[Debian-med-packaging] #779014: ITP: subread, looking for sponsor

Alex Mestiashvili alex at biotec.tu-dresden.de
Fri Mar 13 21:40:12 UTC 2015

On 03/13/2015 09:44 AM, Andreas Tille wrote:
> Hi Alex,
> On Thu, Mar 12, 2015 at 09:37:51PM +0100, Alex Mestiashvili wrote:
>>> However, I'd like to ask for some enhancement.  Since you added
>>> autopkgtests (which is nice) I think you could also provide an
>>> override_auto_test to run the test right at runtime.  Moreover the tests
>>> are running only in the unpackaged source dir.  When I wrote
>>> autopkgtests I always designed these in a way that users can run it
>>> manually as well.  This includes shipping the needed data in a data file
>>> under examples and copy them to a temp dir before running the test
>>> script.  This is OK for autopkgbot and manual user tests.  (I think my
>>> last package implementing this was vsearch if you need an example for
>>> what I wrote.)
>> Thanks for the examples! Initially I planned to put the test directory
>> to the data package, but then I decided that test files are to big and
>> removed them from the package.
>> Also I thought that the tests are important only for the maintainers as
>> they help detect potential problems with the software.
>> To be honest I do not see how they can be useful for the users.
> I'm not a user and can't tell.  So if you are really sure that you want
> to design it that way its fine for me.  However, I'd consider it useful
> to provide a debian/README.test and install it into the doc directory to
> inform users about the extended chances for testing.

My opinion was based on only 1 real user of subread :)
I think you are right, especially when upstream provides tests, they
should be included into package.

For now I decided to pack the entire test directory into 1 archive
instead of installing it as the directory. I think it is good idea because:
1. It takes less space.
2. If it is installed into examples/ as the directory, then the content
is a mixture of gzipped and not gzipped files, which I found quite
annoying. (  if a file is less than 4k, then dh_compress doesn't
compress it ).
And if I do not compress the whole test dir then it is a waste of space.

The tests in debian/tests are not exactly the same as in the upstream
test directory.
I just want to ensure that the binaries work (do not segfault for example) .

>>> Finally, you might consider using help2man for generating some manpages.
>>> I would not really require this for sponsering but if it comes cheap via
>>> help2man I would consider this helpful.  (May be the lastalign page is
>>> inspiring what I mean.)

I have even more hardcore example with bowtie2:

I'll give it a try later.

>>> Kind regards and thanks for your work on this
>>>        Andreas.
>>>> [0] http://anonscm.debian.org/cgit/debian-med/subread.git
>> Thank you for looking on it.
> You are welcome.  (I guess you also noticed two minor commits of mine.)

Yes, I did, actually I expected that lintian would complain about the
template :)

> Just ping me if you consider the package ready for upload.
> Kind regards
>       Andreas.

Best regards,

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