Re: [PATCH] Add Bioconductor importer and updater.

[Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>]

Ludovic Courtès <ludo@gnu.org> writes:

> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
>
>> From 8829683fffc03dec7f2faecea75cdd7831ce1741 Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
>> Date: Wed, 16 Dec 2015 14:45:28 +0100
>> Subject: [PATCH] import: Add Bioconductor importer and updater.
>>
>> * guix/import/cran.scm (bioconductor->guix-package,
>> %bioconductor-updater, latest-bioconductor-release,
>> bioconductor-package?): New procedures.
>> (%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/bioconductor.scm: New file.
>> * guix/scripts/import.scm (importers): Add "bioconductor" importers.
>> * guix/scripts/refresh.scm (%updaters): Add "%bioconductor-updater".
>> * doc/guix.texi: Document Bioconductor importer and updater.
>
> [...]
>
>>  @item cran
>>  the updater for @uref{http://cran.r-project.org/, CRAN} packages;
>> +@item bioconductor
>> +the updater for @uref{http://www.bioconductor.org/, Bioconductor} packages;
>
> “R packages”

Okay.

>> -       (properties ,`(,'quasiquote ((,'upstream-name . ,name))))
>> +       (properties ,`(,'quasiquote ((,'upstream-name . ,name)
>> +                                    (,'r-repository  . ,repository))))
>
> What about adding ‘upstream-name’ only when the upstream name is
> different from the Guix name minus “r-”?

Good idea.

> Regarding ‘r-repository’, I guess it can be inferred from the source
> URL?

[...]

> We could check whether the source URL starts with “mirror://cran”, no?
> And forget about the ‘r-repository’ property?

I think so.  I’ve just updated the patches.

>> +++ b/guix/scripts/import/bioconductor.scm
>
> I was wondering whether this should be a separate script or not.  A
> precedent would be the ELPA importer, which takes a repository name as
> an argument.  We could have done the same with the CRAN importer here.

I would prefer not to have a separate script, because there’s so much
duplication.  I’ll look at the ELPA importer for inspiration.

Should the CRAN importer have its name changed, though?

~~ Ricardo