Additional diploid unit tests

[codecov[bot]]

Codecov Report

Merging #69 into master will increase coverage by 12.03%. The diff coverage is 52.45%.

@@             Coverage Diff             @@
##           master      #69       +/-   ##
===========================================
+ Coverage   35.44%   47.47%   +12.03%     
===========================================
  Files          48       52        +4     
  Lines        3803     4223      +420     
===========================================
+ Hits         1348     2005      +657     
+ Misses       2455     2218      -237     

Impacted Files	Coverage Δ
pastis/io/setup.py	0.00% <0.00%> (ø)
pastis/io/write_struct/pdb.py	11.42% <ø> (ø)
pastis/setup.py	0.00% <0.00%> (ø)
pastis/io/__init__.py	9.30% <9.30%> (ø)
pastis/optimization/piecewise_whole_genome.py	11.63% <10.31%> (+1.20%)	:arrow_up:
pastis/io/read/hiclib.py	16.21% <16.21%> (ø)
pastis/optimization/utils_poisson.py	51.11% <50.56%> (+17.77%)	:arrow_up:
pastis/optimization/initialization.py	62.36% <57.69%> (+0.17%)	:arrow_up:
pastis/optimization/poisson.py	73.22% <65.71%> (+3.17%)	:arrow_up:
pastis/optimization/pastis_algorithms.py	62.15% <71.42%> (+27.45%)	:arrow_up:
... and 18 more

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[gesinecauer]

I think that now that the tests are running, we should go ahead and merge it. Other tests can always be added in a different PR

I actually think I might have a decent amount of unit tests, for now. I essentially imitated the unit tests you had originally, as appropriate for the variety of diploid counts matrix types, and added additional tests of the constraints. Could you let me know if there's anything else I should add at this point?

[gesinecauer]

I'm not sure why codecov/patch isn't successful, or even what that check does...

[NelleV]

codecov checks the coverage of the unit test. The first one checks that the code you've added in this pull request is unit tested, and the other checks that the overall unit test coverage goes up compared to master. The new IO stuff isn't tested. ~I think there is still backward incompatible changes in the io (the function write isn't there anymore).~ (that's not correct -> there's now an io folder)

[NelleV]

Hi @gesinecauer As far as I can tell, the tests are not passing on travis : https://travis-ci.org/github/hiclib/pastis Cheers, N

[gesinecauer]

Is this ready to be merged now?

[NelleV]

Thanks!