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>

gnu: dolphin-emu: Use python-numpy@1.

* gnu/packages/emulators.scm (dolphin-emu)[native-inputs]: Remove
python-numpy, add python-numpy-1.

Change-Id: I1693aa1af04d8c2abca4781b81143cb9a22275d8
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-statannotations.

* gnu/packages/statistics.scm (python-statannotations): New variable.

Change-Id: Ib8a51d7b63c9be9af2addf193c8241569c793569
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-scikit-surprise: Use python-numpy@1.

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

Change-Id: I4ae8d087b602a04ff94ad1ef72c6ef0589938054
Signed-off-by: Rutherther <rutherther@ditigal.xyz>