Remove PSYCO support

Fixes robclewley#74

PyDSTool/Generator/DDEsystem.py

@@ -10,12 +10,6 @@
 from numpy import Inf, NaN, isfinite, sometrue, alltrue, array
 import math, random
 from copy import copy, deepcopy
-try:
-    # use pscyo JIT byte-compiler optimization, if available
-    import psyco
-    HAVE_PSYCO = True
-except ImportError:
-    HAVE_PSYCO = False
 
 # -----------------------------------------------------------------------------
 

PyDSTool/Generator/EmbeddedSysGen.py

@@ -12,12 +12,6 @@
      transpose, shape
 import math, random
 from copy import copy, deepcopy
-try:
-    # use pscyo JIT byte-compiler optimization, if available
-    import psyco
-    HAVE_PSYCO = True
-except ImportError:
-    HAVE_PSYCO = False
 
 
 class EmbeddedSysGen(ctsGen):

PyDSTool/Generator/Euler_ODEsystem.py

@@ -21,13 +21,6 @@
 from copy import copy, deepcopy
 import os, platform, shutil, sys, gc
 
-try:
-    # use psyco JIT byte-compiler optimization, if available
-    import psyco
-    HAVE_PSYCO = True
-except ImportError:
-    HAVE_PSYCO = False
-
 
 class euler_solver(object):
     def __init__(self, rhs):
@@ -94,7 +87,7 @@ def __init__(self, kw):
 
     def addMethods(self):
         # override to add _solver function
-        ODEsystem.addMethods(self, usePsyco=HAVE_PSYCO)
+        ODEsystem.addMethods(self)
         # Jacobian ignored
         self._solver = euler_solver(getattr(self,self.funcspec.spec[1]))
         self._funcreg['_solver'] = ('self', 'euler_solver(getattr(self,' \

PyDSTool/Generator/ExplicitFnGen.py

@@ -14,12 +14,6 @@
 import math, random, types
 from copy import copy, deepcopy
 import six
-try:
-    # use pscyo JIT byte-compiler optimization, if available
-    import psyco
-    HAVE_PSYCO = True
-except ImportError:
-    HAVE_PSYCO = False
 
 
 class ExplicitFnGen(ctsGen):
@@ -75,11 +69,10 @@ def __init__(self, kw):
                                          xinterval, x)
         self._generate_ixmaps()
         self.auxfns = auxfn_container(self)
-        self.addMethods(usePsyco=HAVE_PSYCO)
+        self.addMethods()
 
-    def addMethods(self, usePsyco=False):
-        """Add Python-specific functions to this object's methods,
-        accelerating them with psyco, if it is available."""
+    def addMethods(self):
+        """Add Python-specific functions to this object's methods."""
 
         # Add the auxiliary function specs to this Generator's namespace
         for auxfnname in self.funcspec._pyauxfns:
@@ -107,14 +100,6 @@ def addMethods(self, usePsyco=False):
                 except KeyError:
                     # not a user-defined aux fn
                     pass
-            # bind all the auxfns here
-            if HAVE_PSYCO and usePsyco:
-                psyco.bind(getattr(self, fninfo[1]))
-                try:
-                    psyco.bind(self.auxfns[auxfnname])
-                except KeyError:
-                    # not a user-defined aux fn
-                    pass
         # Add the spec function to this Generator's namespace if
         # target language is python (otherwise integrator exposes it anyway)
         if self.funcspec.targetlang == 'python':
@@ -126,8 +111,6 @@ def addMethods(self, usePsyco=False):
                 raise
             self._funcreg[fninfo[1]] = ('self', fninfo[0])
             setattr(self, fninfo[1], six.create_bound_method(locals()[fninfo[1]], self))
-            if HAVE_PSYCO and usePsyco:
-                psyco.bind(getattr(self, fninfo[1]))
             # Add the auxiliary spec function (if present) to this
             # Generator's namespace
             if self.funcspec.auxspec != '':
@@ -139,8 +122,6 @@ def addMethods(self, usePsyco=False):
                     raise
                 self._funcreg[fninfo[1]] = ('self', fninfo[0])
                 setattr(self, fninfo[1], six.create_bound_method(locals()[fninfo[1]], self))
-                if HAVE_PSYCO and usePsyco:
-                    psyco.bind(getattr(self, fninfo[1]))
 
 
     def compute(self, trajname, ics=None):

PyDSTool/Generator/ImplicitFnGen.py

@@ -13,12 +13,6 @@
 import math, random
 from copy import copy, deepcopy
 import six
-try:
-    # use pscyo JIT byte-compiler optimization, if available
-    import psyco
-    HAVE_PSYCO = True
-except ImportError:
-    HAVE_PSYCO = False
 
 
 class ImplicitFnGen(ctsGen):

PyDSTool/Generator/MapSystem.py

@@ -21,11 +21,6 @@
 import math, random, types
 from copy import copy, deepcopy
 import six
-try:
-    import psyco
-    HAVE_PSYCO = True
-except ImportError:
-    HAVE_PSYCO = False
 
 
 class MapSystem(discGen):
@@ -109,14 +104,6 @@ def addMethods(self):
                 except KeyError:
                     # not a user-defined aux fn
                     pass
-            # bind all the auxfns here
-            if HAVE_PSYCO:
-                psyco.bind(getattr(self, fninfo[1]))
-                try:
-                    psyco.bind(self.auxfns[auxfnname])
-                except KeyError:
-                    # not a user-defined aux fn
-                    pass
         if self.funcspec.targetlang == 'python':
             # Add the spec function to this Generator's namespace
             fninfo = self.funcspec.spec
@@ -131,8 +118,6 @@ def addMethods(self):
                 raise
             self._funcreg[fninfo[1]] = ('self', fnstr)
             setattr(self, fninfo[1], six.create_bound_method(locals()[fninfo[1]], self))
-            if HAVE_PSYCO and not self._solver:
-                psyco.bind(getattr(self, fninfo[1]))
             # Add the auxiliary spec function (if present) to this
             # Generator's namespace
             if self.funcspec.auxspec != '':
@@ -148,8 +133,6 @@ def addMethods(self):
                     raise
                 self._funcreg[fninfo[1]] = ('self', fnstr)
                 setattr(self, fninfo[1], six.create_bound_method(locals()[fninfo[1]], self))
-                if HAVE_PSYCO and not self._solver:
-                    psyco.bind(getattr(self, fninfo[1]))
 
 
     # Method for pickling protocol (setstate same as default)

PyDSTool/Generator/ODEsystem.py

@@ -17,13 +17,6 @@
 import types
 from copy import copy, deepcopy
 import six
-try:
-    # use pscyo JIT byte-compiler optimization, if available
-    import psyco
-    HAVE_PSYCO = True
-except ImportError:
-    HAVE_PSYCO = False
-
 
 
 class ODEsystem(ctsGen):
@@ -100,9 +93,8 @@ def prepDirection(self, dirn):
         return continue_integ
 
 
-    def addMethods(self, usePsyco=False):
-        """Add Python-specific functions to this object's methods,
-        accelerating them with psyco, if it is available."""
+    def addMethods(self):
+        """Add Python-specific functions to this object's methods."""
 
         # Add the auxiliary function specs to this Generator's namespace
         for auxfnname in self.funcspec._pyauxfns:
@@ -130,14 +122,6 @@ def addMethods(self, usePsyco=False):
                 except KeyError:
                     # not a user-defined aux fn
                     pass
-            # bind all the auxfns here
-            if HAVE_PSYCO and usePsyco:
-                psyco.bind(getattr(self, fninfo[1]))
-                try:
-                    psyco.bind(self.auxfns[auxfnname])
-                except KeyError:
-                    # not a user-defined aux fn
-                    pass
         # Add the spec function to this Generator's namespace if
         # target language is python (otherwise integrator exposes it anyway)
         if self.funcspec.targetlang == 'python':
@@ -149,8 +133,6 @@ def addMethods(self, usePsyco=False):
                 raise
             self._funcreg[fninfo[1]] = ('self', fninfo[0])
             setattr(self, fninfo[1], six.create_bound_method(locals()[fninfo[1]], self))
-            if HAVE_PSYCO and usePsyco:
-                psyco.bind(getattr(self, fninfo[1]))
             # Add the auxiliary spec function (if present) to this
             # Generator's namespace
             if self.funcspec.auxspec != '':
@@ -162,8 +144,6 @@ def addMethods(self, usePsyco=False):
                     raise
                 self._funcreg[fninfo[1]] = ('self', fninfo[0])
                 setattr(self, fninfo[1], six.create_bound_method(locals()[fninfo[1]], self))
-                if HAVE_PSYCO and usePsyco:
-                    psyco.bind(getattr(self, fninfo[1]))
 
 
     def haveJacobian(self):

PyDSTool/Generator/Vode_ODEsystem.py

@@ -22,15 +22,6 @@
 import os, platform, shutil, sys, gc
 from scipy.integrate import ode
 
-# PSYCO FUNCTIONS DON'T WORK AS VODE CALLBACK FUNCTIONS!
-#try:
-#    # use psyco JIT byte-compiler optimization, if available
-#    import psyco
-#    HAVE_PSYCO = True
-#except ImportError:
-#    HAVE_PSYCO = False
-HAVE_PSYCO = False
-
 
 class Vode_ODEsystem(ODEsystem):
     """Wrapper for VODE, from SciPy.
@@ -78,7 +69,7 @@ def __init__(self, kw):
 
     def addMethods(self):
         # override to add _solver function
-        ODEsystem.addMethods(self, usePsyco=False)
+        ODEsystem.addMethods(self)
         if self.haveJacobian():
             self._solver = ode(getattr(self,self.funcspec.spec[1]),
                             getattr(self,self.funcspec.auxfns["Jacobian"][1]))

PyDSTool/Generator/baseclasses.py

@@ -16,13 +16,6 @@
 import math, random
 import os
 from copy import copy, deepcopy
-try:
-    # use pscyo JIT byte-compiler optimization, if available
-    import psyco
-    HAVE_PSYCO = True
-except ImportError:
-    HAVE_PSYCO = False
-
 # -----------------------------------------------------------------------------
 
 __all__ = ['ctsGen', 'discGen', 'theGenSpecHelper', 'Generator',

PyDSTool/Toolbox/ParamEst.py

@@ -44,14 +44,6 @@
 
 import math, types
 from copy import copy, deepcopy
-
-try:
-    # use psyco JIT byte-compiler optimization, if available
-    import psyco
-    HAVE_PSYCO = True
-except ImportError:
-    HAVE_PSYCO = False
-
 # ------------------------------------------------------------------------
 
 _pest_classes = ['ParamEst', 'LMpest', 'BoundMin', 'residual_fn_context',
@@ -716,8 +708,7 @@ class ParamEst(Utility):
 
     def __init__(self, **kw):
         self.needKeys = ['freeParams', 'testModel', 'context']
-        self.optionalKeys = ['verbose_level', 'usePsyco',
-                             'residual_fn', 'extra_pars']
+        self.optionalKeys = ['verbose_level', 'residual_fn', 'extra_pars']
         try:
             self.context = kw['context']
             if isinstance(kw['freeParams'], list):
@@ -736,14 +727,6 @@ def __init__(self, **kw):
         except KeyError:
             raise PyDSTool_KeyError('Incorrect argument keys passed')
         self.foundKeys = len(self.needKeys)   # lazy way to achieve this!
-        if 'usePsyco' in kw:
-            if HAVE_PSYCO and kw['usePsyco']:
-                self.usePsyco = True
-            else:
-                self.usePsyco = False
-            self.foundKeys += 1
-        else:
-            self.usePsyco = False
         if 'residual_fn' in kw:
             self.setFn(kw['residual_fn'])
             self.foundKeys += 1
@@ -807,8 +790,6 @@ def setFn(self, fn):
         self.fn = fn
         # reciprocal reference
         self.fn.pest = self
-        if self.usePsyco:
-            psyco.bind(self.fn)
 
 
     def evaluate(self, extra_record_info=None):

examples/pest_test3.py

@@ -188,8 +188,7 @@ def postprocess_test_traj(self, traj):
 ##pest_pars = LMpest(freeParams=['vl', 'gl'],
 ##                 testModel=HH_test_model,
 ##                 context=pest_context,
-##                 verbose_level=2,
-##                 usePsyco=False
+##                 verbose_level=2
 ##                )
 ##
 ##start = clock()

examples/pest_test3_Cintegrator.py

@@ -188,8 +188,7 @@ def postprocess_test_traj(self, traj):
 #pest_pars = LMpest(freeParams=['vl', 'gl'],
 #                 testModel=HH_test_model,
 #                 context=pest_context,
-#                 verbose_level=2,
-#                 usePsyco=True
+#                 verbose_level=2
 #                )
 
 start = clock()

examples/pest_test4_Cintegrator.py

@@ -179,8 +179,7 @@ def postprocess_test_traj(self, traj):
 pest_pars = LMpest(freeParams=['gna', 'gl'],
                  testModel=HH_test_model,
                  context=pest_context,
-                 verbose_level=2,
-                 usePsyco=False
+                 verbose_level=2
                 )
 
 # In case finite difference stepsize needs adjusting