Re: [MoM] Packaging mindthegap (Was: [MoM] Packaging mindthemap)
Hi,
I pushed some other minor changes
Secure URI in watch file:
Very simple - may be caused due to wrong initial advise of mine
Convert remaining Python2 script:
I missed that yesterday in my 2to3 conversion
Just keep on asking if you need more advise for the remaining lintian
issues or the package split.
Kind regards
Andreas.
On Tue, Jul 09, 2019 at 05:11:03PM +0200, Andreas Tille wrote:
> Hi,
>
> our mails crossed. Please read the mail I wrote after building
> the package. I think it answers most of the questions. The one
>
> I: mindthegap: package-contains-documentation-outside-usr-share-doc usr/share/mindthegap/scripts/jenkins/README
> I: mindthegap: package-contains-documentation-outside-usr-share-doc usr/share/mindthegap/test/contig_test/README
> I: mindthegap: package-contains-documentation-outside-usr-share-doc usr/share/mindthegap/test/full_test/README
>
> Could be answerd by: Just move these dirs to
>
> usr/share/doc/mindthegap
>
> Finally these data are not needed to run the package and are basically
> documentation for the user.
>
> I hope everything else is answered by my other mail.
>
> Thanks a lot for your work on this and making that fast progress
>
> Andreas.
>
> On Tue, Jul 09, 2019 at 02:50:06PM +0000, hello@shayandoust.me wrote:
> > Hello!
> >
> > Thanks for your replies. So some good news and an issue. I have worked hard to get autpkgtest, hence I have now used the pre-existing testing scripts to use by creating a patch to make it utilise the system-wide mindthegap installation instead of it expecting a local binary. The pre-existing test scripts also use exit flags / status which makes it easier as I don't need to re-write it. The result I now get is as follows, which looks good:
> >
> > autopkgtest [05:44:25]: test run-unit-test: [-----------------------
> > Invoking simple_test.sh:
> > clean-insert : passed
> > 13-inserts-ref10k : passed
> > 1-SNP : passed
> > 3-SNP*2 : passed
> > snp-before-clean-insert : passed
> > hetero-insert : passed
> > deletion : passed
> > fuzzy-deletion : passed
> > n-in-solid-stretch : passed
> > n-in-before-clean-insert : passed
> > n-after-clean-insert : passed
> > Invoking simple_full_test.sh:
> > full-test find vcf : PASS
> > full-test find breakpoints : PASS
> > full-test fill fasta : PASS
> > full-test fill vcf : PASS
> > contig-test fill fasta : PASS
> > contig-test fill gfa : PASS
> > autopkgtest [05:44:36]: test run-unit-test: -----------------------]
> > autopkgtest [05:44:36]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - -
> > run-unit-test PASS
> > autopkgtest [05:44:36]: @@@@@@@@@@@@@@@@@@@@ summary
> > run-unit-test PASS
> >
> > Now I have corrected the lintian issues, and testing it on my system, the paths are available at either /usr/share/doc/mindthegap or /usr/share/mindthegap depending on what static file it is respectively. I am now left with the following linthian output:
> >
> > I: mindthegap: spelling-error-in-binary usr/bin/MindTheGap writting writing
> > I: mindthegap: hardening-no-bindnow usr/bin/MindTheGap=0Re: mindthegap: new-package-should-close-itp-bug
> > I: mindthegap: description-synopsis-might-not-be-phrased-properly "Performs detection and assembly of DNA insertion variants in NGS read datasets."
> > I: mindthegap: extra-license-file usr/share/doc/mindthegap/LICENSE.gz
> > I: mindthegap: package-contains-documentation-outside-usr-share-doc usr/share/mindthegap/scripts/jenkins/README
> > I: mindthegap: package-contains-documentation-outside-usr-share-doc usr/share/mindthegap/test/contig_test/README
> > I: mindthegap: package-contains-documentation-outside-usr-share-doc usr/share/mindthegap/test/full_test/README
> > E: mindthegap: python-script-but-no-python-dep usr/share/mindthegap/test/scripts/generate_read.py #!python
> > E: mindthegap: python-script-but-no-python-dep usr/share/mindthegap/test/scripts/make_deletions.py #!python
> > E: mindthegap: python-script-but-no-python-dep usr/share/mindthegap/test/scripts/make_snp_deletions.py #!python
> > E: mindthegap: python-script-but-no-python-dep ... use --no-tag-display-limit to see all (or pipe to a file/program)
> >
> > My question is: should I include python as a dependency seeing as linthian is complaining? I initially didn't want to add it as these python files are never used within my autopkgtest, nor do I see why an end user would use these so I thought adding python as a dep would be a dep too many and useless? Please correct me if I should.
> >
> > Now the issue. With my latest commit, it seems like (I really don't know why this happened, I am really certain I popped quilt patches) the files within test and CMakeLists was re-written and is different to what the upstream is. The package building and tests are still successful, but I shouldn't have re-written over these and I am positive I popped them, unless I was really acting stupid at the time and forgot to pop everything. Trying quilt pop -f (-f as these changes are too vast and quilt complains), I cannot package build as it complains I need to dpkg-source --commit(?) first. Doing this will revert back to the initial issue I had with CMake not finding gatb-core even though the patches are still untouched within debian/patches. It's a bit of a headache, as I don't know how to fix this at all. I am also not sure how to revert these commits (if I need to) as all of my autopkgtest changes would get resrt?
> >
> > Hopefully I'm not *too* much of an inconvenience and many thanks :),
> > Shayan Doust
> >
> > July 8, 2019 2:51 PM, "Andreas Tille" <andreas@an3as.eu> wrote:
> >
> > > Hi,
> > >
> > > On Mon, Jul 08, 2019 at 01:59:23PM +0300, merkys@debian.org wrote:
> > >
> > >> @Shayan: I don't have a reference to cite about the severity of lintian
> > >> errors/warnings/..., but I feel errors and warnings must be dealt with.
> > >> Let us know should you need any help with these.
> > >
> > > My *personal* policy is:
> > >
> > > - Errors need to be fixed.
> > > - I try really hard to fix all warnings (but sometimes I fail)
> > > - I try to fix lintian info. Example: I fix spelling mistakes if
> > > I can expect that upstream will accept a patch or if upstream is
> > > dead and Debian is basically upstream. However, if the development
> > > is a moving target but not very probable that upstream will care
> > > about a spelling patch I leave this untouched.
> > > - I don't care about pedantic lintian issues.
> > >
> > > Here is my ~/.lintianrc
> > >
> > > color=always
> > > display-experimental=no
> > > display-info=yes
> > > pedantic=no
> > >
> > > which reflects what I'm caring about and what I'm ignoring.
> > >
> > >> On 2019-07-08 09:46, Andreas Tille wrote:
> > >> @Andrius: Its fun to work with you as co-mentor. A lot less work
> > >> for me!
> > >>
> > >> @Andreas: Same fun here to get my methods reviewed :)
> > >
> > > :-)
> > >
> > > Kind regards
> > >
> > > Andreas.
> > >
> > > --
> > > http://fam-tille.de
> >
> >
>
> --
> http://fam-tille.de
>
>
--
http://fam-tille.de
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