SysBioChalmers / Human-GEM

The generic genome-scale metabolic model of Homo sapiens
https://sysbiochalmers.github.io/Human-GEM-guide/
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feat: automated MACAW tests #840

Closed edkerk closed 1 month ago

edkerk commented 2 months ago

Main improvements in this PR:

As discussed in #827, MACAW duplicate and dead-end metabolite tests are now run for each PR. Summary results should reported as comment in the PR, while the more detailed output is kept in data/macawResults/macaw_results.csv (where a README.md specifies from with PR the results were derived from).

I hereby confirm that I have:

github-actions[bot] commented 2 months ago

This PR has been automatically tested with GH Actions. Here is the output of the macaw test:

Starting dead-end test...
- Found 1373 dead-end metabolites.
- Found 1129 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends.
- Found 1595 reversible reactions that can only carry steady-state fluxes in a single direction due to dead-ends.
Starting duplicate test...
- Skipping redox duplicates because no redox_pairs and/or proton_ids were provided.
- Found 447 reactions that were some type of duplicate:
- 0 were completely identical to at least one other reaction.
- 13 involve the same metabolites but go in the opposite direction or have the opposite reversibility as at least one other reaction.
- 447 involve the same metabolites but with different coefficients as at least one other reaction.

A more detailed output from this test run is also committed to data/macawResults/macaw_results.csv.

Note: In the case of multiple test runs, this post will be edited.