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Do not error on duplicate boundary addition #1401

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Merged
merged 2 commits into from
Aug 26, 2024
Merged

Do not error on duplicate boundary addition #1401

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837b376
Do not error on duplicate boundary addition
oxinabox Aug 23, 2024
95a7c6e
add log message when adding duplicate boundary reaction
oxinabox Aug 26, 2024
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1 change: 1 addition & 0 deletions release-notes/next-release.md
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Expand Up @@ -9,6 +9,7 @@
* Fixed a bug with SBML group parsing that affects the Debian package.

## Other
* Adding a duplicate boundary reaction (with `add_boundary`) no longer errors, but instead just returns the existing reaction.

## Deprecated features

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4 changes: 3 additions & 1 deletion src/cobra/core/model.py
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Expand Up @@ -676,7 +676,9 @@ def add_boundary(
"identifier. Please set the `reaction_id`."
)
if reaction_id in self.reactions:
raise ValueError(f"Boundary reaction '{reaction_id}' already exists.")
# It already exists so just retrieve it.
logger.info(f"Boundary reaction '{reaction_id}' already exists.")
return self.reactions.get_by_id(reaction_id)
name = f"{metabolite.name} {type}"
rxn = Reaction(id=reaction_id, name=name, lower_bound=lb, upper_bound=ub)
rxn.add_metabolites({metabolite: -1})
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6 changes: 3 additions & 3 deletions tests/test_core/test_model.py
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Expand Up @@ -489,9 +489,9 @@ def test_add_existing_boundary(
The allowed types for boundary, see add_boundary() for types.
"""
for metabolite in metabolites:
model.add_boundary(metabolite, reaction_type)
with pytest.raises(ValueError):
model.add_boundary(metabolite, reaction_type)
rxn_added = model.add_boundary(metabolite, reaction_type)
rxn_dup = model.add_boundary(metabolite, reaction_type)
assert rxn_dup is rxn_added


@pytest.mark.parametrize("solver", optlang_solvers)
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