repo stringlengths 7 55 | path stringlengths 4 223 | func_name stringlengths 1 134 | original_string stringlengths 75 104k | language stringclasses 1 value | code stringlengths 75 104k | code_tokens listlengths 19 28.4k | docstring stringlengths 1 46.9k | docstring_tokens listlengths 1 1.97k | sha stringlengths 40 40 | url stringlengths 87 315 | partition stringclasses 1 value |
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click-contrib/click-configfile | tasks/_vendor/pathlib.py | PurePath.with_name | def with_name(self, name):
"""Return a new path with the file name changed."""
if not self.name:
raise ValueError("%r has an empty name" % (self,))
return self._from_parsed_parts(self._drv, self._root,
self._parts[:-1] + [name]) | python | def with_name(self, name):
"""Return a new path with the file name changed."""
if not self.name:
raise ValueError("%r has an empty name" % (self,))
return self._from_parsed_parts(self._drv, self._root,
self._parts[:-1] + [name]) | [
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click-contrib/click-configfile | tasks/_vendor/pathlib.py | PurePath.with_suffix | def with_suffix(self, suffix):
"""Return a new path with the file suffix changed (or added, if none)."""
# XXX if suffix is None, should the current suffix be removed?
drv, root, parts = self._flavour.parse_parts((suffix,))
if drv or root or len(parts) != 1:
raise ValueError("Invalid suffix %r" % (suffix))
suffix = parts[0]
if not suffix.startswith('.'):
raise ValueError("Invalid suffix %r" % (suffix))
name = self.name
if not name:
raise ValueError("%r has an empty name" % (self,))
old_suffix = self.suffix
if not old_suffix:
name = name + suffix
else:
name = name[:-len(old_suffix)] + suffix
return self._from_parsed_parts(self._drv, self._root,
self._parts[:-1] + [name]) | python | def with_suffix(self, suffix):
"""Return a new path with the file suffix changed (or added, if none)."""
# XXX if suffix is None, should the current suffix be removed?
drv, root, parts = self._flavour.parse_parts((suffix,))
if drv or root or len(parts) != 1:
raise ValueError("Invalid suffix %r" % (suffix))
suffix = parts[0]
if not suffix.startswith('.'):
raise ValueError("Invalid suffix %r" % (suffix))
name = self.name
if not name:
raise ValueError("%r has an empty name" % (self,))
old_suffix = self.suffix
if not old_suffix:
name = name + suffix
else:
name = name[:-len(old_suffix)] + suffix
return self._from_parsed_parts(self._drv, self._root,
self._parts[:-1] + [name]) | [
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click-contrib/click-configfile | tasks/_vendor/pathlib.py | Path._raw_open | def _raw_open(self, flags, mode=0o777):
"""
Open the file pointed by this path and return a file descriptor,
as os.open() does.
"""
return self._accessor.open(self, flags, mode) | python | def _raw_open(self, flags, mode=0o777):
"""
Open the file pointed by this path and return a file descriptor,
as os.open() does.
"""
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click-contrib/click-configfile | tasks/_vendor/pathlib.py | Path.iterdir | def iterdir(self):
"""Iterate over the files in this directory. Does not yield any
result for the special paths '.' and '..'.
"""
for name in self._accessor.listdir(self):
if name in ('.', '..'):
# Yielding a path object for these makes little sense
continue
yield self._make_child_relpath(name) | python | def iterdir(self):
"""Iterate over the files in this directory. Does not yield any
result for the special paths '.' and '..'.
"""
for name in self._accessor.listdir(self):
if name in ('.', '..'):
# Yielding a path object for these makes little sense
continue
yield self._make_child_relpath(name) | [
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click-contrib/click-configfile | tasks/_vendor/pathlib.py | Path.absolute | def absolute(self):
"""Return an absolute version of this path. This function works
even if the path doesn't point to anything.
No normalization is done, i.e. all '.' and '..' will be kept along.
Use resolve() to get the canonical path to a file.
"""
# XXX untested yet!
if self.is_absolute():
return self
# FIXME this must defer to the specific flavour (and, under Windows,
# use nt._getfullpathname())
obj = self._from_parts([os.getcwd()] + self._parts, init=False)
obj._init(template=self)
return obj | python | def absolute(self):
"""Return an absolute version of this path. This function works
even if the path doesn't point to anything.
No normalization is done, i.e. all '.' and '..' will be kept along.
Use resolve() to get the canonical path to a file.
"""
# XXX untested yet!
if self.is_absolute():
return self
# FIXME this must defer to the specific flavour (and, under Windows,
# use nt._getfullpathname())
obj = self._from_parts([os.getcwd()] + self._parts, init=False)
obj._init(template=self)
return obj | [
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click-contrib/click-configfile | tasks/_vendor/pathlib.py | Path.resolve | def resolve(self):
"""
Make the path absolute, resolving all symlinks on the way and also
normalizing it (for example turning slashes into backslashes under
Windows).
"""
s = self._flavour.resolve(self)
if s is None:
# No symlink resolution => for consistency, raise an error if
# the path doesn't exist or is forbidden
self.stat()
s = str(self.absolute())
# Now we have no symlinks in the path, it's safe to normalize it.
normed = self._flavour.pathmod.normpath(s)
obj = self._from_parts((normed,), init=False)
obj._init(template=self)
return obj | python | def resolve(self):
"""
Make the path absolute, resolving all symlinks on the way and also
normalizing it (for example turning slashes into backslashes under
Windows).
"""
s = self._flavour.resolve(self)
if s is None:
# No symlink resolution => for consistency, raise an error if
# the path doesn't exist or is forbidden
self.stat()
s = str(self.absolute())
# Now we have no symlinks in the path, it's safe to normalize it.
normed = self._flavour.pathmod.normpath(s)
obj = self._from_parts((normed,), init=False)
obj._init(template=self)
return obj | [
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click-contrib/click-configfile | tasks/_vendor/pathlib.py | Path.open | def open(self, mode='r', buffering=-1, encoding=None,
errors=None, newline=None):
"""
Open the file pointed by this path and return a file object, as
the built-in open() function does.
"""
if sys.version_info >= (3, 3):
return io.open(str(self), mode, buffering, encoding, errors, newline,
opener=self._opener)
else:
return io.open(str(self), mode, buffering, encoding, errors, newline) | python | def open(self, mode='r', buffering=-1, encoding=None,
errors=None, newline=None):
"""
Open the file pointed by this path and return a file object, as
the built-in open() function does.
"""
if sys.version_info >= (3, 3):
return io.open(str(self), mode, buffering, encoding, errors, newline,
opener=self._opener)
else:
return io.open(str(self), mode, buffering, encoding, errors, newline) | [
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click-contrib/click-configfile | tasks/_vendor/pathlib.py | Path.replace | def replace(self, target):
"""
Rename this path to the given path, clobbering the existing
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"""
if sys.version_info < (3, 3):
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self._accessor.replace(self, target) | python | def replace(self, target):
"""
Rename this path to the given path, clobbering the existing
destination if it exists.
"""
if sys.version_info < (3, 3):
raise NotImplementedError("replace() is only available "
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click-contrib/click-configfile | tasks/_vendor/pathlib.py | Path.symlink_to | def symlink_to(self, target, target_is_directory=False):
"""
Make this path a symlink pointing to the given path.
Note the order of arguments (self, target) is the reverse of os.symlink's.
"""
self._accessor.symlink(target, self, target_is_directory) | python | def symlink_to(self, target, target_is_directory=False):
"""
Make this path a symlink pointing to the given path.
Note the order of arguments (self, target) is the reverse of os.symlink's.
"""
self._accessor.symlink(target, self, target_is_directory) | [
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click-contrib/click-configfile | tasks/_vendor/pathlib.py | Path.is_symlink | def is_symlink(self):
"""
Whether this path is a symbolic link.
"""
try:
return S_ISLNK(self.lstat().st_mode)
except OSError as e:
if e.errno != ENOENT:
raise
# Path doesn't exist
return False | python | def is_symlink(self):
"""
Whether this path is a symbolic link.
"""
try:
return S_ISLNK(self.lstat().st_mode)
except OSError as e:
if e.errno != ENOENT:
raise
# Path doesn't exist
return False | [
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click-contrib/click-configfile | tasks/_vendor/pathlib.py | Path.is_block_device | def is_block_device(self):
"""
Whether this path is a block device.
"""
try:
return S_ISBLK(self.stat().st_mode)
except OSError as e:
if e.errno != ENOENT:
raise
# Path doesn't exist or is a broken symlink
# (see https://bitbucket.org/pitrou/pathlib/issue/12/)
return False | python | def is_block_device(self):
"""
Whether this path is a block device.
"""
try:
return S_ISBLK(self.stat().st_mode)
except OSError as e:
if e.errno != ENOENT:
raise
# Path doesn't exist or is a broken symlink
# (see https://bitbucket.org/pitrou/pathlib/issue/12/)
return False | [
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click-contrib/click-configfile | tasks/_vendor/pathlib.py | Path.is_char_device | def is_char_device(self):
"""
Whether this path is a character device.
"""
try:
return S_ISCHR(self.stat().st_mode)
except OSError as e:
if e.errno != ENOENT:
raise
# Path doesn't exist or is a broken symlink
# (see https://bitbucket.org/pitrou/pathlib/issue/12/)
return False | python | def is_char_device(self):
"""
Whether this path is a character device.
"""
try:
return S_ISCHR(self.stat().st_mode)
except OSError as e:
if e.errno != ENOENT:
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creare-com/pydem | pydem/reader/my_types.py | grid_coords_from_corners | def grid_coords_from_corners(upper_left_corner, lower_right_corner, size):
''' Points are the outer edges of the UL and LR pixels. Size is rows, columns.
GC projection type is taken from Points. '''
assert upper_left_corner.wkt == lower_right_corner.wkt
geotransform = np.array([upper_left_corner.lon, -(upper_left_corner.lon - lower_right_corner.lon) / float(size[1]), 0,
upper_left_corner.lat, 0, -(upper_left_corner.lat - lower_right_corner.lat) / float(size[0])])
return GridCoordinates(geotransform=geotransform,
wkt=upper_left_corner.wkt,
y_size=size[0],
x_size=size[1]) | python | def grid_coords_from_corners(upper_left_corner, lower_right_corner, size):
''' Points are the outer edges of the UL and LR pixels. Size is rows, columns.
GC projection type is taken from Points. '''
assert upper_left_corner.wkt == lower_right_corner.wkt
geotransform = np.array([upper_left_corner.lon, -(upper_left_corner.lon - lower_right_corner.lon) / float(size[1]), 0,
upper_left_corner.lat, 0, -(upper_left_corner.lat - lower_right_corner.lat) / float(size[0])])
return GridCoordinates(geotransform=geotransform,
wkt=upper_left_corner.wkt,
y_size=size[0],
x_size=size[1]) | [
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creare-com/pydem | pydem/reader/my_types.py | GridCoordinates.intersects | def intersects(self, other_grid_coordinates):
""" returns True if the GC's overlap. """
ogc = other_grid_coordinates # alias
# for explanation: http://stackoverflow.com/questions/306316/determine-if-two-rectangles-overlap-each-other
# Note the flipped y-coord in this coord system.
ax1, ay1, ax2, ay2 = self.ULC.lon, self.ULC.lat, self.LRC.lon, self.LRC.lat
bx1, by1, bx2, by2 = ogc.ULC.lon, ogc.ULC.lat, ogc.LRC.lon, ogc.LRC.lat
if ((ax1 <= bx2) and (ax2 >= bx1) and (ay1 >= by2) and (ay2 <= by1)):
return True
else:
return False | python | def intersects(self, other_grid_coordinates):
""" returns True if the GC's overlap. """
ogc = other_grid_coordinates # alias
# for explanation: http://stackoverflow.com/questions/306316/determine-if-two-rectangles-overlap-each-other
# Note the flipped y-coord in this coord system.
ax1, ay1, ax2, ay2 = self.ULC.lon, self.ULC.lat, self.LRC.lon, self.LRC.lat
bx1, by1, bx2, by2 = ogc.ULC.lon, ogc.ULC.lat, ogc.LRC.lon, ogc.LRC.lat
if ((ax1 <= bx2) and (ax2 >= bx1) and (ay1 >= by2) and (ay2 <= by1)):
return True
else:
return False | [
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creare-com/pydem | pydem/reader/my_types.py | GridCoordinates.unique_str | def unique_str(self):
""" A string that (ideally) uniquely represents this GC object. This
helps with naming files for caching. 'Unique' is defined as 'If
GC1 != GC2, then GC1.unique_str() != GC2.unique_str()'; conversely,
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..note::Because of length/readability restrictions, this fxn ignores
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Example output:
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unique_str = "_".join(["%.3f" % f for f in self.geotransform] +
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if self.date is not None:
unique_str += '_' + str(self.date)
if self.time is not None:
unique_str += '_' + str(self.time)
return unique_str.replace(':', '_') | python | def unique_str(self):
""" A string that (ideally) uniquely represents this GC object. This
helps with naming files for caching. 'Unique' is defined as 'If
GC1 != GC2, then GC1.unique_str() != GC2.unique_str()'; conversely,
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..note::Because of length/readability restrictions, this fxn ignores
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Example output:
"-180.000_0.250_0.000_90.000_0.000_-0.251_512_612_2013-05-21_12_32_52.945000"
"""
unique_str = "_".join(["%.3f" % f for f in self.geotransform] +
["%d" % d for d in self.x_size, self.y_size]
)
if self.date is not None:
unique_str += '_' + str(self.date)
if self.time is not None:
unique_str += '_' + str(self.time)
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creare-com/pydem | pydem/reader/my_types.py | GridCoordinates._get_x_axis | def _get_x_axis(self):
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# 0,0 is top/left top top/left pixel. Actual x/y coord of that pixel are (.5,.5).
x_centers = np.linspace(.5, self.x_size - .5, self.x_size)
y_centers = x_centers * 0
return (self.geotransform[0]
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"""See http://www.gdal.org/gdal_datamodel.html for details."""
# 0,0 is top/left top top/left pixel. Actual x/y coord of that pixel are (.5,.5).
x_centers = np.linspace(.5, self.x_size - .5, self.x_size)
y_centers = x_centers * 0
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creare-com/pydem | pydem/reader/my_types.py | GridCoordinates._get_y_axis | def _get_y_axis(self):
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# 0,0 is top/left top top/left pixel. Actual x/y coord of that pixel are (.5,.5).
y_centers = np.linspace(.5, self.y_size - .5, self.y_size)
x_centers = y_centers * 0
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"""See http://www.gdal.org/gdal_datamodel.html for details."""
# 0,0 is top/left top top/left pixel. Actual x/y coord of that pixel are (.5,.5).
y_centers = np.linspace(.5, self.y_size - .5, self.y_size)
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creare-com/pydem | pydem/reader/my_types.py | GridCoordinates.raster_to_projection_coords | def raster_to_projection_coords(self, pixel_x, pixel_y):
""" Use pixel centers when appropriate.
See documentation for the GDAL function GetGeoTransform for details. """
h_px_py = np.array([1, pixel_x, pixel_y])
gt = np.array([[1, 0, 0], self.geotransform[0:3], self.geotransform[3:6]])
arr = np.inner(gt, h_px_py)
return arr[2], arr[1] | python | def raster_to_projection_coords(self, pixel_x, pixel_y):
""" Use pixel centers when appropriate.
See documentation for the GDAL function GetGeoTransform for details. """
h_px_py = np.array([1, pixel_x, pixel_y])
gt = np.array([[1, 0, 0], self.geotransform[0:3], self.geotransform[3:6]])
arr = np.inner(gt, h_px_py)
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creare-com/pydem | pydem/reader/my_types.py | GridCoordinates.projection_to_raster_coords | def projection_to_raster_coords(self, lat, lon):
""" Returns pixel centers.
See documentation for the GDAL function GetGeoTransform for details. """
r_px_py = np.array([1, lon, lat])
tg = inv(np.array([[1, 0, 0], self.geotransform[0:3], self.geotransform[3:6]]))
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""" Returns pixel centers.
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r_px_py = np.array([1, lon, lat])
tg = inv(np.array([[1, 0, 0], self.geotransform[0:3], self.geotransform[3:6]]))
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creare-com/pydem | pydem/reader/my_types.py | AbstractDataLayer.reproject_to_grid_coordinates | def reproject_to_grid_coordinates(self, grid_coordinates, interp=gdalconst.GRA_NearestNeighbour):
""" Reprojects data in this layer to match that in the GridCoordinates
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source_dataset = self.grid_coordinates._as_gdal_dataset()
dest_dataset = grid_coordinates._as_gdal_dataset()
rb = source_dataset.GetRasterBand(1)
rb.SetNoDataValue(NO_DATA_VALUE)
rb.WriteArray(np.ma.filled(self.raster_data, NO_DATA_VALUE))
gdal.ReprojectImage(source_dataset, dest_dataset,
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dest_layer = self.clone_traits()
dest_layer.grid_coordinates = grid_coordinates
rb = dest_dataset.GetRasterBand(1)
dest_layer.raster_data = np.ma.masked_values(rb.ReadAsArray(), NO_DATA_VALUE)
return dest_layer | python | def reproject_to_grid_coordinates(self, grid_coordinates, interp=gdalconst.GRA_NearestNeighbour):
""" Reprojects data in this layer to match that in the GridCoordinates
object. """
source_dataset = self.grid_coordinates._as_gdal_dataset()
dest_dataset = grid_coordinates._as_gdal_dataset()
rb = source_dataset.GetRasterBand(1)
rb.SetNoDataValue(NO_DATA_VALUE)
rb.WriteArray(np.ma.filled(self.raster_data, NO_DATA_VALUE))
gdal.ReprojectImage(source_dataset, dest_dataset,
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dest_dataset.GetProjection(),
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dest_layer = self.clone_traits()
dest_layer.grid_coordinates = grid_coordinates
rb = dest_dataset.GetRasterBand(1)
dest_layer.raster_data = np.ma.masked_values(rb.ReadAsArray(), NO_DATA_VALUE)
return dest_layer | [
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creare-com/pydem | pydem/reader/my_types.py | AbstractDataLayer.inpaint | def inpaint(self):
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filled = inpaint.replace_nans(np.ma.filled(self.raster_data, np.NAN).astype(np.float32), 3, 0.01, 2)
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creare-com/pydem | pydem/reader/my_types.py | AbstractRasterDataLayer.interp_value | def interp_value(self, lat, lon, indexed=False):
""" Lookup a pixel value in the raster data, performing linear interpolation
if necessary. Indexed ==> nearest neighbor (*fast*). """
(px, py) = self.grid_coordinates.projection_to_raster_coords(lat, lon)
if indexed:
return self.raster_data[round(py), round(px)]
else:
# from scipy.interpolate import interp2d
# f_interp = interp2d(self.grid_coordinates.x_axis, self.grid_coordinates.y_axis, self.raster_data, bounds_error=True)
# return f_interp(lon, lat)[0]
from scipy.ndimage import map_coordinates
ret = map_coordinates(self.raster_data, [[py], [px]], order=1) # linear interp
return ret[0] | python | def interp_value(self, lat, lon, indexed=False):
""" Lookup a pixel value in the raster data, performing linear interpolation
if necessary. Indexed ==> nearest neighbor (*fast*). """
(px, py) = self.grid_coordinates.projection_to_raster_coords(lat, lon)
if indexed:
return self.raster_data[round(py), round(px)]
else:
# from scipy.interpolate import interp2d
# f_interp = interp2d(self.grid_coordinates.x_axis, self.grid_coordinates.y_axis, self.raster_data, bounds_error=True)
# return f_interp(lon, lat)[0]
from scipy.ndimage import map_coordinates
ret = map_coordinates(self.raster_data, [[py], [px]], order=1) # linear interp
return ret[0] | [
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thefab/tornadis | tornadis/pool.py | ClientPool.get_connected_client | def get_connected_client(self):
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Returns:
A Future object with connected Client instance as a result
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raise tornado.gen.Return(client) | python | def get_connected_client(self):
"""Gets a connected Client object.
If max_size is reached, this method will block until a new client
object is available.
Returns:
A Future object with connected Client instance as a result
(or ClientError if there was a connection problem)
"""
if self.__sem is not None:
yield self.__sem.acquire()
client = None
newly_created, client = self._get_client_from_pool_or_make_it()
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thefab/tornadis | tornadis/pool.py | ClientPool.get_client_nowait | def get_client_nowait(self):
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Returns:
A Client instance (not necessary connected) as result (or None).
"""
if self.__sem is not None:
if self.__sem._value == 0:
return None
self.__sem.acquire()
_, client = self._get_client_from_pool_or_make_it()
return client | python | def get_client_nowait(self):
"""Gets a Client object (not necessary connected).
If max_size is reached, this method will return None (and won't block).
Returns:
A Client instance (not necessary connected) as result (or None).
"""
if self.__sem is not None:
if self.__sem._value == 0:
return None
self.__sem.acquire()
_, client = self._get_client_from_pool_or_make_it()
return client | [
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thefab/tornadis | tornadis/pool.py | ClientPool.connected_client | def connected_client(self):
"""Returns a ContextManagerFuture to be yielded in a with statement.
Returns:
A ContextManagerFuture object.
Examples:
>>> with (yield pool.connected_client()) as client:
# client is a connected tornadis.Client instance
# it will be automatically released to the pool thanks to
# the "with" keyword
reply = yield client.call("PING")
"""
future = self.get_connected_client()
cb = functools.partial(self._connected_client_release_cb, future)
return ContextManagerFuture(future, cb) | python | def connected_client(self):
"""Returns a ContextManagerFuture to be yielded in a with statement.
Returns:
A ContextManagerFuture object.
Examples:
>>> with (yield pool.connected_client()) as client:
# client is a connected tornadis.Client instance
# it will be automatically released to the pool thanks to
# the "with" keyword
reply = yield client.call("PING")
"""
future = self.get_connected_client()
cb = functools.partial(self._connected_client_release_cb, future)
return ContextManagerFuture(future, cb) | [
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thefab/tornadis | tornadis/pool.py | ClientPool.release_client | def release_client(self, client):
"""Releases a client object to the pool.
Args:
client: Client object.
"""
if isinstance(client, Client):
if not self._is_expired_client(client):
LOG.debug('Client is not expired. Adding back to pool')
self.__pool.append(client)
elif client.is_connected():
LOG.debug('Client is expired and connected. Disconnecting')
client.disconnect()
if self.__sem is not None:
self.__sem.release() | python | def release_client(self, client):
"""Releases a client object to the pool.
Args:
client: Client object.
"""
if isinstance(client, Client):
if not self._is_expired_client(client):
LOG.debug('Client is not expired. Adding back to pool')
self.__pool.append(client)
elif client.is_connected():
LOG.debug('Client is expired and connected. Disconnecting')
client.disconnect()
if self.__sem is not None:
self.__sem.release() | [
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thefab/tornadis | tornadis/pool.py | ClientPool.destroy | def destroy(self):
"""Disconnects all pooled client objects."""
while True:
try:
client = self.__pool.popleft()
if isinstance(client, Client):
client.disconnect()
except IndexError:
break | python | def destroy(self):
"""Disconnects all pooled client objects."""
while True:
try:
client = self.__pool.popleft()
if isinstance(client, Client):
client.disconnect()
except IndexError:
break | [
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thefab/tornadis | tornadis/pool.py | ClientPool.preconnect | def preconnect(self, size=-1):
"""(pre)Connects some or all redis clients inside the pool.
Args:
size (int): number of redis clients to build and to connect
(-1 means all clients if pool max_size > -1)
Raises:
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"""
if size == -1 and self.max_size == -1:
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limit = min(size, self.max_size) if size != -1 else self.max_size
clients = yield [self.get_connected_client() for _ in range(0, limit)]
for client in clients:
self.release_client(client) | python | def preconnect(self, size=-1):
"""(pre)Connects some or all redis clients inside the pool.
Args:
size (int): number of redis clients to build and to connect
(-1 means all clients if pool max_size > -1)
Raises:
ClientError: when size == -1 and pool max_size == -1
"""
if size == -1 and self.max_size == -1:
raise ClientError("size=-1 not allowed with pool max_size=-1")
limit = min(size, self.max_size) if size != -1 else self.max_size
clients = yield [self.get_connected_client() for _ in range(0, limit)]
for client in clients:
self.release_client(client) | [
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click-contrib/click-configfile | tasks/_setup.py | setup_path | def setup_path(invoke_minversion=None):
"""Setup python search and add ``TASKS_VENDOR_DIR`` (if available)."""
# print("INVOKE.tasks: setup_path")
if not os.path.isdir(TASKS_VENDOR_DIR):
print("SKIP: TASKS_VENDOR_DIR=%s is missing" % TASKS_VENDOR_DIR)
return
elif os.path.abspath(TASKS_VENDOR_DIR) in sys.path:
# -- SETUP ALREADY DONE:
# return
pass
use_vendor_bundles = os.environ.get("INVOKE_TASKS_USE_VENDOR_BUNDLES", "no")
if need_vendor_bundles(invoke_minversion):
use_vendor_bundles = "yes"
if use_vendor_bundles == "yes":
syspath_insert(0, os.path.abspath(TASKS_VENDOR_DIR))
if setup_path_for_bundle(INVOKE_BUNDLE, pos=1):
import invoke
bundle_path = os.path.relpath(INVOKE_BUNDLE, os.getcwd())
print("USING: %s (version: %s)" % (bundle_path, invoke.__version__))
else:
# -- BEST-EFFORT: May rescue something
syspath_append(os.path.abspath(TASKS_VENDOR_DIR))
setup_path_for_bundle(INVOKE_BUNDLE, pos=len(sys.path))
if DEBUG_SYSPATH:
for index, p in enumerate(sys.path):
print(" %d. %s" % (index, p)) | python | def setup_path(invoke_minversion=None):
"""Setup python search and add ``TASKS_VENDOR_DIR`` (if available)."""
# print("INVOKE.tasks: setup_path")
if not os.path.isdir(TASKS_VENDOR_DIR):
print("SKIP: TASKS_VENDOR_DIR=%s is missing" % TASKS_VENDOR_DIR)
return
elif os.path.abspath(TASKS_VENDOR_DIR) in sys.path:
# -- SETUP ALREADY DONE:
# return
pass
use_vendor_bundles = os.environ.get("INVOKE_TASKS_USE_VENDOR_BUNDLES", "no")
if need_vendor_bundles(invoke_minversion):
use_vendor_bundles = "yes"
if use_vendor_bundles == "yes":
syspath_insert(0, os.path.abspath(TASKS_VENDOR_DIR))
if setup_path_for_bundle(INVOKE_BUNDLE, pos=1):
import invoke
bundle_path = os.path.relpath(INVOKE_BUNDLE, os.getcwd())
print("USING: %s (version: %s)" % (bundle_path, invoke.__version__))
else:
# -- BEST-EFFORT: May rescue something
syspath_append(os.path.abspath(TASKS_VENDOR_DIR))
setup_path_for_bundle(INVOKE_BUNDLE, pos=len(sys.path))
if DEBUG_SYSPATH:
for index, p in enumerate(sys.path):
print(" %d. %s" % (index, p)) | [
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click-contrib/click-configfile | tasks/_setup.py | require_invoke_minversion | def require_invoke_minversion(min_version, verbose=False):
"""Ensures that :mod:`invoke` has at the least the :param:`min_version`.
Otherwise,
:param min_version: Minimal acceptable invoke version (as string).
:param verbose: Indicates if invoke.version should be shown.
:raises: VersionRequirementError=SystemExit if requirement fails.
"""
# -- REQUIRES: sys.path is setup and contains invoke
try:
import invoke
invoke_version = invoke.__version__
except ImportError:
invoke_version = "__NOT_INSTALLED"
if invoke_version < min_version:
message = "REQUIRE: invoke.version >= %s (but was: %s)" % \
(min_version, invoke_version)
message += "\nUSE: pip install invoke>=%s" % min_version
raise VersionRequirementError(message)
INVOKE_VERSION = os.environ.get("INVOKE_VERSION", None)
if verbose and not INVOKE_VERSION:
os.environ["INVOKE_VERSION"] = invoke_version
print("USING: invoke.version=%s" % invoke_version) | python | def require_invoke_minversion(min_version, verbose=False):
"""Ensures that :mod:`invoke` has at the least the :param:`min_version`.
Otherwise,
:param min_version: Minimal acceptable invoke version (as string).
:param verbose: Indicates if invoke.version should be shown.
:raises: VersionRequirementError=SystemExit if requirement fails.
"""
# -- REQUIRES: sys.path is setup and contains invoke
try:
import invoke
invoke_version = invoke.__version__
except ImportError:
invoke_version = "__NOT_INSTALLED"
if invoke_version < min_version:
message = "REQUIRE: invoke.version >= %s (but was: %s)" % \
(min_version, invoke_version)
message += "\nUSE: pip install invoke>=%s" % min_version
raise VersionRequirementError(message)
INVOKE_VERSION = os.environ.get("INVOKE_VERSION", None)
if verbose and not INVOKE_VERSION:
os.environ["INVOKE_VERSION"] = invoke_version
print("USING: invoke.version=%s" % invoke_version) | [
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click-contrib/click-configfile | click_configfile.py | matches_section | def matches_section(section_name):
"""Decorator for SectionSchema classes to define the mapping between
a config section schema class and one or more config sections with
matching name(s).
.. sourcecode::
@matches_section("foo")
class FooSchema(SectionSchema):
pass
@matches_section(["bar", "baz.*"])
class BarAndBazSchema(SectionSchema):
pass
.. sourcecode:: ini
# -- FILE: *.ini
[foo] # USE: FooSchema
...
[bar] # USE: BarAndBazSchema
...
[baz.alice] # USE: BarAndBazSchema
...
"""
section_names = section_name
if isinstance(section_name, six.string_types):
section_names = [section_name]
elif not isinstance(section_name, (list, tuple)):
raise ValueError("%r (expected: string, strings)" % section_name)
def decorator(cls):
class_section_names = getattr(cls, "section_names", None)
if class_section_names is None:
cls.section_names = list(section_names)
else:
# -- BETTER SUPPORT: For multiple decorators
# @matches_section("foo")
# @matches_section("bar.*")
# class Example(SectionSchema):
# pass
# assert Example.section_names == ["foo", "bar.*"]
approved = [name for name in section_names
if name not in cls.section_names]
cls.section_names = approved + cls.section_names
return cls
return decorator | python | def matches_section(section_name):
"""Decorator for SectionSchema classes to define the mapping between
a config section schema class and one or more config sections with
matching name(s).
.. sourcecode::
@matches_section("foo")
class FooSchema(SectionSchema):
pass
@matches_section(["bar", "baz.*"])
class BarAndBazSchema(SectionSchema):
pass
.. sourcecode:: ini
# -- FILE: *.ini
[foo] # USE: FooSchema
...
[bar] # USE: BarAndBazSchema
...
[baz.alice] # USE: BarAndBazSchema
...
"""
section_names = section_name
if isinstance(section_name, six.string_types):
section_names = [section_name]
elif not isinstance(section_name, (list, tuple)):
raise ValueError("%r (expected: string, strings)" % section_name)
def decorator(cls):
class_section_names = getattr(cls, "section_names", None)
if class_section_names is None:
cls.section_names = list(section_names)
else:
# -- BETTER SUPPORT: For multiple decorators
# @matches_section("foo")
# @matches_section("bar.*")
# class Example(SectionSchema):
# pass
# assert Example.section_names == ["foo", "bar.*"]
approved = [name for name in section_names
if name not in cls.section_names]
cls.section_names = approved + cls.section_names
return cls
return decorator | [
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@matches_section("foo")
class FooSchema(SectionSchema):
pass
@matches_section(["bar", "baz.*"])
class BarAndBazSchema(SectionSchema):
pass
.. sourcecode:: ini
# -- FILE: *.ini
[foo] # USE: FooSchema
...
[bar] # USE: BarAndBazSchema
...
[baz.alice] # USE: BarAndBazSchema
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click-contrib/click-configfile | click_configfile.py | assign_param_names | def assign_param_names(cls=None, param_class=None):
"""Class decorator to assign parameter name to instances of :class:`Param`.
.. sourcecode::
@assign_param_names
class ConfigSectionSchema(object):
alice = Param(type=str)
bob = Param(type=str)
assert ConfigSectionSchema.alice.name == "alice"
assert ConfigSectionSchema.bob.name == "bob"
.. sourcecode::
# -- NESTED ASSIGN: Covers also nested SectionSchema subclasses.
@assign_param_names
class ConfigSectionSchema(object):
class Foo(SectionSchema):
alice = Param(type=str)
bob = Param(type=str)
assert ConfigSectionSchema.Foo.alice.name == "alice"
assert ConfigSectionSchema.Foo.bob.name == "bob"
"""
if param_class is None:
param_class = Param
def decorate_class(cls):
for name, value in select_params_from_section_schema(cls, param_class,
deep=True):
# -- ANNOTATE PARAM: By assigning its name
if not value.name:
value.name = name
return cls
# -- DECORATOR LOGIC:
if cls is None:
# -- CASE: @assign_param_names
# -- CASE: @assign_param_names(...)
return decorate_class
else:
# -- CASE: @assign_param_names class X: ...
# -- CASE: assign_param_names(my_class)
# -- CASE: my_class = assign_param_names(my_class)
return decorate_class(cls) | python | def assign_param_names(cls=None, param_class=None):
"""Class decorator to assign parameter name to instances of :class:`Param`.
.. sourcecode::
@assign_param_names
class ConfigSectionSchema(object):
alice = Param(type=str)
bob = Param(type=str)
assert ConfigSectionSchema.alice.name == "alice"
assert ConfigSectionSchema.bob.name == "bob"
.. sourcecode::
# -- NESTED ASSIGN: Covers also nested SectionSchema subclasses.
@assign_param_names
class ConfigSectionSchema(object):
class Foo(SectionSchema):
alice = Param(type=str)
bob = Param(type=str)
assert ConfigSectionSchema.Foo.alice.name == "alice"
assert ConfigSectionSchema.Foo.bob.name == "bob"
"""
if param_class is None:
param_class = Param
def decorate_class(cls):
for name, value in select_params_from_section_schema(cls, param_class,
deep=True):
# -- ANNOTATE PARAM: By assigning its name
if not value.name:
value.name = name
return cls
# -- DECORATOR LOGIC:
if cls is None:
# -- CASE: @assign_param_names
# -- CASE: @assign_param_names(...)
return decorate_class
else:
# -- CASE: @assign_param_names class X: ...
# -- CASE: assign_param_names(my_class)
# -- CASE: my_class = assign_param_names(my_class)
return decorate_class(cls) | [
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.. sourcecode::
@assign_param_names
class ConfigSectionSchema(object):
alice = Param(type=str)
bob = Param(type=str)
assert ConfigSectionSchema.alice.name == "alice"
assert ConfigSectionSchema.bob.name == "bob"
.. sourcecode::
# -- NESTED ASSIGN: Covers also nested SectionSchema subclasses.
@assign_param_names
class ConfigSectionSchema(object):
class Foo(SectionSchema):
alice = Param(type=str)
bob = Param(type=str)
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click-contrib/click-configfile | click_configfile.py | select_params_from_section_schema | def select_params_from_section_schema(section_schema, param_class=Param,
deep=False):
"""Selects the parameters of a config section schema.
:param section_schema: Configuration file section schema to use.
:return: Generator of params
"""
# pylint: disable=invalid-name
for name, value in inspect.getmembers(section_schema):
if name.startswith("__") or value is None:
continue # pragma: no cover
elif inspect.isclass(value) and deep:
# -- CASE: class => SELF-CALL (recursively).
# pylint: disable= bad-continuation
cls = value
for name, value in select_params_from_section_schema(cls,
param_class=param_class, deep=True):
yield (name, value)
elif isinstance(value, param_class):
yield (name, value) | python | def select_params_from_section_schema(section_schema, param_class=Param,
deep=False):
"""Selects the parameters of a config section schema.
:param section_schema: Configuration file section schema to use.
:return: Generator of params
"""
# pylint: disable=invalid-name
for name, value in inspect.getmembers(section_schema):
if name.startswith("__") or value is None:
continue # pragma: no cover
elif inspect.isclass(value) and deep:
# -- CASE: class => SELF-CALL (recursively).
# pylint: disable= bad-continuation
cls = value
for name, value in select_params_from_section_schema(cls,
param_class=param_class, deep=True):
yield (name, value)
elif isinstance(value, param_class):
yield (name, value) | [
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click-contrib/click-configfile | click_configfile.py | parse_config_section | def parse_config_section(config_section, section_schema):
"""Parse a config file section (INI file) by using its schema/description.
.. sourcecode::
import configparser # -- NOTE: Use backport for Python2
import click
from click_configfile import SectionSchema, Param, parse_config_section
class ConfigSectionSchema(object):
class Foo(SectionSchema):
name = Param(type=str)
flag = Param(type=bool)
numbers = Param(type=int, multiple=True)
filenames = Param(type=click.Path(), multiple=True)
parser = configparser.ConfigParser()
parser.read(["foo.ini"])
config_section = parser["foo"]
data = parse_config_section(config_section, ConfigSectionSchema.Foo)
# -- FAILS WITH: click.BadParameter if conversion errors occur.
.. sourcecode:: ini
# -- FILE: foo.ini
[foo]
name = Alice
flag = yes # true, false, yes, no (case-insensitive)
numbers = 1 4 9 16 25
filenames = foo/xxx.txt
bar/baz/zzz.txt
:param config_section: Config section to parse
:param section_schema: Schema/description of config section (w/ Param).
:return: Retrieved data, values converted to described types.
:raises: click.BadParameter, if conversion error occurs.
"""
storage = {}
for name, param in select_params_from_section_schema(section_schema):
value = config_section.get(name, None)
if value is None:
if param.default is None:
continue
value = param.default
else:
value = param.parse(value)
# -- DIAGNOSTICS:
# print(" %s = %s" % (name, repr(value)))
storage[name] = value
return storage | python | def parse_config_section(config_section, section_schema):
"""Parse a config file section (INI file) by using its schema/description.
.. sourcecode::
import configparser # -- NOTE: Use backport for Python2
import click
from click_configfile import SectionSchema, Param, parse_config_section
class ConfigSectionSchema(object):
class Foo(SectionSchema):
name = Param(type=str)
flag = Param(type=bool)
numbers = Param(type=int, multiple=True)
filenames = Param(type=click.Path(), multiple=True)
parser = configparser.ConfigParser()
parser.read(["foo.ini"])
config_section = parser["foo"]
data = parse_config_section(config_section, ConfigSectionSchema.Foo)
# -- FAILS WITH: click.BadParameter if conversion errors occur.
.. sourcecode:: ini
# -- FILE: foo.ini
[foo]
name = Alice
flag = yes # true, false, yes, no (case-insensitive)
numbers = 1 4 9 16 25
filenames = foo/xxx.txt
bar/baz/zzz.txt
:param config_section: Config section to parse
:param section_schema: Schema/description of config section (w/ Param).
:return: Retrieved data, values converted to described types.
:raises: click.BadParameter, if conversion error occurs.
"""
storage = {}
for name, param in select_params_from_section_schema(section_schema):
value = config_section.get(name, None)
if value is None:
if param.default is None:
continue
value = param.default
else:
value = param.parse(value)
# -- DIAGNOSTICS:
# print(" %s = %s" % (name, repr(value)))
storage[name] = value
return storage | [
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import configparser # -- NOTE: Use backport for Python2
import click
from click_configfile import SectionSchema, Param, parse_config_section
class ConfigSectionSchema(object):
class Foo(SectionSchema):
name = Param(type=str)
flag = Param(type=bool)
numbers = Param(type=int, multiple=True)
filenames = Param(type=click.Path(), multiple=True)
parser = configparser.ConfigParser()
parser.read(["foo.ini"])
config_section = parser["foo"]
data = parse_config_section(config_section, ConfigSectionSchema.Foo)
# -- FAILS WITH: click.BadParameter if conversion errors occur.
.. sourcecode:: ini
# -- FILE: foo.ini
[foo]
name = Alice
flag = yes # true, false, yes, no (case-insensitive)
numbers = 1 4 9 16 25
filenames = foo/xxx.txt
bar/baz/zzz.txt
:param config_section: Config section to parse
:param section_schema: Schema/description of config section (w/ Param).
:return: Retrieved data, values converted to described types.
:raises: click.BadParameter, if conversion error occurs. | [
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click-contrib/click-configfile | click_configfile.py | generate_configfile_names | def generate_configfile_names(config_files, config_searchpath=None):
"""Generates all configuration file name combinations to read.
.. sourcecode::
# -- ALGORITHM:
# First basenames/directories are prefered and override other files.
for config_path in reversed(config_searchpath):
for config_basename in reversed(config_files):
config_fname = os.path.join(config_path, config_basename)
if os.path.isfile(config_fname):
yield config_fname
:param config_files: List of config file basenames.
:param config_searchpath: List of directories to look for config files.
:return: List of available configuration file names (as generator)
"""
if config_searchpath is None:
config_searchpath = ["."]
for config_path in reversed(config_searchpath):
for config_basename in reversed(config_files):
config_fname = os.path.join(config_path, config_basename)
if os.path.isfile(config_fname):
# MAYBE: yield os.path.normpath(config_fname)
yield config_fname | python | def generate_configfile_names(config_files, config_searchpath=None):
"""Generates all configuration file name combinations to read.
.. sourcecode::
# -- ALGORITHM:
# First basenames/directories are prefered and override other files.
for config_path in reversed(config_searchpath):
for config_basename in reversed(config_files):
config_fname = os.path.join(config_path, config_basename)
if os.path.isfile(config_fname):
yield config_fname
:param config_files: List of config file basenames.
:param config_searchpath: List of directories to look for config files.
:return: List of available configuration file names (as generator)
"""
if config_searchpath is None:
config_searchpath = ["."]
for config_path in reversed(config_searchpath):
for config_basename in reversed(config_files):
config_fname = os.path.join(config_path, config_basename)
if os.path.isfile(config_fname):
# MAYBE: yield os.path.normpath(config_fname)
yield config_fname | [
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click-contrib/click-configfile | click_configfile.py | select_config_sections | def select_config_sections(configfile_sections, desired_section_patterns):
"""Select a subset of the sections in a configuration file by using
a list of section names of list of section name patters
(supporting :mod:`fnmatch` wildcards).
:param configfile_sections: List of config section names (as strings).
:param desired_section_patterns:
:return: List of selected section names or empty list (as generator).
"""
for section_name in configfile_sections:
for desired_section_pattern in desired_section_patterns:
if fnmatch(section_name, desired_section_pattern):
yield section_name | python | def select_config_sections(configfile_sections, desired_section_patterns):
"""Select a subset of the sections in a configuration file by using
a list of section names of list of section name patters
(supporting :mod:`fnmatch` wildcards).
:param configfile_sections: List of config section names (as strings).
:param desired_section_patterns:
:return: List of selected section names or empty list (as generator).
"""
for section_name in configfile_sections:
for desired_section_pattern in desired_section_patterns:
if fnmatch(section_name, desired_section_pattern):
yield section_name | [
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click-contrib/click-configfile | click_configfile.py | SectionSchema.matches_section | def matches_section(cls, section_name, supported_section_names=None):
"""Indicates if this schema can be used for a config section
by using the section name.
:param section_name: Config section name to check.
:return: True, if this schema can be applied to the config section.
:return: Fals, if this schema does not match the config section.
"""
if supported_section_names is None:
supported_section_names = getattr(cls, "section_names", None)
# pylint: disable=invalid-name
for supported_section_name_or_pattern in supported_section_names:
if fnmatch(section_name, supported_section_name_or_pattern):
return True
# -- OTHERWISE:
return False | python | def matches_section(cls, section_name, supported_section_names=None):
"""Indicates if this schema can be used for a config section
by using the section name.
:param section_name: Config section name to check.
:return: True, if this schema can be applied to the config section.
:return: Fals, if this schema does not match the config section.
"""
if supported_section_names is None:
supported_section_names = getattr(cls, "section_names", None)
# pylint: disable=invalid-name
for supported_section_name_or_pattern in supported_section_names:
if fnmatch(section_name, supported_section_name_or_pattern):
return True
# -- OTHERWISE:
return False | [
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click-contrib/click-configfile | click_configfile.py | ConfigFileReader.collect_config_sections_from_schemas | def collect_config_sections_from_schemas(cls, config_section_schemas=None):
# pylint: disable=invalid-name
"""Derive support config section names from config section schemas.
If no :param:`config_section_schemas` are provided, the schemas from
this class are used (normally defined in the DerivedClass).
:param config_section_schemas: List of config section schema classes.
:return: List of config section names or name patterns (as string).
"""
if config_section_schemas is None:
config_section_schemas = cls.config_section_schemas
collected = []
for schema in config_section_schemas:
collected.extend(schema.section_names)
# -- MAYBE BETTER:
# for name in schema.section_names:
# if name not in collected:
# collected.append(name)
return collected | python | def collect_config_sections_from_schemas(cls, config_section_schemas=None):
# pylint: disable=invalid-name
"""Derive support config section names from config section schemas.
If no :param:`config_section_schemas` are provided, the schemas from
this class are used (normally defined in the DerivedClass).
:param config_section_schemas: List of config section schema classes.
:return: List of config section names or name patterns (as string).
"""
if config_section_schemas is None:
config_section_schemas = cls.config_section_schemas
collected = []
for schema in config_section_schemas:
collected.extend(schema.section_names)
# -- MAYBE BETTER:
# for name in schema.section_names:
# if name not in collected:
# collected.append(name)
return collected | [
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click-contrib/click-configfile | click_configfile.py | ConfigFileReader.process_config_section | def process_config_section(cls, config_section, storage):
"""Process the config section and store the extracted data in
the param:`storage` (as outgoing param).
"""
# -- CONCEPT:
# if not storage:
# # -- INIT DATA: With default parts.
# storage.update(dict(_PERSONS={}))
schema = cls.select_config_schema_for(config_section.name)
if not schema:
message = "No schema found for: section=%s"
raise LookupError(message % config_section.name)
# -- PARSE AND STORE CONFIG SECTION:
section_storage = cls.select_storage_for(config_section.name, storage)
section_data = parse_config_section(config_section, schema)
section_storage.update(section_data) | python | def process_config_section(cls, config_section, storage):
"""Process the config section and store the extracted data in
the param:`storage` (as outgoing param).
"""
# -- CONCEPT:
# if not storage:
# # -- INIT DATA: With default parts.
# storage.update(dict(_PERSONS={}))
schema = cls.select_config_schema_for(config_section.name)
if not schema:
message = "No schema found for: section=%s"
raise LookupError(message % config_section.name)
# -- PARSE AND STORE CONFIG SECTION:
section_storage = cls.select_storage_for(config_section.name, storage)
section_data = parse_config_section(config_section, schema)
section_storage.update(section_data) | [
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click-contrib/click-configfile | click_configfile.py | ConfigFileReader.select_config_schema_for | def select_config_schema_for(cls, section_name):
"""Select the config schema that matches the config section (by name).
:param section_name: Config section name (as key).
:return: Config section schmema to use (subclass of: SectionSchema).
"""
# pylint: disable=cell-var-from-loop, redefined-outer-name
for section_schema in cls.config_section_schemas:
schema_matches = getattr(section_schema, "matches_section", None)
if schema_matches is None:
# -- OTHER SCHEMA CLASS: Reuse SectionSchema functionality.
schema_matches = lambda name: SectionSchema.matches_section(
name, section_schema.section_names)
if schema_matches(section_name):
return section_schema
return None | python | def select_config_schema_for(cls, section_name):
"""Select the config schema that matches the config section (by name).
:param section_name: Config section name (as key).
:return: Config section schmema to use (subclass of: SectionSchema).
"""
# pylint: disable=cell-var-from-loop, redefined-outer-name
for section_schema in cls.config_section_schemas:
schema_matches = getattr(section_schema, "matches_section", None)
if schema_matches is None:
# -- OTHER SCHEMA CLASS: Reuse SectionSchema functionality.
schema_matches = lambda name: SectionSchema.matches_section(
name, section_schema.section_names)
if schema_matches(section_name):
return section_schema
return None | [
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click-contrib/click-configfile | click_configfile.py | ConfigFileReader.select_storage_for | def select_storage_for(cls, section_name, storage):
"""Selects the data storage for a config section within the
:param:`storage`. The primary config section is normally merged into
the :param:`storage`.
:param section_name: Config section (name) to process.
:param storage: Data storage to use.
:return: :param:`storage` or a part of it (as section storage).
"""
section_storage = storage
storage_name = cls.get_storage_name_for(section_name)
if storage_name:
section_storage = storage.get(storage_name, None)
if section_storage is None:
section_storage = storage[storage_name] = dict()
return section_storage | python | def select_storage_for(cls, section_name, storage):
"""Selects the data storage for a config section within the
:param:`storage`. The primary config section is normally merged into
the :param:`storage`.
:param section_name: Config section (name) to process.
:param storage: Data storage to use.
:return: :param:`storage` or a part of it (as section storage).
"""
section_storage = storage
storage_name = cls.get_storage_name_for(section_name)
if storage_name:
section_storage = storage.get(storage_name, None)
if section_storage is None:
section_storage = storage[storage_name] = dict()
return section_storage | [
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:param section_name: Config section (name) to process.
:param storage: Data storage to use.
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click-contrib/click-configfile | tasks/clean.py | clean | def clean(ctx, dry_run=False):
"""Cleanup temporary dirs/files to regain a clean state."""
# -- VARIATION-POINT 1: Allow user to override in configuration-file
directories = ctx.clean.directories
files = ctx.clean.files
# -- VARIATION-POINT 2: Allow user to add more files/dirs to be removed.
extra_directories = ctx.clean.extra_directories or []
extra_files = ctx.clean.extra_files or []
if extra_directories:
directories.extend(extra_directories)
if extra_files:
files.extend(extra_files)
# -- PERFORM CLEANUP:
execute_cleanup_tasks(ctx, cleanup_tasks, dry_run=dry_run)
cleanup_dirs(directories, dry_run=dry_run)
cleanup_files(files, dry_run=dry_run) | python | def clean(ctx, dry_run=False):
"""Cleanup temporary dirs/files to regain a clean state."""
# -- VARIATION-POINT 1: Allow user to override in configuration-file
directories = ctx.clean.directories
files = ctx.clean.files
# -- VARIATION-POINT 2: Allow user to add more files/dirs to be removed.
extra_directories = ctx.clean.extra_directories or []
extra_files = ctx.clean.extra_files or []
if extra_directories:
directories.extend(extra_directories)
if extra_files:
files.extend(extra_files)
# -- PERFORM CLEANUP:
execute_cleanup_tasks(ctx, cleanup_tasks, dry_run=dry_run)
cleanup_dirs(directories, dry_run=dry_run)
cleanup_files(files, dry_run=dry_run) | [
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click-contrib/click-configfile | tasks/clean.py | clean_all | def clean_all(ctx, dry_run=False):
"""Clean up everything, even the precious stuff.
NOTE: clean task is executed first.
"""
cleanup_dirs(ctx.clean_all.directories or [], dry_run=dry_run)
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execute_cleanup_tasks(ctx, cleanup_all_tasks, dry_run=dry_run)
clean(ctx, dry_run=dry_run) | python | def clean_all(ctx, dry_run=False):
"""Clean up everything, even the precious stuff.
NOTE: clean task is executed first.
"""
cleanup_dirs(ctx.clean_all.directories or [], dry_run=dry_run)
cleanup_dirs(ctx.clean_all.extra_directories or [], dry_run=dry_run)
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click-contrib/click-configfile | tasks/clean.py | clean_python | def clean_python(ctx, dry_run=False):
"""Cleanup python related files/dirs: *.pyc, *.pyo, ..."""
# MAYBE NOT: "**/__pycache__"
cleanup_dirs(["build", "dist", "*.egg-info", "**/__pycache__"],
dry_run=dry_run)
if not dry_run:
ctx.run("py.cleanup")
cleanup_files(["**/*.pyc", "**/*.pyo", "**/*$py.class"], dry_run=dry_run) | python | def clean_python(ctx, dry_run=False):
"""Cleanup python related files/dirs: *.pyc, *.pyo, ..."""
# MAYBE NOT: "**/__pycache__"
cleanup_dirs(["build", "dist", "*.egg-info", "**/__pycache__"],
dry_run=dry_run)
if not dry_run:
ctx.run("py.cleanup")
cleanup_files(["**/*.pyc", "**/*.pyo", "**/*$py.class"], dry_run=dry_run) | [
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click-contrib/click-configfile | tasks/clean.py | cleanup_files | def cleanup_files(patterns, dry_run=False, workdir="."):
"""Remove files or files selected by file patterns.
Skips removal if file does not exist.
:param patterns: File patterns, like "**/*.pyc" (as list).
:param dry_run: Dry-run mode indicator (as bool).
:param workdir: Current work directory (default=".")
"""
current_dir = Path(workdir)
python_basedir = Path(Path(sys.executable).dirname()).joinpath("..").abspath()
error_message = None
error_count = 0
for file_pattern in patterns:
for file_ in path_glob(file_pattern, current_dir):
if file_.abspath().startswith(python_basedir):
# -- PROTECT CURRENTLY USED VIRTUAL ENVIRONMENT:
continue
if dry_run:
print("REMOVE: %s (dry-run)" % file_)
else:
print("REMOVE: %s" % file_)
try:
file_.remove_p()
except os.error as e:
message = "%s: %s" % (e.__class__.__name__, e)
print(message + " basedir: "+ python_basedir)
error_count += 1
if not error_message:
error_message = message
if False and error_message:
class CleanupError(RuntimeError): pass
raise CleanupError(error_message) | python | def cleanup_files(patterns, dry_run=False, workdir="."):
"""Remove files or files selected by file patterns.
Skips removal if file does not exist.
:param patterns: File patterns, like "**/*.pyc" (as list).
:param dry_run: Dry-run mode indicator (as bool).
:param workdir: Current work directory (default=".")
"""
current_dir = Path(workdir)
python_basedir = Path(Path(sys.executable).dirname()).joinpath("..").abspath()
error_message = None
error_count = 0
for file_pattern in patterns:
for file_ in path_glob(file_pattern, current_dir):
if file_.abspath().startswith(python_basedir):
# -- PROTECT CURRENTLY USED VIRTUAL ENVIRONMENT:
continue
if dry_run:
print("REMOVE: %s (dry-run)" % file_)
else:
print("REMOVE: %s" % file_)
try:
file_.remove_p()
except os.error as e:
message = "%s: %s" % (e.__class__.__name__, e)
print(message + " basedir: "+ python_basedir)
error_count += 1
if not error_message:
error_message = message
if False and error_message:
class CleanupError(RuntimeError): pass
raise CleanupError(error_message) | [
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click-contrib/click-configfile | tasks/clean.py | path_glob | def path_glob(pattern, current_dir=None):
"""Use pathlib for ant-like patterns, like: "**/*.py"
:param pattern: File/directory pattern to use (as string).
:param current_dir: Current working directory (as Path, pathlib.Path, str)
:return Resolved Path (as path.Path).
"""
if not current_dir:
current_dir = pathlib.Path.cwd()
elif not isinstance(current_dir, pathlib.Path):
# -- CASE: string, path.Path (string-like)
current_dir = pathlib.Path(str(current_dir))
for p in current_dir.glob(pattern):
yield Path(str(p)) | python | def path_glob(pattern, current_dir=None):
"""Use pathlib for ant-like patterns, like: "**/*.py"
:param pattern: File/directory pattern to use (as string).
:param current_dir: Current working directory (as Path, pathlib.Path, str)
:return Resolved Path (as path.Path).
"""
if not current_dir:
current_dir = pathlib.Path.cwd()
elif not isinstance(current_dir, pathlib.Path):
# -- CASE: string, path.Path (string-like)
current_dir = pathlib.Path(str(current_dir))
for p in current_dir.glob(pattern):
yield Path(str(p)) | [
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thefab/tornadis | tornadis/pipeline.py | Pipeline.stack_call | def stack_call(self, *args):
"""Stacks a redis command inside the object.
The syntax is the same than the call() method a Client class.
Args:
*args: full redis command as variable length argument list.
Examples:
>>> pipeline = Pipeline()
>>> pipeline.stack_call("HSET", "key", "field", "value")
>>> pipeline.stack_call("PING")
>>> pipeline.stack_call("INCR", "key2")
"""
self.pipelined_args.append(args)
self.number_of_stacked_calls = self.number_of_stacked_calls + 1 | python | def stack_call(self, *args):
"""Stacks a redis command inside the object.
The syntax is the same than the call() method a Client class.
Args:
*args: full redis command as variable length argument list.
Examples:
>>> pipeline = Pipeline()
>>> pipeline.stack_call("HSET", "key", "field", "value")
>>> pipeline.stack_call("PING")
>>> pipeline.stack_call("INCR", "key2")
"""
self.pipelined_args.append(args)
self.number_of_stacked_calls = self.number_of_stacked_calls + 1 | [
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thefab/tornadis | tornadis/connection.py | Connection.connect | def connect(self):
"""Connects the object to the host:port.
Returns:
Future: a Future object with True as result if the connection
process was ok.
"""
if self.is_connected() or self.is_connecting():
raise tornado.gen.Return(True)
if self.unix_domain_socket is None:
self.__socket = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
if self.tcp_nodelay:
self.__socket.setsockopt(socket.IPPROTO_TCP,
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else:
if not os.path.exists(self.unix_domain_socket):
LOG.warning("can't connect to %s, file does not exist",
self.unix_domain_socket)
raise tornado.gen.Return(False)
self.__socket = socket.socket(socket.AF_UNIX, socket.SOCK_STREAM)
self.__socket.setblocking(0)
self.__periodic_callback.start()
try:
LOG.debug("connecting to %s...", self._redis_server())
self._state.set_connecting()
if self.unix_domain_socket is None:
self.__socket.connect((self.host, self.port))
else:
self.__socket.connect(self.unix_domain_socket)
except socket.error as e:
if (errno_from_exception(e) not in _ERRNO_INPROGRESS and
errno_from_exception(e) not in _ERRNO_WOULDBLOCK):
self.disconnect()
LOG.warning("can't connect to %s", self._redis_server())
raise tornado.gen.Return(False)
self.__socket_fileno = self.__socket.fileno()
self._register_or_update_event_handler()
yield self._state.get_changed_state_future()
if not self.is_connected():
LOG.warning("can't connect to %s", self._redis_server())
raise tornado.gen.Return(False)
else:
LOG.debug("connected to %s", self._redis_server())
self.__socket_fileno = self.__socket.fileno()
self._state.set_connected()
self._register_or_update_event_handler()
raise tornado.gen.Return(True) | python | def connect(self):
"""Connects the object to the host:port.
Returns:
Future: a Future object with True as result if the connection
process was ok.
"""
if self.is_connected() or self.is_connecting():
raise tornado.gen.Return(True)
if self.unix_domain_socket is None:
self.__socket = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
if self.tcp_nodelay:
self.__socket.setsockopt(socket.IPPROTO_TCP,
socket.TCP_NODELAY, 1)
else:
if not os.path.exists(self.unix_domain_socket):
LOG.warning("can't connect to %s, file does not exist",
self.unix_domain_socket)
raise tornado.gen.Return(False)
self.__socket = socket.socket(socket.AF_UNIX, socket.SOCK_STREAM)
self.__socket.setblocking(0)
self.__periodic_callback.start()
try:
LOG.debug("connecting to %s...", self._redis_server())
self._state.set_connecting()
if self.unix_domain_socket is None:
self.__socket.connect((self.host, self.port))
else:
self.__socket.connect(self.unix_domain_socket)
except socket.error as e:
if (errno_from_exception(e) not in _ERRNO_INPROGRESS and
errno_from_exception(e) not in _ERRNO_WOULDBLOCK):
self.disconnect()
LOG.warning("can't connect to %s", self._redis_server())
raise tornado.gen.Return(False)
self.__socket_fileno = self.__socket.fileno()
self._register_or_update_event_handler()
yield self._state.get_changed_state_future()
if not self.is_connected():
LOG.warning("can't connect to %s", self._redis_server())
raise tornado.gen.Return(False)
else:
LOG.debug("connected to %s", self._redis_server())
self.__socket_fileno = self.__socket.fileno()
self._state.set_connected()
self._register_or_update_event_handler()
raise tornado.gen.Return(True) | [
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thefab/tornadis | tornadis/connection.py | Connection.disconnect | def disconnect(self):
"""Disconnects the object.
Safe method (no exception, even if it's already disconnected or if
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"""
if not self.is_connected() and not self.is_connecting():
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LOG.debug("disconnected from %s", self._redis_server()) | python | def disconnect(self):
"""Disconnects the object.
Safe method (no exception, even if it's already disconnected or if
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"""
if not self.is_connected() and not self.is_connecting():
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self._listened_events = 0
except Exception:
pass
self.__socket_fileno = -1
try:
self.__socket.close()
except Exception:
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self._state.set_disconnected()
self._close_callback()
LOG.debug("disconnected from %s", self._redis_server()) | [
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thefab/tornadis | tornadis/connection.py | Connection.write | def write(self, data):
"""Buffers some data to be sent to the host:port in a non blocking way.
So the data is always buffered and not sent on the socket in a
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You can give a WriteBuffer as parameter. The internal Connection
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data (str or WriteBuffer): string (or WriteBuffer) to write to
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"""Buffers some data to be sent to the host:port in a non blocking way.
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data (str or WriteBuffer): string (or WriteBuffer) to write to
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if isinstance(data, WriteBuffer):
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self._write_buffer.append(data)
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self._handle_write()
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click-contrib/click-configfile | tasks/_vendor/path.py | surrogate_escape | def surrogate_escape(error):
"""
Simulate the Python 3 ``surrogateescape`` handler, but for Python 2 only.
"""
chars = error.object[error.start:error.end]
assert len(chars) == 1
val = ord(chars)
val += 0xdc00
return __builtin__.unichr(val), error.end | python | def surrogate_escape(error):
"""
Simulate the Python 3 ``surrogateescape`` handler, but for Python 2 only.
"""
chars = error.object[error.start:error.end]
assert len(chars) == 1
val = ord(chars)
val += 0xdc00
return __builtin__.unichr(val), error.end | [
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click-contrib/click-configfile | tasks/_vendor/path.py | Path._always_unicode | def _always_unicode(cls, path):
"""
Ensure the path as retrieved from a Python API, such as :func:`os.listdir`,
is a proper Unicode string.
"""
if PY3 or isinstance(path, text_type):
return path
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"""
if PY3 or isinstance(path, text_type):
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click-contrib/click-configfile | tasks/_vendor/path.py | Path.namebase | def namebase(self):
""" The same as :meth:`name`, but with one file extension stripped off.
For example,
``Path('/home/guido/python.tar.gz').name == 'python.tar.gz'``,
but
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base, ext = self.module.splitext(self.name)
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""" The same as :meth:`name`, but with one file extension stripped off.
For example,
``Path('/home/guido/python.tar.gz').name == 'python.tar.gz'``,
but
``Path('/home/guido/python.tar.gz').namebase == 'python.tar'``.
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click-contrib/click-configfile | tasks/_vendor/path.py | Path.listdir | def listdir(self, pattern=None):
""" D.listdir() -> List of items in this directory.
Use :meth:`files` or :meth:`dirs` instead if you want a listing
of just files or just subdirectories.
The elements of the list are Path objects.
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pattern = '*'
return [
self / child
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""" D.listdir() -> List of items in this directory.
Use :meth:`files` or :meth:`dirs` instead if you want a listing
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The elements of the list are Path objects.
With the optional `pattern` argument, this only lists
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.. seealso:: :meth:`files`, :meth:`dirs`
"""
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pattern = '*'
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click-contrib/click-configfile | tasks/_vendor/path.py | Path.dirs | def dirs(self, pattern=None):
""" D.dirs() -> List of this directory's subdirectories.
The elements of the list are Path objects.
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"""
return [p for p in self.listdir(pattern) if p.isdir()] | python | def dirs(self, pattern=None):
""" D.dirs() -> List of this directory's subdirectories.
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click-contrib/click-configfile | tasks/_vendor/path.py | Path.files | def files(self, pattern=None):
""" D.files() -> List of the files in this directory.
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""" D.files() -> List of the files in this directory.
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click-contrib/click-configfile | tasks/_vendor/path.py | Path.walkdirs | def walkdirs(self, pattern=None, errors='strict'):
""" D.walkdirs() -> iterator over subdirs, recursively.
With the optional `pattern` argument, this yields only
directories whose names match the given pattern. For
example, ``mydir.walkdirs('*test')`` yields only directories
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return
else:
raise
for child in dirs:
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yield child
for subsubdir in child.walkdirs(pattern, errors):
yield subsubdir | python | def walkdirs(self, pattern=None, errors='strict'):
""" D.walkdirs() -> iterator over subdirs, recursively.
With the optional `pattern` argument, this yields only
directories whose names match the given pattern. For
example, ``mydir.walkdirs('*test')`` yields only directories
with names ending in ``'test'``.
The `errors=` keyword argument controls behavior when an
error occurs. The default is ``'strict'``, which causes an
exception. The other allowed values are ``'warn'`` (which
reports the error via :func:`warnings.warn()`), and ``'ignore'``.
"""
if errors not in ('strict', 'warn', 'ignore'):
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try:
dirs = self.dirs()
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return
elif errors == 'warn':
warnings.warn(
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click-contrib/click-configfile | tasks/_vendor/path.py | Path.walkfiles | def walkfiles(self, pattern=None, errors='strict'):
""" D.walkfiles() -> iterator over files in D, recursively.
The optional argument `pattern` limits the results to files
with names that match the pattern. For example,
``mydir.walkfiles('*.tmp')`` yields only files with the ``.tmp``
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"""
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continue
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continue
else:
raise
if isfile:
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yield child
elif isdir:
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yield f | python | def walkfiles(self, pattern=None, errors='strict'):
""" D.walkfiles() -> iterator over files in D, recursively.
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continue
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click-contrib/click-configfile | tasks/_vendor/path.py | Path.open | def open(self, *args, **kwargs):
""" Open this file and return a corresponding :class:`file` object.
Keyword arguments work as in :func:`io.open`. If the file cannot be
opened, an :class:`~exceptions.OSError` is raised.
"""
with io_error_compat():
return io.open(self, *args, **kwargs) | python | def open(self, *args, **kwargs):
""" Open this file and return a corresponding :class:`file` object.
Keyword arguments work as in :func:`io.open`. If the file cannot be
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click-contrib/click-configfile | tasks/_vendor/path.py | Path.write_text | def write_text(self, text, encoding=None, errors='strict',
linesep=os.linesep, append=False):
r""" Write the given text to this file.
The default behavior is to overwrite any existing file;
to append instead, use the `append=True` keyword argument.
There are two differences between :meth:`write_text` and
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`text` - str/unicode - The text to be written.
`encoding` - str - The Unicode encoding that will be used.
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`errors` - str - How to handle Unicode encoding errors.
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`linesep` - keyword argument - str/unicode - The sequence of
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`append` - keyword argument - bool - Specifies what to do if
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``False``: overwrite it.) The default is ``False``.
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``write_text()`` converts all standard end-of-line sequences
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end-of-line sequence (see :data:`os.linesep`; on Windows, for example,
the end-of-line marker is ``'\r\n'``).
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This applies to Unicode text the same as to 8-bit text, except
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(This is slightly different from when you open a file for
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--- Unicode
If `text` isn't Unicode, then apart from newline handling, the
bytes are written verbatim to the file. The `encoding` and
`errors` arguments are not used and must be omitted.
If `text` is Unicode, it is first converted to :func:`bytes` using the
specified `encoding` (or the default encoding if `encoding`
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"""
if isinstance(text, text_type):
if linesep is not None:
text = U_NEWLINE.sub(linesep, text)
text = text.encode(encoding or sys.getdefaultencoding(), errors)
else:
assert encoding is None
text = NEWLINE.sub(linesep, text)
self.write_bytes(text, append=append) | python | def write_text(self, text, encoding=None, errors='strict',
linesep=os.linesep, append=False):
r""" Write the given text to this file.
The default behavior is to overwrite any existing file;
to append instead, use the `append=True` keyword argument.
There are two differences between :meth:`write_text` and
:meth:`write_bytes`: newline handling and Unicode handling.
See below.
Parameters:
`text` - str/unicode - The text to be written.
`encoding` - str - The Unicode encoding that will be used.
This is ignored if `text` isn't a Unicode string.
`errors` - str - How to handle Unicode encoding errors.
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options. This is ignored if `text` isn't a Unicode
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`linesep` - keyword argument - str/unicode - The sequence of
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`append` - keyword argument - bool - Specifies what to do if
the file already exists (``True``: append to the end of it;
``False``: overwrite it.) The default is ``False``.
--- Newline handling.
``write_text()`` converts all standard end-of-line sequences
(``'\n'``, ``'\r'``, and ``'\r\n'``) to your platform's default
end-of-line sequence (see :data:`os.linesep`; on Windows, for example,
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This applies to Unicode text the same as to 8-bit text, except
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(This is slightly different from when you open a file for
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if isinstance(text, text_type):
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text = U_NEWLINE.sub(linesep, text)
text = text.encode(encoding or sys.getdefaultencoding(), errors)
else:
assert encoding is None
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self.write_bytes(text, append=append) | [
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--- Unicode
If `text` isn't Unicode, then apart from newline handling, the
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click-contrib/click-configfile | tasks/_vendor/path.py | Path.write_lines | def write_lines(self, lines, encoding=None, errors='strict',
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r""" Write the given lines of text to this file.
By default this overwrites any existing file at this path.
This puts a platform-specific newline sequence on every line.
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Use the keyword argument ``append=True`` to append lines to the
file. The default is to overwrite the file.
.. warning ::
When you use this with Unicode data, if the encoding of the
existing data in the file is different from the encoding
you specify with the `encoding=` parameter, the result is
mixed-encoding data, which can really confuse someone trying
to read the file later.
"""
with self.open('ab' if append else 'wb') as f:
for l in lines:
isUnicode = isinstance(l, text_type)
if linesep is not None:
pattern = U_NL_END if isUnicode else NL_END
l = pattern.sub('', l) + linesep
if isUnicode:
l = l.encode(encoding or sys.getdefaultencoding(), errors)
f.write(l) | python | def write_lines(self, lines, encoding=None, errors='strict',
linesep=os.linesep, append=False):
r""" Write the given lines of text to this file.
By default this overwrites any existing file at this path.
This puts a platform-specific newline sequence on every line.
See `linesep` below.
`lines` - A list of strings.
`encoding` - A Unicode encoding to use. This applies only if
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`errors` - How to handle errors in Unicode encoding. This
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linesep - The desired line-ending. This line-ending is
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Use the keyword argument ``append=True`` to append lines to the
file. The default is to overwrite the file.
.. warning ::
When you use this with Unicode data, if the encoding of the
existing data in the file is different from the encoding
you specify with the `encoding=` parameter, the result is
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to read the file later.
"""
with self.open('ab' if append else 'wb') as f:
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if linesep is not None:
pattern = U_NL_END if isUnicode else NL_END
l = pattern.sub('', l) + linesep
if isUnicode:
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click-contrib/click-configfile | tasks/_vendor/path.py | Path.mkdir_p | def mkdir_p(self, mode=0o777):
""" Like :meth:`mkdir`, but does not raise an exception if the
directory already exists. """
try:
self.mkdir(mode)
except OSError:
_, e, _ = sys.exc_info()
if e.errno != errno.EEXIST:
raise
return self | python | def mkdir_p(self, mode=0o777):
""" Like :meth:`mkdir`, but does not raise an exception if the
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click-contrib/click-configfile | tasks/_vendor/path.py | Path.makedirs_p | def makedirs_p(self, mode=0o777):
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""" Like :meth:`makedirs`, but does not raise an exception if the
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click-contrib/click-configfile | tasks/_vendor/path.py | Path.rmdir_p | def rmdir_p(self):
""" Like :meth:`rmdir`, but does not raise an exception if the
directory is not empty or does not exist. """
try:
self.rmdir()
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_, e, _ = sys.exc_info()
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return self | python | def rmdir_p(self):
""" Like :meth:`rmdir`, but does not raise an exception if the
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try:
self.rmdir()
except OSError:
_, e, _ = sys.exc_info()
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click-contrib/click-configfile | tasks/_vendor/path.py | Path.removedirs_p | def removedirs_p(self):
""" Like :meth:`removedirs`, but does not raise an exception if the
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try:
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_, e, _ = sys.exc_info()
if e.errno != errno.ENOTEMPTY and e.errno != errno.EEXIST:
raise
return self | python | def removedirs_p(self):
""" Like :meth:`removedirs`, but does not raise an exception if the
directory is not empty or does not exist. """
try:
self.removedirs()
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_, e, _ = sys.exc_info()
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click-contrib/click-configfile | tasks/_vendor/path.py | Path.remove_p | def remove_p(self):
""" Like :meth:`remove`, but does not raise an exception if the
file does not exist. """
try:
self.unlink()
except OSError:
_, e, _ = sys.exc_info()
if e.errno != errno.ENOENT:
raise
return self | python | def remove_p(self):
""" Like :meth:`remove`, but does not raise an exception if the
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try:
self.unlink()
except OSError:
_, e, _ = sys.exc_info()
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click-contrib/click-configfile | tasks/_vendor/path.py | Path.rmtree_p | def rmtree_p(self):
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try:
self.rmtree()
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""" Like :meth:`rmtree`, but does not raise an exception if the
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click-contrib/click-configfile | tasks/_vendor/path.py | Path.merge_tree | def merge_tree(self, dst, symlinks=False, *args, **kwargs):
"""
Copy entire contents of self to dst, overwriting existing
contents in dst with those in self.
If the additional keyword `update` is True, each
`src` will only be copied if `dst` does not exist,
or `src` is newer than `dst`.
Note that the technique employed stages the files in a temporary
directory first, so this function is not suitable for merging
trees with large files, especially if the temporary directory
is not capable of storing a copy of the entire source tree.
"""
update = kwargs.pop('update', False)
with tempdir() as _temp_dir:
# first copy the tree to a stage directory to support
# the parameters and behavior of copytree.
stage = _temp_dir / str(hash(self))
self.copytree(stage, symlinks, *args, **kwargs)
# now copy everything from the stage directory using
# the semantics of dir_util.copy_tree
dir_util.copy_tree(stage, dst, preserve_symlinks=symlinks,
update=update) | python | def merge_tree(self, dst, symlinks=False, *args, **kwargs):
"""
Copy entire contents of self to dst, overwriting existing
contents in dst with those in self.
If the additional keyword `update` is True, each
`src` will only be copied if `dst` does not exist,
or `src` is newer than `dst`.
Note that the technique employed stages the files in a temporary
directory first, so this function is not suitable for merging
trees with large files, especially if the temporary directory
is not capable of storing a copy of the entire source tree.
"""
update = kwargs.pop('update', False)
with tempdir() as _temp_dir:
# first copy the tree to a stage directory to support
# the parameters and behavior of copytree.
stage = _temp_dir / str(hash(self))
self.copytree(stage, symlinks, *args, **kwargs)
# now copy everything from the stage directory using
# the semantics of dir_util.copy_tree
dir_util.copy_tree(stage, dst, preserve_symlinks=symlinks,
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creare-com/pydem | pydem/reader/gdal_reader.py | GdalReader.__gdal_dataset_default | def __gdal_dataset_default(self):
"""DiskReader implementation."""
if not os.path.exists(self.file_name):
return None
if os.path.splitext(self.file_name)[1].lower() not in self.file_types:
raise RuntimeError('Filename %s does not have extension type %s.' % (self.file_name, self.file_types))
dataset = gdal.OpenShared(self.file_name, gdalconst.GA_ReadOnly)
if dataset is None:
raise ValueError('Dataset %s did not load properly.' % self.file_name)
# Sanity checks.
assert dataset.RasterCount > 0
# Seems okay...
return dataset | python | def __gdal_dataset_default(self):
"""DiskReader implementation."""
if not os.path.exists(self.file_name):
return None
if os.path.splitext(self.file_name)[1].lower() not in self.file_types:
raise RuntimeError('Filename %s does not have extension type %s.' % (self.file_name, self.file_types))
dataset = gdal.OpenShared(self.file_name, gdalconst.GA_ReadOnly)
if dataset is None:
raise ValueError('Dataset %s did not load properly.' % self.file_name)
# Sanity checks.
assert dataset.RasterCount > 0
# Seems okay...
return dataset | [
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thefab/tornadis | tornadis/client.py | Client.connect | def connect(self):
"""Connects the client object to redis.
It's safe to use this method even if you are already connected.
Note: this method is useless with autoconnect mode (default).
Returns:
a Future object with True as result if the connection was ok.
"""
if self.is_connected():
raise tornado.gen.Return(True)
cb1 = self._read_callback
cb2 = self._close_callback
self.__callback_queue = collections.deque()
self._reply_list = []
self.__reader = hiredis.Reader(replyError=ClientError)
kwargs = self.connection_kwargs
self.__connection = Connection(cb1, cb2, **kwargs)
connection_status = yield self.__connection.connect()
if connection_status is not True:
# nothing left to do here, return
raise tornado.gen.Return(False)
if self.password is not None:
authentication_status = yield self._call('AUTH', self.password)
if authentication_status != b'OK':
# incorrect password, return back the result
LOG.warning("impossible to connect: bad password")
self.__connection.disconnect()
raise tornado.gen.Return(False)
if self.db != 0:
db_status = yield self._call('SELECT', self.db)
if db_status != b'OK':
LOG.warning("can't select db %s", self.db)
raise tornado.gen.Return(False)
raise tornado.gen.Return(True) | python | def connect(self):
"""Connects the client object to redis.
It's safe to use this method even if you are already connected.
Note: this method is useless with autoconnect mode (default).
Returns:
a Future object with True as result if the connection was ok.
"""
if self.is_connected():
raise tornado.gen.Return(True)
cb1 = self._read_callback
cb2 = self._close_callback
self.__callback_queue = collections.deque()
self._reply_list = []
self.__reader = hiredis.Reader(replyError=ClientError)
kwargs = self.connection_kwargs
self.__connection = Connection(cb1, cb2, **kwargs)
connection_status = yield self.__connection.connect()
if connection_status is not True:
# nothing left to do here, return
raise tornado.gen.Return(False)
if self.password is not None:
authentication_status = yield self._call('AUTH', self.password)
if authentication_status != b'OK':
# incorrect password, return back the result
LOG.warning("impossible to connect: bad password")
self.__connection.disconnect()
raise tornado.gen.Return(False)
if self.db != 0:
db_status = yield self._call('SELECT', self.db)
if db_status != b'OK':
LOG.warning("can't select db %s", self.db)
raise tornado.gen.Return(False)
raise tornado.gen.Return(True) | [
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thefab/tornadis | tornadis/client.py | Client._close_callback | def _close_callback(self):
"""Callback called when redis closed the connection.
The callback queue is emptied and we call each callback found
with None or with an exception object to wake up blocked client.
"""
while True:
try:
callback = self.__callback_queue.popleft()
callback(ConnectionError("closed connection"))
except IndexError:
break
if self.subscribed:
# pubsub clients
self._reply_list.append(ConnectionError("closed connection"))
self._condition.notify_all() | python | def _close_callback(self):
"""Callback called when redis closed the connection.
The callback queue is emptied and we call each callback found
with None or with an exception object to wake up blocked client.
"""
while True:
try:
callback = self.__callback_queue.popleft()
callback(ConnectionError("closed connection"))
except IndexError:
break
if self.subscribed:
# pubsub clients
self._reply_list.append(ConnectionError("closed connection"))
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thefab/tornadis | tornadis/client.py | Client._read_callback | def _read_callback(self, data=None):
"""Callback called when some data are read on the socket.
The buffer is given to the hiredis parser. If a reply is complete,
we put the decoded reply to on the reply queue.
Args:
data (str): string (buffer) read on the socket.
"""
try:
if data is not None:
self.__reader.feed(data)
while True:
reply = self.__reader.gets()
if reply is not False:
try:
callback = self.__callback_queue.popleft()
# normal client (1 reply = 1 callback)
callback(reply)
except IndexError:
# pubsub clients
self._reply_list.append(reply)
self._condition.notify_all()
else:
break
except hiredis.ProtocolError:
# something nasty occured (corrupt stream => no way to recover)
LOG.warning("corrupted stream => disconnect")
self.disconnect() | python | def _read_callback(self, data=None):
"""Callback called when some data are read on the socket.
The buffer is given to the hiredis parser. If a reply is complete,
we put the decoded reply to on the reply queue.
Args:
data (str): string (buffer) read on the socket.
"""
try:
if data is not None:
self.__reader.feed(data)
while True:
reply = self.__reader.gets()
if reply is not False:
try:
callback = self.__callback_queue.popleft()
# normal client (1 reply = 1 callback)
callback(reply)
except IndexError:
# pubsub clients
self._reply_list.append(reply)
self._condition.notify_all()
else:
break
except hiredis.ProtocolError:
# something nasty occured (corrupt stream => no way to recover)
LOG.warning("corrupted stream => disconnect")
self.disconnect() | [
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thefab/tornadis | tornadis/client.py | Client.call | def call(self, *args, **kwargs):
"""Calls a redis command and returns a Future of the reply.
Args:
*args: full redis command as variable length argument list or
a Pipeline object (as a single argument).
**kwargs: internal private options (do not use).
Returns:
a Future with the decoded redis reply as result (when available) or
a ConnectionError object in case of connection error.
Raises:
ClientError: your Pipeline object is empty.
Examples:
>>> @tornado.gen.coroutine
def foobar():
client = Client()
result = yield client.call("HSET", "key", "field", "val")
"""
if not self.is_connected():
if self.autoconnect:
# We use this method only when we are not contected
# to void performance penaly due to gen.coroutine decorator
return self._call_with_autoconnect(*args, **kwargs)
else:
error = ConnectionError("you are not connected and "
"autoconnect=False")
return tornado.gen.maybe_future(error)
return self._call(*args, **kwargs) | python | def call(self, *args, **kwargs):
"""Calls a redis command and returns a Future of the reply.
Args:
*args: full redis command as variable length argument list or
a Pipeline object (as a single argument).
**kwargs: internal private options (do not use).
Returns:
a Future with the decoded redis reply as result (when available) or
a ConnectionError object in case of connection error.
Raises:
ClientError: your Pipeline object is empty.
Examples:
>>> @tornado.gen.coroutine
def foobar():
client = Client()
result = yield client.call("HSET", "key", "field", "val")
"""
if not self.is_connected():
if self.autoconnect:
# We use this method only when we are not contected
# to void performance penaly due to gen.coroutine decorator
return self._call_with_autoconnect(*args, **kwargs)
else:
error = ConnectionError("you are not connected and "
"autoconnect=False")
return tornado.gen.maybe_future(error)
return self._call(*args, **kwargs) | [
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thefab/tornadis | tornadis/client.py | Client.async_call | def async_call(self, *args, **kwargs):
"""Calls a redis command, waits for the reply and call a callback.
Following options are available (not part of the redis command itself):
- callback
Function called (with the result as argument) when the result
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Args:
*args: full redis command as variable length argument list or
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**kwargs: options as keyword parameters.
Examples:
>>> def cb(result):
pass
>>> client.async_call("HSET", "key", "field", "val", callback=cb)
"""
def after_autoconnect_callback(future):
if self.is_connected():
self._call(*args, **kwargs)
else:
# FIXME
pass
if 'callback' not in kwargs:
kwargs['callback'] = discard_reply_cb
if not self.is_connected():
if self.autoconnect:
connect_future = self.connect()
cb = after_autoconnect_callback
self.__connection._ioloop.add_future(connect_future, cb)
else:
error = ConnectionError("you are not connected and "
"autoconnect=False")
kwargs['callback'](error)
else:
self._call(*args, **kwargs) | python | def async_call(self, *args, **kwargs):
"""Calls a redis command, waits for the reply and call a callback.
Following options are available (not part of the redis command itself):
- callback
Function called (with the result as argument) when the result
is available. If not set, the reply is silently discarded. In
case of errors, the callback is called with a
TornadisException object as argument.
Args:
*args: full redis command as variable length argument list or
a Pipeline object (as a single argument).
**kwargs: options as keyword parameters.
Examples:
>>> def cb(result):
pass
>>> client.async_call("HSET", "key", "field", "val", callback=cb)
"""
def after_autoconnect_callback(future):
if self.is_connected():
self._call(*args, **kwargs)
else:
# FIXME
pass
if 'callback' not in kwargs:
kwargs['callback'] = discard_reply_cb
if not self.is_connected():
if self.autoconnect:
connect_future = self.connect()
cb = after_autoconnect_callback
self.__connection._ioloop.add_future(connect_future, cb)
else:
error = ConnectionError("you are not connected and "
"autoconnect=False")
kwargs['callback'](error)
else:
self._call(*args, **kwargs) | [
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thefab/tornadis | tornadis/utils.py | format_args_in_redis_protocol | def format_args_in_redis_protocol(*args):
"""Formats arguments into redis protocol...
This function makes and returns a string/buffer corresponding to
given arguments formated with the redis protocol.
integer, text, string or binary types are automatically converted
(using utf8 if necessary).
More informations about the protocol: http://redis.io/topics/protocol
Args:
*args: full redis command as variable length argument list
Returns:
binary string (arguments in redis protocol)
Examples:
>>> format_args_in_redis_protocol("HSET", "key", "field", "value")
'*4\r\n$4\r\nHSET\r\n$3\r\nkey\r\n$5\r\nfield\r\n$5\r\nvalue\r\n'
"""
buf = WriteBuffer()
l = "*%d\r\n" % len(args) # noqa: E741
if six.PY2:
buf.append(l)
else: # pragma: no cover
buf.append(l.encode('utf-8'))
for arg in args:
if isinstance(arg, six.text_type):
# it's a unicode string in Python2 or a standard (unicode)
# string in Python3, let's encode it in utf-8 to get raw bytes
arg = arg.encode('utf-8')
elif isinstance(arg, six.string_types):
# it's a basestring in Python2 => nothing to do
pass
elif isinstance(arg, six.binary_type): # pragma: no cover
# it's a raw bytes string in Python3 => nothing to do
pass
elif isinstance(arg, six.integer_types):
tmp = "%d" % arg
if six.PY2:
arg = tmp
else: # pragma: no cover
arg = tmp.encode('utf-8')
elif isinstance(arg, WriteBuffer):
# it's a WriteBuffer object => nothing to do
pass
else:
raise Exception("don't know what to do with %s" % type(arg))
l = "$%d\r\n" % len(arg) # noqa: E741
if six.PY2:
buf.append(l)
else: # pragma: no cover
buf.append(l.encode('utf-8'))
buf.append(arg)
buf.append(b"\r\n")
return buf | python | def format_args_in_redis_protocol(*args):
"""Formats arguments into redis protocol...
This function makes and returns a string/buffer corresponding to
given arguments formated with the redis protocol.
integer, text, string or binary types are automatically converted
(using utf8 if necessary).
More informations about the protocol: http://redis.io/topics/protocol
Args:
*args: full redis command as variable length argument list
Returns:
binary string (arguments in redis protocol)
Examples:
>>> format_args_in_redis_protocol("HSET", "key", "field", "value")
'*4\r\n$4\r\nHSET\r\n$3\r\nkey\r\n$5\r\nfield\r\n$5\r\nvalue\r\n'
"""
buf = WriteBuffer()
l = "*%d\r\n" % len(args) # noqa: E741
if six.PY2:
buf.append(l)
else: # pragma: no cover
buf.append(l.encode('utf-8'))
for arg in args:
if isinstance(arg, six.text_type):
# it's a unicode string in Python2 or a standard (unicode)
# string in Python3, let's encode it in utf-8 to get raw bytes
arg = arg.encode('utf-8')
elif isinstance(arg, six.string_types):
# it's a basestring in Python2 => nothing to do
pass
elif isinstance(arg, six.binary_type): # pragma: no cover
# it's a raw bytes string in Python3 => nothing to do
pass
elif isinstance(arg, six.integer_types):
tmp = "%d" % arg
if six.PY2:
arg = tmp
else: # pragma: no cover
arg = tmp.encode('utf-8')
elif isinstance(arg, WriteBuffer):
# it's a WriteBuffer object => nothing to do
pass
else:
raise Exception("don't know what to do with %s" % type(arg))
l = "$%d\r\n" % len(arg) # noqa: E741
if six.PY2:
buf.append(l)
else: # pragma: no cover
buf.append(l.encode('utf-8'))
buf.append(arg)
buf.append(b"\r\n")
return buf | [
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thefab/tornadis | tornadis/utils.py | ContextManagerFuture._done_callback | def _done_callback(self, wrapped):
"""Internal "done callback" to set the result of the object.
The result of the object if forced by the wrapped future. So this
internal callback must be called when the wrapped future is ready.
Args:
wrapped (Future): the wrapped Future object
"""
if wrapped.exception():
self.set_exception(wrapped.exception())
else:
self.set_result(wrapped.result()) | python | def _done_callback(self, wrapped):
"""Internal "done callback" to set the result of the object.
The result of the object if forced by the wrapped future. So this
internal callback must be called when the wrapped future is ready.
Args:
wrapped (Future): the wrapped Future object
"""
if wrapped.exception():
self.set_exception(wrapped.exception())
else:
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thefab/tornadis | tornadis/utils.py | ContextManagerFuture.result | def result(self):
"""The result method which returns a context manager
Returns:
ContextManager: The corresponding context manager
"""
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# Otherwise return a context manager that cleans up after the block.
@contextlib.contextmanager
def f():
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return f() | python | def result(self):
"""The result method which returns a context manager
Returns:
ContextManager: The corresponding context manager
"""
if self.exception():
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# Otherwise return a context manager that cleans up after the block.
@contextlib.contextmanager
def f():
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enricobacis/lyricwikia | lyricwikia/lyricwikia.py | create_url | def create_url(artist, song):
"""Create the URL in the LyricWikia format"""
return (__BASE_URL__ +
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song=urlize(song))) | python | def create_url(artist, song):
"""Create the URL in the LyricWikia format"""
return (__BASE_URL__ +
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song=urlize(song))) | [
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enricobacis/lyricwikia | lyricwikia/lyricwikia.py | get_lyrics | def get_lyrics(artist, song, linesep='\n', timeout=None):
"""Retrieve the lyrics of the song and return the first one in case
multiple versions are available."""
return get_all_lyrics(artist, song, linesep, timeout)[0] | python | def get_lyrics(artist, song, linesep='\n', timeout=None):
"""Retrieve the lyrics of the song and return the first one in case
multiple versions are available."""
return get_all_lyrics(artist, song, linesep, timeout)[0] | [
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enricobacis/lyricwikia | lyricwikia/lyricwikia.py | get_all_lyrics | def get_all_lyrics(artist, song, linesep='\n', timeout=None):
"""Retrieve a list of all the lyrics versions of a song."""
url = create_url(artist, song)
response = _requests.get(url, timeout=timeout)
soup = _BeautifulSoup(response.content, "html.parser")
lyricboxes = soup.findAll('div', {'class': 'lyricbox'})
if not lyricboxes:
raise LyricsNotFound('Cannot download lyrics')
for lyricbox in lyricboxes:
for br in lyricbox.findAll('br'):
br.replace_with(linesep)
return [lyricbox.text.strip() for lyricbox in lyricboxes] | python | def get_all_lyrics(artist, song, linesep='\n', timeout=None):
"""Retrieve a list of all the lyrics versions of a song."""
url = create_url(artist, song)
response = _requests.get(url, timeout=timeout)
soup = _BeautifulSoup(response.content, "html.parser")
lyricboxes = soup.findAll('div', {'class': 'lyricbox'})
if not lyricboxes:
raise LyricsNotFound('Cannot download lyrics')
for lyricbox in lyricboxes:
for br in lyricbox.findAll('br'):
br.replace_with(linesep)
return [lyricbox.text.strip() for lyricbox in lyricboxes] | [
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melizalab/arf | arf.py | open_file | def open_file(name, mode=None, driver=None, libver=None, userblock_size=None, **kwargs):
"""Open an ARF file, creating as necessary.
Use this instead of h5py.File to ensure that root-level attributes and group
creation property lists are set correctly.
"""
import sys
import os
from h5py import h5p
from h5py._hl import files
try:
# If the byte string doesn't match the default
# encoding, just pass it on as-is. Note Unicode
# objects can always be encoded.
name = name.encode(sys.getfilesystemencoding())
except (UnicodeError, LookupError):
pass
exists = os.path.exists(name)
try:
fcpl = h5p.create(h5p.FILE_CREATE)
fcpl.set_link_creation_order(
h5p.CRT_ORDER_TRACKED | h5p.CRT_ORDER_INDEXED)
except AttributeError:
# older version of h5py
fp = files.File(name, mode=mode, driver=driver,
libver=libver, **kwargs)
else:
fapl = files.make_fapl(driver, libver, **kwargs)
fp = files.File(files.make_fid(name, mode, userblock_size, fapl, fcpl))
if not exists and fp.mode == 'r+':
set_attributes(fp,
arf_library='python',
arf_library_version=__version__,
arf_version=spec_version)
return fp | python | def open_file(name, mode=None, driver=None, libver=None, userblock_size=None, **kwargs):
"""Open an ARF file, creating as necessary.
Use this instead of h5py.File to ensure that root-level attributes and group
creation property lists are set correctly.
"""
import sys
import os
from h5py import h5p
from h5py._hl import files
try:
# If the byte string doesn't match the default
# encoding, just pass it on as-is. Note Unicode
# objects can always be encoded.
name = name.encode(sys.getfilesystemencoding())
except (UnicodeError, LookupError):
pass
exists = os.path.exists(name)
try:
fcpl = h5p.create(h5p.FILE_CREATE)
fcpl.set_link_creation_order(
h5p.CRT_ORDER_TRACKED | h5p.CRT_ORDER_INDEXED)
except AttributeError:
# older version of h5py
fp = files.File(name, mode=mode, driver=driver,
libver=libver, **kwargs)
else:
fapl = files.make_fapl(driver, libver, **kwargs)
fp = files.File(files.make_fid(name, mode, userblock_size, fapl, fcpl))
if not exists and fp.mode == 'r+':
set_attributes(fp,
arf_library='python',
arf_library_version=__version__,
arf_version=spec_version)
return fp | [
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melizalab/arf | arf.py | create_entry | def create_entry(group, name, timestamp, **attributes):
"""Create a new ARF entry under group, setting required attributes.
An entry is an abstract collection of data which all refer to the same time
frame. Data can include physiological recordings, sound recordings, and
derived data such as spike times and labels. See add_data() for information
on how data are stored.
name -- the name of the new entry. any valid python string.
timestamp -- timestamp of entry (datetime object, or seconds since
January 1, 1970). Can be an integer, a float, or a tuple
of integers (seconds, microsceconds)
Additional keyword arguments are set as attributes on created entry.
Returns: newly created entry object
"""
# create group using low-level interface to store creation order
from h5py import h5p, h5g, _hl
try:
gcpl = h5p.create(h5p.GROUP_CREATE)
gcpl.set_link_creation_order(
h5p.CRT_ORDER_TRACKED | h5p.CRT_ORDER_INDEXED)
except AttributeError:
grp = group.create_group(name)
else:
name, lcpl = group._e(name, lcpl=True)
grp = _hl.group.Group(h5g.create(group.id, name, lcpl=lcpl, gcpl=gcpl))
set_uuid(grp, attributes.pop("uuid", None))
set_attributes(grp,
timestamp=convert_timestamp(timestamp),
**attributes)
return grp | python | def create_entry(group, name, timestamp, **attributes):
"""Create a new ARF entry under group, setting required attributes.
An entry is an abstract collection of data which all refer to the same time
frame. Data can include physiological recordings, sound recordings, and
derived data such as spike times and labels. See add_data() for information
on how data are stored.
name -- the name of the new entry. any valid python string.
timestamp -- timestamp of entry (datetime object, or seconds since
January 1, 1970). Can be an integer, a float, or a tuple
of integers (seconds, microsceconds)
Additional keyword arguments are set as attributes on created entry.
Returns: newly created entry object
"""
# create group using low-level interface to store creation order
from h5py import h5p, h5g, _hl
try:
gcpl = h5p.create(h5p.GROUP_CREATE)
gcpl.set_link_creation_order(
h5p.CRT_ORDER_TRACKED | h5p.CRT_ORDER_INDEXED)
except AttributeError:
grp = group.create_group(name)
else:
name, lcpl = group._e(name, lcpl=True)
grp = _hl.group.Group(h5g.create(group.id, name, lcpl=lcpl, gcpl=gcpl))
set_uuid(grp, attributes.pop("uuid", None))
set_attributes(grp,
timestamp=convert_timestamp(timestamp),
**attributes)
return grp | [
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name -- the name of the new entry. any valid python string.
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melizalab/arf | arf.py | create_dataset | def create_dataset(group, name, data, units='', datatype=DataTypes.UNDEFINED,
chunks=True, maxshape=None, compression=None,
**attributes):
"""Create an ARF dataset under group, setting required attributes
Required arguments:
name -- the name of dataset in which to store the data
data -- the data to store
Data can be of the following types:
* sampled data: an N-D numerical array of measurements
* "simple" event data: a 1-D array of times
* "complex" event data: a 1-D array of records, with field 'start' required
Optional arguments:
datatype -- a code defining the nature of the data in the channel
units -- channel units (optional for sampled data, otherwise required)
sampling_rate -- required for sampled data and event data with units=='samples'
Arguments passed to h5py:
maxshape -- make the node resizable up to this shape. Use None for axes that
need to be unlimited.
chunks -- specify the chunk size. The optimal chunk size depends on the
intended use of the data. For single-channel sampled data the
auto-chunking (True) is probably best.
compression -- compression strategy. Can be 'gzip', 'szip', 'lzf' or an integer
in range(10) specifying gzip(N). Only gzip is really portable.
Additional arguments are set as attributes on the created dataset
Returns the created dataset
"""
from numpy import asarray
srate = attributes.get('sampling_rate', None)
# check data validity before doing anything
if not hasattr(data, 'dtype'):
data = asarray(data)
if data.dtype.kind in ('S', 'O', 'U'):
raise ValueError(
"data must be in array with numeric or compound type")
if data.dtype.kind == 'V':
if 'start' not in data.dtype.names:
raise ValueError("complex event data requires 'start' field")
if not isinstance(units, (list, tuple)):
raise ValueError("complex event data requires sequence of units")
if not len(units) == len(data.dtype.names):
raise ValueError("number of units doesn't match number of fields")
if units == '':
if srate is None or not srate > 0:
raise ValueError(
"unitless data assumed time series and requires sampling_rate attribute")
elif units == 'samples':
if srate is None or not srate > 0:
raise ValueError(
"data with units of 'samples' requires sampling_rate attribute")
# NB: can't really catch case where sampled data has units but doesn't
# have sampling_rate attribute
dset = group.create_dataset(
name, data=data, maxshape=maxshape, chunks=chunks, compression=compression)
set_attributes(dset, units=units, datatype=datatype, **attributes)
return dset | python | def create_dataset(group, name, data, units='', datatype=DataTypes.UNDEFINED,
chunks=True, maxshape=None, compression=None,
**attributes):
"""Create an ARF dataset under group, setting required attributes
Required arguments:
name -- the name of dataset in which to store the data
data -- the data to store
Data can be of the following types:
* sampled data: an N-D numerical array of measurements
* "simple" event data: a 1-D array of times
* "complex" event data: a 1-D array of records, with field 'start' required
Optional arguments:
datatype -- a code defining the nature of the data in the channel
units -- channel units (optional for sampled data, otherwise required)
sampling_rate -- required for sampled data and event data with units=='samples'
Arguments passed to h5py:
maxshape -- make the node resizable up to this shape. Use None for axes that
need to be unlimited.
chunks -- specify the chunk size. The optimal chunk size depends on the
intended use of the data. For single-channel sampled data the
auto-chunking (True) is probably best.
compression -- compression strategy. Can be 'gzip', 'szip', 'lzf' or an integer
in range(10) specifying gzip(N). Only gzip is really portable.
Additional arguments are set as attributes on the created dataset
Returns the created dataset
"""
from numpy import asarray
srate = attributes.get('sampling_rate', None)
# check data validity before doing anything
if not hasattr(data, 'dtype'):
data = asarray(data)
if data.dtype.kind in ('S', 'O', 'U'):
raise ValueError(
"data must be in array with numeric or compound type")
if data.dtype.kind == 'V':
if 'start' not in data.dtype.names:
raise ValueError("complex event data requires 'start' field")
if not isinstance(units, (list, tuple)):
raise ValueError("complex event data requires sequence of units")
if not len(units) == len(data.dtype.names):
raise ValueError("number of units doesn't match number of fields")
if units == '':
if srate is None or not srate > 0:
raise ValueError(
"unitless data assumed time series and requires sampling_rate attribute")
elif units == 'samples':
if srate is None or not srate > 0:
raise ValueError(
"data with units of 'samples' requires sampling_rate attribute")
# NB: can't really catch case where sampled data has units but doesn't
# have sampling_rate attribute
dset = group.create_dataset(
name, data=data, maxshape=maxshape, chunks=chunks, compression=compression)
set_attributes(dset, units=units, datatype=datatype, **attributes)
return dset | [
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chunks -- specify the chunk size. The optimal chunk size depends on the
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melizalab/arf | arf.py | create_table | def create_table(group, name, dtype, **attributes):
"""Create a new array dataset under group with compound datatype and maxshape=(None,)"""
dset = group.create_dataset(
name, shape=(0,), dtype=dtype, maxshape=(None,))
set_attributes(dset, **attributes)
return dset | python | def create_table(group, name, dtype, **attributes):
"""Create a new array dataset under group with compound datatype and maxshape=(None,)"""
dset = group.create_dataset(
name, shape=(0,), dtype=dtype, maxshape=(None,))
set_attributes(dset, **attributes)
return dset | [
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melizalab/arf | arf.py | append_data | def append_data(dset, data):
"""Append data to dset along axis 0. Data must be a single element or
a 1D array of the same type as the dataset (including compound datatypes)."""
N = data.shape[0] if hasattr(data, 'shape') else 1
if N == 0:
return
oldlen = dset.shape[0]
newlen = oldlen + N
dset.resize(newlen, axis=0)
dset[oldlen:] = data | python | def append_data(dset, data):
"""Append data to dset along axis 0. Data must be a single element or
a 1D array of the same type as the dataset (including compound datatypes)."""
N = data.shape[0] if hasattr(data, 'shape') else 1
if N == 0:
return
oldlen = dset.shape[0]
newlen = oldlen + N
dset.resize(newlen, axis=0)
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melizalab/arf | arf.py | check_file_version | def check_file_version(file):
"""Check the ARF version attribute of file for compatibility.
Raises DeprecationWarning for backwards-incompatible files, FutureWarning
for (potentially) forwards-incompatible files, and UserWarning for files
that may not have been created by an ARF library.
Returns the version for the file
"""
from distutils.version import StrictVersion as Version
try:
ver = file.attrs.get('arf_version', None)
if ver is None:
ver = file.attrs['arf_library_version']
except KeyError:
raise UserWarning(
"Unable to determine ARF version for {0.filename};"
"created by another program?".format(file))
try:
# if the attribute is stored as a string, it's ascii-encoded
ver = ver.decode("ascii")
except (LookupError, AttributeError):
pass
# should be backwards compatible after 1.1
file_version = Version(ver)
if file_version < Version('1.1'):
raise DeprecationWarning(
"ARF library {} may have trouble reading file "
"version {} (< 1.1)".format(version, file_version))
elif file_version >= Version('3.0'):
raise FutureWarning(
"ARF library {} may be incompatible with file "
"version {} (>= 3.0)".format(version, file_version))
return file_version | python | def check_file_version(file):
"""Check the ARF version attribute of file for compatibility.
Raises DeprecationWarning for backwards-incompatible files, FutureWarning
for (potentially) forwards-incompatible files, and UserWarning for files
that may not have been created by an ARF library.
Returns the version for the file
"""
from distutils.version import StrictVersion as Version
try:
ver = file.attrs.get('arf_version', None)
if ver is None:
ver = file.attrs['arf_library_version']
except KeyError:
raise UserWarning(
"Unable to determine ARF version for {0.filename};"
"created by another program?".format(file))
try:
# if the attribute is stored as a string, it's ascii-encoded
ver = ver.decode("ascii")
except (LookupError, AttributeError):
pass
# should be backwards compatible after 1.1
file_version = Version(ver)
if file_version < Version('1.1'):
raise DeprecationWarning(
"ARF library {} may have trouble reading file "
"version {} (< 1.1)".format(version, file_version))
elif file_version >= Version('3.0'):
raise FutureWarning(
"ARF library {} may be incompatible with file "
"version {} (>= 3.0)".format(version, file_version))
return file_version | [
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] | 71746d9edbe7993a783d4acaf84b9631f3230283 | https://github.com/melizalab/arf/blob/71746d9edbe7993a783d4acaf84b9631f3230283/arf.py#L204-L238 | train |
melizalab/arf | arf.py | set_attributes | def set_attributes(node, overwrite=True, **attributes):
"""Set multiple attributes on node.
If overwrite is False, and the attribute already exists, does nothing. If
the value for a key is None, the attribute is deleted.
"""
aset = node.attrs
for k, v in attributes.items():
if not overwrite and k in aset:
pass
elif v is None:
if k in aset:
del aset[k]
else:
aset[k] = v | python | def set_attributes(node, overwrite=True, **attributes):
"""Set multiple attributes on node.
If overwrite is False, and the attribute already exists, does nothing. If
the value for a key is None, the attribute is deleted.
"""
aset = node.attrs
for k, v in attributes.items():
if not overwrite and k in aset:
pass
elif v is None:
if k in aset:
del aset[k]
else:
aset[k] = v | [
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melizalab/arf | arf.py | keys_by_creation | def keys_by_creation(group):
"""Returns a sequence of links in group in order of creation.
Raises an error if the group was not set to track creation order.
"""
from h5py import h5
out = []
try:
group._id.links.iterate(
out.append, idx_type=h5.INDEX_CRT_ORDER, order=h5.ITER_INC)
except (AttributeError, RuntimeError):
# pre 2.2 shim
def f(name):
if name.find(b'/', 1) == -1:
out.append(name)
group._id.links.visit(
f, idx_type=h5.INDEX_CRT_ORDER, order=h5.ITER_INC)
return map(group._d, out) | python | def keys_by_creation(group):
"""Returns a sequence of links in group in order of creation.
Raises an error if the group was not set to track creation order.
"""
from h5py import h5
out = []
try:
group._id.links.iterate(
out.append, idx_type=h5.INDEX_CRT_ORDER, order=h5.ITER_INC)
except (AttributeError, RuntimeError):
# pre 2.2 shim
def f(name):
if name.find(b'/', 1) == -1:
out.append(name)
group._id.links.visit(
f, idx_type=h5.INDEX_CRT_ORDER, order=h5.ITER_INC)
return map(group._d, out) | [
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melizalab/arf | arf.py | convert_timestamp | def convert_timestamp(obj):
"""Make an ARF timestamp from an object.
Argument can be a datetime.datetime object, a time.struct_time, an integer,
a float, or a tuple of integers. The returned value is a numpy array with
the integer number of seconds since the Epoch and any additional
microseconds.
Note that because floating point values are approximate, the conversion
between float and integer tuple may not be reversible.
"""
import numbers
from datetime import datetime
from time import mktime, struct_time
from numpy import zeros
out = zeros(2, dtype='int64')
if isinstance(obj, datetime):
out[0] = mktime(obj.timetuple())
out[1] = obj.microsecond
elif isinstance(obj, struct_time):
out[0] = mktime(obj)
elif isinstance(obj, numbers.Integral):
out[0] = obj
elif isinstance(obj, numbers.Real):
out[0] = obj
out[1] = (obj - out[0]) * 1e6
else:
try:
out[:2] = obj[:2]
except:
raise TypeError("unable to convert %s to timestamp" % obj)
return out | python | def convert_timestamp(obj):
"""Make an ARF timestamp from an object.
Argument can be a datetime.datetime object, a time.struct_time, an integer,
a float, or a tuple of integers. The returned value is a numpy array with
the integer number of seconds since the Epoch and any additional
microseconds.
Note that because floating point values are approximate, the conversion
between float and integer tuple may not be reversible.
"""
import numbers
from datetime import datetime
from time import mktime, struct_time
from numpy import zeros
out = zeros(2, dtype='int64')
if isinstance(obj, datetime):
out[0] = mktime(obj.timetuple())
out[1] = obj.microsecond
elif isinstance(obj, struct_time):
out[0] = mktime(obj)
elif isinstance(obj, numbers.Integral):
out[0] = obj
elif isinstance(obj, numbers.Real):
out[0] = obj
out[1] = (obj - out[0]) * 1e6
else:
try:
out[:2] = obj[:2]
except:
raise TypeError("unable to convert %s to timestamp" % obj)
return out | [
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melizalab/arf | arf.py | timestamp_to_datetime | def timestamp_to_datetime(timestamp):
"""Convert an ARF timestamp to a datetime.datetime object (naive local time)"""
from datetime import datetime, timedelta
obj = datetime.fromtimestamp(timestamp[0])
return obj + timedelta(microseconds=int(timestamp[1])) | python | def timestamp_to_datetime(timestamp):
"""Convert an ARF timestamp to a datetime.datetime object (naive local time)"""
from datetime import datetime, timedelta
obj = datetime.fromtimestamp(timestamp[0])
return obj + timedelta(microseconds=int(timestamp[1])) | [
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melizalab/arf | arf.py | set_uuid | def set_uuid(obj, uuid=None):
"""Set the uuid attribute of an HDF5 object. Use this method to ensure correct dtype """
from uuid import uuid4, UUID
if uuid is None:
uuid = uuid4()
elif isinstance(uuid, bytes):
if len(uuid) == 16:
uuid = UUID(bytes=uuid)
else:
uuid = UUID(hex=uuid)
if "uuid" in obj.attrs:
del obj.attrs["uuid"]
obj.attrs.create("uuid", str(uuid).encode('ascii'), dtype="|S36") | python | def set_uuid(obj, uuid=None):
"""Set the uuid attribute of an HDF5 object. Use this method to ensure correct dtype """
from uuid import uuid4, UUID
if uuid is None:
uuid = uuid4()
elif isinstance(uuid, bytes):
if len(uuid) == 16:
uuid = UUID(bytes=uuid)
else:
uuid = UUID(hex=uuid)
if "uuid" in obj.attrs:
del obj.attrs["uuid"]
obj.attrs.create("uuid", str(uuid).encode('ascii'), dtype="|S36") | [
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melizalab/arf | arf.py | get_uuid | def get_uuid(obj):
"""Return the uuid for obj, or null uuid if none is set"""
# TODO: deprecate null uuid ret val
from uuid import UUID
try:
uuid = obj.attrs['uuid']
except KeyError:
return UUID(int=0)
# convert to unicode for python 3
try:
uuid = uuid.decode('ascii')
except (LookupError, AttributeError):
pass
return UUID(uuid) | python | def get_uuid(obj):
"""Return the uuid for obj, or null uuid if none is set"""
# TODO: deprecate null uuid ret val
from uuid import UUID
try:
uuid = obj.attrs['uuid']
except KeyError:
return UUID(int=0)
# convert to unicode for python 3
try:
uuid = uuid.decode('ascii')
except (LookupError, AttributeError):
pass
return UUID(uuid) | [
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melizalab/arf | arf.py | count_children | def count_children(obj, type=None):
"""Return the number of children of obj, optionally restricting by class"""
if type is None:
return len(obj)
else:
# there doesn't appear to be any hdf5 function for getting this
# information without inspecting each child, which makes this somewhat
# slow
return sum(1 for x in obj if obj.get(x, getclass=True) is type) | python | def count_children(obj, type=None):
"""Return the number of children of obj, optionally restricting by class"""
if type is None:
return len(obj)
else:
# there doesn't appear to be any hdf5 function for getting this
# information without inspecting each child, which makes this somewhat
# slow
return sum(1 for x in obj if obj.get(x, getclass=True) is type) | [
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melizalab/arf | arf.py | DataTypes._todict | def _todict(cls):
""" generate a dict keyed by value """
return dict((getattr(cls, attr), attr) for attr in dir(cls) if not attr.startswith('_')) | python | def _todict(cls):
""" generate a dict keyed by value """
return dict((getattr(cls, attr), attr) for attr in dir(cls) if not attr.startswith('_')) | [
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singularityhub/singularity-python | singularity/views/utils.py | get_template | def get_template(template_name,fields=None):
'''get_template will return a template in the template folder,
with some substitutions (eg, {'{{ graph | safe }}':"fill this in!"}
'''
template = None
if not template_name.endswith('.html'):
template_name = "%s.html" %(template_name)
here = "%s/cli/app/templates" %(get_installdir())
template_path = "%s/%s" %(here,template_name)
if os.path.exists(template_path):
template = ''.join(read_file(template_path))
if fields is not None:
for tag,sub in fields.items():
template = template.replace(tag,sub)
return template | python | def get_template(template_name,fields=None):
'''get_template will return a template in the template folder,
with some substitutions (eg, {'{{ graph | safe }}':"fill this in!"}
'''
template = None
if not template_name.endswith('.html'):
template_name = "%s.html" %(template_name)
here = "%s/cli/app/templates" %(get_installdir())
template_path = "%s/%s" %(here,template_name)
if os.path.exists(template_path):
template = ''.join(read_file(template_path))
if fields is not None:
for tag,sub in fields.items():
template = template.replace(tag,sub)
return template | [
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singularityhub/singularity-python | singularity/analysis/compare.py | container_similarity_vector | def container_similarity_vector(container1=None,packages_set=None,by=None):
'''container similarity_vector is similar to compare_packages, but intended
to compare a container object (singularity image or singularity hub container)
to a list of packages. If packages_set is not provided, the default used is
'docker-os'. This can be changed to 'docker-library', or if the user wants a custom
list, should define custom_set.
:param container1: singularity image or singularity hub container.
:param packages_set: a name of a package set, provided are docker-os and docker-library
:by: metrics to compare by (files.txt and or folders.txt)
'''
if by == None:
by = ['files.txt']
if not isinstance(by,list):
by = [by]
if not isinstance(packages_set,list):
packages_set = [packages_set]
comparisons = dict()
for b in by:
bot.debug("Starting comparisons for %s" %b)
df = pandas.DataFrame(columns=packages_set)
for package2 in packages_set:
sim = calculate_similarity(container1=container1,
image_package2=package2,
by=b)[b]
name1 = os.path.basename(package2).replace('.img.zip','')
bot.debug("container vs. %s: %s" %(name1,sim))
df.loc["container",package2] = sim
df.columns = [os.path.basename(x).replace('.img.zip','') for x in df.columns.tolist()]
comparisons[b] = df
return comparisons | python | def container_similarity_vector(container1=None,packages_set=None,by=None):
'''container similarity_vector is similar to compare_packages, but intended
to compare a container object (singularity image or singularity hub container)
to a list of packages. If packages_set is not provided, the default used is
'docker-os'. This can be changed to 'docker-library', or if the user wants a custom
list, should define custom_set.
:param container1: singularity image or singularity hub container.
:param packages_set: a name of a package set, provided are docker-os and docker-library
:by: metrics to compare by (files.txt and or folders.txt)
'''
if by == None:
by = ['files.txt']
if not isinstance(by,list):
by = [by]
if not isinstance(packages_set,list):
packages_set = [packages_set]
comparisons = dict()
for b in by:
bot.debug("Starting comparisons for %s" %b)
df = pandas.DataFrame(columns=packages_set)
for package2 in packages_set:
sim = calculate_similarity(container1=container1,
image_package2=package2,
by=b)[b]
name1 = os.path.basename(package2).replace('.img.zip','')
bot.debug("container vs. %s: %s" %(name1,sim))
df.loc["container",package2] = sim
df.columns = [os.path.basename(x).replace('.img.zip','') for x in df.columns.tolist()]
comparisons[b] = df
return comparisons | [
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singularityhub/singularity-python | singularity/analysis/compare.py | compare_singularity_images | def compare_singularity_images(image_paths1, image_paths2=None):
'''compare_singularity_images is a wrapper for compare_containers to compare
singularity containers. If image_paths2 is not defined, pairwise comparison is done
with image_paths1
'''
repeat = False
if image_paths2 is None:
image_paths2 = image_paths1
repeat = True
if not isinstance(image_paths1,list):
image_paths1 = [image_paths1]
if not isinstance(image_paths2,list):
image_paths2 = [image_paths2]
dfs = pandas.DataFrame(index=image_paths1,columns=image_paths2)
comparisons_done = []
for image1 in image_paths1:
fileobj1,tar1 = get_image_tar(image1)
members1 = [x.name for x in tar1]
for image2 in image_paths2:
comparison_id = [image1,image2]
comparison_id.sort()
comparison_id = "".join(comparison_id)
if comparison_id not in comparisons_done:
if image1 == image2:
sim = 1.0
else:
fileobj2,tar2 = get_image_tar(image2)
members2 = [x.name for x in tar2]
c = compare_lists(members1, members2)
sim = information_coefficient(c['total1'],c['total2'],c['intersect'])
delete_image_tar(fileobj2, tar2)
dfs.loc[image1,image2] = sim
if repeat:
dfs.loc[image2,image1] = sim
comparisons_done.append(comparison_id)
delete_image_tar(fileobj1, tar1)
return dfs | python | def compare_singularity_images(image_paths1, image_paths2=None):
'''compare_singularity_images is a wrapper for compare_containers to compare
singularity containers. If image_paths2 is not defined, pairwise comparison is done
with image_paths1
'''
repeat = False
if image_paths2 is None:
image_paths2 = image_paths1
repeat = True
if not isinstance(image_paths1,list):
image_paths1 = [image_paths1]
if not isinstance(image_paths2,list):
image_paths2 = [image_paths2]
dfs = pandas.DataFrame(index=image_paths1,columns=image_paths2)
comparisons_done = []
for image1 in image_paths1:
fileobj1,tar1 = get_image_tar(image1)
members1 = [x.name for x in tar1]
for image2 in image_paths2:
comparison_id = [image1,image2]
comparison_id.sort()
comparison_id = "".join(comparison_id)
if comparison_id not in comparisons_done:
if image1 == image2:
sim = 1.0
else:
fileobj2,tar2 = get_image_tar(image2)
members2 = [x.name for x in tar2]
c = compare_lists(members1, members2)
sim = information_coefficient(c['total1'],c['total2'],c['intersect'])
delete_image_tar(fileobj2, tar2)
dfs.loc[image1,image2] = sim
if repeat:
dfs.loc[image2,image1] = sim
comparisons_done.append(comparison_id)
delete_image_tar(fileobj1, tar1)
return dfs | [
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singularityhub/singularity-python | singularity/analysis/compare.py | compare_containers | def compare_containers(container1=None, container2=None):
'''compare_containers will generate a data structure with common and unique files to
two images. If environmental variable SINGULARITY_HUB is set, will use container
database objects.
:param container1: first container for comparison
:param container2: second container for comparison if either not defined must include
default compares just files
'''
# Get files and folders for each
container1_guts = get_container_contents(split_delim="\n",
container=container1)['all']
container2_guts = get_container_contents(split_delim="\n",
container=container2)['all']
# Do the comparison for each metric
return compare_lists(container1_guts, container2_guts) | python | def compare_containers(container1=None, container2=None):
'''compare_containers will generate a data structure with common and unique files to
two images. If environmental variable SINGULARITY_HUB is set, will use container
database objects.
:param container1: first container for comparison
:param container2: second container for comparison if either not defined must include
default compares just files
'''
# Get files and folders for each
container1_guts = get_container_contents(split_delim="\n",
container=container1)['all']
container2_guts = get_container_contents(split_delim="\n",
container=container2)['all']
# Do the comparison for each metric
return compare_lists(container1_guts, container2_guts) | [
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:param container1: first container for comparison
:param container2: second container for comparison if either not defined must include
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singularityhub/singularity-python | singularity/analysis/compare.py | compare_lists | def compare_lists(list1,list2):
'''compare lists is the lowest level that drives compare_containers and
compare_packages. It returns a comparison object (dict) with the unique,
total, and intersecting things between two lists
:param list1: the list for container1
:param list2: the list for container2
'''
intersect = list(set(list1).intersection(list2))
unique1 = list(set(list1).difference(list2))
unique2 = list(set(list2).difference(list1))
# Return data structure
comparison = {"intersect":intersect,
"unique1": unique1,
"unique2": unique2,
"total1": len(list1),
"total2": len(list2)}
return comparison | python | def compare_lists(list1,list2):
'''compare lists is the lowest level that drives compare_containers and
compare_packages. It returns a comparison object (dict) with the unique,
total, and intersecting things between two lists
:param list1: the list for container1
:param list2: the list for container2
'''
intersect = list(set(list1).intersection(list2))
unique1 = list(set(list1).difference(list2))
unique2 = list(set(list2).difference(list1))
# Return data structure
comparison = {"intersect":intersect,
"unique1": unique1,
"unique2": unique2,
"total1": len(list1),
"total2": len(list2)}
return comparison | [
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:param list1: the list for container1
:param list2: the list for container2 | [
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singularityhub/singularity-python | singularity/analysis/compare.py | calculate_similarity | def calculate_similarity(container1=None,
container2=None,
comparison=None,
metric=None):
'''calculate_similarity will calculate similarity of two containers
by files content, default will calculate
2.0*len(intersect) / total package1 + total package2
Parameters
==========
container1: container 1
container2: container 2 must be defined or
metric a function to take a total1, total2, and intersect count
(we can make this more general if / when more are added)
valid are currently files.txt or folders.txt
comparison: the comparison result object for the tree. If provided,
will skip over function to obtain it.
'''
if metric is None:
metric = information_coefficient
if comparison == None:
comparison = compare_containers(container1=container1,
container2=container2)
return metric(total1=comparison['total1'],
total2=comparison['total2'],
intersect=comparison["intersect"]) | python | def calculate_similarity(container1=None,
container2=None,
comparison=None,
metric=None):
'''calculate_similarity will calculate similarity of two containers
by files content, default will calculate
2.0*len(intersect) / total package1 + total package2
Parameters
==========
container1: container 1
container2: container 2 must be defined or
metric a function to take a total1, total2, and intersect count
(we can make this more general if / when more are added)
valid are currently files.txt or folders.txt
comparison: the comparison result object for the tree. If provided,
will skip over function to obtain it.
'''
if metric is None:
metric = information_coefficient
if comparison == None:
comparison = compare_containers(container1=container1,
container2=container2)
return metric(total1=comparison['total1'],
total2=comparison['total2'],
intersect=comparison["intersect"]) | [
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Parameters
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container1: container 1
container2: container 2 must be defined or
metric a function to take a total1, total2, and intersect count
(we can make this more general if / when more are added)
valid are currently files.txt or folders.txt
comparison: the comparison result object for the tree. If provided,
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