def export_marker(marker: Mapping[str, Iterable[Tuple[str, str]]],
fname: str,
defaultpath: Optional[bool] = True):
"""Export marker pairs to json-File.
Parameters
----------
marker
Marker pairs as from :func:`~pypairs.pairs.sandbag`
fname
Name of the json-File in the writedir (see settings)
defaultpath
Use settings.writedir as root. Default: True
"""
if defaultpath:
fpath = settings.writedir + fname
else:
fpath = fname
try:
write_dict_to_json(marker, fpath)
logg.hint("marker pairs written to: " + str(fpath))
except IOError as e:
msg = "could not write to {}.".format(fpath) + \
"Please verify that the path exists and is writable. Or change `writedir` via `pypairs.settings.writedir`"
logg.error(msg)
logg.error(str(e))
def load_pandas(fname):
"""Load DataFrame or Series"""
try:
return pd.read_csv(fname, index_col=0)
except OSError as e:
logg.error("could not load cached files {}".format(fname))
logg.error(str(e))
def save_pandas(fname, data):
"""Save DataFrame or Series"""
if isinstance(data, DataFrame):
try:
data.to_csv(fname, header=True)
except IOError as e:
logg.warn("could not store cache to {}".format(fname))
logg.warn(str(e))
else:
logg.error("could not save object, `data` must be DataFrame")
def load_marker(fname: str, defaultpath: Optional[bool] = True):
"""Export marker pairs to json-File.
Parameters
----------
fname
Name of the json-File to write to
defaultpath
Use settings.writedir as root. Default: True
"""
if defaultpath:
fpath = settings.writedir + fname
else:
fpath = fname
try:
marker = read_dict_from_json(fpath)
except IOError:
logg.error(
"could not read from {}.\n Please verify that the path exists and is writable."
.format(fpath))
return None
if settings.verbosity > 2:
count_total = 0
count_str = []
for m, p in marker.items():
c = len(p)
count_total += c
count_str.append("\t{}: {}".format(m, c))
logg.hint("loaded {} marker pairs".format(count_total))
for s in count_str:
logg.hint(s)
return marker
def parallel_njit(func: Callable[[], Any],
jitted: Optional[bool] = True) -> Callable[[], Any]:
"""Dynamic decorator for jit-compiled functions.
Adds parallel=True if settings.n_jobs > 1
"""
if jitted is False or settings.enable_jit is False:
logg.warn(
'staring uncompiled processing. Should only be used for debug and testing!'
)
return func
if settings.n_jobs > 1:
if is_win32() is False:
logg.hint('staring parallel processing with {} threads'.format(
settings.n_jobs))
return njit(func, parallel=True, fastmath=settings.enable_fastmath)
else:
logg.error(
'n_jobs is set to {} but multiprocessing is not supported for your platform! '
'falling back to single core... '.format(settings.n_jobs))
return njit(func, fastmath=settings.enable_fastmath)
else:
logg.hint('staring processing with 1 thread')
return njit(func, fastmath=settings.enable_fastmath)