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DAMASK_EICMD
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Merge branch 'PythonImprovements' into pytest

This commit is contained in:
Martin Diehl 2019-11-22 15:42:27 +01:00
parent a26a5738dd fad679a9a5
commit e5e3db8286
4 changed files with 46 additions and 45 deletions
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2
python/damask/__init__.py
View File

@ -2,7 +2,7 @@
import os
with open(os.path.join(os.path.dirname(__file__),'VERSION')) as f:
version = f.readline()[1:-1]
version = f.readline()[1:-1]
name = 'damask'

47
python/damask/asciitable.py
View File

@ -15,7 +15,7 @@ except NameError:
# ------------------------------------------------------------------
class ASCIItable():
"""Read and write to ASCII tables"""
"""Read and write to ASCII tables."""
tmpext = '_tmp' # filename extension for in-place access
@ -27,6 +27,7 @@ class ASCIItable():
labeled = True, # assume table has labels
readonly = False, # no reading from file
):
"""Read and write to ASCII tables."""
self.__IO__ = {'output': [],
'buffered': buffered,
'labeled': labeled, # header contains labels
@ -72,7 +73,7 @@ class ASCIItable():
# ------------------------------------------------------------------
def _removeCRLF(self,
string):
"""Delete any carriage return and line feed from string"""
"""Delete any carriage return and line feed from string."""
try:
return string.replace('\n','').replace('\r','')
except AttributeError:
@ -82,7 +83,7 @@ class ASCIItable():
# ------------------------------------------------------------------
def _quote(self,
what):
"""Quote empty or white space-containing output"""
"""Quote empty or white space-containing output."""
return '{quote}{content}{quote}'.format(
quote = ('"' if str(what)=='' or re.search(r"\s",str(what)) else ''),
content = what)
@ -103,7 +104,7 @@ class ASCIItable():
# ------------------------------------------------------------------
def output_write(self,
what):
"""Aggregate a single row (string) or list of (possibly containing further lists of) rows into output"""
"""Aggregate a single row (string) or list of (possibly containing further lists of) rows into output."""
if isinstance(what, (str, unicode)):
self.__IO__['output'] += [what]
else:
@ -143,7 +144,7 @@ class ASCIItable():
# ------------------------------------------------------------------
def head_read(self):
"""
Get column labels
Get column labels.
by either reading the first row or,
if keyword "head[*]" is present, the last line of the header
@ -154,7 +155,7 @@ class ASCIItable():
pass
firstline = self.__IO__['in'].readline().strip()
m = re.search('(\d+)\s+head', firstline.lower()) # search for "head" keyword
m = re.search(r'(\d+)\s+head', firstline.lower()) # search for "head" keyword
if m: # proper ASCIItable format
@ -194,7 +195,7 @@ class ASCIItable():
# ------------------------------------------------------------------
def head_write(self,
header = True):
"""Write current header information (info + labels)"""
"""Write current header information (info + labels)."""
head = ['{}\theader'.format(len(self.info)+self.__IO__['labeled'])] if header else []
head.append(self.info)
if self.__IO__['labeled']:
@ -205,7 +206,7 @@ class ASCIItable():
# ------------------------------------------------------------------
def head_getGeom(self):
"""Interpret geom header"""
"""Interpret geom header."""
identifiers = {
'grid': ['a','b','c'],
'size': ['x','y','z'],
@ -247,7 +248,7 @@ class ASCIItable():
def labels_append(self,
what,
reset = False):
"""Add item or list to existing set of labels (and switch on labeling)"""
"""Add item or list to existing set of labels (and switch on labeling)."""
if isinstance(what, (str, unicode)):
self.tags += [self._removeCRLF(what)]
else:
@ -261,7 +262,7 @@ class ASCIItable():
# ------------------------------------------------------------------
def labels_clear(self):
"""Delete existing labels and switch to no labeling"""
"""Delete existing labels and switch to no labeling."""
self.tags = []
self.__IO__['labeled'] = False
@ -392,7 +393,7 @@ class ASCIItable():
# ------------------------------------------------------------------
def info_append(self,
what):
"""Add item or list to existing set of infos"""
"""Add item or list to existing set of infos."""
if isinstance(what, (str, unicode)):
self.info += [self._removeCRLF(what)]
else:
@ -403,7 +404,7 @@ class ASCIItable():
# ------------------------------------------------------------------
def info_clear(self):
"""Delete any info block"""
"""Delete any info block."""
self.info = []
# ------------------------------------------------------------------
@ -416,7 +417,7 @@ class ASCIItable():
# ------------------------------------------------------------------
def data_skipLines(self,
count):
"""Wind forward by count number of lines"""
"""Wind forward by count number of lines."""
for i in range(count):
alive = self.data_read()
@ -426,7 +427,7 @@ class ASCIItable():
def data_read(self,
advance = True,
respectLabels = True):
"""Read next line (possibly buffered) and parse it into data array"""
"""Read next line (possibly buffered) and parse it into data array."""
self.line = self.__IO__['readBuffer'].pop(0) if len(self.__IO__['readBuffer']) > 0 \
else self.__IO__['in'].readline().strip() # take buffered content or get next data row from file
@ -446,9 +447,11 @@ class ASCIItable():
# ------------------------------------------------------------------
def data_readArray(self,
labels = []):
"""Read whole data of all (given) labels as numpy array"""
try: self.data_rewind() # try to wind back to start of data
except: pass # assume/hope we are at data start already...
"""Read whole data of all (given) labels as numpy array."""
try:
self.data_rewind() # try to wind back to start of data
except IOError:
pass # assume/hope we are at data start already...
if labels is None or labels == []:
use = None # use all columns (and keep labels intact)
@ -480,7 +483,7 @@ class ASCIItable():
# ------------------------------------------------------------------
def data_write(self,
delimiter = '\t'):
"""Write current data array and report alive output back"""
"""Write current data array and report alive output back."""
if len(self.data) == 0: return True
if isinstance(self.data[0],list):
@ -492,16 +495,16 @@ class ASCIItable():
def data_writeArray(self,
fmt = None,
delimiter = '\t'):
"""Write whole numpy array data"""
"""Write whole numpy array data."""
for row in self.data:
try:
output = [fmt % value for value in row] if fmt else list(map(repr,row))
except:
except Exception:
output = [fmt % row] if fmt else [repr(row)]
try:
self.__IO__['out'].write(delimiter.join(output) + '\n')
except:
except Exception:
pass
# ------------------------------------------------------------------
@ -545,7 +548,7 @@ class ASCIItable():
grid,
type = 'i',
strict = False):
"""Read microstructure data (from .geom format)"""
"""Read microstructure data (from .geom format)."""
def datatype(item):
return int(item) if type.lower() == 'i' else float(item)

39
python/damask/test/test.py → python/damask/test.py
View File

@ -15,7 +15,7 @@ class Test():
variants = []
def __init__(self, **kwargs):
"""New test."""
defaults = {'description': '',
'keep': False,
'accept': False,
@ -118,22 +118,22 @@ class Test():
"""Delete directory tree containing current results."""
try:
shutil.rmtree(self.dirCurrent())
except:
except FileNotFoundError:
logging.warning('removal of directory "{}" not possible...'.format(self.dirCurrent()))
try:
os.mkdir(self.dirCurrent())
return True
except:
except FileExistsError:
logging.critical('creation of directory "{}" failed.'.format(self.dirCurrent()))
return False
def prepareAll(self):
"""Do all necessary preparations for the whole test"""
"""Do all necessary preparations for the whole test."""
return True
def prepare(self,variant):
"""Do all necessary preparations for the run of each test variant"""
"""Do all necessary preparations for the run of each test variant."""
return True
@ -205,9 +205,9 @@ class Test():
for source,target in zip(list(map(mapA,A)),list(map(mapB,B))):
try:
shutil.copy2(source,target)
except:
except FileNotFoundError:
logging.critical('error copying {} to {}'.format(source,target))
raise
raise FileNotFoundError
def copy_Reference2Current(self,sourcefiles=[],targetfiles=[]):
@ -216,9 +216,9 @@ class Test():
for i,f in enumerate(sourcefiles):
try:
shutil.copy2(self.fileInReference(f),self.fileInCurrent(targetfiles[i]))
except:
except FileNotFoundError:
logging.critical('Reference2Current: Unable to copy file "{}"'.format(f))
raise
raise FileNotFoundError
def copy_Base2Current(self,sourceDir,sourcefiles=[],targetfiles=[]):
@ -228,10 +228,10 @@ class Test():
for i,f in enumerate(sourcefiles):
try:
shutil.copy2(os.path.join(source,f),self.fileInCurrent(targetfiles[i]))
except:
except FileNotFoundError:
logging.error(os.path.join(source,f))
logging.critical('Base2Current: Unable to copy file "{}"'.format(f))
raise
raise FileNotFoundError
def copy_Current2Reference(self,sourcefiles=[],targetfiles=[]):
@ -240,9 +240,9 @@ class Test():
for i,f in enumerate(sourcefiles):
try:
shutil.copy2(self.fileInCurrent(f),self.fileInReference(targetfiles[i]))
except:
except FileNotFoundError:
logging.critical('Current2Reference: Unable to copy file "{}"'.format(f))
raise
raise FileNotFoundError
def copy_Proof2Current(self,sourcefiles=[],targetfiles=[]):
@ -251,9 +251,9 @@ class Test():
for i,f in enumerate(sourcefiles):
try:
shutil.copy2(self.fileInProof(f),self.fileInCurrent(targetfiles[i]))
except:
except FileNotFoundError:
logging.critical('Proof2Current: Unable to copy file "{}"'.format(f))
raise
raise FileNotFoundError
def copy_Current2Current(self,sourcefiles=[],targetfiles=[]):
@ -261,9 +261,10 @@ class Test():
for i,f in enumerate(sourcefiles):
try:
shutil.copy2(self.fileInReference(f),self.fileInCurrent(targetfiles[i]))
except:
except FileNotFoundError:
logging.critical('Current2Current: Unable to copy file "{}"'.format(f))
raise
raise FileNotFoundError
def execute_inCurrentDir(self,cmd,streamIn=None,env=None):
@ -437,7 +438,7 @@ class Test():
stdTol = 1.0e-6,
preFilter = 1.0e-9):
"""
Calculate statistics of tables
Calculate statistics of tables.
threshold can be used to ignore small values (a negative number disables this feature)
"""
@ -490,7 +491,7 @@ class Test():
rtol = 1e-5,
atol = 1e-8,
debug = False):
"""Compare multiple tables with np.allclose"""
"""Compare multiple tables with np.allclose."""
if not (isinstance(files, Iterable) and not isinstance(files, str)): # check whether list of files is requested
files = [str(files)]

3
python/damask/test/__init__.py
View File

@ -1,3 +0,0 @@
"""Test functionality."""
from .test import Test # noqa