Merge branch 'properly-close-files' into 'development'
use context manager to ensure that opened files are closed See merge request damask/DAMASK!884
This commit is contained in:
Philip Eisenlohr
commit
b22251a2b9
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@ -2,7 +2,7 @@ import os
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import json
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import functools
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import colorsys
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from typing import Optional, Union, TextIO
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from typing import Optional, Union
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from itertools import chain
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import numpy as np
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@ -344,30 +344,6 @@ class Colormap(mpl.colors.ListedColormap):
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return Colormap(np.array(rev.colors),rev.name[:-4] if rev.name.endswith('_r_r') else rev.name)
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def _get_file_handle(self,
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fname: Union[FileHandle, None],
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suffix: str = '') -> TextIO:
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"""
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Provide file handle.
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Parameters
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----------
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fname : file, str, pathlib.Path, or None
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Name or handle of file.
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If None, colormap name + suffix.
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suffix: str, optional
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Extension to use for colormap file.
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Defaults to empty.
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Returns
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-------
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f : file object
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File handle with write access.
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"""
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return util.open_text(self.name.replace(' ','_')+suffix if fname is None else fname, 'w')
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def save_paraview(self,
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fname: Optional[FileHandle] = None):
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"""
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@ -387,9 +363,9 @@ class Colormap(mpl.colors.ListedColormap):
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'RGBPoints':list(chain.from_iterable([(i,*c) for i,c in enumerate(self.colors.round(6))]))
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}]
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fhandle = self._get_file_handle(fname,'.json')
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json.dump(out,fhandle,indent=4)
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fhandle.write('\n')
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with util.open_text(self.name.replace(' ','_')+'.json' if fname is None else fname, 'w') as fhandle:
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json.dump(out,fhandle,indent=4)
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fhandle.write('\n')
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def save_ASCII(self,
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@ -405,7 +381,9 @@ class Colormap(mpl.colors.ListedColormap):
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"""
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labels = {'RGBA':4} if self.colors.shape[1] == 4 else {'RGB': 3}
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t = Table(labels,self.colors,[f'Creator: {util.execution_stamp("Colormap")}'])
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t.save(self._get_file_handle(fname,'.txt'))
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with util.open_text(self.name.replace(' ','_')+'.txt' if fname is None else fname, 'w') as fhandle:
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t.save(fhandle)
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def save_GOM(self, fname: Optional[FileHandle] = None):
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@ -425,7 +403,8 @@ class Colormap(mpl.colors.ListedColormap):
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+ ' '.join([f' 0 {c[0]} {c[1]} {c[2]} 255 1' for c in reversed((self.colors*255).astype(np.int64))]) \
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+ '\n'
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self._get_file_handle(fname,'.legend').write(GOM_str)
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with util.open_text(self.name.replace(' ','_')+'.legend' if fname is None else fname, 'w') as fhandle:
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fhandle.write(GOM_str)
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def save_gmsh(self,
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@ -443,7 +422,9 @@ class Colormap(mpl.colors.ListedColormap):
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gmsh_str = 'View.ColorTable = {\n' \
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+'\n'.join([f'{c[0]},{c[1]},{c[2]},' for c in self.colors[:,:3]*255]) \
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+'\n}\n'
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self._get_file_handle(fname,'.msh').write(gmsh_str)
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with util.open_text(self.name.replace(' ','_')+'.msh' if fname is None else fname, 'w') as fhandle:
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fhandle.write(gmsh_str)
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@staticmethod
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@ -70,9 +70,9 @@ class LoadcaseGrid(YAML):
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if key not in kwargs:
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kwargs[key] = default
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fhandle = util.open_text(fname,'w')
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try:
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fhandle.write(yaml.dump(self,Dumper=MaskedMatrixDumper,**kwargs))
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except TypeError: # compatibility with old pyyaml
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del kwargs['sort_keys']
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fhandle.write(yaml.dump(self,Dumper=MaskedMatrixDumper,**kwargs))
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with util.open_text(fname,'w') as fhandle:
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try:
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fhandle.write(yaml.dump(self,Dumper=MaskedMatrixDumper,**kwargs))
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except TypeError: # compatibility with old pyyaml
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del kwargs['sort_keys']
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fhandle.write(yaml.dump(self,Dumper=MaskedMatrixDumper,**kwargs))
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@ -277,28 +277,28 @@ class Table:
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Table data from file.
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"""
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f = util.open_text(fname)
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f.seek(0)
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with util.open_text(fname) as f:
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f.seek(0)
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comments = []
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while (line := f.readline().strip()).startswith('#'):
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comments.append(line.lstrip('#').strip())
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labels = line.split()
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comments = []
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while (line := f.readline().strip()).startswith('#'):
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comments.append(line.lstrip('#').strip())
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labels = line.split()
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shapes = {}
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for label in labels:
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tensor_column = re.search(r'[0-9,x]*?:[0-9]*?_',label)
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if tensor_column:
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my_shape = tensor_column.group().split(':',1)[0].split('x')
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shapes[label.split('_',1)[1]] = tuple([int(d) for d in my_shape])
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else:
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vector_column = re.match(r'[0-9]*?_',label)
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if vector_column:
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shapes[label.split('_',1)[1]] = (int(label.split('_',1)[0]),)
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shapes = {}
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for label in labels:
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tensor_column = re.search(r'[0-9,x]*?:[0-9]*?_',label)
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if tensor_column:
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my_shape = tensor_column.group().split(':',1)[0].split('x')
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shapes[label.split('_',1)[1]] = tuple([int(d) for d in my_shape])
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else:
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shapes[label] = (1,)
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vector_column = re.match(r'[0-9]*?_',label)
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if vector_column:
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shapes[label.split('_',1)[1]] = (int(label.split('_',1)[0]),)
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else:
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shapes[label] = (1,)
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data = pd.read_csv(f,names=list(range(len(labels))),sep=r'\s+')
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data = pd.read_csv(f,names=list(range(len(labels))),sep=r'\s+')
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return Table(shapes,data,comments)
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@ -339,10 +339,9 @@ class Table:
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Table data from file.
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"""
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f = util.open_text(fname)
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f.seek(0)
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content = f.readlines()
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with util.open_text(fname) as f:
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f.seek(0)
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content = f.readlines()
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comments = [util.execution_stamp('Table','from_ang')]
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for line in content:
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@ -605,10 +604,9 @@ class Table:
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labels += [f'{util.srepr(self.shapes[l],"x")}:{i+1}_{l}' \
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for i in range(np.prod(self.shapes[l]))]
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f = util.open_text(fname,'w')
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f.write('\n'.join([f'# {c}' for c in self.comments] + [' '.join(labels)])+('\n' if labels else ''))
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try: # backward compatibility
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self.data.to_csv(f,sep=' ',na_rep='nan',index=False,header=False,lineterminator='\n')
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except TypeError:
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self.data.to_csv(f,sep=' ',na_rep='nan',index=False,header=False,line_terminator='\n')
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with util.open_text(fname,'w') as f:
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f.write('\n'.join([f'# {c}' for c in self.comments] + [' '.join(labels)])+('\n' if labels else ''))
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try: # backward compatibility
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self.data.to_csv(f,sep=' ',na_rep='nan',index=False,header=False,lineterminator='\n')
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except TypeError:
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self.data.to_csv(f,sep=' ',na_rep='nan',index=False,header=False,line_terminator='\n')
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@ -197,7 +197,9 @@ class YAML(dict):
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YAML from file.
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"""
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return cls(yaml.load(util.open_text(fname), Loader=SafeLoader))
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with util.open_text(fname) as fhandle:
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return cls(yaml.load(fhandle, Loader=SafeLoader))
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def save(self,
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fname: FileHandle,
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@ -220,12 +222,12 @@ class YAML(dict):
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if 'sort_keys' not in kwargs:
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kwargs['sort_keys'] = False
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fhandle = util.open_text(fname,'w')
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try:
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fhandle.write(yaml.dump(self,Dumper=NiceDumper,**kwargs))
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except TypeError: # compatibility with old pyyaml
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del kwargs['sort_keys']
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fhandle.write(yaml.dump(self,Dumper=NiceDumper,**kwargs))
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with util.open_text(fname,'w') as fhandle:
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try:
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fhandle.write(yaml.dump(self,Dumper=NiceDumper,**kwargs))
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except TypeError: # compatibility with old pyyaml
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del kwargs['sort_keys']
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fhandle.write(yaml.dump(self,Dumper=NiceDumper,**kwargs))
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@property
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@ -8,12 +8,13 @@ import shlex as _shlex
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import re as _re
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import signal as _signal
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import fractions as _fractions
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import contextlib as _contextlib
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from collections import abc as _abc, OrderedDict as _OrderedDict
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from functools import reduce as _reduce, partial as _partial, wraps as _wraps
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import inspect
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from typing import Optional as _Optional, Callable as _Callable, Union as _Union, Iterable as _Iterable, \
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Dict as _Dict, List as _List, Tuple as _Tuple, Literal as _Literal, \
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Any as _Any, TextIO as _TextIO
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Any as _Any, TextIO as _TextIO, Generator as _Generator
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from pathlib import Path as _Path
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import numpy as _np
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@ -193,11 +194,15 @@ def run(cmd: str,
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return stdout, stderr
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@_contextlib.contextmanager
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def open_text(fname: _FileHandle,
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mode: _Literal['r','w'] = 'r') -> _TextIO: # noqa
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mode: _Literal['r','w'] = 'r') -> _Generator[_TextIO, None, None]: # noqa
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"""
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Open a text file.
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Open a text file with Unix line endings
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If a path or string is given, a context manager ensures that
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the file handle is closed.
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If a file handle is given, it remains unmodified.
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Parameters
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----------
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@ -211,8 +216,12 @@ def open_text(fname: _FileHandle,
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f : file handle
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"""
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return fname if not isinstance(fname, (str,_Path)) else \
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open(_Path(fname).expanduser(),mode,newline=('\n' if mode == 'w' else None))
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if isinstance(fname, (str,_Path)):
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fhandle = open(_Path(fname).expanduser(),mode,newline=('\n' if mode == 'w' else None))
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yield fhandle
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fhandle.close()
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else:
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yield fname
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def execution_stamp(class_name: str,
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