fix: require cobra>=0.31.1 to avoid deepcopy RecursionError

[edkerk]

Summary

python3 -m pytest -q was failing 146/1330 tests with RecursionError: maximum recursion depth exceeded from inside copy.deepcopy's _reconstruct, across many unrelated test files.

The root cause is not in geckopy's EcModel. A bare two-object cobra.Model (one Reaction, one Metabolite, no geckopy code involved) reproduces the same RecursionError on copy.deepcopy. The actual cause is cobra.Reaction.__copy__/__deepcopy__: they delegate to super() as a trick to avoid infinitely recursing into themselves, which relies on copy memoizing the in-progress object before recursing into its state. Python 3.14's copy module no longer does that for this code path, so the reaction↔metabolite back-reference that exists in any real cobra model (every reaction holds its metabolites; every metabolite holds the reactions it participates in) sends deepcopy into genuine infinite recursion. This is why the failures spanned reaction- and kcat-related tests across the whole suite rather than being confined to EcModel.copy().

This was already fixed upstream: cobra 0.31.0 ("revise the copy mechanisms") deletes the overriding __copy__/__deepcopy__ methods on Reaction entirely, letting the default copy/__getstate__/__setstate__ machinery (which memoizes correctly) handle it. Verified against cobra 0.32.1.

Changes

• Raise the cobra dependency floor from >=0.29 to >=0.31.1 in pyproject.toml, with a comment explaining why.
• Add a regression test (test_deepcopy_does_not_recurse_on_reaction_metabolite_cycle in tests/test_ec_model.py) that deep-copies an EcModel with a reaction↔metabolite cycle and checks the copy is independent and correctly rebound. Confirmed it reproduces the RecursionError when the pre-0.31.1 Reaction.__copy__/__deepcopy__ overrides are reinstated.
• Add a CHANGELOG.md entry under Unreleased / Fixed.

Test plan

• python3 -m pytest -q --timeout=180 — 1329 passed, 1 deselected, 1 xfailed (was 146 failed before, with cobra <0.31.1)
• tests/test_ec_model.py — 25 passed, including the two new deepcopy tests
• Confirmed the new regression test fails with RecursionError when cobra's pre-0.31.1 Reaction.__copy__/__deepcopy__ are reinstated, and passes with them removed (i.e. cobra>=0.31.1)