[Debian-med-packaging] Bug#894213: No clue yet for building snakemake since there are two dirs in .pybuild

[Andreas Tille]

Hi,

meanwhile I upgraded snakemake to latest upstream in Salsa[1].  I keep
on having trouble with building it:


...
Building DAG of jobs...
Using shell: /bin/bash
Job counts:
        count   jobs
        1       1
        1
Finished job 0.
1 of 1 steps (100%) done
Complete log: /tmp/tmp3rl_vn12/.snakemake/log/2018-06-26T092103.652823.snakemake.log
.E
======================================================================
ERROR: Failure: Exception (snakemake not in PATH. For testing, install snakemake with 'pip install -e .'. You should do this in a separate environment (via conda or virtualenv).)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/nose/failure.py", line 39, in runTest
    raise self.exc_val.with_traceback(self.tb)
  File "/usr/lib/python3/dist-packages/nose/loader.py", line 417, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/lib/python3/dist-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python3/dist-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/lib/python3.6/imp.py", line 235, in load_module
    return load_source(name, filename, file)
  File "/usr/lib/python3.6/imp.py", line 172, in load_source
    module = _load(spec)
  File "<frozen importlib._bootstrap>", line 684, in _load
  File "<frozen importlib._bootstrap>", line 665, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 678, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/build/snakemake-5.1.5/.pybuild/cpython3_3.6_snakemake/build/tests/tests.py", line 22, in <module>
    raise Exception("snakemake not in PATH. For testing, install snakemake with "
Exception: snakemake not in PATH. For testing, install snakemake with 'pip install -e .'. You should do this in a separate environment (via conda or virtualenv).

----------------------------------------------------------------------
Ran 4 tests in 0.227s

FAILED (errors=1)
E: pybuild pybuild:336: test: plugin distutils failed with: exit code=1: cd /build/snakemake-5.1.5/.pybuild/cpython3_3.6_snakemake/build; python3.6 -m nose tests



I think the cause of the issue is that there are two dirs in .pybuild:


# ls -l /build/snakemake-5.1.5/.pybuild
total 8
drwxr-xr-x 3 pbuilder pbuilder 4096 Jun 26 09:20 cpython3_3.6
drwxr-xr-x 3 pbuilder pbuilder 4096 Jun 26 09:20 cpython3_3.6_snakemake


and the latter contains all the installed files while the former is
empty.  How can I prevent this?

Kind regards

        Andreas.


[1] https://salsa.debian.org/med-team/snakemake

-- 
http://fam-tille.de