Makefile added coverage

Makefile

@@ -9,8 +9,8 @@ coverage:
 	coverage html
 	firefox htmlcov/index.html
 
-html:
-	echo "Not implemented"
+clear:
+	coverage erase
 
 publish:
 	@echo "NOOOTE"

tfields/__main__.py

@@ -35,7 +35,7 @@ def run_unittests():
 
 
 
-if __name__ == '__main__':
+if __name__ == '__main__':  # pragma: no cover
     if len(sys.argv) > 1:
         arg = sys.argv.pop(1)
         if arg == 'test':

tfields/core.py

@@ -464,6 +464,7 @@ class Tensors(AbstractNdarray):
             >>> merge2 = tfields.Tensors.merged(*obj_list, coordSys=tfields.bases.CARTESIAN)
             >>> assert merge2.equal([[-0.41614684, 0.90929743, 3.],
             ...                      [3, 3, 3], [5, 1, 3]], atol=1e-8)
+
         """
 
         ''' get most frequent coordSys or predefined coordSys '''

tfields/lib/stats.py

@@ -9,8 +9,6 @@ part of tfields library
 import numpy as np
 import scipy
 import scipy.stats
-import loggingTools
-logger = loggingTools.Logger(__name__)
 
 
 def mode(array, axis=0, bins='auto', range=None):

tfields/lib/util.py

@@ -53,3 +53,34 @@ def flatten(seq, container=None, keep_types=None):
         else:
             container.append(s)
     return container
+
+
+def multi_sort(array, *others, **kwargs):
+    """
+    Sort both lists with list 1
+    Args:
+        array
+        *others
+        **kwargs:
+            method (function): sorting function. Default is 'sorted' 
+            ...: further arguments are passed to method. Default rest is 
+                'key=array[0]'
+    Examples:
+        >>> from tfields.lib.util import multi_sort
+        >>> multi_sort([1,2,3,6,4], [1,2,3,4,5])
+        [[1, 2, 3, 4, 6], [1, 2, 3, 5, 4]]
+        >>> a, b = multi_sort([1,2,3,6,4], [1,2,3,4,5])
+        >>> b
+        [1, 2, 3, 5, 4]
+
+        Expanded to sort as many objects as needed
+        >>> multi_sort([1,2,3,6,4], [1,2,3,4,5], [6,5,4,3,2])
+        [[1, 2, 3, 4, 6], [1, 2, 3, 5, 4], [6, 5, 4, 2, 3]]
+
+    """
+    method = kwargs.pop('method', None)
+    if method is None:
+        method = sorted
+        if 'key' not in kwargs:
+            kwargs['key'] = lambda pair: pair[0]
+    return [list(x) for x in zip(*method(zip(array, *others), **kwargs))]

tfields/mesh3D.py

@@ -723,7 +723,7 @@ class Mesh3D(tfields.TensorMaps):
             return obj, template
         return obj
 
-    def plot(self, **kwargs):
+    def plot(self, **kwargs):  # pragma: no cover
         """
         Forwarding to plotTools.plotMesh
         """
@@ -751,7 +751,7 @@ class Mesh3D(tfields.TensorMaps):
         return tfields.plotting.plotMesh(self, self.faces, **kwargs)
 
 
-if __name__ == '__main__':
+if __name__ == '__main__':  # pragma: no cover
     import doctest
 
     # doctest.run_docstring_examples(Mesh3D.cut, globals())

tfields/planes3D.py

@@ -8,7 +8,6 @@ part of tfields library
 """
 import tfields
 import sympy
-import mplTools as mpt
 
 
 class Planes3D(tfields.TensorFields):
@@ -24,15 +23,15 @@ class Planes3D(tfields.TensorFields):
         return [sympy.Plane(point, normal_vector=vector)
                 for point, vector in zip(self.points, self.vectors)]
 
-    def plot(self, **kwargs):
+    def plot(self, **kwargs):  # pragma: no cover
         """
         forward to Mesh3D plotting
         """
         artists = []
         for i in range(len(self)):
-            artists.append(mpt.plotPlane(self[i],
-                                         self.vectors[0],
-                                         **kwargs))
+            artists.append(tfields.plotting.plotPlane(self[i],
+                                                      self.vectors[0],
+                                                      **kwargs))
         # symbolic = self.symbolic()
         # planeMeshes = [tfields.Mesh3D([pl.arbitrary_point(t=(i + 1) * 1. / 2 * np.pi)
         #                                for i in range(4)],
@@ -41,6 +40,6 @@ class Planes3D(tfields.TensorFields):
         return artists
 
 
-if __name__ == '__main__':
+if __name__ == '__main__':  # pragma: no cover
     import doctest
     doctest.testmod()

tfields/plotting/mpl.py

@@ -64,22 +64,20 @@ def plotMesh(vertices, faces, **kwargs):
     po = tfields.plotting.PlotOptions(kwargs)
     if po.dim == 2:
         full = True
-        import npTools as npt
-        import pyTools
-        mesh = npt.Mesh3D(vertices, faces=faces)
+        mesh = tfields.Mesh3D(vertices, faces=faces)
         xAxis, yAxis, zAxis = po.getXYZAxis()
         facecolors = po.retrieveChain('facecolors', 'color',
                                       default=0,
                                       keep=False)
         if full:
             # implementation that will sort the triangles by zAxis
-            centroids = mesh.getCentroids()
+            centroids = mesh.centroids()
             axesIndices = [0, 1, 2]
             axesIndices.pop(axesIndices.index(xAxis))
             axesIndices.pop(axesIndices.index(yAxis))
             zAxis = axesIndices[0]
             zs = centroids[:, zAxis]
-            zs, faces, facecolors = pyTools.array.getSortedBoth(zs, faces,
+            zs, faces, facecolors = tfields.lib.util.multi_sort(zs, faces,
                                                                 facecolors)
             nFacesInitial = len(faces)
         else:
@@ -87,7 +85,7 @@ def plotMesh(vertices, faces, **kwargs):
             directionVector = np.array([1., 1., 1.])
             directionVector[xAxis] = 0.
             directionVector[yAxis] = 0.
-            normVectors = mesh.triangles.getNormVectors()
+            normVectors = mesh.triangles.norms()
             dotProduct = np.dot(normVectors, directionVector)
             nFacesInitial = len(faces)
             faces = faces[dotProduct > 0]

tfields/points3D.py

@@ -139,7 +139,7 @@ class Points3D(tfields.Tensors):
         return super(Points3D, cls).__new__(cls, tensors, **kwargs)
 
 
-if __name__ == '__main__':
+if __name__ == '__main__':  # pragma: no cover
     import doctest
     doctest.testmod()
     # doctest.run_docstring_examples(Points3D, globals())

tfields/triangles3D.py

@@ -627,6 +627,6 @@ class Triangles3D(tfields.TensorFields):
         return super(Triangles3D, self)._weights(weights, rigid=rigid)
 
 
-if __name__ == '__main__':
+if __name__ == '__main__':  # pragma: no cover
     import doctest
     doctest.testmod()