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2018-01-10gnu: Use one spelling for ‘copyright’.Tobias Geerinckx-Rice
* gnu/packages/gtk.scm: Standardise on ‘copyright’ spelling in file headers. * gnu/packages/pdf.scm: Likewise. * gnu/packages/perl-check.scm: Likewise. * gnu/packages/perl.scm: Likewise. * guix/import/gem.scm: Likewise. * guix/import/hackage.scm: Likewise.
2018-01-08import: crate: Gracefully deal with missing license info.Ludovic Courtès
Reported by Fis Trivial <ybbs.daans@hotmail.com>. Fixes <https://bugs.gnu.org/28987>. * guix/import/crate.scm (crate-fetch): Check whether the "license" info is present.
2017-11-07guix: Add archive support for bioconductor-uri.Ricardo Wurmus
* guix/build-system/r.scm (bioconductor-uri): Also return the archive URL. * guix/import/cran.scm (latest-bioconductor-release, fetch-description): Adjust because bioconductor-uri now returns a list.
2017-11-07import: cran: Use Bioconductor 3.6 helpers.Ricardo Wurmus
* guix/import/cran.scm (bioconductor-mirror-url): Remove procedure. (fetch-description): Extract DESCRIPTION file from tarball for Bioconductor packages. (latest-bioconductor-release): Use latest-bioconductor-package-version.
2017-11-07import: cran: Add support for Bioconductor 3.6.Ricardo Wurmus
* guix/import/cran.scm (%bioconductor-version, %bioconductor-packages-list-url): New variables. (bioconductor-packages-list, latest-bioconductor-package-version): New procedures.
2017-11-07import: utils: Add string helpers.Ricardo Wurmus
* guix/import/utils.scm (read-lines, chunk-lines): New procedures.
2017-10-30Revert "import: cpan: Use HTTPS for home pages."Tobias Geerinckx-Rice
This reverts commit 29f7bf59d5d4d4b848eaedc6766bb4e02cae20d3: HTTPS support at search.cpan.org is unreliable, at best. Don't rely on it.
2017-10-29import: cpan: Use HTTPS for home pages.Tobias Geerinckx-Rice
* guix/import/cpan.scm (cpan-home): Use HTTPS. * tests/cpan.scm ("cpan->guix-package"): Expect it.
2017-10-29import: cpan: Actually use CPAN-HOME.Tobias Geerinckx-Rice
* guix/import/cpan.scm (cpan-module->sexp): Use the CPAN-HOME procedure.
2017-10-29import: cpan: Add trailing "/" to CPAN-HOME.Tobias Geerinckx-Rice
Prevent regression after commit e4bc1727302b0e1e255ea5cf4e2ccf33cafe7296. * guix/import/cpan.scm (cpan-home): Add trailing "/".
2017-10-28import: cpan: Add trailing "/" on home-page.Eric Bavier
This appeases 'guix lint', which otherwise complains about permanent redirects. * guix/import/cpan.scm (cpan-module->sexp): Add trailing "/" on home-page. * tests/cpan.scm ("cpan->guix-package"): Adjust accordingly.
2017-10-28import: cpan: Propagate imported dependencies.Eric Bavier
This is most often the need for perl module dependencies. * guix/import/cpan.scm (cpan-module->sexp): 'inputs -> 'propagated-inputs. * tests/cpan.scm ("cpan->guix-package"): Adjust accordingly.
2017-10-28import: elpa: Do not abort when failing to download the archive.Ludovic Courtès
* guix/import/elpa.scm (elpa-fetch-archive): Use 'http-fetch/cached' directly instead of 'call-with-downloaded-file'. This ensures we don't just abort when networking access is lacking, which is required to allow 'guix refresh -c refresh' to proceed.
2017-10-28import: github: Gracefully handle multiple-URL origins.Ludovic Courtès
* guix/import/github.scm (latest-release)[origin-github-uri]: New procedure. Use it.
2017-10-21Use HTTPS for bioconductor.org.Tobias Geerinckx-Rice
* doc/guix.texi (Invoking guix import, Invoking guix refresh): Use HTTPS for bioconductor.org URLs. * gnu/packages/bioinformatics.scm (r-annotate, r-geneplotter, r-genefilter) (r-deseq2, r-dexseq, r-annotationforge, r-rbgl, r-gseabase, r-category) (r-gostats, r-shortread, r-biocgenerics, r-biocinstaller, r-biocviews) (r-biocstyle, r-bioccheck, r-s4vectors, r-iranges, r-genomeinfodbdata) (r-genomeinfodb, r-xvector, r-genomicranges, r-biobase, r-annotationdbi) (r-biomart, r-biocparallel, r-biostrings, r-rsamtools, r-delayedarray) (r-summarizedexperiment, r-genomicalignments, r-rtracklayer) (r-genomicfeatures, r-graph, r-topgo, r-bsgenome, r-impute, r-seqpattern) (r-seqlogo, r-motifrg, r-bamsignals, r-mutationalpatterns, r-tximport) (r-rhdf5, r-chipseq, r-sva, r-affy, r-vsn, r-mzid, r-msnid) (r-interactivedisplaybase, r-annotationhub)[home-page]: Likewise. * gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene) (r-go-db, r-bsgenome-hsapiens-1000genomes-hs37d5, r-org-hs-eg-db) (r-org-ce-eg-db, r-org-dm-eg-db, r-org-mm-eg-db) (r-bsgenome-hsapiens-ucsc-hg19, r-bsgenome-mmusculus-ucsc-mm9) (r-bsgenome-mmusculus-ucsc-mm10, r-txdb-mmusculus-ucsc-mm10-knowngene) (r-bsgenome-celegans-ucsc-ce6, r-bsgenome-celegans-ucsc-ce10) (r-bsgenome-dmelanogaster-ucsc-dm3, r-copyhelper)[source, home-page]: Likewise. * gnu/packages/statistics.scm (r-rcurl)[source]: Likewise. * guix/build-system/r.scm (bioconductor-uri): Likewise. * guix/import/cran.scm (%cran-url, bioconductor-package?) (bioconductor-data-package?, bioconductor-experiment-package?): Likewise.
2017-10-10import: cpan: Load (gnu packages perl) lazily.Ludovic Courtès
* guix/import/cpan.scm: Remove dependency on (gnu packages perl). (perl-package): New procedure. (%corelist, core-module?): Use it instead of referring to 'perl'.
2017-10-10import: pypi: Remove unneeded import.Ludovic Courtès
* guix/import/pypi.scm: Remove unneeded import.
2017-09-28import: Add generic data to package converter.Ricardo Wurmus
* guix/import/utils.scm (build-system-modules, lookup-build-system-by-name, specs->package-lists, source-spec->object, alist->package): New procedures. * tests/import-utils.scm: Add tests for alist->package.
2017-09-28import: Add package->code.Ricardo Wurmus
* guix/import/print.scm: New file. * tests/print.scm: New file. * Makefile.am (SCM_TESTS): Add new test file. (MODULES): Add print.scm.
2017-09-26upstream: Add new GNOME updater.Ludovic Courtès
Partly fixes <https://bugs.gnu.org/28159>. Reported by Hartmut Goebel <h.goebel@crazy-compilers.com>. * guix/import/gnome.scm: New file. * Makefile.am (MODULES): Add it. * guix/gnu-maintenance.scm (latest-gnome-release) (%gnome-updater): Remove.
2017-09-12import: cpan: Replace '(package-license perl) with 'perl-license.Christopher Baines
The perl-license definition is intended to avoid circular dependencies, so use this as a default when importing packages from CPAN. * guix/import/cpan.scm (string->license): Replace '(package-license perl) with 'perl-license.
2017-07-24import: cpan: Updater returns a list of URLs.Ludovic Courtès
* guix/import/cpan.scm (latest-release): Return a list in the 'urls' field of 'upstream-source'.
2017-06-26import cran: Generate a valid 'license' field for "GPL".Ludovic Courtès
Fixes <http://bugs.gnu.org/27294>. Reported by Joshua Sierles <joshua@joshua.si>. * guix/import/cran.scm (string->license) <"GPL">: Return a quoted list.
2017-06-15guix: Add texlive importer.Ricardo Wurmus
* guix/import/texlive.scm: New file. * guix/scripts/import/texlive.scm: New file. * Makefile.am (MODULES): Add them. * tests/texlive.scm: New file. * Makefile.am (SCM_TESTS): Add it. * guix/scripts/import.scm (importers): Add texlive importer. * doc/guix.texi (Invoking guix import): Document it.
2017-06-15import: pypi: Always use pypi.io URL with downcased package name.Danny Milosavljevic
* guix/import/pypi.scm (make-pypi-sexp): Always use pypi.io URL with downcased package name.
2017-06-07import: cpan: Update CPAN importer to use MetaCPAN v1 API.James Richardson
* guix/import/cpan.scm (module->dist-name, cpan-fetch): Use metacpan.org URLs. * tests/cpan.scm ("cpan->guix-package"): Adjust accordingly. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-05-16import cran: Check if pkg-config is needed.Ricardo Wurmus
* guix/import/cran.scm (needs-pkg-config?): New procedure. (description->package): Use it.
2017-05-16import cran: Refactor "needs-zlib?".Ricardo Wurmus
* guix/import/cran.scm (tarball-files-match-pattern?): New procedure. (needs-zlib?): Implement in terms of "tarball-files-match-pattern?".
2017-05-16import cran: Export package predicates.Ricardo Wurmus
* guix/import/cran.scm (cran-package?, bioconductor-package?, bioconductor-data-package?, bioconductor-experiment-package?): Export procedures.
2017-05-16import cran: Add predicate for Bioconductor experiment packages.Ricardo Wurmus
* guix/import/cran.scm (bioconductor-experiment-package?): New variable.
2017-05-16import cran: Exclude experiment packages in predicate "bioconductor-package?".Ricardo Wurmus
* guix/import/cran.scm (bioconductor-package?): Exclude experiment packages, because they cannot be updated with the default bioconductor updater.
2017-05-16import cran: Fetch DESCRIPTION files from Github mirror.Ricardo Wurmus
* guix/import/cran.scm (%bioconductor-svn-url): Remove variable. (bioconductor-mirror-url): New procedure. (fetch-description): Take a REPOSITORY symbol instead of a BASE-URL string. (cran->guix-package): Pass REPOSITORY symbol to "fetch-description". (latest-cran-release, latest-bioconductor-release): Adjust accordingly. (bioconductor-package?): Update comment about SVN.
2017-05-13import: pypi: Robustify latest-release.Mathieu Othacehe
* guix/import/pypi.scm (latest-release): Check if pypi-fetch has failed. If so return #f, else construct the <upstream-source>.
2017-05-13import: cran: Robustify cran-package?.Mathieu Othacehe
* guix/import/cran.scm (package->upstream-name): Return #f if url start and end index could not be determined. (cran-package?): Check if the upstream-name can be extracted from given package. * tests/cran.scm: Add "r-minimal is not a cran package" to make sure that r-minimal is not detected as a cran package. This fixes a failure of guix refresh on r-minimal because no upsteam-name can be determined from ".../R-version.tar.gz" uri.
2017-05-03ui: Rename '_' to 'G_'.Ludovic Courtès
This avoids collisions with '_' when the latter is used as a 'match' pattern for instance. See <https://lists.gnu.org/archive/html/guix-devel/2017-04/msg00464.html>. * guix/ui.scm: Rename '_' to 'G_'. * po/guix/Makevars (XGETTEXT_OPTIONS): Adjust accordingly. * build-aux/compile-all.scm (warnings): Remove 'format'. * gnu/packages.scm, gnu/services.scm, gnu/services/shepherd.scm, gnu/system.scm, gnu/system/shadow.scm, guix/gnupg.scm, guix/http-client.scm, guix/import/cpan.scm, guix/import/elpa.scm, guix/import/pypi.scm, guix/nar.scm, guix/scripts.scm, guix/scripts/archive.scm, guix/scripts/authenticate.scm, guix/scripts/build.scm, guix/scripts/challenge.scm, guix/scripts/container.scm, guix/scripts/container/exec.scm, guix/scripts/copy.scm, guix/scripts/download.scm, guix/scripts/edit.scm, guix/scripts/environment.scm, guix/scripts/gc.scm, guix/scripts/graph.scm, guix/scripts/hash.scm, guix/scripts/import.scm, guix/scripts/import/cpan.scm, guix/scripts/import/cran.scm, guix/scripts/import/crate.scm, guix/scripts/import/elpa.scm, guix/scripts/import/gem.scm, guix/scripts/import/gnu.scm, guix/scripts/import/hackage.scm, guix/scripts/import/nix.scm, guix/scripts/import/pypi.scm, guix/scripts/import/stackage.scm, guix/scripts/lint.scm, guix/scripts/offload.scm, guix/scripts/pack.scm, guix/scripts/package.scm, guix/scripts/perform-download.scm, guix/scripts/publish.scm, guix/scripts/pull.scm, guix/scripts/refresh.scm, guix/scripts/size.scm, guix/scripts/substitute.scm, guix/scripts/system.scm, guix/ssh.scm, guix/upstream.scm: Use 'G_' instead of '_'. Most of this change was obtained by running: "sed -i -e's/(_ "/(G_ "/g' `find -name \*.scm`".
2017-04-28import: Update Bioconductor release to 3.5.Roel Janssen
* guix/import/cran.scm: Change Bioconductor release to 3.5.
2017-04-05import cran: Distinguish Bioconductor data packages.Ricardo Wurmus
* guix/import/cran.scm (bioconductor-package?): Exclude Bioconductor data packages. (bioconductor-data-package?): New procedure.
2017-03-28Replace (compose not PROC) with simpler idioms.Ludovic Courtès
* gnu/packages/bioinformatics.scm (python-pysam)[arguments] <check>: Use (negate proc) instead of (compose not proc). * guix/import/cran.scm (recursive-import): Likewise. * guix/import/elpa.scm (filter-dependencies): Use 'remove' instead of '(filter (compose not proc) ...)'.
2017-03-28import cran: Automatically add gfortran and zlib when needed.Ricardo Wurmus
* guix/import/cran.scm (needs-fortran?, needs-zlib?): New procedures. (description->package): Use them.
2017-03-17gnu: r: Do not build recommended packages.Ricardo Wurmus
* gnu/packages/statistics.scm (r)[arguments]: Rename phase "build-recommended-packages-reproducibly" to "build-reproducibly"; add configure flag "--without-recommended-packages". * guix/import/cran.scm (default-r-packages): Remove recommended packages. * gnu/packages/python.scm (python-rpy2)[inputs]: Add r-survival. * gnu/packages/bioinformatics.scm (r-ape)[propagated-inputs]: Add r-lattice and r-nlme. (r-vegan)[propagated-inputs]: Add r-mass. (r-genefilter)[propagated-inputs]: Add r-survival. (r-grohmm)[propagated-inputs]: Add r-mass. (r-bioccheck)[propagated-inputs]: Add r-codetools. (r-summarizedexperiment)[propagated-inputs]: Add r-matrix. (r-topgo)[propagated-inputs]: Add r-lattice. (r-sva)[propagated-inputs]: Add r-mgcv. (r-raremetals2)[propagated-inputs]: Add r-mass. (r-vsn)[propagated-inputs]: Add r-lattice. (r-pcamethods)[propagated-inputs]: Add r-mass. * gnu/packages/bioinformatics.scm (r-ggplot2)[propagated-inputs]: Add r-mass. (r-locfit)[propagated-inputs]: Add r-lattice. (r-coda)[propagated-inputs]: Add r-lattice. (r-irlba)[propagated-inputs]: Add r-matrix. (r-glmnet)[propagated-inputs]: Add r-matrix. (r-e1071)[propagated-inputs]: Add r-class. (r-spams)[propagated-inputs]: Add r-lattice and r-matrix. (r-hmisc)[propagated-inputs]: Add r-cluster, r-foreign, r-lattice, r-nnet, and r-rpart. (r-zoo)[propagated-inputs]: Add r-lattice. (r-mixtools)[propagated-inputs]: Add r-boot and r-mass. (r-flexmix)[propagated-inputs]: Add r-lattice and r-nnet. (r-prabclus)[propagated-inputs]: Add r-mass. (r-fpc)[propagated-inputs]: Add r-class, r-cluster, and r-mass. (r-rcppeigen)[propagated-inputs]: Add r-matrix. (r-matrixmodels)[propagated-inputs]: Add r-matrix. (r-lme4)[propagated-inputs]: Add r-mass and r-nlme. (r-pbkrtest)[propagated-inputs]: Add r-mass and r-matrix. (r-car)[propagated-inputs]: Add r-mass, r-mgcv, and r-nnet. (r-tclust)[propagated-inputs]: Add r-cluster.
2017-03-16utils: Move base16 procedures to (guix base16).Ludovic Courtès
* guix/utils.scm (bytevector->base16-string, base16-string->bytevector): Move to... * guix/base16.scm: ... here. New file. * tests/utils.scm ("bytevector->base16-string->bytevector"): Move to... * tests/base16.scm: ... here. New file. * Makefile.am (MODULES): Add guix/base16.scm. (SCM_TESTS): Add tests/base16.scm. * build-aux/download.scm, guix/derivations.scm, guix/docker.scm, guix/import/snix.scm, guix/pk-crypto.scm, guix/scripts/authenticate.scm, guix/scripts/download.scm, guix/scripts/hash.scm, guix/store.scm, tests/hash.scm, tests/pk-crypto.scm: Adjust imports accordingly.
2017-02-14import: stackage: Avoid using (guix ui) in importer code.Federico Beffa
* guix/import/stackage.scm (stackage->guix-package, stackage-lts-info-fetch): Raise 'message' condition instead of using 'leave' from (guix ui). * guix/scripts/import/stackage.scm (guix-import-stackage): Handle conditions.
2017-02-09import: hackage: Handle unknown packages gracefully.Federico Beffa
* guix/import/hackage.scm (hackage-fetch): Add 'guard'.
2017-02-09import: Add stackage importer and updater.Federico Beffa
* guix/import/stackage.scm: New file. * guix/scripts/import/stackage.scm: New file. * Makefile.am (MODULES): Add new files. * guix/scripts/import.scm (importers): Add "stackage". * guix/scripts/refresh.scm (%updaters): Add %stackage-updater. * doc/guix.texi (Invoking 'guix import'): Document the importer. (Invoking 'guix refresh'): Add stackage to option --type valid values. * guix/import/hackage.scm (guix-package->hackage-name, hackage-fetch, hackage-source-url, hackage-cabal-url, hackage-package?): Export them.
2017-02-09import: json: Explicitly ask for JSON data.Federico Beffa
* guix/import/json.scm (json-fetch): Add #:headers to http-fetch call.
2017-02-08import: pypi: Correctly handle multiple-URL origins.Ludovic Courtès
Fixes <https://bugs.gnu.org/25635>. Reported by Sergei Trofimovich <slyfox@inbox.ru>. * guix/import/pypi.scm (guix-package->pypi-name)[url->pypi-name]: New procedure. Rewrite body to match lists in addition to strings. * tests/pypi.scm ("guix-package->pypi-name, several URLs"): New test.
2017-01-28Add (guix memoization).Ludovic Courtès
* guix/combinators.scm (memoize): Remove. * guix/memoization.scm: New file. * Makefile.am (MODULES): Add it. * gnu/packages.scm, gnu/packages/bootstrap.scm, guix/build-system/gnu.scm, guix/build-system/python.scm, guix/derivations.scm, guix/gnu-maintenance.scm, guix/import/cran.scm, guix/import/elpa.scm, guix/modules.scm, guix/scripts/build.scm, guix/scripts/graph.scm, guix/scripts/lint.scm, guix/store.scm, guix/utils.scm: Adjust imports accordingly.
2017-01-28import: github: Better tolerate unexpected file extensions.Ludovic Courtès
* guix/import/github.scm (find-extension): Add ".tbz". (updated-github-url): When 'find-extension' returns #f, use "" for EXT.
2017-01-26import: pypi: Don't add setuptools to propagated-inputs.Carlo Zancanaro
* guix/import/pypi.scm (compute-inputs): Don't add setuptools to the imported package's propagated-inputs.
2017-01-19import: github: Catch HTTP 403 error during fetch.Mathieu OTHACEHE
* guix/import/github.scm (json-fetch*): Catch 403 HTTP error that may be raised if a github token has not been set. Signed-off-by: Mathieu OTHACEHE <m.othacehe@gmail.com> Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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