diff --git a/installation/symlink_Processing.py b/installation/symlink_Processing.py index 5972a7f6a..441e9a9ea 100755 --- a/installation/symlink_Processing.py +++ b/installation/symlink_Processing.py @@ -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 diff --git a/processing/pre/mentat_pbcOnBoxMesh.py b/processing/pre/mentat_pbcOnBoxMesh.py index c171c6ccd..adf0b1aff 100755 --- a/processing/pre/mentat_pbcOnBoxMesh.py +++ b/processing/pre/mentat_pbcOnBoxMesh.py @@ -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]) @@ -197,14 +197,15 @@ 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])) diff --git a/processing/pre/mentat_spectralBox.py b/processing/pre/mentat_spectralBox.py index a61bef57a..e6d138952 100755 --- a/processing/pre/mentat_spectralBox.py +++ b/processing/pre/mentat_spectralBox.py @@ -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): diff --git a/python/damask/__init__.py b/python/damask/__init__.py index 0f343a581..6d65f7cd1 100644 --- a/python/damask/__init__.py +++ b/python/damask/__init__.py @@ -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 diff --git a/python/damask/_environment.py b/python/damask/_environment.py index df690314c..7d12050aa 100644 --- a/python/damask/_environment.py +++ b/python/damask/_environment.py @@ -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) diff --git a/python/damask/_result.py b/python/damask/_result.py index 56c0eac17..e1846cba9 100644 --- a/python/damask/_result.py +++ b/python/damask/_result.py @@ -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))) diff --git a/python/damask/_vtk.py b/python/damask/_vtk.py index 58b43dc1f..72e224bda 100644 --- a/python/damask/_vtk.py +++ b/python/damask/_vtk.py @@ -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) diff --git a/python/damask/solver/_marc.py b/python/damask/solver/_marc.py index 22e9842f5..dfe45a46d 100644 --- a/python/damask/solver/_marc.py +++ b/python/damask/solver/_marc.py @@ -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') diff --git a/python/tests/test_VTK.py b/python/tests/test_VTK.py index 627ea4007..8795e7161 100644 --- a/python/tests/test_VTK.py +++ b/python/tests/test_VTK.py @@ -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)