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2022-08-01gnu: Add r-phyclust.Mădălin Ionel Patrașcu
* gnu/packages/cran.scm (r-phyclust): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-08-02gnu: node-lts: Build with icu4c-71.Efraim Flashner
* gnu/packages/node.scm (node-lts)[inputs]: Replace icu4c-70 with icu4c-71. [native-inputs]: Same.
2022-08-01gnu: Add qtlottie.Maxim Cournoyer
* gnu/packages/qt.scm (qtlottie): New variable.
2022-08-01gnu: telephony: Add a Jami test for a partially defined jami-account.Maxim Cournoyer
* gnu/tests/telephony.scm (%dummy-jami-account-partial): New variable. (make-jami-os): Add a PARTIAL? argument and use it to select the jami-account variant to use. (%jami-os-provisioning-partial): New variable. (run-jami-test): Add a PARTIAL? argument, and use it to select operating system variant. Skip allowed-contacts and moderators test when PARTIAL? is true. (%test-jami-provisioning-partial): New test.
2022-08-01services: configuration: Step back from *unspecified*.Maxim Cournoyer
Fixes <https://issues.guix.gnu.org/56799>. This partially reverts 8cb1a49a3998c39f315a4199b7d4a121a6d66449. Rationale: *unspecified* cannot be serialized thus used as a G-Expression input, which is problematic/inconvenient when using deeply nested records. As an example, jami-service-type was broken when using partially defined <jami-account> records. * gnu/services/configuration.scm (define-maybe-helper): Check against the 'unset symbol. (normalize-field-type+def): Adjust value to 'unset. (define-configuration-helper): Use 'unset as the default value thunk. * gnu/services/file-sharing.scm (serialize-maybe-string): Check against the 'unset symbol. (serialize-maybe-file-object): Likewise. * gnu/services/messaging.scm (define-all-configurations): Use 'unset as value. (raw-content?): Check against 'unset symbol. (prosody-configuration)[http-max-content-size]: Default to 'unset. [http-external-url]: Likewise. [mod-muc]: Likewise. [raw-content]: Likewise. * gnu/services/networking.scm (opendht-configuration): Adjust documentation. * gnu/services/telephony.scm (jami-shepherd-services): Replace *undefined* with the 'unset symbol. * tests/services/configuration.scm ("maybe type, no default"): Check against the 'unset symbol. * doc/guix.texi: Regenerate the opendht-configuration, openvpn-client-configuration and openvpn-server-configuration documentation.
2022-08-01gnu: python-bbknn: Update to 1.5.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bbknn): Update to 1.5.1. [propagated-inputs]: Add python-pandas.
2022-08-01gnu: Add fail2ban.muradm
* gnu/packages/admin.scm (fail2ban): New variable. * gnu/packages/patches/fail2ban-0.11.2_CVE-2021-32749.patch, gnu/packages/patches/fail2ban-0.11.2_fix-setuptools-drop-2to3.patch, gnu/packages/patches/fail2ban-0.11.2_fix-test-suite.patch, gnu/packages/patches/fail2ban-paths-guix-conf.patch, gnu/packages/patches/fail2ban-python310-server-action.patch, gnu/packages/patches/fail2ban-python310-server-actions.patch, gnu/packages/patches/fail2ban-python310-server-jails.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2022-08-01gnu: trilinos-for-dealii-openmpi: Use G-expressions.Paul A. Patience
* gnu/packages/maths.scm (trilinos-for-dealii-openmpi)[arguments]: Use G-expressions. <#:phases>: Remove trailing boolean. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-08-01gnu: trilinos-for-dealii-openmpi: Remove input labels.Paul A. Patience
* gnu/packages/maths.scm (trilinos-for-dealii-openmpi)[native-inputs, inputs, propagated-inputs]: Remove labels. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-08-01gnu: dealii: Update to 9.4.0.Paul A. Patience
* 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>
2022-08-01gnu: dealii: Use G-expressions.Paul A. Patience
* gnu/packages/maths.scm (dealii)[snippet, arguments]: Use G-expressions. (dealii-openmpi)[arguments]: Same. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-08-01gnu: trilinos-for-dealii-openmpi: Fix build.Paul A. Patience
* 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>
2022-08-01gnu: Add r-muscat.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-muscat): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-08-01gnu: mu: Update to 1.8.7.muradm
* 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>
2022-08-01gnu: qutebrowser: Fix indentation.Maxim Cournoyer
* gnu/packages/web-browsers.scm (qutebrowser): Fix indentation.
2022-08-01gnu: qutebrowser: Fix build.Maxim Cournoyer
Fixes <https://issues.guix.gnu.org/56864>, which is a regression introduced with a0beb297a352930b89051ff258a06d78f224d6b9. * 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>
2022-08-01gnu: Add r-millefy.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (r-millefy): New variable.
2022-08-01gnu: exiv2: Fix test failure on ppc64le and aarch64.Marcel van der Boom
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>
2022-08-01gnu: Add python-biblib.Philip McGrath
* gnu/packages/python-xyz.scm (python-biblib): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-08-01services: opensmtpd: Make commands setgid to "smtpq" by default.Maya
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>
2022-08-01gnu: tractor: Update to 3.14.Danial Behzadi
* gnu/packages/tor.scm (tractor): Update to 3.14. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-08-01gnu: Add comma after “i.e.” in descriptions.Paul A. Patience
* 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>
2022-08-01gnu: hdf5-1.8: Add missing comma to linker flag.Paul A. Patience
* gnu/packages/maths.scm (hdf5-1.8)[arguments]<#:phases>: Add missing comma to linker flag. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-08-01gnu: guile-lens: Fix build.Z572
* gnu/packages/guile-xyz.scm (guile-lens) [phases]{run-hall}: replace "dist" to "build-system". Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-08-01gnu: xdot: Build with librsvg-for-system.Denis 'GNUtoo' Carikli
* gnu/packages/graphviz.scm (xdot)[inputs]: Replace librsvg with librsvg-for-system. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-08-01gnu: Add cardpeek.Denis 'GNUtoo' Carikli
* gnu/packages/security-token.scm (cardpeek): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-08-01gnu: python-sep: Update to 1.2.1Sharlatan Hellseher
* gnu/packages/astronomy.scm: (python-sep): Update to 1.2.1. Inherit from libsep Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-08-01gnu: Add libsepSharlatan Hellseher
* gnu/packages/astronomy.scm: (libsep): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2022-08-01gnu: gnutls: Add 3.7.7.Ludovic Courtès
* gnu/packages/tls.scm (gnutls-latest): New variable.
2022-08-01gnu: python-bbknn: Set NUMBA_CACHE_DIR.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bbknn)[arguments]: Add phase 'set-numba-cache-dir.
2022-08-01gnu: python-umap-learn: Disable unreliable test.Ricardo Wurmus
* gnu/packages/machine-learning.scm (python-umap-learn)[arguments]: Disable test_densmap_trustworthiness_on_iris_supervised.
2022-08-01gnu: python-umap-learn: Set NUMBA_CACHE_DIR.Ricardo Wurmus
* gnu/packages/machine-learning.scm (python-umap-learn)[arguments]: Add phase to set NUMBA_CACHE_DIR.
2022-07-31gnu: jami: Apply upstream patch that fixes a usability issue.Maxim Cournoyer
* 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.
2022-07-31gnu: jami: Update to 20220726.1515.da8d1da.Maxim Cournoyer
* 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.
2022-07-31gnu: Deprecate jami-gnome for jami.Maxim Cournoyer
* gnu/packages/jami.scm (jami-gnome): Delete package, deprecating it for jami.
2022-07-31gnu: Remove jami-libclient.Maxim Cournoyer
* gnu/packages/jami.scm (jami-libclient): Delete variable. (libringclient): Likewise. (jami-gnome)[inputs]: Remove jami-libclient. (jami)[inputs]: Likewise.
2022-07-31gnu: libjami: Enable test agent.Maxim Cournoyer
* gnu/packages/jami.scm (libjami)[configure-flags]: Add '--enable-agent' and remove FIXME. [tests?]: Update comment.
2022-07-31gnu: libjami: Update to 20220726.1515.da8d1da.Maxim Cournoyer
* 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.
2022-07-31gnu: Add qtpositioning.Maxim Cournoyer
* gnu/packages/qt.scm (qtpositioning): New variable.
2022-07-31gnu: Add qtnetworkauth, version 6.3.1.Maxim Cournoyer
* gnu/packages/qt.scm (qtnetworkauth): New variable.
2022-07-31gnu: qtnetworkauth: Rename to qtnetworkauth-5.Maxim Cournoyer
Automated with: git grep -l qtnetworkauth | xargs sed 's/\bqtnetworkauth\b/\0-5/g' -i
2022-07-31gnu: Add qttools, version 6.3.1.Maxim Cournoyer
* gnu/packages/qt.scm (qttools): New variable.
2022-07-31gnu: qttools: Rename to qttools-5.Maxim Cournoyer
Automated with: git grep -l qttools | xargs sed 's/\bqttools\b/\0-5/g' -i git checkout NEWS
2022-07-31gnu: Add qt5compat.Maxim Cournoyer
* gnu/packages/qt.scm (qt5compat): New variable.
2022-07-31gnu: Add qtwebengine, version 6.3.1.Maxim Cournoyer
* gnu/packages/qt.scm (qtwebengine): New variable.
2022-07-31gnu: qtwebengine: Rename to qtwebengine-5.Maxim Cournoyer
Automated with: git grep -l qtwebengine | xargs sed 's/\bqtwebengine\b/\0-5/g' -i git checkout NEWS
2022-07-31gnu: Add qtwebchannel, version 6.3.1.Maxim Cournoyer
* gnu/packages/qt.scm (qtwebchannel): New variable.
2022-07-31gnu: qtwebchannel: Rename to qtwebchannel-5.Maxim Cournoyer
Automated via: git grep -l qtwebchannel | xargs sed 's/\bqtwebchannel\b/\0-5/g' -i git checkout NEWS
2022-07-31gnu: Add qtwebsockets, version 6.3.1.Maxim Cournoyer
* gnu/packages/qt.scm (qtwebsockets): New variable.
2022-07-31gnu: qtwebsockets: Rename to qtwebsockets-5.Maxim Cournoyer
Automated via: git grep -l qtwebsockets | xargs sed 's/\bqtwebsockets\b/\0-5/g' -i git checkout NEWS
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