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Re: prinseq(-lite), a dependency of virus seeker



Andreas Tille, on 2020-04-14 09:55:34 +0200:
> Hi Étienne,
> 
> thanks a lot for your work on this package.  As usual I'm CCing my
> answer to the list to make sure others can learn from our discussion as
> well.

Hi Andreas,

I do agree to keep the discussion transparent, no worries.  ;)
Often, I want to edit the header after having sent the message.

> On Sat, Apr 11, 2020 at 08:57:06PM +0200, Étienne Mollier wrote:
> > > Finally d/copyright should be cleaned up.  The Comment should be removed (if you
> > > have done what it says ;-))
> > > Moreover the typical snippet for GPL-3+ is missing.  You need to provide an
> > > extra "License: GPL-3+" paragraph - you'll find lots of examples on your
> > > Debian system.
> > > 
> > > Feel free to ask if you have any questions to my remarks.
> > 
> > Pretty much like a lot of us here I guess, I'm half comfortable
> > with legal components, so wouldn't be against seeing this part
> > being double-checked actually.  I spent some time into
> > Dpkg::Copyright::Scanner(3pm) to get the copyright in a
> > seemingly adequate shape, and tried a few rounds of `cme
> > update dpkg-copyright` to see how it behaves (as provided in
> > Sid, if that is worth mentioning) but comments lasted until I
> > remove them manually.
> > 
> > You don't mind if I tried to keep the legal babbling as short as
> > seems reasonably possible ?  (well, at least with regards to
> > what the cme model accepts...)  I have to write down official
> > authorizations by hand to fullfill my groceries duty, since I
> > have no printer; so, I'm building up some kind of trauma...
> 
> I've commited something what I consider the prefered form by our
> ftpmasters.  There is this short snippet of the GPL text and the hint
> where to find it on a Debian system.  The DEP5 copyright format also
> wants you to use a single License paragraph when having more than
> one Files paragraphs with the same license.  I've just fixed this.

Thanks for mentioning DEP, I was not aware of their existence,
but they are interesting resources indeed:

	https://dep-team.pages.debian.net/

As of formatting the license in the d/copyright file, if there
is a preferred form, then I'll stick to it.  There is this
convenient mechanism to allow several entries to refer to the
same snippet; and as long as copy/paste is not broken, I won't
have to write it by hand anyway.  :)

> I have a question to the files debian/copyright-scan-patterns.yml and
> debian/fill.copyright.blanks.yml.  I admit I have never seen these files
> and I'm wondering for what purpose you injected these.  IMHO these can
> be removed but may be I can learn something from you (which is not
> untypical that I learn from newcomers!)

Using my main personal computer, set to running Sid (maybe the
behavior changed compared to other Debian versions, I haven't
checked), here is what I see when I follow the recommendation of
the d/copyright comment, without .yml files:

	$ scan-copyrights
	The following files were skipped:
	- debian/README.test
	- debian/prinseq-lite-examples.doc-base
	- debian/prinseq-lite-examples.examples
	- debian/prinseq-lite.install
	- debian/prinseq-lite.links
	- debian/prinseq-lite.lintian-overrides
	- debian/tests/run-unit-test
	- example/example1.fasta
	- example/example1.fastq
	- example/example1.gd
	- example/example1.html
	- example/example_readme.txt
	You may want to add a line in debian/copyright-scan-patterns.yml
	or ask the author to add more default patterns to scan
	
	The following paths are missing information:
	- ChangeLog: missing copyright and license
	- debian/TODO: missing copyright and license
	- debian/control: missing copyright and license
	- debian/manpages: missing copyright and license
	- debian/rules: missing copyright and license
	- debian/tests/control: missing copyright and license
	- debian/upstream/metadata: missing copyright and license
	- debian/watch: missing copyright and license
	- prinseq-graphs-noPCA.pl: missing copyright and license
	- prinseq-graphs.pl: missing copyright and license
	- prinseq-lite.pl: missing copyright and license
	You may want to add a line in debian/fill.copyright.blanks.yml
	
	Files: *
	Copyright: 2010-2013, Robert SCHMIEDER
	License: GPL-3+

So, as I understood, those .yml files give hints to build
dynamically the d/copyright file and even update it
automatically with `cme update dpkg-copyright` as upstream
versions are going on, when this information is missing from
upstream files.  I put the three lines here over as is, and
added the following manually at first:

	Files: debian/*
	Copyright: 2020, Étienne Mollier <etienne.mollier@mailoo.org>
	License: GPL-3+

After having built my initial d/copyright file, running manually
the update command led to discrepancies such as:

	Copyright: 2010-2013, Étienne Mollier <etienne.mollier@mailoo.org>

Which is obviously wrong, given the calendar.  Ignoring the
debian/ directory in the copyright-scan-patterns.yml, and
filling the blanks helped stabilize the output, at that moment.

Redoing the same with your modifications, the `cme update
dpkg-copyright` gives a stable output with the appropriate
values.  So, I'm currently under the impression that my not so
conform copyright file was leading to these discrepancies.

> I have further remark to debian/rules and the usage of the debhelper
> tools.  Please inspect my single commits closely.  You have re-invented
> code that is usually done by dh_install, dh_installexamples and dh_link.
> I tried to use single commits to demonstrate the changes.  Please make
> sure you understand every single commit and feel free to ask gere if
> something might remain unclear.

Many thanks for your comprehensive step by step presentation of
the different changes, notably the dh_* ones!  I believe that I
only begin to get an idea of what are, and how to use Debian
helpers.  It looks like I will have a few readings for the next
few days:

	$ apropos dh_ | wc -l
	84

I see several interesting entries there, for cron, pam, etc.
It is nice to see all this automated.

> I'd consider the package ready for upload once you clarified whether
> the debian/*.yml files are needed or not.

As I mentioned, after redoing a few runs `cme update
dpkg-copyright` with the current d/copyright file and without
.yml files, I see d/copyright remains stable with the proper
information.  I'm thus currently under the impression that they
are not strictly needed, although scan-copyright may continue to
suggest changing the scan patterns and filling the blanks.

Since setting them inappropriately may skew the analysis from
scan-copyright, I would currently tend to prefer seeing them
removed as well.

> Thanks a lot for your contribution

You're welcome,
Kind Regards,   :)
-- 
Étienne Mollier <etienne.mollier@mailoo.org>
Fingerprint:  5ab1 4edf 63bb ccff 8b54  2fa9 59da 56fe fff3 882d
Help find cures against the Covid-19 !  Give CPU cycles:
  * Rosetta@home: https://boinc.bakerlab.org/rosetta/
  * Folding@home: https://foldingathome.org/

PS: seeing commit 56adeed480f090c0c21c5bee2e31e13c17102466 by
    the way, good catch!  But I'm at loss understanding how the
    `install` command could have possibly ever worked...

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