Merge remote-tracking branch 'origin/development' into Results.read-.place

.gitlab-ci.yml

@@ -96,7 +96,7 @@ processing:
   stage: python
   script:
     - cd $DAMASKROOT/python
-    - pytest --basetemp=${TESTROOT}/python -v --cov --cov-report=term
+    - COLUMNS=256 pytest --basetemp=${TESTROOT}/python -v --cov --cov-report=term
     - coverage report --fail-under=90
   except:
     - master
@@ -116,7 +116,7 @@ compile_grid_Intel:
   script:
     - module load $IntelCompiler $MPI_Intel $PETSc_Intel
     - cd pytest
-    - pytest -k 'compile and grid' --basetemp=${TESTROOT}/compile_grid_Intel
+    - COLUMNS=256 pytest -k 'compile and grid' --basetemp=${TESTROOT}/compile_grid_Intel
   except:
     - master
     - release
@@ -126,7 +126,7 @@ compile_mesh_Intel:
   script:
     - module load $IntelCompiler $MPI_Intel $PETSc_Intel
     - cd pytest
-    - pytest -k 'compile and mesh' --basetemp=${TESTROOT}/compile_mesh_Intel
+    - COLUMNS=256 pytest -k 'compile and mesh' --basetemp=${TESTROOT}/compile_mesh_Intel
   except:
     - master
     - release
@@ -136,7 +136,7 @@ compile_grid_GNU:
   script:
     - module load $GNUCompiler $MPI_GNU $PETSc_GNU
     - cd pytest
-    - pytest -k 'compile and grid' --basetemp=${TESTROOT}/compile_grid_GNU
+    - COLUMNS=256 pytest -k 'compile and grid' --basetemp=${TESTROOT}/compile_grid_GNU
   except:
     - master
     - release
@@ -146,7 +146,7 @@ compile_mesh_GNU:
   script:
     - module load $GNUCompiler $MPI_GNU $PETSc_GNU
     - cd pytest
-    - pytest -k 'compile and mesh' --basetemp=${TESTROOT}/compile_mesh_GNU
+    - COLUMNS=256 pytest -k 'compile and mesh' --basetemp=${TESTROOT}/compile_mesh_GNU
   except:
     - master
     - release
@@ -156,7 +156,7 @@ compile_Marc:
   script:
     - module load $IntelMarc $HDF5Marc $MSC
     - cd pytest
-    - pytest -k 'compile and Marc' --basetemp=${TESTROOT}/compile_Marc
+    - COLUMNS=256 pytest -k 'compile and Marc' --basetemp=${TESTROOT}/compile_Marc
   except:
     - master
     - release
@@ -191,7 +191,7 @@ core:
   script:
     - module load $IntelCompiler $MPI_Intel $PETSc_Intel
     - cd pytest
-    - pytest -k 'not compile' --basetemp=${TESTROOT}/fortran -v
+    - COLUMNS=256 pytest -k 'not compile' --basetemp=${TESTROOT}/fortran -v
   except:
     - master
     - release

PRIVATE

@@ -1 +1 @@
-Subproject commit 4511a963da5094db309a6a68783f24a23c76da81
+Subproject commit 4ce1f786dc2a613f29b2c8681fcf751d6803d38e

VERSION

@@ -1 +1 @@
-v3.0.0-alpha2-662-gb36ff26cb
+v3.0.0-alpha2-753-g565dab120

python/.gitignore

@@ -2,3 +2,4 @@
 dist
 damask.egg-info
 .coverage
+.coverage.*

python/damask/_configmaterial.py

@@ -157,18 +157,18 @@ class ConfigMaterial(Config):
         f = h5py.File(fname,'r')
 
         if grain_data is None:
-            phase = f['/'.join((b,c,phases))][()].flatten()
+            phase = f['/'.join([b,c,phases])][()].flatten()
-            O = Rotation.from_Euler_angles(f['/'.join((b,c,Euler_angles))]).as_quaternion().reshape(-1,4) # noqa
+            O = Rotation.from_Euler_angles(f['/'.join([b,c,Euler_angles])]).as_quaternion().reshape(-1,4) # noqa
             _,idx = np.unique(np.hstack([O,phase.reshape(-1,1)]),return_index=True,axis=0)
             idx = np.sort(idx)
         else:
-            phase = f['/'.join((b,grain_data,phases))][()]
+            phase = f['/'.join([b,grain_data,phases])][()]
-            O = Rotation.from_Euler_angles(f['/'.join((b,grain_data,Euler_angles))]).as_quaternion() # noqa
+            O = Rotation.from_Euler_angles(f['/'.join([b,grain_data,Euler_angles])]).as_quaternion() # noqa
             idx = np.arange(phase.size)
 
         if cell_ensemble_data is not None and phase_names is not None:
             try:
-                names = np.array([s.decode() for s in f['/'.join((b,cell_ensemble_data,phase_names))]])
+                names = np.array([s.decode() for s in f['/'.join([b,cell_ensemble_data,phase_names])]])
                 phase = names[phase]
             except KeyError:
                 pass

python/damask/_grid.py

@@ -305,18 +305,18 @@ class Grid:
         c = util.DREAM3D_cell_data_group(fname) if cell_data  is None else cell_data
         f = h5py.File(fname, 'r')
 
-        cells  = f['/'.join((b,'_SIMPL_GEOMETRY','DIMENSIONS'))][()]
+        cells  = f['/'.join([b,'_SIMPL_GEOMETRY','DIMENSIONS'])][()]
-        size   = f['/'.join((b,'_SIMPL_GEOMETRY','SPACING'))] * cells
+        size   = f['/'.join([b,'_SIMPL_GEOMETRY','SPACING'])] * cells
-        origin = f['/'.join((b,'_SIMPL_GEOMETRY','ORIGIN'))][()]
+        origin = f['/'.join([b,'_SIMPL_GEOMETRY','ORIGIN'])][()]
 
         if feature_IDs is None:
-            phase = f['/'.join((b,c,phases))][()].reshape(-1,1)
+            phase = f['/'.join([b,c,phases])][()].reshape(-1,1)
-            O = Rotation.from_Euler_angles(f['/'.join((b,c,Euler_angles))]).as_quaternion().reshape(-1,4) # noqa
+            O = Rotation.from_Euler_angles(f['/'.join([b,c,Euler_angles])]).as_quaternion().reshape(-1,4) # noqa
             unique,unique_inverse = np.unique(np.hstack([O,phase]),return_inverse=True,axis=0)
             ma = np.arange(cells.prod()) if len(unique) == cells.prod() else \
                  np.arange(unique.size)[np.argsort(pd.unique(unique_inverse))][unique_inverse]
         else:
-            ma = f['/'.join((b,c,feature_IDs))][()].flatten()
+            ma = f['/'.join([b,c,feature_IDs])][()].flatten()
 
         return Grid(ma.reshape(cells,order='F'),size,origin,util.execution_stamp('Grid','load_DREAM3D'))
 

python/damask/_result.py

@@ -34,7 +34,7 @@ def _read(dataset):
     return np.array(dataset,dtype=dtype)
 
 def _match(requested,existing):
-    """Find matches among two sets of labels"""
+    """Find matches among two sets of labels."""
     def flatten_list(list_of_lists):
         return [e for e_ in list_of_lists for e in e_]
 
@@ -159,7 +159,7 @@ class Result:
             Select from 'set', 'add', and 'del'.
         what : str
             Attribute to change (must be from self.visible).
-        datasets : list of str or bool
+        datasets : str, int, list of str, list of int, or bool
             Name of datasets as list; supports ? and * wildcards.
             True is equivalent to [*], False is equivalent to [].
 
@@ -169,7 +169,7 @@ class Result:
             datasets = '*'
         elif datasets is False or datasets is None:
             datasets = []
-        choice = datasets if hasattr(datasets,'__iter__') and not isinstance(datasets,str) else \
+        choice = list(datasets).copy() if hasattr(datasets,'__iter__') and not isinstance(datasets,str) else \
                 [datasets]
 
         inc = 'inc' if self.version_minor < 12 else 'increment_' # compatibility hack
@@ -1095,7 +1095,7 @@ class Result:
                 for ty in ['phase','homogenization']:
                     for label in self.visible[ty+'s']:
                         for field in self.visible['fields']:
-                            for out in _match(output,f['/'.join((inc,ty,label,field))].keys()):
+                            for out in _match(output,f['/'.join([inc,ty,label,field])].keys()):
                                 name = '/'.join([inc,ty,label,field,out])
                                 shape = f[name].shape[1:]
                                 dtype = f[name].dtype
@@ -1165,29 +1165,29 @@ class Result:
             at_cell_ph = []
             in_data_ph = []
             for c in range(self.N_constituents):
-                at_cell_ph.append({label: np.where(f['/'.join((grp,'phase'))][:,c][name] == label.encode())[0] \
+                at_cell_ph.append({label: np.where(f['/'.join([grp,'phase'])][:,c][name] == label.encode())[0] \
                                           for label in self.visible['phases']})
-                in_data_ph.append({label: f['/'.join((grp,'phase'))][member][at_cell_ph[c][label]][:,c] \
+                in_data_ph.append({label: f['/'.join([grp,'phase'])][member][at_cell_ph[c][label]][:,c] \
                                           for label in self.visible['phases']})
 
-            at_cell_ho = {label: np.where(f['/'.join((grp,'homogenization'))][:][name] == label.encode())[0] \
+            at_cell_ho = {label: np.where(f['/'.join([grp,'homogenization'])][:][name] == label.encode())[0] \
                                  for label in self.visible['homogenizations']}
-            in_data_ho = {label: f['/'.join((grp,'homogenization'))][member][at_cell_ho[label]] \
+            in_data_ho = {label: f['/'.join([grp,'homogenization'])][member][at_cell_ho[label]] \
                                  for label in self.visible['homogenizations']}
 
             for inc in util.show_progress(self.visible['increments']):
 
-                u = _read(f['/'.join((inc,'geometry','u_n' if mode.lower() == 'cell' else 'u_p'))])
+                u = _read(f['/'.join([inc,'geometry','u_n' if mode.lower() == 'cell' else 'u_p'])])
                 v.add(u,'u')
 
                 for ty in ['phase','homogenization']:
                     for field in self.visible['fields']:
                         for label in self.visible[ty+'s']:
-                            if field not in f['/'.join((inc,ty,label))].keys(): continue
+                            if field not in f['/'.join([inc,ty,label])].keys(): continue
                             outs = {}
 
-                            for out in _match(output,f['/'.join((inc,ty,label,field))].keys()):
+                            for out in _match(output,f['/'.join([inc,ty,label,field])].keys()):
-                                data = ma.array(_read(f['/'.join((inc,ty,label,field,out))]))
+                                data = ma.array(_read(f['/'.join([inc,ty,label,field,out])]))
 
                                 if ty == 'phase':
                                     if out+suffixes[0] not in outs.keys():
@@ -1205,7 +1205,7 @@ class Result:
                                     outs[out][at_cell_ho[label]] = data[in_data_ho[label]]
 
                         for label,dataset in outs.items():
-                            v.add(dataset,' / '.join(('/'.join((ty,field,label)),dataset.dtype.metadata['unit'])))
+                            v.add(dataset,' / '.join(['/'.join([ty,field,label]),dataset.dtype.metadata['unit']]))
 
                 v.save(f'{self.fname.stem}_inc{inc[ln:].zfill(N_digits)}')
 
@@ -1236,16 +1236,16 @@ class Result:
             for inc in util.show_progress(self.visible['increments']):
                 r[inc] = {'phase':{},'homogenization':{},'geometry':{}}
 
-                for out in _match(output,f['/'.join((inc,'geometry'))].keys()):
+                for out in _match(output,f['/'.join([inc,'geometry'])].keys()):
-                    r[inc]['geometry'][out] = _read(f['/'.join((inc,'geometry',out))])
+                    r[inc]['geometry'][out] = _read(f['/'.join([inc,'geometry',out])])
 
                 for ty in ['phase','homogenization']:
                     for label in self.visible[ty+'s']:
                         r[inc][ty][label] = {}
-                        for field in _match(self.visible['fields'],f['/'.join((inc,ty,label))].keys()):
+                        for field in _match(self.visible['fields'],f['/'.join([inc,ty,label])].keys()):
                             r[inc][ty][label][field] = {}
-                            for out in _match(output,f['/'.join((inc,ty,label,field))].keys()):
+                            for out in _match(output,f['/'.join([inc,ty,label,field])].keys()):
-                                r[inc][ty][label][field][out] = _read(f['/'.join((inc,ty,label,field,out))])
+                                r[inc][ty][label][field][out] = _read(f['/'.join([inc,ty,label,field,out])])
 
         if prune:   r = util.dict_prune(r)
         if flatten: r = util.dict_flatten(r)
@@ -1303,30 +1303,30 @@ class Result:
             at_cell_ph = []
             in_data_ph = []
             for c in range(self.N_constituents):
-                at_cell_ph.append({label: np.where(f['/'.join((grp,'phase'))][:,c][name] == label.encode())[0] \
+                at_cell_ph.append({label: np.where(f['/'.join([grp,'phase'])][:,c][name] == label.encode())[0] \
                                           for label in self.visible['phases']})
-                in_data_ph.append({label: f['/'.join((grp,'phase'))][member][at_cell_ph[c][label]][:,c] \
+                in_data_ph.append({label: f['/'.join([grp,'phase'])][member][at_cell_ph[c][label]][:,c] \
                                           for label in self.visible['phases']})
 
-            at_cell_ho = {label: np.where(f['/'.join((grp,'homogenization'))][:][name] == label.encode())[0] \
+            at_cell_ho = {label: np.where(f['/'.join([grp,'homogenization'])][:][name] == label.encode())[0] \
                                  for label in self.visible['homogenizations']}
-            in_data_ho = {label: f['/'.join((grp,'homogenization'))][member][at_cell_ho[label]] \
+            in_data_ho = {label: f['/'.join([grp,'homogenization'])][member][at_cell_ho[label]] \
                                  for label in self.visible['homogenizations']}
 
             for inc in util.show_progress(self.visible['increments']):
                 r[inc] = {'phase':{},'homogenization':{},'geometry':{}}
 
-                for out in _match(output,f['/'.join((inc,'geometry'))].keys()):
+                for out in _match(output,f['/'.join([inc,'geometry'])].keys()):
-                    r[inc]['geometry'][out] = _read(f['/'.join((inc,'geometry',out))])
+                    r[inc]['geometry'][out] = _read(f['/'.join([inc,'geometry',out])])
 
                 for ty in ['phase','homogenization']:
                     for label in self.visible[ty+'s']:
-                        for field in _match(self.visible['fields'],f['/'.join((inc,ty,label))].keys()):
+                        for field in _match(self.visible['fields'],f['/'.join([inc,ty,label])].keys()):
                             if field not in r[inc][ty].keys():
                                 r[inc][ty][field] = {}
 
-                            for out in _match(output,f['/'.join((inc,ty,label,field))].keys()):
+                            for out in _match(output,f['/'.join([inc,ty,label,field])].keys()):
-                                data = ma.array(_read(f['/'.join((inc,ty,label,field,out))]))
+                                data = ma.array(_read(f['/'.join([inc,ty,label,field,out])]))
 
                                 if ty == 'phase':
                                     if out+suffixes[0] not in r[inc][ty][field].keys():

python/damask/_table.py

@@ -27,20 +27,69 @@ class Table:
         self.comments = [] if comments_ is None else [c for c in comments_]
         self.data = pd.DataFrame(data=data)
         self.shapes = { k:(v,) if isinstance(v,(np.int64,np.int32,int)) else v for k,v in shapes.items() }
-        self._label_uniform()
+        self._relabel('uniform')
+
 
     def __repr__(self):
         """Brief overview."""
-        return '\n'.join(['# '+c for c in self.comments])+'\n'+self.data.__repr__()
+        self._relabel('shapes')
+        data_repr = self.data.__repr__()
+        self._relabel('uniform')
+        return '\n'.join(['# '+c for c in self.comments])+'\n'+data_repr
+
 
     def __getitem__(self,item):
-        """Return slice according to item."""
+        """
-        return self.__class__(data=self.data[item],shapes=self.shapes,comments=self.comments)
+        Slice the Table according to item.
+
+        Parameters
+        ----------
+        item : row and/or column indexer
+            Slice to select from Table.
+
+        Returns
+        -------
+        slice : Table
+            Sliced part of the Table.
+
+        Examples
+        --------
+        >>> import damask
+        >>> import numpy as np
+        >>> tbl = damask.Table(data=np.arange(12).reshape((4,3)),
+        ...                    shapes=dict(colA=(1,),colB=(1,),colC=(1,)))
+        >>> tbl['colA','colB']
+           colA  colB
+        0     0     1
+        1     3     4
+        2     6     7
+        3     9    10
+        >>> tbl[::2,['colB','colA']]
+           colB  colA
+        0     1     0
+        2     7     6
+        >>> tbl[1:2,'colB']
+           colB
+        1     4
+        2     7
+
+        """
+        item = (item,slice(None,None,None)) if isinstance(item,slice) else \
+               item if isinstance(item[0],slice) else \
+               (slice(None,None,None),item)
+        sliced = self.data.loc[item]
+        cols = np.array(sliced.columns if isinstance(sliced,pd.core.frame.DataFrame) else [item[1]])
+        _,idx = np.unique(cols,return_index=True)
+        return self.__class__(data=sliced,
+                              shapes = {k:self.shapes[k] for k in cols[np.sort(idx)]},
+                              comments=self.comments)
+
 
     def __len__(self):
         """Number of rows."""
         return len(self.data)
 
+
     def __copy__(self):
         """Create deep copy."""
         return copy.deepcopy(self)
@@ -48,21 +97,51 @@ class Table:
     copy = __copy__
 
 
-    def _label_discrete(self):
+    def _label(self,what,how):
-        """Label data individually, e.g. v v v ==> 1_v 2_v 3_v."""
+        """
+        Expand labels according to data shape.
+
+        Parameters
+        ----------
+        what : str or list
+            Labels to expand.
+        how : str
+            Mode of labeling.
+            'uniform' ==> v v v
+            'shapes'  ==> 3:v v v
+            'linear'  ==> 1_v 2_v 3_v
+
+        """
+        what = [what] if isinstance(what,str) else what
         labels = []
-        for label,shape in self.shapes.items():
+        for label in what:
-            size = int(np.prod(shape))
+            shape = self.shapes[label]
-            labels += [('' if size == 1 else f'{i+1}_')+label for i in range(size)]
+            size = np.prod(shape,dtype=int)
-        self.data.columns = labels
+            if   how == 'uniform':
+                labels += [label] * size
+            elif how == 'shapes':
+                labels += [('' if size == 1 or i>0 else f'{util.srepr(shape,"x")}:')+label for i in range(size)]
+            elif how == 'linear':
+                labels += [('' if size == 1 else f'{i+1}_')+label for i in range(size)]
+            else:
+                raise KeyError
+        return labels
 
 
-    def _label_uniform(self):
+    def _relabel(self,how):
-        """Label data uniformly, e.g. 1_v 2_v 3_v ==> v v v."""
+        """
-        labels = []
+        Modify labeling of data in-place.
-        for label,shape in self.shapes.items():
+
-            labels += [label] * int(np.prod(shape))
+        Parameters
-        self.data.columns = labels
+        ----------
+        how : str
+            Mode of labeling.
+            'uniform' ==> v v v
+            'shapes'  ==> 3:v v v
+            'linear'  ==> 1_v 2_v 3_v
+
+        """
+        self.data.columns = self._label(self.shapes,how)
 
 
     def _add_comment(self,label,shape,info):
@@ -72,6 +151,62 @@ class Table:
             self.comments.append(f'{specific} / {general}')
 
 
+    def isclose(self,other,rtol=1e-5,atol=1e-8,equal_nan=True):
+        """
+        Report where values are approximately equal to corresponding ones of other Table.
+
+        Parameters
+        ----------
+        other : Table
+            Table to compare against.
+        rtol : float, optional
+            Relative tolerance of equality.
+        atol : float, optional
+            Absolute tolerance of equality.
+        equal_nan : bool, optional
+            Consider matching NaN values as equal. Defaults to True.
+
+        Returns
+        -------
+        mask : numpy.ndarray bool
+            Mask indicating where corresponding table values are close.
+
+        """
+        return np.isclose( self.data.to_numpy(),
+                          other.data.to_numpy(),
+                          rtol=rtol,
+                          atol=atol,
+                          equal_nan=equal_nan)
+
+
+    def allclose(self,other,rtol=1e-5,atol=1e-8,equal_nan=True):
+        """
+        Test whether all values are approximately equal to corresponding ones of other Table.
+
+        Parameters
+        ----------
+        other : Table
+            Table to compare against.
+        rtol : float, optional
+            Relative tolerance of equality.
+        atol : float, optional
+            Absolute tolerance of equality.
+        equal_nan : bool, optional
+            Consider matching NaN values as equal. Defaults to True.
+
+        Returns
+        -------
+        answer : bool
+            Whether corresponding values are close between both tables.
+
+        """
+        return np.allclose( self.data.to_numpy(),
+                           other.data.to_numpy(),
+                           rtol=rtol,
+                           atol=atol,
+                           equal_nan=equal_nan)
+
+
     @staticmethod
     def load(fname):
         """
@@ -120,12 +255,13 @@ class Table:
 
         return Table(data,shapes,comments)
 
+
     @staticmethod
     def load_ang(fname):
         """
         Load from ang file.
 
-        A valid TSL ang file needs to contains the following columns:
+        A valid TSL ang file has to have the following columns:
 
         - Euler angles (Bunge notation) in radians, 3 floats, label 'eu'.
         - Spatial position in meters, 2 floats, label 'pos'.
@@ -186,11 +322,7 @@ class Table:
             Array of column data.
 
         """
-        if re.match(r'[0-9]*?_',label):
+        data = self.data[label].to_numpy().reshape((-1,)+self.shapes[label])
-            idx,key = label.split('_',1)
-            data = self.data[key].to_numpy()[:,int(idx)-1].reshape(-1,1)
-        else:
-            data = self.data[label].to_numpy().reshape((-1,)+self.shapes[label])
 
         return data.astype(type(data.flatten()[0]))
 
@@ -216,10 +348,12 @@ class Table:
         """
         dup = self.copy()
         dup._add_comment(label,data.shape[1:],info)
-
+        m = re.match(r'(.*)\[((\d+,)*(\d+))\]',label)
-        if re.match(r'[0-9]*?_',label):
+        if m:
-            idx,key = label.split('_',1)
+            key = m.group(1)
-            iloc = dup.data.columns.get_loc(key).tolist().index(True) + int(idx) -1
+            idx = np.ravel_multi_index(tuple(map(int,m.group(2).split(","))),
+                                       self.shapes[key])
+            iloc = dup.data.columns.get_loc(key).tolist().index(True) + idx
             dup.data.iloc[:,iloc] = data
         else:
             dup.data[label]       = data.reshape(dup.data[label].shape)
@@ -322,10 +456,18 @@ class Table:
             Updated table.
 
         """
+        labels_ = [labels] if isinstance(labels,str) else labels.copy()
+        for i,l in enumerate(labels_):
+            m = re.match(r'(.*)\[((\d+,)*(\d+))\]',l)
+            if m:
+                idx = np.ravel_multi_index(tuple(map(int,m.group(2).split(','))),
+                                           self.shapes[m.group(1)])
+                labels_[i] = f'{1+idx}_{m.group(1)}'
+
         dup = self.copy()
-        dup._label_discrete()
+        dup._relabel('linear')
-        dup.data.sort_values(labels,axis=0,inplace=True,ascending=ascending)
+        dup.data.sort_values(labels_,axis=0,inplace=True,ascending=ascending)
-        dup._label_uniform()
+        dup._relabel('uniform')
         dup.comments.append(f'sorted {"ascending" if ascending else "descending"} by {labels}')
         return dup
 

python/damask/util.py

@@ -399,7 +399,7 @@ def DREAM3D_cell_data_group(fname):
     """
     base_group = DREAM3D_base_group(fname)
     with h5py.File(fname,'r') as f:
-        cells = tuple(f['/'.join((base_group,'_SIMPL_GEOMETRY','DIMENSIONS'))][()][::-1])
+        cells = tuple(f['/'.join([base_group,'_SIMPL_GEOMETRY','DIMENSIONS'])][()][::-1])
         cell_data_group = f[base_group].visititems(lambda path,obj: path.split('/')[0] \
                                                    if isinstance(obj,h5py._hl.dataset.Dataset) and np.shape(obj)[:-1] == cells \
                                                    else None)

python/setup.py

@@ -2,6 +2,7 @@ import setuptools
 from pathlib import Path
 import re
 
+# https://www.python.org/dev/peps/pep-0440
 with open(Path(__file__).parent/'damask/VERSION') as f:
   version = re.sub(r'(-([^-]*)).*$',r'.\2',re.sub(r'^v(\d+\.\d+(\.\d+)?)',r'\1',f.readline().strip()))
 

python/tests/test_ConfigMaterial.py

@@ -86,9 +86,12 @@ class TestConfigMaterial:
 
     def test_from_table(self):
         N = np.random.randint(3,10)
-        a = np.vstack((np.hstack((np.arange(N),np.arange(N)[::-1])),np.ones(N*2),np.zeros(N*2),np.ones(N*2),np.ones(N*2))).T
+        a = np.vstack((np.hstack((np.arange(N),np.arange(N)[::-1])),
-        t = Table(a,{'varying':1,'constant':4})
+                       np.ones(N*2),np.zeros(N*2),np.ones(N*2),np.ones(N*2),
-        c = ConfigMaterial.from_table(t,**{'phase':'varying','O':'constant','homogenization':'4_constant'})
+                       np.ones(N*2),
+                      )).T
+        t = Table(a,{'varying':1,'constant':4,'ones':1})
+        c = ConfigMaterial.from_table(t,**{'phase':'varying','O':'constant','homogenization':'ones'})
         assert len(c['material']) == N
         for i,m in enumerate(c['material']):
             assert m['homogenization'] == 1 and (m['constituents'][0]['O'] == [1,0,1,1]).all()

python/tests/test_Grid.py

@@ -407,7 +407,8 @@ class TestGrid:
         z=np.ones(cells.prod())
         z[cells[:2].prod()*int(cells[2]/2):]=0
         t = Table(np.column_stack((coords,z)),{'coords':3,'z':1})
-        g = Grid.from_table(t,'coords',['1_coords','z'])
+        t = t.add('indicator',t.get('coords')[:,0])
+        g = Grid.from_table(t,'coords',['indicator','z'])
         assert g.N_materials == g.cells[0]*2 and (g.material[:,:,-1]-g.material[:,:,0] == cells[0]).all()
 
 

python/tests/test_Result.py

@@ -269,9 +269,8 @@ class TestResult:
         last = default.view('times',default.times_in_range(0,np.inf)[-1])
 
         last.add_stress_Cauchy()
-        with h5py.File(last.fname,'r') as f:
+
-            created_first = default.place('sigma').dtype.metadata['created']
+        created_first = last.place('sigma').dtype.metadata['created']
-        
         created_first = datetime.strptime(created_first,'%Y-%m-%d %H:%M:%S%z')
 
         if overwrite == 'on':
@@ -284,8 +283,8 @@ class TestResult:
             last.add_calculation('sigma','#sigma#*0.0+311.','not the Cauchy stress')
         except ValueError:
             pass
-        with h5py.File(last.fname,'r') as f:
+
-            created_second = last.place('sigma').dtype.metadata['created']
+        created_second = last.place('sigma').dtype.metadata['created']
         created_second = datetime.strptime(created_second,'%Y-%m-%d %H:%M:%S%z')
 
         if overwrite == 'on':

python/tests/test_Table.py

@@ -36,13 +36,33 @@ class TestTable:
         d = default.get('F')
         assert np.allclose(d,1.0) and d.shape[1:] == (3,3)
 
-    def test_get_component(self,default):
+    def test_set(self,default):
-        d = default.get('5_F')
+        d = default.set('F',np.zeros((5,3,3)),'set to zero').get('F')
-        assert np.allclose(d,1.0) and d.shape[1:] == (1,)
+        assert np.allclose(d,0.0) and d.shape[1:] == (3,3)
 
-    @pytest.mark.parametrize('N',[10,40])
+    def test_set_component(self,default):
-    def test_getitem(self,N):
+        d = default.set('F[0,0]',np.zeros((5)),'set to zero').get('F')
-        assert len(Table(np.random.rand(N,1),{'X':1})[:N//2]) == N//2
+        assert np.allclose(d[...,0,0],0.0) and d.shape[1:] == (3,3)
+
+    def test_labels(self,default):
+        assert default.labels == ['F','v','s']
+
+    def test_add(self,default):
+        d = np.random.random((5,9))
+        assert np.allclose(d,default.add('nine',d,'random data').get('nine'))
+
+    def test_isclose(self,default):
+        assert default.isclose(default).all()
+
+    def test_allclose(self,default):
+        assert default.allclose(default)
+
+    @pytest.mark.parametrize('N',[1,3,4])
+    def test_slice(self,default,N):
+        assert len(default[:N]) == 1+N
+        assert len(default[:N,['F','s']]) == 1+N
+        assert default[N:].get('F').shape == (len(default)-N,3,3)
+        assert (default[:N,['v','s']].data == default['v','s'][:N].data).all().all()
 
     @pytest.mark.parametrize('mode',['str','path'])
     def test_write_read(self,default,tmp_path,mode):
@@ -84,21 +104,6 @@ class TestTable:
         with open(ref_path/fname) as f:
             Table.load(f)
 
-    def test_set(self,default):
-        d = default.set('F',np.zeros((5,3,3)),'set to zero').get('F')
-        assert np.allclose(d,0.0) and d.shape[1:] == (3,3)
-
-    def test_set_component(self,default):
-        d = default.set('1_F',np.zeros((5)),'set to zero').get('F')
-        assert np.allclose(d[...,0,0],0.0) and d.shape[1:] == (3,3)
-
-    def test_labels(self,default):
-        assert default.labels == ['F','v','s']
-
-    def test_add(self,default):
-        d = np.random.random((5,9))
-        assert np.allclose(d,default.add('nine',d,'random data').get('nine'))
-
     def test_rename_equivalent(self):
         x = np.random.random((5,13))
         t = Table(x,{'F':(3,3),'v':(3,),'s':(1,)},['random test data'])
@@ -169,15 +174,15 @@ class TestTable:
     def test_sort_component(self):
         x = np.random.random((5,12))
         t = Table(x,{'F':(3,3),'v':(3,)},['random test data'])
-        unsort = t.get('4_F')
+        unsort = t.get('F')[:,1,0]
-        sort   = t.sort_by('4_F').get('4_F')
+        sort   = t.sort_by('F[1,0]').get('F')[:,1,0]
         assert np.all(np.sort(unsort,0)==sort)
 
     def test_sort_revert(self):
         x = np.random.random((5,12))
         t = Table(x,{'F':(3,3),'v':(3,)},['random test data'])
-        sort = t.sort_by('4_F',ascending=False).get('4_F')
+        sort = t.sort_by('F[1,0]',ascending=False).get('F')[:,1,0]
-        assert np.all(np.sort(sort,0)==sort[::-1,:])
+        assert np.all(np.sort(sort,0)==sort[::-1])
 
     def test_sort(self):
         t = Table(np.array([[0,1,],[2,1,]]),
@@ -185,4 +190,4 @@ class TestTable:
                   ['test data'])\
             .add('s',np.array(['b','a']))\
             .sort_by('s')
-        assert np.all(t.get('1_v') == np.array([2,0]).reshape(2,1))
+        assert np.all(t.get('v')[:,0] == np.array([2,0]))

src/YAML_types.f90

@@ -20,16 +20,10 @@ module YAML_types
     procedure(asFormattedString), deferred :: asFormattedString
     procedure :: &
       asScalar     => tNode_asScalar
-    procedure :: &
-      isScalar     => tNode_isScalar
     procedure :: &
       asList       => tNode_asList
-    procedure :: &
-      isList       => tNode_isList
     procedure :: &
       asDict       => tNode_asDict
-    procedure :: &
-      isDict       => tNode_isDict
     procedure :: &
       tNode_get_byIndex            => tNode_get_byIndex
     procedure :: &
@@ -67,9 +61,9 @@ module YAML_types
     procedure :: &
       tNode_get_byKey_as1dString   => tNode_get_byKey_as1dString
     procedure :: &
-      getIndex                     => tNode_get_byKey_asIndex
+      getKey                       => tNode_get_byIndex_asKey
     procedure :: &
-      getKey                       => tNode_getKey_byIndex
+      getIndex                     => tNode_get_byKey_asIndex
     procedure :: &
       contains                     => tNode_contains
     procedure :: &
@@ -129,7 +123,7 @@ module YAML_types
     procedure :: asFormattedString => tList_asFormattedString
     procedure :: append            => tList_append
     procedure :: &
-      as1dFloat    => tList_as1dFloat
+      as1dFloat  => tList_as1dFloat
     procedure :: &
       as2dFloat  => tList_as2dFloat
     procedure :: &
@@ -341,8 +335,6 @@ function tNode_asScalar(self) result(scalar)
   select type(self)
     class is(tScalar)
       scalar => self
-    class default
-      call IO_error(706,ext_msg='Expected "scalar"')
   end select
 
 end function tNode_asScalar
@@ -359,8 +351,6 @@ function tNode_asList(self) result(list)
   select type(self)
     class is(tList)
       list => self
-    class default
-      call IO_error(706,ext_msg='Expected "list"')
   end select
 
 end function tNode_asList
@@ -377,64 +367,11 @@ function tNode_asDict(self) result(dict)
   select type(self)
     class is(tDict)
       dict => self
-    class default
-      call IO_error(706,ext_msg='Expected "dict"')
   end select
 
 end function tNode_asDict
 
 
-!--------------------------------------------------------------------------------------------------
-!> @brief Checks if node is a scalar
-!--------------------------------------------------------------------------------------------------
-function tNode_isScalar(self) result(scalar)
-
-  class(tNode),   intent(in), target :: self
-  logical                            :: scalar
-
-  scalar = .false.
-  select type(self)
-    class is(tScalar)
-      scalar = .true.
-  end select
-
-end function tNode_isScalar
-
-
-!--------------------------------------------------------------------------------------------------
-!> @brief Checks if node is a list
-!--------------------------------------------------------------------------------------------------
-function tNode_isList(self) result(list)
-
-  class(tNode), intent(in), target :: self
-  logical                          :: list
-
-  list = .false.
-  select type(self)
-    class is(tList)
-      list = .true.
-  end select
-
-end function tNode_isList
-
-
-!--------------------------------------------------------------------------------------------------
-!> @brief Checks if node is a dict
-!--------------------------------------------------------------------------------------------------
-function tNode_isDict(self) result(dict)
-
-  class(tNode), intent(in), target :: self
-  logical                          :: dict
-
-  dict = .false.
-  select type(self)
-    class is(tDict)
-      dict = .true.
-  end select
-
-end function tNode_isDict
-
-
 !--------------------------------------------------------------------------------------------------
 !> @brief Access by index
 !--------------------------------------------------------------------------------------------------
@@ -448,14 +385,19 @@ function tNode_get_byIndex(self,i) result(node)
   class(tItem),  pointer :: item
   integer :: j
 
-  self_ => self%asList()
+  select type(self)
+    class is(tList)
+      self_ => self%asList()
+    class default
+      call IO_error(706,ext_msg='Expected list')
+  endselect
+
+  item => self_%first
+
   if (i < 1 .or. i > self_%length) call IO_error(150,ext_msg='tNode_get_byIndex')
 
-  j = 1
+  do j = 2,i
-  item => self_%first
-  do while(j<i)
     item => item%next
-    j = j + 1
   enddo
   node => item%node
 
@@ -475,8 +417,13 @@ function tNode_get_byIndex_asFloat(self,i) result(nodeAsFloat)
   type(tScalar), pointer :: scalar
 
   node   => self%get(i)
-  scalar => node%asScalar()
+  select type(node)
-  nodeAsFloat = scalar%asFloat()
+    class is(tScalar)
+      scalar => node%asScalar()
+      nodeAsFloat = scalar%asFloat()
+    class default
+      call IO_error(706,ext_msg='Expected scalar float')
+  end select
 
 end function tNode_get_byIndex_asFloat
 
@@ -494,8 +441,13 @@ function tNode_get_byIndex_asInt(self,i) result(nodeAsInt)
   type(tScalar), pointer :: scalar
 
   node   => self%get(i)
-  scalar => node%asScalar()
+  select type(node)
-  nodeAsInt = scalar%asInt()
+    class is(tScalar)
+      scalar => node%asScalar()
+      nodeAsInt = scalar%asInt()
+    class default
+      call IO_error(706,ext_msg='Expected scalar integer')
+  end select
 
 end function tNode_get_byIndex_asInt
 
@@ -513,8 +465,13 @@ function tNode_get_byIndex_asBool(self,i) result(nodeAsBool)
   type(tScalar), pointer :: scalar
 
   node   => self%get(i)
-  scalar => node%asScalar()
+  select type(node)
-  nodeAsBool = scalar%asBool()
+    class is(tScalar)
+      scalar => node%asScalar()
+      nodeAsBool = scalar%asBool()
+    class default
+      call IO_error(706,ext_msg='Expected scalar Boolean')
+  endselect
 
 end function tNode_get_byIndex_asBool
 
@@ -532,8 +489,13 @@ function tNode_get_byIndex_asString(self,i) result(nodeAsString)
   type(tScalar), pointer :: scalar
 
   node   => self%get(i)
-  scalar => node%asScalar()
+  select type(node)
-  nodeAsString = scalar%asString()
+    class is(tScalar)
+      scalar => node%asScalar()
+      nodeAsString = scalar%asString()
+    class default
+      call IO_error(706,ext_msg='Expected scalar string')
+  endselect
 
 end function tNode_get_byIndex_asString
 
@@ -547,12 +509,17 @@ function tNode_get_byIndex_as1dFloat(self,i) result(nodeAs1dFloat)
   integer,      intent(in)         :: i
   real(pReal), dimension(:), allocatable :: nodeAs1dFloat
 
-  class(tNode), pointer :: node
+  class(tNode), pointer  :: node
   class(tList),  pointer :: list
 
   node => self%get(i)
-  list => node%asList()
+  select type(node)
-  nodeAs1dFloat = list%as1dFloat()
+    class is(tList)
+      list => node%asList()
+      nodeAs1dFloat = list%as1dFloat()
+    class default
+      call IO_error(706,ext_msg='Expected list of floats')
+  endselect
 
 end function tNode_get_byIndex_as1dFloat
 
@@ -570,8 +537,13 @@ function tNode_get_byIndex_as1dInt(self,i) result(nodeAs1dInt)
   class(tList), pointer :: list
 
   node => self%get(i)
-  list => node%asList()
+  select type(node)
-  nodeAs1dInt = list%as1dInt()
+    class is(tList)
+      list => node%asList()
+      nodeAs1dInt = list%as1dInt()
+    class default
+      call IO_error(706,ext_msg='Expected list of integers')
+  endselect
 
 end function tNode_get_byIndex_as1dInt
 
@@ -589,8 +561,13 @@ function tNode_get_byIndex_as1dBool(self,i) result(nodeAs1dBool)
   class(tList), pointer :: list
 
   node => self%get(i)
-  list => node%asList()
+  select type(node)
-  nodeAs1dBool = list%as1dBool()
+    class is(tList)
+      list => node%asList()
+      nodeAs1dBool = list%as1dBool()
+    class default
+      call IO_error(706,ext_msg='Expected list of Booleans')
+  endselect
 
 end function tNode_get_byIndex_as1dBool
 
@@ -608,8 +585,13 @@ function tNode_get_byIndex_as1dString(self,i) result(nodeAs1dString)
   type(tList),  pointer :: list
 
   node => self%get(i)
-  list => node%asList()
+  select type(node)
-  nodeAs1dString = list%as1dString()
+    class is(tList)
+      list => node%asList()
+      nodeAs1dString = list%as1dString()
+    class default
+      call IO_error(706,ext_msg='Expected list of strings')
+  endselect
 
 end function tNode_get_byIndex_as1dString
 
@@ -617,7 +599,7 @@ end function tNode_get_byIndex_as1dString
 !--------------------------------------------------------------------------------------------------
 !> @brief Returns the key in a dictionary as a string
 !--------------------------------------------------------------------------------------------------
-function tNode_getKey_byIndex(self,i)  result(key)
+function tNode_get_byIndex_asKey(self,i)  result(key)
 
   class(tNode),     intent(in), target  :: self
   integer,          intent(in)          :: i
@@ -627,18 +609,20 @@ function tNode_getKey_byIndex(self,i)  result(key)
   type(tDict), pointer :: dict
   type(tItem), pointer :: item
 
-  dict => self%asDict()
+  select type(self)
-  item => dict%first
+    class is(tDict)
-  do j = 1, dict%length
+      dict => self%asDict()
-    if (j == i) then
+      item => dict%first
-      key = item%key
+      do j = 1, min(i,dict%length)-1
-      exit
+        item => item%next
-    else
+      enddo
-      item => item%next
+    class default
-    endif
+      call IO_error(706,ext_msg='Expected dict')
-  enddo
+  endselect
 
-end function tNode_getKey_byIndex
+  key = item%key
+
+end function tNode_get_byIndex_asKey
 
 
 !-------------------------------------------------------------------------------------------------
@@ -655,25 +639,26 @@ function tNode_contains(self,k)  result(exists)
   type(tDict), pointer :: dict
 
   exists = .false.
-  if (self%isDict()) then
+  select type(self)
-    dict => self%asDict()
+    class is(tDict)
-    do j=1, dict%length
+      dict => self%asDict()
-      if (dict%getKey(j) == k) then
+      do j=1, dict%length
-        exists = .true.
+        if (dict%getKey(j) == k) then
-        return
+          exists = .true.
-      endif
+          return
-    enddo
+        endif
-  elseif (self%isList()) then
+      enddo
-    list => self%asList()
+    class is(tList)
-    do j=1, list%length
+      list => self%asList()
-      if (list%get_asString(j) == k) then
+      do j=1, list%length
-        exists = .true.
+        if (list%get_asString(j) == k) then
-        return
+          exists = .true.
-      endif
+          return
-    enddo
+        endif
-  else
+      enddo
-     call IO_error(706,ext_msg='Expected "list" or "dict"')
+    class default
-  endif
+      call IO_error(706,ext_msg='Expected list or dict')
+  endselect
 
 end function tNode_contains
 
@@ -696,7 +681,12 @@ function tNode_get_byKey(self,k,defaultVal) result(node)
   found = present(defaultVal)
   if (found) node => defaultVal
 
-  self_ => self%asDict()
+  select type(self)
+    class is(tDict)
+      self_ => self%asDict()
+    class default
+      call IO_error(706,ext_msg='Expected dict for key '//k)
+  endselect
 
   j = 1
   item => self_%first
@@ -733,8 +723,13 @@ function tNode_get_byKey_asFloat(self,k,defaultVal) result(nodeAsFloat)
 
   if (self%contains(k)) then
     node => self%get(k)
-    scalar => node%asScalar()
+    select type(node)
-    nodeAsFloat = scalar%asFloat()
+      class is(tScalar)
+        scalar => node%asScalar()
+        nodeAsFloat = scalar%asFloat()
+      class default
+        call IO_error(706,ext_msg='Expected scalar float for key '//k)
+    endselect
   elseif (present(defaultVal)) then
     nodeAsFloat = defaultVal
   else
@@ -759,8 +754,13 @@ function tNode_get_byKey_asInt(self,k,defaultVal) result(nodeAsInt)
 
   if (self%contains(k)) then
     node => self%get(k)
-    scalar => node%asScalar()
+    select type(node)
-    nodeAsInt = scalar%asInt()
+      class is(tScalar)
+        scalar => node%asScalar()
+        nodeAsInt = scalar%asInt()
+      class default
+        call IO_error(706,ext_msg='Expected scalar integer for key '//k)
+    endselect
   elseif (present(defaultVal)) then
     nodeAsInt = defaultVal
   else
@@ -785,8 +785,13 @@ function tNode_get_byKey_asBool(self,k,defaultVal) result(nodeAsBool)
 
   if (self%contains(k)) then
     node => self%get(k)
-    scalar => node%asScalar()
+    select type(node)
-    nodeAsBool = scalar%asBool()
+      class is(tScalar)
+        scalar => node%asScalar()
+        nodeAsBool = scalar%asBool()
+      class default
+        call IO_error(706,ext_msg='Expected scalar Boolean for key '//k)
+    endselect
   elseif (present(defaultVal)) then
     nodeAsBool = defaultVal
   else
@@ -811,8 +816,13 @@ function tNode_get_byKey_asString(self,k,defaultVal) result(nodeAsString)
 
   if (self%contains(k)) then
     node => self%get(k)
-    scalar => node%asScalar()
+    select type(node)
-    nodeAsString = scalar%asString()
+      class is(tScalar)
+        scalar => node%asScalar()
+        nodeAsString = scalar%asString()
+      class default
+        call IO_error(706,ext_msg='Expected scalar string for key '//k)
+    endselect
   elseif (present(defaultVal)) then
     nodeAsString = defaultVal
   else
@@ -839,8 +849,13 @@ function tNode_get_byKey_as1dFloat(self,k,defaultVal,requiredSize) result(nodeAs
 
   if (self%contains(k)) then
     node => self%get(k)
-    list => node%asList()
+    select type(self)
-    nodeAs1dFloat = list%as1dFloat()
+      class is(tList)
+        list => node%asList()
+        nodeAs1dFloat = list%as1dFloat()
+      class default
+        call IO_error(706,ext_msg='Expected 1D float array for key '//k)
+    endselect
   elseif (present(defaultVal)) then
     nodeAs1dFloat = defaultVal
   else
@@ -870,8 +885,13 @@ function tNode_get_byKey_as2dFloat(self,k,defaultVal) result(nodeAs2dFloat)
 
   if(self%contains(k)) then
     node => self%get(k)
-    rows => node%asList()
+    select type(node)
-    nodeAs2dFloat = rows%as2dFloat()
+      class is(tList)
+        rows => node%asList()
+        nodeAs2dFloat = rows%as2dFloat()
+      class default
+        call IO_error(706,ext_msg='Expected 2D float array for key '//k)
+    endselect
   elseif(present(defaultVal)) then
     nodeAs2dFloat = defaultVal
   else
@@ -897,8 +917,13 @@ function tNode_get_byKey_as1dInt(self,k,defaultVal,requiredSize) result(nodeAs1d
 
   if (self%contains(k)) then
     node => self%get(k)
-    list => node%asList()
+    select type(node)
-    nodeAs1dInt = list%as1dInt()
+      class is(tList)
+        list => node%asList()
+        nodeAs1dInt = list%as1dInt()
+      class default
+        call IO_error(706,ext_msg='Expected 1D integer array for key '//k)
+    endselect
   elseif (present(defaultVal)) then
     nodeAs1dInt = defaultVal
   else
@@ -927,8 +952,13 @@ function tNode_get_byKey_as1dBool(self,k,defaultVal) result(nodeAs1dBool)
 
   if (self%contains(k)) then
     node => self%get(k)
-    list => node%asList()
+    select type(node)
-    nodeAs1dBool = list%as1dBool()
+      class is(tList)
+        list => node%asList()
+        nodeAs1dBool = list%as1dBool()
+      class default
+        call IO_error(706,ext_msg='Expected 1D Boolean array for key '//k)
+    endselect
   elseif (present(defaultVal)) then
     nodeAs1dBool = defaultVal
   else
@@ -953,8 +983,13 @@ function tNode_get_byKey_as1dString(self,k,defaultVal) result(nodeAs1dString)
 
   if (self%contains(k)) then
     node => self%get(k)
-    list => node%asList()
+    select type(node)
-    nodeAs1dString = list%as1dString()
+      class is(tList)
+        list => node%asList()
+        nodeAs1dString = list%as1dString()
+      class default
+        call IO_error(706,ext_msg='Expected 1D string array for key '//k)
+    endselect
   elseif (present(defaultVal)) then
     nodeAs1dString = defaultVal
   else
@@ -981,7 +1016,6 @@ function output_as1dString(self)  result(output)                   !ToDo: SR: Re
     output(o) = output_list%get_asString(o)
   enddo
 
-
 end function output_as1dString
 
 
@@ -994,24 +1028,18 @@ function tNode_get_byKey_asIndex(self,key)  result(keyIndex)
   character(len=*), intent(in)          :: key
 
   integer              :: keyIndex
-  integer              :: i
   type(tDict), pointer :: dict
   type(tItem), pointer :: item
 
   dict => self%asDict()
   item => dict%first
-  keyIndex = -1
+  keyIndex = 1
-  do i = 1, dict%length
+  do while (associated(item%next) .and. item%key /= key)
-    if (key == item%key) then
+    item => item%next
-      keyIndex = i
+    keyIndex = keyIndex+1
-      exit
-    else
-      item => item%next
-    endif
   enddo
 
-  if (keyIndex == -1) call IO_error(140,ext_msg=key)
+  if (item%key /= key) call IO_error(140,ext_msg=key)
-
 
 end function tNode_get_byKey_asIndex
 
@@ -1320,7 +1348,7 @@ subroutine tDict_set(self,key,node)
       if (item%key == key) exit
       item => item%next
     end do searchExisting
-    if (.not. item%key == key) then
+    if (item%key /= key) then
       allocate(item%next)
       item => item%next
       self%length = self%length + 1