Merge branch 'github-actions' into 'development'
Using GitHub actions for additional testing See merge request damask/DAMASK!435
This commit is contained in:
commit
af1e27379b
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@ -0,0 +1,46 @@
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name: Test Python Library
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on: [push]
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jobs:
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pip:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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python-version: [3.7, 3.8, 3.9]
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os: [ubuntu-latest, macos-latest]
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install pytest pandas scipy h5py vtk matplotlib pyyaml
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- name: Install and run unit tests
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run: |
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python -m pip install ./python --no-deps -vv --use-feature=in-tree-build
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COLUMNS=256 pytest python
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apt:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Install pytest
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run: |
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python -m pip install --upgrade pip
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pip install pytest
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- name: Install dependencies
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run: >
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sudo apt-get update &&
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sudo apt-get install python3-pip python3-pytest python3-pandas python3-scipy
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python3-h5py python3-vtk7 python3-matplotlib python3-yaml -y
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- name: Run unit tests
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run: |
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export PYTHONPATH=${PWD}/python
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COLUMNS=256 python -m pytest python
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@ -121,7 +121,7 @@ class VTK:
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"""
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"""
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vtk_nodes = vtk.vtkPoints()
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vtk_nodes = vtk.vtkPoints()
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vtk_nodes.SetData(np_to_vtk(nodes))
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vtk_nodes.SetData(np_to_vtk(np.ascontiguousarray(nodes)))
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cells = vtk.vtkCellArray()
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cells = vtk.vtkCellArray()
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cells.SetNumberOfCells(connectivity.shape[0])
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cells.SetNumberOfCells(connectivity.shape[0])
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T = np.concatenate((np.ones((connectivity.shape[0],1),dtype=np.int64)*connectivity.shape[1],
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T = np.concatenate((np.ones((connectivity.shape[0],1),dtype=np.int64)*connectivity.shape[1],
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@ -157,7 +157,7 @@ class VTK:
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"""
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"""
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N = points.shape[0]
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N = points.shape[0]
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vtk_points = vtk.vtkPoints()
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vtk_points = vtk.vtkPoints()
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vtk_points.SetData(np_to_vtk(points))
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vtk_points.SetData(np_to_vtk(np.ascontiguousarray(points)))
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vtk_cells = vtk.vtkCellArray()
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vtk_cells = vtk.vtkCellArray()
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vtk_cells.SetNumberOfCells(N)
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vtk_cells.SetNumberOfCells(N)
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@ -1,5 +1,6 @@
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import pytest
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import pytest
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import numpy as np
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import numpy as np
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import vtk
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from damask import VTK
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from damask import VTK
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from damask import Grid
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from damask import Grid
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@ -410,6 +411,7 @@ class TestGrid:
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@pytest.mark.parametrize('periodic',[True,False])
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@pytest.mark.parametrize('periodic',[True,False])
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@pytest.mark.parametrize('direction',['x','y','z',['x','y'],'zy','xz',['x','y','z']])
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@pytest.mark.parametrize('direction',['x','y','z',['x','y'],'zy','xz',['x','y','z']])
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@pytest.mark.xfail(int(vtk.vtkVersion.GetVTKVersion().split('.')[0])<8, reason='missing METADATA')
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def test_get_grain_boundaries(self,update,ref_path,periodic,direction):
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def test_get_grain_boundaries(self,update,ref_path,periodic,direction):
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grid = Grid.load(ref_path/'get_grain_boundaries_8g12x15x20.vti')
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grid = Grid.load(ref_path/'get_grain_boundaries_8g12x15x20.vti')
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current = grid.get_grain_boundaries(periodic,direction)
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current = grid.get_grain_boundaries(periodic,direction)
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@ -18,6 +18,7 @@ from damask import tensor
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from damask import mechanics
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from damask import mechanics
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from damask import grid_filters
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from damask import grid_filters
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@pytest.fixture
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@pytest.fixture
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def default(tmp_path,ref_path):
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def default(tmp_path,ref_path):
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"""Small Result file in temp location for modification."""
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"""Small Result file in temp location for modification."""
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@ -108,7 +109,7 @@ class TestResult:
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assert np.allclose(in_memory,in_file)
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assert np.allclose(in_memory,in_file)
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@pytest.mark.parametrize('mode',
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@pytest.mark.parametrize('mode',
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['direct',pytest.param('function',marks=pytest.mark.xfail(sys.platform=="darwin",reason='n/a'))])
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['direct',pytest.param('function',marks=pytest.mark.xfail(sys.platform=='darwin',reason='n/a'))])
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def test_add_calculation(self,default,tmp_path,mode):
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def test_add_calculation(self,default,tmp_path,mode):
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if mode == 'direct':
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if mode == 'direct':
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@ -374,6 +375,7 @@ class TestResult:
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@pytest.mark.parametrize('output',['F','*',['P'],['P','F']],ids=range(4))
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@pytest.mark.parametrize('output',['F','*',['P'],['P','F']],ids=range(4))
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@pytest.mark.parametrize('fname',['12grains6x7x8_tensionY.hdf5'],ids=range(1))
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@pytest.mark.parametrize('fname',['12grains6x7x8_tensionY.hdf5'],ids=range(1))
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@pytest.mark.parametrize('inc',[4,0],ids=range(2))
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@pytest.mark.parametrize('inc',[4,0],ids=range(2))
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@pytest.mark.xfail(int(vtk.vtkVersion.GetVTKVersion().split('.')[0])<9, reason='missing "Direction" attribute')
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def test_vtk(self,request,tmp_path,ref_path,update,patch_execution_stamp,patch_datetime_now,output,fname,inc):
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def test_vtk(self,request,tmp_path,ref_path,update,patch_execution_stamp,patch_datetime_now,output,fname,inc):
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result = Result(ref_path/fname).view('increments',inc)
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result = Result(ref_path/fname).view('increments',inc)
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os.chdir(tmp_path)
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os.chdir(tmp_path)
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@ -425,7 +427,8 @@ class TestResult:
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assert sorted(open(tmp_path/fname).read()) == sorted(open(ref_path/fname).read()) # XML is not ordered
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assert sorted(open(tmp_path/fname).read()) == sorted(open(ref_path/fname).read()) # XML is not ordered
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@pytest.mark.skipif(not hasattr(vtk,'vtkXdmfReader'),reason='https://discourse.vtk.org/t/2450')
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@pytest.mark.skipif(not (hasattr(vtk,'vtkXdmfReader') and hasattr(vtk.vtkXdmfReader(),'GetOutput')),
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reason='https://discourse.vtk.org/t/2450')
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def test_XDMF_shape(self,tmp_path,single_phase):
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def test_XDMF_shape(self,tmp_path,single_phase):
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os.chdir(tmp_path)
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os.chdir(tmp_path)
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@ -437,19 +440,14 @@ class TestResult:
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dim_xdmf = reader_xdmf.GetOutput().GetDimensions()
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dim_xdmf = reader_xdmf.GetOutput().GetDimensions()
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bounds_xdmf = reader_xdmf.GetOutput().GetBounds()
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bounds_xdmf = reader_xdmf.GetOutput().GetBounds()
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single_phase.view('increments',0).export_VTK()
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single_phase.view('increments',0).export_VTK(parallel=False)
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fname = os.path.splitext(os.path.basename(single_phase.fname))[0]+'_inc00.vti'
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fname = os.path.splitext(os.path.basename(single_phase.fname))[0]+'_inc00.vti'
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for i in range(10): # waiting for parallel IO
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reader_vti = vtk.vtkXMLImageDataReader()
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reader_vti = vtk.vtkXMLImageDataReader()
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reader_vti.SetFileName(fname)
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reader_vti.SetFileName(fname)
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reader_vti.Update()
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reader_vti.Update()
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dim_vti = reader_vti.GetOutput().GetDimensions()
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dim_vti = reader_vti.GetOutput().GetDimensions()
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bounds_vti = reader_vti.GetOutput().GetBounds()
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bounds_vti = reader_vti.GetOutput().GetBounds()
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if dim_vti == dim_xdmf and bounds_vti == bounds_xdmf:
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assert dim_vti == dim_xdmf and bounds_vti == bounds_xdmf
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return
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time.sleep(.5)
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assert False
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def test_XDMF_invalid(self,default):
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def test_XDMF_invalid(self,default):
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with pytest.raises(TypeError):
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with pytest.raises(TypeError):
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import pytest
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import pytest
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import numpy as np
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import numpy as np
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import numpy.ma as ma
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import numpy.ma as ma
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import vtk
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from damask import VTK
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from damask import VTK
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from damask import grid_filters
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from damask import grid_filters
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new = VTK.load(tmp_path/'with_comments.vtr')
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new = VTK.load(tmp_path/'with_comments.vtr')
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assert new.get_comments() == ['this is a comment']
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assert new.get_comments() == ['this is a comment']
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@pytest.mark.xfail(int(vtk.vtkVersion.GetVTKVersion().split('.')[0])<8, reason='missing METADATA')
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def test_compare_reference_polyData(self,update,ref_path,tmp_path):
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def test_compare_reference_polyData(self,update,ref_path,tmp_path):
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points=np.dstack((np.linspace(0.,1.,10),np.linspace(0.,2.,10),np.linspace(-1.,1.,10))).squeeze()
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points=np.dstack((np.linspace(0.,1.,10),np.linspace(0.,2.,10),np.linspace(-1.,1.,10))).squeeze()
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polyData = VTK.from_poly_data(points)
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polyData = VTK.from_poly_data(points)
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assert polyData.__repr__() == reference.__repr__() and \
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assert polyData.__repr__() == reference.__repr__() and \
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np.allclose(polyData.get('coordinates'),points)
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np.allclose(polyData.get('coordinates'),points)
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@pytest.mark.xfail(int(vtk.vtkVersion.GetVTKVersion().split('.')[0])<8, reason='missing METADATA')
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def test_compare_reference_rectilinearGrid(self,update,ref_path,tmp_path):
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def test_compare_reference_rectilinearGrid(self,update,ref_path,tmp_path):
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cells = np.array([5,6,7],int)
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cells = np.array([5,6,7],int)
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size = np.array([.6,1.,.5])
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size = np.array([.6,1.,.5])
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rectilinearGrid = VTK.from_rectilinear_grid(cells,size)
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rectilinearGrid = VTK.from_rectilinear_grid(cells,size)
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c = grid_filters.coordinates0_point(cells,size).reshape(-1,3,order='F')
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c = grid_filters.coordinates0_point(cells,size).reshape(-1,3,order='F')
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n = grid_filters.coordinates0_node(cells,size).reshape(-1,3,order='F')
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n = grid_filters.coordinates0_node(cells,size).reshape(-1,3,order='F')
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rectilinearGrid.add(c,'cell')
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rectilinearGrid.add(np.ascontiguousarray(c),'cell')
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rectilinearGrid.add(n,'node')
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rectilinearGrid.add(np.ascontiguousarray(n),'node')
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if update:
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if update:
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rectilinearGrid.save(ref_path/'rectilinearGrid')
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rectilinearGrid.save(ref_path/'rectilinearGrid')
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else:
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else:
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