From: "Ludovic Courtès" <ludovic.courtes@inria.fr>
To: Ricardo Wurmus <rekado@elephly.net>
Cc: Timothy Sample <samplet@ngyro.com>,
39885@debbugs.gnu.org, me@tobias.gr,
zimoun <zimon.toutoune@gmail.com>
Subject: bug#39885: Bioconductor URI, fallback and time-machine
Date: Mon, 08 Jan 2024 16:07:28 +0100 [thread overview]
Message-ID: <87y1cz6ez3.fsf@gnu.org> (raw)
In-Reply-To: <878rnwuemq.fsf@elephly.net> (Ricardo Wurmus's message of "Wed, 10 Aug 2022 20:25:00 +0200")
Hi,
(Replying to a 1.5-year-old message…)
Ricardo Wurmus <rekado@elephly.net> skribis:
> I have finally taken the time to review this and implement a first draft
> of a change to the bioconductor importer and updater.
>
> There are some limitations:
>
> - 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.
>
> Perhaps we could operate on the url included in the <upstream-source>
> instead of looking at the *current* package value. We’re only
> accessing “package” once in the url-fetch case, so maybe we can work
> around this problem.
Alternatively, how about writing a custom one-shot tool to change the
‘source’ field of all the Bioconductor packages to ‘git-fetch’?
It may be easier than adjusting (guix upstream) to cater to this
probably unusual case.
> - 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.
OK, sounds acceptable.
> - 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.
Maybe we can build upon Maxime’s patch at
<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.
>
> - the above exception means that we need to litter the importer and
> updater code with extra checks.
>
> With all these notes out of the way I’ll prepare a series of patches
> next.
I don’t think it happened but it’d still be nice. :-)
Thanks,
Ludo’.
next prev parent reply other threads:[~2024-01-08 15:08 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
2024-01-08 15:07 ` Ludovic Courtès [this message]
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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