Ricardo Wurmus <rek...@elephly.net> writes:
> zimoun <zimon.touto...@gmail.com> writes: > >> At the cost of more bandwidth, we could switch from url-fetch to >> git-fetch. > > Let’s do it! I’m tired of Bioconductor archive shenanigans messing with > package availability. 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. - 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. - 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. - “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. -- Ricardo
