gnu: Remove clustal-omega.

Does not build due to failing input argtable@2. No release since 2018.

* gnu/packages/bioinformatics.scm (clustal-omega): Delete variable.

Change-Id: I28d6ce8e44419a4e07dec8a44b23be13af3ca82e

gnu: nss-certs: Relocate to (gnu packages nss).

This is made so that the source can be shared without introducing module
circular dependencies.

* gnu/packages/certs.scm (nss-certs)
(nss-certs-for-test): Move to...
* gnu/packages/nss.scm: ... here.

Adjust the module imports via:

  git grep -l '(gnu packages certs)' |
  xargs sed 's/(gnu packages certs)/(gnu packages nss)/' -i

Change-Id: I56d7bc52ddcdffbced8a162e8db8ea5071b0cb0f

gnu: nanosv: Switch to pyproject.

* gnu/packages/bioinformatics.scm (nanosv):
[source, description]: Run guix style.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:tests?>: Disable them.
<#:phases>: Add phase 'relax-requirements.
[native-inputs]: Add python-setuptools, python-wheel.

Change-Id: If63f2534ae9b0e7cc34c4e5d59fb0947fcbe5d45
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: vembrane: Update to 1.0.7.

* gnu/packages/bioinformatics.scm (vembrane): Update to 1.0.7.
[arguments] <phases>: Remove 'relax-requirements; add 'use-poetry-core.
[native-inputs]: Remove poetry; add python-poetry-core.

Change-Id: I50aca480b3aded3714d6e999efd3d12a4513e6a3

gnu: Pin some golang packages to use go-1.23.

After the defult Golang version was set to 1.24 some of the older
packages which had no fresh version started failing on the 'check phase,
this change pins them to go-1.23 helping to resolve the issue.

Go 1.24 requires non-constant format strings to be explicitly handled.

The errors might look like these:

    non-constant format string in call to (*testing.common).Errorf
    ExampleParseOptionsLifetime refers to unknown identifier: ParseOptionsLifetime

See <https://tip.golang.org/doc/go1.24#vet>.

Change-Id: Ife5093c4fd98af7cea59abf1a9a29351b66602bb

gnu: ivar: Update to 1.4.4, fix build with gcc@14.

* gnu/packages/bioinformatics.scm (ivar): Update to 1.4.4.

Change-Id: Ia7ec6adb465e3256d3f4dfd7e2fb51ae3334261f

gnu: python-liana-py: Update to 1.6.0.

* gnu/packages/bioinformatics.scm (python-liana-py): Update to 1.6.0.
  [arguments] <test-flags>: Skip more problematic tests. Adjust pathe
  for "--ignore" option.
  <phases>: Remove 'relax-requirements.
  [propagated-inputs]: Remove python-decoupler-py; add python-decoupler.
  [native-inputs]: Remove python-black, python-poetry-core, and
  python-pytest-cov; add python-hatchling.

Change-Id: Icfec6a217f828b5e68cccde88fc889b2ee3e32f3

gnu: Add python-decoupler.

This package is a successor of python-decoupler-py with reworked tests
and inputs. Project has changed the license from GPL3+ to BSD-3.

See: <https://github.com/scverse/decoupler/blob/main/CHANGELOG.md#200>

* gnu/packages/bioinformatics.scm (python-decoupler): New variable based
  on python-decoupler-py.
  [source] <url>: Fix permanent redirect.
  [arguments] <test-flags>: Rework skipped tests.
  <phases>: Remove 'relax-requirements.
  [propagated-inputs]: Remove python-ipython, python-matplotlib,
  python-nbsphinx, python-numpy, python-numpydoc, python-omnipath,
  python-scanpy, python-scikit-learn, python-skranger, and
  python-typing-extensions; add python-dcor, python-docrep,
  python-igraph, python-ipywidgets, python-marsilea, python-requests,
  python-session-info2, and python-xgboost.
  [native-inputs]: Remove python-poetry-core; add nss-certs-for-test,
  python-hatchling, python-gseapy, python-memory-profiler, and
  python-scanpy.
  [home-page]: Fix permanent redirect.
  [licenses]: Switch to bsd-3.

(python-decoupler-py): Deprecate package.

Change-Id: Ia517db074c7ac405408731c9a8cfe00e56b8107b

gnu: python-scanpy: Update to 1.11.2.

* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.11.2.
  [arguments] <test-flags>: Run tests in parallel, supported
  upstream. Skipp some more problematic tests.
  <phases>: Remove 'set-numba-cache-dir; add combined 'pre-check.
  [propagated-inputs]: Remove python-session-info; add python-session-info2.
  [native-inputs]: Add python-flaky, python-pytest-xdist, and python-scanorama.

Change-Id: I6a13a7c3449b0d60801daf49e40e6f1fcc48f0c0

gnu: blast+: Update to 2.17.0.

* gnu/packages/bioinformatics.scm (blast+): Update to 2.17.0.

Change-Id: I37b460e057b392a88934a03f9a41d2b445e08f20

gnu: salmon: Update to 1.10.3, fix build.

* gnu/packages/bioinformatics.scm (salmon): Update to 1.10.3.
[inputs]: Update pufferfish sources.

Change-Id: Iba95cc2bc61bbd8bddd1c9b679c9705e260a1364

gnu: r-voltron: Fix tests.

* gnu/packages/bioinformatics.scm (r-voltron): [inputs]: Add which.

Change-Id: Id16ef6a5810f592a349249f1327dc747db9a66b1

gnu: r-hdf5dataframe: Update to 0.0.0-2.1e30e6b.

* gnu/packages/bioinformatics.scm (r-hdf5dataframe): Update to 0.0.0-2.1e30e6b.
[native-inputs]: Add r-testthat.

Change-Id: I4b7b933dd8fe668d03f3e04ccd78336b4efa7e5f

gnu: python-mudata: Update to 0.3.2.

* gnu/packages/bioinformatics.scm (python-mudata): Update to 0.3.2.

Change-Id: I60c2b5d16dd1afddafc5f06231d6c5bf28a4b20c

gnu: python-py2bit: Update to 0.3.3.

* gnu/packages/bioinformatics.scm (python-py2bit): Update to 0.3.3.
[native-inputs]: Add python-setuptools-scm.

Change-Id: Ib7e9d701595501e5da76288e5a8cae32e1dc6739
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: htseq: Switch to pyproject.

* gnu/packages/bioinformatics.scm (htseq):
[build-system]: Switch to pyproject-build-system.
[arguments]: Remove uneeded field.
[native-inputs]: Add python-setuptools, python-wheel.

Change-Id: I5d9ccff56212413d76fa31f02efa5008dd709d97
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: Remove python-hicexplorer.

* gnu/packages/bioinformatics.scm (python-hicexplorer): Delete variable.

Change-Id: If17e4ffd145e889e5281d62470b243b0a2609d20

gnu: sortmerna: Update to 4.3.7.

* gnu/packages/bioinformatics.scm (sortmerna): Update to 4.3.7.

Change-Id: I412f3719549d9f8b2baba49acfedbe0d5ca0f3d9

gnu: sortmerna: Fix build with gcc-14.

* gnu/packages/bioinformatics.scm (sortmerna)[arguments]<#:phases>
{fix-includes}: New phase.

Change-Id: I5c2f6e6456e59ea39f02dd584c6d052c08ff9463

gnu: gdcm: Fix build.

* gnu/packages/bioinformatics.scm (gdcm)[arguments]
<#:configure-flags>: Move excluded tests ...
<#:excluded-tests>: ... to here.

Change-Id: I42cc96a9220e6e5aed1b4fe82ff10835789806e6