def upload(self, from_path, to_path):
"""
:param Text from_path:
:param Text to_path:
"""
# Emulate s3's flat storage by automatically creating directory path
_make_local_path(_os.path.dirname(to_path))
# Write the object to a local file in the sandbox
_copyfile(from_path, to_path)
def copyfile(old_fname, new_fname):
"""
Wrapper to copy a file
"""
if (RANK == 0):
try:
_copyfile(old_fname, new_fname)
except:
_copyfile(old_fname + '.npy', new_fname + '.npy')
def save(self, filename, latex='lualatex'):
with open(self._wdirname / 'Figure_{}.tikz'.format(self.index), 'w') as f:
self.write(f)
rv = _run(['latexmk', "-{}".format(latex), "-silent", "-jobname=Figure_{}".format(self.index),
self.viewdir / 'viewtemplate.tex'], cwd=self._wdir.name)
if rv.returncode != 0:
with open(self._wdirname / 'Figure_{}.log'.format(self.index)) as f:
print(f.read())
else:
_copyfile(self._wdirname / 'Figure_{}.pdf'.format(self.index), filename)
def copyfile(src, dst):
"""
Copy data from src to dst.
Change OVERRIDE mode to specify the operation when dst existed.
Examples
--------
.. code-block :: python
# to change the OVERRIDE operation
from longling.Architecture import config
config.OVERRIDE = False # skip existed dst
config.OVERRIDE = None # use console input to determine
config.OVERRIDE = False # override existed dst
"""
if override_check(dst):
_copyfile(src, dst)
def make_pelican_starter_project(c, path):
_make_sure_path_not_exists_but_parent_directory_does(path)
_mkdir(path)
_make_empty_content_tree(_join(path, 'content'))
_mkdir(_join(path, 'output'))
# skipping Makefile for now
src = _build_starter_dir_path()
# Copy over the config file (warnings without)
this = 'pelicanconf.py'
_copyfile(_join(src, this), _join(path, this))
# Copy the two pages over
head = 'content', 'pages'
for tail in 'my-one-page.md', 'my-other-page.md':
this = (*head, tail)
_copyfile(_join(src, *this), _join(path, *this))
def __init__(self,
root,
base_dir,
use_nestcheck,
transform=None,
overwrite_transformed=False,
**kwargs):
filerootpath = _os.path.join(base_dir, root)
_filerootpath = filerootpath
if transform is not None:
samples = _np.loadtxt(filerootpath + '.txt')
ndims = samples.shape[1] - 2
temp = transform(samples[0, 2:], old_API=True)
ntransform = len(temp) - ndims
_exists = _os.path.isfile(filerootpath + '_transformed.txt')
if not _exists or overwrite_transformed:
transformed = _np.zeros(
(samples.shape[0], samples.shape[1] + ntransform))
transformed[:, :2] = samples[:, :2]
for i in range(samples.shape[0]):
transformed[i, 2:] = transform(samples[i, 2:],
old_API=True)
_np.savetxt(filerootpath + '_transformed.txt', transformed)
filerootpath += '_transformed'
root += '_transformed'
super(NestedBackend, self).__init__(filepath=filerootpath + '.txt',
**kwargs)
if getdist is not None:
# getdist backend
self._gd_bcknd = MCSamples(
root=filerootpath,
settings=self.kde_settings,
sampler='nested',
names=self.names,
ranges=self.bounds,
labels=[self.labels[name] for name in self.names])
self._gd_bcknd.readChains(getdist.chains.chainFiles(filerootpath))
self.use_nestcheck = use_nestcheck
if self.use_nestcheck: # nestcheck backend
if transform is not None:
for ext in ['dead-birth.txt', 'phys_live-birth.txt']:
_exists = _os.path.isfile(filerootpath + ext)
if not _exists or overwrite_transformed:
samples = _np.loadtxt(_filerootpath + ext)
transformed = _np.zeros(
(samples.shape[0], samples.shape[1] + ntransform))
transformed[:, ndims + ntransform:] = samples[:,
ndims:]
for i in range(samples.shape[0]):
transformed[i,:ndims+ntransform] =\
transform(samples[i,:ndims],
old_API=True)
_np.savetxt(filerootpath + ext, transformed)
# .stats file with same root needed, but do not need to modify
# the .stats file contents
if not _os.path.isfile(filerootpath + '.stats'):
if _os.path.isfile(_filerootpath + '.stats'):
try:
from shutil import copyfile as _copyfile
except ImportError:
pass
else:
_copyfile(_filerootpath + '.stats',
filerootpath + '.stats')
try:
kwargs['implementation']
except KeyError:
print('Root %r sampling implementation not specified... '
'assuming MultiNest for nestcheck...')
self._nc_bcknd = process_multinest_run(root, base_dir=base_dir)
else:
if kwargs['implementation'] == 'multinest':
self._nc_bcknd = process_multinest_run(root,
base_dir=base_dir)
elif kwargs['implementation'] == 'polychord':
self._nc_bcknd = process_polychord_run(root,
base_dir=base_dir)
else:
raise ValueError('Cannot process with nestcheck.')
def download(self, from_path, to_path):
"""
:param Text from_path:
:param Text to_path:
"""
_copyfile(from_path, to_path)
def copyfile(src, dst):
print " copying from %s to %s" % (src, dst)
return _copyfile(src, dst)
def download(self, from_path, to_path):
"""
:param Text from_path:
:param Text to_path:
"""
_copyfile(strip_file_header(from_path), strip_file_header(to_path))
