system: Export default gdbinit.

* gnu/system/shadow.scm (%default-gdbinit): Extract from
default-skeletons, export.
(default-skeletons): Use %default-gdbinit.

Change-Id: Ia5188f8083a83ad4cdb96e234dbd730b1bfe0072

system: Export default xdefaults.

* gnu/system/shadow.scm (%default-xdefaults): Extract from
default-skeletons, export.
(default-skeletons): Use %default-xdefaults.

Change-Id: I44018516ec3687a68d32ca5c86c41bc29507a273

system: Export default zprofile.

* gnu/system/shadow.scm (%default-zprofile): Extract from
default-skeletons, export.
(default-skeletons): Use %default-zprofile.

Change-Id: I6c6e158bca2e462a2eae709fbc2c25a2c7f3f8b4

system: Export default bash-profile.

gnu/system/shadow.scm (%default-bash-profile): Extract from
default-skeletons, export.
(default-skeletons): Use %default-bash-profile.

Change-Id: I45641b1091daee3495a5f92bdc1a63050e0cc59e

gnu: abjad-ext-ipython: Fix build.

* gnu/packages/music.scm (abjad-ext-ipython): Fix build.
[propagated-inputs]: Add python-sphinx-autodoc-typehints.

Change-Id: Id20c0527e61b8be194c5387c6c43fdf82ab5ff09

gnu: python-deepdish: Fix build.

* gnu/packages/python-science.scm (python-deepdish): Fix build.
[build-system]: Swap to pyproject-build-system.
[arguments]<#:test-flags>: Silent failing tests.

Change-Id: I4c4df66fc80434aaf5b95a7a62b83e0c1c02a4c6

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

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