Refactor bounds behaviour

[carrascomj]

Related to https://github.com/opencobra/cobrapy/issues/793 Merge this after #272

Description

Previously in cobrapy, setting a lower bound greater than the upper bound (or viceversa) set both bounds to the input value. This was removed in https://github.com/opencobra/cobrapy/pull/1058 and it will raise an error if the bounds are inconsistent.

Implementation

• .bounds was used wherever the intention is to fix the reaction flux to a value.
• Some tests that checked the old behavior were removed or changed.

[codecov[bot]]

Codecov Report

Merging #273 (5c0447f) into devel (879e756) will decrease coverage by 0.80%. The diff coverage is 37.50%.

:exclamation: Current head 5c0447f differs from pull request most recent head 459ce3c. Consider uploading reports for the commit 459ce3c to get more accurate results

@@            Coverage Diff             @@
##            devel     #273      +/-   ##
==========================================
- Coverage   64.41%   63.60%   -0.81%     
==========================================
  Files          58       58              
  Lines        5572     5479      -93     
  Branches      948      941       -7     
==========================================
- Hits         3589     3485     -104     
- Misses       1780     1790      +10     
- Partials      203      204       +1     

Impacted Files	Coverage Δ
cameo/flux_analysis/simulation.py	68.18% <ø> (-0.64%)	:arrow_down:
...ain_design/deterministic/flux_variability_based.py	62.74% <37.50%> (-1.58%)	:arrow_down:
cameo/models/webmodels.py	62.87% <0.00%> (-6.07%)	:arrow_down:
cameo/core/result.py	77.77% <0.00%> (-4.05%)	:arrow_down:
.../strain_design/deterministic/linear_programming.py	21.23% <0.00%> (-2.37%)	:arrow_down:
...ameo/strain_design/heuristic/evolutionary_based.py	44.00% <0.00%> (-1.64%)	:arrow_down:
...sign/heuristic/evolutionary/objective_functions.py	70.35% <0.00%> (-1.42%)	:arrow_down:
cameo/api/designer.py	68.61% <0.00%> (-1.27%)	:arrow_down:
cameo/core/pathway.py	22.05% <0.00%> (-1.13%)	:arrow_down:
...rain_design/heuristic/evolutionary/optimization.py	76.71% <0.00%> (-0.98%)	:arrow_down:
... and 11 more

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[Midnighter]

@carrascomj can I assist you in getting this merged? I'd like to make a new cobrapy release and this is blocking me. Alternatively, can we pin cobrapy to a specific version in cameo so that it doesn't break?

[carrascomj]

@Midnighter Yes, please. This and the parent PR (#272, some docs and escher) are both ready to review. It would wait until cobrapy depends on the latest optlang to pin it here.

[Midnighter]

Moving to latest optlang is exactly why I want to make a new cobrapy release 😆