gnu: python-nptyping: Ignore failing test.

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

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

gnu: python-ncls: Update to 0.0.68.

* gnu/packages/python-xyz.scm (python-ncls): Update to 0.0.68.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-cython, python-pandas, python-pytest,
python-setuptools, python-wheel.

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

gnu: python-cell2cell: Update to 0.7.4.

* gnu/packages/bioinformatics.scm (python-cell2cell): Update to 0.7.4.
[source]{origin}: Relax requirements in snippet.

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

gnu: crossmap: Add missing python-pyparsing native-input.

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

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

gnu: python-bx-python: Update to 0.13.0.

* gnu/packages/bioinformatics.scm (python-bx-python): Update to 0.13.0.

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

gnu: python-cesium: Move to (gnu packages astronomy).

The dependencies of this package are already in (gnu packages astronomy).

* gnu/packages/python-xyz.scm (python-cesium): Move from here…
* gnu/packages/astronomy.scm (python-cesium): …to here.

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

gnu: python-cleanlab: Update to 2.7.1.

* gnu/packages/machine-learning.scm (python-cleanlab): Update to 2.7.1.

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

gnu: pairadise: Add missing native-inputs.

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

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

gnu: python-biom-format: Update to 2.1.16.

* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.16.

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

gnu: Remove python-asynctest.

No updates since 2019, fails to build and has no users in Guix.  See
<https://github.com/Martiusweb/asynctest/issues/163> there is a standard
'unittest.IsolatedAsyncioTestCase' drop-in replacement.

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

Change-Id: If63cfd698a74f86c6895db04e0d7cd02728ae757

gnu: python-asyncua: Fix build.

python-asynctest has not been updated for 6y and fails to build, but
it's optional in tests. This change removes it from native inputs.

* gnu/packages/engineering.scm (python-asyncua): Update to 1.1.5.
[source]: Mention about the third party submodule on recursive option.
[native-inputs]: Remove python-asynctest and python-pytest-runner; add
python-pytest.

Change-Id: I9d268c43ebe97fcaacc5125e1038f6ff371d39b2

gnu: python-asn1tools: Update to 0.167.0 and fix build.

* gnu/packages/python-xyz.scm (python-asn1tools): Update to 0.167.0, fix
build.
[build-system]: Swap to pyproject-build-system.
[arguments] <test-flags>: Skip 7 failing tests.
[native-inputs]: Add python-pytest, python-setuptools, and python-wheel.

Change-Id: I36d12d9bfe2fd6d62a75dd0d30de42a782c4a746

gnu: nikola: Skip one test.

* gnu/packages/python-xyz.scm (nikola) [arguments] <test-flags>: Skip
one test.

Change-Id: I10d4edf07b7c7b4e19020773215da5eae27cd0f4

gnu: gita: Improve package style.

* gnu/packages/version-control.scm (gita): Use G-expressions, refresh
style.
[native-inputs]: Remove git; add git-minimal/pinned.

Change-Id: I61707538f5248e14207aa2ca0931286741697ed8

gnu: gita: Fix indentation.

* gnu/packages/version-control.scm (gita): Fix indentation.

Change-Id: Ib918212b2f6659897c00a4c452776cf0e5d36c35

gnu: gita: Update to 0.16.7.2.

* gnu/packages/version-control.scm (gita): Update to 0.16.7.2.
[build-system]: Swap to pyproject-build-system.
[arguments] <test-flags>: Ignore one test file.
<phases>: Use default 'check, add 'pre-check.
[phases] {install-shell-completions}: Fix path to completion files.
[propagated-inputs]: Remove python-pyyaml; add python-argcomplete.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: I3b53b804c4b436613c5463911716f1a832064517

gnu: Remove python-nose-randomly.

Deprecated: "This repository was archived by the owner on Feb 8,
2019. It is now read-only."; fails to build, has no user in Guix.

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

Change-Id: I1866da62f092fefc7f6167fa8f80ad33402bfb40

gnu: python-biopython-1.73: Make compatible with Python 3.11.

* gnu/packages/bioinformatics.scm (python-biopython-1.73)[arguments]: Add
phases 'python3.11-compatibility, 'numpy-compatibility, 'set-home,
'build-extensions, and 'patch-tests.

Change-Id: Iac6b0638dd5699a7b11862bff9cce1e7b2fee49b

gnu: python-biopython: Update to 1.85.

* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.85.
[arguments]: Add phase 'numpy-compatibility; replace 'check phase.

Change-Id: I4e3ef0d9a357155e36ef61052af4d90f4fa95d5e

gnu: cpp-httplib: Update to 0.20.0.

* gnu/packages/cpp.scm (cpp-httplib): Update to 0.20.0.

Change-Id: I279c00feb30d11b636c122b6ba42ef7bb852012e