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Author SHA1 Message Date
Lars-Dominik Braun 400a7a4c80
build-system: Add pyproject-build-system. 
This is an experimental build system based on python-build-system
that implements PEP 517-compliant builds.

* doc/guix.texi (Build Systems): Add pyproject-build-system section.
* doc/contributing.texi (Python Modules): Mention pyproject.toml and the
PYTHON-TOOLCHAIN package, as well as differences to python-build-system.
* guix/build-system/pyproject.scm,
guix/build/pyproject-build-system.scm,
gnu/packages/aux-files/python/sanity-check-next.py,
gnu/packages/python-commencement.scm: New files.
* Makefile.am (MODULES): Register the new build systems.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add python-commencement.scm.
* gnu/packages/python.scm (python-sans-pip, python-sans-pip-wrapper): New
variables.

Co-authored-by: Marius Bakke <marius@gnu.org>
 2022-10-27 19:43:06 +02:00
Marius Bakke b4e2effb30
gnu: python-pip: Move to (gnu packages python-build). 
* gnu/packages/python-xyz.scm (python-pip): Move from here ...
* gnu/packages/python-build.scm (python-pip): ... to here.
 2022-10-27 19:43:06 +02:00
Lars-Dominik Braun 6e7ed04033
gnu: pypy: Move to separate module. 
This removes the need to import (gnu packages python-xyz) in (gnu packages
python), avoiding issues with circular imports.

* gnu/packages/python.scm (pypy): Move…
* gnu/packages/pypy.scm (pypy): …here
* gnu/local.mk: Register new file.

Co-authored-by: Marius Bakke <marius@gnu.org>
 2022-10-27 19:43:06 +02:00
Lars-Dominik Braun c485a9d8af
gnu: python-setuptools: Move to python-build. 
* gnu/packages/python-xyz.scm (python-setuptools): Move…
* gnu/packages/python-build.scm: …here.
* gnu/packages/chemistry.scm,
gnu/packages/messaging.scm,
gnu/packages/sequoia.scm,
tests/lint.scm: Adjust module imports accordingly.

Co-authored-by: Marius Bakke <marius@gnu.org>
 2022-10-27 19:43:06 +02:00
Marius Bakke cae327a3b0
gnu: Zabbix: Update to 6.0.9. 
* gnu/packages/monitoring.scm (zabbix-agentd): Update to 6.0.9.
 2022-10-27 19:43:06 +02:00
Marius Bakke 593548f063
gnu: zabbix-agentd: Enable TLS support. 
* gnu/packages/monitoring.scm (zabbix-agentd)[arguments]: Pass "--with-gnutls"
in #:configure-flags.
[inputs]: Add GNUTLS.
(zabbix-server): Inherit these changes.
 2022-10-27 19:43:06 +02:00
Ricardo Wurmus 176a501360
gnu: flair: Add missing R packages. 
* gnu/packages/bioinformatics.scm (flair)[propagated-inputs]: Add python-rpy2.
[inputs]: Add r-minimal, r-deseq2, r-drimseq, r-ggplot2, r-lazyeval, r-qqman,
and r-rlang.
[arguments]: Add phase "wrap-executable".
 2022-10-27 18:21:22 +02:00
Nicolas Goaziou 302eae2fc3
gnu: emacs-buttercup: Update to 1.28. 
* gnu/packages/emacs-xyz.scm (emacs-buttercup): Update to 1.28.
 2022-10-27 17:37:40 +02:00
Mădălin Ionel Patrașcu aef2425666
gnu: Add r-aseb. 
* gnu/packages/bioconductor.scm (r-aseb): New variable.
 2022-10-27 16:40:18 +02:00
Mădălin Ionel Patrașcu 695d7720ef
gnu: Add r-asgsca. 
* gnu/packages/bioconductor.scm (r-asgsca): New variable.
 2022-10-27 16:40:18 +02:00
Mădălin Ionel Patrașcu b8b91756ab
gnu: Add r-aspli. 
* gnu/packages/bioconductor.scm (r-aspli): New variable.
 2022-10-27 16:40:18 +02:00
Mădălin Ionel Patrașcu a8e0069f87
gnu: Add r-assessorf. 
* gnu/packages/bioconductor.scm (r-assessorf): New variable.
 2022-10-27 16:40:18 +02:00
Mădălin Ionel Patrașcu f1750236c1
gnu: Add r-asset. 
* gnu/packages/bioconductor.scm (r-asset): New variable.
 2022-10-27 16:40:18 +02:00
Mădălin Ionel Patrașcu c0278aa51e
gnu: Add r-atena. 
* gnu/packages/bioconductor.scm (r-atena): New variable.
 2022-10-27 16:40:18 +02:00
Mădălin Ionel Patrașcu 70d30096b3
gnu: Add r-atsnp. 
* gnu/packages/bioconductor.scm (r-atsnp): New variable.
 2022-10-27 16:40:18 +02:00
Mădălin Ionel Patrașcu 599655dc49
gnu: Add r-attract. 
* gnu/packages/bioconductor.scm (r-attract): New variable.
 2022-10-27 16:40:18 +02:00
Mădălin Ionel Patrașcu 3f755098cb
gnu: Add r-awfisher. 
* gnu/packages/bioconductor.scm (r-awfisher): New variable.
 2022-10-27 16:40:18 +02:00
Mădălin Ionel Patrașcu 930b1e0458
gnu: Add r-awst. 
* gnu/packages/bioconductor.scm (r-awst): New variable.
 2022-10-27 16:40:18 +02:00
Marius Bakke d9686315bd
gnu: ungoogled-chromium: Update to 107.0.5304.68-1. 
* gnu/packages/chromium.scm (%preserved-third-party-files): Adjust for M107.
(%chromium-version): Set to 107.0.5304.68.
(%ungoogled-origin): Update hash.
(%chromium-gcc-patchset, gcc-patch): Remove.
(%gcc-patches): Empty list.
(ungoogled-chromium)[source]: Update hash.
[arguments]: Add clang_base_path and use_system_libwayland_server to
 #:configure-flags.  Adjust substitutions.
[inputs]: Add QTBASE-5.
 2022-10-27 16:15:09 +02:00
Mădălin Ionel Patrașcu 38cc09493c
gnu: Add r-barcodetrackr. 
* gnu/packages/bioconductor.scm (r-barcodetrackr): New variable.
 2022-10-27 15:58:45 +02:00
Mădălin Ionel Patrașcu 01944e0eb8
gnu: Add r-banocc. 
* gnu/packages/bioconductor.scm (r-banocc): New variable.
 2022-10-27 15:57:30 +02:00
Mădălin Ionel Patrașcu fe2be9c0cf
gnu: Add r-bandits. 
* gnu/packages/bioconductor.scm (r-bandits): New variable.
 2022-10-27 15:56:40 +02:00
Mădălin Ionel Patrașcu 9b337c2735
gnu: Add r-bambu. 
* gnu/packages/bioconductor.scm (r-bambu): New variable.
 2022-10-27 15:51:55 +02:00
Mădălin Ionel Patrașcu f0d0b6a0c5
gnu: Add r-badregionfinder. 
* gnu/packages/bioconductor.scm (r-badregionfinder): New variable.
 2022-10-27 15:50:33 +02:00
Mădălin Ionel Patrașcu c969517cec
gnu: Add r-bader. 
* gnu/packages/bioconductor.scm (r-bader): New variable.
 2022-10-27 15:35:22 +02:00
Mădălin Ionel Patrașcu 0ad89a84c3
gnu: Add r-bac. 
* gnu/packages/bioconductor.scm (r-bac): New variable.
 2022-10-27 15:34:01 +02:00
Mădălin Ionel Patrașcu f31b494bb6
gnu: Add r-basespacer. 
* gnu/packages/bioconductor.scm (r-basespacer): New variable.
 2022-10-27 15:30:25 +02:00
Mădălin Ionel Patrașcu 3417a28080
gnu: Add r-eulerr. 
* gnu/packages/cran.scm (r-eulerr): New variable.
 2022-10-27 15:28:22 +02:00
Mădălin Ionel Patrașcu 9f8ab16fb5
gnu: Add r-tximportdata. 
* gnu/packages/bioconductor.scm (r-tximportdata): New variable.
 2022-10-27 15:24:06 +02:00
Mădălin Ionel Patrașcu f180a5990b
gnu: Add r-fishpond. 
* gnu/packages/bioconductor.scm (r-fishpond): New variable.
 2022-10-27 15:19:36 +02:00
Mădălin Ionel Patrașcu fe7b421d05
gnu: Add python-multivelo. 
* gnu/packages/bioinformatics.scm (python-multivelo): New variable.
 2022-10-27 15:15:19 +02:00
Hong.Li@mdc-berlin.de 358a1fdf7b
gnu: Add r-seuratwrappers. 
* gnu/packages/bioinformatics.scm (r-seuratwrappers): New variable.
 2022-10-27 15:03:21 +02:00
Ricardo Wurmus 87763421a9
gnu: r-seurat: Update to 4.2.0. 
* gnu/packages/cran.scm (r-seurat): Update to 4.2.0.
 2022-10-27 15:03:21 +02:00
Ricardo Wurmus 1cc12eace3
gnu: r-seuratobject: Update to 4.1.2. 
* gnu/packages/cran.scm (r-seuratobject): Update to 4.1.2.
 2022-10-27 15:03:21 +02:00
Mădălin Ionel Patrașcu 4b9fa56cad
gnu: Add r-baalchip. 
* gnu/packages/bioconductor.scm (r-baalchip): New variable.
 2022-10-27 13:54:18 +02:00
Mădălin Ionel Patrașcu 8e6a9b23d0
gnu: Add python-jupytext. 
* gnu/packages/python-xyz.scm (python-jupytext): New variable.
 2022-10-27 13:25:15 +02:00
Mădălin Ionel Patrașcu c28598db5b
gnu: Add python-mdit-py-plugins. 
* gnu/packages/python-xyz.scm (python-mdit-py-plugins): New variable.
 2022-10-27 13:25:15 +02:00
Mădălin Ionel Patrașcu 447400c853
gnu: Add python-markdown-it-py. 
* gnu/packages/python-xyz.scm (python-markdown-it-py): New variable.
 2022-10-27 13:25:15 +02:00
Mădălin Ionel Patrașcu d748d4fd6c
gnu: Add python-mdurl. 
* gnu/packages/python-xyz.scm (python-mdurl): New variable.
 2022-10-27 13:25:15 +02:00
Ricardo Wurmus be51ee7ced
gnu: Add ghc-6.0. 
* gnu/packages/haskell.scm (ghc-6.0): New variable.
 2022-10-27 13:25:15 +02:00
Ricardo Wurmus 82791af033
gnu: ghc-4: Build full compiler using provided *.hc files. 
* gnu/packages/haskell.scm (ghc-4)[source]: Remove patch.
[arguments]: Change to build full compiler.
[native-inputs]: Remove default binutils and gcc; add tarball for hc files.
* gnu/packages/patches/ghc-4.patch: Delete patch.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2022-10-27 13:25:15 +02:00
Efraim Flashner bbaf3bcb45
gnu: python-afdko: Skip a test. 
* gnu/packages/fontutils.scm (python-afdko)[arguments]: Adjust custom
'check phase to skip a test.
 2022-10-27 14:13:52 +03:00
Andrew Tropin 95d44c0586
gnu: Add emacs-clj-refactor. 
* gnu/packages/emacs-xyz.scm (emacs-clj-refactor): New variable.
 2022-10-27 09:27:40 +04:00
Andrew Tropin 39dfa2947f
gnu: Add emacs-inflections. 
* gnu/packages/emacs-xyz.scm (emacs-inflections): New variable.
 2022-10-27 09:18:53 +04:00
Tobias Geerinckx-Rice 5dda4c69f0
gnu: xorriso: Update to 1.5.4. 
* gnu/packages/cdrom.scm (xorriso): Update to 1.5.4.
 2022-10-23 02:00:07 +02:00
Tobias Geerinckx-Rice df5cbe529b
gnu: sudo: Update to 1.9.12. 
* gnu/packages/admin.scm (sudo): Update to 1.9.12.
 2022-10-23 02:00:07 +02:00
Tobias Geerinckx-Rice 188acd0aac
gnu: mpv: Prepare for cross-compilation. 
* gnu/packages/video.scm (mpv)[arguments]: Use CC-FOR-TARGET.
 2022-10-23 02:00:07 +02:00
Tobias Geerinckx-Rice 9eea2db6ae
gnu: mpv: Use G-expressions. 
* gnu/packages/video.scm (mpv)[arguments]:
Rewrite as G-expressions.
 2022-10-23 02:00:06 +02:00
Tobias Geerinckx-Rice 51aac125f0
gnu: mpv: Remove input labels. 
* gnu/packages/video.scm (mpv)[inputs]: Remove input labels.
[arguments]: Use SEARCH-INPUT-FILE instead.
 2022-10-23 02:00:06 +02:00
Tobias Geerinckx-Rice 32be0431ff
gnu: mpv: Remove trailing #t from phases. 
* gnu/packages/video.scm (mpv)[arguments]: Don't explicitly return #t
from phases.
 2022-10-23 02:00:06 +02:00