Import cleanups (#82)

doc/sphinx/source/tutorialCVodeDisc.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python 
 # -*- coding: utf-8 -*-
 """
-Tutorial example showing how to use the explicit solver CVode for a discontinious problem. 
+Tutorial example showing how to use the explicit solver CVode for a discontinuous problem. 
 To run the example simply type,
 
     run tutorialCVodeDisc.py (in IPython)

examples/cvode_basic.py

@@ -15,7 +15,7 @@
 # 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 numpy as np
 import nose
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
@@ -37,7 +37,7 @@ def run_example(with_plots=True):
     #Define the rhs
     def f(t,y):
         ydot = -y[0]
-        return N.array([ydot])
+        return np.array([ydot])
 
     #Define an Assimulo problem
     exp_mod = Explicit_Problem(f, y0=4, name = r'CVode Test Example: $\dot y = - y$')
@@ -57,13 +57,13 @@ def f(t,y):
 
     #Plot
     if with_plots:
-        import pylab as P
-        P.plot(t1, y1, color="b")
-        P.plot(t2, y2, color="r")
-        P.title(exp_mod.name)
-        P.ylabel('y')
-        P.xlabel('Time')
-        P.show()
+        import pylab as pl
+        pl.plot(t1, y1, color="b")
+        pl.plot(t2, y2, color="r")
+        pl.title(exp_mod.name)
+        pl.ylabel('y')
+        pl.xlabel('Time')
+        pl.show()
 
     #Basic test
     nose.tools.assert_almost_equal(y2[-1][0], 0.00347746, 5)

examples/cvode_basic_backward.py

@@ -15,7 +15,7 @@
 # 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 numpy as np
 import nose
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
@@ -34,7 +34,7 @@ def run_example(with_plots=True):
     #Define the rhs
     def f(t,y):
         ydot = -y[0]
-        return N.array([ydot])
+        return np.array([ydot])
 
     #Define an Assimulo problem
     exp_mod = Explicit_Problem(f,t0=5, y0=0.02695, name = r'CVode Test Example (reverse time): $\dot y = - y$ ')
@@ -54,12 +54,12 @@ def f(t,y):
 
     #Plot
     if with_plots:
-        import pylab as P
-        P.plot(t, y, color="b")
-        P.title(exp_mod.name)
-        P.ylabel('y')
-        P.xlabel('Time')
-        P.show()
+        import pylab as pl
+        pl.plot(t, y, color="b")
+        pl.title(exp_mod.name)
+        pl.ylabel('y')
+        pl.xlabel('Time')
+        pl.show()
 
     #Basic test
     nose.tools.assert_almost_equal(y[-1][0], 4.00000000, 3)

examples/cvode_gyro.py

@@ -75,12 +75,12 @@ def f(t, u):
 
     # Plot
     if with_plots:
-        import pylab as P
-        P.plot(t, y/10000.)
-        P.xlabel('Time')
-        P.ylabel('States, scaled by $10^4$')
-        P.title(exp_mod.name)
-        P.show()
+        import pylab as pl
+        pl.plot(t, y/10000.)
+        pl.xlabel('Time')
+        pl.ylabel('States, scaled by $10^4$')
+        pl.title(exp_mod.name)
+        pl.show()
 
     #Basic tests
     nose.tools.assert_almost_equal(y[-1][0], 692.800241862)

examples/cvode_stability.py

@@ -15,7 +15,7 @@
 # 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 numpy as np
 import nose
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
@@ -54,9 +54,9 @@ def handle_result(self, solver, t, y):
     def f(t,y):
         yd_0 = y[1]
         yd_1 = my*((1.-y[0]**2)*y[1]-y[0])
-        yd_2 = N.sin(t*y[1])
+        yd_2 = np.sin(t*y[1])
 
-        return N.array([yd_0,yd_1, yd_2])
+        return np.array([yd_0,yd_1, yd_2])
 
     y0 = [2.0,-0.6, 0.1] #Initial conditions
 
@@ -76,20 +76,20 @@ def f(t,y):
 
     #Plot
     if with_plots:
-        import pylab as P
-        P.subplot(211)
-        P.plot(t,y[:,2])
-        P.ylabel("State: $y_1$")
-        P.subplot(212)
-        P.plot(t,exp_mod.order)
-        P.ylabel("Order")
-        P.suptitle(exp_mod.name)
-        P.xlabel("Time")
-        P.show()
+        import pylab as pl
+        pl.subplot(211)
+        pl.plot(t,y[:,2])
+        pl.ylabel("State: $y_1$")
+        pl.subplot(212)
+        pl.plot(t,exp_mod.order)
+        pl.ylabel("Order")
+        pl.suptitle(exp_mod.name)
+        pl.xlabel("Time")
+        pl.show()
 
     #Basic test
     x1 = y[:,0]
-    nose.tools.assert_less(N.abs(float(x1[-1]) - 1.8601438), 1e-1)
+    nose.tools.assert_less(np.abs(float(x1[-1]) - 1.8601438), 1e-1)
 
     return exp_mod, exp_sim
 

examples/cvode_with_disc.py

@@ -15,7 +15,7 @@
 # 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 numpy as np
 import nose
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
@@ -50,7 +50,7 @@ def rhs(self,t,y,sw):
         yd_1 = 0.0
         yd_2 = 0.0
 
-        return N.array([yd_0,yd_1,yd_2])
+        return np.array([yd_0,yd_1,yd_2])
 
     #Sets a name to our function
     name = 'ODE with discontinuities and a function with consistency problem'
@@ -65,7 +65,7 @@ def state_events(self,t,y,sw):
         event_1 = -y[2] + 1.0
         event_2 = -t + 1.0
 
-        return N.array([event_0,event_1,event_2])
+        return np.array([event_0,event_1,event_2])
 
 
     #Responsible for handling the events.
@@ -148,12 +148,12 @@ def run_example(with_plots=True):
 
     #Plot
     if with_plots:
-        import pylab as P
-        P.plot(t,y)
-        P.title(exp_mod.name)
-        P.ylabel('States')
-        P.xlabel('Time')
-        P.show()
+        import pylab as pl
+        pl.plot(t,y)
+        pl.title(exp_mod.name)
+        pl.ylabel('States')
+        pl.xlabel('Time')
+        pl.show()
 
     #Basic test
     nose.tools.assert_almost_equal(y[-1][0],8.0)

examples/cvode_with_initial_sensitivity.py

@@ -15,7 +15,7 @@
 # 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 numpy as np
 import nose
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
@@ -57,12 +57,12 @@ def f(t, y, p):
         yd_1 = k21*y1-(k02+k12)*y2
         yd_2 = k31*y1-k13*y3
 
-        return N.array([yd_0,yd_1,yd_2])
+        return np.array([yd_0,yd_1,yd_2])
 
     #The initial conditions
     y0 = [0.0,0.0,0.0]          #Initial conditions for y
     p0 = [0.0, 0.0, 0.0]  #Initial conditions for parameters
-    yS0 = N.array([[1,0,0],[0,1,0],[0,0,1.]])
+    yS0 = np.array([[1,0,0],[0,1,0],[0,0,1.]])
 
     #Create an Assimulo explicit problem
     exp_mod = Explicit_Problem(f, y0, p0=p0,name='Example: Computing Sensitivities')
@@ -88,39 +88,39 @@ def f(t, y, p):
 
     #Plot
     if with_plots:
-        import pylab as P
+        import pylab as pl
         title_text=r"Sensitivity w.r.t.  ${}$"
         legend_text=r"$\mathrm{{d}}{}/\mathrm{{d}}{}$"
-        P.figure(1)
-        P.subplot(221)
-        P.plot(t, N.array(exp_sim.p_sol[0])[:,0],
-               t, N.array(exp_sim.p_sol[0])[:,1],
-               t, N.array(exp_sim.p_sol[0])[:,2])
-        P.title(title_text.format('p_1'))
-        P.legend((legend_text.format('y_1','p_1'),
+        pl.figure(1)
+        pl.subplot(221)
+        pl.plot(t, np.array(exp_sim.p_sol[0])[:,0],
+               t, np.array(exp_sim.p_sol[0])[:,1],
+               t, np.array(exp_sim.p_sol[0])[:,2])
+        pl.title(title_text.format('p_1'))
+        pl.legend((legend_text.format('y_1','p_1'),
                   legend_text.format('y_1','p_2'),
                   legend_text.format('y_1','p_3')))
-        P.subplot(222)
-        P.plot(t, N.array(exp_sim.p_sol[1])[:,0],
-               t, N.array(exp_sim.p_sol[1])[:,1],
-               t, N.array(exp_sim.p_sol[1])[:,2])
-        P.title(title_text.format('p_2'))
-        P.legend((legend_text.format('y_2','p_1'),
+        pl.subplot(222)
+        pl.plot(t, np.array(exp_sim.p_sol[1])[:,0],
+               t, np.array(exp_sim.p_sol[1])[:,1],
+               t, np.array(exp_sim.p_sol[1])[:,2])
+        pl.title(title_text.format('p_2'))
+        pl.legend((legend_text.format('y_2','p_1'),
                   legend_text.format('y_2','p_2'),
                   legend_text.format('y_2','p_3')))
-        P.subplot(223)
-        P.plot(t, N.array(exp_sim.p_sol[2])[:,0],
-               t, N.array(exp_sim.p_sol[2])[:,1],
-               t, N.array(exp_sim.p_sol[2])[:,2])
-        P.title(title_text.format('p_3'))
-        P.legend((legend_text.format('y_3','p_1'),
+        pl.subplot(223)
+        pl.plot(t, np.array(exp_sim.p_sol[2])[:,0],
+               t, np.array(exp_sim.p_sol[2])[:,1],
+               t, np.array(exp_sim.p_sol[2])[:,2])
+        pl.title(title_text.format('p_3'))
+        pl.legend((legend_text.format('y_3','p_1'),
                   legend_text.format('y_3','p_2'),
                   legend_text.format('y_3','p_3')))
-        P.subplot(224)
-        P.title('ODE Solution')
-        P.plot(t, y)
-        P.suptitle(exp_mod.name)
-        P.show()
+        pl.subplot(224)
+        pl.title('ODE Solution')
+        pl.plot(t, y)
+        pl.suptitle(exp_mod.name)
+        pl.show()
 
     #Basic test
     nose.tools.assert_almost_equal(y[-1][0], 1577.6552477, 5)

examples/cvode_with_jac.py

@@ -15,12 +15,11 @@
 # 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 numpy as np
 import nose
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 
-
 def run_example(with_plots=True):
     r"""
     Example for demonstrating the use of a user supplied Jacobian
@@ -45,11 +44,11 @@ def run_example(with_plots=True):
     def f(t,y):
         yd_0 = y[1]
         yd_1 = -9.82
-        return N.array([yd_0,yd_1])
+        return np.array([yd_0,yd_1])
 
     #Defines the Jacobian
     def jac(t,y):
-        j = N.array([[0,1.],[0,0]])
+        j = np.array([[0,1.],[0,0]])
         return j
 
     #Defines an Assimulo explicit problem
@@ -71,12 +70,12 @@ def jac(t,y):
 
     #Plot
     if with_plots:
-        import pylab as P
-        P.plot(t,y,linestyle="dashed",marker="o") #Plot the solution
-        P.xlabel('Time')
-        P.ylabel('State')
-        P.title(exp_mod.name)
-        P.show()
+        import pylab as pl
+        pl.plot(t,y,linestyle="dashed",marker="o") #Plot the solution
+        pl.xlabel('Time')
+        pl.ylabel('State')
+        pl.title(exp_mod.name)
+        pl.show()
 
     #Basic tests
     nose.tools.assert_almost_equal(y[-1][0],-121.75000000,4)

examples/cvode_with_jac_sparse.py

@@ -15,8 +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/>.
 
-import numpy as N
-import scipy.sparse as SP
+import numpy as np
+import scipy.sparse as sps
 import nose
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
@@ -50,7 +50,7 @@ def f(t,y):
         yd_0 = -0.04*y[0] + 1e4*y[1]*y[2]
         yd_2 = 3e7*y[1]*y[1]
         yd_1 = -yd_0 - yd_2
-        return N.array([yd_0,yd_1,yd_2])
+        return np.array([yd_0,yd_1,yd_2])
 
     #Defines the Jacobian
     def jac(t,y):
@@ -59,7 +59,7 @@ def jac(t,y):
         rowvals = [0, 1, 0, 1, 2, 0, 1]
         data = [-0.04, 0.04, 1e4*y[2], -1e4*y[2]-6e7*y[1], 6e7*y[1], 1e4*y[1], -1e4*y[1]]
 
-        J = SP.csc_matrix((data, rowvals, colptrs))
+        J = sps.csc_matrix((data, rowvals, colptrs))
         return J
 
     #Defines an Assimulo explicit problem
@@ -85,12 +85,12 @@ def jac(t,y):
 
     #Plot
     if with_plots:
-        import pylab as P
-        P.plot(t,y[:,1],linestyle="dashed",marker="o") #Plot the solution
-        P.xlabel('Time')
-        P.ylabel('State')
-        P.title(exp_mod.name)
-        P.show()
+        import pylab as pl
+        pl.plot(t,y[:,1],linestyle="dashed",marker="o") #Plot the solution
+        pl.xlabel('Time')
+        pl.ylabel('State')
+        pl.title(exp_mod.name)
+        pl.show()
 
     #Basic tests
     nose.tools.assert_almost_equal(y[-1][0],0.9851,3)