opencobra / memote

memote – the genome-scale metabolic model test suite
https://memote.readthedocs.io/
Apache License 2.0
128 stars 28 forks source link

chore: register custom pytest markers to snuff error messages #670

Closed ChristianLieven closed 5 years ago

ChristianLieven commented 5 years ago

This removes the warnings that appear with the most recent version of Pytest under Python 3.6.0 by registering the custom markers we use for parametrization (biomass, essentiality and growth).

Running memote report snapshot on Google Colaboratory (Python 3.6.8) errors with something along these lines: 'biomass' not found in `markers` configuration option

This is recommended by the authors of pytest

Midnighter commented 5 years ago

We probably have to drop Python 2 support since the scientific Python dependencies have already done so.

ChristianLieven commented 5 years ago

drop py2 support

The sooner the better! I'm happy to make a quick and dirty switchover ASAP (import warning and removal of py2 CI). We should probably discuss steps on how to do a full transition (similar to solution 3 suggested here: https://github.com/opencobra/cobrapy/issues/853#issuecomment-515514559)

codecov[bot] commented 5 years ago

Codecov Report

Merging #670 into develop will decrease coverage by 0.05%. The diff coverage is 100%.

Impacted file tree graph

@@             Coverage Diff             @@
##           develop     #670      +/-   ##
===========================================
- Coverage    82.59%   82.54%   -0.06%     
===========================================
  Files           49       49              
  Lines         2597     2601       +4     
  Branches       424      424              
===========================================
+ Hits          2145     2147       +2     
- Misses         366      368       +2     
  Partials        86       86
Impacted Files Coverage Δ
src/memote/suite/collect.py 83.78% <100%> (+0.92%) :arrow_up:
src/memote/suite/cli/runner.py 51.81% <0%> (-0.52%) :arrow_down:

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 709563d...86a52db. Read the comment docs.