cfa4ad61a64e168f2c70344afd96ad3a
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-verde: Update to 1.8.1.

* gnu/packages/geo.scm (python-verde): Update to 1.8.1.
[arguments] <test-flag>: Skip one more test.
[propagated-inputs]: Add python-pykdtree and python-numba.
[native-inputs]: Remove python-wheel; add python-matplotlib and
python-pytest-mpl.

Change-Id: Iaeefd5f40cb553fd0c76556663279f75aa7917ad
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-metacells: Simplify.

* gnu/packages/bioinformatics.scm (python-metacells):
[arguments] <phases>: Merge 'set-numba-cache-dir and 'build-extension
into 'pre-check and just remove local source to prevent rebuilding
expansions for tests, it saves some compute time with the same output.
[native-inputs]: Add pybind11.

Change-Id: I95e6706813cc5d3167593440c714c5091303cb00
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-crosshair: Update to 0.0.101.

* gnu/packages/python-check.scm (python-crosshair): Update to 0.0.101.
[arguments] <test-flags>: Rework skipped tests, pass more.
<phases>: Remove 'fix-dependencies; add 'relax-requirements.
[native-inputs]: Remove python-wheel.
[propagated-inputs]: Add python-pygls.

Change-Id: I5b9c84d165c09ce62d364dbbd2da7108dc2eda1c
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-pygls.

* gnu/packages/python-xyz.scm (python-pygls): New variable.

Change-Id: Ifb4bf0277f87fec87161f57ec09b8916ee5de077
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-lsprotocol.

* gnu/packages/python-xyz.scm (python-lsprotocol): New variable.

Change-Id: Id12df328f4c8f51f9c45914fba8f4991857f7596
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-fastcluster: Update to 1.3.0.

* 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>

gnu: python-cvxpy: Update to 1.7.5.

* 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>

gnu: python-scs: Update to 3.2.10.

* 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>

gnu: Add scs.

* gnu/packages/maths.scm (scs): New variable.

Change-Id: Iea504b64a1da5cb4d446fe6461bbf4b2a47f4139
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-osqp: Update to 1.0.5.

* 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>