repository_name stringclasses 316
values | func_path_in_repository stringlengths 6 223 | func_name stringlengths 1 134 | language stringclasses 1
value | func_code_string stringlengths 57 65.5k | func_documentation_string stringlengths 1 46.3k | split_name stringclasses 1
value | func_code_url stringlengths 91 315 | called_functions listlengths 1 156 ⌀ | enclosing_scope stringlengths 2 1.48M |
|---|---|---|---|---|---|---|---|---|---|
kennethreitz/records | records.py | RecordCollection.dataset | python | def dataset(self):
# Create a new Tablib Dataset.
data = tablib.Dataset()
# If the RecordCollection is empty, just return the empty set
# Check number of rows by typecasting to list
if len(list(self)) == 0:
return data
# Set the column names as headers on Ta... | A Tablib Dataset representation of the RecordCollection. | train | https://github.com/kennethreitz/records/blob/ecd857266c5e7830d657cbe0196816314790563b/records.py#L170-L188 | [
"def _reduce_datetimes(row):\n \"\"\"Receives a row, converts datetimes to strings.\"\"\"\n\n row = list(row)\n\n for i in range(len(row)):\n if hasattr(row[i], 'isoformat'):\n row[i] = row[i].isoformat()\n return tuple(row)\n"
] | class RecordCollection(object):
"""A set of excellent Records from a query."""
def __init__(self, rows):
self._rows = rows
self._all_rows = []
self.pending = True
def __repr__(self):
return '<RecordCollection size={} pending={}>'.format(len(self), self.pending)
def __it... |
kennethreitz/records | records.py | RecordCollection.all | python | def all(self, as_dict=False, as_ordereddict=False):
# By calling list it calls the __iter__ method
rows = list(self)
if as_dict:
return [r.as_dict() for r in rows]
elif as_ordereddict:
return [r.as_dict(ordered=True) for r in rows]
return rows | Returns a list of all rows for the RecordCollection. If they haven't
been fetched yet, consume the iterator and cache the results. | train | https://github.com/kennethreitz/records/blob/ecd857266c5e7830d657cbe0196816314790563b/records.py#L190-L202 | null | class RecordCollection(object):
"""A set of excellent Records from a query."""
def __init__(self, rows):
self._rows = rows
self._all_rows = []
self.pending = True
def __repr__(self):
return '<RecordCollection size={} pending={}>'.format(len(self), self.pending)
def __it... |
kennethreitz/records | records.py | RecordCollection.first | python | def first(self, default=None, as_dict=False, as_ordereddict=False):
# Try to get a record, or return/raise default.
try:
record = self[0]
except IndexError:
if isexception(default):
raise default
return default
# Cast and return.
... | Returns a single record for the RecordCollection, or `default`. If
`default` is an instance or subclass of Exception, then raise it
instead of returning it. | train | https://github.com/kennethreitz/records/blob/ecd857266c5e7830d657cbe0196816314790563b/records.py#L207-L226 | [
"def isexception(obj):\n \"\"\"Given an object, return a boolean indicating whether it is an instance\n or subclass of :py:class:`Exception`.\n \"\"\"\n if isinstance(obj, Exception):\n return True\n if isclass(obj) and issubclass(obj, Exception):\n return True\n return False\n"
] | class RecordCollection(object):
"""A set of excellent Records from a query."""
def __init__(self, rows):
self._rows = rows
self._all_rows = []
self.pending = True
def __repr__(self):
return '<RecordCollection size={} pending={}>'.format(len(self), self.pending)
def __it... |
kennethreitz/records | records.py | RecordCollection.one | python | def one(self, default=None, as_dict=False, as_ordereddict=False):
# Ensure that we don't have more than one row.
try:
self[1]
except IndexError:
return self.first(default=default, as_dict=as_dict, as_ordereddict=as_ordereddict)
else:
raise ValueError(... | Returns a single record for the RecordCollection, ensuring that it
is the only record, or returns `default`. If `default` is an instance
or subclass of Exception, then raise it instead of returning it. | train | https://github.com/kennethreitz/records/blob/ecd857266c5e7830d657cbe0196816314790563b/records.py#L228-L241 | [
"def first(self, default=None, as_dict=False, as_ordereddict=False):\n \"\"\"Returns a single record for the RecordCollection, or `default`. If\n `default` is an instance or subclass of Exception, then raise it\n instead of returning it.\"\"\"\n\n # Try to get a record, or return/raise default.\n try... | class RecordCollection(object):
"""A set of excellent Records from a query."""
def __init__(self, rows):
self._rows = rows
self._all_rows = []
self.pending = True
def __repr__(self):
return '<RecordCollection size={} pending={}>'.format(len(self), self.pending)
def __it... |
kennethreitz/records | records.py | Database.get_connection | python | def get_connection(self):
if not self.open:
raise exc.ResourceClosedError('Database closed.')
return Connection(self._engine.connect()) | Get a connection to this Database. Connections are retrieved from a
pool. | train | https://github.com/kennethreitz/records/blob/ecd857266c5e7830d657cbe0196816314790563b/records.py#L285-L292 | null | class Database(object):
"""A Database. Encapsulates a url and an SQLAlchemy engine with a pool of
connections.
"""
def __init__(self, db_url=None, **kwargs):
# If no db_url was provided, fallback to $DATABASE_URL.
self.db_url = db_url or DATABASE_URL
if not self.db_url:
... |
kennethreitz/records | records.py | Database.query | python | def query(self, query, fetchall=False, **params):
with self.get_connection() as conn:
return conn.query(query, fetchall, **params) | Executes the given SQL query against the Database. Parameters can,
optionally, be provided. Returns a RecordCollection, which can be
iterated over to get result rows as dictionaries. | train | https://github.com/kennethreitz/records/blob/ecd857266c5e7830d657cbe0196816314790563b/records.py#L294-L300 | [
"def get_connection(self):\n \"\"\"Get a connection to this Database. Connections are retrieved from a\n pool.\n \"\"\"\n if not self.open:\n raise exc.ResourceClosedError('Database closed.')\n\n return Connection(self._engine.connect())\n"
] | class Database(object):
"""A Database. Encapsulates a url and an SQLAlchemy engine with a pool of
connections.
"""
def __init__(self, db_url=None, **kwargs):
# If no db_url was provided, fallback to $DATABASE_URL.
self.db_url = db_url or DATABASE_URL
if not self.db_url:
... |
kennethreitz/records | records.py | Database.bulk_query | python | def bulk_query(self, query, *multiparams):
with self.get_connection() as conn:
conn.bulk_query(query, *multiparams) | Bulk insert or update. | train | https://github.com/kennethreitz/records/blob/ecd857266c5e7830d657cbe0196816314790563b/records.py#L302-L306 | [
"def get_connection(self):\n \"\"\"Get a connection to this Database. Connections are retrieved from a\n pool.\n \"\"\"\n if not self.open:\n raise exc.ResourceClosedError('Database closed.')\n\n return Connection(self._engine.connect())\n"
] | class Database(object):
"""A Database. Encapsulates a url and an SQLAlchemy engine with a pool of
connections.
"""
def __init__(self, db_url=None, **kwargs):
# If no db_url was provided, fallback to $DATABASE_URL.
self.db_url = db_url or DATABASE_URL
if not self.db_url:
... |
kennethreitz/records | records.py | Database.query_file | python | def query_file(self, path, fetchall=False, **params):
with self.get_connection() as conn:
return conn.query_file(path, fetchall, **params) | Like Database.query, but takes a filename to load a query from. | train | https://github.com/kennethreitz/records/blob/ecd857266c5e7830d657cbe0196816314790563b/records.py#L308-L312 | [
"def get_connection(self):\n \"\"\"Get a connection to this Database. Connections are retrieved from a\n pool.\n \"\"\"\n if not self.open:\n raise exc.ResourceClosedError('Database closed.')\n\n return Connection(self._engine.connect())\n"
] | class Database(object):
"""A Database. Encapsulates a url and an SQLAlchemy engine with a pool of
connections.
"""
def __init__(self, db_url=None, **kwargs):
# If no db_url was provided, fallback to $DATABASE_URL.
self.db_url = db_url or DATABASE_URL
if not self.db_url:
... |
kennethreitz/records | records.py | Database.bulk_query_file | python | def bulk_query_file(self, path, *multiparams):
with self.get_connection() as conn:
conn.bulk_query_file(path, *multiparams) | Like Database.bulk_query, but takes a filename to load a query from. | train | https://github.com/kennethreitz/records/blob/ecd857266c5e7830d657cbe0196816314790563b/records.py#L314-L318 | [
"def get_connection(self):\n \"\"\"Get a connection to this Database. Connections are retrieved from a\n pool.\n \"\"\"\n if not self.open:\n raise exc.ResourceClosedError('Database closed.')\n\n return Connection(self._engine.connect())\n"
] | class Database(object):
"""A Database. Encapsulates a url and an SQLAlchemy engine with a pool of
connections.
"""
def __init__(self, db_url=None, **kwargs):
# If no db_url was provided, fallback to $DATABASE_URL.
self.db_url = db_url or DATABASE_URL
if not self.db_url:
... |
kennethreitz/records | records.py | Database.transaction | python | def transaction(self):
conn = self.get_connection()
tx = conn.transaction()
try:
yield conn
tx.commit()
except:
tx.rollback()
finally:
conn.close() | A context manager for executing a transaction on this Database. | train | https://github.com/kennethreitz/records/blob/ecd857266c5e7830d657cbe0196816314790563b/records.py#L321-L332 | [
"def get_connection(self):\n \"\"\"Get a connection to this Database. Connections are retrieved from a\n pool.\n \"\"\"\n if not self.open:\n raise exc.ResourceClosedError('Database closed.')\n\n return Connection(self._engine.connect())\n",
"def close(self):\n self._conn.close()\n sel... | class Database(object):
"""A Database. Encapsulates a url and an SQLAlchemy engine with a pool of
connections.
"""
def __init__(self, db_url=None, **kwargs):
# If no db_url was provided, fallback to $DATABASE_URL.
self.db_url = db_url or DATABASE_URL
if not self.db_url:
... |
kennethreitz/records | records.py | Connection.query | python | def query(self, query, fetchall=False, **params):
# Execute the given query.
cursor = self._conn.execute(text(query), **params) # TODO: PARAMS GO HERE
# Row-by-row Record generator.
row_gen = (Record(cursor.keys(), row) for row in cursor)
# Convert psycopg2 results to RecordCo... | Executes the given SQL query against the connected Database.
Parameters can, optionally, be provided. Returns a RecordCollection,
which can be iterated over to get result rows as dictionaries. | train | https://github.com/kennethreitz/records/blob/ecd857266c5e7830d657cbe0196816314790563b/records.py#L355-L374 | [
"def all(self, as_dict=False, as_ordereddict=False):\n \"\"\"Returns a list of all rows for the RecordCollection. If they haven't\n been fetched yet, consume the iterator and cache the results.\"\"\"\n\n # By calling list it calls the __iter__ method\n rows = list(self)\n\n if as_dict:\n retur... | class Connection(object):
"""A Database connection."""
def __init__(self, connection):
self._conn = connection
self.open = not connection.closed
def close(self):
self._conn.close()
self.open = False
def __enter__(self):
return self
def __exit__(self, exc, ... |
kennethreitz/records | records.py | Connection.bulk_query | python | def bulk_query(self, query, *multiparams):
self._conn.execute(text(query), *multiparams) | Bulk insert or update. | train | https://github.com/kennethreitz/records/blob/ecd857266c5e7830d657cbe0196816314790563b/records.py#L376-L379 | null | class Connection(object):
"""A Database connection."""
def __init__(self, connection):
self._conn = connection
self.open = not connection.closed
def close(self):
self._conn.close()
self.open = False
def __enter__(self):
return self
def __exit__(self, exc, ... |
kennethreitz/records | records.py | Connection.query_file | python | def query_file(self, path, fetchall=False, **params):
# If path doesn't exists
if not os.path.exists(path):
raise IOError("File '{}' not found!".format(path))
# If it's a directory
if os.path.isdir(path):
raise IOError("'{}' is a directory!".format(path))
... | Like Connection.query, but takes a filename to load a query from. | train | https://github.com/kennethreitz/records/blob/ecd857266c5e7830d657cbe0196816314790563b/records.py#L381-L397 | null | class Connection(object):
"""A Database connection."""
def __init__(self, connection):
self._conn = connection
self.open = not connection.closed
def close(self):
self._conn.close()
self.open = False
def __enter__(self):
return self
def __exit__(self, exc, ... |
kennethreitz/records | records.py | Connection.bulk_query_file | python | def bulk_query_file(self, path, *multiparams):
# If path doesn't exists
if not os.path.exists(path):
raise IOError("File '{}'' not found!".format(path))
# If it's a directory
if os.path.isdir(path):
raise IOError("'{}' is a directory!".format(path))
# ... | Like Connection.bulk_query, but takes a filename to load a query
from. | train | https://github.com/kennethreitz/records/blob/ecd857266c5e7830d657cbe0196816314790563b/records.py#L399-L416 | null | class Connection(object):
"""A Database connection."""
def __init__(self, connection):
self._conn = connection
self.open = not connection.closed
def close(self):
self._conn.close()
self.open = False
def __enter__(self):
return self
def __exit__(self, exc, ... |
kennethreitz/maya | maya/compat.py | comparable | python | def comparable(klass):
# On Python 2, __cmp__ will just work, so no need to add extra methods:
if not is_py3:
return klass
def __eq__(self, other):
c = self.__cmp__(other)
if c is NotImplemented:
return c
return c == 0
def __ne__(self, other):
c = s... | Class decorator that ensures support for the special C{__cmp__} method.
On Python 2 this does nothing.
On Python 3, C{__eq__}, C{__lt__}, etc. methods are added to the class,
relying on C{__cmp__} to implement their comparisons. | train | https://github.com/kennethreitz/maya/blob/774b141d91a83a5d77cb5351db3d02bf50564b21/maya/compat.py#L43-L102 | null | # -*- coding: utf-8 -*-
"""
maya.compat
~~~~~~~~~~~~~~~
This module handles import compatibility issues between Python 2 and
Python 3.
"""
import sys
# -------
# Pythons
# -------
# Syntax sugar.
_ver = sys.version_info
# : Python 2.x?
is_py2 = (_ver[0] == 2)
# : Python 3.x?
is_py3 = (_ver[0] == 3)
# ---------
# Spec... |
kennethreitz/maya | maya/core.py | validate_class_type_arguments | python | def validate_class_type_arguments(operator):
def inner(function):
def wrapper(self, *args, **kwargs):
for arg in args + tuple(kwargs.values()):
if not isinstance(arg, self.__class__):
raise TypeError(
'unorderable types: {}() {} {}()'... | Decorator to validate all the arguments to function
are of the type of calling class for passed operator | train | https://github.com/kennethreitz/maya/blob/774b141d91a83a5d77cb5351db3d02bf50564b21/maya/core.py#L22-L43 | null | # ___ __ ___ _ _ ___
# || \/ | ||=|| \\// ||=||
# || | || || // || ||
import email.utils
import time
import functools
from datetime import timedelta, datetime as Datetime
import re
import pytz
import humanize
import dateparser
import pendulum
import snaptime
from tzlocal import get_localzone
from dateutil.re... |
kennethreitz/maya | maya/core.py | validate_arguments_type_of_function | python | def validate_arguments_type_of_function(param_type=None):
def inner(function):
def wrapper(self, *args, **kwargs):
type_ = param_type or type(self)
for arg in args + tuple(kwargs.values()):
if not isinstance(arg, type_):
raise TypeError(
... | Decorator to validate the <type> of arguments in
the calling function are of the `param_type` class.
if `param_type` is None, uses `param_type` as the class where it is used.
Note: Use this decorator on the functions of the class. | train | https://github.com/kennethreitz/maya/blob/774b141d91a83a5d77cb5351db3d02bf50564b21/maya/core.py#L46-L77 | null | # ___ __ ___ _ _ ___
# || \/ | ||=|| \\// ||=||
# || | || || // || ||
import email.utils
import time
import functools
from datetime import timedelta, datetime as Datetime
import re
import pytz
import humanize
import dateparser
import pendulum
import snaptime
from tzlocal import get_localzone
from dateutil.re... |
kennethreitz/maya | maya/core.py | utc_offset | python | def utc_offset(time_struct=None):
if time_struct:
ts = time_struct
else:
ts = time.localtime()
if ts[-1]:
offset = time.altzone
else:
offset = time.timezone
return offset | Returns the time offset from UTC accounting for DST
Keyword Arguments:
time_struct {time.struct_time} -- the struct time for which to
return the UTC offset.
If None, use current local time. | train | https://github.com/kennethreitz/maya/blob/774b141d91a83a5d77cb5351db3d02bf50564b21/maya/core.py#L369-L387 | null | # ___ __ ___ _ _ ___
# || \/ | ||=|| \\// ||=||
# || | || || // || ||
import email.utils
import time
import functools
from datetime import timedelta, datetime as Datetime
import re
import pytz
import humanize
import dateparser
import pendulum
import snaptime
from tzlocal import get_localzone
from dateutil.re... |
kennethreitz/maya | maya/core.py | when | python | def when(string, timezone='UTC', prefer_dates_from='current_period'):
"
settings = {
'TIMEZONE': timezone,
'RETURN_AS_TIMEZONE_AWARE': True,
'TO_TIMEZONE': 'UTC',
'PREFER_DATES_FROM': prefer_dates_from,
}
dt = dateparser.parse(string, settings=settings)
if dt is None... | Returns a MayaDT instance for the human moment specified.
Powered by dateparser. Useful for scraping websites.
Examples:
'next week', 'now', 'tomorrow', '300 years ago', 'August 14, 2015'
Keyword Arguments:
string -- string to be parsed
timezone -- timezone referenced from (defaul... | train | https://github.com/kennethreitz/maya/blob/774b141d91a83a5d77cb5351db3d02bf50564b21/maya/core.py#L710-L739 | [
"def wrapper(self, *args, **kwargs):\n type_ = param_type or type(self)\n for arg in args + tuple(kwargs.values()):\n if not isinstance(arg, type_):\n raise TypeError(\n (\n 'Invalid Type: {}.{}() accepts only the '\n 'arguments of type \"... | # ___ __ ___ _ _ ___
# || \/ | ||=|| \\// ||=||
# || | || || // || ||
import email.utils
import time
import functools
from datetime import timedelta, datetime as Datetime
import re
import pytz
import humanize
import dateparser
import pendulum
import snaptime
from tzlocal import get_localzone
from dateutil.re... |
kennethreitz/maya | maya/core.py | parse | python | def parse(string, timezone='UTC', day_first=False, year_first=True, strict=False):
"
options = {}
options['tz'] = timezone
options['day_first'] = day_first
options['year_first'] = year_first
options['strict'] = strict
dt = pendulum.parse(str(string), **options)
return MayaDT.from_dateti... | Returns a MayaDT instance for the machine-produced moment specified.
Powered by pendulum.
Accepts most known formats. Useful for working with data.
Keyword Arguments:
string -- string to be parsed
timezone -- timezone referenced from (default: 'UTC')
day_first -- if true, the first... | train | https://github.com/kennethreitz/maya/blob/774b141d91a83a5d77cb5351db3d02bf50564b21/maya/core.py#L742-L767 | [
"def wrapper(self, *args, **kwargs):\n type_ = param_type or type(self)\n for arg in args + tuple(kwargs.values()):\n if not isinstance(arg, type_):\n raise TypeError(\n (\n 'Invalid Type: {}.{}() accepts only the '\n 'arguments of type \"... | # ___ __ ___ _ _ ___
# || \/ | ||=|| \\// ||=||
# || | || || // || ||
import email.utils
import time
import functools
from datetime import timedelta, datetime as Datetime
import re
import pytz
import humanize
import dateparser
import pendulum
import snaptime
from tzlocal import get_localzone
from dateutil.re... |
kennethreitz/maya | maya/core.py | _seconds_or_timedelta | python | def _seconds_or_timedelta(duration):
if isinstance(duration, int):
dt_timedelta = timedelta(seconds=duration)
elif isinstance(duration, timedelta):
dt_timedelta = duration
else:
raise TypeError(
'Expects argument as `datetime.timedelta` object '
'or seconds in... | Returns `datetime.timedelta` object for the passed duration.
Keyword Arguments:
duration -- `datetime.timedelta` object or seconds in `int` format. | train | https://github.com/kennethreitz/maya/blob/774b141d91a83a5d77cb5351db3d02bf50564b21/maya/core.py#L770-L786 | null | # ___ __ ___ _ _ ___
# || \/ | ||=|| \\// ||=||
# || | || || // || ||
import email.utils
import time
import functools
from datetime import timedelta, datetime as Datetime
import re
import pytz
import humanize
import dateparser
import pendulum
import snaptime
from tzlocal import get_localzone
from dateutil.re... |
kennethreitz/maya | maya/core.py | intervals | python | def intervals(start, end, interval):
interval = _seconds_or_timedelta(interval)
current_timestamp = start
while current_timestamp.epoch < end.epoch:
yield current_timestamp
current_timestamp = current_timestamp.add(
seconds=interval.total_seconds()
) | Yields MayaDT objects between the start and end MayaDTs given,
at a given interval (seconds or timedelta). | train | https://github.com/kennethreitz/maya/blob/774b141d91a83a5d77cb5351db3d02bf50564b21/maya/core.py#L799-L811 | [
"def _seconds_or_timedelta(duration):\n \"\"\"Returns `datetime.timedelta` object for the passed duration.\n\n Keyword Arguments:\n duration -- `datetime.timedelta` object or seconds in `int` format.\n \"\"\"\n if isinstance(duration, int):\n dt_timedelta = timedelta(seconds=duration)\n ... | # ___ __ ___ _ _ ___
# || \/ | ||=|| \\// ||=||
# || | || || // || ||
import email.utils
import time
import functools
from datetime import timedelta, datetime as Datetime
import re
import pytz
import humanize
import dateparser
import pendulum
import snaptime
from tzlocal import get_localzone
from dateutil.re... |
kennethreitz/maya | maya/core.py | MayaDT.add | python | def add(self, **kwargs):
return self.from_datetime(
pendulum.instance(self.datetime()).add(**kwargs)
) | Returns a new MayaDT object with the given offsets. | train | https://github.com/kennethreitz/maya/blob/774b141d91a83a5d77cb5351db3d02bf50564b21/maya/core.py#L142-L146 | [
"def datetime(self, to_timezone=None, naive=False):\n \"\"\"Returns a timezone-aware datetime...\n Defaulting to UTC (as it should).\n\n Keyword Arguments:\n to_timezone {str} -- timezone to convert to (default: None/UTC)\n naive {bool} -- if True,\n the tzinfo is simpl... | class MayaDT(object):
"""The Maya Datetime object."""
__EPOCH_START = (1970, 1, 1)
def __init__(self, epoch):
super(MayaDT, self).__init__()
self._epoch = epoch
def __repr__(self):
return '<MayaDT epoch={}>'.format(self._epoch)
def __str__(self):
return self.rfc282... |
kennethreitz/maya | maya/core.py | MayaDT.subtract | python | def subtract(self, **kwargs):
return self.from_datetime(
pendulum.instance(self.datetime()).subtract(**kwargs)
) | Returns a new MayaDT object with the given offsets. | train | https://github.com/kennethreitz/maya/blob/774b141d91a83a5d77cb5351db3d02bf50564b21/maya/core.py#L148-L152 | [
"def datetime(self, to_timezone=None, naive=False):\n \"\"\"Returns a timezone-aware datetime...\n Defaulting to UTC (as it should).\n\n Keyword Arguments:\n to_timezone {str} -- timezone to convert to (default: None/UTC)\n naive {bool} -- if True,\n the tzinfo is simpl... | class MayaDT(object):
"""The Maya Datetime object."""
__EPOCH_START = (1970, 1, 1)
def __init__(self, epoch):
super(MayaDT, self).__init__()
self._epoch = epoch
def __repr__(self):
return '<MayaDT epoch={}>'.format(self._epoch)
def __str__(self):
return self.rfc282... |
kennethreitz/maya | maya/core.py | MayaDT.snap | python | def snap(self, instruction):
return self.from_datetime(snaptime.snap(self.datetime(), instruction)) | Returns a new MayaDT object modified by the given instruction.
Powered by snaptime. See https://github.com/zartstrom/snaptime
for a complete documentation about the snaptime instructions. | train | https://github.com/kennethreitz/maya/blob/774b141d91a83a5d77cb5351db3d02bf50564b21/maya/core.py#L158-L165 | [
"def datetime(self, to_timezone=None, naive=False):\n \"\"\"Returns a timezone-aware datetime...\n Defaulting to UTC (as it should).\n\n Keyword Arguments:\n to_timezone {str} -- timezone to convert to (default: None/UTC)\n naive {bool} -- if True,\n the tzinfo is simpl... | class MayaDT(object):
"""The Maya Datetime object."""
__EPOCH_START = (1970, 1, 1)
def __init__(self, epoch):
super(MayaDT, self).__init__()
self._epoch = epoch
def __repr__(self):
return '<MayaDT epoch={}>'.format(self._epoch)
def __str__(self):
return self.rfc282... |
kennethreitz/maya | maya/core.py | MayaDT.local_timezone | python | def local_timezone(self):
if self._local_tz.zone in pytz.all_timezones:
return self._local_tz.zone
return self.timezone | Returns the name of the local timezone. | train | https://github.com/kennethreitz/maya/blob/774b141d91a83a5d77cb5351db3d02bf50564b21/maya/core.py#L180-L185 | null | class MayaDT(object):
"""The Maya Datetime object."""
__EPOCH_START = (1970, 1, 1)
def __init__(self, epoch):
super(MayaDT, self).__init__()
self._epoch = epoch
def __repr__(self):
return '<MayaDT epoch={}>'.format(self._epoch)
def __str__(self):
return self.rfc282... |
kennethreitz/maya | maya/core.py | MayaDT.__dt_to_epoch | python | def __dt_to_epoch(dt):
# Assume UTC if no datetime is provided.
if dt.tzinfo is None:
dt = dt.replace(tzinfo=pytz.utc)
epoch_start = Datetime(*MayaDT.__EPOCH_START, tzinfo=pytz.timezone('UTC'))
return (dt - epoch_start).total_seconds() | Converts a datetime into an epoch. | train | https://github.com/kennethreitz/maya/blob/774b141d91a83a5d77cb5351db3d02bf50564b21/maya/core.py#L194-L200 | null | class MayaDT(object):
"""The Maya Datetime object."""
__EPOCH_START = (1970, 1, 1)
def __init__(self, epoch):
super(MayaDT, self).__init__()
self._epoch = epoch
def __repr__(self):
return '<MayaDT epoch={}>'.format(self._epoch)
def __str__(self):
return self.rfc282... |
kennethreitz/maya | maya/core.py | MayaDT.from_struct | python | def from_struct(klass, struct, timezone=pytz.UTC):
struct_time = time.mktime(struct) - utc_offset(struct)
dt = Datetime.fromtimestamp(struct_time, timezone)
return klass(klass.__dt_to_epoch(dt)) | Returns MayaDT instance from a 9-tuple struct
It's assumed to be from gmtime(). | train | https://github.com/kennethreitz/maya/blob/774b141d91a83a5d77cb5351db3d02bf50564b21/maya/core.py#L212-L219 | [
"def utc_offset(time_struct=None):\n \"\"\"\n Returns the time offset from UTC accounting for DST\n\n Keyword Arguments:\n time_struct {time.struct_time} -- the struct time for which to\n return the UTC offset.\n If No... | class MayaDT(object):
"""The Maya Datetime object."""
__EPOCH_START = (1970, 1, 1)
def __init__(self, epoch):
super(MayaDT, self).__init__()
self._epoch = epoch
def __repr__(self):
return '<MayaDT epoch={}>'.format(self._epoch)
def __str__(self):
return self.rfc282... |
kennethreitz/maya | maya/core.py | MayaDT.datetime | python | def datetime(self, to_timezone=None, naive=False):
if to_timezone:
dt = self.datetime().astimezone(pytz.timezone(to_timezone))
else:
dt = Datetime.utcfromtimestamp(self._epoch)
dt.replace(tzinfo=self._tz)
# Strip the timezone info if requested to do so.
... | Returns a timezone-aware datetime...
Defaulting to UTC (as it should).
Keyword Arguments:
to_timezone {str} -- timezone to convert to (default: None/UTC)
naive {bool} -- if True,
the tzinfo is simply dropped (default: False) | train | https://github.com/kennethreitz/maya/blob/774b141d91a83a5d77cb5351db3d02bf50564b21/maya/core.py#L238-L259 | [
"def datetime(self, to_timezone=None, naive=False):\n \"\"\"Returns a timezone-aware datetime...\n Defaulting to UTC (as it should).\n\n Keyword Arguments:\n to_timezone {str} -- timezone to convert to (default: None/UTC)\n naive {bool} -- if True,\n the tzinfo is simpl... | class MayaDT(object):
"""The Maya Datetime object."""
__EPOCH_START = (1970, 1, 1)
def __init__(self, epoch):
super(MayaDT, self).__init__()
self._epoch = epoch
def __repr__(self):
return '<MayaDT epoch={}>'.format(self._epoch)
def __str__(self):
return self.rfc282... |
kennethreitz/maya | maya/core.py | MayaDT.iso8601 | python | def iso8601(self):
# Get a timezone-naive datetime.
dt = self.datetime(naive=True)
return '{}Z'.format(dt.isoformat()) | Returns an ISO 8601 representation of the MayaDT. | train | https://github.com/kennethreitz/maya/blob/774b141d91a83a5d77cb5351db3d02bf50564b21/maya/core.py#L269-L273 | [
"def datetime(self, to_timezone=None, naive=False):\n \"\"\"Returns a timezone-aware datetime...\n Defaulting to UTC (as it should).\n\n Keyword Arguments:\n to_timezone {str} -- timezone to convert to (default: None/UTC)\n naive {bool} -- if True,\n the tzinfo is simpl... | class MayaDT(object):
"""The Maya Datetime object."""
__EPOCH_START = (1970, 1, 1)
def __init__(self, epoch):
super(MayaDT, self).__init__()
self._epoch = epoch
def __repr__(self):
return '<MayaDT epoch={}>'.format(self._epoch)
def __str__(self):
return self.rfc282... |
kennethreitz/maya | maya/core.py | MayaDT.slang_date | python | def slang_date(self, locale="en"):
"
dt = pendulum.instance(self.datetime())
try:
return _translate(dt, locale)
except KeyError:
pass
delta = humanize.time.abs_timedelta(
timedelta(seconds=(self.epoch - now().epoch)))
format_string =... | Returns human slang representation of date.
Keyword Arguments:
locale -- locale to translate to, e.g. 'fr' for french.
(default: 'en' - English) | train | https://github.com/kennethreitz/maya/blob/774b141d91a83a5d77cb5351db3d02bf50564b21/maya/core.py#L335-L356 | [
"def now():\n \"\"\"Returns a MayaDT instance for this exact moment.\"\"\"\n epoch = time.time()\n return MayaDT(epoch=epoch)\n",
"def _translate(dt, target_locale):\n en = default_loader.get_locale(\"en\")\n target = default_loader.get_locale(target_locale)\n naturaldate = humanize.naturaldate(... | class MayaDT(object):
"""The Maya Datetime object."""
__EPOCH_START = (1970, 1, 1)
def __init__(self, epoch):
super(MayaDT, self).__init__()
self._epoch = epoch
def __repr__(self):
return '<MayaDT epoch={}>'.format(self._epoch)
def __str__(self):
return self.rfc282... |
kennethreitz/maya | maya/core.py | MayaDT.slang_time | python | def slang_time(self, locale="en"):
"
dt = self.datetime()
return pendulum.instance(dt).diff_for_humans(locale=locale) | Returns human slang representation of time.
Keyword Arguments:
locale -- locale to translate to, e.g. 'fr' for french.
(default: 'en' - English) | train | https://github.com/kennethreitz/maya/blob/774b141d91a83a5d77cb5351db3d02bf50564b21/maya/core.py#L358-L366 | [
"def datetime(self, to_timezone=None, naive=False):\n \"\"\"Returns a timezone-aware datetime...\n Defaulting to UTC (as it should).\n\n Keyword Arguments:\n to_timezone {str} -- timezone to convert to (default: None/UTC)\n naive {bool} -- if True,\n the tzinfo is simpl... | class MayaDT(object):
"""The Maya Datetime object."""
__EPOCH_START = (1970, 1, 1)
def __init__(self, epoch):
super(MayaDT, self).__init__()
self._epoch = epoch
def __repr__(self):
return '<MayaDT epoch={}>'.format(self._epoch)
def __str__(self):
return self.rfc282... |
dunovank/jupyter-themes | jupyterthemes/__init__.py | get_themes | python | def get_themes():
styles_dir = os.path.join(package_dir, 'styles')
themes = [os.path.basename(theme).replace('.less', '')
for theme in glob('{0}/*.less'.format(styles_dir))]
return themes | return list of available themes | train | https://github.com/dunovank/jupyter-themes/blob/421016c2e4fed75fa1830d664c10478d9bd25ed1/jupyterthemes/__init__.py#L20-L25 | null | import os
import sys
from argparse import ArgumentParser
from glob import glob
from . import stylefx
from . import jtplot
# path to local site-packages/jupyterthemes
package_dir = os.path.dirname(os.path.realpath(__file__))
modules = glob(os.path.dirname(__file__) + "/*.py")
__all__ = [os.path.basename(f)[:-3] for f i... |
dunovank/jupyter-themes | jupyterthemes/__init__.py | install_theme | python | def install_theme(theme=None,
monofont=None,
monosize=11,
nbfont=None,
nbfontsize=13,
tcfont=None,
tcfontsize=13,
dffontsize=93,
outfontsize=85,
mathfontsize=100,
... | Install theme to jupyter_customcss with specified font, fontsize,
md layout, and toolbar pref | train | https://github.com/dunovank/jupyter-themes/blob/421016c2e4fed75fa1830d664c10478d9bd25ed1/jupyterthemes/__init__.py#L28-L112 | [
"def reset_default(verbose=False):\n \"\"\"Remove custom.css and custom fonts\"\"\"\n paths = [jupyter_custom, jupyter_nbext]\n\n for fpath in paths:\n custom = '{0}{1}{2}.css'.format(fpath, os.sep, 'custom')\n try:\n os.remove(custom)\n except Exception:\n pass\n... | import os
import sys
from argparse import ArgumentParser
from glob import glob
from . import stylefx
from . import jtplot
# path to local site-packages/jupyterthemes
package_dir = os.path.dirname(os.path.realpath(__file__))
modules = glob(os.path.dirname(__file__) + "/*.py")
__all__ = [os.path.basename(f)[:-3] for f i... |
dunovank/jupyter-themes | jupyterthemes/jtplot.py | infer_theme | python | def infer_theme():
themes = [os.path.basename(theme).replace('.less', '')
for theme in glob('{0}/*.less'.format(styles_dir))]
if os.path.exists(theme_name_file):
with open(theme_name_file) as f:
theme = f.readlines()[0]
if theme not in themes:
theme = 'd... | checks jupyter_config_dir() for text file containing theme name
(updated whenever user installs a new theme) | train | https://github.com/dunovank/jupyter-themes/blob/421016c2e4fed75fa1830d664c10478d9bd25ed1/jupyterthemes/jtplot.py#L62-L76 | null | import os
import sys
import re
from glob import glob
import matplotlib as mpl
from jupyter_core.paths import jupyter_config_dir
# path to install (~/.jupyter/custom/)
jupyter_custom = os.path.join(jupyter_config_dir(), 'custom')
# path to local site-packages/jupyterthemes
package_dir = os.path.dirname(os.path.realpath... |
dunovank/jupyter-themes | jupyterthemes/jtplot.py | style | python | def style(theme=None, context='paper', grid=True, gridlines=u'-', ticks=False, spines=True, fscale=1.2, figsize=(8., 7.)):
# set context and font rc parameters, return rcdict
rcdict = set_context(context=context, fscale=fscale, figsize=figsize)
# read in theme name from ~/.jupyter/custom/current_theme.txt... | main function for styling matplotlib according to theme
::Arguments::
theme (str): 'oceans16', 'grade3', 'chesterish', 'onedork', 'monokai', 'solarizedl', 'solarizedd'. If no theme name supplied the currently installed notebook theme will be used.
context (str): 'paper' (Default), 'notebook', 'tal... | train | https://github.com/dunovank/jupyter-themes/blob/421016c2e4fed75fa1830d664c10478d9bd25ed1/jupyterthemes/jtplot.py#L79-L109 | [
"def infer_theme():\n \"\"\" checks jupyter_config_dir() for text file containing theme name\n (updated whenever user installs a new theme)\n \"\"\"\n themes = [os.path.basename(theme).replace('.less', '')\n for theme in glob('{0}/*.less'.format(styles_dir))]\n if os.path.exists(them... | import os
import sys
import re
from glob import glob
import matplotlib as mpl
from jupyter_core.paths import jupyter_config_dir
# path to install (~/.jupyter/custom/)
jupyter_custom = os.path.join(jupyter_config_dir(), 'custom')
# path to local site-packages/jupyterthemes
package_dir = os.path.dirname(os.path.realpath... |
dunovank/jupyter-themes | jupyterthemes/jtplot.py | set_style | python | def set_style(rcdict, theme=None, grid=True, gridlines=u'-', ticks=False, spines=True):
# extract style and color info for theme
styleMap, clist = get_theme_style(theme)
# extract style variables
figureFace = styleMap['figureFace']
axisFace = styleMap['axisFace']
textColor = styleMap['textColo... | This code has been modified from seaborn.rcmod.set_style()
::Arguments::
rcdict (str): dict of "context" properties (filled by set_context())
theme (str): name of theme to use when setting color properties
grid (bool): turns off axis grid if False (default: True)
ticks (bool): remove... | train | https://github.com/dunovank/jupyter-themes/blob/421016c2e4fed75fa1830d664c10478d9bd25ed1/jupyterthemes/jtplot.py#L113-L188 | [
"def get_theme_style(theme):\n \"\"\"\n read-in theme style info and populate styleMap (dict of with mpl.rcParams)\n and clist (list of hex codes passed to color cylcler)\n ::Arguments::\n theme (str): theme name\n ::Returns::\n styleMap (dict): dict containing theme-specific colors for... | import os
import sys
import re
from glob import glob
import matplotlib as mpl
from jupyter_core.paths import jupyter_config_dir
# path to install (~/.jupyter/custom/)
jupyter_custom = os.path.join(jupyter_config_dir(), 'custom')
# path to local site-packages/jupyterthemes
package_dir = os.path.dirname(os.path.realpath... |
dunovank/jupyter-themes | jupyterthemes/jtplot.py | set_context | python | def set_context(context='paper', fscale=1., figsize=(8., 7.)):
# scale all the parameters by the same factor depending on the context
scaling = dict(paper=.8, notebook=1, talk=1.3, poster=1.6)[context]
context_dict = {k: v * scaling for k, v in base_context.items()}
# scale default figsize
figX, fi... | Most of this code has been copied/modified from seaborn.rcmod.plotting_context()
::Arguments::
context (str): 'paper', 'notebook', 'talk', or 'poster'
fscale (float): font-size scalar applied to axes ticks, legend, labels, etc. | train | https://github.com/dunovank/jupyter-themes/blob/421016c2e4fed75fa1830d664c10478d9bd25ed1/jupyterthemes/jtplot.py#L191-L212 | null | import os
import sys
import re
from glob import glob
import matplotlib as mpl
from jupyter_core.paths import jupyter_config_dir
# path to install (~/.jupyter/custom/)
jupyter_custom = os.path.join(jupyter_config_dir(), 'custom')
# path to local site-packages/jupyterthemes
package_dir = os.path.dirname(os.path.realpath... |
dunovank/jupyter-themes | jupyterthemes/jtplot.py | figsize | python | def figsize(x=8, y=7., aspect=1.):
# update rcparams with adjusted figsize params
mpl.rcParams.update({'figure.figsize': (x*aspect, y)}) | manually set the default figure size of plots
::Arguments::
x (float): x-axis size
y (float): y-axis size
aspect (float): aspect ratio scalar | train | https://github.com/dunovank/jupyter-themes/blob/421016c2e4fed75fa1830d664c10478d9bd25ed1/jupyterthemes/jtplot.py#L215-L223 | null | import os
import sys
import re
from glob import glob
import matplotlib as mpl
from jupyter_core.paths import jupyter_config_dir
# path to install (~/.jupyter/custom/)
jupyter_custom = os.path.join(jupyter_config_dir(), 'custom')
# path to local site-packages/jupyterthemes
package_dir = os.path.dirname(os.path.realpath... |
dunovank/jupyter-themes | jupyterthemes/jtplot.py | get_theme_style | python | def get_theme_style(theme):
styleMap, clist = get_default_jtstyle()
if theme == 'default':
return styleMap, clist
syntaxVars = ['@yellow:', '@orange:', '@red:', '@magenta:', '@violet:', '@blue:', '@cyan:', '@green:']
get_hex_code = lambda line: line.split(':')[-1].split(';')[0][-7:]
theme... | read-in theme style info and populate styleMap (dict of with mpl.rcParams)
and clist (list of hex codes passed to color cylcler)
::Arguments::
theme (str): theme name
::Returns::
styleMap (dict): dict containing theme-specific colors for figure properties
clist (list): list of colors... | train | https://github.com/dunovank/jupyter-themes/blob/421016c2e4fed75fa1830d664c10478d9bd25ed1/jupyterthemes/jtplot.py#L226-L258 | [
"def remove_non_colors(clist):\n checkHex = r'^#(?:[0-9a-fA-F]{3}){1,2}$'\n return [clr for clr in clist if re.search(checkHex, clr)]\n",
"def get_default_jtstyle():\n styleMap = {'axisFace': 'white',\n 'figureFace': 'white',\n 'textColor': '.15',\n 'edgeColor... | import os
import sys
import re
from glob import glob
import matplotlib as mpl
from jupyter_core.paths import jupyter_config_dir
# path to install (~/.jupyter/custom/)
jupyter_custom = os.path.join(jupyter_config_dir(), 'custom')
# path to local site-packages/jupyterthemes
package_dir = os.path.dirname(os.path.realpath... |
dunovank/jupyter-themes | jupyterthemes/jtplot.py | reset | python | def reset():
colors = [(0., 0., 1.), (0., .5, 0.), (1., 0., 0.), (.75, .75, 0.),
(.75, .75, 0.), (0., .75, .75), (0., 0., 0.)]
for code, color in zip("bgrmyck", colors):
rgb = mpl.colors.colorConverter.to_rgb(color)
mpl.colors.colorConverter.colors[code] = rgb
mpl.colors.colo... | full reset of matplotlib default style and colors | train | https://github.com/dunovank/jupyter-themes/blob/421016c2e4fed75fa1830d664c10478d9bd25ed1/jupyterthemes/jtplot.py#L276-L287 | null | import os
import sys
import re
from glob import glob
import matplotlib as mpl
from jupyter_core.paths import jupyter_config_dir
# path to install (~/.jupyter/custom/)
jupyter_custom = os.path.join(jupyter_config_dir(), 'custom')
# path to local site-packages/jupyterthemes
package_dir = os.path.dirname(os.path.realpath... |
dunovank/jupyter-themes | jupyterthemes/stylefx.py | less_to_css | python | def less_to_css(style_less):
with fileOpen(tempfile, 'w') as f:
f.write(style_less)
os.chdir(package_dir)
style_css = lesscpy.compile(tempfile)
style_css += '\n\n'
return style_css | write less-compiled css file to jupyter_customcss in jupyter_dir | train | https://github.com/dunovank/jupyter-themes/blob/421016c2e4fed75fa1830d664c10478d9bd25ed1/jupyterthemes/stylefx.py#L69-L77 | [
"def fileOpen(filename, mode):\n if sys.version_info[0]==3:\n return open(filename, mode, encoding='utf8', errors='ignore')\n else:\n return open(filename, mode)\n"
] | import os, sys
import lesscpy
from shutil import copyfile, rmtree
from jupyter_core.paths import jupyter_config_dir, jupyter_data_dir
from glob import glob
from tempfile import mkstemp
# path to local site-packages/jupyterthemes
package_dir = os.path.dirname(os.path.realpath(__file__))
# path to user jupyter-themes d... |
dunovank/jupyter-themes | jupyterthemes/stylefx.py | set_font_properties | python | def set_font_properties(style_less,
nbfont=None,
tcfont=None,
monofont=None,
monosize=11,
tcfontsize=13,
nbfontsize=13,
prfontsize=95,
... | Parent function for setting notebook, text/md, and
codecell font-properties | train | https://github.com/dunovank/jupyter-themes/blob/421016c2e4fed75fa1830d664c10478d9bd25ed1/jupyterthemes/stylefx.py#L120-L179 | [
"def convert_fontsizes(fontsizes):\n # if triple digits, move decimal (105 --> 10.5)\n fontsizes = [str(fs) for fs in fontsizes]\n for i, fs in enumerate(fontsizes):\n if len(fs) >= 3:\n fontsizes[i] = '.'.join([fs[:-1], fs[-1]])\n elif int(fs) > 25:\n fontsizes[i] = '.'... | import os, sys
import lesscpy
from shutil import copyfile, rmtree
from jupyter_core.paths import jupyter_config_dir, jupyter_data_dir
from glob import glob
from tempfile import mkstemp
# path to local site-packages/jupyterthemes
package_dir = os.path.dirname(os.path.realpath(__file__))
# path to user jupyter-themes d... |
dunovank/jupyter-themes | jupyterthemes/stylefx.py | import_fonts | python | def import_fonts(style_less, fontname, font_subdir):
ftype_dict = {'woff2': 'woff2',
'woff': 'woff',
'ttf': 'truetype',
'otf': 'opentype',
'svg': 'svg'}
define_font = (
"@font-face {{font-family: {fontname};\n\tfont-weight:"
... | Copy all custom fonts to ~/.jupyter/custom/fonts/ and
write import statements to style_less | train | https://github.com/dunovank/jupyter-themes/blob/421016c2e4fed75fa1830d664c10478d9bd25ed1/jupyterthemes/stylefx.py#L182-L218 | [
"def send_fonts_to_jupyter(font_file_path):\n fname = font_file_path.split(os.sep)[-1]\n copyfile(font_file_path, os.path.join(jupyter_custom_fonts, fname))\n"
] | import os, sys
import lesscpy
from shutil import copyfile, rmtree
from jupyter_core.paths import jupyter_config_dir, jupyter_data_dir
from glob import glob
from tempfile import mkstemp
# path to local site-packages/jupyterthemes
package_dir = os.path.dirname(os.path.realpath(__file__))
# path to user jupyter-themes d... |
dunovank/jupyter-themes | jupyterthemes/stylefx.py | style_layout | python | def style_layout(style_less,
theme='grade3',
cursorwidth=2,
cursorcolor='default',
cellwidth='980',
lineheight=170,
margins='auto',
vimext=False,
toolbar=False,
nbname... | Set general layout and style properties of text and code cells | train | https://github.com/dunovank/jupyter-themes/blob/421016c2e4fed75fa1830d664c10478d9bd25ed1/jupyterthemes/stylefx.py#L221-L326 | [
"def fileOpen(filename, mode):\n if sys.version_info[0]==3:\n return open(filename, mode, encoding='utf8', errors='ignore')\n else:\n return open(filename, mode)\n",
"def toggle_settings(\n toolbar=False, nbname=False, hideprompt=False, kernellogo=False):\n \"\"\"Toggle main notebook... | import os, sys
import lesscpy
from shutil import copyfile, rmtree
from jupyter_core.paths import jupyter_config_dir, jupyter_data_dir
from glob import glob
from tempfile import mkstemp
# path to local site-packages/jupyterthemes
package_dir = os.path.dirname(os.path.realpath(__file__))
# path to user jupyter-themes d... |
dunovank/jupyter-themes | jupyterthemes/stylefx.py | toggle_settings | python | def toggle_settings(
toolbar=False, nbname=False, hideprompt=False, kernellogo=False):
toggle = ''
if toolbar:
toggle += 'div#maintoolbar {margin-left: 8px !important;}\n'
toggle += '.toolbar.container {width: 100% !important;}\n'
else:
toggle += 'div#maintoolbar {display: n... | Toggle main notebook toolbar (e.g., buttons), filename,
and kernel logo. | train | https://github.com/dunovank/jupyter-themes/blob/421016c2e4fed75fa1830d664c10478d9bd25ed1/jupyterthemes/stylefx.py#L329-L364 | null | import os, sys
import lesscpy
from shutil import copyfile, rmtree
from jupyter_core.paths import jupyter_config_dir, jupyter_data_dir
from glob import glob
from tempfile import mkstemp
# path to local site-packages/jupyterthemes
package_dir = os.path.dirname(os.path.realpath(__file__))
# path to user jupyter-themes d... |
dunovank/jupyter-themes | jupyterthemes/stylefx.py | set_mathjax_style | python | def set_mathjax_style(style_css, mathfontsize):
jax_style = """<script>
MathJax.Hub.Config({
"HTML-CSS": {
/*preferredFont: "TeX",*/
/*availableFonts: ["TeX", "STIX"],*/
styles: {
scale: %d,
".MathJax_Display": {
"f... | Write mathjax settings, set math fontsize | train | https://github.com/dunovank/jupyter-themes/blob/421016c2e4fed75fa1830d664c10478d9bd25ed1/jupyterthemes/stylefx.py#L400-L420 | null | import os, sys
import lesscpy
from shutil import copyfile, rmtree
from jupyter_core.paths import jupyter_config_dir, jupyter_data_dir
from glob import glob
from tempfile import mkstemp
# path to local site-packages/jupyterthemes
package_dir = os.path.dirname(os.path.realpath(__file__))
# path to user jupyter-themes d... |
dunovank/jupyter-themes | jupyterthemes/stylefx.py | set_vim_style | python | def set_vim_style(theme):
vim_jupyter_nbext = os.path.join(jupyter_nbext, 'vim_binding')
if not os.path.isdir(vim_jupyter_nbext):
os.makedirs(vim_jupyter_nbext)
vim_less = '@import "styles{}";\n'.format(''.join([os.sep, theme]))
with open(vim_style, 'r') as vimstyle:
vim_less += vims... | Add style and compatibility with vim notebook extension | train | https://github.com/dunovank/jupyter-themes/blob/421016c2e4fed75fa1830d664c10478d9bd25ed1/jupyterthemes/stylefx.py#L424-L445 | null | import os, sys
import lesscpy
from shutil import copyfile, rmtree
from jupyter_core.paths import jupyter_config_dir, jupyter_data_dir
from glob import glob
from tempfile import mkstemp
# path to local site-packages/jupyterthemes
package_dir = os.path.dirname(os.path.realpath(__file__))
# path to user jupyter-themes d... |
dunovank/jupyter-themes | jupyterthemes/stylefx.py | reset_default | python | def reset_default(verbose=False):
paths = [jupyter_custom, jupyter_nbext]
for fpath in paths:
custom = '{0}{1}{2}.css'.format(fpath, os.sep, 'custom')
try:
os.remove(custom)
except Exception:
pass
try:
delete_font_files()
except Exception:
... | Remove custom.css and custom fonts | train | https://github.com/dunovank/jupyter-themes/blob/421016c2e4fed75fa1830d664c10478d9bd25ed1/jupyterthemes/stylefx.py#L448-L471 | [
"def check_directories():\n # Ensure all install dirs exist\n if not os.path.isdir(jupyter_home):\n os.makedirs(jupyter_home)\n if not os.path.isdir(jupyter_custom):\n os.makedirs(jupyter_custom)\n if not os.path.isdir(jupyter_custom_fonts):\n os.makedirs(jupyter_custom_fonts)\n ... | import os, sys
import lesscpy
from shutil import copyfile, rmtree
from jupyter_core.paths import jupyter_config_dir, jupyter_data_dir
from glob import glob
from tempfile import mkstemp
# path to local site-packages/jupyterthemes
package_dir = os.path.dirname(os.path.realpath(__file__))
# path to user jupyter-themes d... |
dunovank/jupyter-themes | jupyterthemes/stylefx.py | set_nb_theme | python | def set_nb_theme(name):
from IPython.core.display import HTML
styles_dir = os.path.join(package_dir, 'styles/compiled/')
css_path = glob('{0}/{1}.css'.format(styles_dir, name))[0]
customcss = open(css_path, "r").read()
return HTML(''.join(['<style> ', customcss, ' </style>'])) | Set theme from within notebook | train | https://github.com/dunovank/jupyter-themes/blob/421016c2e4fed75fa1830d664c10478d9bd25ed1/jupyterthemes/stylefx.py#L474-L481 | null | import os, sys
import lesscpy
from shutil import copyfile, rmtree
from jupyter_core.paths import jupyter_config_dir, jupyter_data_dir
from glob import glob
from tempfile import mkstemp
# path to local site-packages/jupyterthemes
package_dir = os.path.dirname(os.path.realpath(__file__))
# path to user jupyter-themes d... |
cs01/gdbgui | gdbgui/htmllistformatter.py | HtmlListFormatter.get_marked_up_list | python | def get_marked_up_list(self, tokensource):
# import ipdb; ipdb.set_trace()
source = self._format_lines(tokensource)
if self.hl_lines:
source = self._highlight_lines(source)
if not self.nowrap:
if self.linenos == 2:
source = self._wrap_inlinelinenos... | an updated version of pygments.formatter.format_unencoded | train | https://github.com/cs01/gdbgui/blob/5367f87554f8f7c671d1f4596c133bf1303154f0/gdbgui/htmllistformatter.py#L9-L36 | null | class HtmlListFormatter(HtmlFormatter):
"""A custom pygments class to format html. Returns a list of source code.
Each element of the list corresponds to a line of (marked up) source code.
"""
|
cs01/gdbgui | gdbgui/SSLify.py | get_ssl_context | python | def get_ssl_context(private_key, certificate):
if (
certificate
and os.path.isfile(certificate)
and private_key
and os.path.isfile(private_key)
):
context = ssl.SSLContext(ssl.PROTOCOL_TLSv1_2)
context.load_cert_chain(certificate, private_key)
return conte... | Get ssl context from private key and certificate paths.
The return value is used when calling Flask.
i.e. app.run(ssl_context=get_ssl_context(,,,)) | train | https://github.com/cs01/gdbgui/blob/5367f87554f8f7c671d1f4596c133bf1303154f0/gdbgui/SSLify.py#L90-L104 | null | """Module to enable SSL for Flask application. Adapted from
https://github.com/kennethreitz/flask-sslify
"""
import os
import ssl
from flask import request, redirect
YEAR_IN_SECS = 31536000
class SSLify(object):
"""Secures your Flask App."""
def __init__(
self, app=None, age=YEAR_IN_SECS, subdomain... |
cs01/gdbgui | gdbgui/SSLify.py | SSLify.init_app | python | def init_app(self, app):
app.config.setdefault("SSLIFY_SUBDOMAINS", False)
app.config.setdefault("SSLIFY_PERMANENT", False)
app.config.setdefault("SSLIFY_SKIPS", None)
self.hsts_include_subdomains = (
self.hsts_include_subdomains or app.config["SSLIFY_SUBDOMAINS"]
)
... | Configures the specified Flask app to enforce SSL. | train | https://github.com/cs01/gdbgui/blob/5367f87554f8f7c671d1f4596c133bf1303154f0/gdbgui/SSLify.py#L28-L41 | null | class SSLify(object):
"""Secures your Flask App."""
def __init__(
self, app=None, age=YEAR_IN_SECS, subdomains=False, permanent=False, skips=None
):
self.app = app
self.hsts_age = age
self.hsts_include_subdomains = subdomains
self.permanent = permanent
self.... |
cs01/gdbgui | gdbgui/SSLify.py | SSLify.set_hsts_header | python | def set_hsts_header(self, response):
# Should we add STS header?
if request.is_secure and not self.skip:
response.headers.setdefault("Strict-Transport-Security", self.hsts_header)
return response | Adds HSTS header to each response. | train | https://github.com/cs01/gdbgui/blob/5367f87554f8f7c671d1f4596c133bf1303154f0/gdbgui/SSLify.py#L82-L87 | null | class SSLify(object):
"""Secures your Flask App."""
def __init__(
self, app=None, age=YEAR_IN_SECS, subdomains=False, permanent=False, skips=None
):
self.app = app
self.hsts_age = age
self.hsts_include_subdomains = subdomains
self.permanent = permanent
self.... |
cs01/gdbgui | gdbgui/backend.py | csrf_protect_all_post_and_cross_origin_requests | python | def csrf_protect_all_post_and_cross_origin_requests():
success = None
if is_cross_origin(request):
logger.warning("Received cross origin request. Aborting")
abort(403)
if request.method in ["POST", "PUT"]:
token = session.get("csrf_token")
if token == request.form.get("csrf_... | returns None upon success | train | https://github.com/cs01/gdbgui/blob/5367f87554f8f7c671d1f4596c133bf1303154f0/gdbgui/backend.py#L116-L133 | [
"def is_cross_origin(request):\n \"\"\"Compare headers HOST and ORIGIN. Remove protocol prefix from ORIGIN, then\n compare. Return true if they are not equal\n example HTTP_HOST: '127.0.0.1:5000'\n example HTTP_ORIGIN: 'http://127.0.0.1:5000'\n \"\"\"\n origin = request.environ.get(\"HTTP_ORIGIN\"... | #!/usr/bin/env python
"""
A server that provides a graphical user interface to the gnu debugger (gdb).
https://github.com/cs01/gdbgui
"""
import argparse
import binascii
from distutils.spawn import find_executable
from flask import (
Flask,
session,
request,
Response,
render_template,
jsonify,... |
cs01/gdbgui | gdbgui/backend.py | is_cross_origin | python | def is_cross_origin(request):
origin = request.environ.get("HTTP_ORIGIN")
host = request.environ.get("HTTP_HOST")
if origin is None:
# origin is sometimes omitted by the browser when origin and host are equal
return False
if origin.startswith("http://"):
origin = origin.replace(... | Compare headers HOST and ORIGIN. Remove protocol prefix from ORIGIN, then
compare. Return true if they are not equal
example HTTP_HOST: '127.0.0.1:5000'
example HTTP_ORIGIN: 'http://127.0.0.1:5000' | train | https://github.com/cs01/gdbgui/blob/5367f87554f8f7c671d1f4596c133bf1303154f0/gdbgui/backend.py#L136-L152 | null | #!/usr/bin/env python
"""
A server that provides a graphical user interface to the gnu debugger (gdb).
https://github.com/cs01/gdbgui
"""
import argparse
import binascii
from distutils.spawn import find_executable
from flask import (
Flask,
session,
request,
Response,
render_template,
jsonify,... |
cs01/gdbgui | gdbgui/backend.py | csrf_protect | python | def csrf_protect(f):
@wraps(f)
def wrapper(*args, **kwargs):
token = session.get("csrf_token", None)
if token is None or token != request.environ.get("HTTP_X_CSRFTOKEN"):
logger.warning("Received invalid csrf token. Aborting")
abort(403)
# call original request h... | A decorator to add csrf protection by validing the X_CSRFTOKEN
field in request header | train | https://github.com/cs01/gdbgui/blob/5367f87554f8f7c671d1f4596c133bf1303154f0/gdbgui/backend.py#L155-L168 | null | #!/usr/bin/env python
"""
A server that provides a graphical user interface to the gnu debugger (gdb).
https://github.com/cs01/gdbgui
"""
import argparse
import binascii
from distutils.spawn import find_executable
from flask import (
Flask,
session,
request,
Response,
render_template,
jsonify,... |
cs01/gdbgui | gdbgui/backend.py | setup_backend | python | def setup_backend(
serve=True,
host=DEFAULT_HOST,
port=DEFAULT_PORT,
debug=False,
open_browser=True,
browsername=None,
testing=False,
private_key=None,
certificate=None,
LLDB=False,
):
app.config["LLDB"] = LLDB
kwargs = {}
ssl_context = get_ssl_context(private_key, c... | Run the server of the gdb gui | train | https://github.com/cs01/gdbgui/blob/5367f87554f8f7c671d1f4596c133bf1303154f0/gdbgui/backend.py#L180-L260 | [
"def get_ssl_context(private_key, certificate): # noqa\n return None\n",
"def get_ssl_context(private_key, certificate):\n \"\"\"Get ssl context from private key and certificate paths.\n The return value is used when calling Flask.\n i.e. app.run(ssl_context=get_ssl_context(,,,))\n \"\"\"\n if ... | #!/usr/bin/env python
"""
A server that provides a graphical user interface to the gnu debugger (gdb).
https://github.com/cs01/gdbgui
"""
import argparse
import binascii
from distutils.spawn import find_executable
from flask import (
Flask,
session,
request,
Response,
render_template,
jsonify,... |
cs01/gdbgui | gdbgui/backend.py | dbprint | python | def dbprint(*args):
if app and app.debug:
if USING_WINDOWS:
print("DEBUG: " + " ".join(args))
else:
CYELLOW2 = "\33[93m"
NORMAL = "\033[0m"
print(CYELLOW2 + "DEBUG: " + " ".join(args) + NORMAL) | print only if app.debug is truthy | train | https://github.com/cs01/gdbgui/blob/5367f87554f8f7c671d1f4596c133bf1303154f0/gdbgui/backend.py#L283-L292 | null | #!/usr/bin/env python
"""
A server that provides a graphical user interface to the gnu debugger (gdb).
https://github.com/cs01/gdbgui
"""
import argparse
import binascii
from distutils.spawn import find_executable
from flask import (
Flask,
session,
request,
Response,
render_template,
jsonify,... |
cs01/gdbgui | gdbgui/backend.py | run_gdb_command | python | def run_gdb_command(message):
controller = _state.get_controller_from_client_id(request.sid)
if controller is not None:
try:
# the command (string) or commands (list) to run
cmd = message["cmd"]
controller.write(cmd, read_response=False)
except Exception:
... | Endpoint for a websocket route.
Runs a gdb command.
Responds only if an error occurs when trying to write the command to
gdb | train | https://github.com/cs01/gdbgui/blob/5367f87554f8f7c671d1f4596c133bf1303154f0/gdbgui/backend.py#L347-L366 | [
"def get_controller_from_client_id(self, client_id):\n for controller, client_ids in self.controller_to_client_ids.items():\n if client_id in client_ids:\n return controller\n\n return None\n"
] | #!/usr/bin/env python
"""
A server that provides a graphical user interface to the gnu debugger (gdb).
https://github.com/cs01/gdbgui
"""
import argparse
import binascii
from distutils.spawn import find_executable
from flask import (
Flask,
session,
request,
Response,
render_template,
jsonify,... |
cs01/gdbgui | gdbgui/backend.py | send_msg_to_clients | python | def send_msg_to_clients(client_ids, msg, error=False):
if error:
stream = "stderr"
else:
stream = "stdout"
response = [{"message": None, "type": "console", "payload": msg, "stream": stream}]
for client_id in client_ids:
logger.info("emiting message to websocket client id " + cl... | Send message to all clients | train | https://github.com/cs01/gdbgui/blob/5367f87554f8f7c671d1f4596c133bf1303154f0/gdbgui/backend.py#L369-L382 | null | #!/usr/bin/env python
"""
A server that provides a graphical user interface to the gnu debugger (gdb).
https://github.com/cs01/gdbgui
"""
import argparse
import binascii
from distutils.spawn import find_executable
from flask import (
Flask,
session,
request,
Response,
render_template,
jsonify,... |
cs01/gdbgui | gdbgui/backend.py | read_and_forward_gdb_output | python | def read_and_forward_gdb_output():
while True:
socketio.sleep(0.05)
controllers_to_remove = []
controller_items = _state.controller_to_client_ids.items()
for controller, client_ids in controller_items:
try:
try:
response = controller.g... | A task that runs on a different thread, and emits websocket messages
of gdb responses | train | https://github.com/cs01/gdbgui/blob/5367f87554f8f7c671d1f4596c133bf1303154f0/gdbgui/backend.py#L418-L460 | [
"def send_msg_to_clients(client_ids, msg, error=False):\n \"\"\"Send message to all clients\"\"\"\n if error:\n stream = \"stderr\"\n else:\n stream = \"stdout\"\n\n response = [{\"message\": None, \"type\": \"console\", \"payload\": msg, \"stream\": stream}]\n\n for client_id in client... | #!/usr/bin/env python
"""
A server that provides a graphical user interface to the gnu debugger (gdb).
https://github.com/cs01/gdbgui
"""
import argparse
import binascii
from distutils.spawn import find_executable
from flask import (
Flask,
session,
request,
Response,
render_template,
jsonify,... |
cs01/gdbgui | gdbgui/backend.py | get_extra_files | python | def get_extra_files():
FILES_TO_SKIP = ["src/gdbgui.js"]
THIS_DIR = os.path.dirname(os.path.abspath(__file__))
extra_dirs = [THIS_DIR]
extra_files = []
for extra_dir in extra_dirs:
for dirname, _, files in os.walk(extra_dir):
for filename in files:
filepath = os.p... | returns a list of files that should be watched by the Flask server
when in debug mode to trigger a reload of the server | train | https://github.com/cs01/gdbgui/blob/5367f87554f8f7c671d1f4596c133bf1303154f0/gdbgui/backend.py#L471-L487 | null | #!/usr/bin/env python
"""
A server that provides a graphical user interface to the gnu debugger (gdb).
https://github.com/cs01/gdbgui
"""
import argparse
import binascii
from distutils.spawn import find_executable
from flask import (
Flask,
session,
request,
Response,
render_template,
jsonify,... |
cs01/gdbgui | gdbgui/backend.py | gdbgui | python | def gdbgui():
interpreter = "lldb" if app.config["LLDB"] else "gdb"
gdbpid = request.args.get("gdbpid", 0)
initial_gdb_user_command = request.args.get("initial_gdb_user_command", "")
add_csrf_token_to_session()
THEMES = ["monokai", "light"]
# fmt: off
initial_data = {
"csrf_token":... | Render the main gdbgui interface | train | https://github.com/cs01/gdbgui/blob/5367f87554f8f7c671d1f4596c133bf1303154f0/gdbgui/backend.py#L525-L562 | [
"def add_csrf_token_to_session():\n if \"csrf_token\" not in session:\n session[\"csrf_token\"] = binascii.hexlify(os.urandom(20)).decode(\"utf-8\")\n"
] | #!/usr/bin/env python
"""
A server that provides a graphical user interface to the gnu debugger (gdb).
https://github.com/cs01/gdbgui
"""
import argparse
import binascii
from distutils.spawn import find_executable
from flask import (
Flask,
session,
request,
Response,
render_template,
jsonify,... |
cs01/gdbgui | gdbgui/backend.py | get_last_modified_unix_sec | python | def get_last_modified_unix_sec():
path = request.args.get("path")
if path and os.path.isfile(path):
try:
last_modified = os.path.getmtime(path)
return jsonify({"path": path, "last_modified_unix_sec": last_modified})
except Exception as e:
return client_error(... | Get last modified unix time for a given file | train | https://github.com/cs01/gdbgui/blob/5367f87554f8f7c671d1f4596c133bf1303154f0/gdbgui/backend.py#L654-L666 | [
"def client_error(obj):\n return jsonify(obj), 400\n"
] | #!/usr/bin/env python
"""
A server that provides a graphical user interface to the gnu debugger (gdb).
https://github.com/cs01/gdbgui
"""
import argparse
import binascii
from distutils.spawn import find_executable
from flask import (
Flask,
session,
request,
Response,
render_template,
jsonify,... |
cs01/gdbgui | gdbgui/backend.py | read_file | python | def read_file():
path = request.args.get("path")
start_line = int(request.args.get("start_line"))
end_line = int(request.args.get("end_line"))
start_line = max(1, start_line) # make sure it's not negative
try:
highlight = json.loads(request.args.get("highlight", "true"))
except Except... | Read a file and return its contents as an array | train | https://github.com/cs01/gdbgui/blob/5367f87554f8f7c671d1f4596c133bf1303154f0/gdbgui/backend.py#L671-L743 | [
"def client_error(obj):\n return jsonify(obj), 400\n"
] | #!/usr/bin/env python
"""
A server that provides a graphical user interface to the gnu debugger (gdb).
https://github.com/cs01/gdbgui
"""
import argparse
import binascii
from distutils.spawn import find_executable
from flask import (
Flask,
session,
request,
Response,
render_template,
jsonify,... |
cs01/gdbgui | gdbgui/backend.py | main | python | def main():
parser = get_parser()
args = parser.parse_args()
if args.debug:
logger.setLevel(logging.NOTSET)
initialize_preferences()
if args.version:
print(__version__)
return
cmd = args.cmd or args.args
if args.no_browser and args.browser:
print("Cannot ... | Entry point from command line | train | https://github.com/cs01/gdbgui/blob/5367f87554f8f7c671d1f4596c133bf1303154f0/gdbgui/backend.py#L927-L997 | [
"def setup_backend(\n serve=True,\n host=DEFAULT_HOST,\n port=DEFAULT_PORT,\n debug=False,\n open_browser=True,\n browsername=None,\n testing=False,\n private_key=None,\n certificate=None,\n LLDB=False,\n):\n \"\"\"Run the server of the gdb gui\"\"\"\n app.config[\"LLDB\"] = LLDB... | #!/usr/bin/env python
"""
A server that provides a graphical user interface to the gnu debugger (gdb).
https://github.com/cs01/gdbgui
"""
import argparse
import binascii
from distutils.spawn import find_executable
from flask import (
Flask,
session,
request,
Response,
render_template,
jsonify,... |
cs01/gdbgui | gdbgui/backend.py | warn_startup_with_shell_off | python | def warn_startup_with_shell_off(platform, gdb_args):
darwin_match = re.match("darwin-(\d+)\..*", platform)
on_darwin = darwin_match is not None and int(darwin_match.groups()[0]) >= 16
if on_darwin:
shell_is_off = "startup-with-shell off" in gdb_args
return not shell_is_off
return False | return True if user may need to turn shell off
if mac OS version is 16 (sierra) or higher, may need to set shell off due
to os's security requirements
http://stackoverflow.com/questions/39702871/gdb-kind-of-doesnt-work-on-macos-sierra | train | https://github.com/cs01/gdbgui/blob/5367f87554f8f7c671d1f4596c133bf1303154f0/gdbgui/backend.py#L1000-L1011 | null | #!/usr/bin/env python
"""
A server that provides a graphical user interface to the gnu debugger (gdb).
https://github.com/cs01/gdbgui
"""
import argparse
import binascii
from distutils.spawn import find_executable
from flask import (
Flask,
session,
request,
Response,
render_template,
jsonify,... |
yoeo/guesslang | guesslang/guesser.py | Guess.language_name | python | def language_name(self, text: str) -> str:
values = extract(text)
input_fn = _to_func(([values], []))
pos: int = next(self._classifier.predict_classes(input_fn=input_fn))
LOGGER.debug("Predicted language position %s", pos)
return sorted(self.languages)[pos] | Predict the programming language name of the given source code.
:param text: source code.
:return: language name | train | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/guesslang/guesser.py#L61-L72 | [
"def extract(text: str) -> List[float]:\n \"\"\"Transform the text into a vector of float values.\n The vector is a representation of the text.\n\n :param text: the text to represent\n :return: representation\n \"\"\"\n return _normalize(_vectorize(split(text)))\n",
"def _to_func(vector: DataSet... | class Guess:
"""Guess the programming language of a source code.
:param model_dir: Guesslang machine learning model directory.
"""
def __init__(self, model_dir: Optional[str] = None) -> None:
model_data = model_info(model_dir)
#: `tensorflow` model directory
self.model_dir: st... |
yoeo/guesslang | guesslang/guesser.py | Guess.scores | python | def scores(self, text: str) -> Dict[str, float]:
values = extract(text)
input_fn = _to_func(([values], []))
prediction = self._classifier.predict_proba(input_fn=input_fn)
probabilities = next(prediction).tolist()
sorted_languages = sorted(self.languages)
return dict(zip(s... | A score for each language corresponding to the probability that
the text is written in the given language.
The score is a `float` value between 0.0 and 1.0
:param text: source code.
:return: language to score dictionary | train | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/guesslang/guesser.py#L74-L87 | [
"def extract(text: str) -> List[float]:\n \"\"\"Transform the text into a vector of float values.\n The vector is a representation of the text.\n\n :param text: the text to represent\n :return: representation\n \"\"\"\n return _normalize(_vectorize(split(text)))\n",
"def _to_func(vector: DataSet... | class Guess:
"""Guess the programming language of a source code.
:param model_dir: Guesslang machine learning model directory.
"""
def __init__(self, model_dir: Optional[str] = None) -> None:
model_data = model_info(model_dir)
#: `tensorflow` model directory
self.model_dir: st... |
yoeo/guesslang | guesslang/guesser.py | Guess.probable_languages | python | def probable_languages(
self,
text: str,
max_languages: int = 3) -> Tuple[str, ...]:
scores = self.scores(text)
# Sorted from the most probable language to the least probable
sorted_scores = sorted(scores.items(), key=itemgetter(1), reverse=True)
lang... | List of most probable programming languages,
the list is ordered from the most probable to the least probable one.
:param text: source code.
:param max_languages: maximum number of listed languages.
:return: languages list | train | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/guesslang/guesser.py#L89-L116 | [
"def scores(self, text: str) -> Dict[str, float]:\n \"\"\"A score for each language corresponding to the probability that\n the text is written in the given language.\n The score is a `float` value between 0.0 and 1.0\n\n :param text: source code.\n :return: language to score dictionary\n \"\"\"\n... | class Guess:
"""Guess the programming language of a source code.
:param model_dir: Guesslang machine learning model directory.
"""
def __init__(self, model_dir: Optional[str] = None) -> None:
model_data = model_info(model_dir)
#: `tensorflow` model directory
self.model_dir: st... |
yoeo/guesslang | guesslang/guesser.py | Guess.learn | python | def learn(self, input_dir: str) -> float:
if self.is_default:
LOGGER.error("Cannot learn using default model")
raise GuesslangError('Cannot learn using default "readonly" model')
languages = self.languages
LOGGER.info("Extract training data")
extensions = [ext f... | Learn languages features from source files.
:raise GuesslangError: when the default model is used for learning
:param input_dir: source code files directory.
:return: learning accuracy | train | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/guesslang/guesser.py#L118-L164 | [
"def search_files(source: str, extensions: List[str]) -> List[Path]:\n \"\"\"Retrieve files located the source directory and its subdirectories,\n whose extension match one of the listed extensions.\n\n :raise GuesslangError: when there is not enough files in the directory\n :param source: directory nam... | class Guess:
"""Guess the programming language of a source code.
:param model_dir: Guesslang machine learning model directory.
"""
def __init__(self, model_dir: Optional[str] = None) -> None:
model_data = model_info(model_dir)
#: `tensorflow` model directory
self.model_dir: st... |
yoeo/guesslang | tools/report_graph.py | main | python | def main():
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument(
'reportfile', type=argparse.FileType('r'),
help="test report file generated by `guesslang --test TESTDIR`")
parser.add_argument(
'-d', '--debug', default=False, action='store_true',
help="... | Report graph creator command line | train | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/tools/report_graph.py#L25-L42 | [
"def config_logging(debug: bool = False) -> None:\n \"\"\"Set-up application and `tensorflow` logging.\n\n :param debug: show or hide debug messages\n \"\"\"\n if debug:\n level = 'DEBUG'\n tf_level = tf.logging.INFO\n else:\n level = 'INFO'\n tf_level = tf.logging.ERROR\n... | #!/usr/bin/env python3
"""
Create a graph from a Guesslang test report.
"""
import argparse
import json
import logging
from pathlib import Path
import shutil
import tempfile
import webbrowser
from guesslang.config import config_logging
LOGGER = logging.getLogger(__name__)
RESOURCES_DIR = Path(__file__).parent.jo... |
yoeo/guesslang | guesslang/utils.py | search_files | python | def search_files(source: str, extensions: List[str]) -> List[Path]:
files = [
path for path in Path(source).glob('**/*')
if path.is_file() and path.suffix.lstrip('.') in extensions]
nb_files = len(files)
LOGGER.debug("Total files found: %d", nb_files)
if nb_files < NB_FILES_MIN:
... | Retrieve files located the source directory and its subdirectories,
whose extension match one of the listed extensions.
:raise GuesslangError: when there is not enough files in the directory
:param source: directory name
:param extensions: list of file extensions
:return: filenames | train | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/guesslang/utils.py#L30-L52 | null | """A set of tools to process files"""
import logging
import multiprocessing
from pathlib import Path
import random
import signal
from typing import List, Dict, Sequence, Tuple
import numpy as np
from guesslang.extractor import extract
LOGGER = logging.getLogger(__name__)
random.seed()
FILE_ENCODINGS = ('utf-8', ... |
yoeo/guesslang | guesslang/utils.py | extract_from_files | python | def extract_from_files(
files: List[Path],
languages: Dict[str, List[str]]) -> DataSet:
enumerator = enumerate(sorted(languages.items()))
rank_map = {ext: rank for rank, (_, exts) in enumerator for ext in exts}
with multiprocessing.Pool(initializer=_process_init) as pool:
file_itera... | Extract arrays of features from the given files.
:param files: list of paths
:param languages: language name =>
associated file extension list
:return: features | train | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/guesslang/utils.py#L55-L73 | [
"def _to_arrays(features: List[Tuple[List[float], int]]) -> DataSet:\n # Flatten and split the dataset\n ranks = []\n content_vectors = []\n for content_vector, rank in features:\n ranks.append(rank)\n content_vectors.append(content_vector)\n\n # Convert lists into numpy arrays\n ret... | """A set of tools to process files"""
import logging
import multiprocessing
from pathlib import Path
import random
import signal
from typing import List, Dict, Sequence, Tuple
import numpy as np
from guesslang.extractor import extract
LOGGER = logging.getLogger(__name__)
random.seed()
FILE_ENCODINGS = ('utf-8', ... |
yoeo/guesslang | guesslang/utils.py | safe_read_file | python | def safe_read_file(file_path: Path) -> str:
for encoding in FILE_ENCODINGS:
try:
return file_path.read_text(encoding=encoding)
except UnicodeError:
pass # Ignore encoding error
raise GuesslangError('Encoding not supported for {!s}'.format(file_path)) | Read a text file. Several text encodings are tried until
the file content is correctly decoded.
:raise GuesslangError: when the file encoding is not supported
:param file_path: path to the input file
:return: text file content | train | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/guesslang/utils.py#L106-L120 | null | """A set of tools to process files"""
import logging
import multiprocessing
from pathlib import Path
import random
import signal
from typing import List, Dict, Sequence, Tuple
import numpy as np
from guesslang.extractor import extract
LOGGER = logging.getLogger(__name__)
random.seed()
FILE_ENCODINGS = ('utf-8', ... |
yoeo/guesslang | guesslang/config.py | config_logging | python | def config_logging(debug: bool = False) -> None:
if debug:
level = 'DEBUG'
tf_level = tf.logging.INFO
else:
level = 'INFO'
tf_level = tf.logging.ERROR
logging_config = config_dict('logging.json')
for logger in logging_config['loggers'].values():
logger['level'] =... | Set-up application and `tensorflow` logging.
:param debug: show or hide debug messages | train | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/guesslang/config.py#L53-L70 | [
"def config_dict(name: str) -> Dict[str, Any]:\n \"\"\"Load a JSON configuration dict from Guesslang config directory.\n\n :param name: the JSON file name.\n :return: configuration\n \"\"\"\n try:\n content = resource_string(PACKAGE, DATADIR.format(name)).decode()\n except DistributionNotFo... | """Load configuration from guesslang `config` directory"""
import json
import logging.config
from pathlib import Path
import platform
from typing import cast, Dict, Any, Tuple, Optional
from pkg_resources import (
Requirement, resource_string, resource_filename, DistributionNotFound)
import tensorflow as tf
LO... |
yoeo/guesslang | guesslang/config.py | config_dict | python | def config_dict(name: str) -> Dict[str, Any]:
try:
content = resource_string(PACKAGE, DATADIR.format(name)).decode()
except DistributionNotFound as error:
LOGGER.warning("Cannot load %s from packages: %s", name, error)
content = DATA_FALLBACK.joinpath(name).read_text()
return cast(D... | Load a JSON configuration dict from Guesslang config directory.
:param name: the JSON file name.
:return: configuration | train | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/guesslang/config.py#L73-L85 | null | """Load configuration from guesslang `config` directory"""
import json
import logging.config
from pathlib import Path
import platform
from typing import cast, Dict, Any, Tuple, Optional
from pkg_resources import (
Requirement, resource_string, resource_filename, DistributionNotFound)
import tensorflow as tf
LO... |
yoeo/guesslang | guesslang/config.py | model_info | python | def model_info(model_dir: Optional[str] = None) -> Tuple[str, bool]:
if model_dir is None:
try:
model_dir = resource_filename(PACKAGE, DATADIR.format('model'))
except DistributionNotFound as error:
LOGGER.warning("Cannot load model from packages: %s", error)
model... | Retrieve Guesslang model directory name,
and tells if it is the default model.
:param model_dir: model location, if `None` default model is selected
:return: selected model directory with an indication
that the model is the default or not | train | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/guesslang/config.py#L88-L110 | null | """Load configuration from guesslang `config` directory"""
import json
import logging.config
from pathlib import Path
import platform
from typing import cast, Dict, Any, Tuple, Optional
from pkg_resources import (
Requirement, resource_string, resource_filename, DistributionNotFound)
import tensorflow as tf
LO... |
yoeo/guesslang | guesslang/config.py | ColorLogFormatter.format | python | def format(self, record: logging.LogRecord) -> str:
if platform.system() != 'Linux': # Avoid funny logs on Windows & MacOS
return super().format(record)
record.msg = (
self.STYLE[record.levelname] + record.msg + self.STYLE['END'])
record.levelname = (
self.S... | Format log records to produce colored messages.
:param record: log record
:return: log message | train | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/guesslang/config.py#L37-L50 | null | class ColorLogFormatter(logging.Formatter):
"""Logging formatter that prints pretty colored log messages"""
STYLE = {
# Log messages styles
'DEBUG': '\033[94m',
'INFO': '\033[0m',
'WARNING': '\033[93m',
'ERROR': '\033[1;91m',
'CRITICAL': '\033[1;95m',
# O... |
yoeo/guesslang | tools/download_github_repo.py | main | python | def main():
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument(
'githubtoken',
help="Github OAuth token, see https://developer.github.com/v3/oauth/")
parser.add_argument('destination', help="location of the downloaded repos")
parser.add_argument(
'-n', '--... | Github repositories downloaded command line | train | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/tools/download_github_repo.py#L54-L87 | [
"def config_logging(debug: bool = False) -> None:\n \"\"\"Set-up application and `tensorflow` logging.\n\n :param debug: show or hide debug messages\n \"\"\"\n if debug:\n level = 'DEBUG'\n tf_level = tf.logging.INFO\n else:\n level = 'INFO'\n tf_level = tf.logging.ERROR\n... | #!/usr/bin/env python3
"""
Download repos from Github.
The repositories source files will be used to feed Guesslang model.
"""
import argparse
from contextlib import closing
import functools
import logging
from pathlib import Path
import random
import time
from urllib.parse import quote_plus
import requests
from ... |
yoeo/guesslang | tools/download_github_repo.py | retry | python | def retry(default=None):
def decorator(func):
"""Retry decorator"""
@functools.wraps(func)
def _wrapper(*args, **kw):
for pos in range(1, MAX_RETRIES):
try:
return func(*args, **kw)
except (RuntimeError, requests.ConnectionErr... | Retry functions after failures | train | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/tools/download_github_repo.py#L117-L140 | null | #!/usr/bin/env python3
"""
Download repos from Github.
The repositories source files will be used to feed Guesslang model.
"""
import argparse
from contextlib import closing
import functools
import logging
from pathlib import Path
import random
import time
from urllib.parse import quote_plus
import requests
from ... |
yoeo/guesslang | tools/make_keywords.py | main | python | def main():
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument('learn', help="learning source codes directory")
parser.add_argument('keywords', help="output keywords file, JSON")
parser.add_argument(
'-n', '--nbkeywords', type=int, default=10000,
help="the number ... | Keywords generator command line | train | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/tools/make_keywords.py#L29-L87 | [
"def config_logging(debug: bool = False) -> None:\n \"\"\"Set-up application and `tensorflow` logging.\n\n :param debug: show or hide debug messages\n \"\"\"\n if debug:\n level = 'DEBUG'\n tf_level = tf.logging.INFO\n else:\n level = 'INFO'\n tf_level = tf.logging.ERROR\n... | #!/usr/bin/env python3
"""
Statistically generate keywords.
Spot the most representative keywords from the learning files.
"""
import argparse
from collections import Counter
import gc
import hashlib
import json
import logging
from operator import itemgetter
from pathlib import Path
from guesslang.config import co... |
yoeo/guesslang | guesslang/__main__.py | main | python | def main() -> None:
try:
_real_main()
except GuesslangError as error:
LOGGER.critical("Failed: %s", error)
sys.exit(-1)
except KeyboardInterrupt:
LOGGER.critical("Cancelled!")
sys.exit(-2) | Run command line | train | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/guesslang/__main__.py#L19-L28 | [
"def _real_main() -> None:\n # Get the arguments\n parser = argparse.ArgumentParser(description=__doc__)\n parser.add_argument(\n '-i', '--input-file', type=argparse.FileType('r'), default=sys.stdin,\n help=\"source code file. Default is standard input (stdin)\")\n parser.add_argument(\n ... | """Guess the programming language of a given source file"""
import argparse
import json
import logging
from pathlib import Path
import sys
import time
from typing import Any, TextIO
from guesslang import Guess, GuesslangError, config_logging
LOGGER = logging.getLogger(__name__)
REPORT_FILENAME = 'report-{}.json'
... |
yoeo/guesslang | guesslang/extractor.py | split | python | def split(text: str) -> List[str]:
return [word for word in SEPARATOR.split(text) if word.strip(' \t')] | Split a text into a list of tokens.
:param text: the text to split
:return: tokens | train | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/guesslang/extractor.py#L34-L40 | null | """Extract features (floats vector) that represent a given text"""
import logging
import re
import math
from typing import cast, Dict, Tuple, List
from guesslang.config import config_dict
LOGGER = logging.getLogger(__name__)
CONTENT_SIZE = 2**10
SPECIAL_KEYWORDS = {'num': '<number>', 'var': '<variable>'}
KEYWORDS... |
yoeo/guesslang | tools/unzip_repos.py | main | python | def main():
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('source', help="location of the downloaded repos")
parser.add_argument('destination', help="location of the extracted files")
parser.add_argument(... | Files extractor command line | train | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/tools/unzip_repos.py#L30-L65 | [
"def config_logging(debug: bool = False) -> None:\n \"\"\"Set-up application and `tensorflow` logging.\n\n :param debug: show or hide debug messages\n \"\"\"\n if debug:\n level = 'DEBUG'\n tf_level = tf.logging.INFO\n else:\n level = 'INFO'\n tf_level = tf.logging.ERROR\n... | #!/usr/bin/env python3
"""
Extract files from downloaded repositories to prepare Guesslang learning:
* testing files and learning files are retrieved from different repositories
* they are stored into two different subdirectories
* a limited number of files for each language are retrieved per repository
"""
impo... |
moonso/vcf_parser | vcf_parser/utils/build_models.py | build_models_dict | python | def build_models_dict(annotated_models):
logger = getLogger(__name__)
logger.debug("Parsing models {0}".format(annotated_models)
)
parsed_models = {}
for family_annotation in annotated_models:
family_id = family_annotation.split(':')[0]
logger.debug("Parsing family {0}".format(family... | Take a list with annotated genetic inheritance patterns for each
family and returns a dictionary with family_id as key and a list of
genetic models as value.
Args:
annotated_models : A list on the form ['1:AD','2:AR_comp|AD_dn']
Returns:
parsed_models : A dictionary on... | train | https://github.com/moonso/vcf_parser/blob/8e2b6724e31995e0d43af501f25974310c6b843b/vcf_parser/utils/build_models.py#L3-L31 | null | from logging import getLogger
def build_models_dict(annotated_models):
"""
Take a list with annotated genetic inheritance patterns for each
family and returns a dictionary with family_id as key and a list of
genetic models as value.
Args:
annotated_models : A list on the form ['1:AD','2... |
moonso/vcf_parser | vcf_parser/utils/split_variants.py | split_variants | python | def split_variants(variant_dict, header_parser, allele_symbol='0'):
logger = getLogger(__name__)
logger.info("Allele symbol {0}".format(allele_symbol))
alternatives = variant_dict['ALT'].split(',')
reference = variant_dict['REF']
number_of_values = 1
# Go through each of the alternative alleles:... | Checks if there are multiple alternative alleles and splitts the
variant.
If there are multiple alternatives the info fields, vep annotations
and genotype calls will be splitted in the correct way
Args:
variant_dict: a dictionary with the variant information
Yields:
varia... | train | https://github.com/moonso/vcf_parser/blob/8e2b6724e31995e0d43af501f25974310c6b843b/vcf_parser/utils/split_variants.py#L13-L120 | [
"def build_info_string(info):\n \"\"\"\n Build a new vcf INFO string based on the information in the info_dict.\n\n The info is a dictionary with vcf info keys as keys and lists of vcf values\n as values. If there is no value False is value in info\n\n Args:\n info (dict): A dictionary with in... | import sys
from logging import getLogger
if sys.version_info < (2, 7):
from ordereddict import OrderedDict
else:
from collections import OrderedDict
from vcf_parser import Genotype
from vcf_parser.utils import (build_vep_string, split_genotype, build_info_string)
def split_variants(variant_dict, header_pars... |
moonso/vcf_parser | vcf_parser/utils/rank_scores.py | build_rank_score_dict | python | def build_rank_score_dict(rank_scores):
logger = getLogger(__name__)
logger.debug("Checking rank scores: {0}".format(rank_scores))
scores = {}
for family in rank_scores:
entry = family.split(':')
try:
family_id = entry[0]
logger.debug("Extracting rank score for fa... | Take a list with annotated rank scores for each family and returns a
dictionary with family_id as key and a list of genetic models as value.
Args:
rank_scores : A list on the form ['1:12','2:20']
Returns:
scores : A dictionary with family id:s as key and scores as value
... | train | https://github.com/moonso/vcf_parser/blob/8e2b6724e31995e0d43af501f25974310c6b843b/vcf_parser/utils/rank_scores.py#L3-L34 | null | from logging import getLogger
def build_rank_score_dict(rank_scores):
"""
Take a list with annotated rank scores for each family and returns a
dictionary with family_id as key and a list of genetic models as value.
Args:
rank_scores : A list on the form ['1:12','2:20']
Returns:
... |
moonso/vcf_parser | vcf_parser/utils/check_info.py | check_info_annotation | python | def check_info_annotation(annotation, info, extra_info, alternatives, individuals=[]):
number = extra_info['Number']
if is_number(number):
number_of_entrys = float(number)
if number_of_entrys != 0:
if len(annotation) != number_of_entrys:
raise SyntaxError("Info f... | Check if the info annotation corresponds to the metadata specification
Arguments:
annotation (list): The annotation from the vcf file
info (str): Name of the info field
extra_info (dict): The metadata specification
alternatives (list): A list with the alternative variants
... | train | https://github.com/moonso/vcf_parser/blob/8e2b6724e31995e0d43af501f25974310c6b843b/vcf_parser/utils/check_info.py#L18-L72 | [
"def is_number(s):\n \"\"\"\n Take a string and determin if it is a number\n\n Arguments:\n s (str): A string\n\n Returns:\n bool: True if it is a number, False otherwise\n \"\"\"\n try:\n float(s)\n return True\n except ValueError:\n return False\n"
] | def is_number(s):
"""
Take a string and determin if it is a number
Arguments:
s (str): A string
Returns:
bool: True if it is a number, False otherwise
"""
try:
float(s)
return True
except ValueError:
return False
def check_info_annotation(annotatio... |
moonso/vcf_parser | vcf_parser/utils/format_variant.py | format_variant | python | def format_variant(line, header_parser, check_info=False):
logger = getLogger(__name__)
individuals = []
vcf_header = header_parser.header
individuals = header_parser.individuals
variant_line = line.rstrip().split('\t')
logger.debug("Checking if variant line is malformed")
if len(vcf_he... | Yield the variant in the right format.
If the variants should be splitted on alternative alles one variant
for each alternative will be yielded.
Arguments:
line (str): A string that represents a variant line in the vcf format
header_parser (HeaderParser): A HeaderParser object
... | train | https://github.com/moonso/vcf_parser/blob/8e2b6724e31995e0d43af501f25974310c6b843b/vcf_parser/utils/format_variant.py#L10-L137 | [
"def check_info_annotation(annotation, info, extra_info, alternatives, individuals=[]):\n \"\"\"\n Check if the info annotation corresponds to the metadata specification\n\n Arguments:\n annotation (list): The annotation from the vcf file\n info (str): Name of the info field\n extra_in... | from __future__ import absolute_import
from logging import getLogger
from vcf_parser import Genotype
from . import (build_info_dict, build_vep_annotation, check_info_annotation,
build_compounds_dict, build_rank_score_dict, build_models_dict)
def format_variant(line, header_parser, check_info=False):
"""
Yie... |
moonso/vcf_parser | vcf_parser/utils/build_info.py | build_info_string | python | def build_info_string(info):
info_list = []
for annotation in info:
if info[annotation]:
info_list.append('='.join([annotation, ','.join(info[annotation])]))
else:
info_list.append(annotation)
return ';'.join(info_list) | Build a new vcf INFO string based on the information in the info_dict.
The info is a dictionary with vcf info keys as keys and lists of vcf values
as values. If there is no value False is value in info
Args:
info (dict): A dictionary with information from the vcf file
Returns:
... | train | https://github.com/moonso/vcf_parser/blob/8e2b6724e31995e0d43af501f25974310c6b843b/vcf_parser/utils/build_info.py#L10-L33 | null | import sys
import logging
if sys.version_info < (2, 7):
from ordereddict import OrderedDict
else:
from collections import OrderedDict
def build_info_string(info):
"""
Build a new vcf INFO string based on the information in the info_dict.
The info is a dictionary with vcf info keys as keys and li... |
moonso/vcf_parser | vcf_parser/utils/build_info.py | build_info_dict | python | def build_info_dict(vcf_info):
logger = logging.getLogger(__name__)
logger.debug("Building info dict")
info_dict = OrderedDict()
for info in vcf_info.split(';'):
info = info.split('=')
if len(info) > 1:
# If the INFO entry is like key=value, we store the value as a list
... | Build a dictionary from the info of a vcf line
The dictionary will have the info keys as keys and info values as values.
Values will allways be lists that are splitted on ','
Arguments:
vcf_info (str): A string with vcf info
Returns:
info_dict (OrderedDict): A ordered dict... | train | https://github.com/moonso/vcf_parser/blob/8e2b6724e31995e0d43af501f25974310c6b843b/vcf_parser/utils/build_info.py#L35-L62 | null | import sys
import logging
if sys.version_info < (2, 7):
from ordereddict import OrderedDict
else:
from collections import OrderedDict
def build_info_string(info):
"""
Build a new vcf INFO string based on the information in the info_dict.
The info is a dictionary with vcf info keys as keys and li... |
moonso/vcf_parser | vcf_parser/utils/split_genotype.py | split_genotype | python | def split_genotype(genotype, gt_format, alternative_number, allele_symbol = '0'):
logger = getLogger(__name__)
logger.info("Allele symbol {0}".format(allele_symbol))
splitted_genotype = genotype.split(':')
logger.debug("Parsing genotype {0}".format(splitted_genotype))
splitted_gt_format = gt_f... | Take a genotype call and make a new one that is working for the new
splitted variant
Arguments:
genotype (str): The original genotype call
gt_format (str): The format of the gt call
alternative_number (int): What genotype call should we return
allele_symbol (str): How should... | train | https://github.com/moonso/vcf_parser/blob/8e2b6724e31995e0d43af501f25974310c6b843b/vcf_parser/utils/split_genotype.py#L3-L92 | null | from logging import getLogger
def split_genotype(genotype, gt_format, alternative_number, allele_symbol = '0'):
"""
Take a genotype call and make a new one that is working for the new
splitted variant
Arguments:
genotype (str): The original genotype call
gt_format (str): The format of ... |
moonso/vcf_parser | vcf_parser/header_parser.py | HeaderParser.parse_header_line | python | def parse_header_line(self, line):
self.header = line[1:].rstrip().split('\t')
if len(self.header) < 9:
self.header = line[1:].rstrip().split()
self.individuals = self.header[9:] | docstring for parse_header_line | train | https://github.com/moonso/vcf_parser/blob/8e2b6724e31995e0d43af501f25974310c6b843b/vcf_parser/header_parser.py#L178-L183 | null | class HeaderParser(object):
"""Parses a file with family info and creates a family object with individuals."""
def __init__(self):
super(HeaderParser, self).__init__()
self.logger = getLogger(__name__)
self.info_lines=[]
self.info_dict=OrderedDict()
#This is a dictionary ... |
moonso/vcf_parser | vcf_parser/header_parser.py | HeaderParser.print_header | python | def print_header(self):
lines_to_print = []
lines_to_print.append('##fileformat='+self.fileformat)
if self.filedate:
lines_to_print.append('##fileformat='+self.fileformat)
for filt in self.filter_dict:
lines_to_print.append(self.filter_dict[filt])
... | Returns a list with the header lines if proper format | train | https://github.com/moonso/vcf_parser/blob/8e2b6724e31995e0d43af501f25974310c6b843b/vcf_parser/header_parser.py#L185-L205 | null | class HeaderParser(object):
"""Parses a file with family info and creates a family object with individuals."""
def __init__(self):
super(HeaderParser, self).__init__()
self.logger = getLogger(__name__)
self.info_lines=[]
self.info_dict=OrderedDict()
#This is a dictionary ... |
moonso/vcf_parser | vcf_parser/header_parser.py | HeaderParser.add_info | python | def add_info(self, info_id, number, entry_type, description):
info_line = '##INFO=<ID={0},Number={1},Type={2},Description="{3}">'.format(
info_id, number, entry_type, description
)
self.logger.info("Adding info line to vcf: {0}".format(info_line))
self.parse_meta_data(info_li... | Add an info line to the header.
Arguments:
info_id (str): The id of the info line
number (str): Integer or any of [A,R,G,.]
entry_type (str): Any of [Integer,Float,Flag,Character,String]
description (str): A description of the info line | train | https://github.com/moonso/vcf_parser/blob/8e2b6724e31995e0d43af501f25974310c6b843b/vcf_parser/header_parser.py#L238-L254 | [
"def parse_meta_data(self, line):\n \"\"\"Parse a vcf metadataline\"\"\"\n line = line.rstrip()\n line_info = line[2:].split('=')\n match = False\n\n if line_info[0] == 'fileformat':\n try:\n self.fileformat = line_info[1]\n except IndexError:\n raise SyntaxError(\... | class HeaderParser(object):
"""Parses a file with family info and creates a family object with individuals."""
def __init__(self):
super(HeaderParser, self).__init__()
self.logger = getLogger(__name__)
self.info_lines=[]
self.info_dict=OrderedDict()
#This is a dictionary ... |
moonso/vcf_parser | vcf_parser/header_parser.py | HeaderParser.add_version_tracking | python | def add_version_tracking(self, info_id, version, date, command_line=''):
other_line = '##Software=<ID={0},Version={1},Date="{2}",CommandLineOptions="{3}">'.format(
info_id, version, date, command_line)
self.other_dict[info_id] = other_line
return | Add a line with information about which software that was run and when
to the header.
Arguments:
info_id (str): The id of the info line
version (str): The version of the software used
date (str): Date when software was run
command_line (str): The... | train | https://github.com/moonso/vcf_parser/blob/8e2b6724e31995e0d43af501f25974310c6b843b/vcf_parser/header_parser.py#L338-L353 | null | class HeaderParser(object):
"""Parses a file with family info and creates a family object with individuals."""
def __init__(self):
super(HeaderParser, self).__init__()
self.logger = getLogger(__name__)
self.info_lines=[]
self.info_dict=OrderedDict()
#This is a dictionary ... |
moonso/vcf_parser | vcf_parser/utils/build_compounds.py | build_compounds_dict | python | def build_compounds_dict(compounds):
logger = getLogger(__name__)
logger.debug("Parsing compounds: {0}".format(compounds))
parsed_compounds = {}
for family_info in compounds:
logger.debug("Parsing entry {0}".format(family_info))
splitted_family_info = family_info.split(':')
... | Take a list with annotated compound variants for each family and
returns a dictionary with family_id as key and a list of dictionarys
that holds the information about the compounds.
Args:
compounds : A list that can be either on the form
[
... | train | https://github.com/moonso/vcf_parser/blob/8e2b6724e31995e0d43af501f25974310c6b843b/vcf_parser/utils/build_compounds.py#L3-L66 | null | from logging import getLogger
def build_compounds_dict(compounds):
"""
Take a list with annotated compound variants for each family and
returns a dictionary with family_id as key and a list of dictionarys
that holds the information about the compounds.
Args:
compounds : A list that can... |
moonso/vcf_parser | vcf_parser/cli/command_line.py | cli | python | def cli(variant_file, vep, split, outfile, verbose, silent, check_info,
allele_symbol, logfile, loglevel):
from vcf_parser import logger, init_log
if not loglevel:
if verbose:
loglevel = 'INFO'
init_log(logger, logfile, loglevel)
nr_of_variants = 0
start = datetime.now(... | Tool for parsing vcf files.
Prints the vcf file to output.
If --split/-s is used all multiallelic calls will be splitted and printed
as single variant calls.
For more information, please see github.com/moonso/vcf_parser. | train | https://github.com/moonso/vcf_parser/blob/8e2b6724e31995e0d43af501f25974310c6b843b/vcf_parser/cli/command_line.py#L93-L163 | [
"def init_log(logger, filename=None, loglevel=None):\n \"\"\"\n Initializes the log file in the proper format.\n\n Arguments:\n\n filename (str): Path to a file. Or None if logging is to\n be disabled.\n loglevel (str): Determines the level of the log output.\n \"\"... | #!/usr/bin/env python
# encoding: utf-8
"""
vcf_parser
Command Line Interface for vcf_parser
Created by Måns Magnusson on 2014-12-12.
Copyright (c) 2014 __MoonsoInc__. All rights reserved.
"""
from __future__ import print_function
import sys
import os
import click
from pprint import pprint as pp
from datetime impo... |
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