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Re: Broadinstitute catch - elegant way to disable tests requiring online access?



Hi Steffen,

On 28/07/21 01:06 PM, Steffen Möller wrote:
> Hi Nilesh,
> > >  The import of pristine-tar has worked after removing .gitattributes, but
> > >  then the git lfs references were still in the tarball and the
> > >  upstream  branch. pristine-tar could be pushed, but then the other branches would
> > >  trigger git lfs errors when pushed to salsa. Only after having all fasta.gz
> > >  lfs files removed, the upload went smoothly and you all now find this on
> > >  https://salsa.debian.org/med-team/broad-catch
> > >  
> >  Is that really intended?
> >  We would not be able to run tests in this case since you essentially
> >  ended
> >  up repacking it , since several tests seem to be using that data.
> >  
> >  BTW, I tried to do a little solution for the lfs thingy, for it to not
> >  store "references" and committed it to my personal repository[1]
> >  Can you have a look and let me know if it looks sensible?
> >  
> >  Also, you might as well want to have a look at pristine-lfs[2] which
> >  could
> >  be interesting to use. I've attempted to use this too, please consider
> >  taking a look
> >  I admit, I'm not very used to the lfs workflow, so something could be
> >  wrong
> >  for sure.
> >  
> >  Not sure why the CI fails though -- probably it does not work fine with
> >  lfs, but just thinking of it as a ground for more ideas here :)
> >  I can clone it locally in a different space and re-produce the tarball,
> >  and
> >  I fixed a few tests (not all) -- please consider trying once and let me
> >  know
> > [Edit]: all tests pass now on a clean chroot for me
> 
> You have outperformed yourself on this one. Thank you tons!
> 
> I just removed the broad-catch repository of mine from salsa, please
> kindly inject what you have, instead. I am saying that also since
> apparently my SALSA_TOKEN apparently does not have authority to adjust
> the CI settings.

Pushed to med-team salsa

https://salsa.debian.org/med-team/broad-catch

> May I also ask you to upload the package?

I actually wanted to ask a few things before that:

0) Are my changes even correct - is this the way out?
This is my first time packaging a lfs based repository

1) When I did the changes, I realised then that the size of repository
 goes really, really huge

$ du -sh broad-catch
785M	broad-catch

(well, a good portion of this is due to both pristine-tar and
pristine-lfs branches)

So do we really want to go that way? I was initially of the impression
that it would be a few megs, but that's quite unfortunately not the case
We can alternatively go with what you pushed earlier and disable tests
instead

2) If we intend to upload this as is, then we really, _really_ need to
either remove installation of all the example fasta files, or we need to
do a separate -examples binary package

3) Would FTP masters be happy with this? Is such a large size OK to go
into the archive?

4) Is the package *that* useful to do that sort of solution for the
same?

5) Is it easy to long-term maintain it in the current state?

I admit, my connection would not be so reliable to upload all of it in
one shot - atleast not today.

@Andreas, can you take over the uploading work?
And would you also chime into the discussion here?

> Next steps would be tell routine-update not to try updating this one. I
> can do that.

I think uscan will work fine on this. The next step would be to
introduce pristine-lfs support instead, I guess?

> And then I would like someone from upstream to comment on
> this package and direct us a bit on what else would be good to have in
> Debian to help their cause. My "plan" about that is to just go the
> official route and introduce the package in a github issue - if it is a
> regular user of that package replying, I guess we are just about as happy.

Yes, that sounds sensible
However, I mightn't have a lot of time to spend over this

Nilesh

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