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Re: bedtools 2.29.2+dfsg-6

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[1].
> 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[2].

[2] 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 <etienne.mollier@mailoo.org>
Fingerprint:  8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
Sent from /dev/pts/2, please excuse my verbosity.

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