Merge branch 'util_open' into 'development'

centralize opening of text files

See merge request damask/DAMASK!555

python/damask/_colormap.py

@@ -2,7 +2,6 @@ import os
 import json
 import functools
 import colorsys
-from pathlib import Path
 from typing import Union, TextIO
 
 import numpy as np
@@ -325,12 +324,7 @@ class Colormap(mpl.colors.ListedColormap):
             File handle with write access.
 
         """
-        if fname is None:
-            return open(self.name.replace(' ','_')+suffix, 'w', newline='\n')
-        elif isinstance(fname, (str, Path)):
-            return open(Path(fname).expanduser(), 'w', newline='\n')
-        else:
-            return fname
+        return util.open_text(self.name.replace(' ','_')+suffix if fname is None else fname, 'w')
 
 
     def save_paraview(self,

python/damask/_config.py

@@ -2,7 +2,6 @@ import copy
 from io import StringIO
 from collections.abc import Iterable
 import abc
-from pathlib import Path
 from typing import Union, Dict, Any, Type, TypeVar
 
 import numpy as np
@@ -10,6 +9,7 @@ import yaml
 
 from ._typehints import FileHandle
 from . import Rotation
+from . import util
 
 MyType = TypeVar('MyType', bound='Config')
 
@@ -144,10 +144,7 @@ class Config(dict):
             Configuration from file.
 
         """
-        fhandle = open(Path(fname).expanduser(),newline='\n') if isinstance(fname, (str, Path)) else \
-                  fname
-
-        return cls(yaml.safe_load(fhandle))
+        return cls(yaml.safe_load(util.open_text(fname)))
 
     def save(self,
              fname: FileHandle,
@@ -163,9 +160,6 @@ class Config(dict):
             Keyword arguments parsed to yaml.dump.
 
         """
-        fhandle = open(Path(fname).expanduser(),'w',newline='\n') if isinstance(fname, (str, Path)) else \
-                  fname
-
         if 'width' not in kwargs:
             kwargs['width'] = 256
         if 'default_flow_style' not in kwargs:
@@ -173,6 +167,7 @@ class Config(dict):
         if 'sort_keys' not in kwargs:
             kwargs['sort_keys'] = False
 
+        fhandle = util.open_text(fname,'w')
         try:
             fhandle.write(yaml.dump(self,Dumper=NiceDumper,**kwargs))
         except TypeError:                                                                           # compatibility with old pyyaml

python/damask/_result.py

@@ -1538,7 +1538,7 @@ class Result:
                                                                                                         np.prod(shape))}
                                 data_items[-1].text = f'{os.path.split(self.fname)[1]}:{name}'
 
-        with open(self.fname.with_suffix('.xdmf').name,'w',newline='\n') as f:
+        with util.open_text(self.fname.with_suffix('.xdmf').name,'w') as f:
             f.write(xml.dom.minidom.parseString(ET.tostring(xdmf).decode()).toprettyxml())
 
 
@@ -1803,7 +1803,7 @@ class Result:
             if type(obj) == h5py.Dataset and  _match(output,[name]):
                 d = obj.attrs['description'] if h5py3 else obj.attrs['description'].decode()
                 if not Path(name).exists() or overwrite:
-                    with open(name,'w',newline='\n') as f_out: f_out.write(obj[0].decode())
+                    with util.open_text(name,'w') as f_out: f_out.write(obj[0].decode())
                     print(f'Exported {d} to "{name}".')
                 else:
                     print(f'"{name}" exists, {d} not exported.')

python/damask/_table.py

@@ -1,6 +1,5 @@
 import re
 import copy
-from pathlib import Path
 from typing import Union, Tuple, List
 
 import pandas as pd
@@ -260,7 +259,7 @@ class Table:
             Table data from file.
 
         """
-        f = open(Path(fname).expanduser(),newline='\n') if isinstance(fname, (str, Path)) else fname
+        f = util.open_text(fname)
         f.seek(0)
 
         comments = []
@@ -281,7 +280,7 @@ class Table:
                 else:
                     shapes[label] = (1,)
 
-        data = pd.read_csv(f,names=list(range(len(labels))),sep=r'\s+',lineterminator='\n')
+        data = pd.read_csv(f,names=list(range(len(labels))),sep=r'\s+')
 
         return Table(shapes,data,comments)
 
@@ -312,7 +311,7 @@ class Table:
             Table data from file.
 
         """
-        f = open(Path(fname).expanduser(),newline='\n') if isinstance(fname, (str, Path)) else fname
+        f = util.open_text(fname)
         f.seek(0)
 
         content = f.readlines()
@@ -594,7 +593,7 @@ class Table:
                     labels += [f'{util.srepr(self.shapes[l],"x")}:{i+1}_{l}' \
                               for i in range(np.prod(self.shapes[l]))]
 
-        f = open(Path(fname).expanduser(),'w',newline='\n') if isinstance(fname, (str, Path)) else fname
+        f = util.open_text(fname,'w')
 
         f.write('\n'.join([f'# {c}' for c in self.comments] + [' '.join(labels)])+('\n' if labels else ''))
         self.data.to_csv(f,sep=' ',na_rep='nan',index=False,header=False,line_terminator='\n')

python/damask/util.py

@@ -10,20 +10,21 @@ import signal
 import fractions
 from collections import abc
 from functools import reduce, partial
-from typing import Callable, Union, Iterable, Sequence, Dict, List, Tuple, Literal, Any, Collection
+from typing import Callable, Union, Iterable, Sequence, Dict, List, Tuple, Literal, Any, Collection, TextIO
 from pathlib import Path
 
 import numpy as np
 import h5py
 
 from . import version
-from ._typehints import FloatSequence, NumpyRngSeed, IntCollection
+from ._typehints import FloatSequence, NumpyRngSeed, IntCollection, FileHandle
 
 # limit visibility
 __all__=[
          'srepr',
          'emph', 'deemph', 'warn', 'strikeout',
          'run',
+         'open_text',
          'natural_sort',
          'show_progress',
          'scale_to_coprime',
@@ -206,7 +207,25 @@ def run(cmd: str,
     return stdout, stderr
 
 
-execute = run
+def open_text(fname: FileHandle,
+              mode: Literal['r','w'] = 'r') -> TextIO:
+    """
+    Open a text file.
+
+    Parameters
+    ----------
+    fname : file, str, or pathlib.Path
+        Name or handle of file.
+    mode: {'r','w'}, optional
+        Access mode: 'r'ead or 'w'rite, defaults to 'r'.
+
+    Returns
+    -------
+    f : file handle
+
+    """
+    return fname if not isinstance(fname, (str,Path)) else \
+           open(Path(fname).expanduser(),mode,newline=('\n' if mode == 'w' else None))
 
 
 def natural_sort(key: str) -> List[Union[int, str]]:

python/tests/test_util.py

@@ -12,19 +12,19 @@ from damask import util
 class TestUtil:
 
     @pytest.mark.xfail(sys.platform == 'win32', reason='echo is not a Windows command')
-    def test_execute_direct(self):
-        out,err = util.execute('echo test')
+    def test_run_direct(self):
+        out,err = util.run('echo test')
         assert out=='test\n' and err==''
 
     @pytest.mark.xfail(sys.platform == 'win32', reason='echo is not a Windows command')
-    def test_execute_env(self):
-        out,err = util.execute('sh -c "echo $test_for_execute"',env={'test_for_execute':'test'})
+    def test_run_env(self):
+        out,err = util.run('sh -c "echo $test_for_execute"',env={'test_for_execute':'test'})
         assert out=='test\n' and err==''
 
     @pytest.mark.xfail(sys.platform == 'win32', reason='false is not a Windows command')
-    def test_execute_runtime_error(self):
+    def test_run_runtime_error(self):
         with pytest.raises(RuntimeError):
-            util.execute('false')
+            util.run('false')
 
     @pytest.mark.parametrize('input,output',
                             [