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Author SHA1 Message Date
Efraim Flashner
0f967dde76
home: services: zsh: Use unified zprofile. 
* gnu/home/services/shells.scm (zsh-file-zprofile): Use the zprofile
defined in (gnu system shadow) as a base.

Change-Id: Iaf4c4f66d1ccbc0bd0166136b3d082229bdec201
 2024-01-17 11:11:10 +02:00
Efraim Flashner
5ef5095ab1
system: default-zprofile: Sync with home zprofile. 
The removed fields are already sourced in /etc/profile.

* gnu/system/shadow.scm (%default-zprofile): Sync with default zprofile
from (gnu home services shells).

Change-Id: I419eadf636344e23e8fd2f7006efa81f45527756
 2024-01-17 11:11:10 +02:00
Efraim Flashner
1e8ac2c41b
system: Add default guix-home-config. 
* gnu/system/shadow.scm (%deafult-skeleton-home-config): New variable.
(default-skeletons): Add it.

Change-Id: Ida4cca8b1b3674491a4f18d94bc1b12d426575ba
 2024-01-17 11:11:10 +02:00
Efraim Flashner
3ca02f0304
system: Export default guile config. 
* gnu/system/shadow.scm (%default-dotguile): Extract from
default-skeletons, export.
(default-skeletons): Use %default-dotguile.

Change-Id: Ibe91b3b517ae542bd28070a08e14152f87ed75ec
 2024-01-17 11:11:09 +02:00
Efraim Flashner
33136e0426
system: Export default nanorc. 
* gnu/system/shadow.scm (%default-nanorc): Extract from
default-skeletons, export.
(default-skeletons): Use %default-nanorc.

Change-Id: I0d07b13ed4894b1152a08b96d9ef8527dde073ce
 2024-01-17 11:11:09 +02:00
Efraim Flashner
eef3babfdb
system: Export default gdbinit. 
* gnu/system/shadow.scm (%default-gdbinit): Extract from
default-skeletons, export.
(default-skeletons): Use %default-gdbinit.

Change-Id: Ia5188f8083a83ad4cdb96e234dbd730b1bfe0072
 2024-01-17 11:11:09 +02:00
Efraim Flashner
7292838874
system: Export default xdefaults. 
* gnu/system/shadow.scm (%default-xdefaults): Extract from
default-skeletons, export.
(default-skeletons): Use %default-xdefaults.

Change-Id: I44018516ec3687a68d32ca5c86c41bc29507a273
 2024-01-17 11:11:09 +02:00
Efraim Flashner
6a9e4b0639
system: Export default zprofile. 
* gnu/system/shadow.scm (%default-zprofile): Extract from
default-skeletons, export.
(default-skeletons): Use %default-zprofile.

Change-Id: I6c6e158bca2e462a2eae709fbc2c25a2c7f3f8b4
 2024-01-17 11:11:09 +02:00
Efraim Flashner
cdcb2e78d2
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
 2024-01-17 11:11:03 +02:00
Wilko Meyer
2f3d6ff968
teams: Add Wilko Meyer to kernel. 
* etc/teams.scm: Add Wilko Meyer.

Change-Id: Ia7b85a090a4d8e81689bd137e1d12cb3708aa760
Signed-off-by: Leo Famulari <leo@famulari.name>
 2024-01-16 20:47:52 -05:00
Sharlatan Hellseher
d99670e33e
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
 2024-01-16 21:43:30 +00:00
Sharlatan Hellseher
d79fd9adc3
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
 2024-01-16 21:43:30 +00:00
Ricardo Wurmus
01bf69177d
import/cran: Add more invalid package names and translations. 
These were encountered in a mass import of Bioconductor packages.

* guix/import/cran.scm (invalid-packages): Add "rtools".
(transform-sysname): Add aliases for Python and bioinformatics packages.

Change-Id: I97e13cee10c2ee85d4b9296d91afccbdbcec4946
 2024-01-16 22:36:39 +01:00
Ricardo Wurmus
171ac4fa4f
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
 2024-01-16 19:40:50 +01:00
Ricardo Wurmus
9a9f05f1f2
gnu: Add samtools-1.14. 
* gnu/packages/bioinformatics.scm (samtools-1.14): New variable.

Change-Id: I0bd35b3865d7a417f55f1f768f7eb0c78a795e0f
 2024-01-16 19:35:37 +01:00
Ricardo Wurmus
e0369ba57d
gnu: samtools: Update to 1.19. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.19.
[source]: Simplify snippet.

Change-Id: If0e02bbbc8e0443eb418c078dc47525f432d7ebe
 2024-01-16 19:31:35 +01:00
Ricardo Wurmus
eda31ffaab
gnu: htslib: Update to 1.19. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.19.

Change-Id: I4d66d8ce37bfd335411a2acc6060f9a8c20c9e4a
 2024-01-16 19:22:03 +01:00
Ricardo Wurmus
cb1f38cc78
gnu: htscodecs: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (htscodecs): Update to 1.6.0.

Change-Id: Ibd5be30e8fbe7fe5d0ef494c1b1e0cd9ec3333cc
 2024-01-16 19:17:39 +01:00
Ricardo Wurmus
20606ca9af
gnu: Add python-prisma. 
* gnu/packages/databases.scm (python-prisma): New variable.

Change-Id: I7df9b5600fb49ef46a73678323bc29993f35fae2
 2024-01-16 15:40:35 +01:00
Ricardo Wurmus
224f8d543b
gnu: Add python-strenum. 
* gnu/packages/python-xyz.scm (python-strenum): New variable.

Change-Id: I6b6d64024db9358ea0a65cfd6c7cd6f94747de42
 2024-01-16 15:33:57 +01:00
Ricardo Wurmus
f4d2371808
gnu: python-readpaf: Explicitly disable tests. 
* gnu/packages/bioinformatics.scm (python-readpaf)[arguments]: Disable tests.

Change-Id: I28ddfa46675b74bd5073c12e5d33bcbf9dee8252
 2024-01-16 14:52:21 +01:00
Ricardo Wurmus
b8085c9240
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
 2024-01-16 14:52:21 +01:00
Efraim Flashner
8520f00d69
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
 2024-01-16 14:24:10 +02:00
Efraim Flashner
5ce1512b0f
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
 2024-01-16 14:24:10 +02:00
Efraim Flashner
cb3f833aaa
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
 2024-01-16 14:24:10 +02:00
Efraim Flashner
eb194090e2
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
 2024-01-16 14:24:10 +02:00
Efraim Flashner
feb96b1d15
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
 2024-01-16 14:24:07 +02:00
Ricardo Wurmus
15d3de9d36
gnu: gourmet: Add missing input. 
* gnu/packages/nutrition.scm (gourmet)[inputs]: Add python-toml.

Change-Id: I53bc9b0247c6dc32c5ec6e3cc518dbc982362bd2
 2024-01-16 12:44:38 +01:00
Ricardo Wurmus
73221c441f
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
 2024-01-16 12:44:38 +01:00
Ricardo Wurmus
7d10e49dfc
gnu: python-clingraph: Update to 1.1.2. 
* gnu/packages/potassco.scm (python-clingraph): Update to 1.1.2.

Change-Id: I5910853d39389ff9ad981543204fd8ef1445e495
 2024-01-16 12:44:37 +01:00
Ricardo Wurmus
dc1719cba4
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
 2024-01-16 12:44:37 +01:00
Ricardo Wurmus
579b35ddd1
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
 2024-01-16 12:44:37 +01:00
Ricardo Wurmus
ae42b55d85
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
 2024-01-16 12:44:37 +01:00
Ricardo Wurmus
53c65baa3d
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
 2024-01-16 12:44:37 +01:00
Ricardo Wurmus
e31e5928ae
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
 2024-01-16 12:44:37 +01:00
Ricardo Wurmus
076e891754
gnu: python-telomerecat: Disable tests. 
* gnu/packages/bioinformatics.scm (python-telomerecat)[arguments]: Disable tests.

Change-Id: I0422ae1e563374a8cc408fc9584cfb7b0e880e95
 2024-01-16 12:44:37 +01:00
Ricardo Wurmus
c3210ae8e2
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
 2024-01-16 12:44:37 +01:00
Ricardo Wurmus
8ef784e84c
gnu: python-adjusttext: Disable tests. 
* gnu/packages/python-xyz.scm (python-adjusttext)[arguments]: Disable tests.

Change-Id: Ib1002de20a6e301f43bb34f64f7299d4316d8a67
 2024-01-16 12:44:37 +01:00
Ricardo Wurmus
65d021a950
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
 2024-01-16 12:44:37 +01:00
Ricardo Wurmus
a8c1d812a0
gnu: python-pandas: Update to 1.5.3. 
* gnu/packages/python-science.scm (python-pandas): Update to 1.5.3.
[build-system]: Use pyproject-build-system.
[arguments]: Use G-expression; move test flags to #:test-flags; add phase
'patch-build-system; fix substitution of "which" executable; remove
'enable-parallel-build; remove custom 'check phase; add 'pre-check phase.
[propagated-inputs]: Add python-matplotlib.
[native-inputs]: Replace python-cython with python-cython-0.29.35.

Change-Id: I9d09971f707b925f469e29be67fe040c181314ff
 2024-01-16 12:44:37 +01:00
Ricardo Wurmus
fbe0233575
gnu: python-click-default-group: Update to 1.2.4. 
* gnu/packages/python-xyz.scm (python-click-default-group): Update to 1.2.4.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-flit-core and python-pytest.

Change-Id: I7e617ee57499542b7e832bb5ea24417b70e8cf85
 2024-01-16 12:44:37 +01:00
Ricardo Wurmus
016d136d89
gnu: datasette: Update to 1.0a7. 
* gnu/packages/databases.scm (datasette): Update to 1.0a7.
[propagated-inputs]: Add python-asyncinject and python-sqlite-utils.

Change-Id: If713cd0f115c8092f9cc200daa850f9a78a20f6b
 2024-01-16 12:44:37 +01:00
Ricardo Wurmus
e8f68ea334
gnu: Add python-asyncinject. 
* gnu/packages/python-xyz.scm (python-asyncinject): New variable.

Change-Id: I2647e8340bca2efabc222d19155d330b1a5ff16f
 2024-01-16 12:44:37 +01:00
Ricardo Wurmus
186aa138a6
gnu: python-metpy: Update to 1.6.0. 
* gnu/packages/geo.scm (python-metpy): Update to 1.6.0.
[arguments]: Add phases 'fix-version-check and 'hide-imp-deprecation-warnings.
[native-inputs]: Add python-packaging; remove python-shapely and
python-cartopy.

Change-Id: I4a46a5e60b1904699475608146f2a09aefc07624
 2024-01-16 12:44:36 +01:00
Ricardo Wurmus
0c6db478ec
gnu: python-pint: Add missing input. 
This is a follow-up to commit 23b8601cd2cf90ed11a51ca6db133083433e74d8.
Without this input the version string will be 0.0.0.

* gnu/packages/python-xyz.scm (python-pint)[native-inputs]: Add
python-setuptools-scm.

Change-Id: Id621e459f119d7268cdcc41ef93bcae135e842d1
 2024-01-16 12:44:36 +01:00
Ricardo Wurmus
cda0f029d6
gnu: python-hicexplorer: Make compatible with latest scipy. 
* gnu/packages/bioinformatics.scm (python-hicexplorer)[arguments]: Add
'scipy-compatibility phase.

Change-Id: I31e9058b7fd4ff9245837d5f1cd145b569ec35ad
 2024-01-16 12:44:36 +01:00
Ricardo Wurmus
3ce25c212f
gnu: python-hicmatrix: Update to 17.1. 
* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 17.1.
[arguments]: Remove.

Change-Id: I6b1230d703d0dc1a88ee61a84cc6cd95f7eeb6f9
 2024-01-16 12:44:36 +01:00
Ricardo Wurmus
998df6e047
gnu: python-scikit-optimize: Make compatible with latest sklearn. 
* gnu/packages/python-science.scm (python-scikit-optimize)[source]: Add
snippet to fix outdated use of "max_features" option.

Change-Id: I4272ffc82b4951315b74b4adee27527e8d513fca
 2024-01-16 12:44:36 +01:00
Ricardo Wurmus
50dbb9561f
gnu: python-fit-nbinom: Disable tests. 
* gnu/packages/python-xyz.scm (python-fit-nbinom)[arguments]: Disable tests.

Change-Id: I980480a3326dccc67930d34474832712005d1bb2
 2024-01-16 12:44:36 +01:00
Ricardo Wurmus
6b4c911a99
gnu: scvelo: Make compatible with latest matplotlib. 
* gnu/packages/bioinformatics.scm (scvelo)[arguments]: Add phase
'matplotlib-compatibility.

Change-Id: Ia761821c8aa1e516525cff7c680db471a5908e5f
 2024-01-16 12:44:36 +01:00