add compare.py which contains functions for comparing.

[akaviaLab]

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• [X] description of feature Added functions for comparing models, metabolites, reactions, groups, genes. This is an adaptation of a function I used to compare XML and MAT models of the same file.

I'm not sure what tests to add for this. Maybe we can replace the test.test_io.conftest.py compare_mdoels() function with this one.

• [ ] tests added/passed
• [ ] add an entry to the next release

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 47.91667% with 75 lines in your changes are missing coverage. Please review.

Project coverage is 83.52%. Comparing base (c3376da) to head (4b92ed9). Report is 162 commits behind head on devel.

Files	Patch %	Lines
src/cobra/util/compare.py	36.11%	67 Missing and 2 partials :warning:
src/cobra/core/solution.py	79.31%	5 Missing and 1 partial :warning:

Additional details and impacted files

@@            Coverage Diff             @@
##            devel    #1206      +/-   ##
==========================================
- Coverage   84.44%   83.52%   -0.93%     
==========================================
  Files          66       67       +1     
  Lines        5511     5602      +91     
  Branches     1265     1289      +24     
==========================================
+ Hits         4654     4679      +25     
- Misses        557      617      +60     
- Partials      300      306       +6     

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[Midnighter]

I'm a bit unsure if this should be in the cobrapy package, part of a cookbook, or possibly a cobra-tools package or so. Let's discuss at the dev meeting!

[cdiener]

Since the test suite is now separated, maybe this could also live there? There is some value to have it for testing purposes...

[akaviaLab]

I'd be happy to move it to the testing suite. This really helped me working on MAT import to make sure it is the same as SBML. If I move it to the testing suite, how thorough should the testing of the compare function be? I'm working on testing that it gives the appropriate results, but I'm not sure that is appropriate/necessary if it lives in the testing suite.

[akaviaLab]

Would you like me to move the compare function to tests? I can do that.