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mojaie/chorus | chorus/v2000reader.py | atoms | def atoms(lines):
"""Parse atom block into atom objects
Returns:
dict: networkx nodes
"""
# Convert sdf style charge to actual charge
conv_charge_table = {0: 0, 1: 3, 2: 2, 3: 1, 4: 0, 5: -1, 6: -2, 7: -3}
results = {}
for i, line in enumerate(lines):
symbol = line[31:34].rs... | python | def atoms(lines):
"""Parse atom block into atom objects
Returns:
dict: networkx nodes
"""
# Convert sdf style charge to actual charge
conv_charge_table = {0: 0, 1: 3, 2: 2, 3: 1, 4: 0, 5: -1, 6: -2, 7: -3}
results = {}
for i, line in enumerate(lines):
symbol = line[31:34].rs... | [
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mojaie/chorus | chorus/v2000reader.py | bonds | def bonds(lines, atoms):
"""Parse bond block into bond objects
Returns:
dict: networkx adjacency dict
"""
# Convert sdf style stereobond (see chem.model.bond.Bond)
conv_stereo_table = {0: 0, 1: 1, 3: 3, 4: 3, 6: 2}
results = {a: {} for a in atoms}
for line in lines:
bond = B... | python | def bonds(lines, atoms):
"""Parse bond block into bond objects
Returns:
dict: networkx adjacency dict
"""
# Convert sdf style stereobond (see chem.model.bond.Bond)
conv_stereo_table = {0: 0, 1: 1, 3: 3, 4: 3, 6: 2}
results = {a: {} for a in atoms}
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mojaie/chorus | chorus/v2000reader.py | properties | def properties(lines):
"""Parse properties block
Returns:
dict: {property_type: (atom_index, value)}
"""
results = {}
for i, line in enumerate(lines):
type_ = line[3:6]
if type_ not in ["CHG", "RAD", "ISO"]:
continue # Other properties are not supported yet
... | python | def properties(lines):
"""Parse properties block
Returns:
dict: {property_type: (atom_index, value)}
"""
results = {}
for i, line in enumerate(lines):
type_ = line[3:6]
if type_ not in ["CHG", "RAD", "ISO"]:
continue # Other properties are not supported yet
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mojaie/chorus | chorus/v2000reader.py | add_properties | def add_properties(props, mol):
"""apply properties to the molecule object
Returns:
None (alter molecule object directly)
"""
if not props:
return
# The properties supersedes all charge and radical values in the atom block
for _, atom in mol.atoms_iter():
atom.charge = 0... | python | def add_properties(props, mol):
"""apply properties to the molecule object
Returns:
None (alter molecule object directly)
"""
if not props:
return
# The properties supersedes all charge and radical values in the atom block
for _, atom in mol.atoms_iter():
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mojaie/chorus | chorus/v2000reader.py | molecule | def molecule(lines):
"""Parse molfile part into molecule object
Args:
lines (list): lines of molfile part
Raises:
ValueError: Symbol not defined in periodictable.yaml
(Polymer expression not supported yet)
"""
count_line = lines[3]
num_atoms = int(count_line... | python | def molecule(lines):
"""Parse molfile part into molecule object
Args:
lines (list): lines of molfile part
Raises:
ValueError: Symbol not defined in periodictable.yaml
(Polymer expression not supported yet)
"""
count_line = lines[3]
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mojaie/chorus | chorus/v2000reader.py | mol_supplier | def mol_supplier(lines, no_halt, assign_descriptors):
"""Yields molecules generated from CTAB text
Args:
lines (iterable): CTAB text lines
no_halt (boolean):
True: shows warning messages for invalid format and go on.
False: throws an exception for it and stop parsing.
... | python | def mol_supplier(lines, no_halt, assign_descriptors):
"""Yields molecules generated from CTAB text
Args:
lines (iterable): CTAB text lines
no_halt (boolean):
True: shows warning messages for invalid format and go on.
False: throws an exception for it and stop parsing.
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mojaie/chorus | chorus/v2000reader.py | mols_from_text | def mols_from_text(text, no_halt=True, assign_descriptors=True):
"""Returns molecules generated from sdfile text
Throws:
StopIteration: if the text does not have molecule
ValueError: if Unsupported symbol is found
"""
if isinstance(text, bytes):
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else:
... | python | def mols_from_text(text, no_halt=True, assign_descriptors=True):
"""Returns molecules generated from sdfile text
Throws:
StopIteration: if the text does not have molecule
ValueError: if Unsupported symbol is found
"""
if isinstance(text, bytes):
t = tx.decode(text)
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mojaie/chorus | chorus/v2000reader.py | mol_from_text | def mol_from_text(text, assign_descriptors=True):
"""Parse CTAB text and return first one as a Compound object.
Throws:
StopIteration: if the text does not have molecule
ValueError: if Unsupported symbol is found
"""
cg = mols_from_text(text, False, assign_descriptors)
return next(c... | python | def mol_from_text(text, assign_descriptors=True):
"""Parse CTAB text and return first one as a Compound object.
Throws:
StopIteration: if the text does not have molecule
ValueError: if Unsupported symbol is found
"""
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mojaie/chorus | chorus/v2000reader.py | mol_from_file | def mol_from_file(path, assign_descriptors=True):
"""Parse CTAB file and return first one as a Compound object."""
cs = mols_from_file(path, False, assign_descriptors)
return next(cs) | python | def mol_from_file(path, assign_descriptors=True):
"""Parse CTAB file and return first one as a Compound object."""
cs = mols_from_file(path, False, assign_descriptors)
return next(cs) | [
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brutus/wdiffhtml | wdiffhtml/settings.py | load_from_resource | def load_from_resource(name):
"""
Returns the contents of a file resource.
If the resource exists in the users data directory, it is used instead
of the default resource.
"""
filepath = Path(USER_DIR) / name
if filepath.exists():
with filepath.open() as fh:
return fh.read()
else:
return ... | python | def load_from_resource(name):
"""
Returns the contents of a file resource.
If the resource exists in the users data directory, it is used instead
of the default resource.
"""
filepath = Path(USER_DIR) / name
if filepath.exists():
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return fh.read()
else:
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micolous/python-slackrealtime | src/slackrealtime/__init__.py | connect | def connect(token, protocol=RtmProtocol, factory=WebSocketClientFactory, factory_kwargs=None, api_url=None, debug=False):
"""
Creates a new connection to the Slack Real-Time API.
Returns (connection) which represents this connection to the API server.
"""
if factory_kwargs is None:
factory_kwargs = dict()
me... | python | def connect(token, protocol=RtmProtocol, factory=WebSocketClientFactory, factory_kwargs=None, api_url=None, debug=False):
"""
Creates a new connection to the Slack Real-Time API.
Returns (connection) which represents this connection to the API server.
"""
if factory_kwargs is None:
factory_kwargs = dict()
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xlfe/reticul8 | python/reticul8/block_compressor.py | block_compressor.next_block | def next_block(self):
"""
This could probably be improved; at the moment it starts by trying to overshoot the
desired compressed block size, then it reduces the input bytes one by one until it
has met the required block size
"""
assert self.pos <= self.input_len
... | python | def next_block(self):
"""
This could probably be improved; at the moment it starts by trying to overshoot the
desired compressed block size, then it reduces the input bytes one by one until it
has met the required block size
"""
assert self.pos <= self.input_len
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mesbahamin/chronophore | chronophore/chronophore.py | set_up_logging | def set_up_logging(log_file, console_log_level):
"""Configure logging settings and return a logger object."""
logger = logging.getLogger()
logger.setLevel(logging.DEBUG)
fh = logging.FileHandler(str(log_file))
fh.setLevel(logging.DEBUG)
ch = logging.StreamHandler()
ch.setLevel(console_log_le... | python | def set_up_logging(log_file, console_log_level):
"""Configure logging settings and return a logger object."""
logger = logging.getLogger()
logger.setLevel(logging.DEBUG)
fh = logging.FileHandler(str(log_file))
fh.setLevel(logging.DEBUG)
ch = logging.StreamHandler()
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mesbahamin/chronophore | chronophore/chronophore.py | main | def main():
"""Run Chronophore based on the command line arguments."""
args = get_args()
# Make Chronophore's directories and files in $HOME
DATA_DIR = pathlib.Path(appdirs.user_data_dir(__title__))
LOG_FILE = pathlib.Path(appdirs.user_log_dir(__title__), 'debug.log')
os.makedirs(str(DATA_DIR),... | python | def main():
"""Run Chronophore based on the command line arguments."""
args = get_args()
# Make Chronophore's directories and files in $HOME
DATA_DIR = pathlib.Path(appdirs.user_data_dir(__title__))
LOG_FILE = pathlib.Path(appdirs.user_log_dir(__title__), 'debug.log')
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zsimic/runez | src/runez/logsetup.py | _ContextFilter.filter | def filter(self, record):
"""Determines if the record should be logged and injects context info into the record. Always returns True"""
fmt = LogManager.spec.context_format
if fmt:
data = self.context.to_dict()
if data:
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"""Determines if the record should be logged and injects context info into the record. Always returns True"""
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zsimic/runez | src/runez/logsetup.py | LogManager.enable_faulthandler | def enable_faulthandler(cls, signum=signal.SIGUSR1):
"""
Enable dumping thread stack traces when specified signals are received, similar to java's handling of SIGQUIT
Note: this must be called from the surviving process in case of daemonization.
Note that SIGQUIT does not work in all en... | python | def enable_faulthandler(cls, signum=signal.SIGUSR1):
"""
Enable dumping thread stack traces when specified signals are received, similar to java's handling of SIGQUIT
Note: this must be called from the surviving process in case of daemonization.
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zsimic/runez | src/runez/logsetup.py | LogManager.override_spec | def override_spec(cls, **kwargs):
"""OVerride 'spec' and '_default_spec' with given values"""
cls._default_spec.set(**kwargs)
cls.spec.set(**kwargs) | python | def override_spec(cls, **kwargs):
"""OVerride 'spec' and '_default_spec' with given values"""
cls._default_spec.set(**kwargs)
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zsimic/runez | src/runez/logsetup.py | LogManager._fix_logging_shortcuts | def _fix_logging_shortcuts(cls):
"""
Fix standard logging shortcuts to correctly report logging module.
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- actually use %(name) and care about it being correct
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"""
Fix standard logging shortcuts to correctly report logging module.
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dfm/casjobs | casjobs.py | CasJobs._parse_single | def _parse_single(self, text, tagname):
"""
A hack to get the content of the XML responses from the CAS server.
## Arguments
* `text` (str): The XML string to parse.
* `tagname` (str): The tag that contains the info that we want.
## Returns
* `content` (str): ... | python | def _parse_single(self, text, tagname):
"""
A hack to get the content of the XML responses from the CAS server.
## Arguments
* `text` (str): The XML string to parse.
* `tagname` (str): The tag that contains the info that we want.
## Returns
* `content` (str): ... | [
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dfm/casjobs | casjobs.py | CasJobs.quick | def quick(self, q, context=None, task_name="quickie", system=False):
"""
Run a quick job.
## Arguments
* `q` (str): The SQL query.
## Keyword Arguments
* `context` (str): Casjobs context used for this query.
* `task_name` (str): The task name.
* `syste... | python | def quick(self, q, context=None, task_name="quickie", system=False):
"""
Run a quick job.
## Arguments
* `q` (str): The SQL query.
## Keyword Arguments
* `context` (str): Casjobs context used for this query.
* `task_name` (str): The task name.
* `syste... | [
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dfm/casjobs | casjobs.py | CasJobs.submit | def submit(self, q, context=None, task_name="casjobs", estimate=30):
"""
Submit a job to CasJobs.
## Arguments
* `q` (str): The SQL query.
## Keyword Arguments
* `context` (str): Casjobs context used for this query.
* `task_name` (str): The task name.
... | python | def submit(self, q, context=None, task_name="casjobs", estimate=30):
"""
Submit a job to CasJobs.
## Arguments
* `q` (str): The SQL query.
## Keyword Arguments
* `context` (str): Casjobs context used for this query.
* `task_name` (str): The task name.
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## Arguments
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## Keyword Arguments
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dfm/casjobs | casjobs.py | CasJobs.status | def status(self, job_id):
"""
Check the status of a job.
## Arguments
* `job_id` (int): The job to check.
## Returns
* `code` (int): The status.
* `status` (str): The human-readable name of the current status.
"""
params = {"jobid": job_id}
... | python | def status(self, job_id):
"""
Check the status of a job.
## Arguments
* `job_id` (int): The job to check.
## Returns
* `code` (int): The status.
* `status` (str): The human-readable name of the current status.
"""
params = {"jobid": job_id}
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dfm/casjobs | casjobs.py | CasJobs.monitor | def monitor(self, job_id, timeout=5):
"""
Monitor the status of a job.
## Arguments
* `job_id` (int): The job to check.
* `timeout` (float): The time to wait between checks (in sec).
## Returns
* `code` (int): The status.
* `status` (str): The human-re... | python | def monitor(self, job_id, timeout=5):
"""
Monitor the status of a job.
## Arguments
* `job_id` (int): The job to check.
* `timeout` (float): The time to wait between checks (in sec).
## Returns
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* `timeout` (float): The time to wait between checks (in sec).
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dfm/casjobs | casjobs.py | CasJobs.request_output | def request_output(self, table, outtype):
"""
Request the output for a given table.
## Arguments
* `table` (str): The name of the table to export.
* `outtype` (str): The type of output. Must be one of:
CSV - Comma Seperated Values
DataSet - XML DataS... | python | def request_output(self, table, outtype):
"""
Request the output for a given table.
## Arguments
* `table` (str): The name of the table to export.
* `outtype` (str): The type of output. Must be one of:
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dfm/casjobs | casjobs.py | CasJobs.get_output | def get_output(self, job_id, outfn):
"""
Download an output file given the id of the output request job.
## Arguments
* `job_id` (int): The id of the _output_ job.
* `outfn` (str): The file where the output should be stored.
May also be a file-like object with a 'wr... | python | def get_output(self, job_id, outfn):
"""
Download an output file given the id of the output request job.
## Arguments
* `job_id` (int): The id of the _output_ job.
* `outfn` (str): The file where the output should be stored.
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dfm/casjobs | casjobs.py | CasJobs.request_and_get_output | def request_and_get_output(self, table, outtype, outfn):
"""
Shorthand for requesting an output file and then downloading it when
ready.
## Arguments
* `table` (str): The name of the table to export.
* `outtype` (str): The type of output. Must be one of:
CSV... | python | def request_and_get_output(self, table, outtype, outfn):
"""
Shorthand for requesting an output file and then downloading it when
ready.
## Arguments
* `table` (str): The name of the table to export.
* `outtype` (str): The type of output. Must be one of:
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dfm/casjobs | casjobs.py | CasJobs.drop_table | def drop_table(self, table):
"""
Drop a table from the MyDB context.
## Arguments
* `table` (str): The name of the table to drop.
"""
job_id = self.submit("DROP TABLE %s"%table, context="MYDB")
status = self.monitor(job_id)
if status[0] != 5:
... | python | def drop_table(self, table):
"""
Drop a table from the MyDB context.
## Arguments
* `table` (str): The name of the table to drop.
"""
job_id = self.submit("DROP TABLE %s"%table, context="MYDB")
status = self.monitor(job_id)
if status[0] != 5:
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dfm/casjobs | casjobs.py | CasJobs.count | def count(self, q):
"""
Shorthand for counting the results of a specific query.
## Arguments
* `q` (str): The query to count. This will be executed as:
`"SELECT COUNT(*) %s" % q`.
## Returns
* `count` (int): The resulting count.
"""
q = "SEL... | python | def count(self, q):
"""
Shorthand for counting the results of a specific query.
## Arguments
* `q` (str): The query to count. This will be executed as:
`"SELECT COUNT(*) %s" % q`.
## Returns
* `count` (int): The resulting count.
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dfm/casjobs | casjobs.py | CasJobs.list_tables | def list_tables(self):
"""
Lists the tables in mydb.
## Returns
* `tables` (list): A list of strings with all the table names from mydb.
"""
q = 'SELECT Distinct TABLE_NAME FROM information_schema.TABLES'
res = self.quick(q, context='MYDB', task_name='listtables... | python | def list_tables(self):
"""
Lists the tables in mydb.
## Returns
* `tables` (list): A list of strings with all the table names from mydb.
"""
q = 'SELECT Distinct TABLE_NAME FROM information_schema.TABLES'
res = self.quick(q, context='MYDB', task_name='listtables... | [
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ncraike/fang | examples/multiple_dependencies.py | multiply_and_add | def multiply_and_add(n):
'''Multiply the given number n by some configured multiplier, and
then add a configured offset.'''
multiplier, offset = di.resolver.unpack(multiply_and_add)
return (multiplier * n) + offset | python | def multiply_and_add(n):
'''Multiply the given number n by some configured multiplier, and
then add a configured offset.'''
multiplier, offset = di.resolver.unpack(multiply_and_add)
return (multiplier * n) + offset | [
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mastro35/flows | flows/Actions/InputTailAction.py | TailAction.flush_buffer | def flush_buffer(self):
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self.buffer.clear()
self.send_message(return_value)
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"""Add `values` to global logging context"""
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mojaie/chorus | chorus/draw/helper.py | display_terminal_carbon | def display_terminal_carbon(mol):
"""Set visible=True to the terminal carbon atoms.
"""
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a.visible = True | python | def display_terminal_carbon(mol):
"""Set visible=True to the terminal carbon atoms.
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mojaie/chorus | chorus/draw/helper.py | equalize_terminal_double_bond | def equalize_terminal_double_bond(mol):
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"""Show equalized double bond if it is connected to terminal atom.
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mojaie/chorus | chorus/draw/helper.py | spine_to_terminal_wedge | def spine_to_terminal_wedge(mol):
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mojaie/chorus | chorus/draw/helper.py | format_ring_double_bond | def format_ring_double_bond(mol):
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mol.require("Topology")
mol.require("ScaleAndCenter")
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vertices = [mol.atom(n).coords for n in r]
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... | python | def format_ring_double_bond(mol):
"""Set double bonds around the ring.
"""
mol.require("Topology")
mol.require("ScaleAndCenter")
for r in sorted(mol.rings, key=len, reverse=True):
vertices = [mol.atom(n).coords for n in r]
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mojaie/chorus | chorus/draw/helper.py | ready_to_draw | def ready_to_draw(mol):
"""Shortcut function to prepare molecule to draw.
Overwrite this function for customized appearance.
It is recommended to clone the molecule before draw
because all the methods above are destructive.
"""
copied = molutil.clone(mol)
# display_terminal_carbon(mol)
e... | python | def ready_to_draw(mol):
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copied = molutil.clone(mol)
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adblair/configloader | configloader/__init__.py | ConfigLoader.update_from_object | def update_from_object(self, obj, criterion=lambda key: key.isupper()):
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Update dict from the attributes of a module, class or other object.
By default only attributes with all-uppercase names will be retrieved.
Use the ``criterion`` argument to modify that behaviour.
:arg o... | python | def update_from_object(self, obj, criterion=lambda key: key.isupper()):
"""
Update dict from the attributes of a module, class or other object.
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adblair/configloader | configloader/__init__.py | ConfigLoader.update_from_env_namespace | def update_from_env_namespace(self, namespace):
"""
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dictionary keys. For example, if the following environment variables
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... | python | def update_from_env_namespace(self, namespace):
"""
Update dict from any environment variables that have a given prefix.
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adblair/configloader | configloader/__init__.py | ConfigLoader.update_from | def update_from(
self,
obj=None,
yaml_env=None,
yaml_file=None,
json_env=None,
json_file=None,
env_namespace=None,
):
"""
Update dict from several sources at once.
This is simply a convenience method... | python | def update_from(
self,
obj=None,
yaml_env=None,
yaml_file=None,
json_env=None,
json_file=None,
env_namespace=None,
):
"""
Update dict from several sources at once.
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adblair/configloader | configloader/__init__.py | ConfigLoader.namespace | def namespace(self, namespace, key_transform=lambda key: key):
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>>> from configloader import ConfigLoader
>>> config = ConfigLoader(
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ehansis/ozelot | ozelot/etl/util.py | render_diagram | def render_diagram(root_task, out_base, max_param_len=20, horizontal=False, colored=False):
"""Render a diagram of the ETL pipeline
All upstream tasks (i.e. requirements) of :attr:`root_task` are rendered.
Nodes are, by default, styled as simple rects. This style is augmented by any
:attr:`diagram_sty... | python | def render_diagram(root_task, out_base, max_param_len=20, horizontal=False, colored=False):
"""Render a diagram of the ETL pipeline
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ehansis/ozelot | ozelot/etl/util.py | sanitize | def sanitize(s,
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form='NFKC',
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"""Normalize a string
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s (unicode string): input unicode string
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gmdzy2010/dingtalk_sdk_gmdzy2010 | dingtalk_sdk_gmdzy2010/authority_request.py | PersistentCodeRequest.get_ticket_for_sns_token | def get_ticket_for_sns_token(self):
"""This is a shortcut for getting the sns_token, as a post data of
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self.logger.info("%s\t%s" % (self.request_method, self.request_url))
return {
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"""This is a shortcut for getting the sns_token, as a post data of
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ehansis/ozelot | examples/superheroes/superheroes/models.py | reinitialize | def reinitialize():
"""Drop all tables for all models, then re-create them
"""
from ozelot import client
# import all additional models needed in this project
# noinspection PyUnresolvedReferences
from ozelot.orm.target import ORMTargetMarker
client = client.get_client()
base.Base.drop... | python | def reinitialize():
"""Drop all tables for all models, then re-create them
"""
from ozelot import client
# import all additional models needed in this project
# noinspection PyUnresolvedReferences
from ozelot.orm.target import ORMTargetMarker
client = client.get_client()
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ncraike/fang | fang/dependency_register.py | DependencyRegister._unwrap_func | def _unwrap_func(cls, decorated_func):
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This unwraps a decorated func, returning the inner wrapped func.
This may become unnecessary with Python 3.4's inspect.unwrap().
'''
if click is not None:
# Workaround for click.command() decorator not setting
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ncraike/fang | fang/dependency_register.py | DependencyRegister._register_dependent | def _register_dependent(self, dependent, resource_name):
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Register a mapping of the dependent to resource name.
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'''
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Register a mapping of the dependent to resource name.
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ncraike/fang | fang/dependency_register.py | DependencyRegister.register | def register(self, resource_name, dependent=None):
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thorgate/django-esteid | esteid/middleware.py | BaseIdCardMiddleware.verify_ocsp | def verify_ocsp(cls, certificate, issuer):
""" Runs OCSP verification and returns error code - 0 means success
"""
return OCSPVerifier(certificate, issuer,
cls.get_ocsp_url(),
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""" Runs OCSP verification and returns error code - 0 means success
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lsst-sqre/documenteer | documenteer/requestsutils.py | requests_retry_session | def requests_retry_session(
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session=None):
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Parameters
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retries : `int`, optional
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lsst-sqre/documenteer | documenteer/sphinxconfig/technoteconf.py | configure_technote | def configure_technote(meta_stream):
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thorgate/django-esteid | esteid/config.py | ocsp_responder_certificate_path | def ocsp_responder_certificate_path():
"""Get ocsp responder certificate path
Test: TEST_of_SK_OCSP_RESPONDER_2011.pem
Live: sk-ocsp-responder-certificates.pem
Note: These files are distributed under esteid/certs
:return:
"""
certificate_path = getattr(settings, 'ESTEID_OCSP_RESPONDER_CER... | python | def ocsp_responder_certificate_path():
"""Get ocsp responder certificate path
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miguelgrinberg/Flask-MarrowMailer | flask_marrowmailer.py | Mailer.new | def new(self, **kwargs):
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brutus/wdiffhtml | wdiffhtml/__init__.py | wdiff | def wdiff(
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Returns the results of `wdiff` in a HTML compatible format.
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mesbahamin/chronophore | chronophore/config.py | _load_config | def _load_config(config_file):
"""Load settings from config file and return them as a dict. If the
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:param config_file: `pathlib.Path` object. Path to config file.
:return: Dictionary of config options.
"""
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mesbahamin/chronophore | chronophore/config.py | _load_options | def _load_options(parser):
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mesbahamin/chronophore | chronophore/config.py | _use_default | def _use_default(config_file):
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:param config_file: `pathlib.Path` object. Path to config file.
:return: `ConfigParser` object with the values loaded.
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"""Write default values to a config file. If another config file
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mojaie/chorus | chorus/model/graphmol.py | Compound.add_atom | def add_atom(self, key, atom):
"""Set an atom. Existing atom will be overwritten."""
self.graph.add_node(key, atom=atom) | python | def add_atom(self, key, atom):
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mojaie/chorus | chorus/model/graphmol.py | Compound.atoms_iter | def atoms_iter(self):
"""Iterate over atoms."""
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"""Iterate over atoms."""
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mojaie/chorus | chorus/model/graphmol.py | Compound.add_bond | def add_bond(self, key1, key2, bond):
"""Set a bond. Existing bond will be overwritten."""
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mojaie/chorus | chorus/model/graphmol.py | Compound.bonds_iter | def bonds_iter(self):
"""Iterate over bonds."""
for u, v, bond in self.graph.edges.data("bond"):
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"""Iterate over bonds."""
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mojaie/chorus | chorus/model/graphmol.py | Compound.neighbors | def neighbors(self, key):
"""Return dict of neighbor atom index and connecting bond."""
return {n: attr["bond"] for n, attr in self.graph[key].items()} | python | def neighbors(self, key):
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mojaie/chorus | chorus/model/graphmol.py | Compound.neighbors_iter | def neighbors_iter(self):
"""Iterate over atoms and return its neighbors."""
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mojaie/chorus | chorus/model/graphmol.py | Compound.clear | def clear(self):
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mojaie/chorus | chorus/draw/qt.py | Qt._convert | def _convert(self, pos):
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lsst-sqre/documenteer | documenteer/sphinxrunner.py | run_sphinx | def run_sphinx(root_dir):
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Root directory of the Sphinx project and content source. This directory
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Antojitos/guacamole-cli | src/guacamole_cli/__init__.py | get_settings | def get_settings(config_file):
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"""Search and load a configuration file."""
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ShadowBlip/Neteria | neteria/encryption.py | Encryption.encrypt | def encrypt(self, message, public_key):
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message (string): The string to encrypt.
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ShadowBlip/Neteria | neteria/encryption.py | Encryption.decrypt | def decrypt(self, message):
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Returns:
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"""
# Unserialize the encrypted message
message = json.loads(message)
... | python | def decrypt(self, message):
"""Decrypts a string using our own private key object.
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message (string): The string of the message to decrypt.
Returns:
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mastro35/flows | flows/Actions/InputWatchdogAction.py | DannyFileSystemEventHandler.on_any_event | def on_any_event(self, event):
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mastro35/flows | flows/Actions/InputWatchdogAction.py | DannyFileSystemEventHandler.on_created | def on_created(self, event):
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mastro35/flows | flows/Actions/InputWatchdogAction.py | DannyFileSystemEventHandler.on_deleted | def on_deleted(self, event):
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mastro35/flows | flows/Actions/InputWatchdogAction.py | WatchdogAction.on_created | def on_created(self, event):
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zsimic/runez | src/runez/heartbeat.py | Heartbeat.start | def start(cls):
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wesleybeckner/salty | salty/visualization.py | parity_plot | def parity_plot(X, Y, model, devmodel, axes_labels=None):
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A standard method of creating parity plots between predicted and
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Parameters
----------
X: array
experimental input data
Y: array
experimental output data
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potash/drain | drain/data.py | expand_dates | def expand_dates(df, columns=[]):
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potash/drain | drain/data.py | binarize | def binarize(df, category_classes, all_classes=True, drop=True,
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Binarize specified categoricals. Works inplace!
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potash/drain | drain/data.py | select_regexes | def select_regexes(strings, regexes):
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select subset of strings matching a regex
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select subset of strings matching a regex
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potash/drain | drain/data.py | parse_delta | def parse_delta(s):
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untwisted/untwisted | untwisted/iputils.py | ip_to_long | def ip_to_long (ip):
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lsst-sqre/documenteer | documenteer/sphinxext/lsstdocushare.py | lsst_doc_shortlink_role | def lsst_doc_shortlink_role(name, rawtext, text, lineno, inliner,
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Example::
:ldm:`151`
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options = options or {}
content = content or []
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DocuShare handles.
Example::
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lsst-sqre/documenteer | documenteer/bin/refreshlsstbib.py | run | def run():
"""Command line entrypoint for the ``refresh-lsst-bib`` program.
"""
args = parse_args()
if args.verbose:
log_level = logging.DEBUG
else:
log_level = logging.INFO
logging.basicConfig(
level=log_level,
format='%(asctime)s %(levelname)s %(name)s: %(messa... | python | def run():
"""Command line entrypoint for the ``refresh-lsst-bib`` program.
"""
args = parse_args()
if args.verbose:
log_level = logging.DEBUG
else:
log_level = logging.INFO
logging.basicConfig(
level=log_level,
format='%(asctime)s %(levelname)s %(name)s: %(messa... | [
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lsst-sqre/documenteer | documenteer/stackdocs/build.py | run_build_cli | def run_build_cli():
"""Command line entrypoint for the ``build-stack-docs`` program.
"""
args = parse_args()
if args.verbose:
log_level = logging.DEBUG
else:
log_level = logging.INFO
logging.basicConfig(
level=log_level,
format='%(asctime)s %(levelname)s %(name)... | python | def run_build_cli():
"""Command line entrypoint for the ``build-stack-docs`` program.
"""
args = parse_args()
if args.verbose:
log_level = logging.DEBUG
else:
log_level = logging.INFO
logging.basicConfig(
level=log_level,
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lsst-sqre/documenteer | documenteer/stackdocs/build.py | parse_args | def parse_args():
"""Create an argument parser for the ``build-stack-docs`` program.
Returns
-------
args : `argparse.Namespace`
Parsed argument object.
"""
parser = argparse.ArgumentParser(
description="Build a Sphinx documentation site for an EUPS stack, "
... | python | def parse_args():
"""Create an argument parser for the ``build-stack-docs`` program.
Returns
-------
args : `argparse.Namespace`
Parsed argument object.
"""
parser = argparse.ArgumentParser(
description="Build a Sphinx documentation site for an EUPS stack, "
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lsst-sqre/documenteer | documenteer/stackdocs/build.py | discover_setup_packages | def discover_setup_packages():
"""Summarize packages currently set up by EUPS, listing their
set up directories and EUPS version names.
Returns
-------
packages : `dict`
Dictionary with keys that are EUPS package names. Values are
dictionaries with fields:
- ``'dir'``: absolut... | python | def discover_setup_packages():
"""Summarize packages currently set up by EUPS, listing their
set up directories and EUPS version names.
Returns
-------
packages : `dict`
Dictionary with keys that are EUPS package names. Values are
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packages : `dict`
Dictionary with keys that are EUPS package names. Values are
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lsst-sqre/documenteer | documenteer/stackdocs/build.py | find_table_file | def find_table_file(root_project_dir):
"""Find the EUPS table file for a project.
Parameters
----------
root_project_dir : `str`
Path to the root directory of the main documentation project. This
is the directory containing the ``conf.py`` file and a ``ups``
directory.
Retu... | python | def find_table_file(root_project_dir):
"""Find the EUPS table file for a project.
Parameters
----------
root_project_dir : `str`
Path to the root directory of the main documentation project. This
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lsst-sqre/documenteer | documenteer/stackdocs/build.py | list_packages_in_eups_table | def list_packages_in_eups_table(table_text):
"""List the names of packages that are required by an EUPS table file.
Parameters
----------
table_text : `str`
The text content of an EUPS table file.
Returns
-------
names : `list` [`str`]
List of package names that are require... | python | def list_packages_in_eups_table(table_text):
"""List the names of packages that are required by an EUPS table file.
Parameters
----------
table_text : `str`
The text content of an EUPS table file.
Returns
-------
names : `list` [`str`]
List of package names that are require... | [
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lsst-sqre/documenteer | documenteer/stackdocs/build.py | find_package_docs | def find_package_docs(package_dir, skippedNames=None):
"""Find documentation directories in a package using ``manifest.yaml``.
Parameters
----------
package_dir : `str`
Directory of an EUPS package.
skippedNames : `list` of `str`, optional
List of package or module names to skip whe... | python | def find_package_docs(package_dir, skippedNames=None):
"""Find documentation directories in a package using ``manifest.yaml``.
Parameters
----------
package_dir : `str`
Directory of an EUPS package.
skippedNames : `list` of `str`, optional
List of package or module names to skip whe... | [
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Parameters
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package_dir : `str`
Directory of an EUPS package.
skippedNames : `list` of `str`, optional
List of package or module names to skip when creating links.
Returns
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