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08 Jan 2024 16:07:30 +0100 From: Ludovic =?UTF-8?Q?Court=C3=A8s?= In-Reply-To: <878rnwuemq.fsf@elephly.net> (Ricardo Wurmus's message of "Wed, 10 Aug 2022 20:25:00 +0200") References: <87lesqmmrr.fsf@gmail.com> <87bktmtmol.fsf@elephly.net> <878rnwuemq.fsf@elephly.net> Date: Mon, 08 Jan 2024 16:07:28 +0100 Message-ID: <87y1cz6ez3.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: bug-guix@gnu.org List-Id: Bug reports for GNU Guix List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: bug-guix-bounces+larch=yhetil.org@gnu.org Sender: bug-guix-bounces+larch=yhetil.org@gnu.org X-Migadu-Country: US X-Migadu-Flow: FLOW_IN X-Migadu-Scanner: mx13.migadu.com X-Migadu-Spam-Score: -3.89 X-Spam-Score: -3.89 X-Migadu-Queue-Id: D91E2154C1 X-TUID: qY6jTqyFHC9N Hi, (Replying to a 1.5-year-old message=E2=80=A6) Ricardo Wurmus 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 =E2=80=9Curl-fetch=E2=80=9D to =E2= =80=9Cgit-fetch=E2=80=9D. > That=E2=80=99s because =E2=80=9Cpackage-update=E2=80=9D in (guix upstre= am) decides whether to > use package-update/url-fetch or package-update/git-fetch based on the > *current* package value=E2=80=99s origin fetch procedure. For the swit= ch 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 > instead of looking at the *current* package value. We=E2=80=99re only > accessing =E2=80=9Cpackage=E2=80=9D once in the url-fetch case, so mayb= e we can work > around this problem. Alternatively, how about writing a custom one-shot tool to change the =E2=80=98source=E2=80=99 field of all the Bioconductor packages to =E2=80= =98git-fetch=E2=80=99? 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 =E2=80=94 so we have to include the commit hash and a re= vision > counter in the version string. OK, sounds acceptable. > - the updater doesn=E2=80=99t work on version expressions like (git-versi= on > "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=E2=80=99s patch at ? > - =E2=80=9Cexperiment=E2=80=9D or =E2=80=9Cdata=E2=80=9D packages are not= kept in Git. They only exist > as volatile tarballs that will be overwritten. Thankfully, they don=E2= =80=99t > 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=E2=80=99ll prepare a series of patc= hes > next. I don=E2=80=99t think it happened but it=E2=80=99d still be nice. :-) Thanks, Ludo=E2=80=99.