First steps toward Python 3.11 & Cython3

doc/sphinx/source/markup.py

@@ -113,7 +113,7 @@ def mark_solvers():
         elif solver[1] == "DAE_OVER":
             file.write('    mod = '+problem_name+'(res, y0, yd0, t0)\n\n')
         else:
-            print "Unknown solver type"
+            print("Unknown solver type")
         file.write('.. note::\n\n')
         file.write('    For complex problems, it is recommended to check the available :doc:`examples <examples>` and the documentation in the problem class, :class:`'+problem_name+ ' <assimulo.problem.'+problem_name+'>`. It is also recommended to define your problem as a subclass of :class:`'+problem_name+ ' <assimulo.problem.'+problem_name+'>`.\n\n')
         file.write('.. warning::\n\n')

setup.py

@@ -15,14 +15,15 @@
 # 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 distutils.core import setup, Extension
-import numpy as np
 import logging
 import sys 
 import os
-import shutil as SH
+import shutil
 import ctypes.util
 import argparse
 from os.path import isfile, join
+import numpy as np
+import numpy.distutils.core as ndc
 
 def str2bool(v):
     return v.lower() in ("yes", "true", "t", "1")
@@ -76,7 +77,7 @@ def remove_prefix(name, prefix):
 import numpy.distutils as nd
 
 try:
-    from Cython.Distutils import build_ext
+    # from Cython.Distutils import build_ext ## TODO: obsolete?
     from Cython.Build import cythonize
 except ImportError:
     msg="Please upgrade to a newer Cython version, >= 0.18."
@@ -105,7 +106,7 @@ def create_dir(self,d):
     def copy_file(self,fi, to_dir):
         # copies only files not directories
         if not os.path.isdir(fi):
-            SH.copy2(fi, to_dir)
+            shutil.copy2(fi, to_dir)
     def copy_all_files(self,file_list, from_dir, to_dir):
         logging.debug('fromdir {}  todir {}'.format(from_dir,to_dir))
         for f in file_list:
@@ -114,8 +115,8 @@ def copy_all_files(self,file_list, from_dir, to_dir):
             else:
                 self.copy_file(f,to_dir)
     def __init__(self,args, thirdparty_methods):
-        # args[0] are optinal arguments given above
-        # args[1] are argumenets passed to distutils 
+        # args[0] are optional arguments given above
+        # args[1] are arguments passed to distutils 
         self.distutil_args=args[1]
         if args[0].prefix:
             self.prefix = args[0].prefix.replace('/',os.sep)   # required in this way for cygwin etc.
@@ -167,10 +168,11 @@ def fortran_compiler_flags(self):
         nd.fcompiler.intel.IntelVisualFCompiler.get_flags=fortran_compiler_flags
 
         self.platform = 'linux'
-        if 'win' in sys.platform: self.platform = 'win'
-        if 'darwin' in sys.platform: self.platform = 'mac' 
+        if 'win' in sys.platform: 
+            self.platform = 'win'
+        if 'darwin' in sys.platform: 
+            self.platform = 'mac' 
 
-        self.is_python3 = True if sys.version_info.major >= 3 else False
         logging.debug('Platform {}'.format(self.platform))
 
         if args[0].sundials_home:
@@ -241,8 +243,9 @@ def create_assimulo_dirs_and_populate(self):
         for f in self.filelist_thirdparty.items():
             logging.debug('Thirdparty method {} file {} copied'.format(f[0],f[1]))
             self.copy_all_files(f[1],os.path.join("thirdparty", f[0]), self.desThirdParty[f[0]])
+            license_name = f[0].upper() if f[0].upper() != "RADAU5" else "HAIRER"
             try:   
-                SH.copy2(os.path.join("thirdparty",f[0],"LICENSE_{}".format(f[0].upper())),self.desLib)
+                shutil.copy2(os.path.join("thirdparty", f[0], "LICENSE_{}".format(license_name)), self.desLib)
             except IOError:
                 logging.warning('No license file {} found.'.format("LICENSE_{}".format(f[0].upper())))
 
@@ -262,8 +265,8 @@ def create_assimulo_dirs_and_populate(self):
         if self.extra_fortran_link_files:
             for extra_fortran_lib in self.extra_fortran_link_files:
                 path_extra_fortran_lib = ctypes.util.find_library(extra_fortran_lib)
-                if path_extra_fortran_lib != None:
-                    SH.copy2(path_extra_fortran_lib,self.desSrc)
+                if path_extra_fortran_lib is not None:
+                    shutil.copy2(path_extra_fortran_lib,self.desSrc)
                 else:
                     logging.debug("Could not find Fortran link file: "+str(extra_fortran_lib))
 
@@ -469,18 +472,24 @@ def cython_extensionlists(self):
 
         # Cythonize main modules 
         ext_list = cythonize([os.path.join("assimulo", "explicit_ode.pyx")], 
-                             include_path=[".", "assimulo"], force = True)
+                             include_path=[".", "assimulo"],
+                             force = True,
+                             compiler_directives={'language_level' : "3str"})
         ext_list[-1].include_dirs += ["assimulo", self.incdirs]
         ext_list[-1].sources += [os.path.join("assimulo", "ode_event_locator.c")]
 
         remaining_pyx = ["algebraic", "implicit_ode", "ode", "problem", "special_systems", "support"]
         ext_list += cythonize([os.path.join("assimulo", "{}.pyx".format(x)) for x in remaining_pyx], 
-                              include_path=[".", "assimulo"], force = True)
+                              include_path=[".", "assimulo"],
+                              force = True,
+                              compiler_directives={'language_level' : "3str"})
 
         # Cythonize Solvers
         # Euler
         ext_list += cythonize([os.path.join("assimulo", "solvers", "euler.pyx")], 
-                              include_path=[".", "assimulo", os.path.join("assimulo", "solvers")], force = True)
+                              include_path=[".", "assimulo", os.path.join("assimulo", "solvers")],
+                              force = True,
+                              compiler_directives={'language_level' : "3str"},)
 
         # SUNDIALS
         if self.with_SUNDIALS:
@@ -491,7 +500,9 @@ def cython_extensionlists(self):
             #CVode and IDA
             ext_list += cythonize(["assimulo" + os.path.sep + "solvers" + os.path.sep + "sundials.pyx"], 
                                  include_path=[".","assimulo","assimulo" + os.sep + "lib"],
-                                 compile_time_env=compile_time_env, force=True)
+                                 compile_time_env=compile_time_env,
+                                 force=True,
+                                 compiler_directives={'language_level' : "3str"})
             ext_list[-1].include_dirs = [np.get_include(), "assimulo","assimulo"+os.sep+"lib", self.incdirs]
             ext_list[-1].library_dirs = [self.libdirs]
 
@@ -510,7 +521,9 @@ def cython_extensionlists(self):
             #Kinsol
             ext_list += cythonize(["assimulo"+os.path.sep+"solvers"+os.path.sep+"kinsol.pyx"], 
                         include_path=[".","assimulo","assimulo"+os.sep+"lib"],
-                        compile_time_env=compile_time_env, force=True)
+                        compile_time_env=compile_time_env,
+                        force=True,
+                        compiler_directives={'language_level' : "3str"})
             ext_list[-1].include_dirs = [np.get_include(), "assimulo","assimulo"+os.sep+"lib", self.incdirs]
             ext_list[-1].library_dirs = [self.libdirs]
             ext_list[-1].libraries = ["sundials_kinsol", "sundials_nvecserial"]
@@ -523,7 +536,8 @@ def cython_extensionlists(self):
         ## Radau5
         ext_list += cythonize([os.path.join("assimulo","thirdparty","radau5","radau5ode.pyx")],
                             include_path=[".", "assimulo", os.path.join("assimulo", "lib")],
-                            force = True)
+                            force = True,
+                            compiler_directives={'language_level' : "3str"})
         ext_list[-1].include_dirs = [np.get_include(), "assimulo", os.path.join("assimulo", "lib"),
                                     os.path.join("assimulo","thirdparty","radau5"),
                                     self.incdirs]
@@ -573,8 +587,7 @@ def cython_extensionlists(self):
             el.extra_compile_args += self.flag_32bit + self.extra_c_flags
 
         for el in ext_list:
-            if self.is_python3:
-                el.cython_directives = {"language_level": 3} 
+            # el.cython_directives = {"language_level": "3str"} ## TODO: Redundant?
             el.extra_link_args += extra_link_flags
         return ext_list
 
@@ -718,7 +731,6 @@ def fortran_extensionlists(self):
                for pck in  thirdparty_methods for place in ['thirdparty','lib']]
 logging.debug(license_info)
 
-import numpy.distutils.core as ndc
 ndc.setup(name=NAME,
       version=VERSION,
       license=LICENSE,
@@ -741,4 +753,3 @@ def fortran_extensionlists(self):
 
 if change_dir:
     os.chdir(curr_dir) #Change back to original directory
-

src/__init__.py

@@ -30,7 +30,7 @@ def wrap(func):
 
 try:
     import os
-    curr_dir = os.path.dirname(os.path.abspath(__file__));
+    curr_dir = os.path.dirname(os.path.abspath(__file__))
     _fpath=os.path.join(curr_dir,'version.txt')
     with open(_fpath, 'r') as f:
         __version__=f.readline().strip()

src/algebraic.pyx

@@ -15,6 +15,8 @@
 # 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/>.
 
+# distutils: define_macros=NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
+
 import numpy as N
 cimport numpy as N
 from timeit import default_timer as timer

src/explicit_ode.pyx

@@ -15,6 +15,8 @@
 # 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/>.
 
+# distutils: define_macros=NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
+
 from ode cimport ODE     
 from problem import Explicit_Problem, Delay_Explicit_Problem, SingPerturbed_Problem, cExplicit_Problem
 
@@ -48,7 +50,7 @@ cdef void c2py_d(N.ndarray[double, ndim=1, mode='c'] dest, double* source, int d
     """Copy (double *) C vector to 1D numpy array."""
     memcpy(N.PyArray_DATA(dest), source, dim*sizeof(double))
 
-cdef int callback_event(int n_y, int n_g, double t, double* y_in, double* g_out, void* f_event_EXT):
+cdef int callback_event(int n_y, int n_g, double t, double* y_in, double* g_out, void* f_event_EXT) noexcept:
     """Event indicator callback function to event_locator.c"""
     cdef N.ndarray[double, ndim=1, mode="c"]y_py = N.empty(n_y, dtype = N.double)
     c2py_d(y_py, y_in, n_y)
@@ -58,7 +60,7 @@ cdef int callback_event(int n_y, int n_g, double t, double* y_in, double* g_out,
     py2c_d(g_out, g_high, n_g)
     return ret
 
-cdef int callback_interp(int n, double t, double* y_out, void* f_interp_EXT):
+cdef int callback_interp(int n, double t, double* y_out, void* f_interp_EXT) noexcept:
     """Interpolation callback function to event_locator.c"""
     y_interp = (<object>f_interp_EXT)(t)
     py2c_d(y_out, y_interp, n)

src/implicit_ode.pyx

@@ -15,6 +15,8 @@
 # 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/>.
 
+# 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

src/lib/sundials_callbacks_ida_cvode.pxi

@@ -16,6 +16,7 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import cython
+import traceback
 from assimulo.exception import AssimuloRecoverableError
 
 cdef int cv_rhs(realtype t, N_Vector yv, N_Vector yvdot, void* problem_data):
@@ -750,11 +751,11 @@ cdef void cv_err(int error_code, const char *module, const char *function, char
     cdef ProblemData pData = <ProblemData>problem_data
 
     if error_code > 0 and pData.verbose > 0: #Warning
-        print '[CVode Warning]', msg
+        print('[CVode Warning]', msg)
 
     if pData.verbose > 2: #Verbosity is greater than NORMAL, print warnings and errors
         if error_code < 0: #Error
-            print '[CVode Error]', msg
+            print('[CVode Error]', msg)
 
 cdef void ida_err(int error_code, const char *module, const char *function, char *msg, void *problem_data):
     """
@@ -763,11 +764,11 @@ cdef void ida_err(int error_code, const char *module, const char *function, char
     cdef ProblemData pData = <ProblemData>problem_data
 
     if error_code > 0 and pData.verbose > 0: #Warning
-        print '[IDA Warning]', msg
+        print('[IDA Warning]', msg)
 
     if pData.verbose > 2: #Verbosity is greater than NORMAL, print warnings and errors
         if error_code < 0: #Error
-            print '[IDA Error]', msg
+            print('[IDA Error]', msg)
 
 
 cdef class ProblemData:

src/lib/sundials_callbacks_kinsol.pxi

@@ -16,6 +16,7 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import cython
+import traceback
 from assimulo.exception import AssimuloRecoverableError
 
 IF SUNDIALS_VERSION >= (3,0,0):
@@ -229,9 +230,9 @@ cdef void kin_err(int err_code, const char *module, const char *function, char *
     else:
         category = 0
 
-    print "Error occured in <function: %s>."%function
-    print "<message: %s>"%msg
-    #print "<functionNorm: %g, scaledStepLength: %g, tolerance: %g>"%(fnorm, snorm, pData.TOL)
+    print("Error occured in <function: %s>."%function)
+    print("<message: %s>"%msg)
+    #print("<functionNorm: %g, scaledStepLength: %g, tolerance: %g>"%(fnorm, snorm, pData.TOL))
 
 
 cdef void kin_info(const char *module, const char *function, char *msg, void *eh_data):
@@ -246,8 +247,8 @@ cdef void kin_info(const char *module, const char *function, char *msg, void *eh
 
     pData.log.append([module, function, msg])
 
-    #print "KinsolInfo <calling_function:%s>"%function
-    #print "<message: %s>"%msg
+    #print("KinsolInfo <calling_function:%s>"%function)
+    #print("<message: %s>"%msg)
     """
     # Get the number of iterations
     KINGetNumNonlinSolvIters(kin_mem, &nniters)
@@ -262,9 +263,9 @@ cdef void kin_info(const char *module, const char *function, char *msg, void *eh
     
     
     if ("KINSolInit" in function or "KINSol" in function) and "nni" in msg:
-        print "<iteration_index:%d>"%nniters
-        print "ivs", N_VGetArrayPointer(kin_mem->kin_uu), block->n);
-        print "<scaled_residual_norm:%E>", kin_mem->kin_fnorm);
+        print("<iteration_index:%d>"%nniters)
+        print("ivs", N_VGetArrayPointer(kin_mem->kin_uu), block->n))
+        print("<scaled_residual_norm:%E>", kin_mem->kin_fnorm))
         print "residuals", 
             realtype* f = N_VGetArrayPointer(kin_mem->kin_fval);
             f[i]*residual_scaling_factors[i]

src/ode.pyx

@@ -15,6 +15,8 @@
 # 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/>.
 
+# distutils: define_macros=NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
+
 import numpy as N
 cimport numpy as N
 from timeit import default_timer as timer
@@ -555,9 +557,9 @@ cdef class ODE:
         """
         cdef i = 0
         for i in self.event_data:
-            print 'Time, t = %e'%i[0]
-            print '  Event info, ', i[1]
-        print 'Number of events: ', len(self.event_data)
+            print('Time, t = %e'%i[0])
+            print('Event info, ', i[1])
+        print('Number of events: ', len(self.event_data))
 
     def print_statistics(self, verbose=NORMAL):
         """

src/problem.pyx

@@ -15,6 +15,8 @@
 # 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/>.
 
+# distutils: define_macros=NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
+
 import numpy as N
 cimport numpy as N
 

src/solvers/euler.pyx

@@ -15,6 +15,8 @@
 # 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/>.
 
+# distutils: define_macros=NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
+
 cimport numpy as N
 import numpy as N
 import numpy.linalg as LIN
@@ -363,7 +365,8 @@ cdef class ImplicitEuler(Explicit_ODE):
         """
         This calculates the next step in the integration.
         """
-        cdef double new_norm, old_norm
+        cdef double new_norm = 0
+        cdef double old_norm = 0
         cdef double tn1 = t+h
         cdef N.ndarray yn = y.copy() #Old y
         #cdef N.ndarray yn1 = y.copy() #First newton guess

src/solvers/kinsol.pyx

@@ -423,7 +423,7 @@ cdef class KINSOL(Algebraic):
         if flag < 0:
             raise KINSOLError(flag)
         if flag == KIN_STEP_LT_STPTOL:
-            print 'Scaled step length too small. Either an approximate solution or a local minimum is reached. Check value of residual.'
+            print('Scaled step length too small. Either an approximate solution or a local minimum is reached. Check value of residual.')
 
         self.store_statistics()
 

src/solvers/odepack.py

@@ -186,7 +186,7 @@ def integrate_start(self, t, y):
         """
         Helper program for the initialization of LSODAR
         """
-        #print ' We have rkstarter {} and rkstarter_active {}'.format(self.rkstarter, self._rkstarter_active)
+        #print('We have rkstarter {} and rkstarter_active {}'.format(self.rkstarter, self._rkstarter_active))
         if not(self.rkstarter>1 and self._rkstarter_active):
             # first call or classical restart after a discontinuity
             ISTATE=1
@@ -409,7 +409,7 @@ def state_events(t,y):
             opts["output_index"] = output_index
         # deciding on restarting options
         self._rkstarter_active = True if ISTATE == 3 and self.rkstarter > 1 else False
-        #print 'rkstarter_active set to {} and ISTATE={}'.format(self._rkstarter_active, ISTATE)
+        #print('rkstarter_active set to {} and ISTATE={}'.format(self._rkstarter_active, ISTATE))
 
         #Retrieving statistics
         self.statistics["nstatefcns"]            += IWORK[9]