gnu: Remove python-watchgod.

* gnu/packages/python-xyz.scm (python-watchgod): Delete variable.

Change-Id: I52cbd0577de38bb21094ed8f6ee5ef14741634e0
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Remove python-statannot.

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>

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

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

Change-Id: Ib7ea70587df75876a01e44899b7aebdd121f19fb
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-peaks2utr: Use python-numpy@1.

* gnu/packages/bioinformatics.scm (python-peaks2utr):
[propagated-inputs]: Remove python-numpy; add python-numpy-1.

Change-Id: I9aacc181e7fd2330c7ed46f14902701aba843fe8
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pandapower: Update to 3.3.0.

* gnu/packages/engineering.scm (python-pandapower): Update to 3.3.0.
[source]: Switch to git-fetch.
[arguments] <test-flags>: Run tests in parallel, supported by upstream.
<phases>: Add 'relax-requirements.
[propagated-inputs]: Add python-pandera, python-geopandas, python-lxml,
python-matplotlib, python-openpyxl, python-pyproj, and
python-shapely.
[native-inputs]: Remove python-pyproj, python-wheel, and unzip; add
python-nbmake and python-pytest-xdist.

Change-Id: I26e0f5ab3efa299beb1acf6ced4dfa3d15f7df3f
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-deepdiff: Update to 8.6.1.

* gnu/packages/python-xyz.scm (python-deepdiff): Update to 8.6.1.
[native-inputs]: Add python-uuid6.

Change-Id: Ife7367c5772c8bba067e698f01b974cf2bfb4bfb
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-uuid6.

* gnu/packages/python-xyz.scm (python-uuid6): New variable.

Change-Id: I3bf9d83706763ac3ed360005831dbfa3f775c368
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

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

* gnu/packages/maths.scm (python-orthopy):
[propagated-inputs]: Remove python-numpy; add python-numpy-1.
[native-inputs]: Remove python-wheel.

Change-Id: I574e885dd7ef3522160cb287e4094c6ed4a05181
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

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

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

Change-Id: I9fa1bf6e8b8110350d5524740653e02d99e36a91
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-metpy: Update to 1.7.1.

* gnu/packages/geo.scm (python-metpy): Update to 1.7.1.

Change-Id: I93c3600f1549d70c18acdb0b8652ffc3fbe7642c
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-mathics-core: Use python-numpy@1.

* gnu/packages/maths.scm (python-mathics-core):
[arguments] <tests?>: Disable for now.
[propagated-inputs]: Remove python-numpy; add python-numpy-1.

Change-Id: I39be334cd670b0e747429887f5a92505bd7be154
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pysm3: Relax requirements for NumPy and SciPy.

* gnu/packages/astronomy.scm (python-pysm3):
[phases] {relax-requirements}: New phase.

Change-Id: I856c43fe9aa7d83cdb9fc71aa8687bf6648e0ba6
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-lifelines: Simplify tests.

* gnu/packages/statistics.scm (python-lifelines):
[arguments] <test-flags>: Rework skipped tests to improve determinism of
them.
[native-inputs]: Remove python-pytest-xdist and python-wheel; add
python-jinja2.

Change-Id: Ia468acbfff3714662620e1196f4ea8fe72a308df
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pytoolconfig: Reduce closure size.

* gnu/packages/python-xyz.scm (python-pytoolconfig): Update to 1.3.1.
[propagated-inputs]: Remove python-pydantic, python-sphinx,
python-sphinx-autodoc-typehints, python-sphinx-rtd-theme, and
python-tabulate.

Change-Id: Ifd1831f64dcb14afaddf9a1b6d445b0b67e94bbd
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pandas-stubs: Update to 2.3.3.251219.

* 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>

gnu: python-liana-py: Update to 1.6.1.

* gnu/packages/bioinformatics.scm (python-liana-py): Update to 1.6.1.
[arguments] <test-flags>: Skip 2 more tests.

Change-Id: Ic73e742be564798cc349b91966beeeb6561a72fa
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-decoupler: Update to 2.1.2.

* gnu/packages/bioinformatics.scm (python-decoupler): Update to 2.1.2.
[phases]{relax-requirements}: New phases.

Change-Id: Iaa57b2d4ef96d661a68310c64c6f2e2b8aee520b
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-iced: Update to 0.6.0.

* gnu/packages/bioinformatics.scm (python-iced): Update to 0.6.0.
[native-inputs]: Remove python-wheel; add python-cython.

Change-Id: I9fa0c3f1e1e4972349007d82095ddda7ae65e0b1
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-hyperopt: Fix build.

* gnu/packages/machine-learning.scm (python-hyperopt):
[arguments] <test-flags>: Move test logic from custom 'check phase here.
<phases>: Use default 'check.
[propagated-inputs]: Remove python-numpy; add python-numpy-1 and
python-scikit-learn.

Change-Id: Ic5b8b5a2ed37417e4869b8b00110367778b2c632
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-tortoise-orm: Update to 0.25.3.

* gnu/packages/databases.scm (python-tortoise-orm): Update to 0.25.3.
[arguments] <test-flags>: Skip only one test, run them in parallel.
[propagated-inputs]: Remove python-asyncmy, and python-rapidjson; add
python-anyio, python-asyncodbc, python-orjson, python-psycopg,
python-psycopg-pool, and python-pyodbc.
[native-inputs]: Remove python-ayncodbc, python-psycopg,
python-psycopg-pool, python-pyodbc, and python-poetry-core; add
python-cython, and
python-pdm-backend, python-pytest-xdist.

Change-Id: I4e2c7b8f083bd649c313c26b77c0dd2110a9689c
Signed-off-by: Rutherther <rutherther@ditigal.xyz>