Merge branch 'PythonImprovements' into pytest
This commit is contained in:
commit
e5e3db8286
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@ -15,7 +15,7 @@ except NameError:
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# ------------------------------------------------------------------
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class ASCIItable():
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"""Read and write to ASCII tables"""
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"""Read and write to ASCII tables."""
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tmpext = '_tmp' # filename extension for in-place access
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@ -27,6 +27,7 @@ class ASCIItable():
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labeled = True, # assume table has labels
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readonly = False, # no reading from file
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):
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"""Read and write to ASCII tables."""
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self.__IO__ = {'output': [],
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'buffered': buffered,
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'labeled': labeled, # header contains labels
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@ -72,7 +73,7 @@ class ASCIItable():
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# ------------------------------------------------------------------
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def _removeCRLF(self,
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string):
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"""Delete any carriage return and line feed from string"""
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"""Delete any carriage return and line feed from string."""
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try:
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return string.replace('\n','').replace('\r','')
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except AttributeError:
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@ -82,7 +83,7 @@ class ASCIItable():
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# ------------------------------------------------------------------
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def _quote(self,
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what):
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"""Quote empty or white space-containing output"""
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"""Quote empty or white space-containing output."""
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return '{quote}{content}{quote}'.format(
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quote = ('"' if str(what)=='' or re.search(r"\s",str(what)) else ''),
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content = what)
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@ -103,7 +104,7 @@ class ASCIItable():
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# ------------------------------------------------------------------
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def output_write(self,
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what):
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"""Aggregate a single row (string) or list of (possibly containing further lists of) rows into output"""
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"""Aggregate a single row (string) or list of (possibly containing further lists of) rows into output."""
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if isinstance(what, (str, unicode)):
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self.__IO__['output'] += [what]
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else:
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@ -143,7 +144,7 @@ class ASCIItable():
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# ------------------------------------------------------------------
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def head_read(self):
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"""
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Get column labels
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Get column labels.
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by either reading the first row or,
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if keyword "head[*]" is present, the last line of the header
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@ -154,7 +155,7 @@ class ASCIItable():
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pass
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firstline = self.__IO__['in'].readline().strip()
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m = re.search('(\d+)\s+head', firstline.lower()) # search for "head" keyword
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m = re.search(r'(\d+)\s+head', firstline.lower()) # search for "head" keyword
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if m: # proper ASCIItable format
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@ -194,7 +195,7 @@ class ASCIItable():
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# ------------------------------------------------------------------
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def head_write(self,
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header = True):
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"""Write current header information (info + labels)"""
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"""Write current header information (info + labels)."""
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head = ['{}\theader'.format(len(self.info)+self.__IO__['labeled'])] if header else []
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head.append(self.info)
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if self.__IO__['labeled']:
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@ -205,7 +206,7 @@ class ASCIItable():
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# ------------------------------------------------------------------
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def head_getGeom(self):
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"""Interpret geom header"""
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"""Interpret geom header."""
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identifiers = {
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'grid': ['a','b','c'],
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'size': ['x','y','z'],
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@ -247,7 +248,7 @@ class ASCIItable():
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def labels_append(self,
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what,
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reset = False):
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"""Add item or list to existing set of labels (and switch on labeling)"""
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"""Add item or list to existing set of labels (and switch on labeling)."""
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if isinstance(what, (str, unicode)):
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self.tags += [self._removeCRLF(what)]
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else:
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@ -261,7 +262,7 @@ class ASCIItable():
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# ------------------------------------------------------------------
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def labels_clear(self):
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"""Delete existing labels and switch to no labeling"""
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"""Delete existing labels and switch to no labeling."""
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self.tags = []
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self.__IO__['labeled'] = False
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@ -392,7 +393,7 @@ class ASCIItable():
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# ------------------------------------------------------------------
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def info_append(self,
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what):
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"""Add item or list to existing set of infos"""
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"""Add item or list to existing set of infos."""
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if isinstance(what, (str, unicode)):
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self.info += [self._removeCRLF(what)]
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else:
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@ -403,7 +404,7 @@ class ASCIItable():
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# ------------------------------------------------------------------
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def info_clear(self):
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"""Delete any info block"""
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"""Delete any info block."""
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self.info = []
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# ------------------------------------------------------------------
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@ -416,7 +417,7 @@ class ASCIItable():
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# ------------------------------------------------------------------
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def data_skipLines(self,
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count):
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"""Wind forward by count number of lines"""
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"""Wind forward by count number of lines."""
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for i in range(count):
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alive = self.data_read()
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@ -426,7 +427,7 @@ class ASCIItable():
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def data_read(self,
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advance = True,
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respectLabels = True):
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"""Read next line (possibly buffered) and parse it into data array"""
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"""Read next line (possibly buffered) and parse it into data array."""
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self.line = self.__IO__['readBuffer'].pop(0) if len(self.__IO__['readBuffer']) > 0 \
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else self.__IO__['in'].readline().strip() # take buffered content or get next data row from file
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@ -446,9 +447,11 @@ class ASCIItable():
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# ------------------------------------------------------------------
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def data_readArray(self,
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labels = []):
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"""Read whole data of all (given) labels as numpy array"""
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try: self.data_rewind() # try to wind back to start of data
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except: pass # assume/hope we are at data start already...
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"""Read whole data of all (given) labels as numpy array."""
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try:
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self.data_rewind() # try to wind back to start of data
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except IOError:
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pass # assume/hope we are at data start already...
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if labels is None or labels == []:
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use = None # use all columns (and keep labels intact)
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@ -480,7 +483,7 @@ class ASCIItable():
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# ------------------------------------------------------------------
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def data_write(self,
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delimiter = '\t'):
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"""Write current data array and report alive output back"""
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"""Write current data array and report alive output back."""
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if len(self.data) == 0: return True
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if isinstance(self.data[0],list):
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@ -492,16 +495,16 @@ class ASCIItable():
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def data_writeArray(self,
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fmt = None,
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delimiter = '\t'):
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"""Write whole numpy array data"""
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"""Write whole numpy array data."""
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for row in self.data:
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try:
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output = [fmt % value for value in row] if fmt else list(map(repr,row))
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except:
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except Exception:
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output = [fmt % row] if fmt else [repr(row)]
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try:
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self.__IO__['out'].write(delimiter.join(output) + '\n')
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except:
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except Exception:
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pass
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# ------------------------------------------------------------------
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@ -545,7 +548,7 @@ class ASCIItable():
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grid,
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type = 'i',
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strict = False):
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"""Read microstructure data (from .geom format)"""
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"""Read microstructure data (from .geom format)."""
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def datatype(item):
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return int(item) if type.lower() == 'i' else float(item)
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@ -15,7 +15,7 @@ class Test():
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variants = []
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def __init__(self, **kwargs):
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"""New test."""
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defaults = {'description': '',
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'keep': False,
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'accept': False,
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@ -118,22 +118,22 @@ class Test():
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"""Delete directory tree containing current results."""
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try:
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shutil.rmtree(self.dirCurrent())
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except:
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except FileNotFoundError:
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logging.warning('removal of directory "{}" not possible...'.format(self.dirCurrent()))
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try:
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os.mkdir(self.dirCurrent())
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return True
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except:
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except FileExistsError:
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logging.critical('creation of directory "{}" failed.'.format(self.dirCurrent()))
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return False
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def prepareAll(self):
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"""Do all necessary preparations for the whole test"""
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"""Do all necessary preparations for the whole test."""
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return True
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def prepare(self,variant):
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"""Do all necessary preparations for the run of each test variant"""
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"""Do all necessary preparations for the run of each test variant."""
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return True
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@ -205,9 +205,9 @@ class Test():
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for source,target in zip(list(map(mapA,A)),list(map(mapB,B))):
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try:
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shutil.copy2(source,target)
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except:
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except FileNotFoundError:
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logging.critical('error copying {} to {}'.format(source,target))
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raise
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raise FileNotFoundError
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def copy_Reference2Current(self,sourcefiles=[],targetfiles=[]):
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@ -216,9 +216,9 @@ class Test():
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for i,f in enumerate(sourcefiles):
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try:
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shutil.copy2(self.fileInReference(f),self.fileInCurrent(targetfiles[i]))
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except:
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except FileNotFoundError:
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logging.critical('Reference2Current: Unable to copy file "{}"'.format(f))
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raise
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raise FileNotFoundError
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def copy_Base2Current(self,sourceDir,sourcefiles=[],targetfiles=[]):
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@ -228,10 +228,10 @@ class Test():
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for i,f in enumerate(sourcefiles):
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try:
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shutil.copy2(os.path.join(source,f),self.fileInCurrent(targetfiles[i]))
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except:
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except FileNotFoundError:
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logging.error(os.path.join(source,f))
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logging.critical('Base2Current: Unable to copy file "{}"'.format(f))
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raise
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raise FileNotFoundError
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def copy_Current2Reference(self,sourcefiles=[],targetfiles=[]):
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@ -240,9 +240,9 @@ class Test():
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for i,f in enumerate(sourcefiles):
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try:
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shutil.copy2(self.fileInCurrent(f),self.fileInReference(targetfiles[i]))
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except:
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except FileNotFoundError:
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logging.critical('Current2Reference: Unable to copy file "{}"'.format(f))
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raise
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raise FileNotFoundError
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def copy_Proof2Current(self,sourcefiles=[],targetfiles=[]):
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@ -251,9 +251,9 @@ class Test():
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for i,f in enumerate(sourcefiles):
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try:
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shutil.copy2(self.fileInProof(f),self.fileInCurrent(targetfiles[i]))
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except:
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except FileNotFoundError:
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logging.critical('Proof2Current: Unable to copy file "{}"'.format(f))
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raise
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raise FileNotFoundError
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def copy_Current2Current(self,sourcefiles=[],targetfiles=[]):
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@ -261,9 +261,10 @@ class Test():
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for i,f in enumerate(sourcefiles):
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try:
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shutil.copy2(self.fileInReference(f),self.fileInCurrent(targetfiles[i]))
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except:
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except FileNotFoundError:
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logging.critical('Current2Current: Unable to copy file "{}"'.format(f))
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raise
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raise FileNotFoundError
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def execute_inCurrentDir(self,cmd,streamIn=None,env=None):
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@ -437,7 +438,7 @@ class Test():
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stdTol = 1.0e-6,
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preFilter = 1.0e-9):
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"""
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Calculate statistics of tables
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Calculate statistics of tables.
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threshold can be used to ignore small values (a negative number disables this feature)
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"""
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@ -490,7 +491,7 @@ class Test():
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rtol = 1e-5,
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atol = 1e-8,
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debug = False):
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"""Compare multiple tables with np.allclose"""
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"""Compare multiple tables with np.allclose."""
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if not (isinstance(files, Iterable) and not isinstance(files, str)): # check whether list of files is requested
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files = [str(files)]
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@ -1,3 +0,0 @@
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"""Test functionality."""
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from .test import Test # noqa
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