Merge branch 'polishing-for-release' into 'development'

Polishing for release

See merge request damask/DAMASK!206

PRIVATE

@@ -1 +1 @@
-Subproject commit a16d1e45a2ed925e12244b0879b9d7e5a58d973b
+Subproject commit 1ca2223c68475bbcb9da633353dbe4a98c18db0d

README

@@ -8,6 +8,6 @@ Max-Planck-Str. 1
 40237 Düsseldorf
 Germany
 
-Email: DAMASK@mpie.de
+damask@mpie.de
 https://damask.mpie.de
 https://magit1.mpie.de

python/.coveragerc

@@ -2,4 +2,3 @@
 omit = tests/*
        damask/_asciitable.py
        damask/_test.py
-       damask/config/*

python/damask/__init__.py

@@ -24,5 +24,4 @@ from .             import solver           # noqa
 Environment = _
 from ._asciitable  import ASCIItable       # noqa
 from ._test        import Test             # noqa
-from .config       import Material         # noqa
 from .util         import extendableOption # noqa

python/damask/config/__init__.py

@@ -1,3 +0,0 @@
-"""Aggregator for configuration file handling."""
-
-from .material import Material    # noqa

python/damask/config/material.py

@@ -1,282 +0,0 @@
-import re
-import os
-
-from damask import util
-
-class Section():
-  def __init__(self,data = {'__order__':[]},part = ''):
-    """New material.config section."""
-    classes = {
-                'homogenization':Homogenization,
-                'microstructure':Microstructure,
-                'crystallite':Crystallite,
-                'phase':Phase,
-                'texture':Texture,
-              }
-    self.parameters = {}
-    for key in data:
-      self.parameters[key] = data[key] if isinstance(data[key], list) else [data[key]]
-
-    if '__order__' not in self.parameters:
-      self.parameters['__order__'] = list(self.parameters.keys())
-    if part.lower() in classes:
-      self.__class__ = classes[part.lower()]
-      self.__init__(data)
-
-  def add_multiKey(self,key,data):
-    multiKey = '(%s)'%key
-    if multiKey not in self.parameters: self.parameters[multiKey] = []
-    if multiKey not in self.parameters['__order__']: self.parameters['__order__'] += [multiKey]
-    self.parameters[multiKey] += [[item] for item in data] if isinstance(data, list) else [[data]]
-
-  def data(self):
-    return self.parameters
-
-
-class Homogenization(Section):
-  def __init__(self,data = {'__order__':[]}):
-    """New material.config <homogenization> section."""
-    Section.__init__(self,data)
-
-
-class Crystallite(Section):
-  def __init__(self,data = {'__order__':[]}):
-    """New material.config <crystallite> section."""
-    Section.__init__(self,data)
-
-
-class Phase(Section):
-  def __init__(self,data = {'__order__':[]}):
-    """New material.config <Phase> section."""
-    Section.__init__(self,data)
-
-
-class Microstructure(Section):
-  def __init__(self,data = {'__order__':[]}):
-    """New material.config <microstructure> section."""
-    Section.__init__(self,data)
-
-
-class Texture(Section):
-  def __init__(self,data = {'__order__':[]}):
-    """New material.config <texture> section."""
-    Section.__init__(self,data)
-
-  def add_component(self,theType,properties):
-
-    scatter  = properties['scatter']  if 'scatter'  in list(map(str.lower,list(properties.keys()))) else 0.0
-    fraction = properties['fraction'] if 'fraction' in list(map(str.lower,list(properties.keys()))) else 1.0
-
-    try:
-      multiKey = theType.lower()
-    except AttributeError:
-      pass
-
-    if multiKey == 'gauss':
-      self.add_multiKey(multiKey,'phi1 %g\tPhi %g\tphi2 %g\tscatter %g\tfraction %g'%(
-                                        properties['eulers'][0],
-                                        properties['eulers'][1],
-                                        properties['eulers'][2],
-                                        scatter,
-                                        fraction,
-                                        )
-                        )
-
-
-class Material():
-  """Read, manipulate, and write material.config files."""
-
-  def __init__(self,verbose=True):
-    """Generates ordered list of parts."""
-    self.parts = [
-            'homogenization',
-            'crystallite',
-            'phase',
-            'texture',
-            'microstructure',
-            ]
-    self.data = {
-            'homogenization': {'__order__': []},
-            'microstructure': {'__order__': []},
-            'crystallite':    {'__order__': []},
-            'phase':          {'__order__': []},
-            'texture':        {'__order__': []},
-            }
-    self.verbose = verbose
-
-  def __repr__(self):
-    """Returns current data structure in material.config format."""
-    me = []
-    for part in self.parts:
-      if self.verbose: print(f'processing <{part}>')
-      me += ['',
-             '#'*100,
-             f'<{part}>',
-             '#'*100,
-            ]
-      for section in self.data[part]['__order__']:
-        me += [f'[{section}] {"#"+"-"*max(0,96-len(section))}']
-        for key in self.data[part][section]['__order__']:
-          if key.startswith('(') and key.endswith(')'):                       # multiple (key)
-            me += [f'{key}\t{" ".join(values)}' for values in self.data[part][section][key]]
-          else:                                                               # plain key
-            me += [f'{key}\t{util.srepr(self.data[part][section][key]," ")}']
-    return '\n'.join(me) + '\n'
-
-  def parse(self, part=None, sections=[], content=None):
-
-    re_part = re.compile(r'^<(.+)>$')                     # pattern for part
-    re_sec  = re.compile(r'^\[(.+)\]$')                   # pattern for section
-
-    name_section = ''
-    active = False
-
-    for line in content:
-      line = line.split('#')[0].strip()                   # kill comments and extra whitespace
-      line = line.split('/echo/')[0].strip()              # remove '/echo/' tags
-      line = line.lower()                                 # be case insensitive
-
-      if line:                                            # content survives...
-        match_part = re_part.match(line)
-        if match_part:                                    # found <...> separator
-          active = (match_part.group(1) == part)          # only active in <part>
-          continue
-        if active:
-          match_sec  = re_sec.match(line)
-          if match_sec:                                   # found [section]
-            name_section = match_sec.group(1)             # remember name ...
-            if '__order__' not in self.data[part]: self.data[part]['__order__'] = []
-            self.data[part]['__order__'].append(name_section)  # ... and position
-            self.data[part][name_section] = {'__order__':[]}
-            continue
-
-          if sections == [] or name_section in sections:  # possibly restrict to subset
-            items = line.split()
-            if items[0] not in self.data[part][name_section]:         # first encounter of key?
-              self.data[part][name_section][items[0]] = []            # create item
-              self.data[part][name_section]['__order__'].append(items[0])
-            if items[0].startswith('(') and items[0].endswith(')'):   # multiple "(key)"
-              self.data[part][name_section][items[0]].append(items[1:])
-            else:                                                     # plain key
-              self.data[part][name_section][items[0]] = items[1:]
-
-
-
-  def read(self,filename=None):
-    """Read material.config file."""
-    def recursiveRead(filename):
-      """Takes care of include statements like '{}'."""
-      result = []
-      re_include  = re.compile(r'^{(.+)}$')
-      with open(filename) as f: lines = f.readlines()
-      for line in lines:
-        match = re_include.match(line.split()[0]) if line.strip() else False
-        result += [line] if not match else \
-                  recursiveRead(match.group(1) if match.group(1).startswith('/') else
-                                os.path.normpath(os.path.join(os.path.dirname(filename),match.group(1))))
-      return result
-
-    c = recursiveRead(filename)
-    for p in self.parts:
-      self.parse(part=p, content=c)
-
-  def write(self,filename='material.config', overwrite=False):
-    """Write to material.config."""
-    i = 0
-    outname = filename
-    while os.path.exists(outname) and not overwrite:
-     i += 1
-     outname = f'{filename}_{i}'
-
-    if self.verbose: print(f'Writing material data to {outname}')
-    with open(outname,'w') as f:
-      f.write(str(self))
-    return outname
-
-  def add_section(self, part=None, section=None, initialData=None, merge=False):
-    """Add Update."""
-    part    = part.lower()
-    section = section.lower()
-    if part not in self.parts: raise Exception(f'invalid part {part}')
-
-    if not isinstance(initialData, dict):
-      initialData = initialData.data()
-
-    if section not in self.data[part]: self.data[part]['__order__'] += [section]
-    if section in self.data[part] and merge:
-      for existing in self.data[part][section]['__order__']:                               # replace existing
-        if existing in initialData['__order__']:
-          if existing.startswith('(') and existing.endswith(')'):                          # multiple (key)
-            self.data[part][section][existing] += initialData[existing]                    # add new multiple entries to existing ones
-          else:                                                                            # regular key
-            self.data[part][section][existing] = initialData[existing]                     # plain replice
-      for new in initialData['__order__']:                                                 # merge new content
-        if new not in self.data[part][section]['__order__']:
-          self.data[part][section][new] = initialData[new]
-          self.data[part][section]['__order__'] += [new]
-    else:
-      self.data[part][section] = initialData
-
-
-
-
-  def add_microstructure(self, section='',
-                               components={},      # dict of phase,texture, and fraction lists
-                        ):
-    """Experimental! Needs expansion to multi-constituent microstructures..."""
-    microstructure = Microstructure()
-    # make keys lower case (http://stackoverflow.com/questions/764235/dictionary-to-lowercase-in-python)
-    components=dict((k.lower(), v) for k,v in components.items())
-
-    for key in ['phase','texture','fraction','crystallite']:
-      if isinstance(components[key], list):
-        for i, x in enumerate(components[key]):
-          try:
-            components[key][i] = x.lower()
-          except AttributeError:
-            pass
-      else:
-        try:
-          components[key] = [components[key].lower()]
-        except AttributeError:
-          components[key] = [components[key]]
-
-    for (phase,texture,fraction,crystallite) in zip(components['phase'],components['texture'],
-                                                    components['fraction'],components['crystallite']):
-      microstructure.add_multiKey('constituent','phase %i\ttexture %i\tfraction %g\ncrystallite %i'%(
-                                    self.data['phase']['__order__'].index(phase)+1,
-                                    self.data['texture']['__order__'].index(texture)+1,
-                                    fraction,
-                                    self.data['crystallite']['__order__'].index(crystallite)+1))
-
-    self.add_section('microstructure',section,microstructure)
-
-
-  def change_value(self, part=None,
-                         section=None,
-                         key=None,
-                         value=None):
-    if not isinstance(value,list):
-      if not isinstance(value,str):
-        value = '%s'%value
-      value = [value]
-    newlen = len(value)
-    oldval = self.data[part.lower()][section.lower()][key.lower()]
-    oldlen = len(oldval)
-    print('changing %s:%s:%s from %s to %s '%(part.lower(),section.lower(),key.lower(),oldval,value))
-    self.data[part.lower()][section.lower()][key.lower()] = value
-    if newlen is not oldlen:
-      print('Length of value was changed from %i to %i!'%(oldlen,newlen))
-
-
-  def add_value(self, part=None,
-                  section=None,
-                  key=None,
-                  value=None):
-    if not isinstance(value,list):
-      if not isinstance(value,str):
-        value = '%s'%value
-      value = [value]
-    print('adding %s:%s:%s with value %s '%(part.lower(),section.lower(),key.lower(),value))
-    self.data[part.lower()][section.lower()][key.lower()] = value
-    self.data[part.lower()][section.lower()]['__order__'] += [key.lower()]

python/setup.py

@@ -16,12 +16,11 @@ setuptools.setup(
     packages=setuptools.find_packages(),
     include_package_data=True,
     install_requires = [
-        "pandas",
+        "pandas",                                                                                   # requires numpy
         "scipy",
-        "h5py",
+        "h5py",                                                                                     # requires numpy
         "vtk",
-        "matplotlib",
+        "matplotlib",                                                                               # requires numpy, pillow
-        "PIL",
     ],
     classifiers = [
         "Intended Audience :: Science/Research",