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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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8 changes: 8 additions & 0 deletions src/cobra/flux_analysis/fastcc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,8 @@

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

from .helpers import normalize_cutoff
Expand Down Expand Up @@ -33,6 +35,12 @@ def _find_sparse_mode(
The list of reactions to consider as consistent.

"""
warn("As of 2021, release V... 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 "
"(the cobrapy implementation) and its matlab implementation "
"present in the cobra toolbox, "
"see: https://github.com/opencobra/cobrapy/issues/1154")
if rxns:
obj_vars = []
vars_and_cons = []
Expand Down
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