[Debian-med-packaging] Bug#878498: snakemake FTBFS with Python 3.6 as default

[Andreas Tille]

control: tags -1 help

Hi,

I've upgraded snakemake in Git to latest upstream but its featuring the
same issue.  I'm pretty sure you Python people know a simple answer for
this issue.

Any help would be welcome

      Andreas.

On Sat, Oct 14, 2017 at 05:33:22AM +0300, Adrian Bunk wrote:
> Source: snakemake
> Version: 3.10.0-1
> Severity: serious
> Tags: buster sid
> 
> https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/snakemake.html
> 
> ...
> ======================================================================
> 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 418, 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/1st/snakemake-3.10.0/.pybuild/pythonX.Y_3.6/build/tests/tests.py", line 21, 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 0.535s
> 
> FAILED (errors=1)
> E: pybuild pybuild:283: test: plugin distutils failed with: exit code=1: cd /build/1st/snakemake-3.10.0/.pybuild/pythonX.Y_3.6/build; python3.6 -m nose tests
> dh_auto_test: pybuild --test --test-nose -i python{version} -p 3.6 returned exit code 13
> debian/rules:18: recipe for target 'build' failed
> make: *** [build] Error 25
> 
> 
> 
> The problem is the the following line in debian/rules:
> 
>   export PATH:=$(CURDIR)/.pybuild/pythonX.Y_3.5/build/bin:$(PATH)
> 
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