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?.
There was an inconsistency between tarball-needs-fortran? and
directory-needs-fortran?.
* guix/import/cran.scm (directory-needs-fortran?): Match .f files too.
Extracting the source tarball multiple times is very slow and a
speedup of >2x (without network I/O) can be achieved by coalescing all
NEEDS-X? functions into a single one, which extracts a tarball only once.
* guix/import/cran.scm (tarball-needs-fortran?): Remove unused function.
(needs-fortran?): Ditto.
(tarball-files-match-pattern?): Ditto.
(tarball-needs-zlib?): Ditto.
(needs-zlib?): Ditto.
(tarball-needs-pkg-config?): Ditto.
(needs-pkg-config?): Ditto.
(source-dir->dependencies): New function.
(source->dependencies): New function.
(description->package): Use it.
Assumes we use package variable names, not package specification names.
* guix/import/cran.scm (invalid-packages): Add more invalid names.
(transform-sysname): Transform more package names.
These importer don't support importing a specific version, thus the updater
does neither. Issue an error message in case version is given.
* guix/import/cpan.scm (latest-release),
guix/import/elpa.scm (latest-release),
guix/import/hackage.scm (latest-release),
guix/import/minetest.scm (latest-minetest-release),
guix/import/opam.scm (latest-release): Add #:version argument,
issue error if version is given.
* guix/import/cran.scm (latest-cran-release): Same.
(latest-bioconductor-release) Same. <version>: rename to <latest-version>.
* guix/import/stackage.scm (latest-lts-release): For each generated updater,
add #:version argument and issue error if version is given.
The next commits will make the functions, which are currently importing the
latest version of a package, change into importing the latest or a given
version of the package (for those updaters supporting specifying a version).
Thus the name ‘latest‘ is no longer appropriate.
* guix/upstream.scm (upstream-updater) Rename field [latest] to
[import]. (lookup-updater, package-latest-release) Adjust fieldname
accordingly.
* guix/gnu-maintenance.scm (%gnu-updater, %gnu-ftp-updater,
%savannah-updater, %sourceforge-updater, %xorg-updater,
%kernel.org-updater, %generic-html-updater),
guix/import/cpan.scm (%cpan-updater),
guix/import/cran.scm (%cran-updater, %bioconductor-updater),
guix/import/crate.scm (%crate-updater),
guix/import/egg.scm (%egg-updater),
guix/import/elpa.scm (%elpa-updater),
guix/import/gem.scm (%gem-updater),
guix/import/git.scm (%generic-git-updater),
guix/import/github.scm (%github-updater),
guix/import/gnome.scm (%gnome-updater),
guix/import/hackage.scm (%hackage-updater),
guix/import/hexpm.scm (%hexpm-updater),
guix/import/kde.scm (%kde-updater),
guix/import/launchpad.scm (%launchpad-updater),
guix/import/minetest.scm (%minetest-updater),
guix/import/opam.scm (%opam-updater),
guix/import/pypi.scm (%pypi-updater),
guix/import/stackage.scm (%stackage-updater),
tests/import-github.scm (found-sexp)
tests/transformations.scm ("options->transformation, with-latest"):
Adjust fieldname accordingly.
* guix/import/cran.scm (string->license): Add more match clauses.
(string->licenses): Split license conjunctions at "|" and apply
string->license on each license.
(description->package): Use string->licenses.
