Add coveralls configuration

[HannesHolste]

Resolves #3.

If you want, you can add the little coverage % indicator to the README, which you need to generate since I don't have access.

[antgonza]

I think you created this PR vs. updating the existing open one, right? Wanna close the other one (duplicated pushes)?

I think you are missing: https://github.com/qiita-spots/qp-deblur/blob/master/.travis.yml#L40

[HannesHolste]

I created this one because semantically it's a separate issue from the 2 algorithm PRs. I was thinking you can merge this PR first, then the other ones if approved.

And thanks, good catch. Encountering this problem with nosetests --with-coverage though. I tried googling for 10min and reading docs but didn't find a meaningful solution. Have you run into this before?

$ nosetests --with-coverage
........................
Name    Stmts   Miss Branch BrPart  Cover
-----------------------------------------
Traceback (most recent call last):
  File "/home/travis/miniconda3/envs/mdsa/bin/nosetests", line 6, in <module>
    sys.exit(nose.run_exit())
  File "/home/travis/miniconda3/envs/mdsa/lib/python2.7/site-packages/nose/core.py", line 121, in __init__
    **extra_args)
  File "/home/travis/miniconda3/envs/mdsa/lib/python2.7/unittest/main.py", line 95, in __init__
    self.runTests()
  File "/home/travis/miniconda3/envs/mdsa/lib/python2.7/site-packages/nose/core.py", line 207, in runTests
    result = self.testRunner.run(self.test)
  File "/home/travis/miniconda3/envs/mdsa/lib/python2.7/site-packages/nose/core.py", line 66, in run
    result.printErrors()
  File "/home/travis/miniconda3/envs/mdsa/lib/python2.7/site-packages/nose/result.py", line 110, in printErrors
    self.config.plugins.report(self.stream)
  File "/home/travis/miniconda3/envs/mdsa/lib/python2.7/site-packages/nose/plugins/manager.py", line 99, in __call__
    return self.call(*arg, **kw)
  File "/home/travis/miniconda3/envs/mdsa/lib/python2.7/site-packages/nose/plugins/manager.py", line 167, in simple
    result = meth(*arg, **kw)
  File "/home/travis/miniconda3/envs/mdsa/lib/python2.7/site-packages/nose/plugins/cover.py", line 190, in report
    self.coverInstance.report(modules, file=stream)
  File "/home/travis/miniconda3/envs/mdsa/lib/python2.7/site-packages/coverage/control.py", line 985, in report
    return reporter.report(morfs, outfile=file)
  File "/home/travis/miniconda3/envs/mdsa/lib/python2.7/site-packages/coverage/summary.py", line 140, in report
    raise CoverageException("No data to report.")

coverage.misc.CoverageException: No data to report.
The command "nosetests --with-coverage" exited with 1.

[antgonza]

The issue is with .coveragerc, I think these values should be:

omit =
    mdsa/tests*
    */__init__.py
    */*/__init__.py
    data*
include = scripts/* mdsa/*

[ElDeveloper]

I recently saw a similar problem in one of our other repos, ended up doing something like this:

nosetests --with-coverage --cover-package=mdsa

I got rid of the coveragerc thing altogether.

[HannesHolste]

@antgonza. I tried your suggestion but same error msg:

# this file is based on the examples provided on scikit-learn's .coveragerc

[run]
omit =
    mdsa/tests*
    */*/__init__.py
    data*
source = mdsa
branch = True
include = scripts/* mdsa/*

[report]
exclude_lines =
    pragma: no cover
    def __repr__
    raise NotImplementedError
    if __name__ == .__main__.:
omit =
    mdsa/tests*
    */*/__init__.py
    data*

@ElDeveloper: That worked.

Thanks for suggestions, guys. I made changes and rebased. Ready to merge after review.

[coveralls]

Changes Unknown when pulling c7d35318ae30b4e1aef0b671cb32af47e7e1bdf6 on HannesHolste:coveralls into \ on biocore:master**.

[coveralls]

Changes Unknown when pulling c7d35318ae30b4e1aef0b671cb32af47e7e1bdf6 on HannesHolste:coveralls into \ on biocore:master**.

[ElDeveloper]

Wonderful, thanks @HannesHolste! 👍