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2023-06-01gnu: Add python-ete3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-ete3): New variable.
2023-06-01gnu: parallel: Update to 20230522.Andy Tai
* gnu/packages/parallel.scm (parallel): Update to 20230522. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01gnu: zenity: Update to 3.44.1.Greg Hogan
* gnu/packages/gnome.scm (zenity): Update to 3.44.1. [native-inputs]: Add gtk+:bin. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01gnu: iperf: Update to 3.13.Greg Hogan
* gnu/packages/networking.scm (iperf): Update to 3.13. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01gnu: iotop: Update to 1.23.Greg Hogan
* gnu/packages/linux.scm (iotop): Update to 1.23. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01gnu: html-xml-utils: Update to 8.6.Greg Hogan
* gnu/packages/xml.scm (html-xml-utils): Update to 8.6. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01gnu: hstr: Update to 3.1.Greg Hogan
* gnu/packages/shellutils.scm (hstr): Update to 3.1. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01gnu: glances: Update to 3.4.0.3.Greg Hogan
* gnu/packages/python-xyz.scm (glances): Update to 3.4.0.3. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01gnu: fish: Update to 3.6.1.Greg Hogan
* gnu/packages/shells.scm (fish): Update to 3.6.1. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01gnu: fio: Update to 3.35.Greg Hogan
* gnu/packages/benchmark.scm (fio): Update to 3.35. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01gnu: atop: Update to 2.9.0.Greg Hogan
* gnu/packages/admin.scm (atop): Update to 2.9.0. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2023-06-01gnu: openblas: Update make-flags comments and coding style.Efraim Flashner
* gnu/packages/maths.scm (openblas)[arguments]: In the make-flags use the target-* macros. Adjust the wording describing why the different architectures have the flags they do.
2023-06-01gnu: openblas: Update architectures we provide substitutes for.Efraim Flashner
* gnu/packages/maths.scm (openblas)[arguments]: Adjust the substitutable? flag to only not provide substitutes when building for powerpc-linux. Adjust the comment accordingly.
2023-06-01gnu: openblas-ilp64: Add powerpc64le-linux as a supported system.Efraim Flashner
* gnu/packages/maths.scm (openblas-ilp64)[supported-systems]: Add powerpc64le-linux.
2023-06-01gnu: r-mbecs: Fix indentation.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-mbecs)[arguments]: Adjust indentation and spelling of comment.
2023-06-01gnu: Add squashfuse.Ricardo Wurmus
* gnu/packages/file-systems.scm (squashfuse): New variable.
2023-06-01gnu: Add r-mbecs.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-mbecs): New variable.
2023-05-31gnu: Remove linux-libre 6.2.Leo Famulari
This kernel series is no longer supported upstream. * gnu/packages/linux.scm (linux-libre-6.2-version, linux-libre-6.2-gnu-revision, deblob-scripts-6.2, linux-libre-6.2-pristine-source, linux-libre-6.2-source, linux-libre-headers-6.2, linux-libre-6.2): Remove variables. * gnu/packages/aux-files/linux-libre/6.2-arm.conf, gnu/packages/aux-files/linux-libre/6.2-arm64.conf, gnu/packages/aux-files/linux-libre/6.2-i686.conf, gnu/packages/aux-files/linux-libre/6.2-x86_64.conf: Delete files. * Makefile.am (AUX_FILES): Remove them.
2023-05-31gnu: linux-libre 4.14: Update to 4.14.316.Leo Famulari
* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.316. (linux-libre-4.14-pristine-source): Update hash.
2023-05-31gnu: linux-libre 4.19: Update to 4.19.284.Leo Famulari
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.284. (linux-libre-4.19-pristine-source): Update hash.
2023-05-31gnu: linux-libre 5.4: Update to 5.4.244.Leo Famulari
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.244. (linux-libre-5.4-pristine-source): Update hash.
2023-05-31gnu: linux-libre 5.10: Update to 5.10.181.Leo Famulari
* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.181. (linux-libre-5.10-pristine-source): Update hash.
2023-05-31gnu: linux-libre 5.15: Update to 5.15.114.Leo Famulari
* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.114. (linux-libre-5.15-pristine-source): Update hash.
2023-05-31gnu: linux-libre 6.1: Update to 6.1.31.Leo Famulari
* gnu/packages/linux.scm (linux-libre-6.1-version): Update to 6.1.31. (linux-libre-6.1-pristine-source): Update hash.
2023-05-31gnu: linux-libre: Update to 6.3.5.Leo Famulari
* gnu/packages/linux.scm (linux-libre-6.3-version): Update to 6.3.5. (linux-libre-6.3-pristine-source): Update hash.
2023-05-31tests: Use quasiquoted 'match' patterns for package sexps.Ludovic Courtès
Turns out it's easier to read. * tests/cpan.scm ("cpan->guix-package"): Use a quasiquoted pattern. * tests/elpa.scm (eval-test-with-elpa): Likewise. * tests/gem.scm ("gem->guix-package") ("gem->guix-package with a specific version") ("gem-recursive-import") ("gem-recursive-import with a specific version"): Likewise. * tests/hexpm.scm ("hexpm-recursive-import"): Likewise. * tests/opam.scm ("opam->guix-package"): Likewise. * tests/pypi.scm ("pypi->guix-package, no wheel") ("pypi->guix-package, wheels") ("pypi->guix-package, no usable requirement file.") ("pypi->guix-package, package name contains \"-\" followed by digits"): Likewise. * tests/texlive.scm ("texlive->guix-package"): Likewise.
2023-05-31gnu: Add updater input properties for R and Python packages.Ludovic Courtès
* gnu/packages/cran.scm (r-glue, r-xfun, r-vctrs) (r-lifecycle): Turn comment about r-knitr into 'properties' field. * gnu/packages/mpi.scm (python-mpi4py)[properties]: New field.
2023-05-31upstream: Honor package properties for ignored and extra inputs.Ludovic Courtès
* guix/upstream.scm (update-package-inputs)[filtered-inputs] [regular-inputs, native-inputs, propagated-inputs]: New procedures. Use them in 'update-field' calls. * tests/guix-refresh.sh (GUIX_TEST_UPDATER_TARGETS): Add "libreoffice" to the dependencies of "the-test-package". Add 'updater-ignored-inputs' property to "the-test-package". * doc/guix.texi (Invoking guix refresh): Document it.
2023-05-31import: gem: Updater provides input list.Ludovic Courtès
* guix/import/gem.scm (import-release): Add 'inputs' field. * tests/gem.scm ("package-latest-release"): New test.
2023-05-31import: gem: Factorize "bundler" special case for name mapping.Ludovic Courtès
* guix/import/gem.scm (ruby-package-name): Add "bundler" special case. (gem->guix-package): Adjust accordingly. * tests/gem.scm ("gem-recursive-import") ("gem-recursive-import with a specific version"): Remove "ruby-bundler" from the expected packages.
2023-05-31import: elpa: Updater provides input list.Ludovic Courtès
* guix/import/elpa.scm (elpa-dependency->upstream-input): New procedure. (latest-release): Add 'inputs' field. * tests/elpa.scm ("package-latest-release"): New test.
2023-05-31import: cpan: Updater provides input list.Ludovic Courtès
* guix/import/cpan.scm (latest-release): Add 'inputs' field. * tests/cpan.scm ("package-latest-release"): New test.
2023-05-31import: cpan: Represent dependencies as <upstream-input> records.Ludovic Courtès
* guix/import/cpan.scm (cpan-name->downstream-name) (cran-dependency->upstream-input, cran-module-inputs): New procedures. (cpan-module->sexp)[guix-name, convert-inputs]: Remove. [maybe-inputs]: Adjust to deal with <upstream-input>. Use 'cpan-name->downstream-name' instead of 'guix-name'. Add call to 'cpan-module-inputs' and adjust calls to 'maybe-inputs'. No longer emit input labels. * tests/cpan.scm ("cpan->guix-package"): Adjust test accordingly.
2023-05-31import: cpan: Remove unary 'string-append' call.Ludovic Courtès
* guix/import/cpan.scm (package->upstream-name): Remove useless 'string-append'.
2023-05-31tests: upstream: Restore test that was skipped.Ludovic Courtès
This test was being skipped since ea6fb108f6a3a53d48ea187b1f82b5f7ffce00a7. * tests/upstream.scm ("coalesce-sources same version"): Compare a serialized form of <upstream-source>.
2023-05-31upstream: Remove <upstream-input-change> and related code.Ludovic Courtès
* guix/upstream.scm (<upstream-input-change>): Remove. (changed-inputs): Remove. * tests/upstream.scm (test-package, test-new-package) ("changed-inputs returns no changes") ("changed-inputs returns changes to plain input list") ("changed-inputs returns changes to all plain input lists"): Remove.
2023-05-31upstream: 'update-package-source' edits input fields.Ludovic Courtès
Previously, 'guix refresh r-ggplot2 -u' and similar commands would print of list of input changes that would have to be made manually. With this change, 'guix refresh -u' takes care of updating input fields automatically. * guix/upstream.scm (update-package-inputs): New procedure. (update-package-source): Call it when 'upstream-source-inputs' returns true. * guix/scripts/refresh.scm (update-package): Remove iteration over the result of 'changed-inputs'. * guix/import/test.scm (available-updates): Add support for input lists. * tests/guix-refresh.sh (GUIX_TEST_UPDATER_TARGETS): Add input list for "the-test-package". Make sure 'guix refresh -u' updates 'inputs' accordingly. * doc/guix.texi (Invoking guix refresh): Mention it.
2023-05-31diagnostics: Factorize 'absolute-location'.Ludovic Courtès
* guix/scripts/style.scm (absolute-location): Move to... * guix/diagnostics.scm (absolute-location): ... here. * guix/upstream.scm (update-package-source): Use it.
2023-05-31upstream: Replace 'input-changes' field by 'inputs'.Ludovic Courtès
Returning the expected list of inputs rather than changes relative to the current package definition is less ambiguous and offers more possibilities for further processing. * guix/upstream.scm (<upstream-source>)[input-changes]: Remove. [inputs]: New field. (<upstream-input>): New record type. * guix/upstream.scm (upstream-input-type-predicate) (input-type-filter, upstream-source-regular-inputs) (upstream-source-native-inputs, upstream-source-propagated-inputs): New procedures. (changed-inputs): Expect an <upstream-source> as its second argument. Adjust accordingly. * guix/import/pypi.scm (distribution-sha256): New procedure. (maybe-inputs): Expect a list of <upstream-input>. (compute-inputs): Rewrite to return a list of <upstream-input>. (pypi-package-inputs, pypi-package->upstream-source): New procedures. (make-pypi-sexp): Use it. * guix/import/stackage.scm (latest-lts-release): Define 'cabal'. Replace 'input-changes' field by 'inputs'. * guix/scripts/refresh.scm (update-package): Use 'changed-inputs' instead of 'upstream-source-input-changes'. * tests/cran.scm ("description->package"): Adjust order of inputs. * tests/pypi.scm (default-sha256, default-sha256/base32): New variables. (foo-json): Add 'digests' entry. ("pypi->guix-package, no wheel"): Check HASH against DEFAULT-SHA256/BASE32. ("pypi->guix-package, wheels"): Likewise. ("pypi->guix-package, no usable requirement file."): Likewise. ("pypi->guix-package, package name contains \"-\" followed by digits"): Likewise. ("package-latest-release"): New test. * tests/upstream.scm (test-package-sexp): Remove. ("changed-inputs returns no changes"): Rewrite to use <upstream-source>. (test-new-package-sexp): Remove. ("changed-inputs returns changes to plain input list"): Rewrite. ("changed-inputs returns changes to all plain input lists"): Likewise. ("changed-inputs returns changes to labelled input list") ("changed-inputs returns changes to all labelled input lists"): Remove. * guix/import/cran.scm (maybe-inputs): Expect PACKAGE-INPUTS to be a list of <upstream-input>. (source-dir->dependencies): Return a list of <upstream-input>. (vignette-builders): Likewise. (uri-helper, cran-package-source-url) (cran-package-propagated-inputs, cran-package-inputs): New procedures. (description->package): Use them instead of local definitions. (latest-cran-release): Replace 'input-changes' field by 'inputs'. (latest-bioconductor-release): Likewise. (format-inputs): Remove. * guix/import/hackage.scm (cabal-package-inputs): New procedure. (hackage-module->sexp): Use it. [maybe-inputs]: Expect a list of <upstream-input>.
2023-05-31doc: Mention 'guix refresh -u' for third-party channels.Ludovic Courtès
* doc/guix.texi (Invoking guix refresh): Show how to run 'guix refresh -u' on a third-party channel.
2023-05-31import: json: Add #:timeout to 'json-fetch'.Ludovic Courtès
* guix/import/json.scm (json-fetch): Add #:timeout and pass it to 'http-fetch'.
2023-05-31import: utils: 'call-with-networking-exception-handler' doesn't unwind.Ludovic Courtès
That way backtraces show where the error actually originates from. * guix/import/utils.scm (call-with-networking-exception-handler): Rewrite using 'with-exception-handler'.
2023-05-31tests: pypi: Rewrite tests using a local HTTP server.Ludovic Courtès
* guix/import/pypi.scm (%pypi-base-url): New variable. (pypi-fetch): Use it. * tests/pypi.scm (foo-json): Compute URLs relative to '%local-url'. (test-json-1, test-json-2, test-source-hash): Remove. (file-dump): New procedure. (with-pypi): New macro. ("pypi->guix-package, no wheel") ("pypi->guix-package, wheels") ("pypi->guix-package, no usable requirement file.") ("pypi->guix-package, package name contains \"-\" followed by digits"): Rewrite using 'with-pypi'.
2023-05-31tests: http: Allow responses to specify a path.Ludovic Courtès
* guix/tests/http.scm (%local-url): Add #:path parameter and honor it. (call-with-http-server)[responses]: Add extra clause with 'path'. [bad-request]: New variable. [server-body]: Handle three-element clauses. Wrap 'run-server' call in 'parameterize'.
2023-05-31tests: pypi: Factorize tarball and wheel file creation.Ludovic Courtès
* tests/pypi.scm (sample-directory): New variable. (pypi-tarball, wheel-file): New procedures. ("pypi->guix-package, no wheel") ("pypi->guix-package, wheels") ("pypi->guix-package, no usable requirement file.") ("pypi->guix-package, package name contains \"-\" followed by digits"): Use them.
2023-05-31transformations: Add "--tune" to "--help-transform".Ludovic Courtès
* guix/transformations.scm (show-transformation-options-help/detailed): Add '--tune'.
2023-05-31nls: Update translation keys for guix gc.Remco van 't Veer
* po/*/*.po (guix/scripts/gc.scm): Round MiBs in user feedback. Signed-off-by: Florian Pelz <pelzflorian@pelzflorian.de>
2023-05-31guix gc: Round MiBs in user feedback.Remco van 't Veer
* guix/scripts/gc.scm (guix-gc): Round MiBs in user feedback. Signed-off-by: Florian Pelz <pelzflorian@pelzflorian.de>
2023-05-31gnu: r-desctools: Update to 0.99.49.Ricardo Wurmus
* gnu/packages/statistics.scm (r-desctools): Update to 0.99.49. [propagated-inputs]: Add r-withr.
2023-05-31gnu: r-rrcov: Update to 1.7-3.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rrcov): Update to 1.7-3.
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