From: zimoun <zimon.toutoune@gmail.com>
To: Ricardo Wurmus <rekado@elephly.net>
Cc: Timothy Sample <samplet@ngyro.com>, 39885@debbugs.gnu.org, me@tobias.gr
Subject: bug#39885: Bioconductor URI, fallback and time-machine
Date: Fri, 09 Sep 2022 19:23:12 +0200 [thread overview]
Message-ID: <865yhwpim7.fsf@gmail.com> (raw)
In-Reply-To: <878rnwuemq.fsf@elephly.net>
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@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
next prev parent reply other threads:[~2022-09-09 17:32 UTC|newest]
Thread overview: 31+ messages / expand[flat|nested] mbox.gz Atom feed top
2020-03-03 15:59 bug#39885: Bioconductor URI, fallback and time-machine zimoun
2020-03-23 21:20 ` Ricardo Wurmus
2020-05-21 23:29 ` zimoun
2020-06-24 11:07 ` zimoun
2020-06-28 20:14 ` Ludovic Courtès
2020-06-29 17:36 ` zimoun
2020-06-29 20:42 ` Ludovic Courtès
2020-11-19 14:22 ` zimoun
2021-11-22 19:48 ` zimoun
2022-07-18 16:03 ` zimoun
2022-07-18 16:21 ` Ricardo Wurmus
2022-08-10 18:25 ` Ricardo Wurmus
2022-08-10 19:44 ` Maxime Devos
2022-08-10 19:48 ` Maxime Devos
2022-09-09 17:23 ` zimoun [this message]
2024-01-08 15:07 ` Ludovic Courtès
2024-01-08 15:34 ` Ricardo Wurmus
2024-01-11 16:11 ` Simon Tournier
2023-12-22 13:40 ` bug#39885: Bioconductor tarballs are not archived Ludovic Courtès
2024-01-08 9:09 ` Simon Tournier
2024-01-08 15:02 ` Ludovic Courtès
2024-01-10 12:41 ` Ricardo Wurmus
2024-01-10 15:23 ` Simon Tournier
2024-01-19 15:46 ` Timothy Sample
2024-01-23 9:10 ` Ludovic Courtès
2024-02-14 15:23 ` Simon Tournier
2024-02-16 16:14 ` Timothy Sample
2024-02-19 16:50 ` Simon Tournier
2024-02-21 18:16 ` Timothy Sample
2023-12-22 20:57 ` bug#39885: Bioconductor URI, fallback and time-machine Ludovic Courtès
2024-01-02 9:20 ` Simon Tournier
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