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Merge branch 'migrate-to-pathlib' into 'development' 

Migrate to pathlib

See merge request damask/DAMASK!177
This commit is contained in:
Anderson Wallace Paiva do Nascimento 2020-06-24 14:54:36 +02:00
parent deaf055f88 a9c61ede69
commit 3d93a5ff00
9 changed files with 99 additions and 114 deletions
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56
installation/symlink_Processing.py
View File

@ -1,56 +1,30 @@
#!/usr/bin/env python3
# Makes postprocessing routines accessible from everywhere.
import os
import sys
from pathlib import Path
import damask
damaskEnv = damask.Environment()
baseDir = damaskEnv.relPath('processing/')
binDir = damaskEnv.relPath('bin/')
env = damask.Environment()
bin_dir = env.root_dir/Path('bin')
if not os.path.isdir(binDir):
os.mkdir(binDir)
if not bin_dir.exists():
bin_dir.mkdir()
#define ToDo list
processing_subDirs = ['pre',
'post',
]
sys.stdout.write('\nsymbolic linking...\n')
for sub_dir in ['pre','post']:
the_dir = env.root_dir/Path('processing')/Path(sub_dir)
for subDir in processing_subDirs:
theDir = os.path.abspath(os.path.join(baseDir,subDir))
sys.stdout.write('\n'+binDir+' ->\n'+theDir+damask.util.deemph(' ...')+'\n')
for theFile in os.listdir(theDir):
theName,theExt = os.path.splitext(theFile)
if theExt in ['.py']:
src = os.path.abspath(os.path.join(theDir,theFile))
sym_link = os.path.abspath(os.path.join(binDir,theName))
if os.path.lexists(sym_link):
os.remove(sym_link)
output = theName+damask.util.deemph(theExt)
else:
output = damask.util.emph(theName)+damask.util.deemph(theExt)
sys.stdout.write(damask.util.deemph('... ')+output+'\n')
os.symlink(src,sym_link)
for the_file in the_dir.glob('*.py'):
src = the_dir/the_file
dst = bin_dir/Path(the_file.with_suffix('').name)
if dst.is_file(): dst.unlink() # dst.unlink(True) for Python >3.8
dst.symlink_to(src)
sys.stdout.write('\npruning broken links...\n')
brokenLinks = 0
for filename in os.listdir(binDir):
path = os.path.join(binDir,filename)
if os.path.islink(path) and not os.path.exists(path):
sys.stdout.write(' '+damask.util.delete(path)+'\n')
os.remove(path)
brokenLinks += 1
sys.stdout.write(('none.' if brokenLinks == 0 else '')+'\n')
for filename in bin_dir.glob('*'):
if not filename.is_file():
filename.unlink

23
processing/pre/mentat_pbcOnBoxMesh.py
View File

@ -6,7 +6,7 @@ import numpy as np
from optparse import OptionParser
import damask
sys.path.append(damask.solver.Marc().libraryPath())
sys.path.append(str(damask.solver.Marc().library_path))
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
@ -198,13 +198,14 @@ def add_servoLinks(mfd_data,active=[True,True,True]): # directions on which to
if mfd_data[i]['uid'] == 1705: del mfd_data[i]
mfd_data.insert(i, links)
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Set up servo linking to achieve periodic boundary conditions for a regular hexahedral mesh.
Use *py_connection to operate on model presently opened in MSC.Mentat.
""", version = scriptID)
parser.add_option('-p', '--port',
@ -229,10 +230,7 @@ if remote and filenames != []:
if filenames == []: filenames = [None]
if remote:
try: import py_mentat
except:
damask.util.croak('no valid Mentat release found.')
sys.exit(-1)
import py_mentat
damask.util.report(scriptName, 'waiting to connect...')
filenames = [os.path.join(tempfile._get_default_tempdir(), next(tempfile._get_candidate_names()) + '.mfd')]
@ -240,14 +238,14 @@ if remote:
py_mentat.py_connect('',options.port)
py_mentat.py_send('*set_save_formatted on')
py_mentat.py_send('*save_as_model "{}" yes'.format(filenames[0]))
py_mentat.py_get_int("nnodes()") # hopefully blocks until file is written
except:
damask.util.croak('failed. try setting Tools/Python/"Run as Separate Process" & "Initiate".')
sys.exit()
py_mentat.py_get_int("nnodes()")
except py_mentat.InputError as err:
damask.util.croak('{}. Try Tools/Python/"Run as Separate Process" & "Initiate".'.format(err))
sys.exit(-1)
damask.util.croak( 'connected...')
for name in filenames:
while remote and not os.path.exists(name): time.sleep(0.5) # wait for Mentat to write MFD file
while remote and not os.path.exists(name): time.sleep(0.5)
with open( name,'r') if name is not None else sys.stdin as fileIn:
damask.util.report(scriptName, name)
mfd = parseMFD(fileIn)
@ -257,5 +255,4 @@ for name in filenames:
fileOut.write(asMFD(mfd))
if remote:
try: py_mentat.py_send('*open_model "{}"'.format(filenames[0]))
except: damask.util.croak('lost connection on sending open command for "{}".'.format(filenames[0]))
py_mentat.py_send('*open_model "{}"'.format(filenames[0]))

2
processing/pre/mentat_spectralBox.py
View File

@ -9,7 +9,7 @@ import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
sys.path.append(damask.solver.Marc().libraryPath())
sys.path.append(str(damask.solver.Marc().library_path))
#-------------------------------------------------------------------------------------------------
def outMentat(cmd,locals):

4
python/damask/__init__.py
View File

@ -1,9 +1,9 @@
"""Tools for pre and post processing of DAMASK simulations."""
import os as _os
from pathlib import Path as _Path
import re as _re
name = 'damask'
with open(_os.path.join(_os.path.dirname(__file__),'VERSION')) as _f:
with open(_Path(__file__).parent/_Path('VERSION')) as _f:
version = _re.sub(r'^v','',_f.readline().strip())
# make classes directly accessible as damask.Class

25
python/damask/_environment.py
View File

@ -1,11 +1,11 @@
import os
from pathlib import Path
import tkinter
class Environment:
def __init__(self):
"""Read and provide values of DAMASK configuration."""
self.options = self._get_options()
try:
tk = tkinter.Tk()
self.screen_width = tk.winfo_screenwidth()
@ -15,17 +15,8 @@ class Environment:
self.screen_width = 1024
self.screen_height = 768
def relPath(self,relative = '.'):
"""Return absolute path from path relative to DAMASK root."""
return os.path.join(self.rootDir(),relative)
def rootDir(self):
"""Return DAMASK root path."""
return os.path.normpath(os.path.join(os.path.realpath(__file__),'../../../'))
def _get_options(self):
@property
def options(self):
options = {}
for item in ['DAMASK_NUM_THREADS',
'MSC_ROOT',
@ -34,3 +25,13 @@ class Environment:
options[item] = os.environ[item] if item in os.environ else None
return options
@property
def root_dir(self):
"""Return DAMASK root path."""
return Path(__file__).parents[2]
# for compatibility
def rootDir(self):
return str(self.root_dir)

19
python/damask/_result.py
View File

@ -6,6 +6,7 @@ import os
import datetime
import xml.etree.ElementTree as ET
import xml.dom.minidom
from pathlib import Path
from functools import partial
import h5py
@ -88,7 +89,7 @@ class Result:
'con_physics': self.con_physics, 'mat_physics': self.mat_physics
}
self.fname = os.path.abspath(fname)
self.fname = Path(fname).absolute()
self._allow_modification = False
@ -1056,14 +1057,17 @@ class Result:
Parameters
----------
func : function
Callback function that calculates a new dataset from one or more datasets per HDF5 group.
Callback function that calculates a new dataset from one or
more datasets per HDF5 group.
datasets : dictionary
Details of the datasets to be used: label (in HDF5 file) and arg (argument to which the data is parsed in func).
Details of the datasets to be used: label (in HDF5 file) and
arg (argument to which the data is parsed in func).
args : dictionary, optional
Arguments parsed to func.
"""
pool = multiprocessing.Pool(int(Environment().options['DAMASK_NUM_THREADS']))
num_threads = Environment().options['DAMASK_NUM_THREADS']
pool = multiprocessing.Pool(int(num_threads) if num_threads is not None else None)
lock = multiprocessing.Manager().Lock()
groups = self.groups_with_datasets(datasets.values())
@ -1190,7 +1194,7 @@ class Result:
'Dimensions': '{} {} {} {}'.format(*self.grid,np.prod(shape))}
data_items[-1].text='{}:{}'.format(os.path.split(self.fname)[1],name)
with open(os.path.splitext(self.fname)[0]+'.xdmf','w') as f:
with open(self.fname.with_suffix('.xdmf').name,'w') as f:
f.write(xml.dom.minidom.parseString(ET.tostring(xdmf).decode()).toprettyxml())
@ -1266,7 +1270,4 @@ class Result:
u = self.read_dataset(self.get_dataset_location('u_n' if mode.lower() == 'cell' else 'u_p'))
v.add(u,'u')
file_out = '{}_inc{}'.format(os.path.splitext(os.path.basename(self.fname))[0],
inc[3:].zfill(N_digits))
v.write(file_out)
v.write('{}_inc{}'.format(self.fname.stem,inc[3:].zfill(N_digits)))

12
python/damask/_vtk.py
View File

@ -1,4 +1,4 @@
import os
from pathlib import Path
import pandas as pd
import numpy as np
@ -126,8 +126,8 @@ class VTK:
vtkUnstructuredGrid, and vtkPolyData.
"""
ext = os.path.splitext(fname)[1]
if ext == '.vtk':
ext = Path(fname).suffix
if ext == '.vtk' or dataset_type:
reader = vtk.vtkGenericDataObjectReader()
reader.SetFileName(fname)
reader.Update()
@ -176,10 +176,10 @@ class VTK:
writer = vtk.vtkXMLPolyDataWriter()
default_ext = writer.GetDefaultFileExtension()
name, ext = os.path.splitext(fname)
ext = Path(fname).suffix
if ext and ext != '.'+default_ext:
raise ValueError('Given extension {} is not .{}'.format(ext,default_ext))
writer.SetFileName('{}.{}'.format(name,default_ext))
raise ValueError('Given extension {} does not match default .{}'.format(ext,default_ext))
writer.SetFileName(str(Path(fname).with_suffix('.'+default_ext)))
writer.SetCompressorTypeToZLib()
writer.SetDataModeToBinary()
writer.SetInputData(self.geom)

36
python/damask/solver/_marc.py
View File

@ -1,7 +1,7 @@
import os
import subprocess
import shlex
import string
from pathlib import Path
from .._environment import Environment
@ -19,28 +19,24 @@ class Marc:
"""
self.solver = 'Marc'
try:
self.version = int(version)
except TypeError:
self.version = -1
self.version = version
#--------------------------
def libraryPath(self):
@property
def library_path(self):
path_MSC = Environment().options['MSC_ROOT']
path_lib = '{}/mentat{}/shlib/linux64'.format(path_MSC,self.version)
path_lib = Path('{}/mentat{}/shlib/linux64'.format(path_MSC,self.version))
return path_lib if os.path.exists(path_lib) else ''
return path_lib if path_lib.is_dir() else None
#--------------------------
def toolsPath(self):
@property
def tools_path(self):
path_MSC = Environment().options['MSC_ROOT']
path_tools = '{}/marc{}/tools'.format(path_MSC,self.version)
path_tools = Path('{}/marc{}/tools'.format(path_MSC,self.version))
return path_tools if os.path.exists(path_tools) else ''
return path_tools if path_tools.is_dir() else None
#--------------------------
@ -53,21 +49,21 @@ class Marc:
):
damaskEnv = Environment()
env = Environment()
user = os.path.join(damaskEnv.relPath('src'),'DAMASK_marc{}.{}'.format(self.version,'f90' if compile else 'marc'))
if not os.path.isfile(user):
user = env.root_dir/Path('src/DAMASK_marc{}'.format(self.version)).with_suffix('.f90' if compile else '.marc')
if not user.is_file():
raise FileNotFoundError("DAMASK4Marc ({}) '{}' not found".format(('source' if compile else 'binary'),user))
# Define options [see Marc Installation and Operation Guide, pp 23]
script = 'run_damask_{}mp'.format(optimization)
cmd = os.path.join(self.toolsPath(),script) + \
cmd = str(self.tools_path/Path(script)) + \
' -jid ' + model + '_' + job + \
' -nprocd 1 -autorst 0 -ci n -cr n -dcoup 0 -b no -v no'
if compile: cmd += ' -u ' + user + ' -save y'
else: cmd += ' -prog ' + os.path.splitext(user)[0]
if compile: cmd += ' -u ' + str(user) + ' -save y'
else: cmd += ' -prog ' + str(user.with_suffix(''))
print('job submission {} compilation: {}'.format('with' if compile else 'without',user))
if logfile: log = open(logfile, 'w')

34
python/tests/test_VTK.py
View File

@ -17,18 +17,24 @@ class TestVTK:
size = np.random.random(3) + 1.0
origin = np.random.random(3)
v = VTK.from_rectilinearGrid(grid,size,origin)
s = v.__repr__()
string = v.__repr__()
v.write(os.path.join(tmp_path,'rectilinearGrid'))
v = VTK.from_file(os.path.join(tmp_path,'rectilinearGrid.vtr'))
assert(s == v.__repr__())
vtr = VTK.from_file(os.path.join(tmp_path,'rectilinearGrid.vtr'))
with open(os.path.join(tmp_path,'rectilinearGrid.vtk'),'w') as f:
f.write(string)
vtk = VTK.from_file(os.path.join(tmp_path,'rectilinearGrid.vtk'),'VTK_rectilinearGrid')
assert(string == vtr.__repr__() == vtk.__repr__())
def test_polyData(self,tmp_path):
points = np.random.rand(3,100)
v = VTK.from_polyData(points)
s = v.__repr__()
string = v.__repr__()
v.write(os.path.join(tmp_path,'polyData'))
v = VTK.from_file(os.path.join(tmp_path,'polyData.vtp'))
assert(s == v.__repr__())
vtp = VTK.from_file(os.path.join(tmp_path,'polyData.vtp'))
with open(os.path.join(tmp_path,'polyData.vtk'),'w') as f:
f.write(string)
vtk = VTK.from_file(os.path.join(tmp_path,'polyData.vtk'),'polyData')
assert(string == vtp.__repr__() == vtk.__repr__())
@pytest.mark.parametrize('cell_type,n',[
('VTK_hexahedron',8),
@ -41,7 +47,17 @@ class TestVTK:
nodes = np.random.rand(n,3)
connectivity = np.random.choice(np.arange(n),n,False).reshape(-1,n)
v = VTK.from_unstructuredGrid(nodes,connectivity,cell_type)
s = v.__repr__()
string = v.__repr__()
v.write(os.path.join(tmp_path,'unstructuredGrid'))
v = VTK.from_file(os.path.join(tmp_path,'unstructuredGrid.vtu'))
assert(s == v.__repr__())
vtu = VTK.from_file(os.path.join(tmp_path,'unstructuredGrid.vtu'))
with open(os.path.join(tmp_path,'unstructuredGrid.vtk'),'w') as f:
f.write(string)
vtk = VTK.from_file(os.path.join(tmp_path,'unstructuredGrid.vtk'),'unstructuredgrid')
assert(string == vtu.__repr__() == vtk.__repr__())
@pytest.mark.parametrize('name,dataset_type',[('this_file_does_not_exist.vtk',None),
('this_file_does_not_exist.vtk','vtk'),
('this_file_does_not_exist.vtx', None)])
def test_invalid_dataset_type(self,dataset_type,name):
with pytest.raises(TypeError):
VTK.from_file('this_file_does_not_exist.vtk',dataset_type)