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Added warning to inform users of known bug and issues fastcc.py #1427

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Added warning to inform users of known bug and issues fastcc.py #1427

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e949381
Added warning to inform users of known bug and issues fastcc.py
dagl1 Feb 19, 2025
5c6e879
Change: Reformulated warning message in fastcc.py
dagl1 Feb 20, 2025
2ac2a53
Removed empty line fastcc.py
dagl1 Feb 20, 2025
45042ae
Added note to use find_blocked_reactions instead: fastcc.py
dagl1 Feb 21, 2025
e105a1a
fix: ran using black 25.1.0
dagl1 Feb 21, 2025
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10 changes: 10 additions & 0 deletions src/cobra/flux_analysis/fastcc.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
"""Provide an implementation of FASTCC."""

from typing import TYPE_CHECKING, List, Optional
from warnings import warn
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Linting will complain about the empty line above.

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Sorry I think I might not understand, the original is:

""Provide an implementation of FASTCC."""

from typing import TYPE_CHECKING, List, Optional

from optlang.symbolics import Zero

from .helpers import normalize_cutoff

Should there not be an empty line between the built-in functions, but empty lines between: built-ins, other packages, other modules? If so I understand, otherwise I am a bit lost


from optlang.symbolics import Zero

Expand Down Expand Up @@ -33,6 +34,15 @@ def _find_sparse_mode(
The list of reactions to consider as consistent.

"""
warn(
"Use find_blocked_reactions instead as "
"this function contains a known bug "
"which allows reactions with zero net flux to be considered active,"
" as well as known discrepancies between this function "
"and its Matlab implementation "
"present in the COBRA toolbox. "
"Please, see https://github.com/opencobra/cobrapy/issues/1154 for more information."
)
if rxns:
obj_vars = []
vars_and_cons = []
Expand Down
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