Creating a file for the code shared by all _frequencies functions

[jonbrenas]

Addresses #664 .

I moved the functions to enable the computation of frequencies and the plotting functions (which required to define a new AnophelesFrequency class). I still want to move the tests of the plotting functions to their own file instead of test_snp_frq.py.

[jonbrenas]

The tests for the plotting functions are still only on SNP frequencies. Is that good enough?

[jonbrenas]

@alimanfoo, I might have found a solution that works for what I wanted to do (namely, import shared testing functions for plotting frequencies into the various test_*_frq.pys) by telling pytest to ignore them when it reaches their file (it means that the tests now return the number of "passed", "skipped", "failed" tests (as well as warnings). I checked that when the tests are actually run when called in the relevant file, they would show a failure if they failed (i.e., they are not skipped when explicitly called).

[alimanfoo]

Hi @jonbrenas, thanks so much. A few comments...

[alimanfoo]

This relies on the ID appearing first within the attributes. Is there a safer and more obvious way to get the IDs? E.g., via gff3_parse_attributes() in util module?

[alimanfoo]

@alimanfoo, I might have found a solution that works for what I wanted to do (namely, import shared testing functions for plotting frequencies into the various test_*_frq.pys) by telling pytest to ignore them when it reaches their file (it means that the tests now return the number of "passed", "skipped", "failed" tests (as well as warnings). I checked that when the tests are actually run when called in the relevant file, they would show a failure if they failed (i.e., they are not skipped when explicitly called).

Thanks @jonbrenas. As suggested in the code review above, it might be even better to name these utility functions like "check_..." instead of "test_..." then no need for skipping.

If the importing of functions between test modules seems to work then I guess we're OK! I still don't understand the mechanics of how pytest imports test modules. But if you've confirmed it works then no objection.

[jonbrenas]

Thanks @alimanfoo. This all makes a lot of sense.

[codecov]

Codecov Report

Attention: Patch coverage is 97.00000% with 6 lines in your changes missing coverage. Please review.

Project coverage is 94.96%. Comparing base (cc1ce67) to head (8c0a432).
Report is 123 commits behind head on master.

Files with missing lines	Patch %	Lines
malariagen_data/anoph/frq_base.py	96.79%	6 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #690      +/-   ##
==========================================
+ Coverage   94.57%   94.96%   +0.39%     
==========================================
  Files          40       45       +5     
  Lines        4187     4612     +425     
==========================================
+ Hits         3960     4380     +420     
- Misses        227      232       +5     

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