Hi John, John Marshall, on 2021-01-17 16:35:36 +0000: > Étienne Mollier wrote: > > I noticed current bedtools 2.29.2+dfsg-5 fails to migrate to > > testing, so I pushed a fix. > > The problem being that the bedtools-test package's symlink to > the htsutil executable located in the bedtools package is not > adequately copied when the test files are copied to /tmp, so > needs to be fixed up in the run-unit-test script. > > This is kind of ridiculous: htsutil would be better off in the > bedtools-test package, and if it was a real non-symlink file > there it would be copied to $AUTOPKGTEST_TMP just fine. Is > there a real technical reason why the bedtools-test package > should be noarch? This executable would be much more naturally > in the bedtools-test package rather than cluttering up the > main bedtools package when it is of no interest to users, and > then all this hackery would be avoided. Technically speaking, the existing bedtools-test package moving to Arch: any will need one instance per architecture, so growing the size of the archive. Also I think the Arch: all component will need removal from the archive, so that the package migrates to testing. I welcome comments, as I am not completely at ease with these aspects of the archive though. Other than that, moving htsutil to bedtools-test does not seem that difficult, and I pushed a branch htsutil-move ready for further comments.  https://salsa.debian.org/med-team/bedtools/-/merge_requests/1 I acknowledge that the situation seems not ideal. I don't think it is dire either though, and stabilisation is coming. In any case, Thanks for your remark, I was not entirely aware of the status of the htsutil executable as a component purely of testing purpose. > (I have prepared an upstream patch to make the test suite use > htsutil via an environment variable that you could override > similarly to $BT, but really there's no particular need to do > that so I would ideally prefer not to apply it. But if doing > so would help you not push an unwanted > /usr/lib/bedtools/test/htsutil directory and executable onto > users' machines, I could be convinced to do so!) Kind Regards, -- Étienne Mollier <email@example.com> Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent from /dev/pts/2, please excuse my verbosity.
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