gnu: python-pyspoa: Switch to pyproject.

* gnu/packages/bioinformatics.scm (python-pyspoa):
[build-system]: Switch to pyproject-build-system.
[arguments]: Improve style.
<#:phases>: Migrate phase 'check to <#:test-backend, #:test-flags>.
[native-inputs]: Add python-setuptools.

Change-Id: Ib38a5779d6b73050126c377f6b0c5d5a53ef25aa
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pypairix: Fix package.

The package was missing binaries, which were not produced because
CFLAGS were effectively ignored.

* gnu/packages/bioinformatics.scm (python-pypairix)[arguments]
<#:phases>: Add phase 'respect-CFLAGS.

Change-Id: Id982af5f5a0c43c6fc20e109a5419913e47882e9
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: flair: Switch to pyproject.

* gnu/packages/bioinformatics.scm (flair):
[build-system]: Switch to pyproject-build-system.
[arguments]<#:phases>: Remove phases 'build and 'install.

Change-Id: Iaf2e75c1830faae61dcab542a733773b621aa93c
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-liana-py: Don't propagate python-numpydoc.

* gnu/packages/bioinformatics.scm (python-liana-py)
[propagated-inputs]: Remove python-numpydoc.
[native-inputs]: Add python-numpydoc.

Change-Id: I3691a1db99010926b80de7aed5b29e5602210aa2
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-scanrbp: Include data in package.

* gnu/packages/bioinformatics.scm (python-scanrbp): Fix build and include data.
[native-inputs]: Remove python-wheel.
<#:phases>: Add 'patchpath and 'copy-data phases. Replace 'check phase.

Change-Id: Ie61792f696f59383789cac89bf9f354f0ce1d188
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-biothings-client: Update to 0.4.1.

* gnu/packages/bioinformatics.scm (python-biothings-client): Update to 0.4.1.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-setuptools.
[propagated-inputs]: Add python-httpx.

Change-Id: I3d5c9ea79fd23a8291074f32d37adfede4e0e238
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-drep: Skip additional test.

* gnu/packages/bioinformatics.scm (python-drep)[arguments]
<#:test-flags>: Skip additional test.

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

gnu: scregseg: Skip 'sanity-check phase.

* gnu/packages/bioinformatics.scm (scregseg)
[arguments]<#:phases>: Skip 'sanity-check phase.
[native-inputs]: Add python-pytest.

Change-Id: If28faf66025e79210850080a18b8ce35d9ec6504
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-coolbox: Fix inputs.

* gnu/packages/bioinformatics.scm (python-coolbox)
[native-inputs]: Remove python-pybbi.
[propagated-inputs]: Add python-pybbi.

Change-Id: Ic748f66b71b0aa489e8c0800b21cb23592f285a4
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-genomepy: Update to 0.16.3.

* gnu/packages/bioinformatics.scm (python-genomepy): Update to 0.16.3.
[source]: Switch to git-fetch.
[native-inputs]: Remove python-pytest.

Change-Id: Iab4a30e7fb4ff31243ae0c210155a2d1896bd3cb
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pygam: Update to 0.12.0.

* gnu/packages/bioinformatics.scm (python-pygam): Update to 0.12.0.
[arguments] <test-flags>: Skip one test.
<phases>: Remove 'patch-pyproject.
[propagated-inputs]: Remove python-black, python-flake8, python-ipython,
and python-poetry-core.
[native-inputs]: Remove python-pytest-cov; add python-matplotlib and
python-setuptools.

Change-Id: I5b3b95deb2bbe455582d4c74fe672c62b9aa8ff4
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-phenograph: Fix tests.

* gnu/packages/bioinformatics.scm (python-phenograph):
[arguments] <test-flags>: Skip 3 more tests.
<phases>: Remove 'disable-leiden-test, and move logic to <#:test-flags>.
[propagated-inputs]: Remove python-numpy; add python-numpy-1.
[native-inputs]: Remove python-wheel.

Change-Id: Id7a7cb67adb13749bde59ad93d5c1125f2903065
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Remove fanc.

* gnu/packages/bioinformatics.scm (fanc): Delete variable.

Change-Id: I6ecb68155c021a67ff548bb2bd3bb6052676dc3a
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-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-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-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>