haddocking / pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.
https://haddocking.github.io/pdb-tools/
Apache License 2.0
384 stars 113 forks source link

Add GitHub actions for testing #108

Closed joaomcteixeira closed 2 years ago

joaomcteixeira commented 3 years ago

Closes #100

joaomcteixeira commented 3 years ago

Build is passing well, but tests are failing while passing locally. Git actions is closing I/O before time

ValueError: I/O operation on closed file

needs research...

codecov[bot] commented 2 years ago

Codecov Report

Merging #108 (2b3f199) into master (4cbefcc) will increase coverage by 0.83%. The diff coverage is 97.42%.

@@            Coverage Diff             @@
##           master     #108      +/-   ##
==========================================
+ Coverage   82.34%   83.18%   +0.83%     
==========================================
  Files          47       48       +1     
  Lines        3711     3878     +167     
  Branches      767      798      +31     
==========================================
+ Hits         3056     3226     +170     
+ Misses        465      463       -2     
+ Partials      190      189       -1     
Impacted Files Coverage Δ
pdbtools/pdb_fetch.py 0.00% <0.00%> (ø)
pdbtools/pdb_tidy.py 82.01% <91.30%> (+7.21%) :arrow_up:
pdbtools/pdb_selaltloc.py 92.05% <96.71%> (+1.90%) :arrow_up:
pdbtools/__init__.py 100.00% <100.00%> (ø)
pdbtools/pdb_b.py 85.18% <100.00%> (+0.18%) :arrow_up:
pdbtools/pdb_chain.py 84.61% <100.00%> (+0.19%) :arrow_up:
pdbtools/pdb_chainbows.py 87.50% <100.00%> (+0.19%) :arrow_up:
pdbtools/pdb_chainxseg.py 94.54% <100.00%> (+0.10%) :arrow_up:
pdbtools/pdb_chkensemble.py 87.64% <100.00%> (+0.14%) :arrow_up:
pdbtools/pdb_delchain.py 84.81% <100.00%> (+0.19%) :arrow_up:
... and 38 more

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JoaoRodrigues commented 2 years ago

OK, summary after a ton of tinkering:

  1. Github Actions are utterly broken when it comes to handling TTYs. See https://github.com/actions/runner/issues/241
  2. Because of the above, I had to disable Win testing.
  3. Separated coverage/linting/building/testing to avoid redundancy and help manage different OSes.
  4. Some tests are failing on Python 2.7, @joaomcteixeira: they are about pdb_selaltloc!
  5. Added flake8 linting to CI.