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2022-04-15gnu: elementary-xfce-icon-theme: Update to 0.16....* gnu/packages/xfce.scm (elementary-xfce-icon-theme): Update to 0.16. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Michael Rohleder
2022-04-15gnu: xfce4-terminal: Update to 1.0.0....* gnu/packages/xfce.scm (xfce4-terminal): Update to 1.0.0. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Zhu Zihao
2022-04-15gnu: Add python-verspec....* gnu/packages/python.xyz.scm (python-verspec): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Vincent Prat
2022-04-15gnu: Add python-shtab....* gnu/packages/python-xyz.scm (python-shtab): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Vincent Prat
2022-04-15gnu: shepherd: Support cross-compilation....Reported by phodina <phodina@protonmail.com>. * gnu/packages/admin.scm (shepherd-0.9)[arguments]: New field. [native-inputs]: Add GUILE-FIBERS-1.1. Ludovic Courtès
2022-04-15gnu: mblaze: Offer contrib executables....* gnu/packages/mail.scm (mblaze)[outputs, inputs]: New fields. [arguments]: Add #:modules. Add 'install-contrib' phase. Signed-off-by: Ludovic Courtès <ludo@gnu.org> B. Wilson
2022-04-15gnu: streamlink: Update to 3.2.0....* gnu/packages/video.scm (streamlink): Update to 3.2.0. [inputs]: Add python-lxml and python-pycountry, remove python-iso3166 and python-iso639. [arguments]<#:phases>{check}: Use pytest. Co-authored-by: Ludovic Courtès <ludo@gnu.org> Chadwain Holness
2022-04-15gnu: python-lxml: Add 4.7.1....* gnu/packages/xml.scm (python-lxml-4.7): New variable. Ludovic Courtès
2022-04-15gnu: cl-nfiles: Update to 0.4.0....* gnu/packages/lisp-xyz.scm (sbcl-nfiles): Update to 0.4.0. [inputs]: Add sbcl-quri. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net> André A. Gomes
2022-04-15gnu: python-hmmlearn: Remove cythonized file....* gnu/packages/machine-learning.scm (python-hmmlearn)[source]: Add snippet to remove cythonized file. Efraim Flashner
2022-04-14gnu: python-aiohttp: Remove cythonized files....* gnu/packages/python-web.scm (python-aiohttp)[source]: Add snippet to remove cythonized files. Efraim Flashner
2022-04-14gnu: python-pywavelets: Remove cythonized files....* gnu/packages/python-xyz.scm (python-pywavelets)[source]: Add snippet to remove cythonized files. [native-inputs]: Add python-cython. Efraim Flashner
2022-04-14gnu: python-igraph: Update to 0.9.10....* gnu/packages/graph.scm (python-igraph): Update to 0.9.10. Efraim Flashner
2022-04-14gnu: igraph: Update to 0.9.8....* gnu/packages/graph.scm (igraph): Update to 0.9.8. Efraim Flashner
2022-04-14gnu: scregseg: Remove cythonized file....* gnu/packages/bioinformatics.scm (scregseg)[source]: Add snippet to remove cythonized file. Efraim Flashner
2022-04-14gnu: cl-py4cl: Update to 0.0.0-1.2f2a008....* gnu/packages/lisp-xyz.scm (sbcl-py4cl): Update to 0.0.0-1.2f2a008. [arguments]<#:phases>: Adjust substitutions to renamed files. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net> Paul A. Patience
2022-04-14gnu: Add emacs-org-modern....* gnu/packages/emacs-xyz.scm (emacs-org-modern): New variable. Signed-off-by: Raghav Gururajan <rg@raghavgururajan.name> jgart
2022-04-14gnu: Add cl-numpy-file-format....* gnu/packages/lisp-xyz.scm (cl-numpy-file-format, ecl-numpy-file-format, sbcl-numpy-file-format): New variables. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net> Paul A. Patience
2022-04-14gnu: cl-who: Update to 1.1.4-3.07dafe9....* gnu/packages/lisp-xyz.scm (sbcl-cl-who): Update to 1.1.4-3.07dafe9. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net> Foo Chuan Wei
2022-04-14gnu: linux-libre 5.10: Update to 5.10.111....* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.111. (linux-libre-5.10-pristine-source): Update hash. Leo Famulari
2022-04-14gnu: linux-libre 5.15: Update to 5.15.34....* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.34. (linux-libre-5.15-pristine-source): Update hash. Leo Famulari
2022-04-14gnu: linux-libre: Update to 5.16.20....* gnu/packages/linux.scm (linux-libre-5.16-version): Update to 5.16.20. (linux-libre-5.16-pristine-source): Update hash. Leo Famulari
2022-04-14gnu: linux-libre 5.17: Update to 5.17.3....* gnu/packages/linux.scm (linux-libre-5.17-version): Update to 5.17.3. (linux-libre-5.17-pristine-source): Update hash. Leo Famulari
2022-04-14gnu: Update linux-libre 5.17 configuration files....This option that adds new hardware support appeared after the 5.17 release. * gnu/packages/aux-files/linux-libre/5.17-arm.conf, gnu/packages/aux-files/linux-libre/5.17-arm64.conf, gnu/packages/aux-files/linux-libre/5.17-i686.conf, gnu/packages/aux-files/linux-libre/5.17-x86_64.conf: Enable support for Realtek Ethernet switch chips. Leo Famulari
2022-04-14gnu: Add r-xcir....* gnu/packages/bioconductor.scm (r-xcir): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net> Mădălin Ionel Patrașcu
2022-04-14gnu: sundials: Remove input labels....* gnu/packages/maths.scm (sundials)[native-inputs, inputs]: Remove labels. (sundials-openmpi)[inputs]: Remove labels. Ludovic Courtès
2022-04-14gnu: sundials: Update to 6.1.1....* gnu/packages/maths.scm (sundials): Update to 6.1.1. [inputs]: Add PETSC. (sundials-openmpi)[inputs]: Remove PETSC. [arguments]: Remove now unnecessary flags. Change "MPI_ENABLE" to "ENABLE_MPI". Ludovic Courtès
2022-04-14gnu: guile-fibers@1.1: Support cross-compilation....Fixes <https://issues.guix.gnu.org/54793>. Reported by Mathieu Othacehe <othacehe@gnu.org>. * gnu/packages/guile-xyz.scm (guile-fibers-1.1)[arguments]: Add 'support-cross-compilation' phase. Ludovic Courtès
2022-04-14gnu: r-illuminahumanmethylation450kanno-ilmn12-hg19: Move to annotation section....* gnu/packages/bioconductor.scm (r-illuminahumanmethylation450kanno-ilmn12-hg19): Move this variable up to the annotation section. Ricardo Wurmus
2022-04-14gnu: r-snplocs-hsapiens-dbsnp144-grch37: Move to annotation section....* gnu/packages/bioconductor.scm (r-snplocs-hsapiens-dbsnp144-grch37): Move this variable up to the annotation section. Ricardo Wurmus
2022-04-14gnu: r-chromvarmotifs: Move to (gnu packages bioinformatics)....* gnu/packages/bioconductor.scm (r-chromvarmotifs): Move this variable from here... * gnu/packages/bioinformatics.scm (r-chromvarmotifs): ...to here. Ricardo Wurmus
2022-04-14gnu: r-absseq: Move out of experiments section....* gnu/packages/bioconductor.scm (r-absseq): Move definition out of experiments section. Ricardo Wurmus
2022-04-14gnu: r-abarray: Move out of experiments section....* gnu/packages/bioconductor.scm (r-abarray): Move definition out of experiments section. Ricardo Wurmus
2022-04-14gnu: r-aneufinder: Move to packages section....* gnu/packages/bioconductor.scm (r-aneufinder): Move this definition out of the section for Bioconductor experiments packages. Ricardo Wurmus
2022-04-14gnu: Add r-absseq....* gnu/packages/bioconductor.scm (r-absseq): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Mădălin Ionel Patrașcu
2022-04-14gnu: Add r-abarray....* gnu/packages/bioconductor.scm (r-abarray): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Mădălin Ionel Patrașcu
2022-04-14gnu: Add r-acde....* gnu/packages/bioconductor.scm (r-acde): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Mădălin Ionel Patrașcu
2022-04-14gnu: Add r-wppi....* gnu/packages/bioconductor.scm (r-wppi): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Mădălin Ionel Patrașcu
2022-04-14gnu: Add r-acme....* gnu/packages/bioconductor.scm (r-acme): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Mădălin Ionel Patrașcu
2022-04-14gnu: Add r-acgh....* gnu/packages/bioconductor.scm (r-acgh): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Mădălin Ionel Patrașcu
2022-04-14gnu: libfprint: Fix build, add python for the tests....* gnu/packages/freedesktop.scm (libfprint)[native-inputs]: Add python-minimal as it's needed by the tests. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Attila Lendvai
2022-04-14gnu: Add r-ace....* gnu/packages/bioconductor.scm (r-ace): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Mădălin Ionel Patrașcu
2022-04-14gnu: r-catalyst: Update description....* gnu/packages/bioconductor.scm (r-catalyst)[description]: Add Texinfo markup and clarify a sentence. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Mădălin Ionel Patrașcu
2022-04-14gnu: r-tcgabiolinks: Update to 2.22.4....* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.22.4. Ricardo Wurmus
2022-04-14gnu: r-omnipathr: Update to 3.2.8....* gnu/packages/bioconductor.scm (r-omnipathr): Update to 3.2.8. Ricardo Wurmus
2022-04-14gnu: r-bgeedb: Update to 2.20.1....* gnu/packages/bioconductor.scm (r-bgeedb): Update to 2.20.1. Ricardo Wurmus
2022-04-14gnu: r-gviz: Update to 1.38.4....* gnu/packages/bioconductor.scm (r-gviz): Update to 1.38.4. Ricardo Wurmus
2022-04-14gnu: r-catalyst: Update to 1.18.1....* gnu/packages/bioconductor.scm (r-catalyst): Update to 1.18.1. Ricardo Wurmus
2022-04-14gnu: r-mscoreutils: Update to 1.6.2....* gnu/packages/bioconductor.scm (r-mscoreutils): Update to 1.6.2. Ricardo Wurmus
2022-04-14gnu: r-singler: Update to 1.8.1....* gnu/packages/bioconductor.scm (r-singler): Update to 1.8.1. Ricardo Wurmus
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sg-tooltip'>* guix/serialization.scm (read-contents): Remove. (read-file-type, fold-archive): New procedures. (restore-file): Rewrite in terms of 'fold-archive'. * tests/nar.scm ("write-file-tree + fold-archive") ("write-file-tree + fold-archive, flat file"): New tests. Ludovic Courtès 2019-12-11import: crate: Better handle license expressions....* guix/import/crate.scm (%dual-license-rx): Removed function. (crate->guix-package): Handle most of the multi-licensing cases. * tests/crate.scm (licenses): Add tests for some licenses. Co-authored-by: Ludovic Courtès <ludo@gnu.org> Brice Waegeneire 2019-12-11import: crate: Add recursive import test....* tests/crate.scm (test-crate): Rename to... (test-foo-crate): ... this. (test-dependencies): Rename to... (test-foo-dependencies): ... this. (test-root-crate, test-root-dependencies, test-intermediate-1-crate) (test-intermediate-1-dependencies, test-intermediate-2-crate) (test-intermediate-2-dependencies, test-leaf-alice-crate) (test-leaf-alice-dependencies, test-leaf-bob-crate) (test-leaf-bob-dependencies): New variables. ("crate->guix-package"): Adjust accordingly. ("cargo-recursive-import"): New test. Co-authored-by: Ludovic Courtès <ludo@gnu.org> Brian Leung 2019-12-11import: utils: 'recursive-import' returns a list rather than a stream....* guix/import/utils.scm (recursive-import): Remove 'list->stream' call. * guix/scripts/import/cran.scm (guix-import-cran): Remove 'stream->list' call. * guix/scripts/import/crate.scm (guix-import-crate): Likewise. * guix/scripts/import/elpa.scm (guix-import-elpa): Likewise. * guix/scripts/import/gem.scm (guix-import-gem): Likewise. * guix/scripts/import/hackage.scm (guix-import-hackage): Likewise. * guix/scripts/import/opam.scm (guix-import-opam): Likewise. * guix/scripts/import/pypi.scm (guix-import-pypi): Likewise. * guix/scripts/import/stackage.scm (guix-import-stackage): Likewise. * tests/gem.scm ("gem-recursive-import"): Likewise. * tests/import-utils.scm ("recursive-import"): Likewise. Co-authored-by: Brian Leung <bkleung89@gmail.com> Ludovic Courtès 2019-12-11import: utils: 'recursive-import' returns packages in topological order....* guix/import/utils.scm (topological-sort): New procedure. (recursive-import): Rewrite to use it. * tests/import-utils.scm ("recursive-import"): New test. * guix/import/cran.scm (cran->guix-package): Always return two values. * guix/scripts/import/cran.scm (guix-import-cran): Remove 'reverse' call on 'cran-recursive-import' result. * guix/scripts/import/crate.scm (guix-import-crate): Likewise. * guix/scripts/import/elpa.scm (guix-import-elpa): Likewise. * guix/scripts/import/gem.scm (guix-import-gem): Likewise. * guix/scripts/import/hackage.scm (guix-import-hackage): Likewise. * guix/scripts/import/opam.scm (guix-import-opam): Likewise. * guix/scripts/import/pypi.scm (guix-import-pypi): Likewise. * guix/scripts/import/stackage.scm (guix-import-stackage): Likewise. * tests/gem.scm ("gem-recursive-import"): Change the order of package expressions accordingly. Ludovic Courtès 2019-12-10tests: processes: Skip tests if running with binfmt....* tests/processes.scm (binfmt-misc?): New procedure, (test-assert*): new procedure that skips the test if binfmt-misc? returns Mathieu Othacehe 2019-12-08lint: Add '--load-path' option....* guix/scripts/lint.scm (%options): Add '--load-path' option. * doc/guix.texi: Document it. * tests/guix-lint.sh: Test it. Signed-off-by: Ludovic Courtès <ludo@gnu.org> zimoun 2019-12-07derivations: Add 'derivation-input-fold'....* guix/derivations.scm (derivation-input-fold): New procedure. (substitution-oracle)[closure]: Rewrite in terms of 'derivation-input-fold'. * tests/derivations.scm ("derivation-input-fold"): New test. Ludovic Courtès 2019-12-01tests: lzlib: Do not fail if lzlib in not available....* tests/lzlib.scm: Use test-assert* for all test cases, so that there are no failures if lzlib is unavailable. Mathieu Othacehe 2019-11-30gexp: 'local-file' properly resolves non-literal relative file names....* guix/gexp.scm (local-file): Distinguish the case where FILE is a literal string and when it's not. Add a clause for when FILE is not a literal string. * tests/gexp.scm ("local-file, non-literal relative file name"): New test. * doc/guix.texi (G-Expressions): Update accordingly. Ludovic Courtès 2019-11-29tests: Fix race condition in profile locking test....Previously, there was a possibility that "guix install emacs" would grab the lock before "guix package -m $module_dir/manifest.scm". When that happened, the test would start building Emacs and all its dependencies, which could take a while and some disk space. This is a followup to b1fb663404894268b5ee92c040f12c52c0bee425. * tests/guix-package.sh: In profile locking test, emit "$module_dir/ready" from the manifest and wait for it to exist before running "guix install emacs". Ludovic Courtès 2019-11-27substitute: Make '%allow-unauthenticated-substitutes?' public....* guix/scripts/substitute.scm (warn-about-missing-authentication): New procedure. (%allow-unauthenticated-substitutes?): Turn into a public parameter and use 'warn-about-missing-authentication'. (valid-narinfo?): Adjust accordingly. * tests/substitute.scm (call-with-narinfo): Likewise. Ludovic Courtès 2019-11-26tests: Avoid unnecessary use of 'mock'....* tests/build-utils.scm ("wrap-script, simple case"): Use the real 'which' instead of mocking it. Ludovic Courtès 2019-11-26tests: Avoid (catch 'srfi-34 …) form....* tests/build-utils.scm ("wrap-script, raises condition"): Use 'guard' instead of "catch 'srfi-34". Ludovic Courtès
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