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values | func_name stringlengths 1 134 | docstring stringlengths 1 46.9k | path stringlengths 4 223 | original_string stringlengths 75 104k | code stringlengths 75 104k | docstring_tokens listlengths 1 1.97k | repo stringlengths 7 55 | language stringclasses 1
value | url stringlengths 87 315 | code_tokens listlengths 19 28.4k | sha stringlengths 40 40 |
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train | ClientPool.connected_client | Returns a ContextManagerFuture to be yielded in a with statement.
Returns:
A ContextManagerFuture object.
Examples:
>>> with (yield pool.connected_client()) as client:
# client is a connected tornadis.Client instance
# it will be automati... | tornadis/pool.py | def connected_client(self):
"""Returns a ContextManagerFuture to be yielded in a with statement.
Returns:
A ContextManagerFuture object.
Examples:
>>> with (yield pool.connected_client()) as client:
# client is a connected tornadis.Client instance
... | def connected_client(self):
"""Returns a ContextManagerFuture to be yielded in a with statement.
Returns:
A ContextManagerFuture object.
Examples:
>>> with (yield pool.connected_client()) as client:
# client is a connected tornadis.Client instance
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train | ClientPool.release_client | Releases a client object to the pool.
Args:
client: Client object. | tornadis/pool.py | def release_client(self, client):
"""Releases a client object to the pool.
Args:
client: Client object.
"""
if isinstance(client, Client):
if not self._is_expired_client(client):
LOG.debug('Client is not expired. Adding back to pool')
... | def release_client(self, client):
"""Releases a client object to the pool.
Args:
client: Client object.
"""
if isinstance(client, Client):
if not self._is_expired_client(client):
LOG.debug('Client is not expired. Adding back to pool')
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train | ClientPool.destroy | Disconnects all pooled client objects. | tornadis/pool.py | def destroy(self):
"""Disconnects all pooled client objects."""
while True:
try:
client = self.__pool.popleft()
if isinstance(client, Client):
client.disconnect()
except IndexError:
break | def destroy(self):
"""Disconnects all pooled client objects."""
while True:
try:
client = self.__pool.popleft()
if isinstance(client, Client):
client.disconnect()
except IndexError:
break | [
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train | ClientPool.preconnect | (pre)Connects some or all redis clients inside the pool.
Args:
size (int): number of redis clients to build and to connect
(-1 means all clients if pool max_size > -1)
Raises:
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Args:
size (int): number of redis clients to build and to connect
(-1 means all clients if pool max_size > -1)
Raises:
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size (int): number of redis clients to build and to connect
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train | setup_path | Setup python search and add ``TASKS_VENDOR_DIR`` (if available). | tasks/_setup.py | def setup_path(invoke_minversion=None):
"""Setup python search and add ``TASKS_VENDOR_DIR`` (if available)."""
# print("INVOKE.tasks: setup_path")
if not os.path.isdir(TASKS_VENDOR_DIR):
print("SKIP: TASKS_VENDOR_DIR=%s is missing" % TASKS_VENDOR_DIR)
return
elif os.path.abspath(TASKS_VE... | def setup_path(invoke_minversion=None):
"""Setup python search and add ``TASKS_VENDOR_DIR`` (if available)."""
# print("INVOKE.tasks: setup_path")
if not os.path.isdir(TASKS_VENDOR_DIR):
print("SKIP: TASKS_VENDOR_DIR=%s is missing" % TASKS_VENDOR_DIR)
return
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train | require_invoke_minversion | Ensures that :mod:`invoke` has at the least the :param:`min_version`.
Otherwise,
:param min_version: Minimal acceptable invoke version (as string).
:param verbose: Indicates if invoke.version should be shown.
:raises: VersionRequirementError=SystemExit if requirement fails. | tasks/_setup.py | def require_invoke_minversion(min_version, verbose=False):
"""Ensures that :mod:`invoke` has at the least the :param:`min_version`.
Otherwise,
:param min_version: Minimal acceptable invoke version (as string).
:param verbose: Indicates if invoke.version should be shown.
:raises: VersionRequirem... | def require_invoke_minversion(min_version, verbose=False):
"""Ensures that :mod:`invoke` has at the least the :param:`min_version`.
Otherwise,
:param min_version: Minimal acceptable invoke version (as string).
:param verbose: Indicates if invoke.version should be shown.
:raises: VersionRequirem... | [
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train | matches_section | Decorator for SectionSchema classes to define the mapping between
a config section schema class and one or more config sections with
matching name(s).
.. sourcecode::
@matches_section("foo")
class FooSchema(SectionSchema):
pass
@matches_section(["bar", "baz.*"])
... | click_configfile.py | def matches_section(section_name):
"""Decorator for SectionSchema classes to define the mapping between
a config section schema class and one or more config sections with
matching name(s).
.. sourcecode::
@matches_section("foo")
class FooSchema(SectionSchema):
pass
... | def matches_section(section_name):
"""Decorator for SectionSchema classes to define the mapping between
a config section schema class and one or more config sections with
matching name(s).
.. sourcecode::
@matches_section("foo")
class FooSchema(SectionSchema):
pass
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train | assign_param_names | Class decorator to assign parameter name to instances of :class:`Param`.
.. sourcecode::
@assign_param_names
class ConfigSectionSchema(object):
alice = Param(type=str)
bob = Param(type=str)
assert ConfigSectionSchema.alice.name == "alice"
assert ConfigSec... | click_configfile.py | def assign_param_names(cls=None, param_class=None):
"""Class decorator to assign parameter name to instances of :class:`Param`.
.. sourcecode::
@assign_param_names
class ConfigSectionSchema(object):
alice = Param(type=str)
bob = Param(type=str)
assert ConfigS... | def assign_param_names(cls=None, param_class=None):
"""Class decorator to assign parameter name to instances of :class:`Param`.
.. sourcecode::
@assign_param_names
class ConfigSectionSchema(object):
alice = Param(type=str)
bob = Param(type=str)
assert ConfigS... | [
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train | select_params_from_section_schema | Selects the parameters of a config section schema.
:param section_schema: Configuration file section schema to use.
:return: Generator of params | click_configfile.py | def select_params_from_section_schema(section_schema, param_class=Param,
deep=False):
"""Selects the parameters of a config section schema.
:param section_schema: Configuration file section schema to use.
:return: Generator of params
"""
# pylint: disable=inva... | def select_params_from_section_schema(section_schema, param_class=Param,
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"""Selects the parameters of a config section schema.
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:return: Generator of params
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train | parse_config_section | Parse a config file section (INI file) by using its schema/description.
.. sourcecode::
import configparser # -- NOTE: Use backport for Python2
import click
from click_configfile import SectionSchema, Param, parse_config_section
class ConfigSectionSchema(object):
c... | click_configfile.py | def parse_config_section(config_section, section_schema):
"""Parse a config file section (INI file) by using its schema/description.
.. sourcecode::
import configparser # -- NOTE: Use backport for Python2
import click
from click_configfile import SectionSchema, Param, parse_config_... | def parse_config_section(config_section, section_schema):
"""Parse a config file section (INI file) by using its schema/description.
.. sourcecode::
import configparser # -- NOTE: Use backport for Python2
import click
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train | generate_configfile_names | Generates all configuration file name combinations to read.
.. sourcecode::
# -- ALGORITHM:
# First basenames/directories are prefered and override other files.
for config_path in reversed(config_searchpath):
for config_basename in reversed(config_files):
con... | click_configfile.py | def generate_configfile_names(config_files, config_searchpath=None):
"""Generates all configuration file name combinations to read.
.. sourcecode::
# -- ALGORITHM:
# First basenames/directories are prefered and override other files.
for config_path in reversed(config_searchpath):
... | def generate_configfile_names(config_files, config_searchpath=None):
"""Generates all configuration file name combinations to read.
.. sourcecode::
# -- ALGORITHM:
# First basenames/directories are prefered and override other files.
for config_path in reversed(config_searchpath):
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train | select_config_sections | Select a subset of the sections in a configuration file by using
a list of section names of list of section name patters
(supporting :mod:`fnmatch` wildcards).
:param configfile_sections: List of config section names (as strings).
:param desired_section_patterns:
:return: List of selected section n... | click_configfile.py | def select_config_sections(configfile_sections, desired_section_patterns):
"""Select a subset of the sections in a configuration file by using
a list of section names of list of section name patters
(supporting :mod:`fnmatch` wildcards).
:param configfile_sections: List of config section names (as stri... | def select_config_sections(configfile_sections, desired_section_patterns):
"""Select a subset of the sections in a configuration file by using
a list of section names of list of section name patters
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train | SectionSchema.matches_section | Indicates if this schema can be used for a config section
by using the section name.
:param section_name: Config section name to check.
:return: True, if this schema can be applied to the config section.
:return: Fals, if this schema does not match the config section. | click_configfile.py | def matches_section(cls, section_name, supported_section_names=None):
"""Indicates if this schema can be used for a config section
by using the section name.
:param section_name: Config section name to check.
:return: True, if this schema can be applied to the config section.
... | def matches_section(cls, section_name, supported_section_names=None):
"""Indicates if this schema can be used for a config section
by using the section name.
:param section_name: Config section name to check.
:return: True, if this schema can be applied to the config section.
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train | ConfigFileReader.collect_config_sections_from_schemas | Derive support config section names from config section schemas.
If no :param:`config_section_schemas` are provided, the schemas from
this class are used (normally defined in the DerivedClass).
:param config_section_schemas: List of config section schema classes.
:return: List of confi... | click_configfile.py | def collect_config_sections_from_schemas(cls, config_section_schemas=None):
# pylint: disable=invalid-name
"""Derive support config section names from config section schemas.
If no :param:`config_section_schemas` are provided, the schemas from
this class are used (normally defined in the... | def collect_config_sections_from_schemas(cls, config_section_schemas=None):
# pylint: disable=invalid-name
"""Derive support config section names from config section schemas.
If no :param:`config_section_schemas` are provided, the schemas from
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train | ConfigFileReader.process_config_section | Process the config section and store the extracted data in
the param:`storage` (as outgoing param). | click_configfile.py | def process_config_section(cls, config_section, storage):
"""Process the config section and store the extracted data in
the param:`storage` (as outgoing param).
"""
# -- CONCEPT:
# if not storage:
# # -- INIT DATA: With default parts.
# storage.update(dict... | def process_config_section(cls, config_section, storage):
"""Process the config section and store the extracted data in
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train | ConfigFileReader.select_config_schema_for | Select the config schema that matches the config section (by name).
:param section_name: Config section name (as key).
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train | ConfigFileReader.select_storage_for | Selects the data storage for a config section within the
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:param section_name: Config section (name) to process.
:param storage: Data storage to use.
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train | clean | Cleanup temporary dirs/files to regain a clean state. | tasks/clean.py | def clean(ctx, dry_run=False):
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# -- VARIATION-POINT 1: Allow user to override in configuration-file
directories = ctx.clean.directories
files = ctx.clean.files
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# -- VARIATION-POINT 1: Allow user to override in configuration-file
directories = ctx.clean.directories
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train | clean_all | Clean up everything, even the precious stuff.
NOTE: clean task is executed first. | tasks/clean.py | def clean_all(ctx, dry_run=False):
"""Clean up everything, even the precious stuff.
NOTE: clean task is executed first.
"""
cleanup_dirs(ctx.clean_all.directories or [], dry_run=dry_run)
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"""Clean up everything, even the precious stuff.
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train | clean_python | Cleanup python related files/dirs: *.pyc, *.pyo, ... | tasks/clean.py | def clean_python(ctx, dry_run=False):
"""Cleanup python related files/dirs: *.pyc, *.pyo, ..."""
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train | cleanup_files | Remove files or files selected by file patterns.
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train | path_glob | Use pathlib for ant-like patterns, like: "**/*.py"
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:param current_dir: Current working directory (as Path, pathlib.Path, str)
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train | Pipeline.stack_call | Stacks a redis command inside the object.
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Args:
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The syntax is the same than the call() method a Client class.
Args:
*args: full redis command as variable length argument list.
Examples:
>>> pipeline = Pipeline()
>>> pipelin... | def stack_call(self, *args):
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The syntax is the same than the call() method a Client class.
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train | Connection.connect | Connects the object to the host:port.
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Returns:
Future: a Future object with True as result if the connection
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train | Connection.disconnect | Disconnects the object.
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Safe method (no exception, even if it's already disconnected or if
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You can give a WriteBuffer as parameter. The internal Connection
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train | surrogate_escape | Simulate the Python 3 ``surrogateescape`` handler, but for Python 2 only. | tasks/_vendor/path.py | def surrogate_escape(error):
"""
Simulate the Python 3 ``surrogateescape`` handler, but for Python 2 only.
"""
chars = error.object[error.start:error.end]
assert len(chars) == 1
val = ord(chars)
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return __builtin__.unichr(val), error.end | def surrogate_escape(error):
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Simulate the Python 3 ``surrogateescape`` handler, but for Python 2 only.
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train | Path._always_unicode | Ensure the path as retrieved from a Python API, such as :func:`os.listdir`,
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Ensure the path as retrieved from a Python API, such as :func:`os.listdir`,
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For example,
``Path('/home/guido/python.tar.gz').name == 'python.tar.gz'``,
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""" The same as :meth:`name`, but with one file extension stripped off.
For example,
``Path('/home/guido/python.tar.gz').name == 'python.tar.gz'``,
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``Path('/home/guido/python.tar.gz').namebase == 'python.tar'``.
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base, ext = self.module... | def namebase(self):
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items whose names match the gi... | tasks/_vendor/path.py | def listdir(self, pattern=None):
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The elements of the list are Path objects.
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Keyword arguments work as in :func:`io.open`. If the file cannot be
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train | Path.write_text | r""" Write the given text to this file.
The default behavior is to overwrite any existing file;
to append instead, use the `append=True` keyword argument.
There are two differences between :meth:`write_text` and
:meth:`write_bytes`: newline handling and Unicode handling.
See be... | tasks/_vendor/path.py | def write_text(self, text, encoding=None, errors='strict',
linesep=os.linesep, append=False):
r""" Write the given text to this file.
The default behavior is to overwrite any existing file;
to append instead, use the `append=True` keyword argument.
There are two diff... | def write_text(self, text, encoding=None, errors='strict',
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By default this overwrites any existing file at this path.
This puts a platform-specific newline sequence on every line.
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r""" Write the given lines of text to this file.
By default this overwrites any existing file at this path.
This puts a platform-specific newline sequence on every line.
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By default this overwrites any existing file at this path.
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""" Like :meth:`mkdir`, but does not raise an exception if the
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directory is not empty or does not exist. """
try:
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train | Path.rmtree_p | Like :meth:`rmtree`, but does not raise an exception if the
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_, e, _ = sys.exc_info()
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train | Path.merge_tree | Copy entire contents of self to dst, overwriting existing
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train | create_url | Create the URL in the LyricWikia format | lyricwikia/lyricwikia.py | def create_url(artist, song):
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"""Retrieve the lyrics of the song and return the first one in case
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return get_all_lyrics(artist, song, linesep, timeout)[0] | def get_lyrics(artist, song, linesep='\n', timeout=None):
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train | open_file | Open an ARF file, creating as necessary.
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data -- the data to store
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train | create_table | Create a new array dataset under group with compound datatype and maxshape=(None,) | arf.py | def create_table(group, name, dtype, **attributes):
"""Create a new array dataset under group with compound datatype and maxshape=(None,)"""
dset = group.create_dataset(
name, shape=(0,), dtype=dtype, maxshape=(None,))
set_attributes(dset, **attributes)
return dset | def create_table(group, name, dtype, **attributes):
"""Create a new array dataset under group with compound datatype and maxshape=(None,)"""
dset = group.create_dataset(
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train | append_data | Append data to dset along axis 0. Data must be a single element or
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train | check_file_version | Check the ARF version attribute of file for compatibility.
Raises DeprecationWarning for backwards-incompatible files, FutureWarning
for (potentially) forwards-incompatible files, and UserWarning for files
that may not have been created by an ARF library.
Returns the version for the file | arf.py | def check_file_version(file):
"""Check the ARF version attribute of file for compatibility.
Raises DeprecationWarning for backwards-incompatible files, FutureWarning
for (potentially) forwards-incompatible files, and UserWarning for files
that may not have been created by an ARF library.
Returns t... | def check_file_version(file):
"""Check the ARF version attribute of file for compatibility.
Raises DeprecationWarning for backwards-incompatible files, FutureWarning
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train | set_attributes | Set multiple attributes on node.
If overwrite is False, and the attribute already exists, does nothing. If
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"""Set multiple attributes on node.
If overwrite is False, and the attribute already exists, does nothing. If
the value for a key is None, the attribute is deleted.
"""
aset = node.attrs
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train | keys_by_creation | Returns a sequence of links in group in order of creation.
Raises an error if the group was not set to track creation order. | arf.py | def keys_by_creation(group):
"""Returns a sequence of links in group in order of creation.
Raises an error if the group was not set to track creation order.
"""
from h5py import h5
out = []
try:
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train | convert_timestamp | Make an ARF timestamp from an object.
Argument can be a datetime.datetime object, a time.struct_time, an integer,
a float, or a tuple of integers. The returned value is a numpy array with
the integer number of seconds since the Epoch and any additional
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Note that because floating poin... | arf.py | def convert_timestamp(obj):
"""Make an ARF timestamp from an object.
Argument can be a datetime.datetime object, a time.struct_time, an integer,
a float, or a tuple of integers. The returned value is a numpy array with
the integer number of seconds since the Epoch and any additional
microseconds.
... | def convert_timestamp(obj):
"""Make an ARF timestamp from an object.
Argument can be a datetime.datetime object, a time.struct_time, an integer,
a float, or a tuple of integers. The returned value is a numpy array with
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train | timestamp_to_datetime | Convert an ARF timestamp to a datetime.datetime object (naive local time) | arf.py | def timestamp_to_datetime(timestamp):
"""Convert an ARF timestamp to a datetime.datetime object (naive local time)"""
from datetime import datetime, timedelta
obj = datetime.fromtimestamp(timestamp[0])
return obj + timedelta(microseconds=int(timestamp[1])) | def timestamp_to_datetime(timestamp):
"""Convert an ARF timestamp to a datetime.datetime object (naive local time)"""
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obj = datetime.fromtimestamp(timestamp[0])
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train | set_uuid | Set the uuid attribute of an HDF5 object. Use this method to ensure correct dtype | arf.py | def set_uuid(obj, uuid=None):
"""Set the uuid attribute of an HDF5 object. Use this method to ensure correct dtype """
from uuid import uuid4, UUID
if uuid is None:
uuid = uuid4()
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train | get_uuid | Return the uuid for obj, or null uuid if none is set | arf.py | def get_uuid(obj):
"""Return the uuid for obj, or null uuid if none is set"""
# TODO: deprecate null uuid ret val
from uuid import UUID
try:
uuid = obj.attrs['uuid']
except KeyError:
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# convert to unicode for python 3
try:
uuid = uuid.decode('ascii')... | def get_uuid(obj):
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# TODO: deprecate null uuid ret val
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train | count_children | Return the number of children of obj, optionally restricting by class | arf.py | def count_children(obj, type=None):
"""Return the number of children of obj, optionally restricting by class"""
if type is None:
return len(obj)
else:
# there doesn't appear to be any hdf5 function for getting this
# information without inspecting each child, which makes this somewha... | def count_children(obj, type=None):
"""Return the number of children of obj, optionally restricting by class"""
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train | DataTypes._todict | generate a dict keyed by value | arf.py | def _todict(cls):
""" generate a dict keyed by value """
return dict((getattr(cls, attr), attr) for attr in dir(cls) if not attr.startswith('_')) | def _todict(cls):
""" generate a dict keyed by value """
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train | get_template | get_template will return a template in the template folder,
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'''get_template will return a template in the template folder,
with some substitutions (eg, {'{{ graph | safe }}':"fill this in!"}
'''
template = None
if not template_name.endswith('.html'):
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here = "%... | def get_template(template_name,fields=None):
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'''
template = None
if not template_name.endswith('.html'):
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train | container_similarity_vector | container similarity_vector is similar to compare_packages, but intended
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to a list of packages. If packages_set is not provided, the default used is
'docker-os'. This can be changed to 'docker-library', or if the user wants a cu... | singularity/analysis/compare.py | def container_similarity_vector(container1=None,packages_set=None,by=None):
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train | compare_singularity_images | compare_singularity_images is a wrapper for compare_containers to compare
singularity containers. If image_paths2 is not defined, pairwise comparison is done
with image_paths1 | singularity/analysis/compare.py | def compare_singularity_images(image_paths1, image_paths2=None):
'''compare_singularity_images is a wrapper for compare_containers to compare
singularity containers. If image_paths2 is not defined, pairwise comparison is done
with image_paths1
'''
repeat = False
if image_paths2 is None:
... | def compare_singularity_images(image_paths1, image_paths2=None):
'''compare_singularity_images is a wrapper for compare_containers to compare
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train | compare_containers | compare_containers will generate a data structure with common and unique files to
two images. If environmental variable SINGULARITY_HUB is set, will use container
database objects.
:param container1: first container for comparison
:param container2: second container for comparison if either not defined ... | singularity/analysis/compare.py | def compare_containers(container1=None, container2=None):
'''compare_containers will generate a data structure with common and unique files to
two images. If environmental variable SINGULARITY_HUB is set, will use container
database objects.
:param container1: first container for comparison
:param ... | def compare_containers(container1=None, container2=None):
'''compare_containers will generate a data structure with common and unique files to
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train | compare_lists | compare lists is the lowest level that drives compare_containers and
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train | calculate_similarity | calculate_similarity will calculate similarity of two containers
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container1: container 1
container2: container 2 must be defined or
metric a function to take a total... | singularity/analysis/compare.py | def calculate_similarity(container1=None,
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train | package_node | package node aims to package a (present working node) for a user into
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train | unpack_node | unpackage node is intended to unpackage a node that was packaged with
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2. Transfer the package somewhere that Singularity is installed | singularity/package/clone.py | def unpack_node(image_path,name=None,output_folder=None,size=None):
'''unpackage node is intended to unpackage a node that was packaged with
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train | get_build_template | get_build template returns a string or file for a particular build template, which is
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:param template_name: the name of the template to retrieve in build/scripts
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:param template_name: the name of the template to retrieve in build/scripts
:pa... | def get_build_template(template_name,params=None,to_file=None):
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:param file_path: the full path to the file to sniff
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train | get_script | get_script will return a build script_name, if it is included
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:param script_name: the name of the script to look for | singularity/build/utils.py | def get_script(script_name):
'''get_script will return a build script_name, if it is included
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'''
install_dir = get_installdir()
script_path = "%s/build/scripts/%s"... | def get_script(script_name):
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:param output_folder: the output folder to create the zip in. If not
:param zip_name: the name of the zipfile to return.
specifi... | def zip_up(file_list,zip_name,output_folder=None):
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train | get_image_hashes | get_image_hashes returns the hash for an image across all levels. This is the quickest,
easiest way to define a container's reproducibility on each level. | singularity/analysis/reproduce/hash.py | def get_image_hashes(image_path, version=None, levels=None):
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'''
if levels is None:
levels = get_levels(version=version)
hashes = dict... | def get_image_hashes(image_path, version=None, levels=None):
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train | get_image_hash | get_image_hash will generate a sha1 hash of an image, depending on a level
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train | get_content_hashes | get_content_hashes is like get_image_hash, but it returns a complete dictionary
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version=None,
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... | singularityhub/singularity-python | python | https://github.com/singularityhub/singularity-python/blob/498c3433724b332f7493fec632d8daf479f47b82/singularity/analysis/reproduce/hash.py#L124-L162 | [
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train | get_image_file_hash | get_image_hash will return an md5 hash of the file based on a criteria level.
:param level: one of LOW, MEDIUM, HIGH
:param image_path: full path to the singularity image | singularity/analysis/reproduce/hash.py | def get_image_file_hash(image_path):
'''get_image_hash will return an md5 hash of the file based on a criteria level.
:param level: one of LOW, MEDIUM, HIGH
:param image_path: full path to the singularity image
'''
hasher = hashlib.md5()
with open(image_path, "rb") as f:
for chunk in ite... | def get_image_file_hash(image_path):
'''get_image_hash will return an md5 hash of the file based on a criteria level.
:param level: one of LOW, MEDIUM, HIGH
:param image_path: full path to the singularity image
'''
hasher = hashlib.md5()
with open(image_path, "rb") as f:
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train | container_difference | container_difference will return a data structure to render an html
tree (graph) of the differences between two images or packages. The second
container is subtracted from the first
:param container: the primary container object (to subtract from)
:param container_subtract: the second container object ... | singularity/views/trees.py | def container_difference(container=None,container_subtract=None,image_package=None,
image_package_subtract=None,comparison=None):
'''container_difference will return a data structure to render an html
tree (graph) of the differences between two images or packages. The second
contai... | def container_difference(container=None,container_subtract=None,image_package=None,
image_package_subtract=None,comparison=None):
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train | container_similarity | container_sim will return a data structure to render an html tree
(graph) of the intersection (commonalities) between two images or packages
:param container1: the first container object
:param container2: the second container object if either not defined, need
:param image_package1: a packaged contain... | singularity/views/trees.py | def container_similarity(container1=None,container2=None,image_package1=None,
image_package2=None,comparison=None):
'''container_sim will return a data structure to render an html tree
(graph) of the intersection (commonalities) between two images or packages
:param container1: the... | def container_similarity(container1=None,container2=None,image_package1=None,
image_package2=None,comparison=None):
'''container_sim will return a data structure to render an html tree
(graph) of the intersection (commonalities) between two images or packages
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train | container_tree | tree will render an html tree (graph) of a container | singularity/views/trees.py | def container_tree(container=None,image_package=None):
'''tree will render an html tree (graph) of a container
'''
guts = get_container_contents(container=container,
image_package=image_package,
split_delim="\n")
# Make the tree and r... | def container_tree(container=None,image_package=None):
'''tree will render an html tree (graph) of a container
'''
guts = get_container_contents(container=container,
image_package=image_package,
split_delim="\n")
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train | make_container_tree | make_container_tree will convert a list of folders and files into a json structure that represents a graph.
:param folders: a list of folders in the image
:param files: a list of files in the folder
:param parse_files: return 'files' lookup in result, to associate ID of node with files (default True)
:p... | singularity/views/trees.py | def make_container_tree(folders,files,path_delim="/",parse_files=True):
'''make_container_tree will convert a list of folders and files into a json structure that represents a graph.
:param folders: a list of folders in the image
:param files: a list of files in the folder
:param parse_files: return 'fi... | def make_container_tree(folders,files,path_delim="/",parse_files=True):
'''make_container_tree will convert a list of folders and files into a json structure that represents a graph.
:param folders: a list of folders in the image
:param files: a list of files in the folder
:param parse_files: return 'fi... | [
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train | make_package_tree | make package tree will make a dendrogram comparing a matrix of packages
:param matrix: a pandas df of packages, with names in index and columns
:param labels: a list of labels corresponding to row names, will be
pulled from rows if not defined
:param title: a title for the plot, if not defined, will be ... | singularity/views/trees.py | def make_package_tree(matrix=None,labels=None,width=25,height=10,title=None,font_size=None):
'''make package tree will make a dendrogram comparing a matrix of packages
:param matrix: a pandas df of packages, with names in index and columns
:param labels: a list of labels corresponding to row names, will be
... | def make_package_tree(matrix=None,labels=None,width=25,height=10,title=None,font_size=None):
'''make package tree will make a dendrogram comparing a matrix of packages
:param matrix: a pandas df of packages, with names in index and columns
:param labels: a list of labels corresponding to row names, will be
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train | make_interactive_tree | make interactive tree will return complete html for an interactive tree
:param title: a title for the plot, if not defined, will be left out. | singularity/views/trees.py | def make_interactive_tree(matrix=None,labels=None):
'''make interactive tree will return complete html for an interactive tree
:param title: a title for the plot, if not defined, will be left out.
'''
from scipy.cluster.hierarchy import (
dendrogram,
linkage,
to_tree
)
... | def make_interactive_tree(matrix=None,labels=None):
'''make interactive tree will return complete html for an interactive tree
:param title: a title for the plot, if not defined, will be left out.
'''
from scipy.cluster.hierarchy import (
dendrogram,
linkage,
to_tree
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train | add_node | add_node will add a node to it's parent | singularity/views/trees.py | def add_node(node, parent):
'''add_node will add a node to it's parent
'''
newNode = dict(node_id=node.id, children=[])
parent["children"].append(newNode)
if node.left: add_node(node.left, newNode)
if node.right: add_node(node.right, newNode) | def add_node(node, parent):
'''add_node will add a node to it's parent
'''
newNode = dict(node_id=node.id, children=[])
parent["children"].append(newNode)
if node.left: add_node(node.left, newNode)
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train | label_tree | label tree will again recursively label the tree
:param n: the root node, usually d3['children'][0]
:param lookup: the node/id lookup | singularity/views/trees.py | def label_tree(n,lookup):
'''label tree will again recursively label the tree
:param n: the root node, usually d3['children'][0]
:param lookup: the node/id lookup
'''
if len(n["children"]) == 0:
leaves = [lookup[n["node_id"]]]
else:
leaves = reduce(lambda ls, c: ls + label_tree(c... | def label_tree(n,lookup):
'''label tree will again recursively label the tree
:param n: the root node, usually d3['children'][0]
:param lookup: the node/id lookup
'''
if len(n["children"]) == 0:
leaves = [lookup[n["node_id"]]]
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train | extract_apps | extract app will extract metadata for one or more apps
Parameters
==========
image: the absolute path to the image
app_name: the name of the app under /scif/apps | singularity/analysis/apps.py | def extract_apps(image, app_names):
''' extract app will extract metadata for one or more apps
Parameters
==========
image: the absolute path to the image
app_name: the name of the app under /scif/apps
'''
apps = dict()
if isinstance(app_names, tuple):
app_names... | def extract_apps(image, app_names):
''' extract app will extract metadata for one or more apps
Parameters
==========
image: the absolute path to the image
app_name: the name of the app under /scif/apps
'''
apps = dict()
if isinstance(app_names, tuple):
app_names... | [
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train | run_command | run_command uses subprocess to send a command to the terminal.
:param cmd: the command to send, should be a list for subprocess
:param error_message: the error message to give to user if fails,
if none specified, will alert that command failed.
:param sudopw: if specified (not None) command will be run ... | singularity/utils.py | def run_command(cmd, sudo=False):
'''run_command uses subprocess to send a command to the terminal.
:param cmd: the command to send, should be a list for subprocess
:param error_message: the error message to give to user if fails,
if none specified, will alert that command failed.
:param sudopw: if ... | def run_command(cmd, sudo=False):
'''run_command uses subprocess to send a command to the terminal.
:param cmd: the command to send, should be a list for subprocess
:param error_message: the error message to give to user if fails,
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train | download_repo | download_repo
:param repo_url: the url of the repo to clone from
:param destination: the full path to the destination for the repo | singularity/utils.py | def download_repo(repo_url, destination, commit=None):
'''download_repo
:param repo_url: the url of the repo to clone from
:param destination: the full path to the destination for the repo
'''
command = "git clone %s %s" % (repo_url, destination)
os.system(command)
return destination | def download_repo(repo_url, destination, commit=None):
'''download_repo
:param repo_url: the url of the repo to clone from
:param destination: the full path to the destination for the repo
'''
command = "git clone %s %s" % (repo_url, destination)
os.system(command)
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train | get_tags | get tags will return a list of tags that describe the software in an image,
meaning inside of a paricular folder. If search_folder is not defined, uses lib
:param container: if provided, will use container as image. Can also provide
:param image_package: if provided, can be used instead of container
:pa... | singularity/analysis/classify.py | def get_tags(container=None,
search_folders=None,
file_list=None,
return_unique=True):
'''get tags will return a list of tags that describe the software in an image,
meaning inside of a paricular folder. If search_folder is not defined, uses lib
:param container: if p... | def get_tags(container=None,
search_folders=None,
file_list=None,
return_unique=True):
'''get tags will return a list of tags that describe the software in an image,
meaning inside of a paricular folder. If search_folder is not defined, uses lib
:param container: if p... | [
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... | singularityhub/singularity-python | python | https://github.com/singularityhub/singularity-python/blob/498c3433724b332f7493fec632d8daf479f47b82/singularity/analysis/classify.py#L51-L91 | [
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train | file_counts | file counts will return a list of files that match one or more regular expressions.
if no patterns is defined, a default of readme is used. All patterns and files are made
case insensitive.
Parameters
==========
:param container: if provided, will use container as image. Can also provide
:param... | singularity/analysis/classify.py | def file_counts(container=None,
patterns=None,
image_package=None,
file_list=None):
'''file counts will return a list of files that match one or more regular expressions.
if no patterns is defined, a default of readme is used. All patterns and files are made
... | def file_counts(container=None,
patterns=None,
image_package=None,
file_list=None):
'''file counts will return a list of files that match one or more regular expressions.
if no patterns is defined, a default of readme is used. All patterns and files are made
... | [
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"fi... | singularityhub/singularity-python | python | https://github.com/singularityhub/singularity-python/blob/498c3433724b332f7493fec632d8daf479f47b82/singularity/analysis/classify.py#L99-L130 | [
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