Re: [MoM] Packaging mindthegap (Was: [MoM] Packaging mindthemap)
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
W: 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
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