integrator python 2.7 and 3.x compatible

README.md

@@ -70,21 +70,20 @@ However, here is a small example using the above oscillating CRN.
             [['C', 'A'],['A','A'],0.9]]
 >>> RG = ReactionGraph(crn)
 >>> filename, odename = RG.write_ODE_lib(filename='ozzy.py')
->>> print 'Wrote ODE system file:', filename
+>>> print('Wrote ODE system file:', filename)
 Wrote ODE system file: ozzy.py
 ```
 
 Then go ahead and execute `ozzy.py`
 ```sh
-~$ python ./ozzy.py --p0 1=1e-6 2=2e-6 3=5e-6
+~$ python ./ozzy.py --p0 1=1e-6 2=2e-6 3=5e-6 --t8 1e8 --pyplot ozzy.pdf
 ```
 
 ... or load it as python library.
 
 ```py
->>> import imp
->>> _temp = imp.load_source(odename, filename)
->>> integrate = getattr(_temp, 'integrate')
+>>> from crnsimulator import get_integrator
+>>> integrate = get_integrator(odename, filename)
 >>> integrate(args) # args = <argparse.ArgumentParser()>
 ```
 
@@ -100,5 +99,5 @@ Then go ahead and execute `ozzy.py`
 ```
 
 ## Version
-0.5
+0.6
 

crnsimulator/__init__.py

@@ -6,9 +6,9 @@
 # Use at your own risk.
 #
 #
-__version__ = "v0.5"
+__version__ = "v0.6"
 
 from crnsimulator.crn_parser import parse_crn_string, parse_crn_file
 from crnsimulator.reactiongraph import ReactionGraph
-from crnsimulator.solver import writeODElib
+from crnsimulator.solver import writeODElib, get_integrator
 from crnsimulator.odelib_template import ode_plotter

crnsimulator/solver.py

@@ -11,6 +11,22 @@
 from builtins import range
 import crnsimulator.odelib_template
 
+def get_integrator(odename, filename):
+    """Workaround to avoid deprecation warnings for the imp module.
+    """
+    try: # Python 3.7
+        import types
+        import importlib.machinery
+
+        loader = importlib.machinery.SourceFileLoader(odename, filename)
+        mod = types.ModuleType(loader.name)
+        loader.exec_module(mod)
+
+        return getattr(mod, 'integrate')
+    except ImportError as err: # Python 2.7
+        import imp
+        _temp = imp.load_source(odename, filename)
+        return getattr(_temp, 'integrate')
 
 def writeODElib(svars, odeM, jacobian=None, rdict=None, concvect=None,
                 odename='odesystem', filename='./odesystem', template=None):

scripts/crnsimulator

@@ -7,14 +7,13 @@
 # Use at your own risk.
 #
 #
+from __future__ import absolute_import, division, print_function
 
-from __future__ import print_function
 import os
 import sys
-import imp
 import argparse
 
-from crnsimulator import ReactionGraph, __version__
+from crnsimulator import ReactionGraph, get_integrator, __version__
 from crnsimulator.odelib_template import add_integrator_args
 from crnsimulator.crn_parser import parse_crn_string, ParseException
 
@@ -89,7 +88,7 @@ def main(args):
     # **************** #
     # WRITE ODE SYSTEM #
     # ................ #
-    if not args.force and os.path.exists(filename):
+    if filename != 'odesystem.py' and not args.force and os.path.exists(filename):
         print('# Reading ODE system from existing file:', filename)
     else:
         # ******************* #
@@ -119,8 +118,7 @@ def main(args):
         print('# Simulating the ODE system, change parameters using:')
         print("#  python {} --help ".format(filename))
 
-        _temp = imp.load_source(odename, filename)
-        integrate = getattr(_temp, 'integrate')
+        integrate = get_integrator(odename, filename)
 
         # ********************* #
         # ARGUMENT PROCESSING 2 #

setup.py

@@ -9,7 +9,7 @@
 
 setup(
     name='crnsimulator',
-    version="0.5",
+    version="0.6",
     description='Simulate CRNs using ODEs.',
     long_description=LONG_DESCRIPTION,
     author='Stefan Badelt',

tests/test_solver.py

@@ -1,10 +1,10 @@
 from __future__ import unicode_literals
 
 import os
-import imp
 import unittest
 from argparse import ArgumentParser
 
+from crnsimulator import get_integrator
 from crnsimulator.reactiongraph import ReactionGraph, ReactionNode
 from crnsimulator.crn_parser import parse_crn_string
 from crnsimulator.odelib_template import add_integrator_args
@@ -46,8 +46,7 @@ def test_crn(self):
         RG = ReactionGraph(crn)
 
         filename, odename = RG.write_ODE_lib(filename=self.filename)
-        _temp = imp.load_source(odename, filename)
-        integrate = getattr(_temp, 'integrate')
+        integrate = get_integrator(odename, filename)
 
         self.args.p0 = ['1=0.5']
         self.args.t_log = 10
@@ -86,8 +85,7 @@ def test_crn_sympy_imports(self):
         RG = ReactionGraph(crn)
 
         filename, odename = RG.write_ODE_lib(filename=self.filename)
-        _temp = imp.load_source(odename, filename)
-        integrate = getattr(_temp, 'integrate')
+        integrate = get_integrator(odename, filename)
 
         self.args.p0 = ['S=0.5', 'cos=0.2']
         self.args.t_log = 10