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2016-01-20import: Add Bioconductor importer and updater.Ricardo Wurmus
* guix/import/cran.scm (%bioconductor-updater, latest-bioconductor-release, bioconductor-package?): New procedures. (cran->guix-package): Support repositories other than CRAN. (%bioconductor-url, %bioconductor-svn-url): New variables. (description->package): Update signature to distinguish between packages from different repositories. (latest-release): Rename procedure ... (latest-cran-release): ... to this. (cran-package?): Do not assume all R packages are available on CRAN. * tests/cran.scm: Update tests. * guix/scripts/import/cran.scm: Add "--archive" option and default to CRAN. * guix/scripts/refresh.scm (%updaters): Add "%bioconductor-updater". * doc/guix.texi: Document Bioconductor importer and updater.
2016-01-19derivations: Add test in keep-going mode.Ludovic Courtès
* tests/derivations.scm ("derivation fails but keep going"): New test.
2016-01-19Merge branch 'master' into core-updatesMark H Weaver
2016-01-18derivations: Add test for #:leaked-env-vars.Ludovic Courtès
* tests/derivations.scm ("derivation #:leaked-env-vars"): New test.
2016-01-13tests: Use sed instead of grep as a package with no dependencies.Ludovic Courtès
* tests/graph.scm ("node-edges"): Choose SED instead of GREP as the example.
2016-01-06utils: Add 'ensure-keyword-arguments'.Ludovic Courtès
* guix/utils.scm (delkw, ensure-keyword-arguments): New procedures. * tests/utils.scm ("ensure-keyword-arguments"): New test.
2016-01-05guix package: Allow multiple '--search' flags.Ludovic Courtès
* guix/scripts/package.scm (find-packages-by-description): Change 'rx' parameter to 'regexps'. [matches-all?, matches-one?]: New procedures. Use them. (process-query): Collect regexps from all 'search' queries, and pass them to 'find-packages-by-description'. * tests/guix-package.sh: Add tests. * doc/guix.texi (Invoking guix package): Document it.
2016-01-02graph: %BAG-WITH-ORIGINS-NODE-TYPE includes the origin's guile.Ludovic Courtès
Before that it would include #f for most origins since that the default value of 'origin-patch-guile'. * guix/scripts/graph.scm (bag-node-edges): When 'origin-patch-guile' returns #f, use (default-guile). * tests/graph.scm ("bag DAG, including origins"): Check for an edge from O to (default-guile).
2016-01-02graph: %BAG-EMERGED-NODE-TYPE filters out origins.Ludovic Courtès
Fixes <http://bugs.gnu.org/22280>. Reported by Leo Famulari <leo@famulari.name>. * guix/scripts/graph.scm (%bag-emerged-node-type)[edges]: Mimic %BAG-NODE-TYPE. This is a followup to 38b92da.
2015-12-30guix build: Augment %PATCH-PATH when -L is passed.Ludovic Courtès
Fixes <http://bugs.gnu.org/22259>. Reported by Nikolay Merinov <nikolay.merinov@member.fsf.org>. * guix/scripts/build.scm (%standard-build-options) <-L>: Augment %PATCH-PATH. * tests/guix-package.sh: Add test.
2015-12-20profiles: Honor search paths of propagated inputs.Ludovic Courtès
Fixes <http://bugs.gnu.org/22073>. Reported by Federico Beffa <beffa@ieee.org>. * guix/profiles.scm (package->manifest-entry): Use 'package-transitive-native-search-paths' when computing 'search-paths' field. * tests/profiles.scm ("package->manifest-entry, search paths"): New test.
2015-12-20packages: Add 'package-transitive-native-search-paths'.Ludovic Courtès
* guix/packages.scm (package-transitive-native-search-paths): New procedure. * tests/packages.scm ("package-transitive-native-search-paths"): New test.
2015-12-14gexp: 'local-file' resolves relative file names.Ludovic Courtès
* guix/gexp.scm (<local-file>): Rename constructor to '%%local-file'. Add 'absolute' field. (%local-file, extract-directory, absolute-file-name): New procedures. (current-source-directory): New macro. (local-file): Adjust call to '%local-file'. (local-file-absolute-file-name): New procedure. (local-file-compiler): Force the 'absolute' field. * tests/guix-system.sh: Test whether 'local-file' canonicalization works. * doc/guix.texi (G-Expressions): Adjust.
2015-12-13graph: Add synthetic test.Ludovic Courtès
* tests/graph.scm ("node-transitive-edges, no duplicates"): New test.
2015-12-11import: cran: Parse DESCRIPTION instead of HTML.Ricardo Wurmus
* guix/import/cran.scm (description->alist, listify, beautify-description, description->package): New procedures. (table-datum, downloads->url, nodes->text, cran-sxml->sexp): Remove proceduces. (latest-release): Use parsed DESCRIPTION instead of SXML. * tests/cran.scm: Rewrite to match importer.
2015-12-09derivations: Determine what's built in 'check' mode.Ludovic Courtès
* guix/derivations.scm (substitution-oracle): Add #:mode parameter and honor it. (derivation-prerequisites-to-build): Likewise. [derivation-built?]: Take it into account. * guix/ui.scm (show-what-to-build): Add #:mode parameter. Pass it to 'substitute-oracle' and 'derivations-prerequisites-to-build'. * tests/derivations.scm ("derivation-prerequisites-to-build in 'check' mode"): New test.
2015-12-08store: Allow clients to request multiple builds.Ludovic Courtès
* guix/store.scm (set-build-options): Add #:rounds parameter and honor it. * tests/store.scm ("build multiple times"): New test.
2015-12-07gnu-maintenance: Add tests for 'release-file?'.Ludovic Courtès
* tests/gnu-maintenance.scm: New file. * Makefile.am (SCM_TESTS): Add it. * guix/gnu-maintenance.scm (release-file?): Export.
2015-12-03store: Add mode parameter to 'build-paths'.Ludovic Courtès
* guix/store.scm (%protocol-version): Set minor to 15. (build-mode): New enumerate type. (build-things): Add 'mode' parameter; pass it to the RPC. * tests/store.scm ("build-things, check mode"): New check.
2015-11-28lint: Do not report already-patched vulnerabilities.Ludovic Courtès
* guix/scripts/lint.scm (patch-file-name): New procedure. (check-vulnerabilities): Use it to filter out patched vulnerabilities. * tests/lint.scm ("cve: one patched vulnerability"): New test.
2015-11-26lint: Add "cve" checker.Ludovic Courtès
Fixes <http://bugs.gnu.org/21289>. * guix/scripts/lint.scm (package-name->cpe-name, package-vulnerabilities) (check-vulnerabilities): New procedures. * guix/scripts/lint.scm (%checkers): Add "cve" checker. * tests/lint.scm ("cve", "cve: one vulnerability"): New tests. * doc/guix.texi (Invoking guix lint): Mention it.
2015-11-26Add (guix cve).Ludovic Courtès
* guix/cve.scm, tests/cve-sample.xml, tests/cve.scm: New files. * Makefile.am (MODULES): Add guix/cve.scm. (SCM_TESTS): Add tests/cve.scm. (EXTRA_DIST): Add tests/cve-sample.scm.
2015-11-26import: hackage: Add new tests.Federico Beffa
* tests/hackage.scm (eval-test-with-cabal): Add optional argument. (test-cabal-3): New variable and test. (test-read-cabal-1): Exercise more parsing variants.
2015-11-26utils: Add 'canonical-newline-port'.Federico Beffa
* guix/utils.scm (canonical-newline-port): New procedure. * tests/utils.scm ("canonical-newline-port"): New test.
2015-11-24services: dmd: Error out upon unmet dmd requirements.Ludovic Courtès
* gnu/services/dmd.scm (assert-no-duplicates): Rename to... (assert-valid-graph): ... this. [provisions]: New variable. [assert-satisfied-requirements]: New procedure. Use it. * tests/guix-system.sh: Add test with unmet dmd requirements.
2015-11-23graph: Add '%bag-with-origins-node-type'.Ludovic Courtès
* guix/scripts/graph.scm (bag-node-edges): Remove 'filter' call. Add case for 'origin'. (%bag-node-type)[edges]: Add filtering here. (%bag-with-origins-node-type): New variable. (%node-types): Add it. * tests/graph.scm ("bag DAG, including origins"): New test. * tests/guix-graph.sh: Add 'bag-with-origins'. * doc/guix.texi (Invoking guix graph): Document it.
2015-11-23guix download: Fail when more than one URL is passed.Ludovic Courtès
* guix/scripts/download.scm (guix-download)[parse-option]: Call 'leave' when passed an extra argument. * tests/guix-download.sh: Add test.
2015-11-21environment: Correctly handle abnormal exits.Ludovic Courtès
Fixes <http://bugs.gnu.org/21958>. * guix/scripts/environment.scm (status->exit-code): New procedure. (exit/status, primitive-exit/status): Use it. * tests/guix-environment-container.sh: Add test.
2015-11-21tests: Skip 'guix-container-environment.sh' when support is missing.Ludovic Courtès
Fixes <http://bugs.gnu.org/21410>. Reported by Alex Vong <alexvong1995@gmail.com>. * tests/guix-environment-container.sh: Exit with 77 when '((@@ (guix scripts environment) assert-container-features))' fails.
2015-11-21graph: Add procedures to query a node's edges.Ludovic Courtès
* guix/graph.scm (%node-edges, node-edges, node-back-edges) (node-transitive-edges): New procedures. * tests/graph.scm ("node-edges") ("node-transitive-edges + node-back-edges"): New tests.
2015-11-21Add (guix graph).Ludovic Courtès
* guix/scripts/graph.scm (<node-type>, <graph-backend>, emit-prologue) (emit-epilogue, emit-node, emit-edge, %graphviz-backend, export-graph): Move to... * guix/graph.scm: ... here. New file. * guix/scripts/system.scm, tests/graph.scm: Use it. * Makefile.am (MODULES): Add it.
2015-11-11guix gc: Error out when extra arguments are passed.Ludovic Courtès
Fixes <http://bugs.gnu.org/21817>. Reported by Petter Berntsen <petter@mykolab.ch>. * guix/scripts/gc.scm (guix-gc)[assert-no-extra-arguments]: New procedure. Use it for actions 'collect-garbage', 'optimize', and 'verify'. * tests/guix-gc.sh: Add tests.
2015-11-11guix package: '--search-paths' can report combined search paths.Ludovic Courtès
Partly fixes <http://bugs.gnu.org/20255>. * guix/scripts/package.scm (search-path-environment-variables): Change 'profile' to 'profiles'; expect it to be a list. (display-search-paths): Likewise. (%default-options): Remove 'profile' entry. (%options) <--profile>: Keep previous values associated with 'profile' in RESULT. (guix-package)[process-actions, process-query]: Handle the possible lack of 'profile' pair in OPTS.
2015-11-04tests: Use the canonical current directory name.Ludovic Courtès
* tests/guix-environment-container.sh (current_dir): New variable. Use it when grepping "mounts".
2015-11-04tests: Skip 'program-file' test when shebang is too long.Ludovic Courtès
* tests/gexp.scm ("program-file"): Skip when SHEBANG is too long.
2015-11-03import: pypi: Use "pypi-uri" instead of building the URL manually.Cyril Roelandt
* guix/import/pypi.scm (make-pypi-sexp): Use "pypi-uri". * tests/pypi.scm: Update the tests accordingly.
2015-11-03build: container: Add feature test predicates.David Thompson
* gnu/build/linux-container.scm (user-namespace-supported?, unprivileged-user-namespace-supported?, setgroups-supported?): New procedures. * tests/container.scm: Use predicates. * tests/syscalls.scm: Likewise.
2015-11-02tests: Set 'SHELL' for 'guix environment'.Ludovic Courtès
* tests/guix-environment.sh: Export 'SHELL'.
2015-11-01tests: Make sure the daemon dumps directory entries deterministically.Ludovic Courtès
* tests/store.scm ("write-file & export-path yield the same result"): New test.
2015-10-30scripts: environment: Allow lists of packages in expressions.David Thompson
* guix/scripts/environment.scm (options/resolve-packages): Match against lists of packages when evaluating expressions. * tests/guix-environment.sh: Add test. * doc/guix.texi ("invoking guix environment"): Add docs.
2015-10-29scripts: environment: Allow mixing regular and ad-hoc packages.David Thompson
This patch changes the --ad-hoc flag to be positional. That is, the packages that appear before --ad-hoc are interpreted as packages whose inputs should be in the environment; the packages that appear after are interpreted as packages to be directly added to the environment. * guix/scripts/environment.scm (tag-package-arg, compact): New procedures. (%options): Tweak the handlers for --load and --expression options. (options/resolve-packages): Preserve package mode tag. (parse-args): Tweak argument handler to use package tagging procedure. (guix-environment): Apply ad-hoc behavior on a per package basis. * tests/guix-environment.sh: Add test. * doc/guix.texi ("invoking guix environment"): Document new behavior of --ad-hoc.
2015-10-28tests: Print the mounts visible in the container.Ludovic Courtès
* tests/guix-environment-container.sh: Print the content of $tmpdir/mounts.
2015-10-28scripts: build: Add --file option.David Thompson
* guix/scripts/build.scm (show-help): Add help text for --file option. (%options): Add --file option. (options/resolve-packages): Handle 'file' options. * tests/guix-build.sh: Add tests. * doc/guix.texi ("invoking guix build"): Add doc.
2015-10-28substitute: Honor all the specified server URLs.Ludovic Courtès
* guix/scripts/substitute.scm (lookup-narinfos/diverse): New procedure. (lookup-narinfo): Use it. (process-query): Change #:cache-url to #:cache-urls. [valid?]: Remove 'narinfo?' check, which is no longer necessary. Use 'lookup-narinfos/diverse' instead of 'lookup-narinfos'. (process-substitution): Change #:cache-url to #:cache-urls. (%cache-url): Rename to... (%cache-urls): ... this. Turn into a list. (guix-substitute): Remove 'getaddrinfo' test with early exit. Adjust calls to 'process-query' and 'process-substitution'. * tests/substitute.scm: Change '%cache-url' to '%cache-urls'.
2015-10-25scripts: environment: Add --container option.David Thompson
* guix/scripts/system.scm (specification->file-system-mapping): Move from here... * guix/ui.scm (specification->file-system-mapping): ... to here. * guix/scripts/enviroment.scm (show-help): Show help for new options. (%options): Add --container --network, --expose, and --share options. (%network-configuration-files): New variable. (launch-environment, launch-environment/container, requisites*, inputs->requisites): New procedures. (guix-environment): Spawn new process in a container when requested. * doc/guix.texi (Invoking guix environment): Document it. * tests/guix-environment-container.sh: New file. * Makefile.am (SH_TESTS): Add it.
2015-10-20Add 'guix challenge'.Ludovic Courtès
* guix/scripts/challenge.scm, tests/challenge.scm: New files. * Makefile.am (MODULES): Add the former. (SCM_TESTS): Add the latter. * doc.am (SUBCOMMANDS): Add 'challenge'. * doc/guix.texi (Substitutes): Add xref to 'guix challenge'. (Invoking guix challenge): New node. * doc/contributing.texi (Submitting Patches): Add note about using 'guix challenge'. * po/guix/POTFILES.in: Add guix/scripts/challenge.scm.
2015-10-19guix archive: Add '--extract'.Ludovic Courtès
* guix/scripts/archive.scm (show-help, %options): Add --extract. (guix-archive): Honor it. * tests/guix-archive.sh: Test it. * doc/guix.texi (Invoking guix archive): Document it.
2015-10-14services: Add 'dmd-service-back-edges'.Ludovic Courtès
* gnu/services/dmd.scm (dmd-service-back-edges): New procedure. * tests/services.scm ("dmd-service-back-edges"): New test.
2015-10-14services: Export 'service-back-edges'.Ludovic Courtès
* gnu/services.scm: Export 'service-back-edges' and <service-type> accessors. * tests/services.scm ("service-back-edges"): New test.
2015-10-10services: Introduce extensible services.Ludovic Courtès
This patch rewrites GuixSD services to make them extensible. * gnu-system.am (GNU_SYSTEM_MODULES): Add gnu/services/dbus.scm. * gnu/services.scm (<service>): Replace with new record type. (<service-extension>, <service-type>): New record types. (write-service-type, compute-boot-script, second-argument): New procedures. (%boot-service, boot-service-type): New variables. (file-union, directory-union, modprobe-wrapper, activation-service->script, activation-script, gexps->activation-gexp): New procedures. (activation-service-type, %activation-service): New variables. (etc-directory, files->etc-directory, etc-service): New procedures. (etc-service-type, setuid-program-service, firmware-service-type): New variables. (firmware->activation-gexp): New procedure. (&service-error, &missing-target-service-error, &ambiguous-target-service-error): New condition types. (service-back-edges, fold-services): New procedures. * gnu/services/avahi.scm (<avahi-configuration>): New record type. (configuration-file): Replace keyword parameters with a single 'config' parameter. (%avahi-accounts, %avahi-activation, avahi-service-type): New variables. (avahi-dmd-service): New procedure. (avahi-service): Rewrite using 'service' and 'avahi-configuration'. * gnu/services/base.scm (%root-file-system-dmd-service, root-file-system-service-type): New variables. (root-file-system-service): Use them. (file-system->dmd-service-name): New procedure. (file-system-service-type): New variable. (file-system-service): Use it. Replace keyword parameters with a single 'file-system' object. (user-unmount-service-type): New variable. (user-unmount-service): Use it. (user-processes-service-type): New variable. (user-processes-service): Use it. (host-name-service-type): New variable. (host-name-service): Use it. (console-keymap-service-type): New variable. (console-keymap-service): Use it. (console-font-service-type): New variable. (console-font-service): Use it. (mingetty-pam-service, mingetty-dmd-service): New procedures. (mingetty-service-type): New variable. (mingetty-service): Use it. (nscd-dmd-service): New procedure. (nscd-activation, nscd-service-type): New variables. (nscd-service): Use the latter. (syslog-service-type): New variable. (syslog-service): Use it. (<guix-configuration>): New record type. (%default-guix-configuration): New variable. (guix-dmd-service, guix-accounts, guix-activation): New procedures. (guix-service-type): New variable. (guix-service): Replace list of keyword parameters with a single 'config' parameter. Rewrite using 'service'. (<udev-configuration>): New record type. (udev-dmd-service): New procedure. (udev-service-type): New variable. (udev-service): Use it. (device-mapping-service-type): New variable. (device-mapping-service): Use it. (swap-service-type): New variable. (swap-service): Use it. * gnu/services/databases.scm (<postgresql-configuration>): New record type. (%postgresql-accounts, postgresql-activation): New variables. (postgresql-dmd-service): New procedure. (postgresql-service): Rewrite using 'service' and 'postgresql-configuration'. * gnu/services/dbus.scm: New file. * gnu/services/desktop.scm (dbus-configuration-directory, dbus-service): Remove. (wrapped-dbus-service): New procedure. (<upower-configuration>): New record type. (upower-configuration-file): Replace keyword parameters with single <upower-configuration> parameter. (%upower-accounts, %upower-activation): New variables. (upower-dbus-service, upower-dmd-service): New procedures. (upower-service-type): New variable. (upower-service): Rewrite using 'service' and 'upower-configuration'. (%colord-activation, %colord-accounts): New variables. (colord-dmd-service): New procedure. (colord-service-type): New variable. (colord-service): Rewrite using 'service'. (<geoclue-configuration>): New record type. (geoclue-configuration-file): Replace keyword parameters with a single 'config' parameter. (geoclue-dbus-service, geoclue-dmd-service): New procedures. (%geoclue-accounts, geoclue-service-type): New variables. (geoclue-service): Rewrite using 'service' and 'geoclue-configuration'. (%polkit-accounts, %polkit-pam-services, polkit-service-type): New variables. (polkit-dmd-service): New procedure. (polkit-service): Rewrite using 'service'. (<elogind-configuration>)[elogind]: New field. (elogind-dmd-service): New procedure. (elogind-service-type): New variable. (elogind-service): Rewrite using 'service'. (%desktop-services): Remove argument to 'dbus-service'. Remove 'map' over %BASE-SERVICES. * gnu/services/dmd.scm (dmd-boot-gexp): New procedure. (dmd-root-service-type, %dmd-root-service): New variables. (dmd-service-type): New macro. (<dmd-service>): New record type. * gnu/services/lirc.scm (<lirc-configuration>): New record type. (%lirc-activation): New variable. (lirc-dmd-service): New procedure. (lirc-service-type): New variable. (lirc-service): Rewrite using 'service' and 'lirc-configuration'. * gnu/services/networking.scm (<static-networking>): New record type. (static-networking-service-type): New variable. (static-networking-service): Rewrite using 'service' and 'static-networking'. (dhcp-client-service-type): New variable. (dhcp-client-service): Rewrite using 'service'. (<ntp-configuration>): New record type. (ntp-dmd-service): New procedure. (ntp-service-type): New variable. (ntp-service): New procedure. (%tor-accounts, tor-service-type): New variable. (tor-dmd-service): New procedure. (tor-service): Rewrite using 'service'. (<bitlbee-configuration>): New record type. (bitlbee-dmd-service): New procedure. (%bitlbee-accounts, %bitlbee-activation, bitlbee-service-type): New variables. (bitlbee-service): Rewrite using 'service'. (%wicd-activation): New variable. (wicd-dmd-service): New procedure. (wicd-service-type): New variable. (wicd-service): Rewrite using 'service'. * gnu/services/ssh.scm (<lsh-configuration>): New record type. (activation): Rename to... (lsh-initialization): ... this. (lsh-activation, lsh-dmd-service, lsh-pam-services): New procedures. (lsh-service-type): New variable. (lsh-service): Rewrite using 'service' and 'lsh-configuration'. * gnu/services/web.scm (<nginx-configuration>): New record type. (%nginx-accounts): New variable. (nginx-activation, nginx-dmd-service): New procedures. (nginx-service-type): New variable. (nginx-service): Rewrite using 'service' and 'nginx-configuration'. * gnu/services/xorg.scm (<slim-configuration>): New record type. (slim-pam-service, slim-dmd-service): New procedures. (slim-service-type): New variable. (slim-service): Rewrite using 'service' and 'slim-configuration'. * gnu/system.scm (file-union): Remove. (other-file-system-services): Adjust to new 'file-system-service' signature. (essential-services): Add #:container? parameter. Add %DMD-ROOT-SERVICE, %ACTIVATION-SERVICE, and calls to 'pam-root-service', 'account-service', 'operating-system-etc-service', and a SETUID-PROGRAM-SERVICE instance. (operating-system-services): Pass #:container? to 'essential-services. (etc-directory): Remove. (operating-system-etc-service): New procedure. Rewrite as a call to 'etc-service'. (operating-system-accounts): Change to not return accounts required by services. (operating-system-etc-directory): Rewrite as a call to 'fold-services' and 'etc-directory'. (user-group->gexp, user-account->gexp, modprobe-wrapper): Remove. (operating-system-activation-script): Rewrite as a call to 'fold-services' and 'activation-service->script'. (operating-system-boot-script): Likewise. (operating-system-derivation): Add call to 'lower-object'. (emacs-site-file, emacs-site-directory, shells-file): Change to use 'computed-file' and 'scheme-file' instead of the monadic procedures. * gnu/system/install.scm (cow-store-service-type): New variable. (cow-store-service): Rewrite using 'service'. (/etc/configuration-files): New procedure. (configuration-template-service-type, %configuration-template-service): New variables. (configuration-template-service): Remove. (installation-services): Adjust accordingly. Adjust argument to 'guix-service'. * gnu/system/linux.scm (/etc-entry, pam-root-service): New procedures. (pam-root-service-type): New variable. * gnu/system/shadow.scm (user-group->gexp, user-account->gexp, account-activation, etc-skel, account-service): New procedures. (account-service-type): New variable. * tests/services.scm: New file. * doc/guix.texi (Base Services, Desktop Services): Adjust accordingly. (Defining Services): Rewrite. * doc/images/service-graph.dot: New file. * doc.am (DOT_FILES): Add it. * po/guix/POTFILES.in: Add gnu/services.scm.
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