GNU bug report logs - #39885
Bioconductor URI, fallback and time-machine

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From: zimoun <zimon.toutoune <at> gmail.com>
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: Timothy Sample <samplet <at> ngyro.com>, 39885 <at> debbugs.gnu.org, me <at> tobias.gr
Subject: bug#39885: Bioconductor URI, fallback and time-machine
Date: Fri, 09 Sep 2022 19:23:12 +0200

Hi Ricardo,

I am late.  This message landed when I was traveling for holidays. :-)

On Wed, 10 Aug 2022 at 20:25, Ricardo Wurmus <rekado <at> elephly.net> wrote:

> - we cannot use the updater to go from “url-fetch” to “git-fetch”.
>   That’s because “package-update” in (guix upstream) decides whether to
>   use package-update/url-fetch or package-update/git-fetch based on the
>   *current* package value’s origin fetch procedure.  For the switch we
>   can hack around this (adding an exception for bioconductor packages),
>   but there is no pretty way to do this in a generic fashion that could
>   be committed.

It appears to me acceptable to have an exception.  Or even to do it just
once as a big replacement of Bioconductor packages.

> - the repositories at https://git.bioconductor.org/package/NAME do not
>   tag package versions.  The only method of organization is branches
>   that are named after *Bioconductor releases* (not package releases),
>   e.g. RELEASE_3_15.  We can only determine the package version by
>   reading its DESCRIPTION file or by looking up the version index for
>   all Bioconductor packages (we do that already).  This means that there
>   could be different commits for the same package version in the same
>   release branch — so we have to include the commit hash and a revision
>   counter in the version string.

This is the most annoying part.  Indeed, when I check out some
Bioconductor Git repositories, I am always confused by their Git
structure.

From my understanding, the tarball you fetch from bioconductor.org has
the same content than the commit tagged “Bioconductor release”
(RELEASE_X_Y).  The content of the upstream release can mismatch the
content of the Bioconductor tarball release.

I do not know how it would be complicated or inaccurate to consider the
package version from the Bioconductor index and assign this version to
the commit tagged RELEASE_X_Y.  This commit would appear in the Guix
package definition though.  Or maybe we transparently could RELEASE_X_Y
to determine this commit.


> - the updater doesn’t work on version expressions like (git-version
>   "1.12" revision commit).  It expects to be able to replace literal
>   strings.  Because of that my changes let the importer generate a
>   string literal such as "1.12-0.cafebab" without a let-bound commit
>   string.

Maxime pointed patch#53144 [1] but I have not looked at it yet.


1: <https://issues.guix.gnu.org/53144#13>


> - “experiment” or “data” packages are not kept in Git.  They only exist
>   as volatile tarballs that will be overwritten.  Thankfully, they don’t
>   change all that often, so they have a good chance of making it into
>   our archives.

That’s an interesting question for Disarchive and Software Heritage.


Cheers,
simon

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