Merge branch 'github-actions' into 'development'

Using GitHub actions for additional testing

See merge request damask/DAMASK!435

.github/workflows/.python.yml

@@ -0,0 +1,46 @@
+name: Test Python Library
+on: [push]
+
+jobs:
+  pip:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: [3.7, 3.8, 3.9]
+        os: [ubuntu-latest, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install pytest pandas scipy h5py vtk matplotlib pyyaml
+      - name: Install and run unit tests
+        run: |
+          python -m pip install ./python --no-deps -vv --use-feature=in-tree-build
+          COLUMNS=256 pytest python
+
+  apt:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Install pytest
+        run: |
+          python -m pip install --upgrade pip
+          pip install pytest
+      - name: Install dependencies
+        run: >
+          sudo apt-get update &&
+          sudo apt-get install python3-pip python3-pytest python3-pandas python3-scipy
+          python3-h5py python3-vtk7 python3-matplotlib python3-yaml -y
+      - name: Run unit tests
+        run: |
+          export PYTHONPATH=${PWD}/python
+          COLUMNS=256 python -m pytest python

python/damask/_vtk.py

@@ -121,7 +121,7 @@ class VTK:
 
         """
         vtk_nodes = vtk.vtkPoints()
-        vtk_nodes.SetData(np_to_vtk(nodes))
+        vtk_nodes.SetData(np_to_vtk(np.ascontiguousarray(nodes)))
         cells = vtk.vtkCellArray()
         cells.SetNumberOfCells(connectivity.shape[0])
         T = np.concatenate((np.ones((connectivity.shape[0],1),dtype=np.int64)*connectivity.shape[1],
@@ -157,7 +157,7 @@ class VTK:
         """
         N = points.shape[0]
         vtk_points = vtk.vtkPoints()
-        vtk_points.SetData(np_to_vtk(points))
+        vtk_points.SetData(np_to_vtk(np.ascontiguousarray(points)))
 
         vtk_cells = vtk.vtkCellArray()
         vtk_cells.SetNumberOfCells(N)

python/tests/test_Grid.py

@@ -1,5 +1,6 @@
 import pytest
 import numpy as np
+import vtk
 
 from damask import VTK
 from damask import Grid
@@ -410,6 +411,7 @@ class TestGrid:
 
     @pytest.mark.parametrize('periodic',[True,False])
     @pytest.mark.parametrize('direction',['x','y','z',['x','y'],'zy','xz',['x','y','z']])
+    @pytest.mark.xfail(int(vtk.vtkVersion.GetVTKVersion().split('.')[0])<8, reason='missing METADATA')
     def test_get_grain_boundaries(self,update,ref_path,periodic,direction):
         grid = Grid.load(ref_path/'get_grain_boundaries_8g12x15x20.vti')
         current = grid.get_grain_boundaries(periodic,direction)

python/tests/test_Result.py

@@ -18,6 +18,7 @@ from damask import tensor
 from damask import mechanics
 from damask import grid_filters
 
+
 @pytest.fixture
 def default(tmp_path,ref_path):
     """Small Result file in temp location for modification."""
@@ -108,7 +109,7 @@ class TestResult:
         assert np.allclose(in_memory,in_file)
 
     @pytest.mark.parametrize('mode',
-        ['direct',pytest.param('function',marks=pytest.mark.xfail(sys.platform=="darwin",reason='n/a'))])
+        ['direct',pytest.param('function',marks=pytest.mark.xfail(sys.platform=='darwin',reason='n/a'))])
     def test_add_calculation(self,default,tmp_path,mode):
 
         if mode == 'direct':
@@ -374,6 +375,7 @@ class TestResult:
     @pytest.mark.parametrize('output',['F','*',['P'],['P','F']],ids=range(4))
     @pytest.mark.parametrize('fname',['12grains6x7x8_tensionY.hdf5'],ids=range(1))
     @pytest.mark.parametrize('inc',[4,0],ids=range(2))
+    @pytest.mark.xfail(int(vtk.vtkVersion.GetVTKVersion().split('.')[0])<9, reason='missing "Direction" attribute')
     def test_vtk(self,request,tmp_path,ref_path,update,patch_execution_stamp,patch_datetime_now,output,fname,inc):
         result = Result(ref_path/fname).view('increments',inc)
         os.chdir(tmp_path)
@@ -425,7 +427,8 @@ class TestResult:
 
         assert sorted(open(tmp_path/fname).read()) == sorted(open(ref_path/fname).read())           # XML is not ordered
 
-    @pytest.mark.skipif(not hasattr(vtk,'vtkXdmfReader'),reason='https://discourse.vtk.org/t/2450')
+    @pytest.mark.skipif(not (hasattr(vtk,'vtkXdmfReader') and hasattr(vtk.vtkXdmfReader(),'GetOutput')),
+                        reason='https://discourse.vtk.org/t/2450')
     def test_XDMF_shape(self,tmp_path,single_phase):
         os.chdir(tmp_path)
 
@@ -437,19 +440,14 @@ class TestResult:
         dim_xdmf = reader_xdmf.GetOutput().GetDimensions()
         bounds_xdmf = reader_xdmf.GetOutput().GetBounds()
 
-        single_phase.view('increments',0).export_VTK()
+        single_phase.view('increments',0).export_VTK(parallel=False)
         fname = os.path.splitext(os.path.basename(single_phase.fname))[0]+'_inc00.vti'
-        for i in range(10):                                                                         # waiting for parallel IO
-            reader_vti = vtk.vtkXMLImageDataReader()
-            reader_vti.SetFileName(fname)
-            reader_vti.Update()
-            dim_vti = reader_vti.GetOutput().GetDimensions()
-            bounds_vti = reader_vti.GetOutput().GetBounds()
-            if dim_vti == dim_xdmf and bounds_vti == bounds_xdmf:
-                return
-            time.sleep(.5)
-
-        assert False
+        reader_vti = vtk.vtkXMLImageDataReader()
+        reader_vti.SetFileName(fname)
+        reader_vti.Update()
+        dim_vti = reader_vti.GetOutput().GetDimensions()
+        bounds_vti = reader_vti.GetOutput().GetBounds()
+        assert dim_vti == dim_xdmf and bounds_vti == bounds_xdmf
 
     def test_XDMF_invalid(self,default):
         with pytest.raises(TypeError):

python/tests/test_VTK.py

@@ -5,6 +5,7 @@ import time
 import pytest
 import numpy as np
 import numpy.ma as ma
+import vtk
 
 from damask import VTK
 from damask import grid_filters
@@ -162,6 +163,7 @@ class TestVTK:
         new = VTK.load(tmp_path/'with_comments.vtr')
         assert new.get_comments() == ['this is a comment']
 
+    @pytest.mark.xfail(int(vtk.vtkVersion.GetVTKVersion().split('.')[0])<8, reason='missing METADATA')
     def test_compare_reference_polyData(self,update,ref_path,tmp_path):
         points=np.dstack((np.linspace(0.,1.,10),np.linspace(0.,2.,10),np.linspace(-1.,1.,10))).squeeze()
         polyData = VTK.from_poly_data(points)
@@ -173,14 +175,15 @@ class TestVTK:
              assert polyData.__repr__() == reference.__repr__() and \
                     np.allclose(polyData.get('coordinates'),points)
 
+    @pytest.mark.xfail(int(vtk.vtkVersion.GetVTKVersion().split('.')[0])<8, reason='missing METADATA')
     def test_compare_reference_rectilinearGrid(self,update,ref_path,tmp_path):
         cells = np.array([5,6,7],int)
         size  = np.array([.6,1.,.5])
         rectilinearGrid = VTK.from_rectilinear_grid(cells,size)
         c = grid_filters.coordinates0_point(cells,size).reshape(-1,3,order='F')
         n = grid_filters.coordinates0_node(cells,size).reshape(-1,3,order='F')
-        rectilinearGrid.add(c,'cell')
-        rectilinearGrid.add(n,'node')
+        rectilinearGrid.add(np.ascontiguousarray(c),'cell')
+        rectilinearGrid.add(np.ascontiguousarray(n),'node')
         if update:
              rectilinearGrid.save(ref_path/'rectilinearGrid')
         else: