More fixes for Cython3

setup.py

@@ -176,8 +176,8 @@ def fortran_compiler_flags(self):
         logging.debug('Platform {}'.format(self.platform))
 
         if args[0].sundials_home:
-            self.incdirs = os.path.join(self.sundialsdir,'include')
-            self.libdirs = os.path.join(self.sundialsdir,'lib')
+            self.incdirs = os.path.join(self.sundialsdir, 'include')
+            self.libdirs = os.path.join(self.sundialsdir, 'lib')
         elif 'win' in self.platform:
             self.incdirs = ''
             self.libdirs = ''
@@ -420,7 +420,7 @@ def check_SUNDIALS(self):
                                 break
                     if os.path.exists(os.path.join(self.libdirs,'sundials_nvecserial.lib')) and not os.path.exists(os.path.join(self.libdirs,'libsundials_nvecserial.a')):
                         sundials_with_msvc = True
-            except Exception as e:
+            except Exception:
                 if os.path.exists(os.path.join(os.path.join(self.incdirs,'arkode'), 'arkode.h')): #This was added in 2.6
                     sundials_version = (2,6,0)
                     logging.debug('SUNDIALS 2.6 found.')

src/algebraic.pyx

@@ -21,8 +21,8 @@ import numpy as N
 cimport numpy as N
 from timeit import default_timer as timer
 
-from exception import Algebraic_Exception, AssimuloException
-from problem import Algebraic_Problem
+from assimulo.exception import Algebraic_Exception, AssimuloException
+from assimulo.problem import Algebraic_Problem
 
 include "constants.pxi" #Includes the constants (textual include)
 

src/explicit_ode.pyx

@@ -25,7 +25,7 @@ import numpy as N
 cimport numpy as N
 from timeit import default_timer as timer
 
-from assimulo.ode cimport ODE     
+from assimulo.ode cimport ODE
 from assimulo.explicit_ode cimport Explicit_ODE, f_event_locator
 
 from assimulo.problem import Explicit_Problem, Delay_Explicit_Problem, SingPerturbed_Problem, cExplicit_Problem

src/implicit_ode.pxd

@@ -15,12 +15,10 @@
 # You should have received a copy of the GNU Lesser General Public License
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
-
-from ode cimport ODE
 import numpy as N
 cimport numpy as N
 
+from assimulo.ode cimport ODE
 
 cdef class Implicit_ODE(ODE):
     cpdef _simulate(self, double t0, double tfinal,N.ndarray output_list,int COMPLETE_STEP, int INTERPOLATE_OUTPUT,int TIME_EVENT)
-

src/implicit_ode.pyx

@@ -17,18 +17,16 @@
 
 # distutils: define_macros=NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
 
-from ode cimport ODE
-from problem import Implicit_Problem, cImplicit_Problem, Overdetermined_Problem
-from problem import cExplicit_Problem
-
 import itertools
 import sys
+import warnings
 import numpy as N
 cimport numpy as N
-
-from exception import TerminateSimulation, TimeLimitExceeded
 from timeit import default_timer as timer
-import warnings
+
+from assimulo.ode cimport ODE
+from assimulo.problem import Implicit_Problem, cExplicit_Problem, cImplicit_Problem, Overdetermined_Problem
+from assimulo.exception import TerminateSimulation, TimeLimitExceeded
 
 realtype = float
 

src/lib/sundials_callbacks.pxi

@@ -21,7 +21,7 @@ import cython
 # Module functions
 #=================
 
-cdef N_Vector N_VNewEmpty_Euclidean(long int n):
+cdef N_Vector N_VNewEmpty_Euclidean(long int n) noexcept:
     IF SUNDIALS_VERSION >= (6,0,0):
         cdef SUNDIALS.SUNContext ctx = NULL
         cdef void * comm = NULL
@@ -32,7 +32,7 @@ cdef N_Vector N_VNewEmpty_Euclidean(long int n):
     v.ops.nvwrmsnorm = v.ops.nvwl2norm #Overwrite the WRMS norm to the 2-Norm
     return v
 
-cdef inline N_Vector arr2nv(x):
+cdef inline N_Vector arr2nv(x) noexcept:
     x=N.array(x)
     cdef long int n = len(x)
     cdef N.ndarray[realtype, ndim=1,mode='c'] ndx=x
@@ -47,7 +47,7 @@ cdef inline N_Vector arr2nv(x):
     memcpy((<N_VectorContent_Serial>v.content).data, data_ptr, n*sizeof(realtype))
     return v
 
-cdef inline N_Vector arr2nv_euclidean(x):
+cdef inline N_Vector arr2nv_euclidean(x) noexcept:
     x=N.array(x)
     cdef long int n = len(x)
     cdef N.ndarray[realtype, ndim=1,mode='c'] ndx=x
@@ -56,33 +56,33 @@ cdef inline N_Vector arr2nv_euclidean(x):
     memcpy((<N_VectorContent_Serial>v.content).data, data_ptr, n*sizeof(realtype))
     return v
 
-cdef inline void arr2nv_inplace(x, N_Vector out):
+cdef inline void arr2nv_inplace(x, N_Vector out) noexcept:
     x=N.array(x)
     cdef long int n = len(x)
     cdef N.ndarray[realtype, ndim=1,mode='c'] ndx=x
     cdef void* data_ptr=PyArray_DATA(ndx)
     memcpy((<N_VectorContent_Serial>out.content).data, data_ptr, n*sizeof(realtype))
 
-cdef inline N.ndarray nv2arr(N_Vector v):
+cdef inline N.ndarray nv2arr(N_Vector v) noexcept:
     cdef long int n = (<N_VectorContent_Serial>v.content).length
     cdef realtype* v_data = (<N_VectorContent_Serial>v.content).data
     cdef N.ndarray[realtype, ndim=1, mode='c'] x=N.empty(n)
     memcpy(PyArray_DATA(x), v_data, n*sizeof(realtype))
     return x
 
-cdef inline void nv2arr_inplace(N_Vector v, N.ndarray o):
+cdef inline void nv2arr_inplace(N_Vector v, N.ndarray o) noexcept:
     cdef long int n = (<N_VectorContent_Serial>v.content).length
     cdef realtype* v_data = (<N_VectorContent_Serial>v.content).data
     memcpy(PyArray_DATA(o), v_data, n*sizeof(realtype))
 
-cdef inline void nv2mat_inplace(int Ns, N_Vector *v, N.ndarray o):
+cdef inline void nv2mat_inplace(int Ns, N_Vector *v, N.ndarray o) noexcept:
     cdef long int i,j, Nf
     for i in range(Ns):
         Nf = (<N_VectorContent_Serial>v[i].content).length
         for j in range(Nf):
             o[j,i] = (<N_VectorContent_Serial>v[i].content).data[j]
 
-cdef inline realtype2arr(realtype *data, int n):
+cdef inline realtype2arr(realtype *data, int n) noexcept:
     """Create new numpy array from realtype*"""
     cdef N.ndarray[realtype, ndim=1, mode='c'] x=N.empty(n)
     memcpy(PyArray_DATA(x), data, n*sizeof(realtype))

src/lib/sundials_callbacks_ida_cvode.pxi

@@ -19,7 +19,7 @@ import cython
 import traceback
 from assimulo.exception import AssimuloRecoverableError
 
-cdef int cv_rhs(realtype t, N_Vector yv, N_Vector yvdot, void* problem_data):
+cdef int cv_rhs(realtype t, N_Vector yv, N_Vector yvdot, void* problem_data) noexcept:
     """
     This method is used to connect the Assimulo.Problem.f to the Sundials
     right-hand-side function.
@@ -57,7 +57,7 @@ cdef int cv_rhs(realtype t, N_Vector yv, N_Vector yvdot, void* problem_data):
 
 cdef int cv_sens_rhs_all(int Ns, realtype t, N_Vector yv, N_Vector yvdot,
                          N_Vector *yvS, N_Vector *yvSdot, void *problem_data, 
-                         N_Vector tmp1, N_Vector tmp2):
+                         N_Vector tmp1, N_Vector tmp2) noexcept:
 
     cdef ProblemData pData = <ProblemData>problem_data
     cdef N.ndarray y = pData.work_y
@@ -92,7 +92,7 @@ IF SUNDIALS_VERSION >= (3,0,0):
     @cython.boundscheck(False)
     @cython.wraparound(False)
     cdef int cv_jac_sparse(realtype t, N_Vector yv, N_Vector fy, SUNMatrix Jac,
-                    void *problem_data, N_Vector tmp1, N_Vector tmp2, N_Vector tmp3):
+                    void *problem_data, N_Vector tmp1, N_Vector tmp2, N_Vector tmp3) noexcept:
         """
         This method is used to connect the Assimulo.Problem.jac to the Sundials
         Sparse Jacobian function.
@@ -146,7 +146,7 @@ ELSE:
     @cython.boundscheck(False)
     @cython.wraparound(False)
     cdef int cv_jac_sparse(realtype t, N_Vector yv, N_Vector fy, SlsMat Jacobian,
-                    void *problem_data, N_Vector tmp1, N_Vector tmp2, N_Vector tmp3):
+                    void *problem_data, N_Vector tmp1, N_Vector tmp2, N_Vector tmp3) noexcept:
         """
         This method is used to connect the Assimulo.Problem.jac to the Sundials
         Sparse Jacobian function.
@@ -213,7 +213,7 @@ ELSE:
 
 IF SUNDIALS_VERSION >= (3,0,0):
     cdef int cv_jac(realtype t, N_Vector yv, N_Vector fy, SUNMatrix Jac, 
-                void *problem_data, N_Vector tmp1, N_Vector tmp2, N_Vector tmp3):
+                void *problem_data, N_Vector tmp1, N_Vector tmp2, N_Vector tmp3) noexcept:
         """
         This method is used to connect the Assimulo.Problem.jac to the Sundials
         Jacobian function.
@@ -264,7 +264,7 @@ IF SUNDIALS_VERSION >= (3,0,0):
         return CVDLS_SUCCESS
 ELSE:
     cdef int cv_jac(long int Neq, realtype t, N_Vector yv, N_Vector fy, DlsMat Jacobian, 
-                    void *problem_data, N_Vector tmp1, N_Vector tmp2, N_Vector tmp3):
+                    void *problem_data, N_Vector tmp1, N_Vector tmp2, N_Vector tmp3) noexcept:
         """
         This method is used to connect the Assimulo.Problem.jac to the Sundials
         Jacobian function.
@@ -315,7 +315,7 @@ ELSE:
 
 
 cdef int cv_jacv(N_Vector vv, N_Vector Jv, realtype t, N_Vector yv, N_Vector fyv,
-				    void *problem_data, N_Vector tmp):
+				    void *problem_data, N_Vector tmp) noexcept:
     """
     This method is used to connect the Assimulo.Problem.jacv to the Sundials
     Jacobian times vector function.
@@ -365,7 +365,7 @@ cdef int cv_jacv(N_Vector vv, N_Vector Jv, realtype t, N_Vector yv, N_Vector fyv
 IF SUNDIALS_VERSION >= (3,0,0):
     cdef int cv_prec_setup(realtype t, N_Vector yy, N_Vector fyy,
                       bint jok, bint *jcurPtr,
-                      realtype gamma, void *problem_data):
+                      realtype gamma, void *problem_data) noexcept:
         """
         For information see CVODES documentation 4.6.9
         """
@@ -387,7 +387,7 @@ IF SUNDIALS_VERSION >= (3,0,0):
     cdef int cv_prec_solve(realtype t, N_Vector yy, N_Vector fyy,
                       N_Vector rr, N_Vector z,
                       realtype gamma, realtype delta,
-                      int lr, void *problem_data):
+                      int lr, void *problem_data) noexcept:
         """
         For information see CVODES documentation 4.6.8
         """
@@ -412,7 +412,7 @@ ELSE:
                       bint jok, bint *jcurPtr,
                       realtype gamma, void *problem_data,
                       N_Vector tmp1, N_Vector tmp2,
-                      N_Vector tmp3):
+                      N_Vector tmp3) noexcept:
         """
         For information see CVODES documentation 4.6.9
         """
@@ -434,7 +434,7 @@ ELSE:
     cdef int cv_prec_solve(realtype t, N_Vector yy, N_Vector fyy,
                       N_Vector rr, N_Vector z,
                       realtype gamma, realtype delta,
-                      int lr, void *problem_data, N_Vector tmp):
+                      int lr, void *problem_data, N_Vector tmp) noexcept:
         """
         For information see CVODES documentation 4.6.8
         """
@@ -461,9 +461,9 @@ cdef int cv_prec(realtype t, N Vector yv, N Vector fyv,
          void *problem_data, N Vector tmp):
     
     cdef ProblemData pData = <ProblemData>problem_data
-    cdef N.ndarray y  = nv2arr(yv)
+    cdef N.ndarray y = nv2arr(yv)
     cdef N.ndarray fy = nv2arr(fyv)
-    cdef N.ndarray r  = nv2arr(rv)
+    cdef N.ndarray r = nv2arr(rv)
     cdef int i
     
     cdef realtype* zptr=(<N_VectorContent_Serial>z.content).data
@@ -480,7 +480,7 @@ cdef int cv_prec(realtype t, N Vector yv, N Vector fyv,
         return SPGMR_PSOLVE_FAIL_UNREC
 """
 
-cdef int cv_root(realtype t, N_Vector yv, realtype *gout,  void* problem_data):
+cdef int cv_root(realtype t, N_Vector yv, realtype *gout, void* problem_data) noexcept:
     """
     This method is used to connect the Assimulo.Problem.state_events to the Sundials
     Root-finding function.
@@ -503,9 +503,9 @@ cdef int cv_root(realtype t, N_Vector yv, realtype *gout,  void* problem_data):
 
         return CV_SUCCESS
     except Exception:
-        return CV_RTFUNC_FAIL  # Unrecoverable Error
+        return CV_RTFUNC_FAIL # Unrecoverable Error
 
-cdef int ida_res(realtype t, N_Vector yv, N_Vector yvdot, N_Vector residual, void* problem_data):
+cdef int ida_res(realtype t, N_Vector yv, N_Vector yvdot, N_Vector residual, void* problem_data) noexcept:
     """
     This method is used to connect the Assimulo.Problem.f to the Sundials
     residual function.
@@ -559,7 +559,7 @@ cdef int ida_res(realtype t, N_Vector yv, N_Vector yvdot, N_Vector residual, voi
 
 IF SUNDIALS_VERSION >= (3,0,0):
     cdef int ida_jac(realtype t, realtype c, N_Vector yv, N_Vector yvdot, N_Vector residual, SUNMatrix Jac,
-                 void *problem_data, N_Vector tmp1, N_Vector tmp2, N_Vector tmp3):
+                 void *problem_data, N_Vector tmp1, N_Vector tmp2, N_Vector tmp3) noexcept:
         """
         This method is used to connect the Assimulo.Problem.jac to the Sundials
         Jacobian function.
@@ -612,7 +612,7 @@ IF SUNDIALS_VERSION >= (3,0,0):
                 return IDADLS_JACFUNC_UNRECVR
 ELSE:
     cdef int ida_jac(long int Neq, realtype t, realtype c, N_Vector yv, N_Vector yvdot, N_Vector residual, DlsMat Jacobian,
-                 void* problem_data, N_Vector tmp1, N_Vector tmp2, N_Vector tmp3):
+                 void* problem_data, N_Vector tmp1, N_Vector tmp2, N_Vector tmp3) noexcept:
         """
         This method is used to connect the Assimulo.Problem.jac to the Sundials
         Jacobian function.
@@ -664,7 +664,7 @@ ELSE:
                 return IDADLS_JACFUNC_UNRECVR
 
 
-cdef int ida_root(realtype t, N_Vector yv, N_Vector yvdot, realtype *gout,  void* problem_data):
+cdef int ida_root(realtype t, N_Vector yv, N_Vector yvdot, realtype *gout, void* problem_data) noexcept:
     """
     This method is used to connect the Assimulo.Problem.state_events to the Sundials
     root function.
@@ -693,7 +693,7 @@ cdef int ida_root(realtype t, N_Vector yv, N_Vector yvdot, realtype *gout,  void
         return IDA_RTFUNC_FAIL  # Unrecoverable Error
 
 cdef int ida_jacv(realtype t, N_Vector yy, N_Vector yp, N_Vector rr, N_Vector vv, N_Vector Jv, realtype cj,
-				    void *problem_data, N_Vector tmp1, N_Vector tmp2):
+				    void *problem_data, N_Vector tmp1, N_Vector tmp2) noexcept:
     """
     This method is used to connect the Assimulo.Problem.jacv to the Sundials
     Jacobian times vector function.
@@ -744,7 +744,7 @@ cdef int ida_jacv(realtype t, N_Vector yy, N_Vector yp, N_Vector rr, N_Vector vv
 # Error handling callback functions
 # =================================
 
-cdef void cv_err(int error_code, const char *module, const char *function, char *msg, void *problem_data):
+cdef void cv_err(int error_code, const char *module, const char *function, char *msg, void *problem_data) noexcept:
     """
     This method overrides the default handling of error messages.
     """
@@ -757,7 +757,7 @@ cdef void cv_err(int error_code, const char *module, const char *function, char
         if error_code < 0: #Error
             print('[CVode Error]', msg)
 
-cdef void ida_err(int error_code, const char *module, const char *function, char *msg, void *problem_data):
+cdef void ida_err(int error_code, const char *module, const char *function, char *msg, void *problem_data) noexcept:
     """
     This method overrides the default handling of error messages.
     """