gnu: python-flask-seasurf: Update to 2.0.0.

* gnu/packages/python-web.scm (python-flask-seasurf): Update to 2.0.0.

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

gnu: python-django-rq: Update to 3.0.0.

* gnu/packages/django.scm (python-django-rq): Update to 3.0.0.
[arguments]{test-flags}: Ignore failing tests.
{phases}: Replace 'check phase replacement by a simpler 'pre-check
configuration phase.
[native-inputs]: Add python-pytest, python-pytest-django.
[propagated-inputs]: Add python-redis, python-pyaml.

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

gnu: Remove python-cookies.

This is a leaf package in python, broken and undevelopped for 10 years.

* gnu/packages/python-web.scm (python-cookies): Delete variable.

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

gnu: python-port-for: Update to 0.7.4.

* gnu/packages/python-web.scm (python-port-for): Update to 0.7.4.
[build-system]: Switch to pyproject.
[native-inputs]: Remove python-mock.  Add python-setuptools,
python-wheel.

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

gnu: python-rq-scheduler: Update to 0.14.

* gnu/packages/databases.scm (python-rq-scheduler): Update to 0.14.
[build-system]: Switch to pyproject.
[arguments]{test-flags}: Ignore failing tests.  They fail because of
mcron's requirements to be run with root when -u flag is used.
{phases}: Remove 'check phase replacement.
[native-inputs]: Add python-crontab, python-freezegun, python-pytest,
python-setuptools, python-wheel.  Remove which.

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

gnu: python-stone: Update to 3.3.9.

* gnu/packages/python-xyz.scm (python-stone): Update to 3.3.9.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject.
[arguments]: Remove field.
[propagated-inputs]: Add python-jinja2, python-packaging.
[native-inputs]: Add python-setuptools, python-wheel. Remove
python-coverage, python-mock.

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

gnu: python-crontab: Update to 3.2.0.

* gnu/packages/python-xyz.scm (python-crontab): Update to 3.2.0.
[build-system]: Switch to pyproject.
[arguments]{test-flags}: Ignore test.
{phases}: Remove phase 'disable-failing-tests. Add phase
default-to-mcron.
[inputs]: Add mcron.
[native-inputs]: Add python-pytest, python-setuptools, python-wheel.

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

gnu: python-rq: Update to 2.3.1.

* gnu/packages/databases.scm (python-rq): Update to 2.3.1.
[build-system]: Switch to pyproject.
[arguments]{phases}: Delete 'check phase replacement. Improve style.
[native-inputs]: Add python-hatchling.

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

gnu: python-furl: Update to 2.1.4.

* gnu/packages/python-web.scm (python-furl): Update to 2.1.4.
[build-system]: Swtich to pyproject.
[arguments]{test-flags}: Ignore failing tests.
[propagated-inputs]: Sort.
[native-inputs]: Add python-pytest, python-setuptools, python-wheel.

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

gnu: python-pgpy: Fix tests.

* gnu/packages/python-crypto.scm (python-pgpy): Fix tests.
[build-system]: Switch to pyproject.
[arguments]{phases}: Remove argument.
{test-flags}: Ignore failing tests.
[native-inputs]: Add python-setuptools.

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

gnu: python-duniterpy: Update to 1.2.1.

* gnu/packages/finance.scm (python-duniterpy): Update to 1.2.1.
[source]: Switch to git-fetch to get tests.
[arguments]: Remove field.
[native-inputs]: Replace python-poetry-core by
python-poetry-core-next.  Add python-pytest.
[propagated-inputs]: Remove python-attrs.

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

gnu: Add python-poetry-core-next.

* gnu/packages/python-build.scm (python-poetry-core-next): New variable.

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

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>