69b0a847fb
import: hackage: Do not repeat inputs in native-inputs.
...
* guix/import/hackage.scm (hackage-module->sexp): Do not repeat inputs again
in native-inputs. native-inputs should only contain packages that are not
already listed in inputs.
2018-10-28 13:51:20 +05:30
7277d06d8b
gnu: Use pypi.org.
...
<pypi.io> redirects to <pypi.org>.
* guix/build-system/python.scm (pypi-uri): Replace pypi.io with pypi.org.
* guix/import/pypi.scm (pypi-url?): Likewise.
* tests/pypi.scm: Likewise.
2018-10-18 23:46:33 -04:00
ad0082afe0
import: json: Handle the error case.
...
* guix/import/json.scm (json-fetch-alist): Handle the error case.
2018-10-16 23:17:36 +02:00
127586adfb
guix: import: stackage: Fix JSON accessors.
...
* guix/import/stackage.scm (lts-info-ghc-version, lst-info-packages): Use
assoc-ref for accessing parsed JSON.
2018-10-01 12:12:08 +02:00
ca71942445
Switch to Guile-Gcrypt.
...
This removes (guix hash) and (guix pk-crypto), which now live as part of
Guile-Gcrypt (version 0.1.0.)
* guix/gcrypt.scm, guix/hash.scm, guix/pk-crypto.scm,
tests/hash.scm, tests/pk-crypto.scm: Remove.
* configure.ac: Test for Guile-Gcrypt. Remove LIBGCRYPT and
LIBGCRYPT_LIBDIR assignments.
* m4/guix.m4 (GUIX_ASSERT_LIBGCRYPT_USABLE): Remove.
* README: Add Guile-Gcrypt to the dependencies; move libgcrypt as
"required unless --disable-daemon".
* doc/guix.texi (Requirements): Likewise.
* gnu/packages/bash.scm, guix/derivations.scm, guix/docker.scm,
guix/git.scm, guix/http-client.scm, guix/import/cpan.scm,
guix/import/cran.scm, guix/import/crate.scm, guix/import/elpa.scm,
guix/import/gnu.scm, guix/import/hackage.scm,
guix/import/texlive.scm, guix/import/utils.scm, guix/nar.scm,
guix/pki.scm, guix/scripts/archive.scm,
guix/scripts/authenticate.scm, guix/scripts/download.scm,
guix/scripts/hash.scm, guix/scripts/pack.scm,
guix/scripts/publish.scm, guix/scripts/refresh.scm,
guix/scripts/substitute.scm, guix/store.scm,
guix/store/deduplication.scm, guix/tests.scm, tests/base32.scm,
tests/builders.scm, tests/challenge.scm, tests/cpan.scm,
tests/crate.scm, tests/derivations.scm, tests/gem.scm,
tests/nar.scm, tests/opam.scm, tests/pki.scm,
tests/publish.scm, tests/pypi.scm, tests/store-deduplication.scm,
tests/store.scm, tests/substitute.scm: Adjust imports.
* gnu/system/vm.scm: Likewise.
(guile-sqlite3&co): Rename to...
(gcrypt-sqlite3&co): ... this. Add GUILE-GCRYPT.
(expression->derivation-in-linux-vm)[config]: Remove.
(iso9660-image)[config]: Remove.
(qemu-image)[config]: Remove.
(system-docker-image)[config]: Remove.
* guix/scripts/pack.scm: Adjust imports.
(guile-sqlite3&co): Rename to...
(gcrypt-sqlite3&co): ... this. Add GUILE-GCRYPT.
(self-contained-tarball)[build]: Call 'make-config.scm' without
#:libgcrypt argument.
(squashfs-image)[libgcrypt]: Remove.
[build]: Call 'make-config.scm' without #:libgcrypt.
(docker-image)[config, json]: Remove.
[build]: Add GUILE-GCRYPT to the extensions Remove (guix config) from
the imported modules.
* guix/self.scm (specification->package): Remove "libgcrypt", add
"guile-gcrypt".
(compiled-guix): Remove #:libgcrypt.
[guile-gcrypt]: New variable.
[dependencies]: Add it.
[*core-modules*]: Remove #:libgcrypt from 'make-config.scm' call.
Add #:extensions.
[*config*]: Remove #:libgcrypt from 'make-config.scm' call.
(%dependency-variables): Remove %libgcrypt.
(make-config.scm): Remove #:libgcrypt.
* build-aux/build-self.scm (guile-gcrypt): New variable.
(make-config.scm): Remove #:libgcrypt.
(build-program)[fake-gcrypt-hash]: New variable.
Add (gcrypt hash) to the imported modules. Adjust load path
assignments.
* gnu/packages/package-management.scm (guix)[propagated-inputs]: Add
GUILE-GCRYPT.
[arguments]: In 'wrap-program' phase, add GUILE-GCRYPT to the search
path.
2018-09-04 17:25:11 +02:00
ac906cb7bb
import: pypi: Support recursive importing.
...
* guix/import/pypi.scm (guess-requirements): Use upstream names.
(compute-inputs): Return the upstream dependency names as an additional value.
(make-pypi-sexp): Likewise.
(pypi->guix-package): Memoize it.
(pypi-recursive-import): New procedure.
* guix/scripts/import/pypi.scm (show-help, %options): Accept "recursive"
option.
(guix-import-pypi): Use pypi-recursive-import.
* doc/guix.texi (Invoking guix import): Document it.
2018-08-30 15:22:22 +02:00
e37f889404
import: pypi: Also guess dependencies from *.egg-info/requires.txt.
...
* guix/import/pypi.scm (guess-requirements): Extract "requires.txt" from the
egg-info directory in addition to "requirements.txt"; strip off version
constraints; use call-with-temporary-directory.
2018-08-30 15:22:14 +02:00
a3ece51a29
import: stackage: Support recursive importing.
...
* guix/import/hackage.scm (hackage-name->package-name): Export procedure.
* guix/import/stackage.scm (lts-info-packages-lts-info): Fix match expression.
(stackage-recursive-import): New procedure.
(stackage->guix-package): Memoize results.
* guix/scripts/import/stackage.scm (show-help, %options,
guix-import-stackage): Support recursive importing.
* doc/guix.texi (Invoking guix import): Document option.
2018-08-30 15:22:06 +02:00
bab4dc58f7
import: github: Filter out tags that don't look like version numbers.
...
* guix/import/github.scm (latest-released-version): Filter out RELEASE
if it doesn't start with digit.
2018-08-20 16:32:18 +02:00
45c01189cc
import: github: Get /tags when /releases returns the empty list.
...
This allows "guix refresh" to work for many packages where it would
previously fail with "no updater for PACKAGE".
* guix/import/github.scm (fetch-releases-or-tags): New procedure.
(latest-released-version): Use it instead of calling 'json-fetch'.
Adjust 'hash-ref' call.
2018-08-20 16:32:18 +02:00
2766282f5a
import: github: Request API v3 in the 'Accept' header.
...
* guix/import/json.scm (json-fetch): Add #:headers argument and honor it.
* guix/import/github.scm (latest-released-version): Pass #:headers to
'json-fetch'.
2018-08-20 16:32:18 +02:00
a928596162
import: hackage: Support recursive importing.
...
* guix/import/hackage.scm (hackage-recursive-import): New procedure.
(hackage-module->sexp): Return dependencies alongside dependencies.
(hackage->guix-package): Memoize results.
* guix/scripts/import/hackage.scm (show-help, %options, guix-import-hackage):
Support recursive importing.
* doc/guix.texi (Invoking guix import): Document option.
2018-08-11 18:53:46 +02:00
9aba9b1278
Migrate search.cpan.org home pages to metacpan.org.
...
The venerable search.cpan.org has retired[0].
[0]: https://log.perl.org/2018/05/goodbye-search-dot-cpan-dot-org.html
* guix/import/cpan.scm (cpan-home): Generate metacpan.org home page URIs.
Update all previously generated ones in (gnu packages) to their
canonical new homes.
2018-08-11 17:22:31 +02:00
f60784228a
import: cabal, hackage: Avoid error when custom setup section is missing.
...
Fixes <https://debbugs.gnu.org/32387 >.
* guix/import/cabal.scm (eval-cabal): Avoid mis-match when the custom-setup
section cannot be created.
* guix/import/hackage.scm (cabal-custom-setup-dependencies->names): Do not
crash when cabal-package-custom-setup returns #F.
2018-08-07 20:39:12 +02:00
d804d0b9ef
import: hackage: Emit native-inputs in the importer.
...
* guix/import/cabal.scm (cabal-custom-setup-dependencies): Export.
(cabal-package-custom-setup): Export.
(<cabal-package>): New field "custom-setup".
(make-cabal-package): Modify.
(eval-cabal): Modify.
* guix/import/hackage.scm (cabal-dependencies->names): Factor out...
(cabal-test-dependencies->names): ...this.
(cabal-custom-setup-dependencies->names): New procedure.
(hackage-module->sexp): Modify.
2018-07-27 11:42:53 +02:00
8440db459a
import: PyPI: Update redirected URL.
...
* guix/import/pypi.scm (guix-package->pypi-name, pypi->guix-package): Update
docstrings.
(pypi-package?): Test for pypi.org, too.
(pypi-fetch): s/pypi.python.org/pypi.org/
* tests/pypi.scm ("guix-package->pypi-name, new URL style",
"pypi->guix-package", "pypi->guix-package, wheels"): Likewise.
2018-07-24 17:42:04 +02:00
e29067d22e
import: hackage: Fix typo.
...
* guix/import/cabal.scm (cabal-custom-setuo-name): Rename to...
(cabal-custom-setup-name): ...this.
2018-07-13 15:23:40 +02:00
e39a44f340
import: hackage: Evaluate "-any" and "-none" version comparison operators.
...
* guix/import/cabal.scm (eval-cabal): Modify.
* tests/hackage.scm (test-cabal-4): New variable and test.
(test-cabal-5): New variable and test.
(test-cabal-6): New variable and test.
2018-07-12 20:35:04 +02:00
ecba50bb79
import: hackage: Support "-any" and "-none" version comparison operators.
...
* guix/import/cabal.scm (make-cabal-parser): Modify.
(is-any): New variable.
(is-none): New variable.
(lex-any): New procedure.
(lex-none): New procedure.
(lex-word): Modify.
(eval-cabal): Modify.
2018-07-12 09:06:48 +02:00
314b63e0b4
import: hackage: Support "custom-setup" field.
...
Fixes <https://bugs.gnu.org/23961 >.
* guix/import/cabal.scm (make-cabal-parser): Modify.
(is-custom-setup): New variable.
(lex-custom-setup): New procedure.
(is-id): Modify.
(lex-version): Modify.
(<cabal-custom-setup>): New record type.
(eval-cabal): Modify.
(dependencies): Add parameter.
2018-07-12 09:06:48 +02:00
88388766f7
import: gem: Add recursive import.
...
* doc/guix.texi (Invoking guix import): Document gem recursive import.
* guix/import/gem.scm (gem->guix-package): Return package and dependencies
values.
(gem-recursive-import): New procedure.
* guix/scripts/import/gem.scm (show-help, %options): Add recursive option.
(guix-import-gem): Use 'gem-recursive-import'.
* tests/gem.scm (test-json): Rename to 'test-foo-json'.
("gem->guix-package"): Use 'test-foo-json'.
(test-bar-json, test-bundler-json): New variables.
("gem-recursive-import"): New test.
2018-07-11 07:08:54 +03:00
b24443bff9
guix: Add opam importer.
...
* guix/scripts/import.scm (importers): Add opam.
* guix/scripts/import/opam.scm: New file.
* guix/import/opam.scm: New file.
* tests/opam.scm: New file.
* Makefile.am: Add them.
* doc/guix.texi (Invoking guix import): Document it.
2018-07-10 10:11:01 +02:00
ae6fa00af0
import: elpa: Check if 'fetch-elpa-package' rest argument is null.
...
* guix/import/elpa.scm (fetch-elpa-package): Check if 'rest' is null.
2018-07-03 07:19:13 +03:00
e8cb9c01c6
build: Remove checks for 'nix-instantiate'.
...
* guix/import/snix.scm (open-nixpkgs): Use "nix-instantiate"
unconditionally.
* configure.ac: Remove check for 'nix-instantiate'.
* guix/config.scm.in (%nix-instantiate): Remove.
* guix/self.scm (%dependency-variables): Remove '%nix-instantiate'.
(make-config.scm): Remove it from the generated "config.scm".
* build-aux/build-self.scm (%dependency-variables, make-config.scm):
Likewise.
2018-06-18 23:19:51 +02:00
38212ff7b9
import: utils: Import more dependencies.
...
* guix/import/utils.scm (recursive-import): Import more dependencies.
2018-06-12 19:51:03 +03:00
3edf0d53a4
import: json: Consolidate duplicate json-fetch functionality.
...
* guix/import/json.scm (json-fetch): Return a list or hash table.
(json-fetch-alist): New procedure.
* guix/import/github.scm (json-fetch*): Remove.
(latest-released-version): Use json-fetch.
* guix/import/cpan.scm (module->dist-name): Use json-fetch-alist.
(cpan-fetch): Likewise.
* guix/import/crate.scm (crate-fetch): Likewise.
* guix/import/gem.scm (rubygems-fetch): Likewise.
* guix/import/pypi.scm (pypi-fetch): Likewise.
* guix/import/stackage.scm (stackage-lts-info-fetch): Likewise.
2018-06-10 22:15:12 +02:00
62d78ec076
import: elpa: Remove unused (gnu packages) module.
...
* guix/import/elpa.scm: Remove unused (gnu packages) module.
2018-06-08 17:05:18 +03:00
74032da3a2
import: elpa: Add recursive import.
...
* doc/guix.texi (Invoking guix import): Document elpa recursive import.
* guix/import/elpa.scm (elpa-package->sexp): Return package and
dependencies values.
(elpa-guix-name, elpa-recursive-import): New procedures.
* guix/scripts/import/elpa.scm (show-help, %options): Add recursive
option.
(guix-import-elpa): Use 'elpa-recursive-import'.
2018-06-08 14:58:33 +03:00
ae9e5d6602
import: utils: Add recursive-import.
...
* guix/import/cran.scm (cran-guix-name, cran-recursive-import): New
procedures.
(recursive-import): Remove procedure.
* guix/import/utils.scm (guix-name, recursive-import): New procedures.
* guix/scripts/import/cran.scm (guix-import-cran): Use
'cran-recursive-import' procedure.
2018-06-08 14:58:33 +03:00
41f17554d8
import: cran: Update to Bioconductor 3.7.
...
* guix/import/cran.scm (%bioconductor-version): Update to 3.7.
2018-06-02 13:39:13 +02:00
4a78fd4617
Correct name and Email for ng0.
...
* .mailmap: Correct name and Email for ng0.
* Makefile.am, doc/guix.texi, etc/completion/fish/guix.fish
gnu/packages/accessibility.scm, gnu/packages/admin.scm,
gnu/packages/audio.scm, gnu/packages/autotools.scm,
gnu/packages/cdrom.scm, gnu/packages/check.scm,
gnu/packages/cinnamon.scm, gnu/packages/compression.scm,
gnu/packages/crypto.scm, gnu/packages/databases.scm,
gnu/packages/django.scm, gnu/packages/dns.scm,
gnu/packages/emacs.scm, gnu/packages/enlightenment.scm,
gnu/packages/fonts.scm, gnu/packages/fontutils.scm,
gnu/packages/forth.scm, gnu/packages/fvwm.scm,
gnu/packages/games.scm, gnu/packages/gl.scm,
gnu/packages/gnome.scm, gnu/packages/gnunet.scm,
gnu/packages/gnupg.scm, gnu/packages/gnuzilla.scm,
gnu/packages/gtk.scm, gnu/packages/guile-wm.scm,
gnu/packages/guile.scm, gnu/packages/haskell-check.scm,
gnu/packages/haskell-crypto.scm, gnu/packages/haskell.scm,
gnu/packages/image-viewers.scm, gnu/packages/image.scm,
gnu/packages/irc.scm, gnu/packages/language.scm,
gnu/packages/libcanberra.scm, gnu/packages/linux.scm,
gnu/packages/lisp.scm, gnu/packages/lolcode.scm,
gnu/packages/lxde.scm, gnu/packages/lxqt.scm,
gnu/packages/mail.scm, gnu/packages/markup.scm,
gnu/packages/mate.scm, gnu/packages/maths.scm,
gnu/packages/mc.scm, gnu/packages/messaging.scm,
gnu/packages/music.scm, gnu/packages/ncurses.scm,
gnu/packages/networking.scm, gnu/packages/nickle.scm,
gnu/packages/openbox.scm, gnu/packages/pdf.scm,
gnu/packages/perl-check.scm, gnu/packages/perl.scm,
gnu/packages/python-crypto.scm, gnu/packages/python-web.scm,
gnu/packages/python.scm, gnu/packages/qt.scm,
gnu/packages/ruby.scm, gnu/packages/rust.scm,
gnu/packages/scheme.scm, gnu/packages/serialization.scm,
gnu/packages/shells.scm, gnu/packages/ssh.scm,
gnu/packages/suckless.scm, gnu/packages/tbb.scm,
gnu/packages/telephony.scm, gnu/packages/text-editors.scm,
gnu/packages/textutils.scm, gnu/packages/time.scm,
gnu/packages/tls.scm, gnu/packages/tor.scm,
gnu/packages/version-control.scm, gnu/packages/video.scm,
gnu/packages/vim.scm, gnu/packages/web.scm,
gnu/packages/wm.scm, gnu/packages/xdisorg.scm,
gnu/packages/xfce.scm, gnu/packages/xml.scm,
gnu/packages/xorg.scm, gnu/services/certbot.scm,
gnu/services/desktop.scm, gnu/services/version-control.scm,
gnu/services/web.scm, guix/import/hackage.scm,
guix/licenses.scm: Likewise.
Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
2018-03-20 17:17:58 +01:00
9bb1838c3f
import: elpa: Return 'license:gpl3+ for ELPA only.
...
Fixes <https://bugs.gnu.org/30836 >.
Reported by Konrad Hinsen <konrad.hinsen@fastmail.net>.
* guix/import/elpa.scm (elpa-package->sexp): Add LICENSE parameter and
honor it.
(elpa->guix-package): Pass 'license:gpl3+ only when REPO is 'gnu.
2018-03-18 22:26:34 +01:00
07d2fed2f6
import: elpa: Fix typos in documentation strings
...
* guix/import/elpa.scm: Fix typos in docstrings.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-03-18 00:02:05 +01:00
44dd3d579d
import: elpa: use https in download URLs
...
* guix/import/elpa.scm (elpa-url): Use HTTPS.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-03-18 00:02:05 +01:00
b402f4ee34
import: cpan: Drop "v" prefix from version strings.
...
Fixes <https://bugs.gnu.org/30641 >.
Reported by Oleg Pykhalov <go.wigust@gmail.com>.
* guix/import/cpan.scm (cpan-version): Drop the "v" prefix when it is
there.
2018-03-01 14:54:55 +01:00
5e2495d09e
import: utils: 'alist->package' allows false license.
...
Reported by <pkill9@runbox.com>.
Fixes <https://bugs.gnu.org/30470 >.
* guix/import/utils.scm (alist->package): Check whether 'license' is
false and set the 'license' field to #f in this case.
* tests/import-utils.scm ("alist->package with false license"): New
test.
2018-02-16 11:10:12 +01:00
8286215326
gnu: Use one spelling for ‘copyright’.
...
* 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.
2018-01-10 18:21:20 +01:00
1e63ecee0b
import: crate: Gracefully deal with missing license info.
...
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.
2018-01-08 11:45:35 +01:00
25e51b1c45
guix: Add archive support for bioconductor-uri.
...
* 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.
2017-11-07 08:14:09 +01:00
27baf50956
import: cran: Use Bioconductor 3.6 helpers.
...
* 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.
2017-11-07 08:13:35 +01:00
84dfdc5759
import: cran: Add support for Bioconductor 3.6.
...
* guix/import/cran.scm (%bioconductor-version,
%bioconductor-packages-list-url): New variables.
(bioconductor-packages-list, latest-bioconductor-package-version): New
procedures.
2017-11-07 08:13:34 +01:00
6b46b04f91
import: utils: Add string helpers.
...
* guix/import/utils.scm (read-lines, chunk-lines): New procedures.
2017-11-07 08:07:51 +01:00
b5c7574b2f
Revert "import: cpan: Use HTTPS for home pages."
...
This reverts commit 29f7bf59d5d4d4b848eaedc6766bb4e02cae20d3: HTTPS support
at search.cpan.org is unreliable, at best. Don't rely on it.
2017-10-30 17:20:42 +01:00
29f7bf59d5
import: cpan: Use HTTPS for home pages.
...
* guix/import/cpan.scm (cpan-home): Use HTTPS.
* tests/cpan.scm ("cpan->guix-package"): Expect it.
2017-10-29 17:32:35 +01:00
6d176ad379
import: cpan: Actually use CPAN-HOME.
...
* guix/import/cpan.scm (cpan-module->sexp): Use the CPAN-HOME procedure.
2017-10-29 17:32:35 +01:00
73f33b9379
import: cpan: Add trailing "/" to CPAN-HOME.
...
Prevent regression after commit e4bc172730
2017-10-29 17:32:12 +01:00
e4bc172730
import: cpan: Add trailing "/" on home-page.
...
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.
2017-10-28 18:20:59 -05:00
23055424f2
import: cpan: Propagate imported dependencies.
...
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.
2017-10-28 18:20:58 -05:00
0a2ce1ea0a
import: elpa: Do not abort when failing to download the archive.
...
* 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.
2017-10-28 09:45:54 +02:00
90297811a9
import: github: Gracefully handle multiple-URL origins.
...
* guix/import/github.scm (latest-release)[origin-github-uri]: New
procedure. Use it.
2017-10-28 09:45:54 +02:00
5713bbf157
Use HTTPS for bioconductor.org.
...
* 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.
2017-10-21 17:43:40 +02:00
90eaa9419a
import: cpan: Load (gnu packages perl) lazily.
...
* guix/import/cpan.scm: Remove dependency on (gnu packages perl).
(perl-package): New procedure.
(%corelist, core-module?): Use it instead of referring to 'perl'.
2017-10-10 23:12:04 +02:00
b719ddbbbb
import: pypi: Remove unneeded import.
...
* guix/import/pypi.scm: Remove unneeded import.
2017-10-10 23:12:03 +02:00
5e892bc365
import: Add generic data to package converter.
...
* 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.
2017-09-28 13:10:11 +02:00
68a91a183b
import: Add package->code.
...
* guix/import/print.scm: New file.
* tests/print.scm: New file.
* Makefile.am (SCM_TESTS): Add new test file.
(MODULES): Add print.scm.
2017-09-28 13:10:10 +02:00
c1d8b3b3b5
upstream: Add new GNOME updater.
...
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.
2017-09-26 00:35:06 +02:00
01ef804d69
import: cpan: Replace '(package-license perl) with 'perl-license.
...
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.
2017-09-12 23:15:36 +01:00
e956ae16a4
import: cpan: Updater returns a list of URLs.
...
* guix/import/cpan.scm (latest-release): Return a list in the 'urls'
field of 'upstream-source'.
2017-07-24 17:35:26 +02:00
94a400beba
import cran: Generate a valid 'license' field for "GPL".
...
Fixes <http://bugs.gnu.org/27294 >.
Reported by Joshua Sierles <joshua@joshua.si>.
* guix/import/cran.scm (string->license) <"GPL">: Return a quoted list.
2017-06-26 22:52:06 +02:00
afbc94194e
guix: Add texlive importer.
...
* 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.
2017-06-15 17:03:19 +02:00
d1e7ca2df8
import: pypi: Always use pypi.io URL with downcased package name.
...
* guix/import/pypi.scm (make-pypi-sexp): Always use pypi.io URL with
downcased package name.
2017-06-15 09:49:13 +02:00
4679dd6967
import: cpan: Update CPAN importer to use MetaCPAN v1 API.
...
* 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>
2017-06-07 15:06:34 +02:00
17a69cf623
import cran: Check if pkg-config is needed.
...
* guix/import/cran.scm (needs-pkg-config?): New procedure.
(description->package): Use it.
2017-05-16 21:43:35 +02:00
a0f43208cb
import cran: Refactor "needs-zlib?".
...
* guix/import/cran.scm (tarball-files-match-pattern?): New procedure.
(needs-zlib?): Implement in terms of "tarball-files-match-pattern?".
2017-05-16 21:43:15 +02:00
ff8c179ab6
import cran: Export package predicates.
...
* guix/import/cran.scm (cran-package?, bioconductor-package?,
bioconductor-data-package?, bioconductor-experiment-package?): Export
procedures.
2017-05-16 21:42:18 +02:00
daaa270ecc
import cran: Add predicate for Bioconductor experiment packages.
...
* guix/import/cran.scm (bioconductor-experiment-package?): New variable.
2017-05-16 21:40:39 +02:00
c9ffa91fd3
import cran: Exclude experiment packages in predicate "bioconductor-package?".
...
* guix/import/cran.scm (bioconductor-package?): Exclude experiment packages,
because they cannot be updated with the default bioconductor updater.
2017-05-16 21:40:03 +02:00
7c9fcb0825
import cran: Fetch DESCRIPTION files from Github mirror.
...
* 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.
2017-05-16 21:39:06 +02:00
22fc581db3
import: pypi: Robustify latest-release.
...
* guix/import/pypi.scm (latest-release): Check if pypi-fetch has
failed. If so return #f, else construct the <upstream-source>.
2017-05-13 12:40:20 +02:00
db427602d8
import: cran: Robustify cran-package?.
...
* 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.
2017-05-13 12:40:20 +02:00
69daee23af
ui: Rename '_' to 'G_'.
...
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`".
2017-05-03 16:16:17 +02:00
7c3e4660a5
import: Update Bioconductor release to 3.5.
...
* guix/import/cran.scm: Change Bioconductor release to 3.5.
2017-04-28 11:02:26 +02:00
5ae63362ae
import cran: Distinguish Bioconductor data packages.
...
* guix/import/cran.scm (bioconductor-package?): Exclude Bioconductor
data packages.
(bioconductor-data-package?): New procedure.
2017-04-05 18:38:51 +02:00
e1f02f92e9
Replace (compose not PROC) with simpler idioms.
...
* 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) ...)'.
2017-03-28 22:15:44 +02:00
2dca8b2d51
import cran: Automatically add gfortran and zlib when needed.
...
* guix/import/cran.scm (needs-fortran?, needs-zlib?): New procedures.
(description->package): Use them.
2017-03-28 15:37:47 +02:00
aeb64f3cb2
gnu: r: Do not build recommended packages.
...
* 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.
2017-03-17 10:14:02 +01:00
4c0c4db070
utils: Move base16 procedures to (guix base16).
...
* 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.
2017-03-16 22:50:14 +01:00
57075ade97
import: stackage: Avoid using (guix ui) in importer code.
...
* 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.
2017-02-14 08:38:45 +01:00
a4824c60ef
import: hackage: Handle unknown packages gracefully.
...
* guix/import/hackage.scm (hackage-fetch): Add 'guard'.
2017-02-09 19:36:08 +01:00
bc5844d149
import: Add stackage importer and updater.
...
* 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.
2017-02-09 19:36:08 +01:00
81e0bc1834
import: json: Explicitly ask for JSON data.
...
* guix/import/json.scm (json-fetch): Add #:headers to http-fetch call.
2017-02-09 19:36:04 +01:00
4eaac4b722
import: pypi: Correctly handle multiple-URL origins.
...
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.
2017-02-08 16:17:05 +01:00
f9704f179a
Add (guix memoization).
...
* 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.
2017-01-28 18:55:20 +01:00
21f4a7c116
import: github: Better tolerate unexpected file extensions.
...
* guix/import/github.scm (find-extension): Add ".tbz".
(updated-github-url): When 'find-extension' returns #f, use "" for EXT.
2017-01-28 00:38:20 +01:00
2f977d92d3
import: pypi: Don't add setuptools to propagated-inputs.
...
* guix/import/pypi.scm (compute-inputs): Don't add setuptools to the imported
package's propagated-inputs.
2017-01-26 13:44:31 +01:00
d18b79fed8
import: github: Catch HTTP 403 error during fetch.
...
* 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>
2017-01-19 17:17:16 +01:00
608a50b66c
http-client: Provide 'User-Agent' header by default.
...
* guix/http-client.scm (http-fetch): Add #:headers parameter and honor
it. Rename 'auth-header' to 'headers'.
* guix/import/github.scm (json-fetch*): Add comment about required
User-Agent.
2017-01-13 18:24:19 +01:00
4cd5ec801b
import: github: Fix regression on the /releases retrieval.
...
Fixes a regression introduced in
62bd24db39
2017-01-13 18:24:19 +01:00
f1d136957d
build-system: cargo: Handle Cargo.lock file not present.
...
* guix/build-system/cargo.scm (cargo-build): Add src output.
(private-keywords): Add #:outputs.
* guix/build/cargo-build-system.scm (configure): Use /share/rust-source
when replacing inputs.
(build, check): Don't do anything when there isn't a Cargo.lock file
present.
(install): Install sources to src output. When a Cargo.lock file is
present use cargo install to install binaries to out.
* guix/import/crate.scm (make-crate-sexp): Importer uses the src output
for crate inputs by default.
* guix/import/utils.scm (package-names->package-inputs, maybe-inputs,
maybe-native-inputs): Take an optional output argument.
* tests/crate.scm (crate->guix-package test): Update.
Problem reported by Francisco Gómez García <espectalll@kydara.com>.
2017-01-01 18:20:52 +01:00
f53a5514e0
import: crate: Provide a default home-page value.
...
* guix/import/crate.scm (make-crate-sexp): Provide a default home-page
value.
* tests/crate.scm (test-crate): Add repository field.
Problem reported by ng0 <ng0@libertad.pw>.
2017-01-01 18:12:06 +01:00
681a555b83
import: elpa: Import dependencies as propagated-inputs
...
* guix/import/elpa.scm (elpa-package->sexp): Import dependencies as
propagated-inputs.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-12-29 18:22:49 +01:00
36225d4fef
import: elpa: Fix call-with-downloaded-file
...
* guix/import/elpa.scm (call-with-downloaded-file): Make function behaviour
match documentation string.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-12-29 18:22:49 +01:00
62bd24db39
import: github: Use 'json-fetch'.
...
* guix/import/github.scm (json-fetch*): Remove.
(latest-released-version): Adjust accordingly.
2016-12-20 19:14:41 +01:00
4cb7786eff
import: pypi: Match new 'pypi-uri' domain in updater.
...
* guix/import/pypi.scm (pypi-package?): Match pypi.io domain.
2016-12-20 12:57:26 +01:00
fdbc84b056
import cran: Handle HTTP errors.
...
Fixes <http://bugs.gnu.org/23479 >.
* guix/import/cran.scm (fetch-description): Return #f in case of HTTP
errors.
2016-12-17 19:13:42 +01:00
94e907b962
import cran: Add recursive importer.
...
* guix/import/cran.scm (recursive-import): New variable.
(cran->guix-package): Memoize the procedure.
2016-12-17 19:12:55 +01:00
b26abe4f14
import cran: Ignore default R packages.
...
* guix/import/cran.scm (default-r-packages): New variable.
(description->package): Drop default R packages from list of inputs.
2016-12-17 15:56:48 +01:00
ad68f7fa58
import cran: description->package: Also return package dependencies.
...
* guix/import/cran.scm (description->package): Return package
dependencies in addition to generated package expression.
2016-12-17 15:56:48 +01:00
bfa0c752bc
import cran: Move guix-name to top-level.
...
* guix/import/cran.scm (guix-name): Move to top-level.
2016-12-17 15:56:48 +01:00
2e5f32ce1b
import cran: Remove more invalid characters from package names.
...
* guix/import/cran.scm (guix-name): Replace period and underscore with
dash; always prepend package names with "r-".
2016-12-17 15:56:47 +01:00
Arun Isaac