Rename compartment-backed PySB mapping IDs to _c, fixes #113

[Copilot]

This updates the affected PySB v2 cases to use _c for mapping IDs that point to compartment-scaled species values.

• Mapping ID cleanup

  • Renames compartment-backed mapping IDs in PySB cases 0010, 0011, 0013, and 0017:
    • A → A_c
    • B → B_c
  • Updates the corresponding condition-table references to keep the PEtab entities aligned with the mapping table.

• Regenerated checked-in case artifacts

  • Refreshes the generated _conditions.tsv and _mapping.tsv files for those four cases so the checked-in artifacts match the source definitions.

Example of the intended rename:

problem.add_condition("c0", B_c=2)
problem.add_mapping("A_c", "A_() ** compartment")
problem.add_mapping("B_c", "B_() ** compartment")

[Copilot]

Pull request overview

This pull request standardizes PEtab v2 PySB case mapping identifiers for compartment-scaled species by renaming A/B mapping IDs to A_c/B_c in the affected cases, and adds a regression test to ensure all v2 cases pass PEtab linting.

Changes:

• Renamed compartment-backed mapping IDs (A→A_c, B→B_c) and updated condition references in PySB v2 cases 0010, 0011, 0013, and 0017.
• Regenerated checked-in _mapping.tsv and _conditions.tsv artifacts for those cases to match the updated source definitions.
• Added a pytest regression test that lints all v2.0.0 cases for both SBML and PySB formats.

Reviewed changes

Copilot reviewed 13 out of 13 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
test/test_general.py	Adds a regression test to lint all v2.0.0 cases (sbml + pysb).
petabtests/cases/v2.0.0/pysb/0010/0010.py	Updates condition keys and mapping IDs to use _c suffix.
petabtests/cases/v2.0.0/pysb/0010/_mapping.tsv	Renames mapping entity IDs to A_c/B_c.
petabtests/cases/v2.0.0/pysb/0010/_conditions.tsv	Updates condition target IDs to B_c.
petabtests/cases/v2.0.0/pysb/0011/0011.py	Updates condition keys and mapping IDs to use _c suffix.
petabtests/cases/v2.0.0/pysb/0011/_mapping.tsv	Renames mapping entity IDs to A_c/B_c.
petabtests/cases/v2.0.0/pysb/0011/_conditions.tsv	Updates condition target IDs to B_c.
petabtests/cases/v2.0.0/pysb/0013/0013.py	Updates condition keys and mapping IDs to use _c suffix.
petabtests/cases/v2.0.0/pysb/0013/_mapping.tsv	Renames mapping entity IDs to A_c/B_c.
petabtests/cases/v2.0.0/pysb/0013/_conditions.tsv	Updates condition target IDs to B_c.
petabtests/cases/v2.0.0/pysb/0017/0017.py	Updates condition keys and mapping IDs to use _c suffix.
petabtests/cases/v2.0.0/pysb/0017/_mapping.tsv	Renames mapping entity IDs to A_c/B_c.
petabtests/cases/v2.0.0/pysb/0017/_conditions.tsv	Updates condition target IDs to A_c/B_c.

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