gnu: python-pyro4: Update to 4.82.

* gnu/packages/python-xyz.scm (python-pyro4): Update to 4.82.
[build-system]: Switch to pyproject-build-system.
[arguments]{tests?}: Remove to enable tests.
{test-flags}: Skip missing tests.
{phases}: Add 'check phase replacement.
[native-inputs]: Add python-setuptools, python-wheel.

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

gnu: python-serpent: Update to 1.41.

* gnu/packages/python-xyz.scm (python-serpent): Update to 1.41.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-setuptools, python-wheel.

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

gnu: python-attr: Update to 0.3.2.

* gnu/packages/python-xyz.scm (python-attr): Update to 0.3.2.

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

gnu: python-property-cached: Fix build.

* gnu/packages/python-xyz.scm (python-property-cached): Fix build.
* gnu/packages/patches/python-property-cached-asyncio-3_11.patch: Add
patch.
* gnu/local.mk: Record patch.

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

gnu: Remove pybind11-2.3.

This package is now a leaf package that fails to build.

* gnu/packages/python-xyz.scm (pybind11-2.3): Delete variable.

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

gnu: python-vaex-core: Update to 4.17.1.

* gnu/packages/python-science.scm (python-vaex-core): Update to 4.17.1.
* gnu/packages/patches/python-vaex-core-fix-tsl-use.patch: Add patch.
* gnu/local.mk: Record patch.

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

gnu: python-pytensor: Update to 2.28.3.

* gnu/packages/python-science.scm (python-pytensor): Update to 2.28.3.
[arguments]{test-flags}: Use field.
{phases}: Remove 'check phase replacement. Simplify 'versioneer. Add
phase 'pre-check.

Co-authored-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Change-Id: I8f324863438356ebc1ad3d62e86b5b17c416cd02
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: Add string-view-lite.

* gnu/packages/cpp.scm (string-view-lite): New variable.

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

gnu: python-pytorch-geometric: Skip failing tests.

* gnu/packages/machine-learning.scm (python-pytorch-geometric):
[arguments]{test-flags}: Skip test_type_repr failing test.

Change-Id: I8ec82761a107ed6021c655250f8ab5b1187980c8
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: mageck: Add missing native-inputs.

* gnu/packages/bioinformatics.scm (mageck)[native-inputs]: Add
python-wheel.

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

gnu: autokey: Add missing native-inputs.

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

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

gnu: scregseg: Add missing native-inputs.

* gnu/packages/bioinformatics.scm (scregseg)[native-inputs]: Add
python-wheel.

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

gnu: labelme: Add missing native-inputs.

* gnu/packages/image-processing.scm (labelme)[native-inputs]: Add
python-wheel.

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

gnu: Add clipper2.

* gnu/packages/cpp.scm (clipper2): New variable.

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

gnu: python-numdifftools: Skip some tests.

* gnu/packages/python-science.scm (python-numdifftools) [arguments]
<test-flags>: Skip 7 tests failing with a NumPy 1.26.2.

Change-Id: I5dc5865d0ac1ba47e79aac57d4e1768ecdb590be

gnu: python-mechanize: Update to 0.4.10.

* gnu/packages/python-xyz.scm (python-mechanize): Update to 0.4.10.
[build-system]: Switch to pyproject-build-system.
[arguments]{tests?}: Disable them.
{phases}: Add 'configure-tests phase to setup GUIX_PYTHONPATH.
[native-inputs]: Add python-html5-parser, python-html5lib,
python-lxml, python-service-identity, python-setuptools, python-six,
python-twisted, python-wheel.

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

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>