Allow for extended species names #2600
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Previously, species names (e.g., panFirmicutes_bacterium_CAG_176) could be prefixes of longer model names (e.g., panFirmicutes_bacterium_CAG_176_63_11), which caused extra reactions to be selected and resulted in a dimension mismatch.
Fix applied:
Select all reactions beginning with bacteriumID + "_".
Identify any "child" IDs that also start with this prefix.
Exclude reactions beginning with any childID + "_".
This ensures that only reactions belonging to the intended bacterium are selected, correctly matching the dimensions of the coupling matrix.
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