Merge pull request #121 from simpeg/travis

Rearrange Tests

.travis.yml

@@ -4,6 +4,12 @@ python:
 
 sudo: false
 
+env:
+    - TEST_DIR=tests/utils
+    - TEST_DIR=tests/mesh
+    - TEST_DIR=tests/base
+    - TEST_DIR=tests/examples
+
 # Setup anaconda
 before_install:
   - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda-3.8.3-Linux-x86_64.sh -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-3.8.3-Linux-x86_64.sh -O miniconda.sh; fi
@@ -11,20 +17,17 @@ before_install:
   - ./miniconda.sh -b
   - export PATH=/home/travis/anaconda/bin:/home/travis/miniconda/bin:$PATH
   - conda update --yes conda
-  # The next couple lines fix a crash with multiprocessing on Travis and are not specific to using Miniconda
-  # - sudo rm -rf /dev/shm
-  # - sudo ln -s /run/shm /dev/shm
 
 # Install packages
 install:
-  - conda install --yes pip python=$TRAVIS_PYTHON_VERSION numpy scipy matplotlib cython
+  - conda install --yes pip python=$TRAVIS_PYTHON_VERSION numpy scipy matplotlib cython ipython
   - pip install nose-cov python-coveralls
   # - pip install -r requirements.txt
   - python setup.py install
 
 # Run test
 script:
-  - nosetests --with-cov --cov SimPEG --cov-config .coveragerc -v -s
+  - nosetests $TEST_DIR --with-cov --cov SimPEG --cov-config .coveragerc -v -s
 
 # Calculate coverage
 after_success:

SimPEG/Examples/DCfwd.py

@@ -5,67 +5,73 @@ from matplotlib.mlab import griddata
 
 ## 2D DC forward modeling example with Tensor and Curvilinear Meshes
 
-# Step1: Generate Tensor and Curvilinear Mesh
-sz = [40,40]
-# Tensor Mesh
-tM = Mesh.TensorMesh(sz)
-# Curvilinear Mesh
-rM = Mesh.CurvilinearMesh(Utils.meshutils.exampleLrmGrid(sz,'rotate'))
+def run(plotIt=True):
+    # Step1: Generate Tensor and Curvilinear Mesh
+    sz = [40,40]
+    # Tensor Mesh
+    tM = Mesh.TensorMesh(sz)
+    # Curvilinear Mesh
+    rM = Mesh.CurvilinearMesh(Utils.meshutils.exampleLrmGrid(sz,'rotate'))
 
-# Step2: Direct Current (DC) operator
-def DCfun(mesh, pts):
-    D = mesh.faceDiv
-    G = D.T
-    sigma = 1e-2*np.ones(mesh.nC)
-    Msigi = mesh.getFaceInnerProduct(1./sigma)
-    MsigI = Utils.sdInv(Msigi)
-    A = D*MsigI*G
-    A[-1,-1] /= mesh.vol[-1] # Remove null space
-    rhs = np.zeros(mesh.nC)
-    txind = Utils.meshutils.closestPoints(mesh, pts)
-    rhs[txind] = np.r_[1,-1]
-    return A, rhs
+    # Step2: Direct Current (DC) operator
+    def DCfun(mesh, pts):
+        D = mesh.faceDiv
+        G = D.T
+        sigma = 1e-2*np.ones(mesh.nC)
+        Msigi = mesh.getFaceInnerProduct(1./sigma)
+        MsigI = Utils.sdInv(Msigi)
+        A = D*MsigI*G
+        A[-1,-1] /= mesh.vol[-1] # Remove null space
+        rhs = np.zeros(mesh.nC)
+        txind = Utils.meshutils.closestPoints(mesh, pts)
+        rhs[txind] = np.r_[1,-1]
+        return A, rhs
 
-pts = np.vstack((np.r_[0.25, 0.5], np.r_[0.75, 0.5]))
+    pts = np.vstack((np.r_[0.25, 0.5], np.r_[0.75, 0.5]))
 
-#Step3: Solve DC problem (LU solver)
-AtM, rhstM = DCfun(tM, pts)
-AinvtM = SolverLU(AtM)
-phitM = AinvtM*rhstM
+    #Step3: Solve DC problem (LU solver)
+    AtM, rhstM = DCfun(tM, pts)
+    AinvtM = SolverLU(AtM)
+    phitM = AinvtM*rhstM
 
-ArM, rhsrM = DCfun(rM, pts)
-AinvrM = SolverLU(ArM)
-phirM = AinvrM*rhsrM
+    ArM, rhsrM = DCfun(rM, pts)
+    AinvrM = SolverLU(ArM)
+    phirM = AinvrM*rhsrM
 
-#Step4: Making Figure
-fig, axes = plt.subplots(1,2,figsize=(12*1.2,4*1.2))
-label = ["(a)", "(b)"]
-opts = {}
-vmin, vmax = phitM.min(), phitM.max()
-dat = tM.plotImage(phitM, ax=axes[0], clim=(vmin, vmax), grid=True)
+    if not plotIt: return
 
-#TODO: At the moment Curvilinear Mesh do not have plotimage 
+    #Step4: Making Figure
+    fig, axes = plt.subplots(1,2,figsize=(12*1.2,4*1.2))
+    label = ["(a)", "(b)"]
+    opts = {}
+    vmin, vmax = phitM.min(), phitM.max()
+    dat = tM.plotImage(phitM, ax=axes[0], clim=(vmin, vmax), grid=True)
 
-Xi = tM.gridCC[:,0].reshape(sz[0], sz[1], order='F')
-Yi = tM.gridCC[:,1].reshape(sz[0], sz[1], order='F')
-PHIrM = griddata(rM.gridCC[:,0], rM.gridCC[:,1], phirM, Xi, Yi, interp='linear')
-axes[1].contourf(Xi, Yi, PHIrM, 100, vmin=vmin, vmax=vmax)
+    #TODO: At the moment Curvilinear Mesh do not have plotimage
 
-cb = plt.colorbar(dat[0], ax=axes[0]); cb.set_label("Voltage (V)")
-cb = plt.colorbar(dat[0], ax=axes[1]); cb.set_label("Voltage (V)")
+    Xi = tM.gridCC[:,0].reshape(sz[0], sz[1], order='F')
+    Yi = tM.gridCC[:,1].reshape(sz[0], sz[1], order='F')
+    PHIrM = griddata(rM.gridCC[:,0], rM.gridCC[:,1], phirM, Xi, Yi, interp='linear')
+    axes[1].contourf(Xi, Yi, PHIrM, 100, vmin=vmin, vmax=vmax)
 
-tM.plotGrid(ax=axes[0], **opts)
-axes[0].set_title('TensorMesh')
-rM.plotGrid(ax=axes[1], **opts)
-axes[1].set_title('CurvilinearMesh')
-for i in range(2):
-    axes[i].set_xlim(0.025, 0.975)
-    axes[i].set_ylim(0.025, 0.975)
-    axes[i].text(0., 1.0, label[i], fontsize=20)
-    if i==0:        
-        axes[i].set_ylabel("y")
-    else:
-        axes[i].set_ylabel(" ")
-    axes[i].set_xlabel("x")
+    cb = plt.colorbar(dat[0], ax=axes[0]); cb.set_label("Voltage (V)")
+    cb = plt.colorbar(dat[0], ax=axes[1]); cb.set_label("Voltage (V)")
 
-plt.show()
+    tM.plotGrid(ax=axes[0], **opts)
+    axes[0].set_title('TensorMesh')
+    rM.plotGrid(ax=axes[1], **opts)
+    axes[1].set_title('CurvilinearMesh')
+    for i in range(2):
+        axes[i].set_xlim(0.025, 0.975)
+        axes[i].set_ylim(0.025, 0.975)
+        axes[i].text(0., 1.0, label[i], fontsize=20)
+        if i==0:
+            axes[i].set_ylabel("y")
+        else:
+            axes[i].set_ylabel(" ")
+        axes[i].set_xlabel("x")
+
+    plt.show()
+
+if __name__ == '__main__':
+    run()

SimPEG/Examples/__init__.py

@@ -1 +1 @@
-import Linear
+import Linear, DCfwd

tests/__init__.py

@@ -1,6 +1,3 @@
-from TestUtils import checkDerivative, Rosenbrock, OrderTest, getQuadratic
-
-
 if __name__ == '__main__':
     import os
     import glob

tests/base/__init__.py

@@ -0,0 +1,11 @@
+if __name__ == '__main__':
+    import os
+    import glob
+    import unittest
+    test_file_strings = glob.glob('test_*.py')
+    module_strings = [str[0:len(str)-3] for str in test_file_strings]
+    suites = [unittest.defaultTestLoader.loadTestsFromName(str) for str
+              in module_strings]
+    testSuite = unittest.TestSuite(suites)
+
+    unittest.TextTestRunner(verbosity=2).run(testSuite)

tests/base/test_maps.py

@@ -1,7 +1,6 @@
 import numpy as np
 import unittest
 from SimPEG import *
-from TestUtils import checkDerivative
 from scipy.sparse.linalg import dsolve
 
 TOL = 1e-14

tests/base/test_regularization.py

@@ -1,7 +1,6 @@
 import numpy as np
 import unittest
 from SimPEG import *
-from TestUtils import checkDerivative
 from scipy.sparse.linalg import dsolve
 import inspect
 
@@ -18,12 +17,16 @@ class RegularizationTests(unittest.TestCase):
             if not issubclass(r, Regularization.BaseRegularization):
                 continue
             # if 'Regularization' not in R: continue
-            print 'Check:', R
             mapping = r.mapPair(self.mesh2)
             reg = r(self.mesh2, mapping=mapping)
             m = np.random.rand(mapping.nP)
             reg.mref = m[:]*np.mean(m)
-            passed = checkDerivative(lambda m : [reg.eval(m), reg.evalDeriv(m)], m, plotIt=False)
+
+            print 'Check:', R
+            passed = Tests.checkDerivative(lambda m : [reg.eval(m), reg.evalDeriv(m)], m, plotIt=False)
+            self.assertTrue(passed)
+            print 'Check 2 Deriv:', R
+            passed = Tests.checkDerivative(lambda m : [reg.evalDeriv(m), reg.eval2Deriv(m)], m, plotIt=False)
             self.assertTrue(passed)
 
 

tests/examples/__init__.py

@@ -0,0 +1,11 @@
+if __name__ == '__main__':
+    import os
+    import glob
+    import unittest
+    test_file_strings = glob.glob('test_*.py')
+    module_strings = [str[0:len(str)-3] for str in test_file_strings]
+    suites = [unittest.defaultTestLoader.loadTestsFromName(str) for str
+              in module_strings]
+    testSuite = unittest.TestSuite(suites)
+
+    unittest.TextTestRunner(verbosity=2).run(testSuite)

tests/examples/test_examples.py

@@ -1,13 +1,17 @@
 import unittest
 import sys
-from SimPEG.Examples import Linear
+from SimPEG.Examples import Linear, DCfwd
 import numpy as np
 
 class TestLinear(unittest.TestCase):
-
     def test_running(self):
         Linear.run(100, plotIt=False)
         self.assertTrue(True)
 
+class TestDCfwd(unittest.TestCase):
+    def test_running(self):
+        DCfwd.run(plotIt=False)
+        self.assertTrue(True)
+
 if __name__ == '__main__':
     unittest.main()

tests/mesh/__init__.py

@@ -0,0 +1,11 @@
+if __name__ == '__main__':
+    import os
+    import glob
+    import unittest
+    test_file_strings = glob.glob('test_*.py')
+    module_strings = [str[0:len(str)-3] for str in test_file_strings]
+    suites = [unittest.defaultTestLoader.loadTestsFromName(str) for str
+              in module_strings]
+    testSuite = unittest.TestSuite(suites)
+
+    unittest.TextTestRunner(verbosity=2).run(testSuite)

tests/mesh/test_boundaryPoisson.py

@@ -1,13 +1,12 @@
 import numpy as np
 import scipy.sparse as sp
 import unittest
-from TestUtils import OrderTest
 import matplotlib.pyplot as plt
 from SimPEG import *
 
 MESHTYPES = ['uniformTensorMesh']
 
-class Test1D_InhomogeneousDirichlet(OrderTest):
+class Test1D_InhomogeneousDirichlet(Tests.OrderTest):
     name = "1D - Dirichlet"
     meshTypes = MESHTYPES
     meshDimension = 1
@@ -88,7 +87,7 @@ class Test1D_InhomogeneousDirichlet(OrderTest):
         self.orderTest()
 
 
-class Test2D_InhomogeneousDirichlet(OrderTest):
+class Test2D_InhomogeneousDirichlet(Tests.OrderTest):
     name = "2D - Dirichlet"
     meshTypes = MESHTYPES
     meshDimension = 2
@@ -169,7 +168,7 @@ class Test2D_InhomogeneousDirichlet(OrderTest):
         self.myTest = 'xcJ'
         self.orderTest()
 
-class Test1D_InhomogeneousNeumann(OrderTest):
+class Test1D_InhomogeneousNeumann(Tests.OrderTest):
     name = "1D - Neumann"
     meshTypes = MESHTYPES
     meshDimension = 1
@@ -246,7 +245,7 @@ class Test1D_InhomogeneousNeumann(OrderTest):
         self.myTest = 'xcJ'
         self.orderTest()
 
-class Test2D_InhomogeneousNeumann(OrderTest):
+class Test2D_InhomogeneousNeumann(Tests.OrderTest):
     name = "2D - Neumann"
     meshTypes = MESHTYPES
     meshDimension = 2
@@ -333,7 +332,7 @@ class Test2D_InhomogeneousNeumann(OrderTest):
         self.myTest = 'xcJ'
         self.orderTest()
 
-class Test1D_InhomogeneousMixed(OrderTest):
+class Test1D_InhomogeneousMixed(Tests.OrderTest):
     name = "1D - Mixed"
     meshTypes = MESHTYPES
     meshDimension = 1
@@ -410,7 +409,7 @@ class Test1D_InhomogeneousMixed(OrderTest):
         self.myTest = 'xcJ'
         self.orderTest()
 
-class Test2D_InhomogeneousMixed(OrderTest):
+class Test2D_InhomogeneousMixed(Tests.OrderTest):
     name = "2D - Mixed"
     meshTypes = MESHTYPES
     meshDimension = 2

tests/mesh/test_cylMesh.py

@@ -1,7 +1,6 @@
 import unittest
 import sys
 from SimPEG import *
-from TestUtils import OrderTest
 
 
 class TestCyl2DMesh(unittest.TestCase):
@@ -217,7 +216,7 @@ cyl_row3 = lambda g, xfun, yfun, zfun: np.c_[call3(xfun, g), call3(yfun, g), cal
 cylF2 = lambda M, fx, fy: np.vstack((cyl_row2(M.gridFx, fx, fy), cyl_row2(M.gridFz, fx, fy)))
 
 
-class TestFaceDiv2D(OrderTest):
+class TestFaceDiv2D(Tests.OrderTest):
     name = "FaceDiv"
     meshTypes = MESHTYPES
     meshDimension = 2
@@ -242,7 +241,7 @@ class TestFaceDiv2D(OrderTest):
     def test_order(self):
         self.orderTest()
 
-class TestEdgeCurl2D(OrderTest):
+class TestEdgeCurl2D(Tests.OrderTest):
     name = "EdgeCurl"
     meshTypes = MESHTYPES
     meshDimension = 2
@@ -281,7 +280,7 @@ class TestEdgeCurl2D(OrderTest):
         self.orderTest()
 
 
-# class TestInnerProducts2D(OrderTest):
+# class TestInnerProducts2D(Tests.OrderTest):
 #     """Integrate an function over a unit cube domain using edgeInnerProducts and faceInnerProducts."""
 
 #     meshTypes = MESHTYPES

tests/mesh/test_innerProduct.py

@@ -1,10 +1,9 @@
 import numpy as np
 import unittest
-from TestUtils import OrderTest
-from SimPEG import Utils
+from SimPEG import Utils, Tests
 
 
-class TestInnerProducts(OrderTest):
+class TestInnerProducts(Tests.OrderTest):
     """Integrate an function over a unit cube domain using edgeInnerProducts and faceInnerProducts."""
 
     meshTypes = ['uniformTensorMesh', 'uniformCurv', 'rotateCurv']
@@ -151,7 +150,7 @@ class TestInnerProducts(OrderTest):
         self.orderTest()
 
 
-class TestInnerProducts2D(OrderTest):
+class TestInnerProducts2D(Tests.OrderTest):
     """Integrate an function over a unit cube domain using edgeInnerProducts and faceInnerProducts."""
 
     meshTypes = ['uniformTensorMesh', 'uniformCurv', 'rotateCurv']
@@ -293,7 +292,7 @@ class TestInnerProducts2D(OrderTest):
 
 
 
-class TestInnerProducts1D(OrderTest):
+class TestInnerProducts1D(Tests.OrderTest):
     """Integrate an function over a unit cube domain using edgeInnerProducts and faceInnerProducts."""
 
     meshTypes = ['uniformTensorMesh']

tests/mesh/test_innerProductDerivs.py

@@ -1,7 +1,6 @@
 import numpy as np
 import unittest
 from SimPEG import *
-from TestUtils import checkDerivative
 
 
 class TestInnerProductsDerivs(unittest.TestCase):
@@ -21,7 +20,7 @@ class TestInnerProductsDerivs(unittest.TestCase):
             Md = mesh.getFaceInnerProductDeriv(sig, invProp=invProp, invMat=invMat, doFast=fast)
             return M*v, Md(v)
         print meshType, 'Face', h, rep, fast, ('harmonic' if invProp and invMat else 'standard')
-        return checkDerivative(fun, sig, num=5, plotIt=False)
+        return Tests.checkDerivative(fun, sig, num=5, plotIt=False)
 
     def doTestEdge(self, h, rep, fast, meshType, invProp=False, invMat=False):
         if meshType == 'Curv':
@@ -38,7 +37,7 @@ class TestInnerProductsDerivs(unittest.TestCase):
             Md = mesh.getEdgeInnerProductDeriv(sig, invProp=invProp, invMat=invMat, doFast=fast)
             return M*v, Md(v)
         print meshType, 'Edge', h, rep, fast, ('harmonic' if invProp and invMat else 'standard')
-        return checkDerivative(fun, sig, num=5, plotIt=False)
+        return Tests.checkDerivative(fun, sig, num=5, plotIt=False)
 
     def test_FaceIP_1D_float(self):
         self.assertTrue(self.doTestFace([10],0, False, 'Tensor'))

tests/mesh/test_interpolation.py

@@ -1,8 +1,7 @@
 import numpy as np
 import unittest
-from TestUtils import OrderTest
 from SimPEG.Utils import mkvc
-from SimPEG import Mesh
+from SimPEG import Mesh, Tests
 import unittest
 
 
@@ -23,7 +22,7 @@ cartE3 = lambda M, ex, ey, ez: np.vstack((cart_row3(M.gridEx, ex, ey, ez), cart_
 TOL = 1e-7
 
 
-class TestInterpolation1D(OrderTest):
+class TestInterpolation1D(Tests.OrderTest):
     LOCS = np.random.rand(50)*0.6+0.2
     name = "Interpolation 1D"
     meshTypes = MESHTYPES
@@ -69,7 +68,7 @@ class TestOutliersInterp1D(unittest.TestCase):
         Q = M.getInterpolationMat(np.array([[-1],[0.126],[0.127]]),'CC',zerosOutside=True)
         self.assertTrue(np.linalg.norm(Q*x - np.r_[0,1.004,1.008]) < TOL)
 
-class TestInterpolation2d(OrderTest):
+class TestInterpolation2d(Tests.OrderTest):
     name = "Interpolation 2D"
     LOCS = np.random.rand(50,2)*0.6+0.2
     meshTypes = MESHTYPES
@@ -152,7 +151,7 @@ class TestInterpolation2dCyl_Simple(unittest.TestCase):
         self.assertRaises(Exception,lambda:M.getInterpolationMat(locs, 'Ez'))
 
 
-class TestInterpolation2dCyl(OrderTest):
+class TestInterpolation2dCyl(Tests.OrderTest):
     name = "Interpolation 2D"
     LOCS = np.c_[np.random.rand(4)*0.6+0.2, np.zeros(4), np.random.rand(4)*0.6+0.2]
     meshTypes = ['uniformCylMesh'] # MESHTYPES +
@@ -220,7 +219,7 @@ class TestInterpolation2dCyl(OrderTest):
         self.name = 'Interpolation 2D CYLMESH: Ey'
         self.orderTest()
 
-class TestInterpolation3D(OrderTest):
+class TestInterpolation3D(Tests.OrderTest):
     name = "Interpolation"
     LOCS = np.random.rand(50,3)*0.6+0.2
     meshTypes = MESHTYPES

tests/mesh/test_operators.py

@@ -1,6 +1,6 @@
 import numpy as np
 import unittest
-from TestUtils import OrderTest
+from SimPEG.Tests import OrderTest
 import matplotlib.pyplot as plt
 
 #TODO: 'randomTensorMesh'

tests/mesh/test_tensorMesh.py

@@ -1,8 +1,7 @@
 import numpy as np
 import unittest
 from SimPEG.Mesh import TensorMesh
-from TestUtils import OrderTest
-from SimPEG import Solver
+from SimPEG import Solver, Tests
 
 TOL = 1e-10
 
@@ -91,7 +90,7 @@ class BasicTensorMeshTests(unittest.TestCase):
         M = TensorMesh([[(10.,2)]])
         self.assertLess(np.abs(M.hx - np.r_[10.,10.]).sum(), TOL)
 
-class TestPoissonEqn(OrderTest):
+class TestPoissonEqn(Tests.OrderTest):
     name = "Poisson Equation"
     meshSizes = [10, 16, 20]
 

tests/utils/__init__.py

@@ -0,0 +1,11 @@
+if __name__ == '__main__':
+    import os
+    import glob
+    import unittest
+    test_file_strings = glob.glob('test_*.py')
+    module_strings = [str[0:len(str)-3] for str in test_file_strings]
+    suites = [unittest.defaultTestLoader.loadTestsFromName(str) for str
+              in module_strings]
+    testSuite = unittest.TestSuite(suites)
+
+    unittest.TextTestRunner(verbosity=2).run(testSuite)