Add target for Python tests and test VTKReader

* Add 'pytest' to dependencies for Python module.
* Add test for VTKReader.
  - Add testing .vtu files.
* Define Python test target.

python/CMakeLists.txt

@@ -8,3 +8,12 @@ dune_python_install_package(PATH dorie)
 
 # set cache variable
 set(DORIE_PYTHON_MODULES ${python_paths} CACHE PATH "Paths to the python modules")
+
+# add Python tests
+dune_python_add_test(NAME python_tests
+                     COMMAND ${CMAKE_BINARY_DIR}/run-in-dune-env
+                             python -m pytest -v
+                             ${CMAKE_CURRENT_SOURCE_DIR}/dorie/dorie/test/
+                     WORKING_DIRECTORY
+                        ${CMAKE_CURRENT_SOURCE_DIR}/dorie/dorie/test/
+)

python/dorie/dorie/test/test_vtkreader.py

+import pytest
+import numpy as np
+
+from dorie.utilities.vtktools.vtkreader import VTKReader
+
+VTK_CELL = "vtkreader-cell.vtu"
+VTK_VERTEX = "vtkreader-vertex.vtu"
+DEFAULT_ARRAY = "head"
+ARRAYS = ["head", "flux", "K_0", "Theta", "theta_w"]
+
+# Fixtures ---------------------------------------------------------------
+@pytest.fixture
+def vtk_cell ():
+    """Create a VTKReader for the cell VTK test file"""
+    return VTKReader(VTK_CELL, DEFAULT_ARRAY)
+
+@pytest.fixture
+def vtk_vertex ():
+    """Create a VTKReader for the vertex VTK test file"""
+    return VTKReader(VTK_VERTEX, DEFAULT_ARRAY)
+
+# Tests ------------------------------------------------------------------
+
+def test_init ():
+    """Test if initialization works"""
+    VTKReader(VTK_CELL, DEFAULT_ARRAY)
+    VTKReader(VTK_VERTEX, DEFAULT_ARRAY)
+
+def test_array_set (vtk_cell, vtk_vertex):
+    """Test if all included arrays are found"""
+    for array in ARRAYS:
+        vtk_cell.set_data_array(array)
+        vtk_vertex.set_data_array(array)
+
+    with pytest.raises(RuntimeError):
+        vtk_cell.set_data_array("other")
+
+def test_properties (vtk_cell):
+    """Test the VTKReader properties"""
+    assert np.allclose(vtk_cell.bounds, [[0, 1],
+                                         [0, 1],
+                                         [0, 0]])
+    assert vtk_cell.number_of_components == 1
+
+    vtk_cell.set_data_array("flux")
+    assert vtk_cell.number_of_components == 3
+
+def test_evaluate (vtk_cell, vtk_vertex):
+    """Test the evaluation function"""
+    center = np.mean(vtk_cell.bounds, axis=1)
+
+    # should return scalar
+    with pytest.raises(TypeError):
+        len(vtk_cell.evaluate(center))
+
+    # check return of vector
+    vtk_vertex.set_data_array("flux")
+    assert len(vtk_vertex.evaluate(center)) == 3
+
+    # check values are equal
+    for array in ["head", "K_0", "flux"]:
+        vtk_cell.set_data_array(array)
+        vtk_vertex.set_data_array(array)
+        assert np.allclose(vtk_cell.evaluate(center),
+                           vtk_vertex.evaluate(center))
+
+    # check evaluation errors
+    # position has wrong shape
+    with pytest.raises(ValueError):
+        vtk_vertex.evaluate([0.0, 0.0])
+
+    # position out of bounds
+    pos = vtk_vertex.bounds[:, 1]
+    pos = pos + [1.0, 0.0, 1.0]
+    with pytest.raises(ValueError):
+        vtk_vertex.evaluate(pos)

python/dorie/dorie/test/vtkreader-cell.vtu

+<?xml version="1.0"?>
+<VTKFile type="UnstructuredGrid" version="0.1" byte_order="LittleEndian">
+  <UnstructuredGrid>
+    <Piece NumberOfCells="1" NumberOfPoints="4">
+      <CellData Scalars="head" Vectors="flux">
+        <DataArray type="Float32" Name="head" NumberOfComponents="1" format="binary">
+          BAAAAA==AAAAvw==
+        </DataArray>
+        <DataArray type="Float32" Name="flux" NumberOfComponents="3" format="binary">
+          DAAAAA==AAAAgAAAAIAAAAAA
+        </DataArray>
+        <DataArray type="Float32" Name="K_0" NumberOfComponents="1" format="binary">
+          BAAAAA==pIy4N4==
+        </DataArray>
+        <DataArray type="Float32" Name="theta_w" NumberOfComponents="1" format="binary">
+          BAAAAA==Jh4iPh==
+        </DataArray>
+        <DataArray type="Float32" Name="Theta" NumberOfComponents="1" format="binary">
+          BAAAAA==jKPqPq==
+        </DataArray>
+      </CellData>
+      <Points>
+        <DataArray type="Float32" Name="Coordinates" NumberOfComponents="3" format="binary">
+          MAAAAA==AAAAAAAAAAAAAAAAAACAPwAAAAAAAAAAAAAAAAAAgD8AAAAAAACAPwAAgD8AAAAA
+        </DataArray>
+      </Points>
+      <Cells>
+        <DataArray type="Int32" Name="connectivity" NumberOfComponents="1" format="binary">
+          EAAAAA==AAAAAAEAAAADAAAAAgAAAA==
+        </DataArray>
+        <DataArray type="Int32" Name="offsets" NumberOfComponents="1" format="binary">
+          BAAAAA==BAAAAA==
+        </DataArray>
+        <DataArray type="UInt8" Name="types" NumberOfComponents="1" format="binary">
+          AQAAAA==CQ==
+        </DataArray>
+      </Cells>
+    </Piece>
+  </UnstructuredGrid>
+</VTKFile>

python/dorie/dorie/test/vtkreader-vertex.vtu

+<?xml version="1.0"?>
+<VTKFile type="UnstructuredGrid" version="0.1" byte_order="LittleEndian">
+  <UnstructuredGrid>
+    <Piece NumberOfCells="1" NumberOfPoints="4">
+      <PointData Scalars="head" Vectors="flux">
+        <DataArray type="Float32" Name="head" NumberOfComponents="1" format="binary">
+          EAAAAA==AAAAAAAAAAAAAIC/AACAvw==
+        </DataArray>
+        <DataArray type="Float32" Name="flux" NumberOfComponents="3" format="binary">
+          MAAAAA==AAAAgAAAAIAAAAAAAAAAgAAAAIAAAAAAAAAAgAAAAIAAAAAAAAAAgAAAAIAAAAAA
+        </DataArray>
+        <DataArray type="Float32" Name="K_0" NumberOfComponents="1" format="binary">
+          EAAAAA==pIy4N6SMuDekjLg3pIy4N4==
+        </DataArray>
+        <DataArray type="Float32" Name="theta_w" NumberOfComponents="1" format="binary">
+          EAAAAA==UriePlK4nj6N0Uo9jdFKPd==
+        </DataArray>
+        <DataArray type="Float32" Name="Theta" NumberOfComponents="1" format="binary">
+          EAAAAA==AACAPwAAgD9Xv449V7+OPb==
+        </DataArray>
+      </PointData>
+      <Points>
+        <DataArray type="Float32" Name="Coordinates" NumberOfComponents="3" format="binary">
+          MAAAAA==AAAAAAAAAAAAAAAAAACAPwAAAAAAAAAAAAAAAAAAgD8AAAAAAACAPwAAgD8AAAAA
+        </DataArray>
+      </Points>
+      <Cells>
+        <DataArray type="Int32" Name="connectivity" NumberOfComponents="1" format="binary">
+          EAAAAA==AAAAAAEAAAADAAAAAgAAAA==
+        </DataArray>
+        <DataArray type="Int32" Name="offsets" NumberOfComponents="1" format="binary">
+          BAAAAA==BAAAAA==
+        </DataArray>
+        <DataArray type="UInt8" Name="types" NumberOfComponents="1" format="binary">
+          AQAAAA==CQ==
+        </DataArray>
+      </Cells>
+    </Piece>
+  </UnstructuredGrid>
+</VTKFile>

python/dorie/setup.py

@@ -9,7 +9,8 @@ setup(name='dorie',
     author='Lukas Riedel',
     author_email='dorieteam@iup.uni-heidelberg.de',
     url='https://ts-gitlab.iup.uni-heidelberg.de/dorie/dorie',
-    packages=find_packages(),
+    packages=find_packages(exclude=["dorie.test"]),
+    test_suite='py.test',
     install_requires= ['cycler',
                     'configparser',
                     'h5py',
@@ -18,6 +19,7 @@ setup(name='dorie',
                     'Pillow',
                     'pygmsh',
                     'pyparsing',
+                    'pytest',
                     'python-dateutil',
                     'pytz',
                     'pyyaml',