Merge branch 'properly-close-files' into 'development'

use context manager to ensure that opened files are closed

See merge request damask/DAMASK!884

python/damask/_colormap.py

@@ -2,7 +2,7 @@ import os
 import json
 import functools
 import colorsys
-from typing import Optional, Union, TextIO
+from typing import Optional, Union
 from itertools import chain
 
 import numpy as np
@@ -344,30 +344,6 @@ class Colormap(mpl.colors.ListedColormap):
         return Colormap(np.array(rev.colors),rev.name[:-4] if rev.name.endswith('_r_r') else rev.name)
 
 
-    def _get_file_handle(self,
-                         fname: Union[FileHandle, None],
-                         suffix: str = '') -> TextIO:
-        """
-        Provide file handle.
-
-        Parameters
-        ----------
-        fname : file, str, pathlib.Path, or None
-            Name or handle of file.
-            If None, colormap name + suffix.
-        suffix: str, optional
-            Extension to use for colormap file.
-            Defaults to empty.
-
-        Returns
-        -------
-        f : file object
-            File handle with write access.
-
-        """
-        return util.open_text(self.name.replace(' ','_')+suffix if fname is None else fname, 'w')
-
-
     def save_paraview(self,
                       fname: Optional[FileHandle] = None):
         """
@@ -387,9 +363,9 @@ class Colormap(mpl.colors.ListedColormap):
                 'RGBPoints':list(chain.from_iterable([(i,*c) for i,c in enumerate(self.colors.round(6))]))
                }]
 
-        fhandle = self._get_file_handle(fname,'.json')
+        with util.open_text(self.name.replace(' ','_')+'.json' if fname is None else fname, 'w') as fhandle:
-        json.dump(out,fhandle,indent=4)
+            json.dump(out,fhandle,indent=4)
-        fhandle.write('\n')
+            fhandle.write('\n')
 
 
     def save_ASCII(self,
@@ -405,7 +381,9 @@ class Colormap(mpl.colors.ListedColormap):
         """
         labels = {'RGBA':4} if self.colors.shape[1] == 4 else {'RGB': 3}
         t = Table(labels,self.colors,[f'Creator: {util.execution_stamp("Colormap")}'])
-        t.save(self._get_file_handle(fname,'.txt'))
+
+        with util.open_text(self.name.replace(' ','_')+'.txt' if fname is None else fname, 'w') as fhandle:
+            t.save(fhandle)
 
 
     def save_GOM(self, fname: Optional[FileHandle] = None):
@@ -425,7 +403,8 @@ class Colormap(mpl.colors.ListedColormap):
                 + ' '.join([f' 0 {c[0]} {c[1]} {c[2]} 255 1' for c in reversed((self.colors*255).astype(np.int64))]) \
                 + '\n'
 
-        self._get_file_handle(fname,'.legend').write(GOM_str)
+        with util.open_text(self.name.replace(' ','_')+'.legend' if fname is None else fname, 'w') as fhandle:
+            fhandle.write(GOM_str)
 
 
     def save_gmsh(self,
@@ -443,7 +422,9 @@ class Colormap(mpl.colors.ListedColormap):
         gmsh_str = 'View.ColorTable = {\n' \
                  +'\n'.join([f'{c[0]},{c[1]},{c[2]},' for c in self.colors[:,:3]*255]) \
                  +'\n}\n'
-        self._get_file_handle(fname,'.msh').write(gmsh_str)
+
+        with util.open_text(self.name.replace(' ','_')+'.msh' if fname is None else fname, 'w') as fhandle:
+            fhandle.write(gmsh_str)
 
 
     @staticmethod

python/damask/_loadcasegrid.py

@@ -70,9 +70,9 @@ class LoadcaseGrid(YAML):
             if key not in kwargs:
                 kwargs[key] = default
 
-        fhandle = util.open_text(fname,'w')
+        with util.open_text(fname,'w') as fhandle:
-        try:
+            try:
-            fhandle.write(yaml.dump(self,Dumper=MaskedMatrixDumper,**kwargs))
+                fhandle.write(yaml.dump(self,Dumper=MaskedMatrixDumper,**kwargs))
-        except TypeError:                                                                           # compatibility with old pyyaml
+            except TypeError:                                                                       # compatibility with old pyyaml
-            del kwargs['sort_keys']
+                del kwargs['sort_keys']
-            fhandle.write(yaml.dump(self,Dumper=MaskedMatrixDumper,**kwargs))
+                fhandle.write(yaml.dump(self,Dumper=MaskedMatrixDumper,**kwargs))

python/damask/_table.py

@@ -277,28 +277,28 @@ class Table:
             Table data from file.
 
         """
-        f = util.open_text(fname)
+        with util.open_text(fname) as f:
-        f.seek(0)
+            f.seek(0)
 
-        comments = []
+            comments = []
-        while (line := f.readline().strip()).startswith('#'):
+            while (line := f.readline().strip()).startswith('#'):
-            comments.append(line.lstrip('#').strip())
+                comments.append(line.lstrip('#').strip())
-        labels = line.split()
+            labels = line.split()
 
-        shapes = {}
+            shapes = {}
-        for label in labels:
+            for label in labels:
-            tensor_column = re.search(r'[0-9,x]*?:[0-9]*?_',label)
+                tensor_column = re.search(r'[0-9,x]*?:[0-9]*?_',label)
-            if tensor_column:
+                if tensor_column:
-                my_shape = tensor_column.group().split(':',1)[0].split('x')
+                    my_shape = tensor_column.group().split(':',1)[0].split('x')
-                shapes[label.split('_',1)[1]] = tuple([int(d) for d in my_shape])
+                    shapes[label.split('_',1)[1]] = tuple([int(d) for d in my_shape])
-            else:
-                vector_column = re.match(r'[0-9]*?_',label)
-                if vector_column:
-                    shapes[label.split('_',1)[1]] = (int(label.split('_',1)[0]),)
                 else:
-                    shapes[label] = (1,)
+                    vector_column = re.match(r'[0-9]*?_',label)
+                    if vector_column:
+                        shapes[label.split('_',1)[1]] = (int(label.split('_',1)[0]),)
+                    else:
+                        shapes[label] = (1,)
 
-        data = pd.read_csv(f,names=list(range(len(labels))),sep=r'\s+')
+            data = pd.read_csv(f,names=list(range(len(labels))),sep=r'\s+')
 
         return Table(shapes,data,comments)
 
@@ -339,10 +339,9 @@ class Table:
             Table data from file.
 
         """
-        f = util.open_text(fname)
+        with util.open_text(fname) as f:
-        f.seek(0)
+            f.seek(0)
-
+            content = f.readlines()
-        content = f.readlines()
 
         comments = [util.execution_stamp('Table','from_ang')]
         for line in content:
@@ -605,10 +604,9 @@ class Table:
                     labels += [f'{util.srepr(self.shapes[l],"x")}:{i+1}_{l}' \
                               for i in range(np.prod(self.shapes[l]))]
 
-        f = util.open_text(fname,'w')
+        with util.open_text(fname,'w') as f:
-
+            f.write('\n'.join([f'# {c}' for c in self.comments] + [' '.join(labels)])+('\n' if labels else ''))
-        f.write('\n'.join([f'# {c}' for c in self.comments] + [' '.join(labels)])+('\n' if labels else ''))
+            try:                                                                                    # backward compatibility
-        try:                                                                                        # backward compatibility
+                self.data.to_csv(f,sep=' ',na_rep='nan',index=False,header=False,lineterminator='\n')
-            self.data.to_csv(f,sep=' ',na_rep='nan',index=False,header=False,lineterminator='\n')
+            except TypeError:
-        except TypeError:
+                self.data.to_csv(f,sep=' ',na_rep='nan',index=False,header=False,line_terminator='\n')
-            self.data.to_csv(f,sep=' ',na_rep='nan',index=False,header=False,line_terminator='\n')

python/damask/_yaml.py

@@ -197,7 +197,9 @@ class YAML(dict):
             YAML from file.
 
         """
-        return cls(yaml.load(util.open_text(fname), Loader=SafeLoader))
+        with util.open_text(fname) as fhandle:
+            return cls(yaml.load(fhandle, Loader=SafeLoader))
+
 
     def save(self,
              fname: FileHandle,
@@ -220,12 +222,12 @@ class YAML(dict):
         if 'sort_keys' not in kwargs:
             kwargs['sort_keys'] = False
 
-        fhandle = util.open_text(fname,'w')
+        with util.open_text(fname,'w') as fhandle:
-        try:
+            try:
-            fhandle.write(yaml.dump(self,Dumper=NiceDumper,**kwargs))
+                fhandle.write(yaml.dump(self,Dumper=NiceDumper,**kwargs))
-        except TypeError:                                                                           # compatibility with old pyyaml
+            except TypeError:                                                                       # compatibility with old pyyaml
-            del kwargs['sort_keys']
+                del kwargs['sort_keys']
-            fhandle.write(yaml.dump(self,Dumper=NiceDumper,**kwargs))
+                fhandle.write(yaml.dump(self,Dumper=NiceDumper,**kwargs))
 
 
     @property

python/damask/util.py

@@ -8,12 +8,13 @@ import shlex as _shlex
 import re as _re
 import signal as _signal
 import fractions as _fractions
+import contextlib as _contextlib
 from collections import abc as _abc, OrderedDict as _OrderedDict
 from functools import reduce as _reduce, partial as _partial, wraps as _wraps
 import inspect
 from typing import Optional as _Optional, Callable as _Callable, Union as _Union, Iterable as _Iterable, \
                    Dict as _Dict, List as _List, Tuple as _Tuple, Literal as _Literal, \
-                   Any as _Any, TextIO as _TextIO
+                   Any as _Any, TextIO as _TextIO, Generator as _Generator
 from pathlib import Path as _Path
 
 import numpy as _np
@@ -193,11 +194,15 @@ def run(cmd: str,
 
     return stdout, stderr
 
-
+@_contextlib.contextmanager
 def open_text(fname: _FileHandle,
-              mode: _Literal['r','w'] = 'r') -> _TextIO:                                            # noqa
+              mode: _Literal['r','w'] = 'r') -> _Generator[_TextIO, None, None]:                    # noqa
     """
-    Open a text file.
+    Open a text file with Unix line endings
+
+    If a path or string is given, a context manager ensures that
+    the file handle is closed.
+    If a file handle is given, it remains unmodified.
 
     Parameters
     ----------
@@ -211,8 +216,12 @@ def open_text(fname: _FileHandle,
     f : file handle
 
     """
-    return fname if not isinstance(fname, (str,_Path)) else \
+    if isinstance(fname, (str,_Path)):
-           open(_Path(fname).expanduser(),mode,newline=('\n' if mode == 'w' else None))
+        fhandle = open(_Path(fname).expanduser(),mode,newline=('\n' if mode == 'w' else None))
+        yield fhandle
+        fhandle.close()
+    else:
+        yield fname
 
 
 def execution_stamp(class_name: str,