Merge branch 'python-improvements' into 'development'
Python improvements See merge request damask/DAMASK!343
This commit is contained in:
Sharan Roongta
commit
23a3354ac1
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@ -84,7 +84,7 @@ for executable in python python3; do
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done
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secondLevel "Details on $DEFAULT_PYTHON:"
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echo $(ls -la $(which $DEFAULT_PYTHON))
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for module in numpy scipy pandas;do
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for module in numpy scipy pandas matplotlib yaml h5py;do
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thirdLevel $module
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$DEFAULT_PYTHON -c "import $module; \
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print('Version: {}'.format($module.__version__)); \
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@ -94,10 +94,6 @@ thirdLevel vtk
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$DEFAULT_PYTHON -c "import vtk; \
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print('Version: {}'.format(vtk.vtkVersion.GetVTKVersion())); \
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print('Location: {}'.format(vtk.__file__))"
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thirdLevel h5py
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$DEFAULT_PYTHON -c "import h5py; \
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print('Version: {}'.format(h5py.version.version)); \
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print('Location: {}'.format(h5py.__file__))"
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firstLevel "GNU Compiler Collection"
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for executable in gcc g++ gfortran ;do
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@ -103,7 +103,6 @@ class ConfigMaterial(Config):
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"""Check for completeness."""
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ok = True
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for top_level in ['homogenization','phase','material']:
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# ToDo: With python 3.8 as prerequisite we can shorten with :=
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ok &= top_level in self
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if top_level not in self: print(f'{top_level} entry missing')
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@ -203,7 +202,7 @@ class ConfigMaterial(Config):
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"""
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dup = self.copy()
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for i,m in enumerate(dup['material']):
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if ID and i not in ID: continue
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if ID is not None and i not in ID: continue
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for c in m['constituents']:
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if constituent is not None and c not in constituent: continue
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try:
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@ -227,7 +226,7 @@ class ConfigMaterial(Config):
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"""
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dup = self.copy()
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for i,m in enumerate(dup['material']):
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if ID and i not in ID: continue
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if ID is not None and i not in ID: continue
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try:
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m['homogenization'] = mapping[m['homogenization']]
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except KeyError:
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@ -202,7 +202,7 @@ class Grid:
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Geometry file to read.
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"""
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warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.1.0', DeprecationWarning)
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warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.1.0', DeprecationWarning,2)
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try:
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f = open(fname)
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except TypeError:
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@ -541,7 +541,7 @@ class Grid:
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Compress geometry with 'x of y' and 'a to b'.
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"""
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warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.1.0', DeprecationWarning)
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warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.1.0', DeprecationWarning,2)
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header = [f'{len(self.comments)+4} header'] + self.comments \
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+ ['grid a {} b {} c {}'.format(*self.cells),
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'size x {} y {} z {}'.format(*self.size),
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@ -760,7 +760,7 @@ class Grid:
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"""
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if fill is None: fill = np.nanmax(self.material) + 1
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dtype = float if np.isnan(fill) or int(fill) != fill or self.material.dtype==np.float else int
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dtype = float if isinstance(fill,float) or self.material.dtype in np.sctypes['float'] else int
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material = self.material
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# These rotations are always applied in the reference coordinate system, i.e. (z,x,z) not (z,x',z'')
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@ -246,8 +246,8 @@ class VTK:
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raise ValueError('No label defined for numpy.ndarray')
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N_data = data.shape[0]
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d = np_to_vtk((data.astype(np.float32) if data.dtype in [np.float64, np.float128]
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else data).reshape(N_data,-1),deep=True) # avoid large files
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d = np_to_vtk((data.astype(np.single) if data.dtype in [np.double, np.longdouble] else
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data).reshape(N_data,-1),deep=True) # avoid large files
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d.SetName(label)
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if N_data == N_points:
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@ -183,7 +183,7 @@ def scale_to_coprime(v):
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# Python 3.9 provides math.lcm, see https://stackoverflow.com/questions/51716916.
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return a * b // np.gcd(a, b)
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m = (np.array(v) * reduce(lcm, map(lambda x: int(get_square_denominator(x)),v)) ** 0.5).astype(np.int)
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m = (np.array(v) * reduce(lcm, map(lambda x: int(get_square_denominator(x)),v)) ** 0.5).astype(int)
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m = m//reduce(np.gcd,m)
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with np.errstate(invalid='ignore'):
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@ -6,28 +6,29 @@ with open(Path(__file__).parent/'damask/VERSION') as f:
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version = re.sub(r'(-([^-]*)).*$',r'.\2',re.sub(r'^v(\d+\.\d+(\.\d+)?)',r'\1',f.readline().strip()))
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setuptools.setup(
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name="damask",
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name='damask',
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version=version,
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author="The DAMASK team",
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author_email="damask@mpie.de",
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description="DAMASK library",
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long_description="Python library for pre and post processing of DAMASK simulations",
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url="https://damask.mpie.de",
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author='The DAMASK team',
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author_email='damask@mpie.de',
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description='DAMASK library',
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long_description='Python library for pre and post processing of DAMASK simulations',
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url='https://damask.mpie.de',
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packages=setuptools.find_packages(),
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include_package_data=True,
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python_requires = '>=3.6',
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install_requires = [
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"pandas", # requires numpy
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"scipy",
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"h5py", # requires numpy
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"vtk",
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"matplotlib", # requires numpy, pillow
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"pyaml"
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'pandas>=0.24', # requires numpy
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'scipy>=1.2',
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'h5py>=2.9', # requires numpy
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'vtk>=8.1',
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'matplotlib>=3.0', # requires numpy, pillow
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'pyaml>=3.12'
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],
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classifiers = [
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"Intended Audience :: Science/Research",
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"Topic :: Scientific/Engineering",
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"Programming Language :: Python :: 3",
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"License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
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"Operating System :: OS Independent",
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'Intended Audience :: Science/Research',
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'Topic :: Scientific/Engineering',
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'Programming Language :: Python :: 3',
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'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)',
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'Operating System :: OS Independent',
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],
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)
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@ -347,7 +347,7 @@ class TestGrid:
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@pytest.mark.parametrize('approach',['Laguerre','Voronoi'])
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def test_tessellate_bicrystal(self,approach):
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cells = np.random.randint(5,10,3)*2
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size = cells.astype(np.float)
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size = cells.astype(float)
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seeds = np.vstack((size*np.array([0.5,0.25,0.5]),size*np.array([0.5,0.75,0.5])))
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material = np.zeros(cells)
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material[:,cells[1]//2:,:] = 1
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