Hello Shayan,
July 7, 2019 2:03 PM, hello@shayandoust.me wrote:Just with regards to MoM and how imperative communication is, I thought I'd keep you both updated with how it's going. I've been in an emergency trip for the past couple of days, and will be returning at some point later today. Hence I will be continuing where I left off from.I hope you're fine!
On 2019-07-07 23:12, hello@shayandoust.me wrote:I have installed the generated .deb file on my system and it works as expected. I have written a manpage which I have tested to be accessible via 'man mindthegap'. I have modified debian/copyright to reflect on the current project. Running Lintian, I have corrected any errors with regards to the docs. There are no documentations pre-written or available on the upstream repository so I am unsure if I should either exclude this (by removing docs-base which I have already done) or write a documentation base myself.Great!
Regarding the documentation. I am personally reluctant to write documentation myself. First of all, it takes a lot of time; second, this is better done in close coordination with the upstream as they most likely know their software better; and finally, written documentation may quickly get inconsistent with the code by upstream releases. However, manpages are inevitable. Sometimes I manage to even avoid writing them by using help2man, but your manpage is already better than it. It seems that README.md has a lot on the usage of MindTheGap. There might be a way to convert it to a manpage or (less difficult) place it in package's documentation and link there from the manpage.
In addition to this, checking the current repository and my current progress would be much appreciated, as I feel like this is more or less ready.OK. The package builds successfully, but lintian reports a couple of issues.
First of all, the file locations:
W: mindthegap: file-in-unusual-dir usr/test/compare_vcf.sh
W: mindthegap: file-in-unusual-dir usr/test/contig_test/README
W: mindthegap: file-in-unusual-dir usr/test/contig_test/genome-variant.fastaCMake seems to place all the supporting files under /usr. Proper place for these static files are /usr/share/<package-name> or /usr/share/doc/<package-name>. You may correct this behavior by using debian/mindthegap.install with a list of files and their end locations.
Second, copyright:
W: mindthegap source: missing-license-paragraph-in-dep5-copyright gnu affero general public license v3.0 (paragraph at line 10)
W: mindthegap source: space-in-std-shortname-in-dep5-copyright gnu affero general public license v3.0 (paragraph at line 10)Instead of 'License: GNU Affero General Public License v3.0' you should write 'License: AGPL-3.0' with a proper license paragraph (see [1] for example).
W: mindthegap: binary-without-manpage usr/bin/MindTheGap
Change the manpage's filename to match the capitalization of MindTheGap. Create debian/mindthegap.manpages listing debian/mans/mindthegap.1.
W: mindthegap: script-not-executable usr/test/compare_vcf.sh
You may change the permissions prior to installing using 'override_dh_auto_install' in debian/rules.
By the way, autopkgtest fails for me:
autopkgtest [01:55:14]: test run-unit-test: [-----------------------
cp: cannot stat '/usr/share/doc/#PACKAGENAME#/examples/*': No such file or directory
autopkgtest [01:55:15]: test run-unit-test: -----------------------]
autopkgtest [01:55:15]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - -
run-unit-test FAIL non-zero exit status 1Does it work for you?
Best,
Andrius[1] https://salsa.debian.org/science-team/asl/blob/debian/master/debian/copyright
-- Andrius Merkys Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325 LT-10257 Vilnius, Lithuania