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2021-11-17Merge branch 'master' into core-updates-frozenLudovic Courtès
2021-11-16daemon: Do not deduplicate files smaller than 8 KiB....Files smaller than 8 KiB typically represent ~70% of the entries in /gnu/store/.links but only contribute to ~4% of the space savings afforded by deduplication. Not considering these files for deduplication speeds up file insertion in the store and, more importantly, leaves 'removeUnusedLinks' with fewer entries to traverse, thereby speeding it up proportionally. Partly fixes <https://issues.guix.gnu.org/24937>. * config-daemon.ac: Remove symlink hard link check and CAN_LINK_SYMLINK definition. * guix/store/deduplication.scm (%deduplication-minimum-size): New variable. (deduplicate)[loop]: Do not recurse when FILE's size is below %DEDUPLICATION-MINIMUM-SIZE. (dump-port): New procedure. (dump-file/deduplicate)[hash]: Turn into... [dump-and-compute-hash]: ... this thunk. Call 'deduplicate' only when SIZE is greater than %DEDUPLICATION-MINIMUM-SIZE; otherwise call 'dump-port'. * nix/libstore/gc.cc (LocalStore::removeUnusedLinks): Drop files where st.st_size < deduplicationMinSize. * nix/libstore/local-store.hh (deduplicationMinSize): New declaration. * nix/libstore/optimise-store.cc (deduplicationMinSize): New variable. (LocalStore::optimisePath_): Return when PATH is a symlink or smaller than 'deduplicationMinSize'. * tests/derivations.scm ("identical files are deduplicated"): Produce files bigger than %DEDUPLICATION-MINIMUM-SIZE. * tests/nar.scm ("restore-file-set with directories (signed, valid)"): Likewise. * tests/store-deduplication.scm ("deduplicate, below %deduplication-minimum-size"): New test. ("deduplicate", "deduplicate, ENOSPC"): Produce files bigger than %DEDUPLICATION-MINIMUM-SIZE. * tests/store.scm ("substitute, deduplication"): Likewise. Ludovic Courtès
2021-11-16tests: Factorize 'file=?'....* guix/tests.scm (file=?): Add optional 'stat' parameter. Add fast patch comparing inode numbers. * tests/gexp.scm ("imported-files with file-like objects"): Remove 'file=?' procedure and use the one from (guix tests). Ludovic Courtès
2021-11-16build-system/julia: Enable Julia Pkg to find installed packages....Julia's built-in package manager (Pkg) looks for packages in JULIA_DEPOT_PATH/packages/PACKAGENAME/XXXX, where XXXX is a string encoding package UUID and SHA1 of files. The link-depot phase creates a link at the correct location to allow Pkg to find packages that were already installed by Guix. * guix/build/julia-build-system.scm (link-depot): New phase. (%package-path): Modified package path from packages/ to loadpath/. (project.toml->uuid): New procedure, retrive package uuid from TOML file. (precompile, check): Adjust to the change in paths. (%standard-phases): Add link-depot phase. (julia-build): Add julia-package-uuid keyword. * guix/build-system/julia.scm (julia-build): Also use the julia-package-uuid keyword. * gnu/packages/julia-jll.scm (julia-bzip2-jll, julia-cairo-jll, julia-compilersupportlibraries-jll, julia-expat-jll, julia-ffmpeg-jll, julia-fontconfig-jll, julia-freetype2-jll, julia-fribidi-jll, julia-gettext-jll, julia-glib-jll, julia-gr-jll, julia-gumbo-jll, julia-imagemagick-jll, julia-jllwrappers-jll, julia-jpegturbo-jll, julia-lame-jll, julia-libass-jll, julia-libfdk-aac-jll, julia-libffi-jll, julia-libgcrypt-jll, julia-libglvnd-jll, julia-libgpg-error-jll, juli-libiconv-jll, julia-libmount-jll, julia-libpng-jll, julia-libsass-jll, julia-libtiff-jll, julia-libuuid-jll, julia-libvorbis-jll, julia-lzo-jll, julia-mbedtls-jll, julia-ogg-jll, julia-openspecfun-jll, julia-openssl-jll, julia-opus-jll, julia-pcre-jll, julia-pixman-jll, julia-qt5base-jll, julia-wayland-jll, julia-wayland-protocols-jll, julia-x264-jll, julia-x265-jll, julia-xkbcommon-jll, julia-xml2-jll, julia-xorg-libpthread-stubs-jll, julia-xorg-libx11-jll, julia-xorg-libxau-jll, julia-xorg-libxcb-jll, julia-xorg-libxcursor-jll, julia-xorg-libxdmcp-jll, julia-xorg-libxext-jll, julia-xorg-libxfixes-jll, julia-xorg-libxi-jll, julia-xorg-libxinerama-jll, julia-xorg-libxkbfile-jll, julia-xorg-libxrandr-jll, julia-xorg-libxrender-jll, julia-xorg-xcb-util-jll, julia-xorg-xcb-util-keysyms-jll, julia-xorg-xcb-util-renderutil-jll, julia-xorg-xcb-util-wm-jll, julia-xorg-xkbcomp-jll, julia-xorg-xkeyboard-config-jll, julia-xorg-xtrans-jll, julia-xslt-jll, julia-zlib-jll, julia-zstd-jll) [argument]: Adjust the order of the phases to the change in the julia-build-system. * gnu/packages/julia-xyz.scm (julia-bufferedstreams, julia-calculus, julia-dataframes, julia-datavalues, julia-distances, julia-documenter, julia-dualnumbers, julia-ellipsisnotation, julia-expronicon, julia-fileio, julia-fixedpointnumbers, julia-functionwrappers, julia-fuzzycompletions, julia-genericlinearalgebra, julia-genericschur, julia-geometrybasics, julia-imagemagick, julia-infinity, julia-matrixfactorizations, julia-media, julia-missings, julia-nnlib, julia-optimtestproblems, julia-orderedcollections, julia-prettytables, julia-pycall, julia-quadmath, julia-safetests, julia-stackviews) [arguments]: Correct paths to reflect change of %package-path modify order of phases as link-depot needs to run on an unmodified src directory add package-name-uuid keyword argument to packages without Project.toml file. * gnu/packages/julia.scm (julia)[native-search-paths]: Correct paths to reflect change of %package-path modify order of phases as link-depot needs to run on an unmodified src directory. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Jean-Baptiste Volatier
2021-11-14build: wrap-qt-program: Fix typo....* gnu/build/qt-utils.scm (wrap-qt-program): Fix spelling of "program". Vagrant Cascadian
2021-11-14environment: Fix ‘--check’ with exported PS1 variable....If your .bashrc (unnecessarily) exports PS1 and you’re in a non-login shell, Guix crashes: user@popigai:~$ guix shell --check coreutils guix shell: checking the environment variables visible from shell '/bin/bash'... Backtrace: 14 (primitive-load "/home/user/.config/guix/current/bin/g…") In guix/ui.scm: 2206:7 13 (run-guix . _) 2169:10 12 (run-guix-command _ . _) In ice-9/boot-9.scm: 1752:10 11 (with-exception-handler _ _ #:unwind? _ # _) 1752:10 10 (with-exception-handler _ _ #:unwind? _ # _) In guix/store.scm: 658:37 9 (thunk) 1320:8 8 (call-with-build-handler _ _) 1320:8 7 (call-with-build-handler #<procedure 7fe393b7c420 at g…> …) In guix/status.scm: 800:4 6 (call-with-status-report _ _) In guix/scripts/environment.scm: 951:12 5 (_) In guix/store.scm: 2119:24 4 (run-with-store #<store-connection 256.99 7fe39627e500> …) In guix/scripts/environment.scm: 521:35 3 (_ _) In unknown file: 2 (string=? ("PS1" . "${debian_chroot:+($debian_chroot)…") …) In ice-9/boot-9.scm: 1685:16 1 (raise-exception _ #:continuable? _) 1685:16 0 (raise-exception _ #:continuable? _) ice-9/boot-9.scm:1685:16: In procedure raise-exception: In procedure string=: Wrong type argument in position 1 (expecting string): ("PS1" . "${debian_chroot:+($debian_chroot)}\\[\\033[01;32m\\]\\u@\\h\\[\\033[00m\\]:\\[\\033[01;34m\\]\\w\\[\\033[00m\\]${EXTRA}\\$ ") user@popigai:~$ This is because the match pattern doesn’t expect `(vhash-assoc "PS1" actual)` to return a pair. * guix/scripts/environment.scm (validate-child-shell-environment): Change match pattern to expect a pair. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Thiago Jung Bauermann
2021-11-13guix: packages: Clarify that list is a list of <license> records....* guix/packages/packages.scm (<package>): Clarify that the license field takes a list of licenses rather than a generic list. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com> jgart
2021-11-12import: utils: Add more licenses and extend their detection....* guix/import/utils.scm (spdx-string->license): Identify more licenses (CC-BY-4.0, Freetype, HPND). * guix/licenses.scm: Add a comment that mentions "MIT" so that people who grep for MIT end up there. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Attila Lendvai
2021-11-11build: meson: Replace the 'test-target' argument by 'test-options'....This change is motivated by the need to disable the default 30 seconds timeout that Meson uses (see: https://gitlab.gnome.org/GNOME/glib/-/issues/2522), and also by desire to specify extra options to run the check phase without having to override it. * guix/build-system/meson.scm (meson-build) <test-target>: Replace argument with... <test-options>: ... this one. * guix/build/meson-build-system.scm (check): Invoke 'meson test' instead of 'ninja test-target', as the former is configurable via options. * doc/guix.texi (Build Systems) <meson-build-system>: Update doc. Maxim Cournoyer
2021-11-11profiles: Add a gdk-pixbuf-loaders-cache-file hook....This paves the way toward properly fixing https://issues.guix.gnu.org/50957. * guix/profiles.scm (gdk-pixbuf-loaders-cache-file): Add procedure... (%default-profile-hooks): ... and register it as a profile hook. * guix/status.scm (hook-message): Register it here too. Maxim Cournoyer
2021-11-11build: glib-or-gtk: Generate the gdk-pixbuf-loaders cache file in a phase....Adding a profile hook to do so covers most use cases, but it is still necessary to have the gdk-pixbuf loaders cache file computed at build time, as software may expect to find loaders support at that time. * guix/build/glib-or-gtk-build-system.scm: Delete trailing #t. (%gdk-pixbuf-loaders-cache-file-prefix): New variable. (generate-gdk-pixbuf-loaders-cache): New procedure. (generate-gdk-pixbuf-loaders-cache-file): Add procedure... (%standard-phases): ... and register it as a build phase. Maxim Cournoyer
2021-11-11build: glib-or-gtk-build-system: Fix indentation....* guix/build/glib-or-gtk-build-system.scm (gtk-module-directories) (wrap-all-programs): Fix indentation. Maxim Cournoyer
2021-11-11build: glib-or-gtk-build-system: Simplify the wrap-all-programs phase....* guix/build/glib-or-gtk-build-system.scm (wrap-all-programs) <handle-output>: Precisely build the list of variable specifications, rather than relying on a bunch of conditionals. Maxim Cournoyer
2021-11-11guix: packages: Fix repacking of plain tarballs....Fixes <https://issues.guix.gnu.org/50066>. * guix/packages.scm (patch-and-repack): Test for a tarball using tarball? and move the plain file copy to the else clause. Reported-by: Mathieu Othacehe <othacehe@gnu.org> Maxim Cournoyer
2021-11-11build: qt-utils: Don't wrap .X-real files....* guix/build/qt-utils.scm (find-files-to-wrap): Exclude already wrapped programs. This is forbidden in wrap-program now due to a738a663a99. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com> Brendan Tildesley
2021-11-11import: print: Replace packages and origins in 'arguments'....* guix/import/print.scm (package->code)[variable-reference] [object->code]: New procedures. [package-lists->code]: Rewrite in terms of 'object->code'. Pass the 'arguments' field through 'object->code'. * tests/print.scm (pkg-with-arguments, pkg-with-arguments-source): New variables. ("package with arguments"): New test. Ludovic Courtès
2021-11-11import: print: Handle patches that are origins....* guix/import/print.scm (package->code)[source->code]: Handle patches that are origins. * tests/print.scm (pkg-with-origin-input): Add 'patches' field. (pkg-with-origin-patch, pkg-with-origin-patch-source): New variables. ("package with origin patch"): New test. Ludovic Courtès
2021-11-11import: print: Correctly handle URI lists....* guix/import/print.scm (package->code)[factorized-uri-code]: New procedure. [source->code]: Use it, and factorize URI when it's a list. * tests/print.scm (pkg-with-origin-input): Check origin URI to a list. Ludovic Courtès
2021-11-11import: print: Properly render packages with origins as inputs....* guix/import/print.scm (package->code)[source->code]: Check whether VERSION is true before calling 'factorize-uri'. [package-lists->code]: Add clause for inputs that are origins. * tests/print.scm (pkg-with-origin-input, pkg-with-origin-input-source): New variables. ("package with origin input"): New test. Ludovic Courtès
2021-11-11import: cran: Allow imports of a specific version....* guix/import/cran.scm (download): Handle the case where URL is a list. (fetch-description-from-tarball): New procedure. (fetch-description): Add #:version parameter. Honor it when REPOSITORY is 'cran. Use 'fetch-description-from-tarball' when REPOSITORY is 'bioconductor. (description->package): SOURCE-URL may now be a list. (cran->guix-package): Pass VERSION to 'fetch-description'. (cran-recursive-import): Add #:version parameter. * guix/scripts/import/cran.scm (guix-import-cran): Expect a spec rather than a mere package name. * doc/guix.texi (Invoking guix import): Document it. Ludovic Courtès
2021-11-11import: pypi: Allow imports of a specific version....* guix/import/pypi.scm (latest-version): New procedure. (latest-source-release): Rename to... (source-release): ... this. Add 'version' parameter. (latest-wheel-release): Rename to... (wheel-release): ... this. Add 'version' parameter. (pypi->guix-package): Honor 'version' parameter. (pypi-recursive-import): Add 'version' parameter and honor it. * guix/scripts/import/pypi.scm (guix-import-pypi): Expect a spec. Pass it to 'package-name->name+version'. Pass the 'version' parameter. * tests/pypi.scm ("pypi->guix-package, no wheel"): Exercise the #:version parameter. * doc/guix.texi (Invoking guix import): Document it. Ludovic Courtès
2021-11-10store: 'mapm/accumulate-builds' does not compare stores with 'eq?'....Fixes <https://issues.guix.gnu.org/51732>. Regression introduced in 2015d3f042870860efef10e801b93eacc0742d38. The (eq? store expected-store) comparison doesn't work on this branch where the functional cache, with 'cache-object-mapping', is used extensively, thereby changing the store's object identity. * guix/store.scm (build-accumulator): Compare the socket of STORE and EXPECTED-STORE rather than the store themselves. Ludovic Courtès
2021-11-08Merge remote-tracking branch 'origin/master' into core-updates-frozenEfraim Flashner
2021-11-07guix: Upgrade to Bioconductor 3.14....* guix/build-system/r.scm (bioconductor-uri): Bump Bioconductor version to 3.14. * guix/import/cran.scm (%bioconductor-version): Same. Ricardo Wurmus
2021-11-07shell: Actually clean up the profile cache....Previously, most actions would leave the cache as-is because 'guix-environment*' would indirectly call 'exit', and thus its continuation was never reached. * guix/scripts/shell.scm (guix-shell): Move call to 'maybe-remove-expired-cache-entries' to EXIT-HOOK. Ludovic Courtès
2021-11-07import: egg: Allow imports of a specific version....* guix/import/egg.scm (eggs-repository): Change URL. (egg-metadata): Accept optional #:version keyword argument. (egg->guix-package): Accept ‘version’ argument. (egg-recursive-import): Add ‘version’ argument and honor it. * guix/scripts/import/egg.scm (guix-import-egg): Parse a specification instead of just a package name. * doc/guix.texi (Invoking guix import): Document it. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Xinglu Chen
2021-11-07home: services: bash: Add ‘aliases’ field....* doc/guix.texi (Shells Home Services): Document it. * gnu/home/services/shells.scm (bash-serialize-aliases): New procedure. (home-bash-configuration, home-bash-extension): Add ‘aliases’ field. (home-bash-extensions): Adjust accordingly. * guix/scripts/home/import.scm (generate-bash-configuration+modules): Populate the ‘alias’ field. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Xinglu Chen
2021-11-07ui: 'load*' correctly reports 'read-error' in all cases....Previously, 'read-error' exceptions other than "missing closing paren" would not be reported; instead, we'd directly call (exit 1) without printing anything. Fixes <https://issues.guix.gnu.org/51463>. Reported by Alice BRENON <alice.brenon@ens-lyon.fr>. * guix/ui.scm (report-load-error): Report the error without re-throwing upon 'read-error'. * tests/guix-build.sh: Add test. Ludovic Courtès
2021-11-07utils: Define a target-x86-32? and target-x86-64? predicate....* guix/utils.scm (target-x86-32?, target-x86-64?): New predicates. * tests/utils.scm ("target-x86-32?", "target-x86-64?"): New tests. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org> Maxime Devos
2021-11-06environment: Suggest command upon 'execlp' failure....* guix/scripts/environment.scm (launch-environment): Call 'primitive-_exit' upon 'system-error. (suggest-command-name, validate-exit-status): New procedures. (launch-environment/fork): Call 'validate-exit-status'. (launch-environment/container)[exit/status*]: New procedure. Use it instead of 'exit/status'. Ludovic Courtès
2021-11-06profiles: Build the man database only if 'man-db' is in the profile....This allows us to skip the expensive man-db profile hook in most cases. Suggested by Liliana Marie Prikler <liliana.prikler@gmail.com>. * guix/profiles.scm (manual-database/optional): New procedure. (%default-profile-hooks): Use it instead of 'manual-database'. * doc/guix.texi (Documentation): Add footnote about 'man -k' database creation. Ludovic Courtès
2021-11-06import: elpa: Work around Guile 3.0.[5-7] compiler bug....Fixes <https://issues.guix.gnu.org/49006>. Reported by Xinglu Chen <public@yoctocell.xyz>. * guix/import/elpa.scm (elpa-package->sexp)[melpa-recipe]: Add call to 'identity'. Ludovic Courtès
2021-11-03Merge remote-tracking branch 'origin/master' into core-updates-frozenEfraim Flashner
2021-11-02import: stackage: Update to release 18.14....* guix/import/stackage.scm (%default-lts-version): Update to 18.14. Lars-Dominik Braun
2021-10-31Merge remote-tracking branch 'origin/master' into core-updates-frozenEfraim Flashner
2021-10-31ui: Use DISPLAY in SHOW-GUIX-HELP....* guix/ui.scm (show-guix-help): Use DISPLAY where FORMAT isn't needed. Tobias Geerinckx-Rice
2021-10-31ui: Add top-level options to help text....This also makes automated ‘guix --h<Tab>’ completion possible. * guix/ui.scm (show-guix-help): Document that an OPTION's an option, and all valid options. Tobias Geerinckx-Rice
2021-10-31home: import: Avoid duplication of 'manifest->code'....* guix/scripts/home/import.scm (manifest->code): Remove. (manifest+configuration-files->code): New procedure. (import-manifest): Use 'manifest+configuration-files->code' instead of 'manifest->code'. * tests/home-import.scm (eval-test-with-home-environment): Likewise. (match-home-environment-transformations): New procedure. ("manifest->code: No services, package transformations"): New test. Ludovic Courtès
2021-10-31home: import: Factorize triplicated 'version-spec' procedure....* guix/scripts/package.scm (manifest-entry-version-prefix): New procedure, moved from... (export-manifest)[version-spec]: ... here. Adjust caller. * tests/home-import.scm (version-spec): Remove. (eval-test-with-home-environment): Use 'manifest-entry-version-prefix' instead. * guix/scripts/home/import.scm (import-manifest): Likewise. Ludovic Courtès
2021-10-31home: import: Clarify "destination directory"....Suggested by Liliana Marie Prikler <liliana.prikler@gmail.com>. * guix/scripts/home/import.scm (configurations+modules): Rename 'destination-directory' to 'configuration-directory'. Improve docstring. Ludovic Courtès
2021-10-31home: import: Compare procedures with 'eq?'....'procedure-name' is a debugging aid and cannot be reliably used to check for procedure equality. * guix/scripts/home/import.scm (configurations+modules): Remove use of 'procedure-name'. Ludovic Courtès
2021-10-31guix home: import: Call ‘local-file’ with ‘name’...Set the name of the file to just the basename of the file passed to ‘local-file’. * guix/scripts/home/import.scm (basename+remove-dots): New procedure. (generate-bash-configuration+modules): Use it. * tests/home-import.scm (match-home-environment-bash-service): Adjust accordingly. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Xinglu Chen
2021-10-31Add tests for ‘guix home import’....* tests/home-import.scm: New file. * Makefile.am (SCM_TESTS): Add it. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Xinglu Chen
2021-10-31guix home: import: Delete duplicate modules when importing....Two different services might require the same module(s), so delete duplicates when generating the ‘use-modules’ form. * import.scm (manifest->code): Delete duplicate modules. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Xinglu Chen
2021-10-31guix home: import: Don’t use 'slurp-file-gexp'....‘slurp-file-gexp’ is not a bound procedure. * guix/scripts/home/import.scm (generate-bash-configuration+modules): Don’t use ‘slurp-file-gexp’. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Xinglu Chen
2021-10-31guix home: import: Fix module name for Bash service....* guix/scripts/home/import.scm (generate-bash-configuration+modules): Change (gnu home-services bash) to (gnu home-services shells); add (guix gexp). Signed-off-by: Ludovic Courtès <ludo@gnu.org> Xinglu Chen
2021-10-31guix home: import: Allow multiple modules to be imported for each service....Previously, only one module could be imported for each service, e.g., only (gnu home-services shell) could be imported when generating the Bash service declaration. However, for some services, multiple modules might need to be imported in order for it to work. * guix/scripts/home/import.scm (generate-bash-module+configuration): Rename to ... (generate-bash-configuration+modules): ... this. (%files-configurations-alist): Rename to ... (%files+configurations-alist): ... this. (modules+configurations): Rename to ... (configurations+modules): ... this. (manifest->code): Adjust accordingly. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Xinglu Chen
2021-10-31guix home: import: Make the user to specify a destination directory....Copy the appropriate the relevant configuration files to the destination directory, and call ‘local-file’ on them. Without this, ‘guix home import’ will generate a service declaration like this (service home-bash-service-type (home-bash-configuration (bashrc (list (slurp-file-gexp (local-file "/home/yoctocell/.bashrc")))))) but when running ‘guix home reconfigure’, the ~/.bashrc file would be moved, so when running ‘guix home reconfigure’ for the second time, it would read the ~/.bashrc which is itself a symlink to a file the store. * guix/scripts/home/import.scm (generate-bash-module+configuration): Take ‘destination-directory’ parameter (modules+configurations): Copy the user’s configuration file to ‘%destination-directory’. * guix/scripts/home.scm (process-command): Adjust accordingly; create ‘destination’ if it doesn’t exist. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Xinglu Chen
2021-10-30shell: Error out when an unauthorized guix.scm/manifest.scm is found....The previous behavior was confusing: a warning would be printed and 'guix shell' would go on starting an empty environment. Reported by Tobias Geerinckx-Rice <me@tobias.gr>. * guix/scripts/shell.scm (auto-detect-manifest): Change "not loading" case from warning to error. * tests/guix-shell.sh: Adjust accordingly. Ludovic Courtès
2021-10-28packages: Optionally validate Texinfo markup at expansion time....* guix/packages.scm (validate-texinfo): New macro. (<package>)[synopsis, description]: Add 'sanitize' property. Ludovic Courtès