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2023-04-22Merge remote-tracking branch 'origin/master' into core-updatesAndreas Enge
2023-04-21gnu: python-cffsubr: Depend on python-afdko@3.6.1.Ludovic Courtès
This removes the dependency of GNOME on Java: gnome -> font-abattis-cantarell -> ... -> openjdk Discussed at <https://lists.gnu.org/archive/html/guix-devel/2022-10/msg00226.html>. * gnu/packages/fontutils.scm (python-cffsubr)[inputs]: Switch to PYTHON-AFDKO-3.6.1.
2023-04-21gnu: python-afdko: Add version 3.6.1.Ludovic Courtès
* gnu/packages/fontutils.scm (python-afdko-3.6.1): New variable.
2023-04-21gnu: libotr: Fix compilation with glibc 2.35.Ludovic Courtès
* gnu/packages/messaging.scm (libotr)[source]: Add 'snippet'.
2023-04-21Revert "gnu: lxqt-admin: Fix path for timezone file."Leo Famulari
The timezone database should not be depended on by packages, but rather found at runtime in the environment. Otherwise, this package will eventually report the incorrect time, because time zones change regularly. This reverts commit 99c1c7a30c59c3514a4ced6e0cad0e5c2860331d.
2023-04-21gnu: ghc-9.0: Make testsuite compatible with Python 3.10.Lars-Dominik Braun
* gnu/packages/haskell.scm (ghc-9.0)[native-inputs]: Add patch and snippet to ghc-testsuite input.
2023-04-21doc: Update openssh-host documentation.Saku Laesvuori
* doc/guix.texi (Secure Shell): Update openssh-host documentation to match the code. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-04-21home: services: openssh: Add configuration option for jump proxiesSaku Laesvuori
Add a new 'proxy' field to openssh-host to allow ProxyCommand or ProxyJump, but not both, to be configured. Configuring both would cause the serialization order to determine which one is used. Deprecate the 'proxy-command' field because the 'proxy' field replaces it. * gnu/home/services/ssh.scm (proxy-jump->string, proxy-command-or-jump-list?, serialize-proxy-command-or-jump-list, sanitize-proxy-command): New procedure. (proxy-jump, proxy-command): New record type. (openssh-host)[proxy-command]: Mark field as deprecated because OpenSSH can't have ProxyCommand and ProxyJump configured at the same time. * doc/guix.texi (Secure Shell): Update to match the changes to the service. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-04-21gnu: guile-dsv: Update to 0.5.2.Artyom V. Poptsov
* gnu/packages/guile-xyz.scm (guile-dsv): Update to 0.5.2. [native-inputs]: Add "help2man". Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-04-21gnu: Add emacs-gerbil-mode.Juliana Sims
* gnu/packages/emacs-xyz.scm (emacs-gerbil-mode): Add emacs-gerbil-mode. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-04-21gnu: kicad: Update to 7.0.2.Peter Polidoro
* gnu/packages/engineering.scm (kicad): Update to 7.0.2. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-04-21packages: 'package-direct-sources' correctly handles non-origin sources.Ludovic Courtès
Previously 'package-direct-sources' would trigger a wrong-type-arg error when passed a package whose 'source' is not an origin, such as 'ruby-sorbet-runtime'. * guix/packages.scm (package-direct-sources): Call 'expand' if and only if (package-source package) is an origin.
2023-04-21tests: Relax two tests that expected a non-zero error code.Ludovic Courtès
* tests/guix-package-aliases.sh: "guix upgrade foo bar" has always returned zero; adjust accordingly. * tests/guix-refresh.sh: "guix refresh -t test idutils" and similar return zero; adjust accordingly.
2023-04-21gnu: kdoctools: Compile with docbook-xml@4.5.Andreas Enge
* gnu/packages/kde-frameworks.scm (kdoctools): Use docbook-xml-4.5 instead of docbook-xml.
2023-04-21tests: Fix checks for expected failures.Eric Bavier
Addresses <https://issues.guix.gnu.org/62406>. With 'set -e', a return status inverted with '!' does not cause the shell to exit immediately. Instead use '&& false' to indicate an expected failure. * tests/guix-archive.sh, tests/guix-build-branch.sh, tests/guix-build.sh, tests/guix-daemon.sh, tests/guix-download.sh, tests/guix-environment-container.sh, tests/guix-environment.sh, tests/guix-gc.sh, tests/guix-git-authenticate.sh, tests/guix-graph.sh, tests/guix-hash.sh, tests/guix-home.sh, tests/guix-pack-relocatable.sh, tests/guix-pack.sh, tests/guix-package-aliases.sh, tests/guix-package-net.sh, tests/guix-package.sh, tests/guix-refresh.sh, tests/guix-shell.sh, tests/guix-style.sh, tests/guix-system.sh: Replace uses of '! ...' with '... && false' or `test ! ...` as appropriate. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-04-21tests: Fork and exec a new Guile for the marionette REPL.Ludovic Courtès
By merely forking PID 1, details from PID 1 (shepherd) would leak into the marionette process, such as the set of modules in scope and state inherited from the shepherd process (<service> instances, fibers, etc.). Running a fresh Guile instance avoids that. * gnu/tests.scm (marionette-program): New procedure. (marionette-shepherd-service): Change 'start' to use 'make-forkexec-constructor', and run the result of 'marionette-program'.
2023-04-21tests: Use the client 'start-service' procedure.Ludovic Courtès
The previous code worked "by chance": 'start' from (shepherd service) happened to be in scope because the marionette REPL is created by a mere 'primitive-fork', and 'start' happened to kinda work. * gnu/tests/base.scm (run-basic-test): Use 'start-service' from (gnu services herd), not 'start' from (shepherd service), which is not supposed to work. * gnu/tests/install.scm (run-install): Likewise.
2023-04-21services: herd: 'load-services/safe' is synonymous with 'load-services'.Ludovic Courtès
This is a followup to 547965aa27b6a09cadf42130b7ec7db3f1aee61f. * gnu/services/herd.scm (load-services/safe): Make an alias for 'load-services'.
2023-04-21services: nscd: Depend on syslogd.Ludovic Courtès
This gets rid of nscd debug messages on the console at boot time. * gnu/services/base.scm (nscd-shepherd-service): Add dependency on 'syslogd'.
2023-04-21services: postgresql: Add default package.Ludovic Courtès
* gnu/services/databases.scm (<postgresql-configuration>)[postgresql]: Add default value, moved from... (postgresql-service-type)[default-value]: ... here.
2023-04-21services: knot: Add 'configuration' action.Ludovic Courtès
* gnu/services/dns.scm (knot-shepherd-service): Add 'actions' field.
2023-04-21services: rsync: Add 'configuration' action.Ludovic Courtès
* gnu/services/rsync.scm (rsync-shepherd-service): Add 'actions' field.
2023-04-21services: redis: Add 'configuration' action.Ludovic Courtès
* gnu/services/databases.scm (redis-shepherd-service): Add 'actions' field.
2023-04-21services: mysql: Add 'configuration' action.Ludovic Courtès
* gnu/services/databases.scm (mysql-shepherd-service): Add 'actions' field.
2023-04-21services: postgresql: Add 'configuration' action.Ludovic Courtès
* gnu/services/databases.scm (postgresql-shepherd-service): Add 'actions' field.
2023-04-21services: postgresql: Add the 'postgresql' Shepherd service name.Ludovic Courtès
* gnu/services/databases.scm (postgresql-shepherd-service): Add 'postgresql' to 'provision'.
2023-04-21gnu: freerdp: Update to 2.2.0 [security fixes].Maxim Cournoyer
This fixes CVE-2022-39316, CVE-2022-39317, CVE-2022-39318, CVE-2022-39319, CVE-2022-39320, CVE-2022-41877, CVE-2022-39347, CVE-2022-39282, CVE-2022-39283, CVE-2021-41159 and CVE-2021-41160. * gnu/packages/rdesktop.scm (freerdp): Update to 2.2.0. [arguments]: Use gexps. Do not set DOCBOOKXSL_DIR in #:configureflags.
2023-04-21gnu: freerdp: Update to 2.2.0 [security fixes].Maxim Cournoyer
This fixes CVE-2022-39316, CVE-2022-39317, CVE-2022-39318, CVE-2022-39319, CVE-2022-39320, CVE-2022-41877, CVE-2022-39347, CVE-2022-39282, CVE-2022-39283, CVE-2021-41159 and CVE-2021-41160. * gnu/packages/rdesktop.scm (freerdp): Update to 2.2.0. [arguments]: Use gexps. Do not set DOCBOOKXSL_DIR in #:configureflags.
2023-04-21services: syslog: Log auth.info to /var/log/secure in default configuration.Maxim Cournoyer
This causes authentication failures such as those generated by SSH brute force attacks to appear in /var/log/secure, which is picked up by tools such as fail2ban. * gnu/services/base.scm (%default-syslog.conf): Add a auth.info selector for the /var/log/secure log. Series-to: 62802@debbugs.gnu.org
2023-04-21services/syslog: Strip leading white space indent in syslog.conf.Maxim Cournoyer
This is a cosmetic change. * gnu/services/base.scm (%default-syslog.conf): Add a comment referencing the documentation. Strip the extraneous leading trailing white space indent.
2023-04-21services: syslog: Add a reload action.Maxim Cournoyer
* gnu/services/base.scm (syslog-service-type) [actions]: Add a reload action. * doc/guix.texi (Base Services): Document it.
2023-04-21services: syslog: Move configuration to /etc/syslog.conf.Maxim Cournoyer
Having the configuration live at a static location makes it possible to hot-reload it. * gnu/services/base.scm (syslog.conf): New variable. (syslog-etc, syslog-shepherd-service): New procedures. (syslog-service-type): Rewrite using the above new variable and procedures, extending etc-service-type with its configuration file.
2023-04-21gnu: libxml++: Remove fix-documentation phase.Maxim Cournoyer
* gnu/packages/gnome.scm (libxml++) [arguments]: Delete field.
2023-04-21gnu: opensp: Fix build.Maxim Cournoyer
This is a follow up commit to b84d0b81b2. * gnu/packages/xml.scm (opensp) [arguments]: Properly quote.
2023-04-21gnu: bppsuite: Update to 2.4.1.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (bppsuite): Update to 2.4.1. [source]: Remove the commit and use the release version. Changed to the github repo. [arguments]: Remove the disabled parallel-build. [inputs]: Use list. [home-page]: Changed to github page.
2023-04-21gnu: bpp-popgen: Update to 2.4.1.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (bpp-popgen): Update to 2.4.1. [source]: Remove the commit and use the release version. Changed to the github repo. [arguments]: Remove the disabled parallel-build. [home-page]: Changed to new host Université Claude-Bernard Lyon 1.
2023-04-21gnu: Add maffilter.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (maffilter): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2023-04-21gnu: tensorflow: Adjust for Python 3.10 compatibility.Ricardo Wurmus
* gnu/packages/machine-learning.scm (tensorflow)[arguments]: Replace build phase 'python3.9-compatibility with 'python3.10-compatibility; patch for move from "collections" to "collections.abc"; add well-meaning but potentially reckless patch to remove overwrite error for __or__ and __ror__ methods; adjust farmhash sources to build with GCC 11; do not use distutils.sysconfig.
2023-04-21gnu: python-protobuf-3.6: Patch for Python 3.10.Ricardo Wurmus
* gnu/packages/protobuf.scm (python-protobuf-3.6)[arguments]: Patch collections import. [native-inputs]: Add python-setuptools-for-tensorflow.
2023-04-21gnu: python-setuptools-for-tensorflow: Patch for Python 3.10 compatibility.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-setuptools-for-tensorflow)[arguments]: Patch collections imports; remove wininst support.
2023-04-21gnu: grpc-1.16.1: Correct input modifications.Ricardo Wurmus
abseil-cpp is not part of the native-inputs but of the inputs. * gnu/packages/rpc.scm (grpc-1.16.1)[native-inputs]: Only replace protobuf. [inputs]: Replace abseil-cpp.
2023-04-21gnu: python-grpcio: Rebuild Cythonized source files.Ricardo Wurmus
* gnu/packages/rpc.scm (python-grpcio)[source]: Delete generated cpp file. [build-system]: Use pyproject-build-system. [arguments]: Patch setup.py to add grpc headers to search path. [inputs]: Replace abseil-cpp with abseil-cpp-20211102.0; add grpc-for-python-grpcio. [native-inputs]: Add python-cython.
2023-04-21gnu: Add grpc-for-python-grpcio.Ricardo Wurmus
* gnu/packages/rpc.scm (grpc-for-python-grpcio): New variable.
2023-04-21gnu: Add abseil-cpp-20211102.0.Ricardo Wurmus
* gnu/packages/cpp.scm (abseil-cpp-20211102.0): New variable.
2023-04-21gnu: Add bpp-phyl-omics.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (bpp-phyl-omics): New variable.
2023-04-21gnu: Add bpp-seq-omics.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (bpp-seq-omics): New variable.
2023-04-21gnu: bpp-phyl: Update to 2.4.1.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (bpp-phyl): Update to 2.4.1. [source]: Remove the commit and use the release version. Changed to the github repo. [arguments]: Remove the disabled parallel-build and out-of-source. [home-page]: Changed to new host Université Claude-Bernard Lyon 1. [synopsis]: Use proper capitalization.
2023-04-21gnu: bpp-seq: Update to 2.4.1.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (bpp-seq): Update to 2.4.1. [source]: Remove the commit and use the release version. Changed to the github repo. [arguments]: Remove the disabled parallel-build and out-of-source. [home-page]: Changed to new host Université Claude-Bernard Lyon 1.
2023-04-21gnu: bpp-core: Update to 2.4.1.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (bpp-core): Update to 2.4.1. [source]: Remove the commit and use the release version. Changed to the github stored sources. [arguments]: Remove the disabled parallel-build. [home-page]: Changed to new host Université Claude-Bernard Lyon 1.
2023-04-21gnu: luakit: Further improve style.Nicolas Goaziou
This is a followup to d3bc56da0475bc643ccb065483c53c6d28cf8e39. * gnu/packages/web-browsers.scm (luakit)[arguments]<#:phases>: Remove unnecessary INPUTS key. [inputs]: Sort alphabetically.
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