gnu: Add python-strenum.

* gnu/packages/python-xyz.scm (python-strenum): New variable.

Change-Id: I6b6d64024db9358ea0a65cfd6c7cd6f94747de42

gnu: python-readpaf: Explicitly disable tests.

* gnu/packages/bioinformatics.scm (python-readpaf)[arguments]: Disable tests.

Change-Id: I28ddfa46675b74bd5073c12e5d33bcbf9dee8252

gnu: python-pyls-black: Fix build.

* gnu/packages/patches/python-pyls-black-41.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/python-xyz.scm (python-pyls-black)[source]: Add patch.
[build-system]: Use pyproject-build-system.
[arguments]: Disable one failing test.

Change-Id: I14b2982644e58c0b43d76838febc6dfceb220b15

import: crate: Simplify find-crate-version.

* guix/import/crate.scm (find-crate-version): Reuse
nonyanked-crate-versions, max-crate-version-of-semver.

Change-Id: I976a3b5a397f0d6a7d723804a98356544bfc7da3

import: crate: Update to latest semver version.

* guix/import/crate.scm (min-element, max-crate-version-of-semver,
nonyanked-crate-versions): New procedures.
(import-release)[version]: Update to the requested version or the newest
semver-compatible version.

Co-authored by David Elsing <david.elsing@posteo.net>
Change-Id: I72b081147c4eb9faf482f159b7145aaaf9f91f29

doc: Fix mistakes in the manual.

Recommended by Christian Miller.

* doc/guix.texi (Packages with Multiple Outputs): Replace 'a packages'
with 'a package'.
(Invoking guix time-machine): Don't assume knowledge and give an
explicit link to Back to the Future.
(Invoking guix pack): Remove doubled word.
(Build Systems): Same.
(Debugging Build Failures): 'inspect' is not a command to be run.
(Invoking guix import): Remove doubled word.
(Invoking guix size): Remove stray word.
(Invoking guix processes): Replace 'guix environment' with 'guix shell'.
(Base Services): Add missing word.
(Networking Setup): Adjust a/an usage.
(Networking Services): Remove stray symbol.  Add space between two
words.
(Desktop Services): Remove stray symbol from example.
(Database Services): Document default postgresql version.
(Web Services): Adjust indentation.
(Audio Services): Add missing newline.
(Miscellaneous Services): Switch 'get' to 'gets'.
(Bootloader Configuration): Remove stray symbol.
(Secure Shell): Remove marks around accepted values.
(Installing Debugging Files): Replace 'is' with 'it'.
(Full-Source Bootstrap): Remove doubled word.
(Preparing to Use the Bootstrap Binaries): Same.

Change-Id: Ifbf2677dff7642c6531384145363d7611286e48b

gnu: debian-ports-archive-keyring: Update to 2024.01.05.

* gnu/packages/debian.scm (debian-ports-archive-keyring): Update to 2024.01.05.

Change-Id: Ibaa279a91d9e39804eb5cc1bf759ca3afd69e962

gnu: debootstrap: Update to 1.0.134.

* gnu/packages/debian.scm (debootstrap): Update to 1.0.134.
[arguments]: Remove obsolete substitution in 'patch-source phase.

Change-Id: I2a50ae75a43c0970e3ef866e02c49d87094e14eb

gnu: gourmet: Add missing input.

* gnu/packages/nutrition.scm (gourmet)[inputs]: Add python-toml.

Change-Id: I53bc9b0247c6dc32c5ec6e3cc518dbc982362bd2

gnu: python-pyrdfa3: Update to 3.6.2.

* gnu/packages/rdf.scm (python-pyrdfa3): Update to 3.6.2.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom build phases.
[propagated-inputs]: Add python-requests.

Change-Id: Ie8a1a369a569d29c8f43248d03f024e6cc19c004

gnu: python-clingraph: Update to 1.1.2.

* gnu/packages/potassco.scm (python-clingraph): Update to 1.1.2.

Change-Id: I5910853d39389ff9ad981543204fd8ef1445e495

gnu: python-astroml: Make compatible with recent Matplot and Scipy.

* gnu/packages/astronomy.scm (python-astroml)[arguments]: Add phases
'matplotlib-compatibility and 'scipy-compatibility.

Change-Id: Id88cf769f705f9326f41f951403583155bcee58f

gnu: python-bbknn: Update to 1.6.0.

* gnu/packages/bioinformatics.scm (python-bbknn): Update to 1.6.0.
[arguments]: Remove phase 'do-not-fail-to-find-sklearn.
[propagated-inputs]: Add python-pynndescent.
[native-inputs]: Add python-flit-core.

Change-Id: I5fca2d6ca52e54eb7650b3bb24a34a0aa47b1782

gnu: python-geopandas: Update to 0.14.2.

* gnu/packages/geo.scm (python-geopandas): Update to 0.14.2.
[arguments]: Disable test_pandas_kind tests.

Change-Id: I2a49d6ef73a79b84751ce0225757a2b83019cd42

gnu: python-dask: Propagate click.

* gnu/packages/python-xyz.scm (python-dask)[native-inputs]: Move python-click
from here...
[propagated-inputs]: ...to here.

Change-Id: I1a1617d9cb00268d9fc26f4fe6c9ecc6d0a2e375

gnu: python-xarray: Update to 2023.12.0.

* gnu/packages/python-science.scm (python-xarray): Update to 2023.12.0.
[arguments]: Ignore one test file.
[propagated-inputs]: Add python-packaging.

Change-Id: I6b70f59670f7bc8b56787fe3436579db8ac113bb

gnu: python-telomerecat: Disable tests.

* gnu/packages/bioinformatics.scm (python-telomerecat)[arguments]: Disable tests.

Change-Id: I0422ae1e563374a8cc408fc9584cfb7b0e880e95

gnu: python-mysql-connector-python: Defuse time bomb.

Additional tests fail due to expired certificates.  Disable them.

* gnu/packages/python-xyz.scm (python-mysql-connector-python)[arguments]:
Disable six additional tests.

Change-Id: I99b5f15736af89c0281ab7aca56c1bd3958d1a46

gnu: python-adjusttext: Disable tests.

* gnu/packages/python-xyz.scm (python-adjusttext)[arguments]: Disable tests.

Change-Id: Ib1002de20a6e301f43bb34f64f7299d4316d8a67

gnu: python-scikit-bio: Update to 0.5.9.

* gnu/packages/bioinformatics.scm (python-scikit-bio): Update to 0.5.9.
[source]: Add patch.
[arguments]: Disable one test via #:test-flags; adjust 'compatibility phase;
update 'check phase.
[propagated-inputs]: Remove python-cachecontrol, python-lockfile, and
python-scikit-learn; add python-requests.
* gnu/packages/patches/python-scikit-bio-1887.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Change-Id: Ie57b0256cf695e5ea088545cd2102335303a93e7