Your message dated Tue, 02 Jun 2026 16:05:25 +0000
with message-id <[email protected]>
and subject line Bug#1138218: fixed in python-cobra 0.31.1-1
has caused the Debian Bug report #1138218,
regarding python-cobra: infinite recursion and GPR deepcopy failures on Python
3.14
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1138218: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1138218
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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
--- End Message ---
--- Begin Message ---
Source: python-cobra
Source-Version: 0.31.1-1
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
python-cobra, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated python-cobra package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Tue, 02 Jun 2026 17:28:56 +0200
Source: python-cobra
Architecture: source
Version: 0.31.1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1138218
Changes:
python-cobra (0.31.1-1) unstable; urgency=medium
.
* Team upload.
.
[ Ujjwal Sarswat ]
* Fix infinite recursion and GPR deepcopy failures on Python 3.14
Closes: #1138218
.
[ Andreas Tille ]
* DEP3
* New upstream version
* Standards-Version: 4.7.4 (routine-update)
* Drop alien lintiantag
python-package-depends-on-package-from-other-python-variant
* Drop unknown architecture powerpcspe
* Build-Depends: pybuild-plugin-pyproject
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