[BUG] model.copy() fails with python 3.13.0

[mpredl]

Is there an existing issue for this?

• I have searched the existing issues

Problem description

There seems to be a bug when trying to copy a model in python v3.13.0. - cobra v0.29. The error message hints at problems copying the GPR. This issue does not happen in python v3.12.7 - cobra v0.29

Code sample

Code run:

import cobra
text_book_model = cobra.io.load_model("textbook")
text_book_model.copy()

Traceback:

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[3], line 1
----> 1 text_book_model.copy()

File [~/.conda/envs/cf_prediction/1.1/lib/python3.13/site-packages/cobra/core/model.py:426], in Model.copy(self)
    424 for attr, value in reaction.__dict__.items():
    425     if attr not in do_not_copy_by_ref:
--> 426         new_reaction.__dict__[attr] = copy(value)
    427 new_reaction._model = new
    428 new.reactions.append(new_reaction)

File [~/.conda/envs/cf_prediction/1.1/lib/python3.13/copy.py:80], in copy(x)
     78 copier = getattr(cls, "__copy__", None)
     79 if copier is not None:
---> 80     return copier(x)
     82 reductor = dispatch_table.get(cls)
     83 if reductor is not None:

File [~/.conda/envs/cf_prediction/1.1/lib/python3.13/site-packages/cobra/core/gene.py:554], in GPR.__copy__(self)
    552 def __copy__(self) -> "GPR":
    553     """Ensure a correct shallow copy."""
--> 554     return self.copy()

File [~/.conda/envs/cf_prediction/1.1/lib/python3.13/site-packages/cobra/core/gene.py:550], in GPR.copy(self)
    548 def copy(self):
    549     """Copy a GPR."""
--> 550     return deepcopy(self)

File [~/.conda/envs/cf_prediction/1.1/lib/python3.13/copy.py:163], in deepcopy(x, memo, _nil)
    161                 y = x
    162             else:
--> 163                 y = _reconstruct(x, memo, *rv)
    165 # If is its own copy, don't memoize.
    166 if y is not x:

File [~/.conda/envs/cf_prediction/1.1/lib/python3.13/copy.py:254], in _reconstruct(x, memo, func, args, state, listiter, dictiter, deepcopy)
    252 if deep and args:
    253     args = (deepcopy(arg, memo) for arg in args)
--> 254 y = func(*args)
    255 if deep:
    256     memo[id(x)] = y

TypeError: GPR.__init__() takes from 1 to 2 positional arguments but 3 were given

Environment

### Package Information

Package	Version
cobra	0.29.0

Dependency Information

Package	Version
appdirs	1.4.4
black	missing
bumpversion	missing
depinfo	2.2.0
diskcache	5.6.3
future	1.0.0
httpx	0.27.2
importlib-resources	6.4.5
isort	missing
numpy	2.1.3
optlang	1.8.2
pandas	2.2.3
pydantic	2.9.2
python-libsbml	5.20.4
rich	13.9.4
ruamel.yaml	0.18.6
scipy	missing
swiglpk	5.0.10
tox	missing

Build Tools Information

Package	Version
pip	24.3.1
setuptools	75.5.0

Platform Information

Linux	6.1.0-26-amd64-x86_64
CPython	3.13.0

Anything else?

No response