cleaning

dropped support for legacy table

Makefile

@@ -1,7 +1,9 @@
 SHELL = /bin/sh
-########################################################################################
-# Makefile for the installation of DAMASK
-########################################################################################
+
+###################################################################################################
+# One-command-build invoking CMake (meant for developers, should not be part of the distribution)
+###################################################################################################
+
 .PHONY: all
 all: grid mesh
 

python/damask/_colormap.py

@@ -39,20 +39,20 @@ class Colormap(mpl.colors.ListedColormap):
     """
 
     def __add__(self,other):
-        """Concatenate colormaps."""
+        """Concatenate."""
         return Colormap(np.vstack((self.colors,other.colors)),
                         f'{self.name}+{other.name}')
 
     def __iadd__(self,other):
-        """Concatenate colormaps."""
+        """Concatenate (in-place)."""
         return self.__add__(other)
 
     def __invert__(self):
-        """Return inverted colormap."""
+        """Reverse."""
         return self.reversed()
 
     def __repr__(self):
-        """Show colormap as matplotlib figure."""
+        """Show as matplotlib figure."""
         fig = plt.figure(self.name,figsize=(5,.5))
         ax1 = fig.add_axes([0, 0, 1, 1])
         ax1.set_axis_off()
@@ -207,7 +207,7 @@ class Colormap(mpl.colors.ListedColormap):
 
     def reversed(self,name=None):
         """
-        Make a reversed instance of the colormap.
+        Reverse.
 
         Parameters
         ----------

python/damask/_config.py

@@ -31,7 +31,7 @@ class NiceDumper(yaml.SafeDumper):
             return super().represent_data(data)
 
     def ignore_aliases(self, data):
-        """No references."""
+        """Do not use references to existing objects."""
         return True
 
 class Config(dict):

python/damask/_configmaterial.py

@@ -9,14 +9,29 @@ from . import Orientation
 from . import util
 
 class ConfigMaterial(Config):
-    """Material configuration."""
+    """
+    Material configuration.
+
+    Manipulate material configurations for storage in YAML format.
+    A complete material configuration file has the entries 'material',
+    'phase', and 'homogenization'. For use in DAMASK, it needs to be
+    stored as 'material.yaml'.
+    """
 
     _defaults = {'material': [],
                  'homogenization': {},
                  'phase': {}}
 
     def __init__(self,d=_defaults):
-        """Initialize object with default dictionary keys."""
+        """
+        New material configuration.
+
+        Parameters
+        ----------
+        d : dictionary, optional
+            Initial content. Defaults to empty material, homogenization, and phase entries.
+
+        """
         super().__init__(d)
 
 

python/damask/_grid.py

@@ -17,11 +17,18 @@ from . import Rotation
 
 
 class Grid:
-    """Geometry definition for grid solvers."""
+    """
+    Geometry definition for grid solvers.
+
+    Create and manipulate geometry definitions for storage as VTK
+    rectiliear grid files ('.vtr' extension). A grid contains the
+    material ID (referring to the entry in 'material.yaml') and
+    the physical size.
+    """
 
     def __init__(self,material,size,origin=[0.0,0.0,0.0],comments=[]):
         """
-        New grid definition from array of materials, size, and origin.
+        New geometry definition for grid solvers.
 
         Parameters
         ----------

python/damask/_orientation.py

@@ -47,19 +47,30 @@ class Orientation(Rotation):
 
     The Bravais lattice is one of Orientation.lattice_symmetries:
 
-    - aP : triclinic    primitive
-    - mP : monoclinic   primitive
-    - mS : ...          base-centered
-    - oP : orthorhombic primitive
-    - oS : ...          base-centered
-    - oI : ...          body-centered
-    - oF : ...          face-centered
-    - tP : tetragonal   primitive
-    - tI : ...          body-centered
-    - hP : hexagonal    primitive
-    - cP : cubic        primitive
-    - cI : ...          body-centered
-    - cF : ...          face-centered
+    - triclinic
+       - aP : primitive
+
+    - monoclininic
+       - mP : primitive
+       - mS : base-centered
+
+    - orthorhombic
+       - oP : primitive
+       - oS : base-centered
+       - oI : body-centered
+       - oF : face-centered
+
+    - tetragonal
+       - tP : primitive
+       - tI : body-centered
+
+    - hexagonal
+       - hP : primitive
+
+    - cubic
+       - cP : primitive
+       - cI : body-centered
+       - cF : face-centered
 
     and inherits the corresponding crystal family.
     Specifying a Bravais lattice, compared to just the crystal family,
@@ -111,7 +122,7 @@ class Orientation(Rotation):
                  alpha = None,beta = None,gamma = None,
                  degrees = False):
         """
-        Initialize orientation object.
+        New orientation.
 
         Parameters
         ----------

python/damask/_result.py

@@ -26,14 +26,14 @@ h5py3 = h5py.__version__[0] == '3'
 
 class Result:
     """
-    Read and write to DADF5 files.
+    Manipulate and read DADF5 files.
 
     DADF5 (DAMASK HDF5) files contain DAMASK results.
     """
 
     def __init__(self,fname):
         """
-        Open an existing DADF5 file.
+        New result view bound to a HDF5 file.
 
         Parameters
         ----------

python/damask/_rotation.py

@@ -51,7 +51,7 @@ class Rotation:
 
     def __init__(self,rotation = np.array([1.0,0.0,0.0,0.0])):
         """
-        Initialize rotation object.
+        New rotation.
 
         Parameters
         ----------
@@ -140,7 +140,7 @@ class Rotation:
 
 
     def __len__(self):
-        """Length of leading/leftmost dimension of Rotation array."""
+        """Length of leading/leftmost dimension of array."""
         return 0 if self.shape == () else self.shape[0]
 
 
@@ -180,7 +180,7 @@ class Rotation:
 
     def __mul__(self,other):
         """
-        Compose this rotation with other.
+        Compose with other.
 
         Parameters
         ----------
@@ -206,7 +206,7 @@ class Rotation:
 
     def __imul__(self,other):
         """
-        Compose this rotation with other (in-place).
+        Compose with other (in-place).
 
         Parameters
         ----------
@@ -219,7 +219,7 @@ class Rotation:
 
     def __truediv__(self,other):
         """
-        Compose this rotation with inverse of other.
+        Compose with inverse of other.
 
         Parameters
         ----------
@@ -239,7 +239,7 @@ class Rotation:
 
     def __itruediv__(self,other):
         """
-        Compose this rotation with inverse of other (in-place).
+        Compose with inverse of other (in-place).
 
         Parameters
         ----------
@@ -252,7 +252,7 @@ class Rotation:
 
     def __matmul__(self,other):
         """
-        Rotation of vector, second order tensor, or fourth order tensor.
+        Rotate vector, second order tensor, or fourth order tensor.
 
         Parameters
         ----------
@@ -301,7 +301,7 @@ class Rotation:
 
     def append(self,other):
         """
-        Extend rotation array along first dimension with other array(s).
+        Extend array along first dimension with other array(s).
 
         Parameters
         ----------
@@ -313,19 +313,19 @@ class Rotation:
 
 
     def flatten(self,order = 'C'):
-        """Flatten quaternion array."""
+        """Flatten array."""
         return self.copy(rotation=self.quaternion.reshape((-1,4),order=order))
 
 
     def reshape(self,shape,order = 'C'):
-        """Reshape quaternion array."""
+        """Reshape array."""
         if isinstance(shape,(int,np.integer)): shape = (shape,)
         return self.copy(rotation=self.quaternion.reshape(tuple(shape)+(4,),order=order))
 
 
     def broadcast_to(self,shape,mode = 'right'):
         """
-        Broadcast quaternion array to shape.
+        Broadcast array.
 
         Parameters
         ----------
@@ -343,7 +343,7 @@ class Rotation:
 
     def average(self,weights = None):
         """
-        Average rotations along last dimension.
+        Average along last array dimension.
 
         Parameters
         ----------
@@ -382,7 +382,7 @@ class Rotation:
 
     def misorientation(self,other):
         """
-        Calculate misorientation from self to other Rotation.
+        Calculate misorientation to other Rotation.
 
         Parameters
         ----------

python/damask/_table.py

@@ -7,7 +7,7 @@ import numpy as np
 from . import util
 
 class Table:
-    """Store spreadsheet-like data."""
+    """Manipulate multi-dimensional spreadsheet-like data."""
 
     def __init__(self,data,shapes,comments=None):
         """
@@ -77,13 +77,11 @@ class Table:
         """
         Load from ASCII table file.
 
-        In legacy style, the first line indicates the number of
-        subsequent header lines as "N header", with the last header line being
-        interpreted as column labels.
-        Alternatively, initial comments are marked by '#', with the first non-comment line
+        Initial comments are marked by '#', the first non-comment line
         containing the column labels.
-        Vector data column labels are indicated by '1_v, 2_v, ..., n_v'.
-        Tensor data column labels are indicated by '3x3:1_T, 3x3:2_T, ..., 3x3:9_T'.
+
+        - Vector data column labels are indicated by '1_v, 2_v, ..., n_v'.
+        - Tensor data column labels are indicated by '3x3:1_T, 3x3:2_T, ..., 3x3:9_T'.
 
         Parameters
         ----------
@@ -97,21 +95,13 @@ class Table:
             f = fname
             f.seek(0)
 
-        try:
-            N_comment_lines,keyword = f.readline().strip().split(maxsplit=1)
-            if keyword != 'header':
-                raise ValueError
-            else:
-                comments = [f.readline().strip() for i in range(1,int(N_comment_lines))]
-                labels   = f.readline().split()
-        except ValueError:
-            f.seek(0)
-            comments = []
+        f.seek(0)
+        comments = []
+        line = f.readline().strip()
+        while line.startswith('#'):
+            comments.append(line.lstrip('#').strip())
             line = f.readline().strip()
-            while line.startswith('#'):
-                comments.append(line.lstrip('#').strip())
-                line = f.readline().strip()
-            labels = line.split()
+        labels = line.split()
 
         shapes = {}
         for label in labels:
@@ -391,7 +381,7 @@ class Table:
             return dup
 
 
-    def save(self,fname,legacy=False):
+    def save(self,fname):
         """
         Save as plain text file.
 
@@ -399,9 +389,6 @@ class Table:
         ----------
         fname : file, str, or pathlib.Path
             Filename or file for writing.
-        legacy : Boolean, optional
-            Write table in legacy style, indicating header lines by "N header"
-            in contrast to using comment sign ('#') at beginning of lines.
 
         """
         seen = set()
@@ -416,13 +403,10 @@ class Table:
                 labels += [f'{util.srepr(self.shapes[l],"x")}:{i+1}_{l}' \
                           for i in range(np.prod(self.shapes[l]))]
 
-        header = ([f'{len(self.comments)+1} header'] + self.comments) if legacy else \
-                  [f'# {comment}' for comment in self.comments]
-
         try:
             fhandle = open(fname,'w',newline='\n')
         except TypeError:
             fhandle = fname
 
-        for line in header + [' '.join(labels)]: fhandle.write(line+'\n')
+        fhandle.write('\n'.join([f'# {c}' for c in self.comments] + [' '.join(labels)])+'\n')
         self.data.to_csv(fhandle,sep=' ',na_rep='nan',index=False,header=False)

python/damask/_vtk.py

@@ -22,7 +22,7 @@ class VTK:
 
     def __init__(self,vtk_data):
         """
-        Initialize from vtk dataset.
+        New spatial visualization.
 
         Parameters
         ----------

python/damask/util.py

@@ -153,10 +153,12 @@ def scale_to_coprime(v):
         """Denominator of the square of a number."""
         return fractions.Fraction(x ** 2).limit_denominator(MAX_DENOMINATOR).denominator
 
-    def lcm(a, b):
+    def lcm(a,b):
         """Least common multiple."""
-        # Python 3.9 provides math.lcm, see https://stackoverflow.com/questions/51716916.
-        return a * b // np.gcd(a, b)
+        try:
+            return np.lcm(a,b)                                                                      # numpy > 1.18
+        except AttributeError:
+            return a * b // np.gcd(a, b)
 
     m = (np.array(v) * reduce(lcm, map(lambda x: int(get_square_denominator(x)),v)) ** 0.5).astype(int)
     m = m//reduce(np.gcd,m)
@@ -405,7 +407,7 @@ class return_message:
 
     def __init__(self,message):
         """
-        Sets return message.
+        Set return message.
 
         Parameters
         ----------
@@ -429,7 +431,7 @@ class _ProgressBar:
 
     def __init__(self,total,prefix,bar_length):
         """
-        Inititalize a progress bar to current time as basis for ETA estimation.
+        Set current time as basis for ETA estimation.
 
         Parameters
         ----------

python/tests/reference/Orientation/cF_Bain.txt

@@ -1,4 +1,3 @@
-1 header
 1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
 180.0 45.00000000000001 180.0 1 1
 270.0 45.00000000000001 90.0 1 2

python/tests/reference/Orientation/cF_GT.txt

@@ -1,4 +1,3 @@
-1 header
 1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
 146.75362934444064 9.976439066337804 256.395594327347 1 1
 356.59977719102034 43.39784965440254 12.173896584899929 1 2

python/tests/reference/Orientation/cF_GT_prime.txt

@@ -1,4 +1,3 @@
-1 header
 1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
 166.39559432734697 9.976439066337804 236.75362934444058 1 1
 352.1156357053931 43.82007387041961 14.074783631236542 1 2

python/tests/reference/Orientation/cF_KS.txt

@@ -1,4 +1,3 @@
-1 header
 1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
 114.20342833932975 10.52877936550932 204.20342833932972 1 1
 94.3573968784815 80.40593177313954 311.22729452432543 1 2

python/tests/reference/Orientation/cF_NW.txt

@@ -1,4 +1,3 @@
-1 header
 1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
 96.91733794010702 83.13253115922213 314.5844440567886 1 1
 173.082662059893 83.13253115922211 45.41555594321143 1 2

python/tests/reference/Orientation/cF_Pitsch.txt

@@ -1,4 +1,3 @@
-1 header
 1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
 135.41555594321144 83.13253115922213 173.082662059893 1 1
 260.26438968275465 90.0 135.0 1 2

python/tests/reference/Orientation/cI_Bain.txt

@@ -1,4 +1,3 @@
-1 header
 1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
 0.0 45.00000000000001 0.0 1 1
 90.0 45.00000000000001 270.0 1 2

python/tests/reference/Orientation/cI_GT.txt

@@ -1,4 +1,3 @@
-1 header
 1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
 283.60440567265294 9.976439066337804 33.24637065555936 1 1
 167.8261034151001 43.397849654402556 183.40022280897963 1 2

python/tests/reference/Orientation/cI_GT_prime.txt

@@ -1,4 +1,3 @@
-1 header
 1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
 303.24637065555936 9.976439066337804 13.604405672652977 1 1
 165.92521636876344 43.82007387041961 187.88436429460683 1 2

python/tests/reference/Orientation/cI_KS.txt

@@ -1,4 +1,3 @@
-1 header
 1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
 335.7965716606702 10.528779365509317 65.79657166067024 1 1
 228.77270547567446 80.40593177313953 85.64260312151849 1 2

python/tests/reference/Orientation/cI_NW.txt

@@ -1,4 +1,3 @@
-1 header
 1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
 225.41555594321144 83.13253115922213 83.08266205989301 1 1
 134.58444405678856 83.13253115922211 6.917337940107012 1 2

python/tests/reference/Orientation/cI_Pitsch.txt

@@ -1,4 +1,3 @@
-1 header
 1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
 6.9173379401070045 83.13253115922213 44.58444405678856 1 1
 45.0 89.99999999999999 279.7356103172453 1 2

python/tests/test_Table.py

@@ -60,13 +60,6 @@ class TestTable:
             new = Table.load(f)
         assert all(default.data==new.data) and default.shapes == new.shapes
 
-    def test_write_read_legacy_style(self,default,tmp_path):
-        with open(tmp_path/'legacy.txt','w') as f:
-            default.save(f,legacy=True)
-        with open(tmp_path/'legacy.txt') as f:
-            new = Table.load(f)
-        assert all(default.data==new.data) and default.shapes == new.shapes
-
     def test_write_invalid_format(self,default,tmp_path):
         with pytest.raises(TypeError):
             default.save(tmp_path/'shouldnotbethere.txt',format='invalid')