Merge pull request #2151 from Ericgig/misc.cython3

Enable cython 3

.github/workflows/tests.yml

@@ -51,6 +51,7 @@ jobs:
             numpy-requirement: ">=1.20,<1.21"
             scipy-requirement: ">=1.5,<1.6"
             condaforge: 1
+            oldcython: 1
 
           # No MKL runs.  MKL is now the default for conda installations, but
           # not necessarily for pip.
@@ -73,6 +74,7 @@ jobs:
             os: ubuntu-latest
             python-version: "3.10"
             condaforge: 1
+            oldcython: 1
 
           # Python 3.11 and latest numpy
           # Use conda-forge to provide Python 3.11 and latest numpy
@@ -115,6 +117,9 @@ jobs:
           if [[ -z "${{ matrix.nocython }}" ]]; then
             QUTIP_TARGET="$QUTIP_TARGET,runtime_compilation"
           fi
+          if [[ "${{ matrix.oldcython }}" ]]; then
+            pip install cython==0.29.36
+          fi
           export CI_QUTIP_WITH_OPENMP=${{ matrix.openmp }}
           if [[ -z "${{ matrix.nomkl }}" ]]; then
             conda install blas=*=mkl "numpy${{ matrix.numpy-requirement }}" "scipy${{ matrix.scipy-requirement }}"

doc/changes/2151.misc

@@ -0,0 +1 @@
+Enable cython 3

pyproject.toml

@@ -3,7 +3,7 @@ requires = [
     "setuptools",
     "packaging",
     "wheel",
-    "cython>=0.29.20,<3.0.0",
+    "cython>=0.29.20",
     # See https://numpy.org/doc/stable/user/depending_on_numpy.html for
     # the recommended way to build against numpy's C API:
     "oldest-supported-numpy",

qutip/core/_brtools.pyx

@@ -54,11 +54,6 @@ cdef class SpectraCoefficient(Coefficient):
         return self
 
 
-@cython.overflowcheck(True)
-cdef size_t _mul_checked(size_t a, size_t b) except? -1:
-    return a * b
-
-
 cdef Data _apply_trans(Data original, int trans):
     """helper function for matmul_var_data, apply transform."""
     cdef Data out

qutip/core/cy/_element.pyx

@@ -1,5 +1,9 @@
 #cython: language_level=3
-#cython: boundscheck=False, wraparound=False, initializedcheck=False, cdvision=True
+#cython: boundscheck=False
+#cython: wraparound=False
+#cython: initializedcheck=False
+#cython: cdvision=True
+#cython: c_api_binop_methods=True
 
 from .. import data as _data
 from qutip.core.cy.coefficient import coefficient_function_parameters

qutip/core/cy/coefficient.pyx

@@ -1,4 +1,6 @@
 #cython: language_level=3
+#cython: c_api_binop_methods=True
+
 import inspect
 import pickle
 import scipy

qutip/core/data/add.pyx

@@ -33,7 +33,7 @@ __all__ = [
 cdef int _ONE=1
 
 
-cdef void _check_shape(Data left, Data right) nogil except *:
+cdef void _check_shape(Data left, Data right) except * nogil:
     if left.shape[0] != right.shape[0] or left.shape[1] != right.shape[1]:
         raise ValueError(
             "incompatible matrix shapes "

qutip/core/data/base.pyx

@@ -1,4 +1,5 @@
 #cython: language_level=3
+#cython: c_api_binop_methods=True
 
 import numpy as np
 cimport numpy as cnp

qutip/core/data/dispatch.pyx

@@ -59,7 +59,7 @@ cdef class _constructed_specialisation:
     cdef readonly str _short_name
     cdef public str __doc__
     cdef public str __name__
-    cdef public str __module__
+    # cdef public str __module__
     cdef public object __signature__
     cdef readonly str __text_signature__
 
@@ -71,7 +71,7 @@ cdef class _constructed_specialisation:
             + "_"
             + "_".join([x.__name__ for x in types])
         )
-        self.__module__ = dispatcher.__module__
+        # self.__module__ = dispatcher.__module__
         self.__signature__ = dispatcher.__signature__
         self.__text_signature__ = dispatcher.__text_signature__
         self._output = out
@@ -128,7 +128,7 @@ cdef class Dispatcher:
     cdef readonly bint output
     cdef public str __doc__
     cdef public str __name__
-    cdef public str __module__
+    # cdef public str __module__
     cdef public object __signature__
     cdef readonly str __text_signature__
 
@@ -169,6 +169,10 @@ cdef class Dispatcher:
             this.  If not given and `signature_source` is _not_ an instance of
             `inspect.Signature`, then we will attempt to read `__module__` from
             there instead.
+
+            .. note::
+
+                Commented for now because of a bug in cython 3 (cython#5472)
         """
         if isinstance(inputs, str):
             inputs = (inputs,)
@@ -197,10 +201,10 @@ cdef class Dispatcher:
             self.__name__ = signature_source.__name__
         else:
             self.__name__ = 'dispatcher'
-        if module is not None:
-            self.__module__ = module
-        elif not isinstance(signature_source, inspect.Signature):
-            self.__module__ = signature_source.__module__
+        # if module is not None:
+        #     self.__module__ = module
+        # elif not isinstance(signature_source, inspect.Signature):
+        #     self.__module__ = signature_source.__module__
         self.__text_signature__ = self.__name__ + str(self.__signature__)
         if not isinstance(signature_source, inspect.Signature):
             self.__doc__ = inspect.getdoc(signature_source)

qutip/core/data/expect.pxd

@@ -3,14 +3,14 @@
 
 from qutip.core.data cimport CSR, Dense, Data, Dia
 
-cpdef double complex expect_csr(CSR op, CSR state) nogil except *
-cpdef double complex expect_super_csr(CSR op, CSR state) nogil except *
+cpdef double complex expect_csr(CSR op, CSR state) except * nogil
+cpdef double complex expect_super_csr(CSR op, CSR state) except * nogil
 
-cpdef double complex expect_csr_dense(CSR op, Dense state) nogil except *
-cpdef double complex expect_super_csr_dense(CSR op, Dense state) nogil except *
+cpdef double complex expect_csr_dense(CSR op, Dense state) except * nogil
+cpdef double complex expect_super_csr_dense(CSR op, Dense state) except * nogil
 
-cpdef double complex expect_dense(Dense op, Dense state) nogil except *
-cpdef double complex expect_super_dense(Dense op, Dense state) nogil except *
+cpdef double complex expect_dense(Dense op, Dense state) except * nogil
+cpdef double complex expect_super_dense(Dense op, Dense state) except * nogil
 
 cpdef double complex expect_dia(Dia op, Dia state) except *
 cpdef double complex expect_super_dia(Dia op, Dia state) except *

qutip/core/data/expect.pyx

@@ -24,7 +24,7 @@ __all__ = [
     'expect_super_csr_dense', 'expect_super_dia_dense', 'expect_super_data',
 ]
 
-cdef void _check_shape_ket(Data op, Data state) nogil except *:
+cdef void _check_shape_ket(Data op, Data state) except * nogil:
     if (
         op.shape[1] != state.shape[0]  # Matrix multiplication
         or state.shape[1] != 1  # State is ket
@@ -33,7 +33,7 @@ cdef void _check_shape_ket(Data op, Data state) nogil except *:
         raise ValueError("incorrect input shapes "
                          + str(op.shape) + " and " + str(state.shape))
 
-cdef void _check_shape_dm(Data op, Data state) nogil except *:
+cdef void _check_shape_dm(Data op, Data state) except * nogil:
     if (
         op.shape[1] != state.shape[0]  # Matrix multiplication
         or state.shape[0] != state.shape[1]  # State is square
@@ -42,7 +42,7 @@ cdef void _check_shape_dm(Data op, Data state) nogil except *:
         raise ValueError("incorrect input shapes "
                          + str(op.shape) + " and " + str(state.shape))
 
-cdef void _check_shape_super(Data op, Data state) nogil except *:
+cdef void _check_shape_super(Data op, Data state) except * nogil:
     if state.shape[1] != 1:
         raise ValueError("expected a column-stacked matrix")
     if (
@@ -52,7 +52,7 @@ cdef void _check_shape_super(Data op, Data state) nogil except *:
         raise ValueError("incompatible shapes " + str(op.shape) + ", " + str(state.shape))
 
 
-cdef double complex _expect_csr_ket(CSR op, CSR state) nogil except *:
+cdef double complex _expect_csr_ket(CSR op, CSR state) except * nogil:
     """
     Perform the operation
         state.adjoint() @ op @ state
@@ -75,7 +75,7 @@ cdef double complex _expect_csr_ket(CSR op, CSR state) nogil except *:
         out += mul * sum
     return out
 
-cdef double complex _expect_csr_dm(CSR op, CSR state) nogil except *:
+cdef double complex _expect_csr_dm(CSR op, CSR state) except * nogil:
     """
     Perform the operation
         tr(op @ state)
@@ -94,7 +94,7 @@ cdef double complex _expect_csr_dm(CSR op, CSR state) nogil except *:
     return out
 
 
-cpdef double complex expect_super_csr(CSR op, CSR state) nogil except *:
+cpdef double complex expect_super_csr(CSR op, CSR state) except * nogil:
     """
     Perform the operation `tr(op @ state)` where `op` is supplied as a
     superoperator, and `state` is a column-stacked operator.
@@ -112,7 +112,7 @@ cpdef double complex expect_super_csr(CSR op, CSR state) nogil except *:
     return out
 
 
-cpdef double complex expect_csr(CSR op, CSR state) nogil except *:
+cpdef double complex expect_csr(CSR op, CSR state) except * nogil:
     """
     Get the expectation value of the operator `op` over the state `state`.  The
     state can be either a ket or a density matrix.
@@ -125,8 +125,8 @@ cpdef double complex expect_csr(CSR op, CSR state) nogil except *:
     if state.shape[1] == 1:
         return _expect_csr_ket(op, state)
     return _expect_csr_dm(op, state)
-'expect_super_dense',
-cdef double complex _expect_csr_dense_ket(CSR op, Dense state) nogil except *:
+
+cdef double complex _expect_csr_dense_ket(CSR op, Dense state) except * nogil:
     _check_shape_ket(op, state)
     cdef double complex out=0, sum
     cdef size_t row, ptr
@@ -139,7 +139,7 @@ cdef double complex _expect_csr_dense_ket(CSR op, Dense state) nogil except *:
         out += sum * conj(state.data[row])
     return out
 
-cdef double complex _expect_csr_dense_dm(CSR op, Dense state) nogil except *:
+cdef double complex _expect_csr_dense_dm(CSR op, Dense state) except * nogil:
     _check_shape_dm(op, state)
     cdef double complex out=0
     cdef size_t row, ptr_op, ptr_state=0, row_stride, col_stride
@@ -154,7 +154,7 @@ cdef double complex _expect_csr_dense_dm(CSR op, Dense state) nogil except *:
     return out
 
 
-cdef double complex _expect_dense_ket(Dense op, Dense state) nogil except *:
+cdef double complex _expect_dense_ket(Dense op, Dense state) except * nogil:
     _check_shape_ket(op, state)
     cdef double complex out=0, sum
     cdef size_t row, col, op_row_stride, op_col_stride
@@ -169,7 +169,7 @@ cdef double complex _expect_dense_ket(Dense op, Dense state) nogil except *:
         out += sum * conj(state.data[row])
     return out
 
-cdef double complex _expect_dense_dense_dm(Dense op, Dense state) nogil except *:
+cdef double complex _expect_dense_dense_dm(Dense op, Dense state) except * nogil:
     _check_shape_dm(op, state)
     cdef double complex out=0
     cdef size_t row, col, op_row_stride, op_col_stride
@@ -186,7 +186,7 @@ cdef double complex _expect_dense_dense_dm(Dense op, Dense state) nogil except *
     return out
 
 
-cpdef double complex expect_csr_dense(CSR op, Dense state) nogil except *:
+cpdef double complex expect_csr_dense(CSR op, Dense state) except * nogil:
     """
     Get the expectation value of the operator `op` over the state `state`.  The
     state can be either a ket or a density matrix.
@@ -201,7 +201,7 @@ cpdef double complex expect_csr_dense(CSR op, Dense state) nogil except *:
     return _expect_csr_dense_dm(op, state)
 
 
-cpdef double complex expect_dense(Dense op, Dense state) nogil except *:
+cpdef double complex expect_dense(Dense op, Dense state) except * nogil:
     """
     Get the expectation value of the operator `op` over the state `state`.  The
     state can be either a ket or a density matrix.
@@ -216,7 +216,7 @@ cpdef double complex expect_dense(Dense op, Dense state) nogil except *:
     return _expect_dense_dense_dm(op, state)
 
 
-cpdef double complex expect_super_csr_dense(CSR op, Dense state) nogil except *:
+cpdef double complex expect_super_csr_dense(CSR op, Dense state) except * nogil:
     """
     Perform the operation `tr(op @ state)` where `op` is supplied as a
     superoperator, and `state` is a column-stacked operator.
@@ -232,7 +232,7 @@ cpdef double complex expect_super_csr_dense(CSR op, Dense state) nogil except *:
     return out
 
 
-cpdef double complex expect_super_dense(Dense op, Dense state) nogil except *:
+cpdef double complex expect_super_dense(Dense op, Dense state) except * nogil:
     """
     Perform the operation `tr(op @ state)` where `op` is supplied as a
     superoperator, and `state` is a column-stacked operator.

qutip/core/data/inner.pxd

@@ -2,5 +2,5 @@
 
 from qutip.core.data.csr cimport CSR
 
-cpdef double complex inner_csr(CSR left, CSR right, bint scalar_is_ket=*) nogil except *
-cpdef double complex inner_op_csr(CSR left, CSR op, CSR right, bint scalar_is_ket=*) nogil except *
+cpdef double complex inner_csr(CSR left, CSR right, bint scalar_is_ket=*) except * nogil
+cpdef double complex inner_op_csr(CSR left, CSR op, CSR right, bint scalar_is_ket=*) except * nogil

qutip/core/data/inner.pyx

@@ -21,7 +21,7 @@ __all__ = [
 ]
 
 
-cdef void _check_shape_inner(Data left, Data right) nogil except *:
+cdef void _check_shape_inner(Data left, Data right) except * nogil:
     if (
         (left.shape[0] != 1 and left.shape[1] != 1)
         or right.shape[1] != 1
@@ -33,7 +33,7 @@ cdef void _check_shape_inner(Data left, Data right) nogil except *:
             + str(right.shape)
         )
 
-cdef void _check_shape_inner_op(Data left, Data op, Data right) nogil except *:
+cdef void _check_shape_inner_op(Data left, Data op, Data right) except * nogil:
     cdef bint left_shape = left.shape[0] == 1 or left.shape[1] == 1
     cdef bint left_op = (
         (left.shape[0] == 1 and left.shape[1] == op.shape[0])
@@ -72,7 +72,7 @@ cdef double complex _inner_csr_ket_ket(CSR left, CSR right) nogil:
             out += conj(left.data[ptr_l]) * right.data[ptr_r]
     return out
 
-cpdef double complex inner_csr(CSR left, CSR right, bint scalar_is_ket=False) nogil except *:
+cpdef double complex inner_csr(CSR left, CSR right, bint scalar_is_ket=False) except * nogil:
     """
     Compute the complex inner product <left|right>.  The shape of `left` is
     used to determine if it has been supplied as a ket or a bra.  The result of
@@ -95,7 +95,7 @@ cpdef double complex inner_csr(CSR left, CSR right, bint scalar_is_ket=False) no
         return _inner_csr_bra_ket(left, right)
     return _inner_csr_ket_ket(left, right)
 
-cpdef double complex inner_dia(Dia left, Dia right, bint scalar_is_ket=False) nogil except *:
+cpdef double complex inner_dia(Dia left, Dia right, bint scalar_is_ket=False) except * nogil:
     """
     Compute the complex inner product <left|right>.  The shape of `left` is
     used to determine if it has been supplied as a ket or a bra.  The result of
@@ -134,7 +134,7 @@ cpdef double complex inner_dia(Dia left, Dia right, bint scalar_is_ket=False) no
 
     return inner
 
-cpdef double complex inner_dense(Dense left, Dense right, bint scalar_is_ket=False) nogil except *:
+cpdef double complex inner_dense(Dense left, Dense right, bint scalar_is_ket=False) except * nogil:
     """
     Compute the complex inner product <left|right>.  The shape of `left` is
     used to determine if it has been supplied as a ket or a bra.  The result of
@@ -194,7 +194,7 @@ cdef double complex _inner_op_csr_ket_ket(CSR left, CSR op, CSR right) nogil:
     return out
 
 cpdef double complex inner_op_dia(Dia left, Dia op, Dia right,
-                                   bint scalar_is_ket=False) nogil except *:
+                                   bint scalar_is_ket=False) except * nogil:
     """
     Compute the complex inner product <left|op|right>.  The shape of `left` is
     used to determine if it has been supplied as a ket or a bra.  The result of
@@ -238,7 +238,7 @@ cpdef double complex inner_op_dia(Dia left, Dia op, Dia right,
     return inner
 
 cpdef double complex inner_op_csr(CSR left, CSR op, CSR right,
-                                  bint scalar_is_ket=False) nogil except *:
+                                  bint scalar_is_ket=False) except * nogil:
     """
     Compute the complex inner product <left|op|right>.  The shape of `left` is
     used to determine if it has been supplied as a ket or a bra.  The result of

qutip/core/data/matmul.pyx

@@ -59,7 +59,7 @@ __all__ = [
 ]
 
 
-cdef void _check_shape(Data left, Data right, Data out=None) nogil except *:
+cdef void _check_shape(Data left, Data right, Data out=None) except * nogil:
     if left.shape[1] != right.shape[0]:
         raise ValueError(
             "incompatible matrix shapes "

qutip/core/data/norm.pxd

@@ -7,10 +7,10 @@ cpdef double one_csr(CSR matrix) except -1
 cpdef double trace_csr(CSR matrix) except -1
 cpdef double max_csr(CSR matrix) nogil
 cpdef double frobenius_csr(CSR matrix) nogil
-cpdef double l2_csr(CSR matrix) nogil except -1
+cpdef double l2_csr(CSR matrix) except -1 nogil
 
 cpdef double frobenius_dense(Dense matrix) nogil
-cpdef double l2_dense(Dense matrix) nogil except -1
+cpdef double l2_dense(Dense matrix) except -1 nogil
 
 cpdef double one_dia(Dia matrix) except -1
 cpdef double max_dia(Dia matrix) nogil