With SYSTEM* we see a file descriptor leak. See the discussion at
<https://codeberg.org/guix-science/guix-cran-scripts/issues/5>. There is no
such leak when using SPAWN.
* guix/import/cran.scm (fetch-description-from-tarball, source->dependencies):
Use SPAWN instead of SYSTEM*.
Change-Id: Idb13f775317e6d5d426f8675e169f0ebbe246fe2
* guix/import/cran.scm (cran-package-propagated-inputs): Replace lset-union
with actual sets, because the former does not remove duplicates of its
arguments.
Change-Id: I84c57c2426aef656bdd20e30e65b510e27603a64
* guix/import/cran.scm (import-pattern): Also match on single quotes.
(needed-vignettes-inputs-in-directory): Use EXTRACT-IMPORTS.
* tests/import/cran.scm: Add test.
Change-Id: Ie69027992519bd8d886860346f4a359514d8e822
* guix/import/cran.scm (maybe-arguments): Do not overwrite %STANDARD-PHASES
with the definition from MINIFY-BUILD-SYSTEM.
Change-Id: I6e4cd64575ea029665db0d3b3aecdea38c41fe9d
* guix/build-system/r.scm (bioconductor-uri): Update to 3.22.
* guix/import/cran.scm (%bioconductor-version): Set to 3.22.
Change-Id: I53c6b0d1ddc37faad90492103b7d02c210f945d7
* guix/build-system/r.scm (bioconductor-uri): Update version in URI to 3.21.
* guix/import/cran.scm (%bioconductor-version): Update to 3.21.
Change-Id: I216576d42d013a00310cc2230e89567ffb1487a2
* guix/import/utils.scm (find-version): New procedure.
* guix/scripts/refresh.scm (<update-spec>) [partial?]: New field.
(update-spec-partial?): New accessor.
(update-spec): Add a PARTIAL? optional argument.
(update-specification->update-spec) <update-spec>: Call with its new PARTIAL?
optional argument when FALLBACK-VERSION is provided, i.e. when
'--target-version' was used.
(update-package): Remove the PACKAGE and VERSION positional arguments, and
replace them with UPDATE-SPEC. Update doc. Call `package-update' with its
new #:partial-version? argument.
(check-for-package-update) <package-latest-release>: Pass the new
#:partial-version? argument to it.
(guix-refresh) <update-package>: Adjust call accordingly.
(show-help): Udate doc.
* guix/upstream.scm (package-latest-release): Add #:partial-version? argument,
and apply it to the importer call.
(package-update): Add #:partial-version?> argument. Update doc. Pass it to
the `package-latest-release' call.
* guix/gnu-maintenance.scm (rewrite-url): Add #:partial-version? argument.
Update doc. Crawl URL for newer compatible versions when provided.
(import-html-release): Add #:partial-version? argument, and pass it to the
`rewrite-url' call. Use `find-version' to find the best version.
(import-release, import-ftp-release, import-gnu-release)
(import-release*): Add #:partial-version? argument and honor it.
(import-html-updatable-release): Add #:partial-version? argument, and pass it
to the `import-html-release' call.
* guix/import/gnome.scm (import-gnome-release)
<#:partial-version?>: Add new argument and honor it.
* guix/import/texlive.scm (latest-texlive-tag): Rename to...
(texlive-tags): ... this, and have it return all tags.
(texlive->guix-package): Adjust accordingly.
(latest-release): Add a #:partial-version? argument. Update doc.
* guix/import/stackage.scm (latest-lts-release): New #:partial-version?
argument.
* guix/import/pypi.scm (import-release): New #:partial-version? argument; pass
it to `pypi-package->upstream-source'.
* guix/import/opam.scm (latest-release): New #:partial-version? argument.
* guix/import/minetest.scm (latest-minetest-release): New #:partial-version?
argument.
(pypi-package->upstream-source): New #:partial-version? argument. Update doc.
* guix/import/launchpad.scm (latest-released-version): Rename to...
(release-versions): ... this, making it return all versions.
(import-release) <#:partial-version?>: New argument.
* guix/import/kde.scm (import-kde-release)
<#:partial-version?>: New argument. Update doc. Refactor to honor argument.
* guix/import/hexpm.scm (lookup-hexpm): Update doc.
(hexpm-latest-release): Rename to...
(hexpm-releases): ... this; return all release strings.
(hexpm->guix-package): Adjust accordingly.
(import-release): Add and honor a #:partial-version? argument. Update doc.
* guix/import/hackage.scm (import-release): New #:partial-version? argument.
* guix/import/cpan.scm (latest-release): New #:partial-version? argument.
* guix/import/crate.scm (max-crate-version-of-semver): Improve doc.
(import-release): Add a #:partial-version? argument and honor it.
* guix/import/egg.scm (find-latest-version): Rename to...
(get-versions): ... this, returning all versions.
(egg-metadata): Adjust accordingly.
(egg->guix-package): Likewise.
(import-release): Add a new #:partial-version? argument and honor it.
* guix/import/elpa.scm (latest-release): New #:partial-version? argument.
* guix/import/gem.scm (get-versions): New procedure.
(import-release): Add a new #:partial-version? argument and honor it.
* guix/import/git.scm (version-mapping): Update doc; streamline a bit.
(latest-tag): Rename to...
(get-tags): ... this, dropping the #:version keyword and returning the complete
tags alist. Update doc.
(latest-git-tag-version): Rename to...
(get-package-tags): ... this, returning the complete tags alist of the
package. Update doc.
(import-git-release): Add a new #:partial-version? argument and honor it.
Update doc.
* guix/import/github.scm (latest-released-version): Rename to...
(get-package-tags): ... this, returning all tags. Update doc.
(import-release): Add a new #:partial-version? argument and honor it.
* guix/import/cran.scm (latest-cran-release)
(latest-bioconductor-release): Add #:partial-version? argument.
* guix/import/composer.scm (latest-version): Delete procedure.
(composer-fetch): Add #:partial-version? keyword and honor it. Update doc.
(import-release): Likewise.
* guix/import/test.scm (import-release): Add #:partial-version? argument.
* tests/guix-refresh.sh: Add test.
* tests/gem.scm (test-foo-versions-json): New variable.
(package-latest-release): Mock new URL.
* tests/import-git.scm (latest-git-tag-version): New procedure.
* tests/gnu-maintenance.scm (libuv-dist-html)
(libuv-dist-1.46.0-html, libuv-dist-1.44.2-html)
(libuv-html-data): New variables.
(mock-http-fetch/cached): New procedure.
("rewrite-url, without to-version"): Rewrite using the above.
("rewrite-url, partial to-version"): New test.
* doc/guix.texi <"Invoking guix refresh">: Update doc.
Series-to: 75871@debbugs.gnu.org
Change-Id: I092a58b57ac42e54a2fa55e7761e8c6993af8ad4
* guix/import/cran.scm (import-pattern): Comment; capture direct namespace
imports as well as silent imports.
Change-Id: Ia54035d6f230d695aa950adb3e691cbce4f2d416
* guix/import/cran.scm (description->package): Return all R packages, not just
all propagated inputs.
Change-Id: Id1c6ded681e25e29dcef8f8aed1a6be47b36c4a0
Fixes <https://issues.guix.gnu.org/44256>.
* guix/import/cran.scm (cran-package-inputs): Avoid passing "#:method #f", so
that there is only one memoization key in the default case.
(fetch-description): Use the full list returned by BIOCONDUCTOR-URI.
Change-Id: I532812b14f4e4d9542bfb9248555be1b09f7d92f
* guix/import/cran.scm (import-pattern): New variable.
(needed-test-inputs-in-directory, needed-vignettes-inputs-in-directory): New
procedures.
(source-dir->dependencies): Add native inputs from result of
NEEDED-TEST-INPUTS-IN-DIRECTORY and NEEDED-VIGNETTES-INPUTS-IN-DIRECTORY.
(cran-package-inputs): Clean up and delete duplicates from source-derived
inputs.
Change-Id: Id139c144fc6e866e4aaf8f05201b0d2687744fb6
* guix/import/cran.scm (phases-for-inputs): Also add 'set-HOME phase when
R.rsp is among the inputs.
Change-Id: Ib00d981cc623da8ec487086913570f937a76aeb5
* guix/import/cran.scm (description->package): Do not process license as
string when it's missing.
Change-Id: I415fa6be17631f83c2aa7a213683fdf90a868e96
* guix/build-system/r.scm (bioconductor-uri): Use 3.19 URL.
* guix/import/cran.scm (%bioconductor-version): Set to 3.19.
Change-Id: I7a2c4dfcdb2c4cdfef581f823d87e73acc163549
Reported by Alexander Blume at
<https://github.com/BIMSBbioinfo/guix.install/issues/4>.
* guix/import/cran.scm (format-inputs): Use UPSTREAM-INPUT-DOWNSTREAM-NAME
when %INPUT-STYLE is set to 'SPECIFICATION.
Change-Id: I2f0963af197896aafd613b253d8712e41a716e52
* guix/import/cran.scm (phases-for-inputs): Add 'set-HOME phase when
ExperimentHub is among inputs.
Change-Id: Ie3a2443934704eed8694a76a651b806209722421
* guix/import/cran.scm (latest-bioconductor-release): Determine package type
and pass it to LATEST-BIOCONDUCTOR-PACKAGE-VERSION and BIOCONDUCTOR-URI.
(%bioconductor-updater): Compose all bioconductor predicates.
Change-Id: Icef3ae05e28ed0f2796d9abf90e51821d2dfcc4c
* guix/import/cran.scm (phases-for-inputs, maybe-arguments): New procedures.
(description->package): Splice in result of MAYBE-ARGUMENTS.
Change-Id: I578e1903f37c91bf865f0be49b04187ec372ed05
These were encountered in a mass import of Bioconductor packages.
* guix/import/cran.scm (invalid-packages): Add "rtools".
(transform-sysname): Add aliases for Python and bioinformatics packages.
Change-Id: I97e13cee10c2ee85d4b9296d91afccbdbcec4946
This fixes a regression introduced in commit
e6223017d9 causing the selected input style to
be ignored.
* guix/import/cran.scm (format-inputs): New procedure.
(maybe-inputs): Use it.
Change-Id: I0d36f972fcb9888ed2be4ec9360bbcab13c25c5d
This allows users of this module to provide e.g. caching alternatives to the
download and fetch procedures.
* guix/import/cran.scm (%bioconductor-version, download, fetch-description):
Make these variables public.
Change-Id: I9ce14db9be9b8b3314b06fa9eb50a4e24c5dd718
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>.
This was obtained by setting up this environment:
guix shell -D guix --with-input=guile@3.0.9=guile-next \
--with-commit=guile-next=e2ed33ef0445c867fe56c247054aa67e834861f2
-- make -j5
then adding 'unused-module' to (@@ (guix build compiler) %warnings),
building, and checking all the "unused module" warnings and removing
those that were definitely unused.
* guix/import/cran.scm (needs-knitr?): Remove procedure.
(vignette-builders): New procedure.
(description->package): Use vignette-builders instead of needs-knitr?.
Ricardo Wurmus