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biosustain / cameo

cameo - computer aided metabolic engineering & optimization
http://cameo.bio
Apache License 2.0
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fix: predicted pathways containing exch reactions for native compounds #234

Closed phantomas1234 closed 5 years ago

phantomas1234 commented 5 years ago

Fixes #233

A change of model.exchanges in upstream cobrapy has led to the incorporation of DM_ reactions for native compounds (H+, H2O, CO2, etc.) into the PathwayPredictor.model (host model + universal model). The reason for this was that previously predictor.universal_model.exchanges returned a list of all DM... reactions included but after the change in cobrapy it returned []. This list is used to remove DM reactions for native compounds.

I have replaced model.exchanges with model.boundary (which has the same behavior as model.exchanges had in the past) to fix this problem.

codecov[bot] commented 5 years ago

Codecov Report

Merging #234 into devel will increase coverage by 0.01%. The diff coverage is 73.33%.

Impacted file tree graph

@@            Coverage Diff             @@
##            devel     #234      +/-   ##
==========================================
+ Coverage   63.83%   63.85%   +0.01%     
==========================================
  Files          56       56              
  Lines        5126     5126              
  Branches      886      886              
==========================================
+ Hits         3272     3273       +1     
+ Misses       1671     1670       -1     
  Partials      183      183
Impacted Files Coverage Δ
.../strain_design/deterministic/linear_programming.py 21.58% <0%> (ø) :arrow_up:
cameo/flux_analysis/structural.py 50.4% <0%> (ø) :arrow_up:
cameo/flux_analysis/util.py 88.88% <100%> (ø) :arrow_up:
...ain_design/deterministic/flux_variability_based.py 65.92% <100%> (ø) :arrow_up:
cameo/flux_analysis/analysis.py 70.21% <100%> (ø) :arrow_up:
...ain_design/pathway_prediction/pathway_predictor.py 76.37% <100%> (+0.39%) :arrow_up:
...rain_design/heuristic/evolutionary/optimization.py 76.71% <50%> (ø) :arrow_up:
cameo/core/utils.py 67.24% <66.66%> (ø) :arrow_up:

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phantomas1234 commented 5 years ago

@Midnighter I just fixed the broken use of model.exchanges. Nothing more. Obviously, the whole medium loading functionality doesn't make sense anymore in cameo, so feel free to improve in a future pull request.