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fix: merge duplicate pentose phosphate pathway subsystem - #1032

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edkerk merged 1 commit into
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fix/ppp-subsystem-casing
Jul 11, 2026
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fix: merge duplicate pentose phosphate pathway subsystem#1032
edkerk merged 1 commit into
developfrom
fix/ppp-subsystem-casing

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@edkerk edkerk commented Jul 11, 2026

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Main improvements in this PR:

As reported in #1003, the pentose phosphate pathway appears as two subsystems: MAR20070 has its subsystem set to "Pentose Phosphate Pathway" (title case), while the other 25 reactions of the pathway use "Pentose phosphate pathway". The wrong casing was introduced when MAR20070 was added in #551.

  • Correct the subsystem of MAR20070 to "Pentose phosphate pathway", merging the two groups into one.

I hereby confirm that I have:

  • Tested my code on my own computer for running the model
  • Selected develop as a target branch
  • Any removed reactions and metabolites have been moved to the corresponding deprecated identifier lists

…1003)

MAR20070 had its subsystem set to "Pentose Phosphate Pathway" (title
case) when it was added in #551, while the other 25 reactions of that
pathway use "Pentose phosphate pathway". This made the pentose phosphate
pathway appear as two subsystems, one containing only MAR20070. Correct
MAR20070 to "Pentose phosphate pathway" so the two merge into one.
@edkerk

edkerk commented Jul 11, 2026

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No structural change

@edkerk
edkerk merged commit baeb13f into develop Jul 11, 2026
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This PR has been automatically tested with GH Actions. Here is the output of the MACAW test:

Starting dead-end test...
- Found 1384 dead-end metabolites.
- Found 1141 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends.
- Found 1369 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 377 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.
- 377 involve the same metabolites but with different coefficients as at least one other reaction.

This and a more detailed output from MACAW are also committed to data/testResults/.

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

@edkerk edkerk added this to the 2.0.1 milestone Jul 11, 2026
@edkerk edkerk mentioned this pull request Jul 15, 2026
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