func_code_string stringlengths 52 1.94M | func_documentation_string stringlengths 1 47.2k |
|---|---|
def _connect(self):
# Attempt to get a cached connection from the connection pool
try:
connection = self._pool_manager.get(self.pid, self)
LOGGER.debug("Re-using connection for %s", self.pid)
except pool.NoIdleConnectionsError:
if self._pool_manager.i... | Connect to PostgreSQL, either by reusing a connection from the pool
if possible, or by creating the new connection.
:rtype: psycopg2.extensions.connection
:raises: pool.NoIdleConnectionsError |
def _get_cursor(self, connection, name=None):
cursor = connection.cursor(name=name,
cursor_factory=self._cursor_factory)
if name is not None:
cursor.scrollable = True
cursor.withhold = True
return cursor | Return a cursor for the given cursor_factory. Specify a name to
use server-side cursors.
:param connection: The connection to create a cursor on
:type connection: psycopg2.extensions.connection
:param str name: A cursor name for a server side cursor
:rtype: psycopg2.extensions.c... |
def _incr_exceptions(self):
self._pool_manager.get_connection(self.pid, self._conn).exceptions += 1 | Increment the number of exceptions for the current connection. |
def _incr_executions(self):
self._pool_manager.get_connection(self.pid, self._conn).executions += 1 | Increment the number of executions for the current connection. |
def _register_unicode(connection):
psycopg2.extensions.register_type(psycopg2.extensions.UNICODE,
connection)
psycopg2.extensions.register_type(psycopg2.extensions.UNICODEARRAY,
connection) | Register the cursor to be able to receive Unicode string.
:type connection: psycopg2.extensions.connection
:param connection: Where to register things |
def _status(self):
if self._conn.status == psycopg2.extensions.STATUS_BEGIN:
return self.READY
return self._conn.status | Return the current connection status as an integer value.
The status should match one of the following constants:
- queries.Session.INTRANS: Connection established, in transaction
- queries.Session.PREPARED: Prepared for second phase of transaction
- queries.Session.READY: Connected, n... |
def as_dict(self):
if not self.cursor.rowcount:
return {}
self._rewind()
if self.cursor.rowcount == 1:
return dict(self.cursor.fetchone())
else:
raise ValueError('More than one row') | Return a single row result as a dictionary. If the results contain
multiple rows, a :py:class:`ValueError` will be raised.
:return: dict
:raises: ValueError |
def items(self):
if not self.cursor.rowcount:
return []
self.cursor.scroll(0, 'absolute')
return self.cursor.fetchall() | Return all of the rows that are in the result set.
:rtype: list |
def get_current_user():
if pwd is None:
return getpass.getuser()
else:
try:
return pwd.getpwuid(os.getuid())[0]
except KeyError as error:
LOGGER.error('Could not get logged-in user: %s', error) | Return the current username for the logged in user
:rtype: str |
def uri(host='localhost', port=5432, dbname='postgres', user='postgres',
password=None):
if port:
host = '%s:%s' % (host, port)
if password:
return 'postgresql://%s:%s@%s/%s' % (user, password, host, dbname)
return 'postgresql://%s@%s/%s' % (user, host, dbname) | Return a PostgreSQL connection URI for the specified values.
:param str host: Host to connect to
:param int port: Port to connect on
:param str dbname: The database name
:param str user: User to connect as
:param str password: The password to use, None for no password
:return str: The PostgreSQ... |
def uri_to_kwargs(uri):
parsed = urlparse(uri)
default_user = get_current_user()
password = unquote(parsed.password) if parsed.password else None
kwargs = {'host': parsed.hostname,
'port': parsed.port,
'dbname': parsed.path[1:] or default_user,
'user': pars... | Return a URI as kwargs for connecting to PostgreSQL with psycopg2,
applying default values for non-specified areas of the URI.
:param str uri: The connection URI
:rtype: dict |
def urlparse(url):
value = 'http%s' % url[5:] if url[:5] == 'postgresql' else url
parsed = _urlparse.urlparse(value)
path, query = parsed.path, parsed.query
hostname = parsed.hostname if parsed.hostname else ''
return PARSED(parsed.scheme.replace('http', 'postgresql'),
parsed.... | Parse the URL in a Python2/3 independent fashion.
:param str url: The URL to parse
:rtype: Parsed |
def free(self):
self._freed = True
self._cleanup(self.cursor, self._fd) | Release the results and connection lock from the TornadoSession
object. This **must** be called after you finish processing the results
from :py:meth:`TornadoSession.query <queries.TornadoSession.query>` or
:py:meth:`TornadoSession.callproc <queries.TornadoSession.callproc>`
or the conne... |
def _ensure_pool_exists(self):
if self.pid not in self._pool_manager:
self._pool_manager.create(self.pid, self._pool_idle_ttl,
self._pool_max_size, self._ioloop.time) | Create the pool in the pool manager if it does not exist. |
def _connect(self):
future = concurrent.Future()
# Attempt to get a cached connection from the connection pool
try:
connection = self._pool_manager.get(self.pid, self)
self._connections[connection.fileno()] = connection
future.set_result(connection)
... | Connect to PostgreSQL, either by reusing a connection from the pool
if possible, or by creating the new connection.
:rtype: psycopg2.extensions.connection
:raises: pool.NoIdleConnectionsError |
def _create_connection(self, future):
LOGGER.debug('Creating a new connection for %s', self.pid)
# Create a new PostgreSQL connection
kwargs = utils.uri_to_kwargs(self._uri)
try:
connection = self._psycopg2_connect(kwargs)
except (psycopg2.Error, OSError, soc... | Create a new PostgreSQL connection
:param tornado.concurrent.Future future: future for new conn result |
def _execute(self, method, query, parameters=None):
future = concurrent.Future()
def on_connected(cf):
if cf.exception():
future.set_exception(cf.exception())
return
# Get the psycopg2 connection object and cursor
... | Issue a query asynchronously on the server, mogrifying the
parameters against the sql statement and yielding the results
as a :py:class:`Results <queries.tornado_session.Results>` object.
This function reduces duplicate code for callproc and query by getting
the class attribute for the ... |
def _exec_cleanup(self, cursor, fd):
LOGGER.debug('Closing cursor and cleaning %s', fd)
try:
cursor.close()
except (psycopg2.Error, psycopg2.Warning) as error:
LOGGER.debug('Error closing the cursor: %s', error)
self._cleanup_fd(fd)
# If the clean... | Close the cursor, remove any references to the fd in internal state
and remove the fd from the ioloop.
:param psycopg2.extensions.cursor cursor: The cursor to close
:param int fd: The connection file descriptor |
def _cleanup_fd(self, fd, close=False):
self._ioloop.remove_handler(fd)
if fd in self._connections:
try:
self._pool_manager.free(self.pid, self._connections[fd])
except pool.ConnectionNotFoundError:
pass
if close:
... | Ensure the socket socket is removed from the IOLoop, the
connection stack, and futures stack.
:param int fd: The fd # to cleanup |
def _incr_exceptions(self, conn):
self._pool_manager.get_connection(self.pid, conn).exceptions += 1 | Increment the number of exceptions for the current connection.
:param psycopg2.extensions.connection conn: the psycopg2 connection |
def _incr_executions(self, conn):
self._pool_manager.get_connection(self.pid, conn).executions += 1 | Increment the number of executions for the current connection.
:param psycopg2.extensions.connection conn: the psycopg2 connection |
def _on_io_events(self, fd=None, _events=None):
if fd not in self._connections:
LOGGER.warning('Received IO event for non-existing connection')
return
self._poll_connection(fd) | Invoked by Tornado's IOLoop when there are events for the fd
:param int fd: The file descriptor for the event
:param int _events: The events raised |
def _poll_connection(self, fd):
try:
state = self._connections[fd].poll()
except (OSError, socket.error) as error:
self._ioloop.remove_handler(fd)
if fd in self._futures and not self._futures[fd].done():
self._futures[fd].set_exception(
... | Check with psycopg2 to see what action to take. If the state is
POLL_OK, we should have a pending callback for that fd.
:param int fd: The socket fd for the postgresql connection |
def main():
import codecs
setuptools.setup(
name='wcwidth',
version='0.1.7',
description=("Measures number of Terminal column cells "
"of wide-character codes"),
long_description=codecs.open(
os.path.join(HERE, 'README.rst'), 'r', 'utf8').rea... | Setup.py entry point. |
def _do_readme_update(self):
import codecs
import glob
# read in,
data_in = codecs.open(
os.path.join(HERE, 'README.rst'), 'r', 'utf8').read()
# search for beginning and end positions,
pos_begin = data_in.find(self.README_PATCH_FROM)
assert po... | Patch README.rst to reflect the data files used in release. |
def _do_east_asian(self):
self._do_retrieve(self.EAW_URL, self.EAW_IN)
(version, date, values) = self._parse_east_asian(
fname=self.EAW_IN,
properties=(u'W', u'F',)
)
table = self._make_table(values)
self._do_write(self.EAW_OUT, 'WIDE_EASTASIAN', ... | Fetch and update east-asian tables. |
def _do_zero_width(self):
self._do_retrieve(self.UCD_URL, self.UCD_IN)
(version, date, values) = self._parse_category(
fname=self.UCD_IN,
categories=('Me', 'Mn',)
)
table = self._make_table(values)
self._do_write(self.ZERO_OUT, 'ZERO_WIDTH', versi... | Fetch and update zero width tables. |
def _make_table(values):
import collections
table = collections.deque()
start, end = values[0], values[0]
for num, value in enumerate(values):
if num == 0:
table.append((value, value,))
continue
start, end = table.pop()
... | Return a tuple of lookup tables for given values. |
def _do_retrieve(url, fname):
folder = os.path.dirname(fname)
if not os.path.exists(folder):
os.makedirs(folder)
print("{}/ created.".format(folder))
if not os.path.exists(fname):
with open(fname, 'wb') as fout:
print("retrieving {}.".... | Retrieve given url to target filepath fname. |
def _parse_east_asian(fname, properties=(u'W', u'F',)):
version, date, values = None, None, []
print("parsing {} ..".format(fname))
for line in open(fname, 'rb'):
uline = line.decode('utf-8')
if version is None:
version = uline.split(None, 1)[1].r... | Parse unicode east-asian width tables. |
def _parse_category(fname, categories):
version, date, values = None, None, []
print("parsing {} ..".format(fname))
for line in open(fname, 'rb'):
uline = line.decode('utf-8')
if version is None:
version = uline.split(None, 1)[1].rstrip()
... | Parse unicode category tables. |
def _do_write(fname, variable, version, date, table):
# pylint: disable=R0914
# Too many local variables (19/15) (col 4)
print("writing {} ..".format(fname))
import unicodedata
import datetime
import string
utc_now = datetime.datetime.utcnow()
... | Write combining tables to filesystem as python code. |
def report_ucs_msg(ucs, wcwidth_libc, wcwidth_local):
ucp = (ucs.encode('unicode_escape')[2:]
.decode('ascii')
.upper()
.lstrip('0'))
url = "http://codepoints.net/U+{}".format(ucp)
name = unicodedata.name(ucs)
return (u"libc,ours={},{} [--o{}o--] name={} val={} {}"
... | Return string report of combining character differences.
:param ucs: unicode point.
:type ucs: unicode
:param wcwidth_libc: libc-wcwidth's reported character length.
:type comb_py: int
:param wcwidth_local: wcwidth's reported character length.
:type comb_wc: int
:rtype: unicode |
def main(using_locale=('en_US', 'UTF-8',)):
all_ucs = (ucs for ucs in
[unichr(val) for val in range(sys.maxunicode)]
if is_named(ucs) and isnt_combining(ucs))
libc_name = ctypes.util.find_library('c')
if not libc_name:
raise ImportError("Can't find C library.")
... | Program entry point.
Load the entire Unicode table into memory, excluding those that:
- are not named (func unicodedata.name returns empty string),
- are combining characters.
Using ``locale``, for each unicode character string compare libc's
wcwidth with local wcwidth.wcwidth() function;... |
def validate_args(opts):
if opts['--wide'] is None:
opts['--wide'] = 2
else:
assert opts['--wide'] in ("1", "2"), opts['--wide']
if opts['--alignment'] is None:
opts['--alignment'] = 'left'
else:
assert opts['--alignment'] in ('left', 'right'), opts['--alignment']
... | Validate and return options provided by docopt parsing. |
def main(opts):
term = Terminal()
style = Style()
# if the terminal supports colors, use a Style instance with some
# standout colors (magenta, cyan).
if term.number_of_colors:
style = Style(attr_major=term.magenta,
attr_minor=term.bright_cyan,
... | Program entry point. |
def hint_width(self):
return sum((len(self.style.delimiter),
self.wide,
len(self.style.delimiter),
len(u' '),
UCS_PRINTLEN + 2,
len(u' '),
self.style.name_len,)) | Width of a column segment. |
def head_item(self):
delimiter = self.style.attr_minor(self.style.delimiter)
hint = self.style.header_hint * self.wide
heading = (u'{delimiter}{hint}{delimiter}'
.format(delimiter=delimiter, hint=hint))
alignment = lambda *args: (
self.term.rjust(*... | Text of a single column heading. |
def msg_intro(self):
delim = self.style.attr_minor(self.style.delimiter)
txt = self.intro_msg_fmt.format(delim=delim).rstrip()
return self.term.center(txt) | Introductory message disabled above heading. |
def num_columns(self):
if self.term.is_a_tty:
return self.term.width // self.hint_width
return 1 | Number of columns displayed. |
def on_resize(self, *args):
# pylint: disable=W0613
# Unused argument 'args'
self.screen.style.name_len = min(self.screen.style.name_len,
self.term.width - 15)
assert self.term.width >= self.screen.hint_width, (
'Scree... | Signal handler callback for SIGWINCH. |
def _set_lastpage(self):
self.last_page = (len(self._page_data) - 1) // self.screen.page_size | Calculate value of class attribute ``last_page``. |
def display_initialize(self):
echo(self.term.home + self.term.clear)
echo(self.term.move_y(self.term.height // 2))
echo(self.term.center('Initializing page data ...').rstrip())
flushout()
if LIMIT_UCS == 0x10000:
echo('\n\n')
echo(self.term.blink_... | Display 'please wait' message, and narrow build warning. |
def initialize_page_data(self):
if self.term.is_a_tty:
self.display_initialize()
self.character_generator = self.character_factory(self.screen.wide)
page_data = list()
while True:
try:
page_data.append(next(self.character_generator))
... | Initialize the page data for the given screen. |
def page_data(self, idx, offset):
size = self.screen.page_size
while offset < 0 and idx:
offset += size
idx -= 1
offset = max(0, offset)
while offset >= size:
offset -= size
idx += 1
if idx == self.last_page:
of... | Return character data for page of given index and offset.
:param idx: page index.
:type idx: int
:param offset: scrolling region offset of current page.
:type offset: int
:returns: list of tuples in form of ``(ucs, name)``
:rtype: list[(unicode, unicode)] |
def _run_notty(self, writer):
page_idx = page_offset = 0
while True:
npage_idx, _ = self.draw(writer, page_idx + 1, page_offset)
if npage_idx == self.last_page:
# page displayed was last page, quit.
break
page_idx = npage_idx
... | Pager run method for terminals that are not a tty. |
def _run_tty(self, writer, reader):
# allow window-change signal to reflow screen
signal.signal(signal.SIGWINCH, self.on_resize)
page_idx = page_offset = 0
while True:
if self.dirty:
page_idx, page_offset = self.draw(writer,
... | Pager run method for terminals that are a tty. |
def run(self, writer, reader):
self._page_data = self.initialize_page_data()
self._set_lastpage()
if not self.term.is_a_tty:
self._run_notty(writer)
else:
self._run_tty(writer, reader) | Pager entry point.
In interactive mode (terminal is a tty), run until
``process_keystroke()`` detects quit keystroke ('q'). In
non-interactive mode, exit after displaying all unicode points.
:param writer: callable writes to output stream, receiving unicode.
:type writer: call... |
def process_keystroke(self, inp, idx, offset):
if inp.lower() in (u'q', u'Q'):
# exit
return (-1, -1)
self._process_keystroke_commands(inp)
idx, offset = self._process_keystroke_movement(inp, idx, offset)
return idx, offset | Process keystroke ``inp``, adjusting screen parameters.
:param inp: return value of Terminal.inkey().
:type inp: blessed.keyboard.Keystroke
:param idx: page index.
:type idx: int
:param offset: scrolling region offset of current page.
:type offset: int
:returns: ... |
def _process_keystroke_commands(self, inp):
if inp in (u'1', u'2'):
# chose 1 or 2-character wide
if int(inp) != self.screen.wide:
self.screen.wide = int(inp)
self.on_resize(None, None)
elif inp in (u'_', u'-'):
# adjust name l... | Process keystrokes that issue commands (side effects). |
def _process_keystroke_movement(self, inp, idx, offset):
term = self.term
if inp in (u'y', u'k') or inp.code in (term.KEY_UP,):
# scroll backward 1 line
idx, offset = (idx, offset - self.screen.num_columns)
elif inp in (u'e', u'j') or inp.code in (term.KEY_ENTER,... | Process keystrokes that adjust index and offset. |
def draw(self, writer, idx, offset):
# as our screen can be resized while we're mid-calculation,
# our self.dirty flag can become re-toggled; because we are
# not re-flowing our pagination, we must begin over again.
while self.dirty:
self.draw_heading(writer)
... | Draw the current page view to ``writer``.
:param writer: callable writes to output stream, receiving unicode.
:type writer: callable
:param idx: current page index.
:type idx: int
:param offset: scrolling region offset of current page.
:type offset: int
:returns:... |
def draw_heading(self, writer):
if self.dirty == self.STATE_REFRESH:
writer(u''.join(
(self.term.home, self.term.clear,
self.screen.msg_intro, '\n',
self.screen.header, '\n',)))
return True | Conditionally redraw screen when ``dirty`` attribute is valued REFRESH.
When Pager attribute ``dirty`` is ``STATE_REFRESH``, cursor is moved
to (0,0), screen is cleared, and heading is displayed.
:param writer: callable writes to output stream, receiving unicode.
:returns: True if clas... |
def draw_status(self, writer, idx):
if self.term.is_a_tty:
writer(self.term.hide_cursor())
style = self.screen.style
writer(self.term.move(self.term.height - 1))
if idx == self.last_page:
last_end = u'(END)'
else:
... | Conditionally draw status bar when output terminal is a tty.
:param writer: callable writes to output stream, receiving unicode.
:param idx: current page position index.
:type idx: int |
def page_view(self, data):
if self.term.is_a_tty:
yield self.term.move(self.screen.row_begins, 0)
# sequence clears to end-of-line
clear_eol = self.term.clear_eol
# sequence clears to end-of-screen
clear_eos = self.term.clear_eos
# track our current c... | Generator yields text to be displayed for the current unicode pageview.
:param data: The current page's data as tuple of ``(ucs, name)``.
:rtype: generator |
def text_entry(self, ucs, name):
style = self.screen.style
if len(name) > style.name_len:
idx = max(0, style.name_len - len(style.continuation))
name = u''.join((name[:idx], style.continuation if idx else u''))
if style.alignment == 'right':
fmt = u' ... | Display a single column segment row describing ``(ucs, name)``.
:param ucs: target unicode point character string.
:param name: name of unicode point.
:rtype: unicode |
def back_tick(cmd, ret_err=False, as_str=True, raise_err=None):
if raise_err is None:
raise_err = False if ret_err else True
cmd_is_seq = isinstance(cmd, (list, tuple))
proc = Popen(cmd, stdout=PIPE, stderr=PIPE, shell=not cmd_is_seq)
out, err = proc.communicate()
retcode = proc.returnc... | Run command `cmd`, return stdout, or stdout, stderr if `ret_err`
Roughly equivalent to ``check_output`` in Python 2.7
Parameters
----------
cmd : sequence
command to execute
ret_err : bool, optional
If True, return stderr in addition to stdout. If False, just return
stdout... |
def unique_by_index(sequence):
uniques = []
for element in sequence:
if element not in uniques:
uniques.append(element)
return uniques | unique elements in `sequence` in the order in which they occur
Parameters
----------
sequence : iterable
Returns
-------
uniques : list
unique elements of sequence, ordered by the order in which the element
occurs in `sequence` |
def ensure_permissions(mode_flags=stat.S_IWUSR):
def decorator(f):
def modify(filename, *args, **kwargs):
m = chmod_perms(filename) if exists(filename) else mode_flags
if not m & mode_flags:
os.chmod(filename, m | mode_flags)
try:
retu... | decorator to ensure a filename has given permissions.
If changed, original permissions are restored after the decorated
modification. |
def get_install_names(filename):
lines = _cmd_out_err(['otool', '-L', filename])
if not _line0_says_object(lines[0], filename):
return ()
names = tuple(parse_install_name(line)[0] for line in lines[1:])
install_id = get_install_id(filename)
if not install_id is None:
assert name... | Return install names from library named in `filename`
Returns tuple of install names
tuple will be empty if no install names, or if this is not an object file.
Parameters
----------
filename : str
filename of library
Returns
-------
install_names : tuple
tuple of inst... |
def get_install_id(filename):
lines = _cmd_out_err(['otool', '-D', filename])
if not _line0_says_object(lines[0], filename):
return None
if len(lines) == 1:
return None
if len(lines) != 2:
raise InstallNameError('Unexpected otool output ' + '\n'.join(lines))
return lines... | Return install id from library named in `filename`
Returns None if no install id, or if this is not an object file.
Parameters
----------
filename : str
filename of library
Returns
-------
install_id : str
install id of library `filename`, or None if no install id |
def set_install_name(filename, oldname, newname):
names = get_install_names(filename)
if oldname not in names:
raise InstallNameError('{0} not in install names for {1}'.format(
oldname, filename))
back_tick(['install_name_tool', '-change', oldname, newname, filename]) | Set install name `oldname` to `newname` in library filename
Parameters
----------
filename : str
filename of library
oldname : str
current install name in library
newname : str
replacement name for `oldname` |
def set_install_id(filename, install_id):
if get_install_id(filename) is None:
raise InstallNameError('{0} has no install id'.format(filename))
back_tick(['install_name_tool', '-id', install_id, filename]) | Set install id for library named in `filename`
Parameters
----------
filename : str
filename of library
install_id : str
install id for library `filename`
Raises
------
RuntimeError if `filename` has not install id |
def get_rpaths(filename):
try:
lines = _cmd_out_err(['otool', '-l', filename])
except RuntimeError:
return ()
if not _line0_says_object(lines[0], filename):
return ()
lines = [line.strip() for line in lines]
paths = []
line_no = 1
while line_no < len(lines):
... | Return a tuple of rpaths from the library `filename`
If `filename` is not a library then the returned tuple will be empty.
Parameters
----------
filaname : str
filename of library
Returns
-------
rpath : tuple
rpath paths in `filename` |
def dir2zip(in_dir, zip_fname):
z = zipfile.ZipFile(zip_fname, 'w',
compression=zipfile.ZIP_DEFLATED)
for root, dirs, files in os.walk(in_dir):
for file in files:
in_fname = pjoin(root, file)
in_stat = os.stat(in_fname)
# Preserve file per... | Make a zip file `zip_fname` with contents of directory `in_dir`
The recorded filenames are relative to `in_dir`, so doing a standard zip
unpack of the resulting `zip_fname` in an empty directory will result in
the original directory contents.
Parameters
----------
in_dir : str
Director... |
def find_package_dirs(root_path):
package_sdirs = set()
for entry in os.listdir(root_path):
fname = entry if root_path == '.' else pjoin(root_path, entry)
if isdir(fname) and exists(pjoin(fname, '__init__.py')):
package_sdirs.add(fname)
return package_sdirs | Find python package directories in directory `root_path`
Parameters
----------
root_path : str
Directory to search for package subdirectories
Returns
-------
package_sdirs : set
Set of strings where each is a subdirectory of `root_path`, containing
an ``__init__.py`` fi... |
def cmp_contents(filename1, filename2):
with open_readable(filename1, 'rb') as fobj:
contents1 = fobj.read()
with open_readable(filename2, 'rb') as fobj:
contents2 = fobj.read()
return contents1 == contents2 | Returns True if contents of the files are the same
Parameters
----------
filename1 : str
filename of first file to compare
filename2 : str
filename of second file to compare
Returns
-------
tf : bool
True if binary contents of `filename1` is same as binary contents ... |
def get_archs(libname):
if not exists(libname):
raise RuntimeError(libname + " is not a file")
try:
stdout = back_tick(['lipo', '-info', libname])
except RuntimeError:
return frozenset()
lines = [line.strip() for line in stdout.split('\n') if line.strip()]
# For some rea... | Return architecture types from library `libname`
Parameters
----------
libname : str
filename of binary for which to return arch codes
Returns
-------
arch_names : frozenset
Empty (frozen)set if no arch codes. If not empty, contains one or more
of 'ppc', 'ppc64', 'i386... |
def validate_signature(filename):
out, err = back_tick(['codesign', '--verify', filename],
ret_err=True, as_str=True, raise_err=False)
if not err:
return # The existing signature is valid
if 'code object is not signed at all' in err:
return # File has no signatu... | Remove invalid signatures from a binary file
If the file signature is missing or valid then it will be ignored
Invalid signatures are replaced with an ad-hoc signature. This is the
closest you can get to removing a signature on MacOS
Parameters
----------
filename : str
Filepath to a... |
def os_path_relpath(path, start=os.path.curdir):
if not path:
raise ValueError("no path specified")
start_list = [x for x in os.path.abspath(start).split(os.path.sep) if x]
path_list = [x for x in os.path.abspath(path).split(os.path.sep) if x]
# Work out how much of the filepath is shared b... | Return a relative version of a path |
def fuse_trees(to_tree, from_tree, lib_exts=('.so', '.dylib', '.a')):
for from_dirpath, dirnames, filenames in os.walk(from_tree):
to_dirpath = pjoin(to_tree, relpath(from_dirpath, from_tree))
# Copy any missing directories in to_path
for dirname in tuple(dirnames):
to_path ... | Fuse path `from_tree` into path `to_tree`
For each file in `from_tree` - check for library file extension (in
`lib_exts` - if present, check if there is a file with matching relative
path in `to_tree`, if so, use :func:`delocate.tools.lipo_fuse` to fuse the
two libraries together and write into `to_tre... |
def fuse_wheels(to_wheel, from_wheel, out_wheel):
to_wheel, from_wheel, out_wheel = [
abspath(w) for w in (to_wheel, from_wheel, out_wheel)]
with InTemporaryDirectory():
zip2dir(to_wheel, 'to_wheel')
zip2dir(from_wheel, 'from_wheel')
fuse_trees('to_wheel', 'from_wheel')
... | Fuse `from_wheel` into `to_wheel`, write to `out_wheel`
Parameters
---------
to_wheel : str
filename of wheel to fuse into
from_wheel : str
filename of wheel to fuse from
out_wheel : str
filename of new wheel from fusion of `to_wheel` and `from_wheel` |
def delocate_tree_libs(lib_dict, lib_path, root_path):
copied_libs = {}
delocated_libs = set()
copied_basenames = set()
rp_root_path = realpath(root_path)
rp_lib_path = realpath(lib_path)
# Test for errors first to avoid getting half-way through changing the tree
for required, requiring... | Move needed libraries in `lib_dict` into `lib_path`
`lib_dict` has keys naming libraries required by the files in the
corresponding value. Call the keys, "required libs". Call the values
"requiring objects".
Copy all the required libs to `lib_path`. Fix up the rpaths and install
names in the re... |
def copy_recurse(lib_path, copy_filt_func = None, copied_libs = None):
if copied_libs is None:
copied_libs = {}
else:
copied_libs = dict(copied_libs)
done = False
while not done:
in_len = len(copied_libs)
_copy_required(lib_path, copy_filt_func, copied_libs)
... | Analyze `lib_path` for library dependencies and copy libraries
`lib_path` is a directory containing libraries. The libraries might
themselves have dependencies. This function analyzes the dependencies and
copies library dependencies that match the filter `copy_filt_func`. It also
adjusts the dependin... |
def _copy_required(lib_path, copy_filt_func, copied_libs):
# Paths will be prepended with `lib_path`
lib_dict = tree_libs(lib_path)
# Map library paths after copy ('copied') to path before copy ('orig')
rp_lp = realpath(lib_path)
copied2orig = dict((pjoin(rp_lp, basename(c)), c) for c in copied... | Copy libraries required for files in `lib_path` to `lib_path`
Augment `copied_libs` dictionary with any newly copied libraries, modifying
`copied_libs` in-place - see Notes.
This is one pass of ``copy_recurse``
Parameters
----------
lib_path : str
Directory containing libraries
co... |
def delocate_path(tree_path, lib_path,
lib_filt_func = None,
copy_filt_func = filter_system_libs):
if lib_filt_func == "dylibs-only":
lib_filt_func = _dylibs_only
if not exists(lib_path):
os.makedirs(lib_path)
lib_dict = tree_libs(tree_path, lib_filt_... | Copy required libraries for files in `tree_path` into `lib_path`
Parameters
----------
tree_path : str
Root path of tree to search for required libraries
lib_path : str
Directory into which we copy required libraries
lib_filt_func : None or str or callable, optional
If None,... |
def _merge_lib_dict(d1, d2):
for required, requirings in d2.items():
if required in d1:
d1[required].update(requirings)
else:
d1[required] = requirings
return None | Merges lib_dict `d2` into lib_dict `d1` |
def delocate_wheel(in_wheel,
out_wheel = None,
lib_sdir = '.dylibs',
lib_filt_func = None,
copy_filt_func = filter_system_libs,
require_archs = None,
check_verbose = False,
):
if ... | Update wheel by copying required libraries to `lib_sdir` in wheel
Create `lib_sdir` in wheel tree only if we are copying one or more
libraries.
If `out_wheel` is None (the default), overwrite the wheel `in_wheel`
in-place.
Parameters
----------
in_wheel : str
Filename of wheel to ... |
def patch_wheel(in_wheel, patch_fname, out_wheel=None):
in_wheel = abspath(in_wheel)
patch_fname = abspath(patch_fname)
if out_wheel is None:
out_wheel = in_wheel
else:
out_wheel = abspath(out_wheel)
if not exists(patch_fname):
raise ValueError("patch file {0} does not e... | Apply ``-p1`` style patch in `patch_fname` to contents of `in_wheel`
If `out_wheel` is None (the default), overwrite the wheel `in_wheel`
in-place.
Parameters
----------
in_wheel : str
Filename of wheel to process
patch_fname : str
Filename of patch file. Will be applied with ... |
def check_archs(copied_libs, require_archs=(), stop_fast=False):
if isinstance(require_archs, string_types):
require_archs = (['i386', 'x86_64'] if require_archs == 'intel'
else [require_archs])
require_archs = frozenset(require_archs)
bads = []
for depended_lib, de... | Check compatibility of archs in `copied_libs` dict
Parameters
----------
copied_libs : dict
dict containing the (key, value) pairs of (``copied_lib_path``,
``dependings_dict``), where ``copied_lib_path`` is a library real path
that has been copied during delocation, and ``dependings... |
def bads_report(bads, path_prefix=None):
path_processor = ((lambda x : x) if path_prefix is None
else get_rp_stripper(path_prefix))
reports = []
for result in bads:
if len(result) == 3:
depended_lib, depending_lib, missing_archs = result
reports.app... | Return a nice report of bad architectures in `bads`
Parameters
----------
bads : set
set of length 2 or 3 tuples. A length 2 tuple is of form
``(depending_lib, missing_archs)`` meaning that an arch in
`require_archs` was missing from ``depending_lib``. A length 3 tuple
is o... |
def tree_libs(start_path, filt_func=None):
lib_dict = {}
for dirpath, dirnames, basenames in os.walk(start_path):
for base in basenames:
depending_libpath = realpath(pjoin(dirpath, base))
if not filt_func is None and not filt_func(depending_libpath):
continue... | Return analysis of library dependencies within `start_path`
Parameters
----------
start_path : str
root path of tree to search for libraries depending on other libraries.
filt_func : None or callable, optional
If None, inspect all files for library dependencies. If callable,
acc... |
def resolve_rpath(lib_path, rpaths):
if not lib_path.startswith('@rpath/'):
return lib_path
lib_rpath = lib_path.split('/', 1)[1]
for rpath in rpaths:
rpath_lib = realpath(pjoin(rpath, lib_rpath))
if os.path.exists(rpath_lib):
return rpath_lib
warnings.warn(
... | Return `lib_path` with its `@rpath` resolved
If the `lib_path` doesn't have `@rpath` then it's returned as is.
If `lib_path` has `@rpath` then returns the first `rpaths`/`lib_path`
combination found. If the library can't be found in `rpaths` then a
detailed warning is printed and `lib_path` is return... |
def get_prefix_stripper(strip_prefix):
n = len(strip_prefix)
def stripper(path):
return path if not path.startswith(strip_prefix) else path[n:]
return stripper | Return function to strip `strip_prefix` prefix from string if present
Parameters
----------
prefix : str
Prefix to strip from the beginning of string if present
Returns
-------
stripper : func
function such that ``stripper(a_string)`` will strip `prefix` from
``a_string... |
def stripped_lib_dict(lib_dict, strip_prefix):
relative_dict = {}
stripper = get_prefix_stripper(strip_prefix)
for lib_path, dependings_dict in lib_dict.items():
ding_dict = {}
for depending_libpath, install_name in dependings_dict.items():
ding_dict[stripper(depending_libpa... | Return `lib_dict` with `strip_prefix` removed from start of paths
Use to give form of `lib_dict` that appears relative to some base path
given by `strip_prefix`. Particularly useful for analyzing wheels where we
unpack to a temporary path before analyzing.
Parameters
----------
lib_dict : dic... |
def wheel_libs(wheel_fname, filt_func = None):
with TemporaryDirectory() as tmpdir:
zip2dir(wheel_fname, tmpdir)
lib_dict = tree_libs(tmpdir, filt_func)
return stripped_lib_dict(lib_dict, realpath(tmpdir) + os.path.sep) | Return analysis of library dependencies with a Python wheel
Use this routine for a dump of the dependency tree.
Parameters
----------
wheel_fname : str
Filename of wheel
filt_func : None or callable, optional
If None, inspect all files for library dependencies. If callable,
... |
def _open_for_csv(name, mode):
if sys.version_info[0] < 3:
return open_rw(name, mode + 'b')
return open_rw(name, mode, newline='', encoding='utf-8') | Deal with Python 2/3 open API differences |
def rewrite_record(bdist_dir):
info_dirs = glob.glob(pjoin(bdist_dir, '*.dist-info'))
if len(info_dirs) != 1:
raise WheelToolsError("Should be exactly one `*.dist_info` directory")
record_path = pjoin(info_dirs[0], 'RECORD')
record_relpath = relpath(record_path, bdist_dir)
# Unsign whee... | Rewrite RECORD file with hashes for all files in `wheel_sdir`
Copied from :method:`wheel.bdist_wheel.bdist_wheel.write_record`
Will also unsign wheel
Parameters
----------
bdist_dir : str
Path of unpacked wheel file |
def add_platforms(in_wheel, platforms, out_path=None, clobber=False):
in_wheel = abspath(in_wheel)
out_path = dirname(in_wheel) if out_path is None else abspath(out_path)
wf = WheelFile(in_wheel)
info_fname = _get_wheelinfo_name(wf)
# Check what tags we have
in_fname_tags = wf.parsed_filena... | Add platform tags `platforms` to `in_wheel` filename and WHEEL tags
Add any platform tags in `platforms` that are missing from `in_wheel`
filename.
Add any platform tags in `platforms` that are missing from `in_wheel`
``WHEEL`` file.
Parameters
----------
in_wheel : str
Filename o... |
def temporal_betweenness_centrality(tnet=None, paths=None, calc='time'):
if tnet is not None and paths is not None:
raise ValueError('Only network or path input allowed.')
if tnet is None and paths is None:
raise ValueError('No input.')
# if shortest paths are not calculated, calculate ... | Returns temporal betweenness centrality per node.
Parameters
-----------
Input should be *either* tnet or paths.
data : array or dict
Temporal network input (graphlet or contact). nettype: 'bu', 'bd'.
calc : str
either 'global' or 'time'
paths : pandas dataframe
O... |
def volatility(tnet, distance_func_name='default', calc='global', communities=None, event_displacement=None):
r
# Get input (C or G)
tnet, netinfo = process_input(tnet, ['C', 'G', 'TN'])
distance_func_name = check_distance_funciton_input(
distance_func_name, netinfo)
if not isinstance(distan... | r"""
Volatility of temporal networks.
Volatility is the average distance between consecutive time points of graphlets (difference is caclualted either globally or per edge).
Parameters
----------
tnet : array or dict
temporal network input (graphlet or contact). Nettype: 'bu','bd','wu','w... |
def allegiance(community):
N = community.shape[0]
C = community.shape[1]
T = P = np.zeros([N, N])
for t in range(len(community[0, :])):
for i in range(len(community[:, 0])):
for j in range(len(community[:, 0])):
if i == j:
continue
... | Computes the allegiance matrix with values representing the probability that
nodes i and j were assigned to the same community by time-varying clustering methods.
parameters
----------
community : array
array of community assignment of size node,time
returns
-------
P : array
... |
def rand_poisson(nnodes, ncontacts, lam=1, nettype='bu', netinfo=None, netrep='graphlet'):
if isinstance(ncontacts, list):
if len(ncontacts) != nnodes:
raise ValueError(
'Number of contacts, if a list, should be one per node')
if isinstance(lam, list):
if len(lam... | Generate a random network where intervals between contacts are distributed by a poisson distribution
Parameters
----------
nnodes : int
Number of nodes in networks
ncontacts : int or list
Number of expected contacts (i.e. edges). If list, number of contacts for each node.
Any ... |
def temporal_participation_coeff(tnet, communities=None, decay=None, removeneg=False):
r
if communities is None:
if isinstance(tnet, dict):
if 'communities' in tnet.keys():
communities = tnet['communities']
else:
raise ValueError('Community index n... | r'''
Temporal participation coefficient is a measure of diversity of connections across communities for individual nodes.
Parameters
----------
tnet : array, dict
graphlet or contact sequence input. Only positive matrices considered.
communities : array
community vector. Either 1D (... |
def graphlet_stack_plot(netin, ax, q=10, cmap='Reds', gridcolor='k', borderwidth=2, bordercolor=None, Fs=1, timeunit='', t0=1, sharpen='yes', vminmax='minmax'):
r
# Get input type (C, G, TO)
inputType = checkInput(netin)
# Convert TO to C representation
if inputType == 'TO':
netin = netin.co... | r'''
Returns matplotlib axis handle for graphlet_stack_plot. This is a row of transformed connectivity matrices to look like a 3D stack.
Parameters
----------
netin : array, dict
network input (graphlet or contact)
ax : matplotlib ax handles.
q : int
Quality. Increaseing this w... |
def partition_inference(tctc_mat, comp, tau, sigma, kappa):
r
communityinfo = {}
communityinfo['community'] = []
communityinfo['start'] = np.empty(0)
communityinfo['end'] = np.empty(0)
communityinfo['size'] = np.empty(0)
for i, tcomp in enumerate(comp):
# This can go in parallel loop... | r"""
Takes tctc trajectory matrix and returns dataframe where all multi-label communities are listed
Can take a little bit of time with large datasets and optimizaiton could remove some for loops. |
def tctc(data, tau, epsilon, sigma, kappa=0, largedataset=False, rule='flock', noise=None, raw_signal='amplitude', output='array', tempdir=None, njobs=1, largestonly=False):
r
# Get distance matrix
if largedataset:
raise NotImplementedError(
'HDF5 implementation for large datasets is not... | r"""
Runs TCTC community detection
Parameters
----------
data : array
Multiariate series with dimensions: "time, node" that belong to a network.
tau : int
tau specifies the minimum number of time-points of each temporal community must last.
epsilon : float
epsilon specif... |
def temporal_efficiency(tnet=None, paths=None, calc='global'):
r
if tnet is not None and paths is not None:
raise ValueError('Only network or path input allowed.')
if tnet is None and paths is None:
raise ValueError('No input.')
# if shortest paths are not calculated, calculate them
... | r"""
Returns temporal efficiency estimate. BU networks only.
Parameters
----------
Input should be *either* tnet or paths.
data : array or dict
Temporal network input (graphlet or contact). nettype: 'bu', 'bd'.
paths : pandas dataframe
Output of TenetoBIDS.networkmeasure.sho... |
def network_from_array(self, array):
if len(array.shape) == 2:
array = np.array(array, ndmin=3).transpose([1, 2, 0])
teneto.utils.check_TemporalNetwork_input(array, 'array')
uvals = np.unique(array)
if len(uvals) == 2 and 1 in uvals and 0 in uvals:
i, j, ... | impo
Defines a network from an array.
Parameters
----------
array : array
3D numpy array. |
def network_from_df(self, df):
teneto.utils.check_TemporalNetwork_input(df, 'df')
self.network = df
self._update_network() | Defines a network from an array.
Parameters
----------
array : array
Pandas dataframe. Should have columns: \'i\', \'j\', \'t\' where i and j are node indicies and t is the temporal index.
If weighted, should also include \'weight\'. Each row is an edge. |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.