amaharaneko/guix-mirrors
1
1
Fork 0
mirror of https://codeberg.org/guix/guix.git synced 2025-10-02 02:15:12 +00:00
Code Issues Projects Releases Packages Wiki Activity Actions
165601 commits 77 branches 38 tags 712 MiB
Commit graph

4062 commits

Author SHA1 Message Date
Sharlatan Hellseher
bb3dbcde48
gnu: Remove python-mistune-next. 
* gnu/packages/python-xyz.scm (python-mistune-next): Delete variable.
* gnu/packages/bioinformatics.scm (python-schema-salad)
[propagated-inputs]: Remove python-mistune-next; add python-mistune.
* gnu/packages/mail.scm (python-hyperkitty): Likewise.
* gnu/packages/syndication.scm (giara): Likewise.

Change-Id: Iccf5ffde2b2c5a8c9b8e1c0e6ebd6fa7eab9f144
 2024-12-13 20:18:59 +00:00
Nicolas Graves
3c2943b621
gnu: build-system/pyproject: Add missing native-inputs. 
* gnu/packages/bioinformatics.scm (python-ega-download-client)
[native-inputs]: Add python-setuptools and python-wheel.

* gnu/packages/databases.scm (datasette)[native-inputs]: Add
python-pip.

* gnu/packages/django.scm (python-django-localflavor,
python-django-contact-form)[native-inputs]: Add python-setuptools and
python-wheel.

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

* gnu/packages/jupyter.scm (python-jupyterlab-server)[native-inputs]:
Add python-wheel.
(python-nbstripout)[native-inputs]: Add python-setuptools and
python-wheel.

* gnu/packages/machine-learning.scm (python-captum,
python-linear-operator, python-gpytorch)[native-inputs]: Add
python-setuptools.

* gnu/packages/music.scm (abjad, abjad-ext-rmarkers,
abjed-ext-nauert, python-mutagen)[native-inputs]: Add
python-setuptools and python-wheel.

* gnu/packages/package-management.scm
(python-conda-package-handling)[native-inputs]: Add python-setuptools
and python-wheel.
(conda)[native-inputs]: Add python-wheel.

* gnu/packages/python-check.scm (python-pyinstrument,
python-pytest-testmon, python-pytest-trio, python-nbval,
python-pytest-toolbox)[native-inputs]: Add python-setuptools and
python-wheel.
(python-nptyping)[native-inputs]: Add python-setuptools.

* gnu/packages/python-check.scm (python-dask-expr)[native-inputs]:
Add python-setuptools and python-wheel.

* gnu/packages/python-web.scm (parfive, python-aioftp, python-hupper,
python-sanic, python-mechanicalsoup, python-tinycss, python-aiostream,
python-cbor2, gunicorn)[native-inputs]: Add python-setuptools and
python-wheel.

* gnu/packages/python-xyz.scm (python-apprise, python-jaraco-classes,
python-sparse, python-shtab, python-pyan3)[native-inputs]: Add
python-setuptools.
(python-jupytext, python-orderedmultidict, python-identify, python-nodeenv,
python-cfgv, python-zarr, python-multipart, python-nbconvert, python-cram,
python-immutables, python-numpydoc, python-cairosvg, python-unidecode,
python-black, python-multidict, python-mpv-jsonipc, python-humanize,
python-cmd2)[native-inputs]: Add python-setuptools and python-wheel.
(python-partd, python-dask, python-zarr)[native-inputs]: Add
python-wheel.
(python-nbconvert)[propagated-inputs]: Add texlive-etoolbox. Remove
duplicate textlive-jknapltx.
(python-isort)[native-inputs]: Add python-pip.

* gnu/packages/simulation.scm (python-fenics-dijitso)[native-inputs]:
Add python-setuptools and python-wheel.

* gnu/packages/sphinx.scm (python-pydata-sphinx-theme,
python-sphinx-autodoc-typehints)[native-inputs]: Add
python-setuptools.

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

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

* gnu/packages/time.scm (python-arrow, python-dateutil)
[native-inputs]: Add python-setuptools and python-wheel.

* gnu/packages/version-control.scm (pre-commit)[native-inputs]: Add
python-setuptools and python-wheel.  Remove input labels.

* gnu/packages/virtualization.scm (python-qemu-qmp,
python-transient)[native-inputs]: Add python-setuptools and
python-wheel.

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

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

Change-Id: Id61cf8cdc47bd4c2871c0a9c8e9a5bfd51157df0
 2024-12-13 20:18:58 +00:00
Lars-Dominik Braun
6d97c15911
gnu: Add python-setuptools/python-wheel where necessary. 
Changes to pyproject-build-system require explicit dependency on
setuptools/wheel.

Change-Id: Icd7699fc1dc56e974ae7568f2ae916dbf876bea5
 2024-12-13 20:18:25 +00:00
Lars-Dominik Braun
fdc0fefd46
build-system/pyproject: Use python-sans-pip-wrapper as default-python. 
Also adds python-setuptools and python-wheel to relevant packages,
either to native-inputs or to propagated inputs if the pkg_resources
Python module is loaded at runtime.

* guix/build-system/pyproject.scm (default-python): Default to
python-sans-pip-wrapper.

Change-Id: I2d986c2225114f54459dd6bb360913106e52cdf4
 2024-12-13 20:15:41 +00:00
Gabriel Wicki
6f8c8a86d8
gnu: Fix synopsis in miscelaneous packages. 
* gnu/packages/astronomy.scm (calcmysky-qt5): Fix synopsis.
* gnu/packages/base.scm (hello): Fix synopsis.
* gnu/packages/bioinformatics.scm (vembrane): Fix synopsis.
* gnu/packages/browser-extensions.scm (passff): Fix synopsis.
* gnu/packages/browser-extensions.scm (noscript): Fix synopsis.
* gnu/packages/c.scm (orangeduck-mpc): Fix synopsis.
* gnu/packages/cran.scm (r-d3r): Fix synopsis.
* gnu/packages/docbook.scm (docbook-mathml-1.0): Fix synopsis.
* gnu/packages/finance.scm (flowee): Fix synopsis.
* gnu/packages/firmware.scm (seabios): Fix synopsis.
* gnu/packages/games.scm (pinball): Fix synopsis.
(morris): Fix synopsis.
* gnu/packages/gawk.scm (cppawk-egawk): Fix synopsis.
* gnu/packages/gnome.scm (gssdp): Fix synopsis.
* gnu/packages/gstreamer.scm (gst-plugins-espeak): Fix synopsis.
* gnu/packages/heads.scm (musl-cross): Fix synopsis.
* gnu/packages/irc.scm (epic5): Fix synopsis.
* gnu/packages/kde-pim.scm (itinerary): Fix synopsis.
* gnu/packages/kde-plasma.scm (mpvqt): Fix synopsis.
* gnu/packages/lesstif.scm (motif): Fix synopsis.
* gnu/packages/linux.scm (ecryptfs-utils): Fix synopsis.
* gnu/packages/linux.scm (falcosecurity-libs): Fix synopsis.
* gnu/packages/mail.scm (pan): Fix synopsis.
* gnu/packages/messaging.scm (biboumi): Fix synopsis.
* gnu/packages/ocaml.scm (ocaml-ppx-import): Fix synopsis.
* gnu/packages/pascal.scm (p2c): Fix synopsis.
* gnu/packages/pdf.scm (unpaper): Fix synopsis.
* gnu/packages/pure.scm (pure): Fix synopsis.
* gnu/packages/qt.scm (qxlsx-qt5): Fix synopsis.
* gnu/packages/smalltalk.scm (smalltalk): Fix synopsis.
* gnu/packages/sugar.scm (sugar): Fix synopsis.
* gnu/packages/terminals.scm (roxterm): Fix synopsis.
* gnu/packages/virtualization.scm (xen): Fix synopsis.
* gnu/packages/vpn.scm (sshoot): Fix synopsis.
* gnu/packages/web.scm (buku-run): Fix synopsis.

Signed-off-by: Vagrant Cascadian <vagrant@debian.org>
 2024-12-10 22:35:12 -08:00
Gabriel Wicki
8d05f0c8db
gnu: Fix synopsis in various python packages. 
* gnu/packages/python-compression.scm (python-inflate64): Fix synopsis.
* gnu/packages/python-science.scm (python-xarray-dataclasses): Fix synopsis.
* gnu/packages/python-web.scm (python-waybackpack): Fix synopsis.
* gnu/packages/python-xyz.scm (python-mir-eval): Fix synopsis.
(python-restructuredtext-lint): Fix synopsis.  (python-pixelmatch): Fix
synopsis.  (python-google-pasta): Fix synopsis.  (python-xmp-toolkit): Fix
synopsis.
* gnu/packages/bioinformatics.scm (python-mgatk): Fix synopsis.
* gnu/packages/rpc.scm (python-grpc-stubs): Fix synopsis.
* gnu/packages/simulation.scm (python-commonroad-io): Fix synopsis.

Signed-off-by: Vagrant Cascadian <vagrant@debian.org>
 2024-12-10 22:35:06 -08:00
Ricardo Wurmus
3cfd6e11a4
gnu: Add skewer. 
* gnu/packages/bioinformatics.scm (skewer): New variable.

Change-Id: Ieeb95ed7449b91ea853d73ecca05e5436121df6a
 2024-12-04 16:21:07 +01:00
Ricardo Wurmus
b97678925a
gnu: discrover: Add missing input. 
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Add
texlive-etoolbox.

Change-Id: I42075c05a36a031c40c335a668a8b46a7603b4dd
 2024-12-03 17:00:00 +01:00
Ricardo Wurmus
9ba40c620c
gnu: r-btools: Disable tests. 
* gnu/packages/bioinformatics.scm (r-btools)[arguments]: Disable tests.

Change-Id: I0fc83672a3c09908296551b649244ae1993ac01d
 2024-12-03 16:59:59 +01:00
Ricardo Wurmus
79989a9f53
gnu: r-cytoexplorer: Add missing inputs. 
* gnu/packages/bioinformatics.scm (r-cytoexplorer)[native-inputs]: Drop
labels; add r-cytoexplorerdata, r-mockery, and r-testthat.
[arguments]: Add phase 'skip-bad-tests.

Change-Id: I5060b1ae4ad42ae122a46db018f10910340985d6
 2024-12-03 16:59:58 +01:00
Ricardo Wurmus
baef0f8bb3
gnu: Add r-cytoexplorerdata. 
* gnu/packages/bioinformatics.scm (r-cytoexplorerdata): New variable.

Change-Id: I5565dff552f033c951bee5bac474cb05c7034066
 2024-12-03 16:59:58 +01:00
Ricardo Wurmus
61c16f3e55
gnu: r-skitools: Add missing input. 
* gnu/packages/bioinformatics.scm (r-skitools)[native-inputs]: Add
r-bsgenome-hsapiens-ucsc-hg19.

Change-Id: I8331e0df21bda001d6e3ec944f02791c0a9301b6
 2024-12-03 16:59:58 +01:00
Ricardo Wurmus
bd109162b3
gnu: r-scseqcomm: Remove commented inputs. 
* gnu/packages/bioinformatics.scm (r-scseqcomm): Remove comments.

Change-Id: I537f6377da44637674a0413a30ddd6b70a620ad3
 2024-12-03 16:59:58 +01:00
Ricardo Wurmus
0b3aa43797
gnu: r-chromunity: Add missing input. 
* gnu/packages/bioinformatics.scm (r-chromunity)[native-inputs]: Add
r-testthat.

Change-Id: I5d208a5ab0cb63567ab49783d0fbe0733b08161a
 2024-12-03 16:59:58 +01:00
Ricardo Wurmus
64e941ef7a
gnu: r-liana: Add missing input. 
* gnu/packages/bioinformatics.scm (r-liana)[native-inputs]: Add r-testthat.

Change-Id: I04c9c5f60842e1ed0a0415e51c25b46b64a60104
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
f6b6eb26b9
gnu: r-circus: Add missing input. 
* gnu/packages/bioinformatics.scm (r-circus)[native-inputs]: Add r-testthat.

Change-Id: I7178baece0a8134923fd550e2f1cc303f32aaaea
 2024-12-03 16:59:56 +01:00
Ricardo Wurmus
e3bbf678e3
gnu: Remove r-numbat. 
This is a duplicate of a package in (gnu packages bioconductor).

* gnu/packages/bioinformatics.scm (r-numbat): Delete variable.

Change-Id: Ic1f5d9779a594432a0dd8bd0be9059423a2f5b34
 2024-12-03 16:59:56 +01:00
Ricardo Wurmus
dff6f58688
gnu: r-spectre: Disable tests. 
* gnu/packages/bioinformatics.scm (r-spectre)[arguments]: Disable tests.

Change-Id: I7978b05d0c1c2de3ada6b1b490ae36b28171f17c
 2024-12-03 16:59:56 +01:00
Ricardo Wurmus
e2561d2ec8
gnu: r-gchain: Add missing inputs. 
* gnu/packages/bioinformatics.scm (r-gchain)[native-inputs]: Add
r-pwalign and r-testthat.
[arguments]: Add phase 'skip-bad-tests.

Change-Id: Ia11c6e50e0d2886762ec551df3e5d73ef98547f8
 2024-12-03 16:59:56 +01:00
Ricardo Wurmus
5d6561a87d
gnu: r-seraster: Add missing input. 
* gnu/packages/bioinformatics.scm (r-seraster)[native-inputs]: Add r-testthat.

Change-Id: I88fb4a51831aff1b08437ef08adb62e344185a07
 2024-12-03 16:59:55 +01:00
Ricardo Wurmus
88ce625adb
gnu: r-gtrack: Add missing input. 
* gnu/packages/bioinformatics.scm (r-gtrack)[native-inputs]: Add r-testthat.

Change-Id: I7b0cad1b8fd27d88ff766c5a46bd01dae2933422
 2024-12-03 16:59:54 +01:00
Ricardo Wurmus
10296b8cae
gnu: r-doubletcollection: Add missing input and disable tests. 
* gnu/packages/bioinformatics.scm (r-doubletcollection)[native-inputs]: Add
r-testthat.
[arguments]: Disable tests.

Change-Id: I8802f703ecfd8d69e6e457cffb28e34d3f4f2b06
 2024-12-03 16:59:53 +01:00
Ricardo Wurmus
bb939442b0
gnu: r-pando: Add missing inputs and disable tests. 
* gnu/packages/bioinformatics.scm (r-pando)[native-inputs]: Add
r-bsgenome-hsapiens-ucsc-hg38, r-devtools, r-doparallel, and
r-ensdb-hsapiens-v86.
[arguments]: Disable tests.

Change-Id: Ic66679e2b8c4cdb9835ce08dc4dbb0a42e35e291
 2024-12-03 16:59:53 +01:00
Ricardo Wurmus
066b53965c
gnu: r-anpan: Add missing input. 
* gnu/packages/bioinformatics.scm (r-anpan)[native-inputs]: Add r-testthat.

Change-Id: I69be3fa82db5f9c4e1302c9a3bd2d4f5253bde13
 2024-12-03 16:59:53 +01:00
Ricardo Wurmus
5a2ba07676
gnu: r-hdwgcna: Add missing inputs. 
* gnu/packages/bioinformatics.scm (r-hdwgcna)[native-inputs]: Add r-devtools
and r-testthat.

Change-Id: I553d4fc2f1a682e5d552862c5e50a31140528073
 2024-12-03 16:59:52 +01:00
Ricardo Wurmus
4b78a0dde4
gnu: r-ewastools: Add missing inputs. 
* gnu/packages/bioinformatics.scm (r-ewastools)[native-inputs]: Add r-enmix,
r-illuminahumanmethylationepicanno-ilm10b4-hg19, r-minfi, r-stringi, and
r-testthat.

Change-Id: I8ba2b1c46a4898b27874a7dc8648bb142f4b5a70
 2024-12-03 16:59:52 +01:00
Ricardo Wurmus
387ca84d52
gnu: r-bamutils: Add test inputs and disable tests. 
* gnu/packages/bioinformatics.scm (r-bamutils)[arguments]: Disable tests.
[native-inputs]: Add r-testthat and samtools.

Change-Id: I781c38fb59355a51f2cd27a833d7ed5dbe5277ab
 2024-12-03 16:59:52 +01:00
Ricardo Wurmus
bf20a8fb15
gnu: r-bamutils: Update to 0.0.0.9000-2.0a7d2d9. 
* gnu/packages/bioinformatics.scm (r-bamutils): Update to
0.0.0.9000-2.0a7d2d9.

Change-Id: I04e86c2ff1059f23a34615ac6067926cdd9cb355
 2024-12-03 16:59:52 +01:00
Ricardo Wurmus
d352e2ac18
gnu: r-dropbead: Disable tests. 
* gnu/packages/bioinformatics.scm (r-dropbead)[native-inputs]: Add
r-data-table.
[arguments]: Disable tests.

Change-Id: I48c74a7b4253695ab5c877f6f1cebdca6ed42cb7
 2024-12-03 16:59:49 +01:00
Ricardo Wurmus
f8d38c785d
gnu: r-sleuth: Disable tests. 
* gnu/packages/bioinformatics.scm (r-sleuth)[native-inputs]: Add r-testthat.
[arguments]: Disable tests.

Change-Id: Ib060eb18f8964212eb38b7025a35c16f0aca97b9
 2024-12-03 16:59:49 +01:00
Ricardo Wurmus
cc3d2e78ed
gnu: r-ggsankey: Add missing inputs. 
* gnu/packages/bioinformatics.scm (r-ggsankey)[native-inputs]: Add r-testthat.

Change-Id: Iaafb75cc47e89a4a25232003d410f98c304ff021
 2024-12-03 16:59:48 +01:00
Ricardo Wurmus
c777e6ba75
gnu: r-streamgraph: Add missing input. 
* gnu/packages/bioinformatics.scm (r-streamgraph)[native-inputs]: Add
r-testthat.

Change-Id: I1209a467c5a966c916f0d0416c6c1e283ae9226d
 2024-12-03 16:59:48 +01:00
Ricardo Wurmus
dd561e0cf7
gnu: r-signac: Add missing input. 
* gnu/packages/bioinformatics.scm (r-signac)[native-inputs]: Add r-testthat.

Change-Id: I0aacabf77171903cca2bc0f443f77e479b6331b2
 2024-12-03 16:59:48 +01:00
Ricardo Wurmus
32657c03bc
gnu: r-psupertime: Add missing input. 
* gnu/packages/bioinformatics.scm (r-psupertime)[native-inputs]: Add
r-testthat.

Change-Id: I9993547e2e757b4218c2229495a7eaa0c8fecbe2
 2024-12-03 16:59:46 +01:00
Ricardo Wurmus
92301c7a27
gnu: r-demuxmix: Add missing input. 
* gnu/packages/bioinformatics.scm (r-demuxmix)[native-inputs]: Add r-testthat.

Change-Id: Ia09b929b4d5bb521d58fb74f17f1ac91a4d44a60
 2024-12-03 16:59:46 +01:00
Ricardo Wurmus
6ec643fd9d
gnu: r-cmdstanr: Add missing input. 
* gnu/packages/bioinformatics.scm (r-cmdstanr)[native-inputs]: Add
r-testthat.

Change-Id: Idd81b903e9e9a8308703c9ee8dc5583a04854678
 2024-12-03 16:59:46 +01:00
Ricardo Wurmus
0dcdeea3e5
gnu: r-gutils: Add missing input. 
* gnu/packages/bioinformatics.scm (r-gutils)[native-inputs]: Add r-testthat.

Change-Id: I1b5e34441b48bc92bff6538378d2e2bbc7111631
 2024-12-03 16:59:45 +01:00
Ricardo Wurmus
0afafd8b21
gnu: r-rnacrosslinkoo: Add missing inputs. 
* gnu/packages/bioinformatics.scm (r-rnacrosslinkoo)[native-inputs]: Add
r-testthat.

Change-Id: Iedd2dee7a32dcd19a99d25d92b6f453dd197f5b4
 2024-12-03 16:59:42 +01:00
Ricardo Wurmus
d344c8dd7a
gnu: r-bedtorch: Disable tests. 
* gnu/packages/bioinformatics.scm (r-bedtorch)[arguments]: Disable tests.
[native-inputs]: Add r-testthat.

Change-Id: Ia06aca330528eb2b9eea569d5d12db0f12d6511e
 2024-12-03 16:59:42 +01:00
Ricardo Wurmus
ddad87926c
gnu: r-presto: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-presto)[native-inputs]: Add r-testthat.

Change-Id: I3fe5ec83478e384fe34701b0672b6f216255b1d6
 2024-12-03 16:59:41 +01:00
Ricardo Wurmus
0b191fda81
gnu: r-psiplot: Add missing inputs. 
* gnu/packages/bioinformatics.scm (r-psiplot)[native-inputs]: Add r-testthat.

Change-Id: I19ad7216f86968c87abad64313bf09d03e3ad612
 2024-12-03 16:59:41 +01:00
Ricardo Wurmus
132a8451a1
gnu: r-omnipathr/devel: Add missing inputs. 
* gnu/packages/bioinformatics.scm (r-omnipathr/devel)[native-inputs]: Add
r-testthat.

Change-Id: I7e339871d65ed0ff263db14ff9fb0aa1bb3ed0bb
 2024-12-03 16:59:40 +01:00
Ricardo Wurmus
6b2dda4068
gnu: r-millefy: Add missing inputs. 
* gnu/packages/bioinformatics.scm (r-millefy)[native-inputs]: Add r-testthat.

Change-Id: Id5d1f74074f05f1af2e3726e9a9e49f2d63f13c9
 2024-12-03 16:59:39 +01:00
Ricardo Wurmus
65ea023a14
gnu: r-singlet: Add test inputs. 
* gnu/packages/bioinformatics.scm (r-singlet)[native-inputs]: Add r-testthat.

Change-Id: I617f6bbb9e11ef00148571b94a4aaf2d445cfcb2
 2024-12-03 16:59:38 +01:00
Ricardo Wurmus
7b5b76c18c
gnu: r-anndatar: Add test inputs. 
* gnu/packages/bioinformatics.scm (r-anndatar)[native-inputs]: Add r-rhdf5,
r-seuratobject, r-singlecellexperiment, and r-testthat.

Change-Id: I233a1f7216241b5d9d8301e07acdf811edb24a28
 2024-12-03 16:59:36 +01:00
Ricardo Wurmus
d97a67d41d
gnu: homer: Install config.txt. 
* gnu/packages/bioinformatics.scm (homer)[native-inputs]: Add config.txt.
[arguments]: Update 'configure phase to place config.txt in expected location;
patch configuration code to optionally load a user's configuration file.

Change-Id: Ib05c828e751c6568524bbef45997a42fade4545a
 2024-12-02 13:41:08 +01:00
Ricardo Wurmus
af774e2780
gnu: homer: Install homer executable. 
* gnu/packages/bioinformatics.scm (homer)[arguments]: Update 'install phase to
also install "homer" to the bin directory.

Change-Id: Ia2d23fce493f9c10cc43ac126cd83956b4b9bb05
 2024-12-02 13:41:08 +01:00
Efraim Flashner
541abedc0a
Merge remote-tracking branch 'origin/rust-team' 
Change-Id: I6d5c28252f060eeb69eb02fd281e7268bb885b29
 2024-12-02 14:13:39 +02:00
Ricardo Wurmus
2756c660fb
gnu: python-pairtools: Update to 1.1.0-fix. 
* gnu/packages/bioinformatics.scm (python-pairtools): Update to 1.1.0-fix.
[build-system]: Use pyproject-build-system.
[arguments]: Add phase 'patch-setup.py.
[native-inputs]: Add python-pytest-cov, python-setuptools, and python-wheel.

Change-Id: Ifa3c12de228420d8fdd7b0053bb9da80b9b3efe4
 2024-12-02 10:49:06 +01:00
Ricardo Wurmus
207c69e40d
gnu: Add macs-3. 
* gnu/packages/bioinformatics.scm (macs-3): New variable.

Change-Id: I4bc417e90a1e9d6d28226ea4f66ddc035826c2c4
 2024-12-02 10:28:59 +01:00