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{bioinformatics,bioconductor}.scm cleaning?
From: |
zimoun |
Subject: |
{bioinformatics,bioconductor}.scm cleaning? |
Date: |
Wed, 11 Sep 2019 18:10:05 +0200 |
Dear,
Based on the (old) discussion [1] I would like to address this move.
[1] https://lists.gnu.org/archive/html/guix-devel/2018-12/msg00266.html
However, there is already incoherence in bioconductor.scm. :-)
First, the commit c586f427b4 changes `bioconductor-uri` which now
takes optional package type. Thanks Ricardo. :-)
The use of `string-append` in the `uri` field--introduced because of
the annotation and experiment
package--is not expected, right?
Especially, they generally use ".../release/..." without a second
stable URI. Therefore, the future time travel will break.
What is the best: one patch correcting all the packages involved or
one patch per involved package?
Second, all the Bioconductor packages seem to be having a git uri
https://git.bioconductor.org/packages/<name>. And based on the new [2]
`guix lint -c archival` which automatically sends a request to
Software Heritage (SWH) when the fetching method is VCS, it appears to
me a good policy to fix the method to `git-fetch` in the file
`bioconductor.scm`. What do you think ?
>From my knowledge, Bioconductor is not yet archived by them. But even
it will be, archive the source in SWH at the "lint time"--i.e., when
the package is modified in Guix--eases their work and ensures
robustness in time travel from our side. From my opinion, replace
`url-fetch` by `git-fetch` will be a good practise.
What do you think?
[2] https://lists.gnu.org/archive/html/guix-patches/2019-08/msg00580.html
Third, bioconductor.scm contains (3) packages which are not in
Bioconductor 3.9; (r-monocle3, r-cicero-monocle3, r-cistopic). Is it
expected?
All the best,
simon
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