Test cofactor networks generated with the CLI

[jthorton]

Extend the CLI network tests with cofactors to explicitly check that they are included in the transformations.
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[github-actions]

🚨 API breaking changes detected! 🚨

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 92.74%. Comparing base (66476fd) to head (653a752).
Report is 147 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1048      +/-   ##
==========================================
- Coverage   94.46%   92.74%   -1.72%     
==========================================
  Files         135      135              
  Lines       10077    10093      +16     
==========================================
- Hits         9519     9361     -158     
- Misses        558      732     +174     

Flag	Coverage Δ
fast-tests	92.74% <100.00%> (?)
slow-tests	?

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[jthorton]

Python 3.11/12 tests are failing as the name of the cofactor component is not what we expect, see here.

AssertionError: assert 'cofactor1' in {'RFEComponentLabels.COFACTOR1': SmallMoleculeComponent(name=3L9H), 'ligand': SmallMoleculeComponent(name=lig_CHEMBL1078691), 'protein': ProteinComponent(name=), 'solvent': SolventComponent(name=O, Na+, Cl-)}

[github-actions]

🚨 API breaking changes detected! 🚨

[github-actions]

🚨 API breaking changes detected! 🚨

[atravitz]

Just one change to make the enum handling cleaner.

[github-actions]

No API break detected ✅