Hello, All received and acknowledged. Thanks for your time!
Shayan Doust July 10, 2019 7:04 AM, "Andreas Tille" <[email protected]> wrote: > 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, [email protected] 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" <[email protected]> wrote: >> >>> Hi, >>> >>> On Mon, Jul 08, 2019 at 01:59:23PM +0300, [email protected] 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
