Fixing DeprecationWarnings + various typos; fixed Radar solver statis…

…tics

examples/cvode_basic.py

@@ -66,7 +66,7 @@ def f(t,y):
         P.show()
 
     #Basic test
-    nose.tools.assert_almost_equal(float(y2[-1]), 0.00347746, 5)
+    nose.tools.assert_almost_equal(y2[-1][0], 0.00347746, 5)
     nose.tools.assert_almost_equal(exp_sim.get_last_step(), 0.0222169642893, 3)
 
     return exp_mod, exp_sim

examples/cvode_basic_backward.py

@@ -62,7 +62,7 @@ def f(t,y):
         P.show()
 
     #Basic test
-    nose.tools.assert_almost_equal(float(y[-1]), 4.00000000, 3)
+    nose.tools.assert_almost_equal(y[-1][0], 4.00000000, 3)
 
     return exp_mod, exp_sim
 

examples/cvode_stability.py

@@ -68,7 +68,7 @@ def f(t,y):
     exp_sim = CVode(exp_mod) #Create a CVode solver
 
     #Sets the parameters
-    exp_sim.stablimdet = True
+    exp_sim.stablimit = True
     exp_sim.report_continuously = True
 
     #Simulate

examples/cvode_with_disc.py

@@ -84,7 +84,7 @@ def handle_event(self, solver, event_info):
 
             event_info = self.check_eIter(b_mode, a_mode)
 
-            if not True in event_info: #Breaks the iteration loop
+            if True not in event_info: #Breaks the iteration loop
                 break
 
     #Helper function for handle_event

examples/cvode_with_parameters.py

@@ -70,7 +70,7 @@ def f(t, y, p):
     exp_sim.discr = 'BDF'
     exp_sim.rtol = 1.e-4
     exp_sim.atol = N.array([1.0e-8, 1.0e-14, 1.0e-6])
-    exp_sim.sensmethod = 'SIMULTANEOUS' #Defines the sensitvity method used
+    exp_sim.sensmethod = 'SIMULTANEOUS' #Defines the sensitivity method used
     exp_sim.suppress_sens = False       #Dont suppress the sensitivity variables in the error test.
     exp_sim.report_continuously = True
 

examples/cvode_with_parameters_fcn.py

@@ -87,7 +87,7 @@ def fsens(t, y, s, p):
     exp_sim.discr = 'BDF'
     exp_sim.rtol = 1.e-4
     exp_sim.atol = N.array([1.0e-8, 1.0e-14, 1.0e-6])
-    exp_sim.sensmethod = 'SIMULTANEOUS' #Defines the sensitvity method used
+    exp_sim.sensmethod = 'SIMULTANEOUS' #Defines the sensitivity method used
     exp_sim.suppress_sens = False       #Dont suppress the sensitivity variables in the error test.
     exp_sim.report_continuously = True
 

examples/cvode_with_parameters_modified.py

@@ -68,7 +68,7 @@ def f(t, y, p):
     exp_sim.discr = 'BDF'
     exp_sim.rtol = 1.e-4
     exp_sim.atol = N.array([1.0e-8, 1.0e-14, 1.0e-6])
-    exp_sim.sensmethod = 'SIMULTANEOUS' #Defines the sensitvity method used
+    exp_sim.sensmethod = 'SIMULTANEOUS' #Defines the sensitivity method used
     exp_sim.suppress_sens = False       #Dont suppress the sensitivity variables in the error test.
     exp_sim.report_continuously = True
 
@@ -95,4 +95,3 @@ def f(t, y, p):
 
 if __name__=='__main__':
     mod,sim = run_example()
-

examples/cvode_with_preconditioning.py

@@ -53,7 +53,7 @@ def prec_setup(t, y, fy, jok, gamma, data):
         A = np.array([[2.0, 1.0], [3.0, 2.0]])
 
         #If jok is false the jacobian data needs to be recomputed
-        if jok == False:
+        if jok is False:
 
             #Extract the diagonal of the jacobian to form a Jacobi preconditioner
             a0 = A[0, 0] * t * np.cos(y[0])
@@ -64,7 +64,7 @@ def prec_setup(t, y, fy, jok, gamma, data):
             return [True, a]
 
         #If jok is true the existing jacobian data can be reused 
-        if jok == True:
+        if jok is True:
 
             #Return false (jacobian data was reused) and the old data
             return [False, data]

examples/dopri5_basic.py

@@ -56,7 +56,7 @@ def f(t,y):
         P.show()
 
     #Basic test
-    nose.tools.assert_almost_equal(float(y[-1]),0.02695199,5)
+    nose.tools.assert_almost_equal(y[-1][0],0.02695199,5)
 
     return exp_mod, exp_sim
 

examples/dopri5_with_disc.py

@@ -84,7 +84,7 @@ def handle_event(self, solver, event_info):
 
             event_info = self.check_eIter(b_mode, a_mode)
 
-            if not True in event_info: #Breaks the iteration loop
+            if True not in event_info: #Breaks the iteration loop
                 break
 
     #Helper function for handle_event
@@ -163,6 +163,3 @@ def run_example(with_plots=True):
 
 if __name__=="__main__":
     mod,sim = run_example()
-
-
-

examples/euler_basic.py

@@ -61,7 +61,7 @@ def f(t,y):
         P.show()
 
     #Basic test
-    nose.tools.assert_almost_equal(float(y2[-1]), 0.02628193)
+    nose.tools.assert_almost_equal(y2[-1][0], 0.02628193)
 
     return exp_mod, exp_sim
 

examples/euler_vanderpol.py

@@ -92,4 +92,3 @@ def jac(t,y):
 
 if __name__=='__main__':
     mod,sim = run_example()
-

examples/euler_with_disc.py

@@ -84,7 +84,7 @@ def handle_event(self, solver, event_info):
 
             event_info = self.check_eIter(b_mode, a_mode)
 
-            if not True in event_info: #Breaks the iteration loop
+            if True not in event_info: #Breaks the iteration loop
                 break
 
     #Helper function for handle_event
@@ -121,8 +121,6 @@ def init_mode(self, solver):
         solver.y[1] = (-1.0 if solver.sw[1] else 3.0)
         solver.y[2] = (0.0 if solver.sw[2] else 2.0)
 
-
-
 def run_example(with_plots=True):
     r"""
     Example of the use of Euler's method for a differential equation

examples/glimda_vanderpol.py

@@ -17,7 +17,7 @@
 
 import numpy as N
 import nose
-from assimulo.solvers import GLIMDA,IDA
+from assimulo.solvers import GLIMDA
 from assimulo.problem import Implicit_Problem
 
 def run_example(with_plots=True):

examples/ida_basic_backward.py

@@ -62,7 +62,7 @@ def f(t,y,yd):
         P.show()
 
     #Basic test
-    nose.tools.assert_almost_equal(float(y[-1]), 4.00000000, 3)
+    nose.tools.assert_almost_equal(y[-1][0], 4.00000000, 3)
 
     return imp_mod, imp_sim
 

examples/ida_with_disc.py

@@ -87,7 +87,7 @@ def handle_event(self, solver, event_info):
 
             event_info = self.check_eIter(b_mode, a_mode)
 
-            if not True in event_info: #Breaks the iteration loop
+            if True not in event_info: #Breaks the iteration loop
                 break
 
     #Helper function for handle_event
@@ -125,8 +125,6 @@ def init_mode(self, solver):
                                                    #see SUNDIALS IDA documentation
                                                    #on the option 'IDA_YA_YDP_INIT'
 
-
-
 def run_example(with_plots=True):
     r"""
     Example of the use of IDA for an implicit differential equation
@@ -168,6 +166,3 @@ def run_example(with_plots=True):
 
 if __name__=="__main__":
     mod,sim = run_example()
-
-
-

examples/ida_with_initial_sensitivity.py

@@ -79,7 +79,7 @@ def f(t, y, yd,p):
     imp_sim.atol = 1e-6
     imp_sim.pbar = [1,1,1] #pbar is used to estimate the tolerances for the parameters
     imp_sim.report_continuously = True #Need to be able to store the result using the interpolate methods
-    imp_sim.sensmethod = 'SIMULTANEOUS' #Defines the sensitvity method used
+    imp_sim.sensmethod = 'SIMULTANEOUS' #Defines the sensitivity method used
     imp_sim.suppress_sens = False            #Dont suppress the sensitivity variables in the error test.
 
     #Simulate

examples/ida_with_jac.py

@@ -125,4 +125,3 @@ def jac(c,t,y,yd):
 
 if __name__=='__main__':
     mod,sim = run_example()
-

examples/ida_with_parameters.py

@@ -98,4 +98,3 @@ def f(t, y, yd, p):
 
 if __name__=='__main__':
     mod,sim = run_example()
-

examples/ida_with_user_defined_handle_result.py

@@ -115,7 +115,5 @@ def handle_result(solver, t ,y, yd):
 
     return imp_mod, imp_sim
 
-
 if __name__=='__main__':
     mod,sim = run_example()
-

examples/kinsol_basic.py

@@ -15,7 +15,6 @@
 # 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/>.
 
-import numpy as N
 import nose
 from assimulo.solvers import KINSOL
 from assimulo.problem import Algebraic_Problem
@@ -53,4 +52,3 @@ def res(y):
 
 if __name__=='__main__':
     mod, solv = run_example()
-

examples/kinsol_ors.py

@@ -16,7 +16,6 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as N
-import scipy as S
 import scipy.linalg as LIN
 import scipy.io as IO
 import scipy.sparse as SPARSE
@@ -79,7 +78,7 @@ def prec_setup(u,f, uscale, fscale):
     def prec_solve(r):
         return solvePrec(r)
 
-    y0 = S.rand(A.shape[0])
+    y0 = N.random.rand(A.shape[0])
 
     #Define an Assimulo problem
     alg_mod = Algebraic_Problem(res, y0=y0, jac=jac, jacv=jacv, name = 'ORS Example')
@@ -101,10 +100,10 @@ def setup_param(solver):
     setup_param(alg_solver)
     setup_param(alg_solver_prec)
 
-    #Solve orignal system
+    #Solve original system
     y = alg_solver.solve()
 
-    #Solve Preconditionined system
+    #Solve Preconditioned system
     y_prec = alg_solver_prec.solve()
 
     print("Error                 , in y: ", LIN.norm(y-N.ones(len(y))))
@@ -137,4 +136,3 @@ def setup_param(solver):
 
 if __name__=='__main__':
     mod, solv = run_example()
-

examples/kinsol_with_jac.py

@@ -58,4 +58,3 @@ def jac(y):
 
 if __name__=='__main__':
     mod, solv = run_example()
-

examples/lsodar_bouncing_ball.py

@@ -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/>.
 
-import numpy as N
 import nose
+import numpy as N
 from assimulo.solvers import LSODAR
 from assimulo.problem import Explicit_Problem
-import sys
-import os
 
 """
 The bouncing ball example for LSODAR
@@ -155,6 +153,3 @@ def run_example(with_plots=True):
 
 if __name__=="__main__":
     mod,sim = run_example()
-
-
-

examples/lsodar_vanderpol.py

@@ -55,7 +55,7 @@ def f(t,y):
     exp_mod = Explicit_Problem(f,y0, name = "LSODAR: Van der Pol's equation")
 
     #Define an explicit solver
-    exp_sim = LSODAR(exp_mod) #Create a Radau5 solver
+    exp_sim = LSODAR(exp_mod) #Create a LSODAR solver
 
     #Sets the parameters
     exp_sim.atol = 1e-4 #Default 1e-6

examples/lsodar_with_disc.py

@@ -83,7 +83,7 @@ def handle_event(self, solver, event_info):
 
             event_info = self.check_eIter(b_mode, a_mode)
 
-            if not True in event_info: #Breaks the iteration loop
+            if True not in event_info: #Breaks the iteration loop
                 break
 
     #Helper function for handle_event

examples/mech_system_pendulum.py

@@ -15,8 +15,6 @@
 # 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/>.
 
-#import nose
-import assimulo.problem as ap
 import assimulo.special_systems as ass
 import numpy as N
 import nose

examples/radau5ode_with_disc.py

@@ -34,7 +34,7 @@
 #Extend Assimulos problem definition
 class Extended_Problem(Explicit_Problem):
 
-    #Sets the initial conditons directly into the problem
+    #Sets the initial conditions directly into the problem
     y0 = [0.0, -1.0, 0.0]
     sw0 = [False,True,True]
 
@@ -84,7 +84,7 @@ def handle_event(self, solver, event_info):
 
             event_info = self.check_eIter(b_mode, a_mode)
 
-            if not True in event_info: #Breaks the iteration loop
+            if True not in event_info: #Breaks the iteration loop
                 break
 
     #Helper function for handle_event

examples/radau5ode_with_disc_sparse.py

@@ -35,7 +35,7 @@
 #Extend Assimulos problem definition
 class Extended_Problem(Explicit_Problem):
 
-    #Sets the initial conditons directly into the problem
+    #Sets the initial conditions directly into the problem
     y0 = [0.0, -1.0, 0.0]
     sw0 = [False,True,True]
 
@@ -90,7 +90,7 @@ def handle_event(self, solver, event_info):
 
             event_info = self.check_eIter(b_mode, a_mode)
 
-            if not True in event_info: #Breaks the iteration loop
+            if True not in event_info: #Breaks the iteration loop
                 break
 
     #Helper function for handle_event
@@ -127,8 +127,6 @@ def init_mode(self, solver):
         solver.y[1] = (-1.0 if solver.sw[1] else 3.0)
         solver.y[2] = (0.0 if solver.sw[2] else 2.0)
 
-
-
 def run_example(with_plots=True):
     #Create an instance of the problem
     exp_mod = Extended_Problem() #Create the problem
@@ -161,4 +159,3 @@ def run_example(with_plots=True):
 
 if __name__=="__main__":
     mod,sim = run_example()
-

examples/radau5ode_with_jac_sparse.py

@@ -21,7 +21,6 @@
 from assimulo.solvers import Radau5ODE
 from assimulo.problem import Explicit_Problem
 
-
 def run_example(with_plots=True):
     r"""
     Example for demonstrating the use of a user supplied Jacobian (sparse).
@@ -90,10 +89,9 @@ def jac(t,y):
         P.show()
 
     #Basic tests
-    nose.tools.assert_almost_equal(y[-1][0],0.9851,3)
+    nose.tools.assert_almost_equal(y[-1][0], 0.9851, 3)
 
     return exp_mod, exp_sim
 
-
 if __name__=='__main__':
     mod,sim = run_example()

examples/rodasode_vanderpol.py

@@ -93,4 +93,3 @@ def jac(t,y):
 
 if __name__=='__main__':
     mod,sim = run_example()
-

examples/rungekutta34_basic.py

@@ -49,7 +49,7 @@ def f(t,y):
     t, y = exp_sim.simulate(5) #Simulate 5 seconds
 
     #Basic test
-    nose.tools.assert_almost_equal(float(y[-1]),0.02695199,5)
+    nose.tools.assert_almost_equal(y[-1][0], 0.02695199, 5)
 
     #Plot
     if with_plots: