Public bug reported:
```
tests/test_summary/test_reaction_summary.py:104:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cobra/core/reaction.py:1659: in summary
return ReactionSummary(
cobra/summary/reaction_summary.py:73: in __init__
self._reaction = reaction.copy()
^^^^^^^^^^^^^^^
cobra/core/reaction.py:966: in copy
new_reaction = deepcopy(self)
^^^^^^^^^^^^^^
/usr/lib/python3.14/copy.py:138: in deepcopy
y = copier(memo)
^^^^^^^^^^^^
cobra/core/reaction.py:279: in __deepcopy__
setattr(cop, k, deepcopy(v, memo))
^^^^^^^^^^^^^^^^^
/usr/lib/python3.14/copy.py:157: in deepcopy
y = _reconstruct(x, memo, *rv)
^^^^^^^^^^^^^^^^^^^^^^^^^^
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
x = cobra.core.gene.GPR('b3916 or b1723')
memo = {133461221447936: [{}, {'bigg.reaction': 'PFK'}], 133461249907728:
<Reaction PFK at 0x7961de646ed0>, 133461266794368: {}, 133461266805696:
{'bigg.reaction': 'PFK'}}
func = <class 'cobra.core.gene.GPR'>
args = <generator object _reconstruct.<locals>.<genexpr> at 0x7961e274b880>
state = {'_genes': {'b1723', 'b3916'}, 'body': BoolOp(op=Or(),
values=[Name(id='b3916', ctx=Load()), Name(id='b1723', ctx=Load())]),
'type_ignores': []}
listiter = None, dictiter = None
def _reconstruct(x, memo, func, args,
state=None, listiter=None, dictiter=None,
*, deepcopy=deepcopy):
deep = memo is not None
if deep and args:
args = (deepcopy(arg, memo) for arg in args)
> y = func(*args)
^^^^^^^^^^^
E TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3
were given
```
Upstream bug filed: https://github.com/opencobra/cobrapy/issues/1475
Patching (LP: #2154412) causes this issue to crop up. Full details in
the upstream bug report.
I have written a patch for this bug as well, and will create a debian
bug report as well. We should be able to drop the patch after a sync
down the line.
** Affects: python-cobra (Ubuntu)
Importance: Undecided
Assignee: Ujjwal Sarswat (vmpyr)
Status: In Progress
** Tags: ftbfs
** Changed in: python-cobra (Ubuntu)
Status: New => In Progress
** Changed in: python-cobra (Ubuntu)
Assignee: (unassigned) => Ujjwal Sarswat (vmpyr)
** Tags added: ftbfs
--
You received this bug notification because you are a member of Ubuntu
Bugs, which is subscribed to Ubuntu.
https://bugs.launchpad.net/bugs/2154413
Title:
GPR.__deepcopy__ missing: deepcopy(reaction) raises TypeError on
Python 3.14
To manage notifications about this bug go to:
https://bugs.launchpad.net/ubuntu/+source/python-cobra/+bug/2154413/+subscriptions
--
ubuntu-bugs mailing list
[email protected]
https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
