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Paul A. Patience 32bcadc98c
gnu: trilinos-for-dealii-openmpi: Remove input labels. 
* gnu/packages/maths.scm (trilinos-for-dealii-openmpi)[native-inputs,
inputs, propagated-inputs]: Remove labels.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 17:20:26 +02:00
Paul A. Patience a42730183a
gnu: dealii: Update to 9.4.0. 
* gnu/packages/maths.scm (dealii): Update to 9.4.0.
[propagated-inputs]: Replace sundials-5 with sundials.
(dealii-openmpi)[propagated-inputs]: Replace sundials-openmpi-5 with
sundials-openmpi.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 17:20:26 +02:00
Paul A. Patience 6a15bd031f
gnu: dealii: Use G-expressions. 
* gnu/packages/maths.scm (dealii)[snippet, arguments]: Use
G-expressions.
(dealii-openmpi)[arguments]: Same.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 17:20:26 +02:00
Paul A. Patience bbf5e033d4
gnu: trilinos-for-dealii-openmpi: Fix build. 
* gnu/packages/maths.scm (trilinos-for-dealii-openmpi)[native-inputs]:
Add gcc-7 to fix the failing build with newer versions of gcc.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 17:20:26 +02:00
Mădălin Ionel Patrașcu c6800aa31e
gnu: Add r-muscat. 
* gnu/packages/bioconductor.scm (r-muscat): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2022-08-01 16:08:11 +02:00
muradm 7e3234cb70
gnu: mu: Update to 1.8.7. 
* gnu/packages/mail.scm (mu): Update to 1.8.7.
[source]: Fetch from git.
[build-system]: Use meson-build-system.
[native-inputs]: Remove glib:bin and tzdata; add gnupg and texinfo; use new
style.
[inputs]: Remove guile.
[arguments]: Remove obsolete 'patch-configure, 'fix-ffi, and
'check-tz-setup phases.  Rename 'patch-bin-sh-in-tests
to 'patch-bin-references and update it.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2022-08-01 16:03:21 +02:00
Maxim Cournoyer c454cf6343
gnu: qutebrowser: Fix indentation. 
* gnu/packages/web-browsers.scm (qutebrowser): Fix indentation.
 2022-08-01 09:32:28 -04:00
Maxim Cournoyer aea756ea33
gnu: qutebrowser: Fix build. 
Fixes <https://issues.guix.gnu.org/56864>, which is a regression introduced
with a0beb297a3.

* gnu/packages/web-browsers.scm (qutebrowser)
[phases]{wrap-qt-process-path}: Do not use the (no longer valid)
"qtwebengine-5" label; instead, locate QtWebEngineProcess via
'search-input-file'.

Reported-by: Jack Hill <jackhill@jackhill.us>
 2022-08-01 09:32:28 -04:00
Mădălin Ionel Patrașcu 8d7a721400
gnu: Add r-millefy. 
* gnu/packages/bioinformatics.scm (r-millefy): New variable.
 2022-08-01 15:14:47 +02:00
Marcel van der Boom b8df15b748
gnu: exiv2: Fix test failure on ppc64le and aarch64. 
ppc64 and aarch64 do not raise exception and thus output and exit code
for test is different.

See:

  https://github.com/Exiv2/exiv2/issues/365 and
  https://github.com/Exiv2/exiv2/issues/933

* gnu/packages/image.scm (exiv2)[arguments]: Add 'adjust-tests' phase.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 14:08:09 +02:00
Philip McGrath d7ab54cdb1
gnu: Add python-biblib. 
* gnu/packages/python-xyz.scm (python-biblib): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 14:08:09 +02:00
Maya dd3cf14402
services: opensmtpd: Make commands setgid to "smtpq" by default. 
This is a patch that fixes "<executable name>: this program must be setgid smtpq".

* gnu/services/mail.scm (<opensmtpd-configuration>)[setgid-commands?]: New field.
(opensmtpd-set-gids): New procedure.
(opensmtpd-service-type)[extensions]: Add SETUID-PROGRAM-SERVICE-TYPE extension.
* doc/guix.texi (Mail Services): Document it.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 14:08:08 +02:00
Danial Behzadi 432ea6446d
gnu: tractor: Update to 3.14. 
* gnu/packages/tor.scm (tractor): Update to 3.14.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 14:08:08 +02:00
Paul A. Patience d1b60cb65b
gnu: Add comma after “i.e.” in descriptions. 
* gnu/packages/bioconductor.scm (r-anota)[description]: Add comma after
“i.e.”.
* gnu/packages/code.scm (xenon)[description]: Same.
* gnu/packages/cran.scm (r-crosstalk)[description]: Same.
* gnu/packages/python-xyz.scm (python-radon)[description]: Same.
* gnu/packages/statistics.scm (r-logspline)[description]: Same.
* gnu/packages/suckless.scm (tabbed)[description]: Same.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 14:08:08 +02:00
Paul A. Patience e0de48f0e4
gnu: hdf5-1.8: Add missing comma to linker flag. 
* gnu/packages/maths.scm (hdf5-1.8)[arguments]<#:phases>: Add missing
comma to linker flag.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 14:08:08 +02:00
Z572 dee64d4776
gnu: guile-lens: Fix build. 
* gnu/packages/guile-xyz.scm (guile-lens)
[phases]{run-hall}: replace "dist" to "build-system".

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 14:08:08 +02:00
Denis 'GNUtoo' Carikli 49000523d2
gnu: xdot: Build with librsvg-for-system. 
* gnu/packages/graphviz.scm (xdot)[inputs]: Replace librsvg with
  librsvg-for-system.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 14:08:07 +02:00
Denis 'GNUtoo' Carikli 4f57da7668
gnu: Add cardpeek. 
* gnu/packages/security-token.scm (cardpeek): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 14:08:07 +02:00
Sharlatan Hellseher d790ec21e8
gnu: python-sep: Update to 1.2.1 
* gnu/packages/astronomy.scm: (python-sep): Update to 1.2.1.
  Inherit from libsep

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 14:08:07 +02:00
Sharlatan Hellseher 6ad9a094c1
gnu: Add libsep 
* gnu/packages/astronomy.scm: (libsep): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-08-01 14:08:07 +02:00
Ludovic Courtès 5a96748a99
gnu: gnutls: Add 3.7.7. 
* gnu/packages/tls.scm (gnutls-latest): New variable.
 2022-08-01 14:08:07 +02:00
Ludovic Courtès cce7427f95
download: 'url-fetch' closes its HTTP/HTTPS port. 
* guix/build/download.scm (url-fetch)[fetch]: In the http/https case,
close PORT before returning.
 2022-08-01 14:08:07 +02:00
Ricardo Wurmus dc3ad40c6b
gnu: python-bbknn: Set NUMBA_CACHE_DIR. 
* gnu/packages/bioinformatics.scm (python-bbknn)[arguments]: Add phase
'set-numba-cache-dir.
 2022-08-01 12:46:19 +02:00
Ricardo Wurmus 9b1a2dcd5b
gnu: python-umap-learn: Disable unreliable test. 
* gnu/packages/machine-learning.scm (python-umap-learn)[arguments]: Disable
test_densmap_trustworthiness_on_iris_supervised.
 2022-08-01 12:46:19 +02:00
Ricardo Wurmus a69f2cd076
gnu: python-umap-learn: Set NUMBA_CACHE_DIR. 
* gnu/packages/machine-learning.scm (python-umap-learn)[arguments]: Add phase
to set NUMBA_CACHE_DIR.
 2022-08-01 12:46:19 +02:00
Maxim Cournoyer 3a656ea836
gnu: jami: Apply upstream patch that fixes a usability issue. 
* gnu/packages/patches/jami-fix-esc-bug.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/jami.scm (%jami-sources): Apply it.
 2022-07-31 23:08:51 -04:00
Maxim Cournoyer ccf6401d05
gnu: jami: Update to 20220726.1515.da8d1da. 
* gnu/packages/jami.scm (jami): Update to 20220726.1515.da8d1da.
[configure-flags]: New argument.
[phases]{fix-version-string}: Adjust file name.
{use-desktop-opengl}: Delete obsolete phase.
{patch-source}: New phase.
[native-inputs]: Add googletest and vulkan-headers.  Replace qttools-5 with
qttools.
[inputs]: Add libxkbcommon, qt5compat, qtnetworkauth, qtpositioning and
vulkan-loader.  Remove qtwebengine-5, qtwebchannel-5, qtgraphicaleffects,
qtquickcontrols-5 and qtquickcontrols2-5.  Update qtsvg-5, qtmultimedia-5 and
qtdeclarative-5 to their Qt 6 equivalent.
 2022-07-31 21:55:50 -04:00
Maxim Cournoyer f80f1667f1
gnu: Deprecate jami-gnome for jami. 
* gnu/packages/jami.scm (jami-gnome): Delete package, deprecating it for jami.
 2022-07-31 21:55:50 -04:00
Maxim Cournoyer 46f5623cc1
gnu: Remove jami-libclient. 
* gnu/packages/jami.scm (jami-libclient): Delete variable.
(libringclient): Likewise.
(jami-gnome)[inputs]: Remove jami-libclient.
(jami)[inputs]: Likewise.
 2022-07-31 21:55:49 -04:00
Maxim Cournoyer 3d812fea06
gnu: libjami: Enable test agent. 
* gnu/packages/jami.scm (libjami)[configure-flags]: Add '--enable-agent' and
remove FIXME.
[tests?]: Update comment.
 2022-07-31 21:55:49 -04:00
Maxim Cournoyer bdf0fce88e
gnu: libjami: Update to 20220726.1515.da8d1da. 
* gnu/packages/patches/jami-fix-crash-on-quit.patch: Delete file.
* gnu/packages/patches/jami-images-loading.patch: Likewise.
* gnu/packages/patches/jami-libclient-audio-managers.patch: Likewise.
* gnu/packages/patches/jami-memory-usage.patch: Likewise.
* gnu/local.mk (dist_patch_DATA): De-register removed patches.
* gnu/packages/jami.scm (%jami-version): Update to 20220726.1515.da8d1da.
(libjami)[configure-flags]: Add '--disable-static'.
(jami-apply-custom-patches): Adjust for top directory renaming.
(%ffmpeg-default-configure-flags): Add muxer support
for g726 and g726le.  Add demuxer support for g723_1, g726 and g726le.  Add
encoder/decoder support for g726, g726le and g723_1.  Add decoder support for
g729.
(ffmpeg-jami)[patches]: Add 'libopusenc-reload-packet-loss-at-encode'.
(jami-libclient)[native-inputs]: New field.
[inputs]: Add ffmpeg-jami and libxkbcommon.
[propagated-inputs]: Replace qtbase-5 with qtbase.
 2022-07-31 21:55:49 -04:00
Maxim Cournoyer 1f466ed6be
build: qt: Add qtbase argument and wrap Qt environment variables exactly. 
* guix/build-system/qt.scm (default-qtbase): New variable.
(lower) <#:qtbase>: Add argument...
[build-inputs]: ... and propagate it here.
(qt-build): Add qtbase argument.
(qt-cross-build): Likewise.
* guix/build/qt-utils.scm (%default-qt-major-version): New variable.
(variables-for-wrapping): Add qt-major-version argument, and use it to format
the various path prefixes.  Wrap QT environment variables exactly.
(wrap-qt-program*): Add qt-major-version argument, and pass it to
variables-for-wrapping.
(wrap-qt-program): Add qt-major-version argument, and pass it to
wrap-qt-program*.
(wrap-all-qt-programs): Add qtbase argument, and extract the major version
from it, passing it to wrap-qt-program*.
 2022-07-31 21:55:49 -04:00
Maxim Cournoyer a13a687989
gnu: Add qtpositioning. 
* gnu/packages/qt.scm (qtpositioning): New variable.
 2022-07-31 21:55:49 -04:00
Maxim Cournoyer d9e8d7f4aa
gnu: Add qtnetworkauth, version 6.3.1. 
* gnu/packages/qt.scm (qtnetworkauth): New variable.
 2022-07-31 21:55:48 -04:00
Maxim Cournoyer 2e27ccec83
gnu: qtnetworkauth: Rename to qtnetworkauth-5. 
Automated with:

  git grep -l qtnetworkauth | xargs sed 's/\bqtnetworkauth\b/\0-5/g' -i
 2022-07-31 21:55:48 -04:00
Maxim Cournoyer a4784b3273
gnu: Add qttools, version 6.3.1. 
* gnu/packages/qt.scm (qttools): New variable.
 2022-07-31 21:55:48 -04:00
Maxim Cournoyer eef8e2ec46
gnu: qttools: Rename to qttools-5. 
Automated with:

  git grep -l qttools | xargs sed 's/\bqttools\b/\0-5/g' -i
  git checkout NEWS
 2022-07-31 21:55:48 -04:00
Maxim Cournoyer de20b74fc2
gnu: Add qt5compat. 
* gnu/packages/qt.scm (qt5compat): New variable.
 2022-07-31 21:55:47 -04:00
Maxim Cournoyer f1e126c03b
gnu: Add qtwebengine, version 6.3.1. 
* gnu/packages/qt.scm (qtwebengine): New variable.
 2022-07-31 21:55:47 -04:00
Maxim Cournoyer a0beb297a3
gnu: qtwebengine: Rename to qtwebengine-5. 
Automated with:

  git grep -l qtwebengine | xargs sed 's/\bqtwebengine\b/\0-5/g' -i
  git checkout NEWS
 2022-07-31 21:55:47 -04:00
Maxim Cournoyer ef648459df
gnu: Add qtwebchannel, version 6.3.1. 
* gnu/packages/qt.scm (qtwebchannel): New variable.
 2022-07-31 21:55:46 -04:00
Maxim Cournoyer 0938c3e34a
gnu: qtwebchannel: Rename to qtwebchannel-5. 
Automated via:

  git grep -l qtwebchannel | xargs sed 's/\bqtwebchannel\b/\0-5/g' -i
  git checkout NEWS
 2022-07-31 21:55:46 -04:00
Maxim Cournoyer 573055b7ef
gnu: Add qtwebsockets, version 6.3.1. 
* gnu/packages/qt.scm (qtwebsockets): New variable.
 2022-07-31 21:55:46 -04:00
Maxim Cournoyer d15258d991
gnu: qtwebsockets: Rename to qtwebsockets-5. 
Automated via:

  git grep -l qtwebsockets | xargs sed 's/\bqtwebsockets\b/\0-5/g' -i
  git checkout NEWS
 2022-07-31 21:55:46 -04:00
Maxim Cournoyer d90031f799
gnu: qtquickcontrols2: Define as obsoleted by qtdeclarative. 
* gnu/packages/qt.scm (qtquickcontrols2): New variable.
 2022-07-31 21:55:45 -04:00
Maxim Cournoyer 1130fc5991
gnu: qtquickcontrols2: Rename to qtquickcontrols2-5. 
Automated via:

  git grep -l qtquickcontrols2 | xargs sed 's/\bqtquickcontrols2\b/\0-5/g' -i
  git checkout NEWS
 2022-07-31 21:55:45 -04:00
Maxim Cournoyer 65e5e85d28
gnu: qtquickcontrols: Rename to qtquickcontrols-5. 
Automated via:

  git grep -l qtquickcontrols | xargs sed 's/\bqtquickcontrols\b/\0-5/g' -i
  git checkout NEWS
 2022-07-31 21:55:45 -04:00
Maxim Cournoyer 397d05a4bf
gnu: Add qtdeclarative, version 6.3.1. 
* gnu/packages/qt.scm (qtdeclarative): New variable.
 2022-07-31 21:55:44 -04:00
Maxim Cournoyer 735d340ae4
gnu: qtdeclarative: Rename to qtdeclarative-5. 
Automated via the following commands:

  git grep -l '\bqtdeclarative\b' | xargs sed -E 's/qtdeclarative/\0-5/g' -i
  git checkout NEWS
 2022-07-31 21:55:44 -04:00
Maxim Cournoyer 983a061e98
gnu: Add qtmultimedia, version 6.3.1. 
* gnu/packages/qt.scm (qtmultimedia): New variable.
 2022-07-31 21:55:44 -04:00