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r-bioinformatics / edgePy

A Python implementation of edgeR for differential expression analysis
https://edgepy.readthedocs.io
MIT License
96 stars 10 forks source link

Wrap all dynamic/static analysis tools in tox #37

Closed clintval closed 6 years ago

clintval commented 6 years ago

This is a rather large PR as it wraps all of the testing I've set up over the weeks. We run the following dynamic/static analysis tools on our codebase, each requiring configuration and invocation:

Further more, we now build Sphinx documentation which must pass building as well.

The solution to this is to wrap all tools with a frontend for continuous integration with Tox which is compatible with our backend TravisCI service.

@julianstanley could you take a look at how I reorganized the docs/ directory? I deprecated make.bat in favor of building with the Makefile or even better with tox -e py36-docs.

Finally I created instructions for installing, developing, and testing this library in the CONTRIBUTING.md file.

Testing this project against all the above is now as simple as:

❯ cd edgePy
❯ tox

Side-effects:

  1. Coverage is now specified as branch which is a smarter algorithm for determining code coverage and should show us more uninterpreted lines than before.

  2. Until pyproject.toml becomes accepted by the community, we exist between a setup.py, setup.cfg, and requirements-test.txt. Ideally everything in this project would be defined with a single project file and single semantic structure.

Closes #29

codecov[bot] commented 6 years ago

Codecov Report

Merging #37 into master will decrease coverage by 6.2%. The diff coverage is n/a.

@@           Coverage Diff            @@
##           master     #37     +/-   ##
========================================
- Coverage    94.5%   88.3%   -6.3%     
========================================
  Files           4       3      -1     
  Lines         148     146      -2     
  Branches        0      25     +25     
========================================
- Hits          140     129     -11     
  Misses          8       8             
- Partials        0       9      +9
clintval commented 6 years ago

I will merge this now.

@apfejes this may introduce a few merge conflicts with your banch. I'll take on the rebase FYI.