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Author SHA1 Message Date
Lars-Dominik Braun 652c5d8a01
gnu: r-mixedpower: Fix faulty commit. 
Fix previous commit, which did not contain the following changes:

* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/statistics.scm (r-mixedpower)[source]: Use it.
 2022-10-28 10:17:55 +02:00
Jonathan Brielmaier 328fa8b290
gnu: icedove: Update to 102.4.1. 
* gnu/packages/gnuzilla.scm (%icedove-build-id, %icedove-version) Update to 102.4.1.
 2022-10-28 10:02:35 +02:00
Lars-Dominik Braun 332568d3e8
gnu: r-mixedpower: Improve compatibility with R>=4.2. 
Upstream’s fix is incomplete and thus commit
7871447cf5 was insufficient.

* gnu/packages/patches/r-mixedpower-r2power.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/statistics.scm (r-mixedpower)[source]: Use it.
 2022-10-28 09:59:11 +02:00
Maxim Cournoyer 3511ad2857
gnu: rottlog: Apply patch adding a Texinfo direntry. 
Relates to <https://issues.guix.gnu.org/58821>.

* gnu/packages/patches/rottlog-direntry.patch: Add patch.
* gnu/packages/admin.scm (rottlog): Apply it.
* gnu/local.mk (dist_patch_DATA): Register it.
 2022-10-27 23:34:46 -04:00
Maxim Cournoyer ff097b450b
gnu: rottlog: Use gexps and bootstrap Autotools build system. 
* gnu/packages/admin.scm (rottlog) [snippet]: Delete build system files.
Delete trailing #t.  Patch Makefile.am instead of Makefile.in.  Do not patch
INSTALL_RC and INSTALL_SCRIPT variables default values.
[arguments]: Use gexps.  Delete trailing #t.
[make-flags]: Override INSTALL_RC and INSTALL_SCRIPT.
[phases]{fix-configure}: Delete phase.
[native-inputs]: Add autoconf.  Sort inputs.
 2022-10-27 23:34:46 -04:00
Maxim Cournoyer b42b0e6d62
profiles: info-dir-file: Remove install-info '--silent' option. 
Relates to <https://issues.guix.gnu.org/58821>.

Revert 4fef1e850e, which silenced useful
information such as the following warning:

   install-info: warning: no info dir entry in
   `/gnu/store/...-rottlog-0.72.2/share/info/rottlog.info.gz'

Rationale: profile hooks output is now hidden by default, and can be made
visible via the --verbosity option.
 2022-10-27 23:34:45 -04:00
Leo Famulari e04baf43ab
gnu: linux-libre: Update to 5.19.17. 
* gnu/packages/linux.scm (linux-libre-5.19-version): Update to 5.19.17.
(linux-libre-5.19-pristine-source): Update hash.
 2022-10-27 21:02:02 -04:00
Ludovic Courtès d520fdec3c
gnu: findutils: Skip failing test on GNU/Hurd. 
* gnu/packages/base.scm (findutils)[arguments]: Add #:make-flags.
* gnu/packages/commencement.scm (findutils-boot0)[arguments]: Likewise.
 2022-10-28 01:27:22 +02:00
Ludovic Courtès 6c16eb24d1
gnu: grep: Skip failing tests on GNU/Hurd. 
* gnu/packages/base.scm (grep)[arguments]: Add #:make-flags.
 2022-10-28 01:27:22 +02:00
Ludovic Courtès 842b73fd2b
gnu: coreutils: Skip failing tests on GNU/Hurd. 
* gnu/packages/base.scm (coreutils)[arguments]: Add
"tests/df/unreadable.sh" and "test-perror2" to the 'XFAIL_TESTS' list.
 2022-10-28 01:27:21 +02:00
Vagrant Cascadian ac51b9c86d
gnu: swftools: Fix typos. 
* gnu/packages/animation.scm (swftools)[description]: Avoid uses of "allows
  to".
 2022-10-27 14:13:17 -07:00
Marius Bakke f8ce707252
gnu: pypy: Remove unused module imports. 
This is a follow-up to commit 6e7ed04033.

* gnu/packages/pypy.scm: Remove unused modules.
 2022-10-27 21:38:56 +02:00
Marius Bakke e944734ef9
build-system/pyproject: Always run tests verbosely for supported backends. 
* guix/build-system/pyproject.scm (pyproject-build): Default to '() instead of
 #false for TEST-FLAGS.
* guix/build/pyproject-build-system.scm (check): Unconditionally enable
verbose test flags.
* doc/guix.texi (Build Systems): Document this change.
* gnu/packages/fontutils.scm (python-glyphslib)[arguments]: Remove verbosity
from #:test-flags.
* gnu/packages/pdf.scm (python-pydyf, weasyprint)[arguments]: Likewise.
* gnu/packages/python-web.scm (python-openapi-spec-validator)[arguments]: Likewise.
* gnu/packages/python-xyz.scm (python-path, python-tempora)[arguments]: Likewise.
 2022-10-27 21:30:03 +02:00
Marius Bakke 6ef998d54e
build-system/pyproject: Adjust indentation. 
* guix/build/pyproject-build-system.scm: Adjust indentation.
 2022-10-27 21:30:03 +02:00
Marius Bakke f928abac36
gnu: python-deepmerge: Use pyproject-build-system. 
* gnu/packages/python-xyz.scm (python-deepmerge)[build-system]: Set to
PYPROJECT-BUILD-SYSTEM.
[arguments]: Remove obsolete phases.
[native-inputs]: Remove PYTHON-PYPA-BUILD and PYTHON-WHEEL.
 2022-10-27 19:43:08 +02:00
Marius Bakke 7b83b3a77c
gnu: python-scikit-build: Switch to pyproject-build-system. 
* gnu/packages/python-xyz.scm (python-scikit-build)[build-system]: Set to
PYPROJECT-BUILD-SYSTEM.
[arguments]: Remove obsolete phases.
[native-inputs]: Remove PYTHON-PYPA-BUILD and PYTHON-WHEEL.
 2022-10-27 19:43:08 +02:00
Marius Bakke 9ffbcb8a06
gnu: python-cattrs: Use pyproject-build-system. 
* gnu/packages/python-xyz.scm (python-cattrs)[build-system]: Set to
PYPROJECT-BUILD-SYSTEM.
[arguments]: Remove obsolete phases.
[native-inputs]: Remove PYTHON-PYPA-BUILD.
 2022-10-27 19:43:08 +02:00
Marius Bakke d2e88c383b
gnu: python-path: Use pyproject-build-system. 
* gnu/packages/python-xyz.scm (python-path-bootstrap)[build-system]: Switch to
PYPROJECT-BUILD-SYSTEM.
[arguments]: Remove #:phases.
[native-inputs]: Remove PYTHON-PYPA-BUILD.
(python-path): Remove #:phases.  Add #:test-flags.
 2022-10-27 19:43:08 +02:00
Marius Bakke 5e17453f18
gnu: python-openapi-spec-validator: Use pyproject-build-system. 
* gnu/packages/python-web.scm (python-openapi-spec-validator)[build-system]:
Set to PYPROJECT-BUILD-SYSTEM.
[arguments]: Add #:test-flags.  Remove obsolete phases.
[native-inputs]: Remove PYTHON-PYPA-BUILD.
 2022-10-27 19:43:08 +02:00
Marius Bakke 3c685772de
gnu: python-openapi-schema-validator: Use pyproject-build-system. 
* gnu/packages/python-web.scm (python-openapi-schema-validator)[build-system]:
Set to PYPROJECT-BUILD-SYSTEM.
[arguments]: Remove redundant phases.
[native-inputs]: Remove PYTHON-PYPA-BUILD.
 2022-10-27 19:43:08 +02:00
Marius Bakke 7b499ef116
gnu: zabbix-cli: Switch to pyproject-build-system. 
* gnu/packages/monitoring.scm (zabbix-cli)[build-system]: Switch to
PYPROJECT-BUILD-SYSTEM.
[arguments]: Remove check phase.
 2022-10-27 19:43:08 +02:00
Marius Bakke e05e2a7a75
gnu: python-pygmsh: Use pyproject-build-system. 
* gnu/packages/simulation.scm (python-pygmsh)[build-system]: Switch to
PYPROJECT-BUILD-SYSTEM.
[arguments]: Remove redundant phases.
[native-inputs]: Remove PYTHON-PYPA-BUILD.
 2022-10-27 19:43:07 +02:00
Marius Bakke b8efe89eb4
gnu: python-tempora: Switch to pyproject-build-system. 
* gnu/packages/python-xyz.scm (python-tempora)[build-system]: Switch to
PYPROJECT-BUILD-SYSTEM.
[arguments]: Add #:test-flags.  Remove #:phases.
[native-inputs]: Remove PYTHON-PYPA-BUILD.
 2022-10-27 19:43:07 +02:00
Marius Bakke 8bdc4c1547
gnu: python-mypy-protobuf: Switch to pyproject-build-system. 
* gnu/packages/protobuf.scm (python-mypy-protobuf)[build-system]: Switch to
PYPROJECT-BUILD-SYSTEM.
[arguments]: Remove redundant phases.
[native-inputs]: Remove PYTHON-PYPA-BUILD.
 2022-10-27 19:43:07 +02:00
Marius Bakke eecc807ea4
gnu: python-ufolib2: Use pyproject-build-system. 
* gnu/packages/fontutils.scm (python-ufolib2)[build-system]: Switch to
PYPROJECT-BUILD-SYSTEM.
[arguments]: Remove.
[native-inputs]: Remove PYTHON-PYPA-BUILD and PYTHON-WHEEL.
 2022-10-27 19:43:07 +02:00
Marius Bakke 10f8534929
gnu: python-statmake: Use pyproject-build-system. 
* gnu/packages/fontutils.scm (python-statmake)[build-system]: Switch to
PYPROJECT-BUILD-SYSTEM.
[arguments]: Remove redundant phases.
[native-inputs]: Remove PYTHON-PYPA-BUILD.
 2022-10-27 19:43:07 +02:00
Marius Bakke 6f6257a6bc
gnu: python-glyphslib: Use pyproject-build-system. 
* gnu/packages/fontutils.scm (python-glyphslib)[build-system]: Switch to
PYPROJECT-BUILD-SYSTEM.
[arguments]: Add #:test-flags.  Remove #:phases.
[native-inputs]: Remove PYTHON-PYPA-BUILD and PYTHON-WHEEL.
 2022-10-27 19:43:07 +02:00
Marius Bakke df095a1813
gnu: weasyprint: Use pyproject-build-system. 
* gnu/packages/pdf.scm (weasyprint)[build-system]: Switch to
PYPROJECT-BUILD-SYSTEM.
[arguments]: Remove redundant phases.  Add #:test-flags.
[native-inputs]: Remove PYTHON-PYPA-BUILD.
 2022-10-27 19:43:07 +02:00
Marius Bakke 4c8e0b3274
gnu: python-pydyf: Use pyproject-build-system. 
* gnu/packages/pdf.scm (python-pydyf)[build-system]: Switch to
PYPROJECT-BUILD-SYSTEM.
[arguments]: Remove #:phases.  Add #:test-flags.
[native-inputs]: Remove PYTHON-PYPA-BUILD.
 2022-10-27 19:43:07 +02:00
Marius Bakke ee1f51011c
gnu: python-autopage: Use pyproject-build-system. 
* gnu/packages/python-xyz.scm (python-autopage)[build-system]: Switch to
PYPROJECT-BUILD-SYSTEM.
[arguments]: Remove redundant phases.
 2022-10-27 19:43:07 +02:00
Marius Bakke a4fd4db6d1
news: Add entry for 'pyproject-build-system'. 
* etc/news.scm: Add entry.

Co-authored-by: Florian Pelz <pelzflorian@pelzflorian.de>
Co-authored-by: Julien Lepiller <julien@lepiller.eu>
 2022-10-27 19:43:07 +02:00
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