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
576eda6d02
import cran: Handle BSD licenses with LICENSE file.
...
* guix/import/cran.scm (string->license): Add cases for BSD licenses
with LICENSE file.
2016-12-17 15:56:47 +01:00
741d68c20d
import cran: Translate MIT to the Expat license.
...
* guix/import/cran.scm (string->license): Translate "MIT" license to
Expat license.
2016-12-17 15:56:47 +01:00
13f54d081b
import cran: Do not use "or later" licenses by default.
...
* guix/import/cran.scm (string->license): Use exact license versions.
2016-12-17 15:56:39 +01:00
8ac5298786
import: Add updater for rust crates.
...
* guix/import/crate.scm (crate-package?, latest-release,
%crate-updater): New variables.
* guix/scripts/refresh.scm (%updaters): Add crate updater.
* doc/guix.texi: Add crate updater to table.
2016-12-14 16:30:42 +01:00
3e0c036584
import: Add importer for rust crates.
...
* guix/import/crate.scm: New file.
* guix/scripts/import/crate.scm: New file.
* guix/scripts/import.scm (importers): Add crate importer.
* tests/crate.scm: New file.
* doc/guix.texi: Add crate importer to table.
* Makefile.am (MODULES, SCM_TESTS): Add files.
2016-12-14 16:30:42 +01:00
bb3f36ed4c
import: utils: Add some utilities.
...
* guix/import/utils.scm (maybe-inputs, maybe-native-inputs,
package->definition): New variables.
2016-12-14 16:30:42 +01:00
ff55fe5599
import: cpan: Add updater.
...
* guix/import/cpan.scm (module->dist-name): Fetch the field of interest.
(cpan-fetch): Accept release name rather than module name.
(fix-source-url): Rename to ...
(cpan-source-url): ... this. Take metadata as parameter.
(package->upstream-name, cpan-version, cpan-package?, latest-release):
New procedures.
(cpan-module->sexp): Use cpan-version and cpan-source-url.
(%cpan-updater): New variable.
* guix/scripts/refresh.scm (%updaters): Add %CPAN-UPDATER.
2016-12-12 22:22:33 -06:00
d391ad57d6
import: cpan: Move core-module? to top-level.
...
* guix/import/cpan.scm (cpan-module->sexp): Move local core-module?
procedure to ...
(core-module?): ... here.
2016-12-12 22:22:33 -06:00
63773200d7
import: json: Silence json-fetch output.
...
* guix/import/json.scm (json-fetch): Use http-fetch instead of url-fetch
to avoid writing to stdout and a temporary file for each invocation.
* guix/import/gem.scm (rubygems-fetch): Do not redirect json-fetch
output to /dev/null.
* guix/import/pypi.scm (pypi-fetch): Likewise.
2016-12-12 22:22:02 -06:00
c91b368e96
import/cpan: Maybe coerce version to string.
...
* guix/import/cpan.scm (cpan-module->sexp) <version>: Test if version in
meta is string or number. If it is number, coerce to string.
2016-11-14 00:06:09 +01:00
e3100110ce
import: cran: Fix off-by-one error.
...
* guix/import/cran.scm (package->upstream-name): Do not include leading
slash in upstream name URL.
2016-11-03 16:03:28 +01:00
a98470b5be
import cran: Use URL for Bioconductor 3.4.
...
* guix/import/cran.scm (%bioconductor-svn-url): Update to release URL
for version 3.4.
2016-10-26 09:28:06 +02:00
b5c347ad3d
import: pypi: All inputs are propagated-inputs by default.
...
* guix/import/pypi.scm (maybe-inputs): Return inputs as
"propagated-inputs".
2016-10-23 19:23:14 +02:00
b37e1e6428
import: utils: Remove dependency on (json) module.
...
This fixes a regression introduced by commit
fbe9c10128
2016-10-16 19:19:31 +03:00
523b77faef
import: github: Add .love extension.
...
* guix/import/github.scm (find-extension): Add '.love' extension to the
list of extensions checked.
2016-10-10 11:52:03 +03:00
11e296ef30
import: utils: Refactor license->symbol.
...
* guix/import/utils.scm (license->symbol): Work for all licenses.
* tests/import-utils.scm (license->symbol): Add test.
2016-09-28 13:17:15 +02:00
59b2034787
import: utils: Add spdx-string->license.
...
* guix/import/utils.scm (spdx-string->license): New variable.
* guix/licenses.scm (agpl1, fdl1.2+): New variables.
2016-09-28 13:15:31 +02:00
263ac57fc2
import: Move string->license to importers.
...
* guix/import/gem.scm (string->license): Move from (guix import utils).
* guix/import/pypi.scm (string->license): Move from (guix import utils).
2016-09-28 12:47:29 +02:00
fbe9c10128
import: Reorder imports in (guix import utils).
...
* guix/import/utils.scm (define-module): Reorder imports alphabetically.
2016-09-28 12:47:10 +02:00
18f7473504
import: hackage: Default to https urls.
...
* guix/import/hackage.scm (hackage-source-url, hackage-cabal-url): Use https
for hackage.haskell.org.
2016-08-30 22:38:16 +03:00
7a62263ee5
import: cpan: Use tls to query api.metacpan.org.
...
* guix/import/cpan.scm (module->dist-name, cpan-fetch-module): Use tls
for api.metacpan.org.
Signed-off-by: Eric Bavier <bavier@member.fsf.org>
2016-08-30 13:21:07 -05:00
a34b236c17
import: Importers return prefixed licenses.
...
* guix/import/utils.scm
(define-module): Import licenses with license: prefix.
(string->licenses): Use prefixed licenses.
(license->symbol): Return symbols with the prefix license:.
* guix/tests/pypi.scm (pypi->guix-package): Update test cases.
* guix/tests/gem.scm (gem->guix-package): Update test case.
2016-08-28 14:04:50 +02:00
8173ceee1f
import: pypi: Correctly handle new-style URLs.
...
Fixes <http://bugs.gnu.org/23997 >.
* guix/import/pypi.scm (guix-package->pypi-name): Rewrite using
'basename' and 'hyphen-package-name->name+version'.
* tests/pypi.scm ("guix-package->pypi-name, old URL style")
("guix-package->pypi-name, new URL style"): New tests.
2016-07-26 17:49:34 +02:00
Ludovic Courtès