Reported by Leo Famulari <leo@famulari.name>
and Ben Woodcroft <b.woodcroft@uq.edu.au>
at <http://bugs.gnu.org/22752>.
* guix/scripts/refresh.scm: Remove unneeded and harmful import of (guix
import gem).
* guix/import/cran.scm (%bioconductor-updater,
latest-bioconductor-release, bioconductor-package?): New procedures.
(cran->guix-package): Support repositories other than CRAN.
(%bioconductor-url, %bioconductor-svn-url): New variables.
(description->package): Update signature to distinguish between packages
from different repositories.
(latest-release): Rename procedure ...
(latest-cran-release): ... to this.
(cran-package?): Do not assume all R packages are available on CRAN.
* tests/cran.scm: Update tests.
* guix/scripts/import/cran.scm: Add "--archive" option and default to
CRAN.
* guix/scripts/refresh.scm (%updaters): Add "%bioconductor-updater".
* doc/guix.texi: Document Bioconductor importer and updater.
This is a followup to b68d2db, which added a check for updaters at
macro-expansion time. The problem is that, when running 'guix pull',
Guile-JSON is found, so the PyPi updater (say) is added to %UPDATERS,
but then at run time Guile-JSON might be missing.
Reported by orbea on #guix.
* guix/scripts/refresh.scm (maybe-updater): Rewrite as 'syntax-rules'.
Produce code that checks conditions at run time.
(list-updaters): Update docstring.
Reported by Sleep_Walker and Mathieu Lirzin <mthl@gnu.org>.
* guix/scripts/refresh.scm (maybe-updater, list-updaters): New macros.
(%updaters): Use 'list-updaters' instead of 'list'. Make
%PYPI-UPDATER conditional.
* guix/scripts/refresh.scm (%options, show-help): Add --type.
(lookup-updater): New procedure.
(update-package): Add 'updaters' parameter and honor it.
(guix-refresh)[options->updaters]: New procedure.
Use it, and honor --type.
* guix/gnu-maintenance.scm (<gnu-release>): Remove.
(coalesce-releases): Move to upstream.scm. Rename to
'coalesce-sources'; adjust callers.
(releases, latest-release): Return <upstream-source> objects instead
of <gnu-release> objects.
(latest-release*, non-emacs-gnu-package?): New procedures.
(gnu-release-archive-types): Remove.
(%gnu-updater): New variable.
(package-update-path, download-tarball, package-update,
update-package-source): Move to...
* guix/upstream.scm: ... here. New file.
* Makefile.am (MODULES): Add it.
* po/guix/POTFILES.in: Replace gnu-maintenance.scm with upstream.scm.
* guix/scripts/refresh.scm (%updaters): New variable.
(update-package): Adjust to new 'package-update' interface.
(guix-refresh): Adjust to new 'package-update-path'. Remove
'false-if-exception' around it.
* guix/scripts/refresh.scm (guix-refresh): Use 'specification->package'
instead of 'find-packages-by-name'. This allows users to specify
things like "qt-4.8.6".
* doc/guix.texi (Invoking guix refresh): Add an example.
* guix/derivations.scm (derivation-hash): Add comment as to why we keep
the plain `sha256' call.
* guix/scripts/download.scm (guix-download): Use `port-sha256' instead
of (compose sha256 get-bytevector-all).
* guix/scripts/refresh.scm (update-package): Likewise.
* guix/gnu-maintenance.scm (download-tarball): Add a 'key-download'
keyword argument and pass it to 'gnupg-verify*'. Make
'archive-type' a keyword argument.
(package-update): Add a 'key-download' keyword argument. Pass
'archive-type' and 'key-download' keyword arguments to
'download-tarball'.
* guix/gnupg.scm: Import (ice-9 i18n) and (guix ui).
(gnupg-verify*): Add a 'key-download' keyword argument and adjust
'gnupg-verify*' to use it. Make 'server' a keyword argument.
* guix/scripts/refresh.scm (show-help, %options): Add and document
'--key-download'.
(update-package): Add a 'key-download' keyword argument and pass it
to 'package-update'.
(guix-refresh): Pass 'key-download' to 'update-package'. Limit
lines to a maximum of 79 characters.
* guix/scripts/refresh.scm (%options): Add `--key-server' and `--gpg'.
(show-help): Update accordingly.
(update-package): New procedure, formerly in `guix-refresh'.
(guix-refresh): Use it. Parameterize `%openpgp-key-server' and
`%gpg-command'.
* guix/scripts/refresh.scm (guix-refresh): When updating a source file,
gracefully handle the case where TARBALL is #f.
Reported by Nikita Karetnikov <nikita@karetnikov.org>.
* guix/scripts/refresh.scm (%options): Add `--select'.
(show-help): Likewise. Augment initial help text.
(guix-refresh)[core-package?]: New procedure.
Use it when selecting packages.
Ludovic Courtès