gnu: kapidox: Switch to pyproject.

* gnu/packages/kde-frameworks.scm (kapidox):
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-setuptools.

Change-Id: Idedbc3901ddb80969d23cff179abf79743ec13cb
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python2-pycparser: Move to (gnu packages pypy).

* gnu/packages/python-xyz.scm (python2-pycparser): Move from here…
* gnu/packages/pypy.scm (python2-pycparser): …to here.

Change-Id: I368e7fc7c07dcba675c1f7524e7f68145252cf73
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python2-cffi: Move to (gnu packages pypy).

* gnu/packages/libffi.scm (python2-cffi): Move from here…
* gnu/packages/pypy.scm (python2-cffi): …to here.

Change-Id: Ib472d2187a118c1dfec62ea9285d48fe63438fbf
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python2-cffi: Migrate to pyproject and decouple.

Rationale: Decoupling helps us moving the package, and not worry about
inheriting package updates.

* gnu/packages/python-xyz.scm (python2-cffi)
[inherit]: Drop it.
[source]: Decrease version to 1.15.1, which is the last supported
version for Python2. The former build fails with 1.17.0.
[build-system, arguments]: Migrate to pyproject-build-system.
[name, home-page, synopsis, description, license]: Set them
explicitely.

Change-Id: Iea81e4fd3896da044a97043e2d80f5f43b28f50e
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python2-pycparser: Migrate to pyproject and decouple.

Rationale: Decoupling helps us moving the package, and not worry about
inheriting package updates.

* gnu/packages/python-xyz.scm (python2-pycparser)
[inherit]: Drop it.
[build-system, arguments]: Migrate to pyproject-build-system.
[name, home-page, synopsis, description, license]: Set them
explicitely.
[native-inputs]: Add python-setuptools.

Change-Id: Ie55f1fdc60d80ec921acabced218ec758a650cf1
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

build-system: python: Accept pyproject package-with-explicit-python.

* guix/build-system/python.scm (package-with-explicit-python): Accept
pyproject-build-system resolved lazily.

Change-Id: I6e4186b8a7d2ec17afbf6af7d0f9e709cc55e14b
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: duplicity: Remove python-lockfile propagated-input.

* gnu/packages/backup.scm (duplicity)[propagated-input]: Remove
python-lockfile.

Change-Id: Ieaa7330354c96aee0ee4c754419b10380f24acda
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-cachecontrol: Remove python-lockfile propagated-input.

* gnu/packages/python-web.scm (python-cachecontrol)[propagated-input]:
Remove python-lockfile.

Change-Id: I9801a3673d1e655148a7d9a76cb4026c26fca69d
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-daemon: Replace python-lockfile by python-filelock.

* gnu/packages/python-xyz.scm (python-daemon)[propagated-inputs]:
Replace python-lockfile by python-filelock.

* gnu/packages/patches/python-daemon-relax-lockfile.patch: New file
* gnu/local.mk (dist_patch_DATA): Register patch.

Change-Id: Ia12b754065a71b612b0fe626b18e2edc9d158ae7
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pyvista: Ignore failing test.

* gnu/packages/python-science.scm (python-pyvista)[arguments]
<#:test-flags>: Ignore failing test.

Change-Id: I0dba730e92c7fd7e9d7d6273bba3b5e7646278c2
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pyts: Update to 0.13.0-0.4f3d97b.

* gnu/packages/python-science.scm (python-pyts): Update to 0.13.0-0.4f3d97b.
[source]: Switch to git-fetch.
[native-inputs]: Remove python-wheel.
[description]: Improve it.

Change-Id: I64947107888826ad3db8cf1e2e4d3790c6a3e070
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pgmpy: Ignore flaky tests.

* gnu/packages/statistics.scm (python-pgmpy)[arguments]
<#:test-flags>: Ignore additional flaky tests.

Change-Id: I047cf08cde1d6c2157e826e80f6f93e5a9717438
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-drep: Skip additional test.

* gnu/packages/bioinformatics.scm (python-drep)[arguments]
<#:test-flags>: Skip additional test.

Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: scregseg: Skip 'sanity-check phase.

* gnu/packages/bioinformatics.scm (scregseg)
[arguments]<#:phases>: Skip 'sanity-check phase.
[native-inputs]: Add python-pytest.

Change-Id: If28faf66025e79210850080a18b8ce35d9ec6504
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-coolbox: Fix inputs.

* gnu/packages/bioinformatics.scm (python-coolbox)
[native-inputs]: Remove python-pybbi.
[propagated-inputs]: Add python-pybbi.

Change-Id: Ic748f66b71b0aa489e8c0800b21cb23592f285a4
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-sphinx-autodoc-typehints: Update to 2.3.0.

* gnu/packages/sphinx.scm (python-sphinx-autodoc-typehints): Update to 2.3.0.
[arguments] <test-flags>: Rework skpped tests.
[native-inputs]: Remove nss-certs-for-test and python-nptyping.

Change-Id: Iaf7fbcf27dd4334c04acaf0efec27e0d3f140b82
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Remove python-pynbody-1.

* gnu/packages/astronomy.scm (python-pynbody-1): Delete variable.

Fixes: guix/guix#4801
Change-Id: If3461a85679cf0ff46eaeb50bcd0cc4c7eb78b16
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Remove python-aioredis.

* gnu/packages/databases.scm (python-aioredis): Delete variable.

Change-Id: If859740f6bb38fc42ae42df577d0a8c48d2af7c3
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-genomepy: Update to 0.16.3.

* gnu/packages/bioinformatics.scm (python-genomepy): Update to 0.16.3.
[source]: Switch to git-fetch.
[native-inputs]: Remove python-pytest.

Change-Id: Iab4a30e7fb4ff31243ae0c210155a2d1896bd3cb
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-mysql-connector-python: Skip one more test.

* gnu/packages/python-xyz.scm (python-mysql-connector-python):
[phases]{check}: Skip one more test.

Change-Id: I22277bc3cdf0634b166f3198d005c82c37b8796f
Signed-off-by: Rutherther <rutherther@ditigal.xyz>