Public bug reported:
LP buildlog: https://launchpadlibrarian.net/861245115/buildlog_ubuntu-
stonking-amd64.python-cobra_0.29.1-4_BUILDING.txt.gz
```
__________________________________ test_copy ___________________________________
model = <Model e_coli_core at 0x7d52e7f1c650>
def test_copy(model: Model) -> None:
"""Test reaction copying."""
PGI = model.reactions.PGI
> copied = PGI.copy()
^^^^^^^^^^
tests/test_core/test_core_reaction.py:393:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/core/reaction.py:960: in copy
new_reaction = deepcopy(self)
^^^^^^^^^^^^^^
/usr/lib/python3.14/copy.py:138: in deepcopy
y = copier(memo)
^^^^^^^^^^^^
cobra/core/reaction.py:273: in __deepcopy__
cop = deepcopy(super(Reaction, self), memo)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/lib/python3.14/copy.py:157: in deepcopy
y = _reconstruct(x, memo, *rv)
^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/lib/python3.14/copy.py:234: in _reconstruct
y = func(*args)
^^^^^^^^^^^
/usr/lib/python3.14/copy.py:233: in <genexpr>
args = (deepcopy(arg, memo) for arg in args)
^^^^^^^^^^^^^^^^^^^
/usr/lib/python3.14/copy.py:138: in deepcopy
y = copier(memo)
^^^^^^^^^^^^
cobra/core/reaction.py:273: in __deepcopy__
cop = deepcopy(super(Reaction, self), memo)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
E RecursionError: maximum recursion depth exceeded
!!! Recursion detected (same locals & position)
```
Upstream bug filed: https://github.com/opencobra/cobrapy/issues/1474
I have written a patch as a temporary fix. I will file a bug in debian
as well since this issue arises from the use of Python 3.14 and affects
debian as well (they have currently only built with Python 3.13)
I am creating another bug report for test failures arising after
patching this bug.
** Affects: python-cobra (Ubuntu)
Importance: Undecided
Assignee: Ujjwal Sarswat (vmpyr)
Status: In Progress
** Tags: ftbfs
** Tags added: ftbfs
** Changed in: python-cobra (Ubuntu)
Assignee: (unassigned) => Ujjwal Sarswat (vmpyr)
** Changed in: python-cobra (Ubuntu)
Status: New => In Progress
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https://bugs.launchpad.net/bugs/2154412
Title:
RecursionError in Reaction.__deepcopy__ with Python 3.14
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