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127657 Commits (27d017be7aaea12db68529c3ebd5fd3dbd8642b4)

Author SHA1 Message Date
Ludovic Courtès 59d29ebbb2
gnu: psm2: Update to 12.0. 
* gnu/packages/linux.scm (psm2): Update to 12.0.
 2023-11-15 11:36:20 +01:00
Ludovic Courtès 8c1c045a87
gnu: libfabric: Update to 1.19.0. 
* gnu/packages/linux.scm (libfabric): Update to 1.19.0.
 2023-11-15 11:36:20 +01:00
Ludovic Courtès 3f7eeaa57c
gnu: rdma-core: Update to 48.0. 
* gnu/packages/linux.scm (rdma-core): Update to 48.0.
 2023-11-15 11:36:20 +01:00
Ludovic Courtès 975350fab7
gnu: ucx: Update to 1.15.0. 
* gnu/packages/fabric-management.scm (ucx): Update to 1.15.0.
* gnu/packages/patches/ucx-tcp-iface-ioctl.patch: Update for 1.15.0.
 2023-11-15 11:36:20 +01:00
Ludovic Courtès d117c6b422
gnu: opensm: Update to 3.3.24. 
* gnu/packages/fabric-management.scm (opensm): Update to 3.3.24.
 2023-11-15 11:36:20 +01:00
Ludovic Courtès f1f8d56b75
gnu: hwloc: Update to 2.9.3. 
* gnu/packages/mpi.scm (hwloc-2): Update to 2.9.3.
 2023-11-15 11:36:19 +01:00
Ludovic Courtès 96753702a0
gnu: slurm: Add 23.02.6. 
* gnu/packages/parallel.scm (slurm): Update to 23.02.6.
(slurm-22.05): New variable.
 2023-11-15 11:36:19 +01:00
Ludovic Courtès d67fa732f7
gnu: opensm: Use gexps. 
* gnu/packages/fabric-management.scm (opensm)[arguments]: Use gexps.
 2023-11-15 11:36:19 +01:00
Ludovic Courtès ab6f63f3cb
gnu: opensm: Use the right version string for the doc directory. 
Previously, when built with ‘--with-latest=opensm’, the package would
install its documentation under a directory with the wrong version
string.

* gnu/packages/fabric-management.scm (opensm)[arguments]: Use the name
and version of THIS-PACKAGE.
 2023-11-15 11:36:19 +01:00
Ricardo Wurmus b712e563cf
gnu: soci: Add PIE flag. 
* gnu/packages/databases.scm (soci)[arguments]: Set CMAKE_CXX_FLAGS to add
-fPIE.

Change-Id: I79527759d0d35833168f5106a9d6f372375a8ebe
 2023-11-14 23:46:08 +01:00
Josselin Poiret bd0f217321
gnu: agda-1lab: Update to 549fdb1c948a975e90e70f871993a4a4239aa280. 
* gnu/packages/agda.scm (agda-1lab): Update to
549fdb1c948a975e90e70f871993a4a4239aa280.

Change-Id: Iad77350fea5a6378e836cbd18c1f4a51bd5a5f0e
 2023-11-14 13:47:53 +01:00
Josselin Poiret c5c2a82082
gnu: agda-cubical: Update to 0.6. 
* gnu/packages/agda.scm (agda-cubical): Update to 0.6.

Change-Id: I1d6edc44755260e505985fb974c632ec6fff2b49
 2023-11-14 13:47:53 +01:00
Josselin Poiret 5f4b3ccf50
gnu: agda-categories: Adapt to agda-stdlib 1.7.3. 
* gnu/packages/patches/agda-categories-use-stdlib-1.7.3.patch: New patch.
* gnu/packages/agda.scm (agda-categories)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Register it.

Change-Id: I25f16d55f14465a1dae882fd8ec47a95f8598e5c
 2023-11-14 13:47:10 +01:00
Josselin Poiret 7374e14f51
gnu: agda-stdlib: Update to 1.7.3. 
* gnu/packages/agda.scm (agda-stdlib): Update to 1.7.3.

Change-Id: Ic941073814a6a2150d470fc05218dc8d19954445
 2023-11-14 13:30:49 +01:00
Josselin Poiret a521757306
gnu: agda: Update to 2.6.4. 
* gnu/packages/agda.scm (agda): Update to 2.6.4.  Also build with
optimizations and cluster counting support.
* gnu/packages/patches/agda-use-sphinx-5.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Register it.

Change-Id: I98a66678ec401b9201d9fd3a0f606fff9767b4bc
 2023-11-14 13:30:48 +01:00
Josselin Poiret 5cb2574243
gnu: Add ghc-text-icu. 
* gnu/packages/haskell-xyz.scm (ghc-text-icu): New variable.

Change-Id: I553f1fef4e76aeea6d09901917fd5d6032c23d46
 2023-11-14 13:30:45 +01:00
Nicolas Goaziou b25954181c
gnu: emacs-denote: Update to 2.1.0. 
* gnu/packages/emacs-xyz.scm (emacs-denote): Update to 2.1.0.

Change-Id: I4d0f585604ef049480842b4c052edd1aef300e15
 2023-11-14 13:21:41 +01:00
Nicolas Goaziou cb399d96fb
gnu: emacs-org: Update to 9.6.12. 
* gnu/packages/emacs-xyz.scm (emacs-org): Update to 9.6.12.

Change-Id: I0d2b063526f24b7104fcbab972f212e279060f27
 2023-11-14 13:21:41 +01:00
Nicolas Goaziou 3254429a41
gnu: emacs-package-lint: Update to 0.21. 
* gnu/packages/emacs-xyz.scm (emacs-package-lint): Update to 0.21.

Change-Id: I82e28b8e1c211389e99f1947c5c7ddfcba893612
 2023-11-14 13:21:41 +01:00
Nicolas Goaziou 21822095e8
gnu: emacs-compat: Update to 29.1.4.4. 
* gnu/packages/emacs-xyz.scm (emacs-compat): Update to 29.1.4.4.

Change-Id: I11705cb0c2b50bb445711bfdfdb142557aa58b04
 2023-11-14 13:21:40 +01:00
Nicolas Goaziou b5d419b4ab
gnu: emacs-flycheck-grammalecte: Improve package style. 
* gnu/packages/emacs-xyz.scm (emacs-flycheck-grammalecte)[arguments]Use
G-expressions.
<#:exclude>: Remove non-existing excluded file.
<#:emacs>: Use EMACS-NO-X.
<#:phases>: Use G-expressions.

Change-Id: Ic5a3c5e3f5271e75cd369cdd40ce210d7c2b859b
 2023-11-14 13:21:40 +01:00
Nicolas Goaziou a572e55ea5
gnu: emacs-flycheck-grammalecte: Update to 2.4. 
* gnu/packages/emacs-xyz.scm (emacs-flycheck-grammalecte): Update to 2.4.

Change-Id: I372e3e55534606dba6fed2c2d2f00dc27dc76c0e
 2023-11-14 13:21:40 +01:00
Efraim Flashner 3d15e9e5bc
gnu: insight-toolkit-4.12: Fix building. 
* gnu/packages/image-processing.scm (insight-toolkit-4.12)[arguments]:
Add a configure-flag to build with c++14.

Change-Id: I5e7a0a3ed47e4e3f25611147f8e66c58a1bf8a8c
 2023-11-14 08:57:48 +02:00
Efraim Flashner f9f36b08e5
gnu: ffmpeg-2.8: Update to 2.8.22. 
* gnu/packages/video.scm (ffmpeg-2.8): Update to 2.8.22.

Change-Id: I4ab83a07f60692aa43d04a81dd227b56a95a1d74
 2023-11-14 08:16:52 +02:00
Efraim Flashner b3f110184f
gnu: ffmpeg-3.4: Update to 3.4.13. 
* gnu/packages/video.scm (ffmpeg-3.4): Update to 3.4.13.

Change-Id: I9ef7b61dcdeab96d4021150fb57b3739a61376d0
 2023-11-14 08:16:51 +02:00
Efraim Flashner b8dac014b1
gnu: ffmpeg-5: Update to 5.1.4. 
* gnu/packages/video.scm (ffmpeg-5): Update to 5.1.4.

Change-Id: I4ea8faa3bcee2e34287af4461d078850de17154f
 2023-11-14 08:16:45 +02:00
Liliana Marie Prikler 4963d4c6bb
gnu: appstream: Update to 0.16.4. 
* gnu/packages/freedesktop.scm (appstream): Update to 0.16.4.
[arguments]<#:configure-flags>: Add “-Dsystemd=false”.
<#:phases>: Adjust accordingly.

Change-Id: I9c22cbd10681666c20e848dbc1e52ca08431d984
 2023-11-11 01:38:07 +01:00
Liliana Marie Prikler 02555467ce
gnu: libxmlb: Update to 0.3.14. 
* gnu/packages/xml.scm (libxmlb): Update to 0.3.14.

Change-Id: I8571b3f46a5528d04cc2ea013ff2ab0ef4ba19da
 2023-11-11 01:37:59 +01:00
Liliana Marie Prikler a7e831a556
gnu: gtk: Update to 4.12.3. 
* gnu/packages/gtk.scm (gtk): Update to 4.12.3.
[source]: Remove snippet.
[arguments]<#:configure-flags>: Add “--no-suite=headless”.
<#:phases>: Also patch text-color tests in gsk/nodeparser.

Change-Id: Iedabfd12ae4f60f02ea21f427b85aeb6b17d03d6
 2023-11-11 01:19:20 +01:00
Liliana Marie Prikler 72e886328c
Merge branch 'master' into gnome-team 
Change-Id: I88d3789460d1a89917451d80405d89a2824006ac
 2023-11-04 07:43:44 +01:00
Clément Lassieur f54f36b363
gnu: passff-host: Add explicit references to inputs and remove some. 
This removes ‘coreutils’, ‘grep’, ‘sed’, ‘which’, ‘bash-minimal’ and
‘gnu-make’ inputs, which were only used by the Makefile and
install_host_app.sh.  Instead of running install_host_app.sh (through
‘make’) which does a few text substitutions, do the text substitutions with
Scheme code.  This simplifies things and avoids unnecessary native inputs.

* gnu/packages/browser-extensions.scm (passff-host)[build-system]: Change to
copy-build-system.
[arguments]: Copy passff.json and passff.py.  Do text substitutions on
them rather than running make.  Refer to ‘password-store’ and ‘python’ through
inputs rather than directly.
[inputs]: Add PASSWORD-STORE and PYTHON.

Change-Id: I8fdb757516a7c30eae36b15f2a8d91e1445b19a5
 2023-11-04 00:52:39 +01:00
Clément Lassieur 625cfb4c4c
gnu: password-store: Add missing ‘tail’ input. 
* gnu/packages/password-utils.scm (password-store)[arguments]: Add “tail” to
the list of requisites.
[inputs]: Add COREUTILS.

Change-Id: I7f59e6c0abfb5396b9548edaec08d3b0a7c0eb23
 2023-11-04 00:52:38 +01:00
Afkhami, Navid 10d728139d
gnu: Add r-ggbreak. 
* gnu/packages/cran.scm (r-ggbreak): New variable.

Change-Id: I27d62d0110fb56e77dc8cf82581adb6259317c2d
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-11-03 23:39:57 +01:00
Vinicius Monego 479fdc8451
gnu: python-pymc: Update to 5.9.1. 
* gnu/packages/statistics.scm (python-pymc): Update to 5.9.1.

Change-Id: I3d7927e7173f36ba4edeab06bd930c285432c29f
 2023-11-03 19:25:36 -03:00
Vinicius Monego 43d9fa0802
gnu: python-pytensor: Update to 2.17.3. 
* gnu/packages/python-science.scm (python-pytensor): Update to 2.17.3.

Change-Id: I2843aca1df4d43883bf643e6e363bd3700202c45
 2023-11-03 19:25:36 -03:00
Vinicius Monego 1879bfd88f
gnu: python-deepxde: Update to 1.10.0. 
* gnu/packages/machine-learning.scm (python-deepxde): Update to 1.10.0.

Change-Id: Ibc37f9e7df45c49f590beb1dda87236e853b88c1
 2023-11-03 19:25:36 -03:00
Vinicius Monego 96e8502faa
gnu: Add python-emcee. 
* gnu/packages/statistics.scm (python-emcee): New variable.
 2023-11-03 19:25:35 -03:00
Vinicius Monego a7d56852e3
gnu: Add python-salib. 
* gnu/packages/python-science.scm (python-salib): New variable.
 2023-11-03 19:25:35 -03:00
Vinicius Monego 9642b1c7af
gnu: python-openturns: Update to 1.21.1. 
* gnu/packages/statistics.scm (python-openturns): Update to 1.21.1.
 2023-11-03 19:25:35 -03:00
Vinicius Monego a55c3110be
gnu: python-opentsne: Update to 1.0.0. 
* gnu/packages/machine-learning.scm (python-opentsne): Update to 1.0.0.
 2023-11-03 19:25:35 -03:00
Vinicius Monego ef473d3422
gnu: symengine: Update to 0.11.1. 
* gnu/packages/algebra.scm (symengine): Update to 0.11.1.
 2023-11-03 19:25:31 -03:00
Ricardo Wurmus eb93ab2d14
gnu: r-gdata: Remove Excel from description. 
gdata 3.0.0 has removed support for reading Excel files.

* gnu/packages/statistics.scm (r-gdata)[description]: Update it.

Change-Id: Ic4090bc765d330d38136bf1b1dbbb6bb136edd39
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 8be2f44765
gnu: Remove r-sigpathway. 
This package has been removed with the release of Bioconductor 3.18.

* gnu/packages/bioconductor.scm (r-sigpathway): Remove variable.

Change-Id: I5cb9d938f370aa28b196f9cea95fb6024c2e6e37
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 38b5777ec8
gnu: r-rhdf5filters: Simplify. 
* gnu/packages/bioconductor.scm (r-rhdf5filters)[arguments]: Remove
'use-system-libraries phase and pass configure flags to disable bundled
libraries.

Change-Id: I2fb115e7b3df00cccb3f8d6659d465075d21f19b
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 78641cf9da
gnu: r-spams: Build with C++11. 
* gnu/packages/statistics.scm (r-spams)[arguments]: Add phase 'use-c++11.

Change-Id: Ie477af6afe8993919090f6c81e071cee542e69bc
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 142313cf0c
gnu: Remove r-genomegraphs. 
This package had been removed from Bioconductor with release 3.11.

* gnu/packages/bioconductor.scm (r-genomegraphs): Remove variable.

Change-Id: I73cc8cc8546089d91212176939b8c0c0a7afc309
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus 0150529188
gnu: Remove r-wavetiling. 
This package had been removed from Bioconductor since release 3.12.

* gnu/packages/bioconductor.scm (r-wavetiling): Remove variable.

Change-Id: I5eb624d975f0eb170b263266b144eacf11944580
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus abaca151b2
gnu: r-mpo-db: Include HPO sqlite database. 
* gnu/packages/bioconductor.scm (r-mpo-db)[arguments]: Bypass fetching of the
database from the internet when in build environment.
[native-inputs]: Add MPO.sqlite.

Change-Id: Ic7228322b89ce78a85a9bd5ffbd985ccd906d268
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus b30127052e
gnu: r-readwriter: Update to 0.3.2-1.12d32cb. 
* gnu/packages/bioinformatics.scm (r-readwriter): Update to 0.3.2-1.12d32cb.

Change-Id: I412190ce94bee4e7b5fce27db7ef8a72188e74f4
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus c66c66ee3f
gnu: r-hpo-db: Include HPO sqlite database. 
* gnu/packages/bioconductor.scm (r-hpo-db)[arguments]: Bypass fetching of the
database from the internet when in build environment.
[native-inputs]: Add HPO.sqlite.

Change-Id: Ie01605ef2531d992fb85c07bae5cfaabda626ea6
 2023-11-03 22:49:28 +01:00