Troubleshooting

`Convention A requires module-level 'state_vars' list`

The CLI found a callable model function but cannot map y[i] entries to SBML species IDs.

Fix:

state_vars = ["S", "P"]

`Formula contains Python-only prefix 'np.'`

The formula converter rejects Python-specific prefixes because SBML MathML does not use NumPy or Python namespaces.

Fix:

# Bad
"np.exp(-k*t)"

# Good
"exp(-k*t)"

Invalid SBML SId

SBML identifiers must match:

^[A-Za-z_][A-Za-z0-9_]*$

Fix examples:

Bad	Good
`1species`	`species_1`
`k-cat`	`k_cat`
`EGFR Y1068`	`EGFR_Y1068`

PEtab export has no `parameters.tsv`

This is expected when the IR has no parameters. The PEtab writer avoids creating an invalid empty PEtab parameter table.

libSBML unit warnings

Unit warnings often mean the model is structurally valid but units are under-specified or inconsistent. Define parameter units and inspect species units.

Do not ignore errors

Warnings may be acceptable during early modeling. Error and Fatal diagnostics should block release, publication, or downstream fitting.