search

opencobra / memote

memote – the genome-scale metabolic model test suite
https://memote.readthedocs.io/
Apache License 2.0
125 stars 26 forks source link

Implementation Details #576

Closed ChristianLieven closed 5 years ago

ChristianLieven commented 5 years ago

For each test case, I've now included a description of how that particular test is implemented. I hope that this makes it easier for a user to understand the meaning of each test without having to read the source code.

Midnighter commented 5 years ago

I see, I thought your idea was to pull in the docstring of the corresponding 'support' function? I like the descriptions and I'm not against merging but I wonder how brittle/stable these docstrings are?

ChristianLieven commented 5 years ago

I definitely agree that this cannot be a long-term solution. But updating the implementation description relies just as much on the programmer's memory as an update to the docstring of a support function would. In addition, some tests use several support functions while others use none (or indirect). I didn't just c/p the docstrings either, but in many cases tried to detail what is going on succinctly.

In the future, I'd happy to attempt constructing this description automatically.

codecov[bot] commented 5 years ago

Codecov Report

Merging #576 into develop will increase coverage by 0.01%. The diff coverage is 100%.

Impacted file tree graph

@@             Coverage Diff             @@
##           develop     #576      +/-   ##
===========================================
+ Coverage    79.94%   79.95%   +0.01%     
===========================================
  Files           57       57              
  Lines         2927     2929       +2     
  Branches       387      388       +1     
===========================================
+ Hits          2340     2342       +2     
  Misses         521      521              
  Partials        66       66
Impacted Files Coverage Δ
memote/support/consistency.py 97.07% <ø> (ø) :arrow_up:
memote/suite/tests/test_sbo.py 82.22% <ø> (ø) :arrow_up:
memote/suite/tests/test_consistency.py 95.29% <ø> (ø) :arrow_up:
memote/suite/tests/test_thermodynamics.py 100% <ø> (ø) :arrow_up:
memote/suite/tests/test_essentiality.py 50% <ø> (ø) :arrow_up:
memote/support/basic.py 96.66% <ø> (ø) :arrow_up:
memote/suite/tests/test_annotation.py 96.93% <ø> (ø) :arrow_up:
memote/suite/tests/test_matrix.py 100% <ø> (ø) :arrow_up:
memote/suite/tests/test_growth.py 50% <ø> (ø) :arrow_up:
memote/suite/tests/test_basic.py 100% <ø> (ø) :arrow_up:
... and 1 more

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 0606a22...5872943. Read the comment docs.

ChristianLieven commented 5 years ago

Replied to all your comments and rebased this branch, should be good to go!