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>

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

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

Change-Id: I103cc604f51d1af3e4030c64b3bc3cda9fadc77d
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

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

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

Change-Id: I9df15444696ef365861b2fdf40011b86dc0afb1a
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

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

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

Change-Id: I8236576e39b7e6f8b981126cbf67fc55f35db83c
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-salib: Update to 1.5.2.

* gnu/packages/python-science.scm (python-salib): Update to 1.5.2.
[phases]{set-version}: New phase.
[native-inputs]: Remove python-pytest-cov; add python-hatch-vcs.

Change-Id: Ibff2633efa0f7657a40b580a3028cb71f57b923d
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

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

* gnu/packages/bioinformatics.scm (python-muon):
[propagated-inputs]: Remove python-numpy; add python-numpy-1.
[native-inputs]: Remove python-pytest-flake8.

Change-Id: I6b16e7ce8d26ba874d1065766fac875e880f51f2
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pyamg: Update to 5.3.0.

* gnu/packages/python-science.scm (python-pyamg): Update to 5.3.0.
[arguments] <test-flags>: Remove local source instead in phase..
<phases>: Add 'pre-check.
[native-inputs]: Remove python-wheel.

Change-Id: I3f231c1201013b4cbc7a8fbda14937aa0685827e
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pygenometracks: Update to 3.9.

* gnu/packages/bioinformatics.scm (python-pygenometracks): Update to 3.9.
[source]: Switch to git-fetch.
[arguments] <tests?, test-flags>: Enable them.
<phases>: Remove 'remove-invalid-syntax; adjust 'relax-requirements.
[propagated-inputs]: Add python-bx-python, python-pybedtools, and
python-pyfaidx.
[native-inputs]: Remove python-wheel; add python-setuptools.

Change-Id: I364255a3e4d072535a871340588cdff0f30b83ff
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-hicmatrix: Update to 17.2.

* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 17.2.
[arguments] <test-flags>: Skip one test.
<phases>: Remove 'find-blosc2.
[inputs]: Remove c-blosc2.
[native-inputs]: Remove python-wheel.

Change-Id: I45972befc224d9c85858d1c1ac9be885f63cdf01
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: pigx-scrnaseq: Use python-numpy@1.

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

Change-Id: I3bd24084626d2c1720c899a2bae6e9be4ab99c09
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-sbpy: Skip one doc test.

* gnu/packages/astronomy.scm (python-sbpy) [arguments] <test-flags>:
Skip one test.

Change-Id: Ie3c929d9367f596561f67e34f7bebf9024641654
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: scvelo: Update to 0.3.3.

* gnu/packages/bioinformatics.scm (scvelo): Update to 0.3.3.
[source]: Switch to git-fetch.
[arguments] <test-flags>: Run all tests in "tests/core"
<phases>: Remove 'matplotlib-compatibility; add 'set-version.

Change-Id: Iea4f9e9b7d385033b1131644c0145a5fdc3a7db7
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-hic2cool: Fix tests.

* gnu/packages/bioinformatics.scm (python-hic2cool) [arguments]
<test-backend, test-flags>: Use custom.

Change-Id: I1bfacc5b91a31e3bcd9434589d1d9e1a7b4d4076
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-hdf5storage: Use pythno-numpy@1.

* gnu/packages/python-xyz.scm (python-hdf5storage):
[propagated-inputs]: Remove python-numpy; add python-numpy-1.
[native-inputs]: Remove python-wheel.

Change-Id: I1d2e3d4d5b654e4025aa16f4d1aa9230c10a3e0a
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

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

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

Change-Id: Ida842dda2adea1e6a2085ae219b7e95988c14f85
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: coda: Use python-numpy@1.

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

Change-Id: I1419ec3eb9cb4f25b1078908e305c99ec8bd59c4
Signed-off-by: Rutherther <rutherther@ditigal.xyz>