From 5db8c7c6bbdba9dc33bda7135c4d51ced5cf6a8a Mon Sep 17 00:00:00 2001 From: Antonio Rojas Date: Sun, 30 Aug 2026 10:45:56 +0200 Subject: [PATCH 1/6] Use a custom name for C++ list type in braiding.pyx As it is already done in all other instances [1][2] Works around Cython 3.3 bug https://github.com/cython/cython/issues/7939 [1] https://github.com/sagemath/sage/blob/10.10.beta9/src/sage/rings/function_field/riemann_roch.pyx#L22 [2] https://github.com/sagemath/sage/blob/10.10.beta9/src/sage/graphs/graph_decompositions/modular_decomposition.pxd#L2 --- src/sage/libs/braiding.pyx | 62 +++++++++++++++++++------------------- 1 file changed, 31 insertions(+), 31 deletions(-) diff --git a/src/sage/libs/braiding.pyx b/src/sage/libs/braiding.pyx index beb6ad174e4..d678320d12f 100644 --- a/src/sage/libs/braiding.pyx +++ b/src/sage/libs/braiding.pyx @@ -26,26 +26,26 @@ permutation braids. from cysignals.signals cimport sig_on, sig_off -from libcpp.list cimport list +from libcpp.list cimport list as cpplist cdef extern from "braiding.h" namespace "Braiding": - list[list[int]] ConjugatingBraid(int n, list[int] word, list[int] word2) - list[list[int]] LeftNormalForm(int n, list[int] word) - list[list[int]] RightNormalForm(int n, list[int] word) - list[list[int]] GreatestCommonDivisor(int n, list[int] word1, list[int] word2) - list[list[int]] LeastCommonMultiple(int n, list[int] word1, list[int] word2) - list[list[list[int]]] CentralizerGenerators(int n, list[int] word) - list[list[list[int]]] SuperSummitSet(int n, list[int] word) - list[list[list[list[int]]]] UltraSummitSet(int n, list[int] word) - int thurstontype(int n, list[int] word) - int Rigidity_ext(int n, list[int] word) - list[list[list[list[int]]]] SlidingCircuits(int n, list[int] word) - list[list[list[int]]] SendToSSS(int n, list[int] word) - list[list[list[int]]] SendToUSS(int n, list[int] word) - list[list[list[int]]] SendToSC(int n, list[int] word) - list[list[list[int]]] Trajectory(int n, list[int] word) - list[list[list[list[int]]]] CyclicSlidings(int n, list[int] word) + cpplist[cpplist[int]] ConjugatingBraid(int n, cpplist[int] word, cpplist[int] word2) + cpplist[cpplist[int]] LeftNormalForm(int n, cpplist[int] word) + cpplist[cpplist[int]] RightNormalForm(int n, cpplist[int] word) + cpplist[cpplist[int]] GreatestCommonDivisor(int n, cpplist[int] word1, cpplist[int] word2) + cpplist[cpplist[int]] LeastCommonMultiple(int n, cpplist[int] word1, cpplist[int] word2) + cpplist[cpplist[cpplist[int]]] CentralizerGenerators(int n, cpplist[int] word) + cpplist[cpplist[cpplist[int]]] SuperSummitSet(int n, cpplist[int] word) + cpplist[cpplist[cpplist[cpplist[int]]]] UltraSummitSet(int n, cpplist[int] word) + int thurstontype(int n, cpplist[int] word) + int Rigidity_ext(int n, cpplist[int] word) + cpplist[cpplist[cpplist[cpplist[int]]]] SlidingCircuits(int n, cpplist[int] word) + cpplist[cpplist[cpplist[int]]] SendToSSS(int n, cpplist[int] word) + cpplist[cpplist[cpplist[int]]] SendToUSS(int n, cpplist[int] word) + cpplist[cpplist[cpplist[int]]] SendToSC(int n, cpplist[int] word) + cpplist[cpplist[cpplist[int]]] Trajectory(int n, cpplist[int] word) + cpplist[cpplist[cpplist[cpplist[int]]]] CyclicSlidings(int n, cpplist[int] word) def conjugatingbraid(braid1, braid2): @@ -77,7 +77,7 @@ def conjugatingbraid(braid1, braid2): l1 = braid1.Tietze() l2 = braid2.Tietze() sig_on() - cdef list[list[int]] rop = ConjugatingBraid(nstrands, l1, l2) + cdef cpplist[cpplist[int]] rop = ConjugatingBraid(nstrands, l1, l2) sig_off() return rop @@ -108,7 +108,7 @@ def leftnormalform(braid): nstrands = braid.parent().strands() l1 = braid.Tietze() sig_on() - cdef list[list[int]] rop = LeftNormalForm(nstrands, l1) + cdef cpplist[cpplist[int]] rop = LeftNormalForm(nstrands, l1) sig_off() return rop @@ -139,7 +139,7 @@ def rightnormalform(braid): nstrands = braid.parent().strands() l1 = braid.Tietze() sig_on() - cdef list[list[int]] rop = RightNormalForm(nstrands, l1) + cdef cpplist[cpplist[int]] rop = RightNormalForm(nstrands, l1) sig_off() return rop @@ -169,7 +169,7 @@ def greatestcommondivisor(braid1, braid2): l1 = braid1.Tietze() l2 = braid2.Tietze() sig_on() - cdef list[list[int]] rop = GreatestCommonDivisor(nstrands, l1, l2) + cdef cpplist[cpplist[int]] rop = GreatestCommonDivisor(nstrands, l1, l2) sig_off() return rop @@ -199,7 +199,7 @@ def leastcommonmultiple(braid1, braid2): l1 = braid1.Tietze() l2 = braid2.Tietze() sig_on() - cdef list[list[int]] rop = LeastCommonMultiple(nstrands, l1, l2) + cdef cpplist[cpplist[int]] rop = LeastCommonMultiple(nstrands, l1, l2) sig_off() return rop @@ -236,7 +236,7 @@ def centralizer(braid): return [[[0], [i + 1, nstrands - i - 1]] for i in range(nstrands//2 - 1)] + [[[0], [nstrands//2]]] l = braid.Tietze() sig_on() - cdef list[list[list[int]]] rop = CentralizerGenerators(nstrands, l) + cdef cpplist[cpplist[cpplist[int]]] rop = CentralizerGenerators(nstrands, l) sig_off() return rop @@ -263,7 +263,7 @@ def supersummitset(braid): nstrands = braid.parent().strands() b = braid.Tietze() sig_on() - cdef list[list[list[int]]] rop = SuperSummitSet(nstrands, b) + cdef cpplist[cpplist[cpplist[int]]] rop = SuperSummitSet(nstrands, b) sig_off() return rop @@ -293,7 +293,7 @@ def ultrasummitset(braid): nstrands = braid.parent().strands() b = braid.Tietze() sig_on() - cdef list[list[list[list[int]]]] rop = UltraSummitSet(nstrands, b) + cdef cpplist[cpplist[cpplist[cpplist[int]]]] rop = UltraSummitSet(nstrands, b) sig_off() return rop @@ -395,7 +395,7 @@ def sliding_circuits(braid): nstrands = braid.parent().strands() b = braid.Tietze() sig_on() - cdef list[list[list[list[int]]]] rop = SlidingCircuits(nstrands, b) + cdef cpplist[cpplist[cpplist[cpplist[int]]]] rop = SlidingCircuits(nstrands, b) sig_off() return rop @@ -426,7 +426,7 @@ def send_to_sss(braid): nstrands = braid.parent().strands() b = braid.Tietze() sig_on() - cdef list[list[list[int]]] rop = SendToSSS(nstrands, b) + cdef cpplist[cpplist[cpplist[int]]] rop = SendToSSS(nstrands, b) sig_off() return rop @@ -457,7 +457,7 @@ def send_to_uss(braid): nstrands = braid.parent().strands() b = braid.Tietze() sig_on() - cdef list[list[list[int]]] rop = SendToUSS(nstrands, b) + cdef cpplist[cpplist[cpplist[int]]] rop = SendToUSS(nstrands, b) sig_off() return rop @@ -489,7 +489,7 @@ def send_to_sc(braid): nstrands = braid.parent().strands() b = braid.Tietze() sig_on() - cdef list[list[list[int]]] rop = SendToSC(nstrands, b) + cdef cpplist[cpplist[cpplist[int]]] rop = SendToSC(nstrands, b) sig_off() return rop @@ -523,7 +523,7 @@ def trajectory(braid): nstrands = braid.parent().strands() b = braid.Tietze() sig_on() - cdef list[list[list[int]]] rop = Trajectory(nstrands, b) + cdef cpplist[cpplist[cpplist[int]]] rop = Trajectory(nstrands, b) sig_off() return rop @@ -558,6 +558,6 @@ def cyclic_slidings(braid): nstrands = braid.parent().strands() b = braid.Tietze() sig_on() - cdef list[list[list[list[int]]]] rop = CyclicSlidings(nstrands, b) + cdef cpplist[cpplist[cpplist[cpplist[int]]]] rop = CyclicSlidings(nstrands, b) sig_off() return rop From 4dc8455c8db17027fd8d6878b6c498170f46d4ff Mon Sep 17 00:00:00 2001 From: Antonio Rojas Date: Sun, 30 Aug 2026 10:49:51 +0200 Subject: [PATCH 2/6] Explicitly cast to tuple in set_system.pyx Cython 3.3 no longer implicitly converts lists to tuples --- src/sage/matroids/set_system.pyx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/sage/matroids/set_system.pyx b/src/sage/matroids/set_system.pyx index 28ed604b0a7..ac51cea1059 100644 --- a/src/sage/matroids/set_system.pyx +++ b/src/sage/matroids/set_system.pyx @@ -222,7 +222,7 @@ cdef class SetSystem: E.append(mapping[self._E[i]]) else: E.append(self._E[i]) - self._groundset = E + self._groundset = tuple(E) self._idx = {} for i in range(self._groundset_size): self._idx[self._groundset[i]] = i From 0fb37ded8c2485c424ae80cd4f750a520f0ebb20 Mon Sep 17 00:00:00 2001 From: Antonio Rojas Date: Sun, 30 Aug 2026 10:57:00 +0200 Subject: [PATCH 3/6] Fix cython_metaclass crashes with Cython 3.3 Cython 3.3 moved Cython function initialization to a later stage init_after_shared_utility [1] Make sure that this has been run before calling metaclass methods to prevent crashes [1] https://github.com/cython/cython/commit/eee7a607684485e2feb0177da4ea621daf9f1d5c --- src/sage/cpython/cython_metaclass.h | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/src/sage/cpython/cython_metaclass.h b/src/sage/cpython/cython_metaclass.h index c3df3c27d5e..4d1414d910f 100644 --- a/src/sage/cpython/cython_metaclass.h +++ b/src/sage/cpython/cython_metaclass.h @@ -33,6 +33,10 @@ static CYTHON_INLINE PyObject* PyMethodDescr_CallSelf(PyMethodDescrObject* desc, return meth->ml_meth(self, NULL); } +#if defined(CYTHON_HEX_VERSION) && CYTHON_HEX_VERSION >= 0x03030000 +static int __Pyx_InitAfterSharedUtility(void); +#endif + /* * This function calls PyType_Ready(t) and then calls * t.__getmetaclass__(None) (if that method exists) which should @@ -45,6 +49,12 @@ static CYTHON_INLINE int Sage_PyType_Ready(PyTypeObject* t) if (r < 0) return r; +#if defined(CYTHON_HEX_VERSION) && CYTHON_HEX_VERSION >= 0x03030000 + // Ensure Cython function types are initialized before calling metaclass methods. + if (__Pyx_InitAfterSharedUtility() < 0) + return -1; +#endif + // Cython 3 sets Py_TPFLAGS_HEAPTYPE before calling PyType_Ready, // and resets just after the call. We need to reset it earlier, // since otherwise the call to metaclass.__init__ below may have From 0e3f5d3dc9c615dd4fc21189c41f419d94776559 Mon Sep 17 00:00:00 2001 From: Antonio Rojas Date: Sun, 30 Aug 2026 14:11:11 +0200 Subject: [PATCH 5/6] Drop OverflowError test After Cython's __getitem__ implementation rewrite in https://github.com/cython/cython/commit/63a35d40f26930b16c1ed24ea157d926e6ee9707 this gives an IndexError instead --- src/sage/data_structures/list_of_pairs.pyx | 4 ---- 1 file changed, 4 deletions(-) diff --git a/src/sage/data_structures/list_of_pairs.pyx b/src/sage/data_structures/list_of_pairs.pyx index 258320353a0..b9edff5c86f 100644 --- a/src/sage/data_structures/list_of_pairs.pyx +++ b/src/sage/data_structures/list_of_pairs.pyx @@ -67,10 +67,6 @@ cdef class ListOfPairs: Traceback (most recent call last): ... IndexError - sage: l[-1] - Traceback (most recent call last): - ... - OverflowError: can't convert negative value to size_t """ cdef pair_s* pair = self.get(index) return (smallInteger(pair.first), smallInteger(pair.second)) From 04b3333f4f9a3143efe11332dc448b5b112f2e6d Mon Sep 17 00:00:00 2001 From: Samuel Chen <119898205+sacchen@users.noreply.github.com> Date: Tue, 1 Sep 2026 22:55:49 -0700 Subject: [PATCH 6/6] sage.ext.stdsage: pass an empty tuple to tp_new PY_NEW() called tp_new(t, NULL, NULL), but tp_new requires a tuple for the positional arguments. Cython's __cinit__ wrapper reads the tuple's size whenever __cinit__ takes arguments, so PY_NEW() on such a class segfaults with Cython 3.2 and 3.3 alike. Cython 3.3 additionally routes tp_new through a vectorcall adapter that reads the size unconditionally, so classes with a no-argument __cinit__ can fault as well, depending on inlining and optimization level. The call now passes (). Cython compiles this to the module's cached empty tuple, so it is a single load, not an allocation. PY_SET_TP_NEW() is unchanged. The new doctest compiles a base extension type and a derived one with __cinit__(self, *args) and constructs both through PY_NEW(). Against the unpatched header it segfaults with Cython 3.2.9 and 3.3.0 at every optimization level; with the patch both return (). Refs: https://github.com/passagemath/passagemath/pull/2762 Co-Authored-By: Claude Opus 5 Co-Authored-By: Claude Fable 5.1 Claude-Session: https://claude.ai/code/session_01NJQDfzmiW166qBedkq5z1v --- src/sage/ext/stdsage.pxd | 38 +++++++++++++++++++++++++++++++++++++- 1 file changed, 37 insertions(+), 1 deletion(-) diff --git a/src/sage/ext/stdsage.pxd b/src/sage/ext/stdsage.pxd index b1d322cbf2f..1be82887c0a 100644 --- a/src/sage/ext/stdsage.pxd +++ b/src/sage/ext/stdsage.pxd @@ -18,8 +18,44 @@ cdef inline PY_NEW(type t): Return ``t.__new__(t)``. This works even for types like :class:`Integer` where we change ``tp_new`` at runtime (Cython optimizations assume that ``tp_new`` doesn't change). + + TESTS: + + ``tp_new`` must be called with a real (empty) argument tuple, not with + ``NULL``. Cython's ``__cinit__`` wrapper reads the tuple's size whenever + ``__cinit__`` takes arguments, and Cython 3.3 also reads it in the + vectorcall adapter it installs as ``tp_new``; either way a ``NULL`` + argument tuple segfaults. Check both a base extension type and a + derived one, which reaches the base ``tp_new`` through the inheritance + chain:: + + sage: # needs sage.misc.cython + sage: cython( + ....: ''' + ....: from sage.ext.stdsage cimport PY_NEW + ....: + ....: cdef class Base: + ....: cdef public tuple stored + ....: def __cinit__(self, *args): + ....: self.stored = args + ....: + ....: cdef class Derived(Base): + ....: pass + ....: + ....: def new_base(): + ....: return PY_NEW(Base) + ....: + ....: def new_derived(): + ....: return PY_NEW(Derived) + ....: ''') + sage: new_base().stored + () + sage: new_derived().stored + () """ - return (t).tp_new(t, NULL, NULL) + # tp_new requires a tuple for positional arguments. In particular, + # Cython 3.3's vectorcall wrapper reads its size unconditionally. + return (t).tp_new(t, (), NULL) cdef inline void PY_SET_TP_NEW(type dst, type src) noexcept: