[From nobody Tue Jun 2 17:07:04 2026 Received: (at submit) by bugs.debian.org; 29 May 2026 15:13:37 +0000 X-Spam-Checker-Version: SpamAssassin 4.0.1-bugs.debian.org_2005_01_02 (2024-03-25) on buxtehude.debian.org X-Spam-Level: X-Spam-Status: No, score=-18.9 required=4.0 tests=BAYES_00, BODY_INCLUDES_PACKAGE,FOURLA,FVGT_m_MULTI_ODD,GMAIL,HAS_PACKAGE, MD5_SHA1_SUM,NO_RELAYS,XMAILER_REPORTBUG autolearn=ham autolearn_force=no version=4.0.1-bugs.debian.org_2005_01_02 X-Spam-Bayes: score:0.0000 Tokens: new, 59; hammy, 150; neutral, 231; spammy, 0. spammytokens: hammytokens:0.000-+--XDebbugsCc, 0.000-+--X-Debbugs-Cc, 0.000-+--armhf, 0.000-+--H*Ad:N*Bug, 0.000-+--H*Ad:N*Tracking Return-path: <ujjwal.sarswat@canonical.com> Received: via submission by buxtehude.debian.org with esmtp (Exim 4.96) (envelope-from <ujjwal.sarswat@canonical.com>) id 1wSytz-00FrSv-2B for submit@bugs.debian.org; Fri, 29 May 2026 15:13:37 +0000 Content-Type: multipart/mixed; boundary="===============3995393947754011396==" MIME-Version: 1.0 From: Ujjwal Sarswat <ujjwal.sarswat@canonical.com> To: Debian Bug Tracking System <submit@bugs.debian.org> Subject: python-cobra: infinite recursion and GPR deepcopy failures on Python 3.14 Message-ID: <178006760933.1048326.17786925951261145316.reportbug@carbon> X-Mailer: reportbug 13.2.0+ubuntu1 Date: Fri, 29 May 2026 20:43:29 +0530 Delivered-To: submit@bugs.debian.org This is a multi-part MIME message sent by reportbug. --===============3995393947754011396== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline 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: debian-amd64@lists.debian.org, debian-arm@lists.debian.org, debian-powerpc@lists.debian.org, ujjwal.sarswat@canonical.com 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 Usertags: arm64 armhf User: debian-qa@lists.debian.org Usertags: i386 User: debian-powerpc@lists.debian.org 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 --===============3995393947754011396== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="python-cobra_0.29.1-5.debdiff" 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 <ch.diener@gmail.com> +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 --===============3995393947754011396==-- ]