gnu: openmolar: Fix build.

* gnu/packages/medical.scm (openmolar): Fix build.
[build-system]: Switch to pyproject-build-system.
[arguments]{use-setuptools?}: Drop it.
{phases}: Add phase 'set-acceptable-version.
[native-inputs]: Add python-setuptools, python-wheel.

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

gnu: libei: Update to 1.4.0.

* gnu/packages/freedesktop.scm (libei): Update to 1.4.0.
[native-inputs]: Add dbus, python-pyaml. Remove python-black.

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

gnu: python-cu2qu: Fix tests.

* gnu/packages/fontutils.scm (python-cu2qu): Fix tests.
[build-system]: Switch to pyproject-build-system.
[arguments]{test-flags}: Ignore failing test (most likely due to
lagging behing python-fonttools package).
[native-inputs]: Add python-setuptools, python-wheel.
* gnu/packages/python-xyz.scm (python-fonttools-minimal): Add comment.

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

gnu: conan: Update to 2.7.1.

* gnu/packages/package-management.scm (conan): Update to 2.7.1.
[build-system]: Switch to pyproject-build-system.
[arguments]{test-flags}: Use field. Ignore failing tests (old versions
of cmake, performance tests, docker/premake/scons requirements.
{phases}: Refresh phases. Replace 'check phase by a 'configure-tests
phase and the native 'check phase.
[propagated-inputs]: Replace python-urllib3 by python-urllib3-next.
[native-inputs]: Add python-setuptools, python-wheel.

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

gnu: veusz: Update to 3.6.2.

* gnu/packages/maths.scm (veusz): Update to 3.6.2.
[build-system]: Switch to pyproject-build-system.
[arguments]: Improve style, use gexps.
{phases}: Remove phase 'fix-sip-dir. Add phase
'fix-pyqt5-include-dir. Refresh phase 'wrap-executable.
[native-inputs]: Add python-astropy, python-setuptools,
python-wheel. Remove python-sip-4.
[inputs]: Add qtwayland-5.

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

gnu: python-patch-ng: Update to 1.18.1.

* gnu/packages/python-xyz.scm (python-patch-ng): Update to 1.18.1.

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

gnu: cpplint: Update to 2.0.0.

* gnu/packages/cpp.scm (cpplint): Update to 2.0.0.
[arguments]{phases}: Add phase 'patch-build-system.
[native-inputs]: Add python-parameterized, python-pytest-timeout.

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

gnu: umi-tools: Update to 1.1.6.

* gnu/packages/bioinformatics.scm (umi-tools): Update to 1.1.6.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[inputs]: Add python-pybktree, python-scipy.
[native-inputs]: Add python-setuptools, python-wheel.

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

gnu: Add python-pybktree.

* gnu/packages/backup.scm (python-pybktree): New variable.

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

gnu: python-sip: Update to 6.10.0.

* gnu/packages/qt.scm (python-sip): Update to 6.10.0.
[source]: Add snippet to relax python-setuptools requirement.
[native-inputs]: Remove python-wrapper. Add python-wheel. Sort inputs.
[propagated-inputs]: Remove python-tomli, python-wheel. Sort inputs.

* gnu/packages/backup.scm (vorta)[native-inputs]: Add
python-setuptools, python-wheel.

* gnu/packages/python-xyz.scm (python-echo)[native-inputs]: Add
python-setuptools, python-wheel.

* gnu/packages/patches/python-sip-include-dirs.patch: Refresh patch.

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

gnu: python-rstr: Update to 3.2.2. Enable tests.

* gnu/packages/python-xyz.scm (python-rstr): Update to 3.2.2.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]{phases}: Add phase 'pretend-version.
[native-inputs]: Add python-pytest, python-setuptools,
python-setuptools-scm, python-wheel.

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

gnu: taxtastic: Update to 0.11.1.

* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.11.1.
[build-system]: Switch to pyproject-build-system.
[arguments]{test-flags}: Ignore failing test.
{phases}: Improve style with gexp. Update phase
'prepare-directory. Improve phase 'check with test-flags inclusion.
[native-inputs]: Add python-setuptools, python-wheel.
[propagated-inputs]: Sort inputs. Replace python-psycopg2 by both
python-psycopg and python-psycopg2-binary. Add python-sqlparse.

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

gnu: Remove python-pyfasta.

This package is archived and deprecated in favor or python-pyfaidx for
7 years.

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

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

gnu: seqmagick: Update to 0.8.6-0.dee6ab9.

* gnu/packages/bioinformatics.scm (seqmagick): Update to 0.8.6-0.dee6ab9.

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

gnu: rseqc: Switch to pyproject-build-system.

* gnu/packages/bioinformatics.scm (rseqc):
[build-system]: Switch to pyproject-build-system.
[inputs]: Sort inputs. Add python-pyparsing, python-setuptools,
python-wheel.

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

gnu: python-locust: Update to 2.33.2.

* gnu/packages/benchmark.scm (python-locust): Update to 2.33.2.
[arguments]{test-flags}: Add additional missing test.
{phases}: Add phase 'pretend-version. Adapt phase fix-version.
[native-inputs]: Remove python-poetry-core,
python-poetry-dynamic-versioning. Add python-hatchling,
python-hatch-vcs.

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

gnu: python-pyquery: Update to 2.0.1.

* gnu/packages/python-xyz.scm (python-pyquery): Update to 2.0.1.
[build-system]: Switch to pyproject-build-system.
[arguments]{test-flags}: Ignore a test that requires network access.
[native-inputs]: Add python-pytest, python-pytest-cov,
python-requests, python-setuptools, python-webob, python-webtest,
python-wheel.
[propagated-inputs]: Sort inputs.

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

gnu: Remove python-anyjson.

This package is a leaf package in Guix, is stale for 13 years, and its
upstream repository is not even up anymore.

* gnu/packages/python-xyz.scm (python-anyjson): Delete variable.

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

gnu: Remove python-parameterizedtestcase.

This package is a leaf package in Guix, has been abandonned for 11
years (aside from a License change).

* gnu/packages/python-check.scm (python-parameterizedtestcase): Delete variable.

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

gnu: python-pyvcf: Use the fork python-pyvcf3.

* gnu/packages/bioinformatics.scm (python-pyvcf): Define in terms of
'deprecated-package'.
(python-pyvcf3): New variable.
(python-nanosv): Replace python-pyvcf by python-pyvcf3.

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