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
* guix/import/crate.scm (min-element, max-crate-version-of-semver,
nonyanked-crate-versions): New procedures.
(import-release)[version]: Update to the requested version or the newest
semver-compatible version.
Co-authored by David Elsing <david.elsing@posteo.net>
Change-Id: I72b081147c4eb9faf482f159b7145aaaf9f91f29
* doc/guix.texi (Invoking guix import): Mention '--allow-yanked'.
* guix/import/crate.scm (make-crate-sexp): Add yanked? argument. For
yanked packages, use the full version suffixed by "-yanked" for
generated variable names and add a comment and package property.
(crate->guix-package): Add allow-yanked? argument and if it is set to #t,
allow importing yanked crates if no other version matching the
requirements exists.
[find-package-version]: Packages previously marked as yanked are only
included if allow-yanked? is #t and then take the lowest priority.
[find-crate-version]: If allow-yanked? is #t, also consider yanked
versions with the lowest priority.
[dependency-name+version]: Rename to ...
[dependency-name+version+yanked] ...this. Honor allow-yanked? and choose
between an existing package and an upstream package. Exit with an error
message if no version fulfilling the requirement is found.
[version*]: Exit with an error message if the crate version is not found.
(cargo-recursive-import): Add allow-yanked? argument.
* guix/read-print.scm: Export <comment>.
* guix/scripts/import/crate.scm: Add "--allow-yanked".
* tests/crate.scm: Add test 'crate-recursive-import-only-yanked-available'.
[sort-map-dependencies]: Adjust accordingly.
[remove-yanked-info]: New variable.
Adjust test 'crate-recursive-import-honors-existing-packages'.
(test-bar-dependencies): Add yanked dev-dependencies.
(test-leaf-bob-crate): Add yanked versions.
(rust-leaf-bob-3.0.2-yanked): New variable.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
Change-Id: I175d89b39774e6b57dcd1f05bf68718d23866bb7
If --recursive-dev-dependencies is specified, development dependencies
are also included for all recursively imported packages.
* doc/guix.texi (Invoking guix import): Mention --recursive-dev-dependencies.
* guix/import/crate.scm (crate-recursive-import): Add
recursive-dev-dependencies? argument.
* guix/scripts/import/crate.scm (show-help, guix-import-crate): Add
"--recursive-dev-dependencies".
* tests/crate.scm: Test both #f and #t for #:recursive-dev-dependencies?
in the 'cargo-recursive-import' test.
(test-root-dependencies): Add intermediate-c as dev-dependency.
(test-intermediate-c-crate, test-intermediate-c-dependencies): New
variables.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
Change-Id: Iae89794681155d77f128733120e60f03bc297717
* guix/import/crate.scm (crate-recursive-import): Apply memoize outside the
lambda passed to recursive-import in order to actually use the memoization.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
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
* guix/import/go.scm (go-package, go.mod-go-version): New procedures.
(go-module->guix-package): Add the #:go keyword in the generated package
definition if the required go is newer than the default go.
* tests/go.scm (mock-http-get): Use gexps for package arguments.
Change-Id: I8d005740a442330ac307a40a53764c803ceffc4f
* guix/import/go.scm (parse-go.mod)[define-peg-patern require]: Adjust
the peg pattern to reject lines with the 'indirect' comment in them.
Change-Id: I9618bbaa1cb8c6549ced875e3c8d32afc72c3b9b
* guix/import/cabal.scm (eval-cabal)[eval]: Split imports to a
normalized list before mapping over it.
* tests/hackage.scm: Test it.
Change-Id: I39ece019251b6a23a937c8562d2d4a545a6bc7df
Signed-off-by: Lars-Dominik Braun <lars@6xq.net>
Cabal consideres lines to be part of a layout block if they are indented
at least one space more than the field line the block belongs to.
Previously Guix considered lines to be a part of the block if they were
indented at least as much as the first line in it.
This also makes a workaround that enabled if statements to have multiple
elses redundant and removes it.
Fixes: https://issues.guix.gnu.org/35743
* guix/import/cabal.scm (current-indentation*): Renamed from
current-indentation.
(previous-indentation, current-indentation): New variables.
(make-cabal-parser): Remove outdated comment.
[open]: Use previous-indentation + 1 instead of
current-indentation.
[elif-else]: Split to elif and else to allow only one ELSE in an if
statement.
(read-cabal)[parameterize]: Use current-indentation* and previous-indentation.
* tests/hackage.scm (hackage->guix-package test mixed layout): Expect to
pass.
Change-Id: I3a1495b1588a022fabbfe8dad9f3231e578af4f3
Signed-off-by: Lars-Dominik Braun <lars@6xq.net>
* guix/import/stackage.scm (lts-package-version): Call
stackage-package-version only when the package is found.
Change-Id: Ic8d7c1b7a42a9c1a6cbba567e148706507a53ee3
Signed-off-by: Lars-Dominik Braun <lars@6xq.net>
* guix/import/crate.scm (<crate-version>): Add yanked? field.
(crate->guix-package)[find-crate-version]: Remove versions which have
been yanked.
* tests/crate.scm: Adjust tests for new yanked? field.
Fixes <https://issues.guix.gnu.org/issue/66461>.
Reported by Simon Tournier <zimon.toutoune@gmail.com>.
* guix/import/opam.scm (opam->guix-package): Handle lists of licenses.
Signed-off-by: Simon Tournier <zimon.toutoune@gmail.com>
* guix/import/texlive.scm (linked-scripts): Also check for scripts with ".rb" extension.
(tlpdb->package): Add proper RUBY input for Ruby linked scripts.
Asymptote is provided in `asymptote' Guix package. OTOH, asy executable is
not built from TeX Live tree. Therefore, Asymptote package from TeX Live can be ignored.
* guix/import/texlive.scm (translate-depends): Ignore Asymptote package.
* guix/import/texlive.scm (linked-scripts): Also generate scripts from files
with ".tlu" and ".tcl" extensions.
(tlpdb->package): Add appropriate inputs when providing a TCL script.
* guix/import/texlive.scm (texlive-generic-locations): Add "scripts/context/"
since this location is split across multiple packages.
* guix/import/texlive.scm (files->locations): Only single out files from
generic locations, not their sub-directories. E.g., generic location
"scripts/context/lua/" should not fetch "scripts/context/lua/third/" files.
* gnu/packages/tex.scm (texlive-scripts): Include only core scripts along with
their man pages and their dependencies. Also patch them for use in Guix.
(texlive-bin): Simplify package.
[inputs]: Remove "texlive-extra-src" and "texlive-scripts" inputs. Remove
labels from other inputs.
[propagated-inputs]: Add TEXLIVE-SCRIPTS.
[arguments]: Use G-expressions.
<#:configure-flags>: Add "--disable-linked-scripts".
<#:phases>: Remove phases relative to scripts.
* guix/profiles.scm (texlive-font-maps): Fetch executables from both
TEXLIVE-SCRIPTS and TEXLIVE-BIN.
* guix/import/texlive.scm (tlpdb-file): Grab file from TEXLIVE-SCRIPTS instead
of TEXLIVE-BIN.
* guix/import/texlive.scm (tlpdb): Also retrieve so-called binfiles.
(formats):
(linked-scripts): New functions.
(tlpdb->package): Use new functions to set #:LINK-SCRIPTS argument and
possibly INPUTS.
* tests/texlive.scm (%fake-tlpdb): Add test data.
("texlive->guix-package, single script, no extension"):
("texlive->guix-package, multiple scripts, with extensions"):
("texlive->guix-package, script with associated input"): New tests.
* guix/import/texlive.scm (latex-bin-dependency-tree): New function.
(tlpdb->package): Set #:TEXLIVE-LATEX-BIN? when appropriate.
* tests/texlive.scm ("texlive->guix-package, lonely `hyphen-base' dependency
and ARCH"): Update test.
* guix/import/texlive.scm (tlpdb->package): Meta packages should use trivial
build system and an appropriate builder.
* tests/texlive.scm ("texlive->guix-package, meta-package"):
("texlive->guix-package, translate dependencies"): Update tests.
Herman Rimm
Ricardo Wurmus
Efraim Flashner
David Elsing
Nicolas Graves
Saku Laesvuori
Josselin Poiret
Nicolas Goaziou
walky_talky