gnu: python-pysnptools: Fix build and enable tests.

* gnu/packages/bioinformatics.scm (python-pysnptools): Fix build and enable
tests.
[arguments]{test-flags}: Ignore failing tests.
{phases}: Add 'patch-data-path and 'loosen-requirements phases.

(pysnptools-examples-files): Add origin.
(bgen-sample-files): Add origin.

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

gnu: python-bed-reader: Fix build and enable tests.

* gnu/packages/bioinformatics.scm (python-bed-reader): Fix build and enable tests.
[source]{snippet}: Delete bundled website-related javascript.
{patches}: Use the store-cached instead of pooch-cached samples.
[arguments]{tests?}: Enable them.
{cargo-test-flags}: Skip doc tests. Skip failing tests.
{cargo-inputs}: Improve style.
{cargo-development-inputs}: Improve style.
{phases}: Add phases 'set-data-path, 'patch-data-path to use
store-cached samples for library and tests.  Rewrite phase
'prepare-python-module to rely more on the existing info in
pyproject.toml.  Rewrite phase 'check-python entirely, and
marginaly rewrite phase 'install-python-library to match 'check-python
phase style.
{modules}: Adapt accordingly.
{propagated-inputs}: Remove python-pooch. Add python-scipy.

(bed-sample-files): Add origin, used in python-bed-reader.

* gnu/packages/patches/python-bed-reader-use-store-samples.patch: Add
patch.
* gnu/local.mk: Record patch.

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

gnu: python-qasync: Ignore failing test.

* gnu/packages/python-xyz.scm (python-qasync)[arguments]{test-flags}:
Ignore failing tests.

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

gnu: python-pgmpy: Update to 1.0.0.

* gnu/packages/statistics.scm (python-pgmpy): Update to 1.0.0.
[arguments]{test-flags}: Ignore failing tests.
[native-inputs]: Add python-pyro-ppl, python-setuptools, python-wheel,
python-xgboost.

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

gnu: python-botorch: Update to 0.13.0.

* gnu/packages/machine-learning.scm (python-botorch): Update to
0.13.0.
[native-inputs]: Add python-pyre-extensions.

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

gnu: python-gpytorch: Update to 1.14.

* gnu/packages/machine-learning.scm (python-gpytorch): Update to 1.14.
[arguments]{test-flags}: Ignore additional failing test.
[propagated-inputs]: Add python-jaxtyping.
[native-inputs]: Add python-setuptools, python-wheel.

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

gnu: python-botorch: Add missing native-inputs.

* gnu/packages/machine-learning.scm (python-botorch)[native-inputs]:
Add python-setuptools, python-wheel.

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

gnu: python-gpytorch: Remove uneeded inputs.

* gnu/packages/machine-learning.scm (python-gpytorch): Remove uneeded
inputs.
[arguments]{test-flags}: Ignore costly examples tests.
[native-inputs]: Remove python-coverage, python-flake8,
python-flake8-print, python-twine.

Change-Id: Id3b9537d9f3306cc4a8e0eed19aabd5732854813
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-linear-operator: Update to 0.6.

* gnu/packages/machine-learning.scm (python-linear-operator): Update
to 0.6.
[propagated-inputs]: Remove python-typeguard. Add python-mpmath.
[native-inputs]: Remove python-flake8, python-flake8-print,
python-twine. Add python-typeguard, python-wheel.

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

gnu: python-lcapy: Add missing native-inputs.

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

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

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>