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)
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User: ubuntu-devel@lists.ubuntu.com
Usertags: origin-ubuntu stonking ubuntu-patch
User: debian-amd64@lists.debian.org
Usertags: amd64
User: debian-arm@lists.debian.org
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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.

Hello,

Bug #1138218 in python-cobra reported by you has been fixed in the
Git repository and is awaiting an upload. You can see the commit
message below and you can check the diff of the fix at:

https://salsa.debian.org/med-team/python-cobra/-/commit/67e866a1aaa36c7e7ea21dda293b4a8e3d940957

(this message was generated automatically)
-- 
Greetings

https://bugs.debian.org/1138218

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 1138218@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (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 ftpmaster@ftp-master.debian.org)
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 <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
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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