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>

gnu: python-pypika-tortoise: Update to 0.6.3.

* gnu/packages/databases.scm (python-pypika-tortoise): Update to 0.6.3.
[arguments]<test-flags>: Skip one test.
[native-inputs]: Remove python-poetry-core; add python-pdm-backend.

Change-Id: Id29435ec6f4c5962f32020e3cfaadac0911cd373
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pyreadstat: Update to 1.3.2.

* gnu/packages/statistics.scm (python-pyreadstat): Update to 1.3.2.
[arguments] <test-backend, test-flags>: Move custom 'check phase logic here.
<phases>: Remove 'change-home-dir; add 'pre-check.
[inputs]: Add readstat.
[propagated-inputs]: Add python-narwhals-minimal and python-numpy.

* gnu/packages/patches/python-pyreadstat-link-libiconv.patch: Refresh
patch for 1.3.2.

Change-Id: I478c67cb48574178483b6dfe97b5ed7bf9b4c783
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-narwhals: Update to 2.15.0.

* gnu/packages/python-science.scm (python-narwhals): Update to 2.15.0.
[propagated-inputs]: Add python-duckdb, python-packaging, and python-rich.
[native-inputs]: Remove python-duckdb.

Change-Id: I0af82e4cbe2b3c2b3ae3803b77cde5f6c921a1a6
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-narwhals-minimal.

* gnu/packages/python-science.scm (python-narwhals-minimal): New variable.

Change-Id: I972010ea88c649d41227c51256b739a022a350df
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-watchfiles: Update to 1.1.1.

* gnu/packages/python-xyz.scm (python-watchfiles): Update to 1.1.1.

* gnu/packages/rust-crates.scm: (rust-syn-2.0.60,
rust-proc-macro2-1.0.81, rust-filetime-0.2.24,
rust-crossbeam-utils-0.8.19, rust-cc-1.0.96, rust-bitflags-2.7.0): New
variables.

(lookup-cargo-inputs)[python-watchfiles]: Remove rust-autocfg-1.4.0,
rust-bitflags-2.9.0, rust-cc-1.2.19, rust-crossbeam-utils-0.8.21,
rust-filetime-0.2.25, rust-indoc-2.0.6, rust-inotify-0.10.2,
rust-instant-0.1.13, rust-libc-0.2.172, rust-log-0.4.27,
rust-notify-7.0.0, rust-notify-types-1.0.1, rust-portable-atomic-1.11.0,
rust-proc-macro2-1.0.95, rust-pyo3-0.24.1,
rust-pyo3-build-config-0.24.1, rust-pyo3-ffi-0.24.1,
rust-pyo3-macros-0.24.1, rust-pyo3-macros-backend-0.24.1,
rust-python3-dll-a-0.2.13, rust-quote-1.0.40, rust-redox-syscall-0.5.11,
rust-shlex-1.3.0, rust-syn-2.0.100, rust-unicode-ident-1.0.18, and
rust-unindent-0.2.4; add rust-autocfg-1.3.0, rust-bitflags-2.7.0,
rust-cc-1.0.96, rust-crossbeam-utils-0.8.19, rust-filetime-0.2.24,
rust-indoc-2.0.5, rust-inotify-0.11.0, rust-libc-0.2.169,
rust-log-0.4.22, rust-notify-8.0.0, rust-notify-types-2.0.0,
rust-portable-atomic-1.6.0, rust-proc-macro2-1.0.81, rust-pyo3-0.26.0,
rust-pyo3-build-config-0.26.0, rust-pyo3-ffi-0.26.0,
rust-pyo3-macros-0.26.0, rust-pyo3-macros-backend-0.26.0,
rust-python3-dll-a-0.2.14, rust-quote-1.0.36, rust-redox-syscall-0.5.3,
rust-syn-2.0.60, rust-unicode-ident-1.0.12, and rust-unindent-0.2.3.

Change-Id: I197939e4c9061d59708f51bfb8667d81555ea17a

Change-Id: Iec394c08dad5aa5fe063bc06b927e05089231f84
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-libneuroml: Update to 0.6.7.

* gnu/packages/python-science.scm (python-libneuroml): Update to 0.6.7.
[native-inputs]: Remove python-wheel.

Change-Id: I7ef49953a922116bd2c1aeb12ea548d0dd8afb18
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-imagecodecs: Fix build.

* gnu/packages/python-xyz.scm (python-imagecodecs):
[inputs]: Remove python-blosc2; add c-blosc2.

Change-Id: I28487d0a93c8098620b68c5d46caf6d6f55ca108
Signed-off-by: Rutherther <rutherther@ditigal.xyz>