import/cran: Add more invalid package names and translations.

* guix/import/cran.scm (invalid-packages): Add "build-essential".
(transform-sysname): Add aliases for openssl, libxml2, and zlib.

Change-Id: Ia142ebc388dbcd47caf3b2c5165bc21227bc1832

gnu: Add samtools-1.14.

* gnu/packages/bioinformatics.scm (samtools-1.14): New variable.

Change-Id: I0bd35b3865d7a417f55f1f768f7eb0c78a795e0f

gnu: samtools: Update to 1.19.

* gnu/packages/bioinformatics.scm (samtools): Update to 1.19.
[source]: Simplify snippet.

Change-Id: If0e02bbbc8e0443eb418c078dc47525f432d7ebe

gnu: htslib: Update to 1.19.

* gnu/packages/bioinformatics.scm (htslib): Update to 1.19.

Change-Id: I4d66d8ce37bfd335411a2acc6060f9a8c20c9e4a

gnu: htscodecs: Update to 1.6.0.

* gnu/packages/bioinformatics.scm (htscodecs): Update to 1.6.0.

Change-Id: Ibd5be30e8fbe7fe5d0ef494c1b1e0cd9ec3333cc

gnu: Add python-prisma.

* gnu/packages/databases.scm (python-prisma): New variable.

Change-Id: I7df9b5600fb49ef46a73678323bc29993f35fae2

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