Bug#956456: [covid-19] Packaging idseq-dag (Was: [covid] New Contributor for biohackathon)

[Andreas Tille <andreas@an3as.eu>]

Hi Emmanuel,

I've seen your ITP of idseq-dag.  You mentioned

   idseq-dag depends on pytz. I will send the ITP for that package.

I admit its a bit confusing but that package is python3-tz in Debian, is
packaged and I've added it to Build-Depends (amongst other changes).

The current packaging is suffering from failures inside the test suite
looking like this:


======================================================================
ERROR: test_step_single (tests.generate_alignment_viz.GenerateAlignmentVizTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/build/idseq-dag-4.2.3/.pybuild/cpython3_3.8_idseq-dag/build/tests/generate_alignment_viz.py", line 9, in test_step_single
    run_step = IdseqStepSetup.get_step_object(PipelineStepGenerateAlignmentViz, "alignment_viz_out", paired=False)
  File "/build/idseq-dag-4.2.3/.pybuild/cpython3_3.8_idseq-dag/build/tests/idseq_step_setup.py", line 47, in get_step_object
    PipelineFlow.fetch_input_files_from_s3(
  File "/build/idseq-dag-4.2.3/.pybuild/cpython3_3.8_idseq-dag/build/idseq_dag/engine/pipeline_flow.py", line 179, in fetch_input_files_from_s3
    output_file = idseq_dag.util.s3.fetch_from_s3(s3_file, local_dir, allow_s3mi=True)
  File "/build/idseq-dag-4.2.3/.pybuild/cpython3_3.8_idseq-dag/build/idseq_dag/util/s3.py", line 286, in fetch_from_s3
    if is_reference or os.path.abspath(dst).startswith(config["REF_DIR"]):
TypeError: startswith first arg must be str or a tuple of str, not NoneType


The issue is that I had to replace some default dir in a patch[1].
Unfortunately this did not propagated into the config dictionary and
the key "REF_DIR" is not set.  For the moment I gave up here - may
be you want to continue by either fixing my patch or finding a better
way to convince the test suite to write to some place where this is
permitted.

Kind regards

       Andreas.

[1] https://salsa.debian.org/med-team/idseq-dag/-/blob/master/debian/patches/set_default_output_dir_var_tmp.patch

On Sat, Apr 11, 2020 at 12:38:13AM -0300, Emmanuel Arias wrote:
> Hello everybody,
> 
> I am available to help. I will be working on the TODO list [0].
> 
> [0]
> https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/wikis/COVID-19-Hackathon-packages-needing-work
> 
> Cheers,
> Arias Emmanuel
> @eamanu
> yaerobi.com
> 
> 
> On Fri, Apr 10, 2020 at 3:10 AM Olek Wojnar <olek@debian.org> wrote:
> 
> > On 4/9/20 7:37 PM, fancycade wrote:
> > > Thank you for the assistance with this!
> > >
> > > I have uploaded my package to the appropriate repository under the
> > > Python Modules team and will reach out for a RFS.
> >
> > Great, thanks for your contribution!
> >
> > -Olek
> >
> >
> >
> >

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