Package: python-cobra Version: 0.29.1-5 Severity: serious Tags: patch ftbfs Justification: fails to build from source (but built successfully in the past) X-Debbugs-Cc: [email protected], [email protected], [email protected], [email protected] User: [email protected] Usertags: origin-ubuntu stonking ubuntu-patch User: [email protected] Usertags: amd64 User: [email protected] Usertags: arm64 armhf User: [email protected] Usertags: i386 User: [email protected] Usertags: ppc64el
Dear Maintainer, In Python 3.14, two related regressions were introduced in cobrapy: 1. `deepcopy(super(Reaction, self), memo)` no longer short-circuits via the memo dict, causing `Reaction.__deepcopy__` to call itself indefinitely and raise a RecursionError (LP: #2154412, https://github.com/opencobra/cobrapy/issues/1474). 2. `ast.Module.__reduce__` now returns three positional arguments, which `GPR.__init__` cannot accept, causing deepcopy of any model containing GPR objects to fail with a TypeError (LP: #2154413, https://github.com/opencobra/cobrapy/issues/1475). Both failures are triggered by the presence of the custom `__copy__` and `__deepcopy__` overrides on `Reaction`. Removing them lets Python's default copy machinery handle `Reaction` and the `GPR` objects it references correctly, without requiring any manual workaround. The fix is minimal and has been verified against the upstream test suite. Upstream has a fix PR merged and should be available soon in debian after a new release: https://github.com/opencobra/cobrapy/pull/1471 In Ubuntu, the attached patch was applied to achieve the following: * d/p/python-314.patch: remove Reaction.__copy__ and __deepcopy__, fixing infinite recursion and GPR deepcopy failures on Python 3.14 (LP: #2154412, LP: #2154413) Thanks for considering the patch. -- System Information: Debian Release: forky/sid APT prefers resolute-updates APT policy: (500, 'resolute-updates'), (500, 'resolute-security'), (500, 'resolute') Architecture: amd64 (x86_64) Kernel: Linux 7.0.0-15-generic (SMP w/16 CPU threads; PREEMPT) Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled
diff -Nru python-cobra-0.29.1/debian/patches/python-314.patch python-cobra-0.29.1/debian/patches/python-314.patch --- python-cobra-0.29.1/debian/patches/python-314.patch 1970-01-01 05:30:00.000000000 +0530 +++ python-cobra-0.29.1/debian/patches/python-314.patch 2026-05-28 18:00:33.000000000 +0530 @@ -0,0 +1,45 @@ +Description: Remove Reaction.__copy__ and __deepcopy__, broken in Python 3.14 + The super()-based overrides cause infinite recursion and GPR deepcopy + failures in Python 3.14. Removing them lets the default copy machinery + handle both correctly. +Author: Christian Diener <[email protected]> +Origin: upstream, https://github.com/opencobra/cobrapy/commit/c4a09043c0b378bfbecf597d89020b85eafb5737 +Bug: https://github.com/opencobra/cobrapy/issues/1474 +Bug: https://github.com/opencobra/cobrapy/issues/1475 +Last-Update: 2026-05-29 +--- a/src/cobra/core/reaction.py ++++ b/src/cobra/core/reaction.py +@@ -246,33 +246,6 @@ + if self.flux_expression is not None: + set_objective(self.model, {self: value}, additive=True) + +- def __copy__(self) -> "Reaction": +- """Copy the Reaction. +- +- Returns +- ------- +- Reaction +- A new reaction that is a copy of the original reaction. +- """ +- cop = copy(super(Reaction, self)) +- return cop +- +- def __deepcopy__(self, memo: dict) -> "Reaction": +- """Copy the reaction with memo. +- +- Parameters +- ---------- +- memo: dict +- Automatically passed parameter. +- +- Returns +- ------- +- Reaction +- A new reaction that is a deep copy of the original reaction with memo. +- """ +- cop = deepcopy(super(Reaction, self), memo) +- return cop +- + @staticmethod + def _check_bounds(lb: float, ub: float) -> None: + """Check if the lower and upper bounds are valid. diff -Nru python-cobra-0.29.1/debian/patches/series python-cobra-0.29.1/debian/patches/series --- python-cobra-0.29.1/debian/patches/series 2026-02-27 19:43:42.000000000 +0530 +++ python-cobra-0.29.1/debian/patches/series 2026-05-28 18:00:33.000000000 +0530 @@ -6,3 +6,4 @@ remove-appdirs.patch a2b9d00a04b85b8c8eb12e4deba29ce2147896cf.patch pr1452.patch +python-314.patch
