Re: RFS: nim-hts (hts-nim on sheet)
On 01.11.20 19:51, Nilesh Patra wrote:
>
>
> On Mon, 2 Nov 2020 at 00:11, Steffen Möller <steffen_moeller@gmx.de
> <mailto:steffen_moeller@gmx.de>> wrote:
>
> Hi Nilesh,
>
> On 01.11.20 08:34, Nilesh Patra wrote:
> > Hi,
> >
> > On Sun, 1 Nov 2020 at 09:41, Steffen Möller
> <steffen_moeller@gmx.de <mailto:steffen_moeller@gmx.de>
> > <mailto:steffen_moeller@gmx.de <mailto:steffen_moeller@gmx.de>>>
> wrote:
> >
> > Hello,
> >
> > https://salsa.debian.org/med-team/nim-hts
> <https://salsa.debian.org/med-team/nim-hts>
> > <https://salsa.debian.org/med-team/nim-hts
> <https://salsa.debian.org/med-team/nim-hts>> seems ready to upload
> > to me.
> > Please kindly give it some extra eyeballs and typically it
> is Andreas
> > who kindly uploads but feel free to help him out.
> >
> >
> > I took the liberty to do a few changes here:
> >
> > * Added d/watch
> ;) I had deleted mine by accident. Many thanks!
> > * Did repacking to remove binary files which would be otherwise
> > rejected by FTP masters
>
> I saw
>
> tests/HG02002.bam | Bin 435867->
> 0bytes
> tests/HG02002.bam.bai | Bin 16880->
> 0bytes
> tests/other-for-test.bcf.csi | Bin
> 103-> 0bytes
> tests/sa.bam | Bin 35116->
> 0bytes
> tests/sa.bam.bai | Bin 11896->
> 0bytes
> tests/test.bcf.csi | Bin
> 103-> 0bytes
> tests/test.vcf.gz.tbi | Bin
> 103-> 0bytes
> tests/test_files/simple.tsv.gz.csi | Bin
> 112-> 0bytes
>
>
> I regenerated most of these binaries from sources in the rules file.
> Please take a look here[1]
> And the tests pertaining to them are unchanged.
This is nice, indeed.
>
>
> and you have consequently disabled the corresponding tests? This seems
> unfortunate to me.
>
>
> I discarded two of the binaries : |tests/test_files/simple.tsv.gz.csi
> and |tests/other-for-test.bcf.csi||
> since they are either of the form that have undergone a lossy
> transition and the source can't be recovered back, or cannot be
> indexed properly.
> I explained the changes in the header of the patch here[2]
>
> Since not much disk space is invested, I doubt that the FTPmasters
> would
> mind. The files are binary only because they are compressed, not
> because
> they are constructed with some tool that Debian does not have. And
> they
> are not essential for the program but only for testing its
> functionality. I truly confident that this would be ok with the
> FTPmasters.
>
>
> I didn't know about this and I tend to discard binaries fearing
> rejection, but I take your word on this.
> I apologize if I did something stupid here.
>
> [1]
> https://salsa.debian.org/med-team/nim-hts/-/blob/master/debian/rules#L10
> <https://salsa.debian.org/med-team/nim-hts/-/blob/master/debian/rules#L10>
> [2]:
> https://salsa.debian.org/med-team/nim-hts/-/blob/master/debian/patches/disable-test-with-sourceless-file.patch
> <https://salsa.debian.org/med-team/nim-hts/-/blob/master/debian/patches/disable-test-with-sourceless-file.patch>
Certainly not stupid, a bit above my personal ambition for this package,
though :o)
Also, I suggest you contact upstream about it. The idea to generate the
files with the respective latest version of the established tools and
then test the wrapper against their product is a good one. And this is
why FTPmasters typically don't like redistributed binary files.
You more than convinced me. I added you as an uploader - and uploaded.
Many thanks!
Steffen
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