repo stringlengths 7 55 | path stringlengths 4 127 | func_name stringlengths 1 88 | original_string stringlengths 75 19.8k | language stringclasses 1
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brunato/lograptor | lograptor/cache.py | LookupCache.map_value | def map_value(self, value, gid):
"""
Return the value for a group id, applying requested mapping.
Map only groups related to a filter, ie when the basename of
the group is identical to the name of a filter.
"""
base_gid = self.base_gid_pattern.search(gid).group(1)
... | python | def map_value(self, value, gid):
"""
Return the value for a group id, applying requested mapping.
Map only groups related to a filter, ie when the basename of
the group is identical to the name of a filter.
"""
base_gid = self.base_gid_pattern.search(gid).group(1)
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brunato/lograptor | lograptor/cache.py | LookupCache.match_to_dict | def match_to_dict(self, match, gids):
"""
Map values from match into a dictionary.
"""
values = {}
for gid in gids:
try:
values[gid] = self.map_value(match.group(gid), gid)
except IndexError:
pass
return values | python | def match_to_dict(self, match, gids):
"""
Map values from match into a dictionary.
"""
values = {}
for gid in gids:
try:
values[gid] = self.map_value(match.group(gid), gid)
except IndexError:
pass
return values | [
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brunato/lograptor | lograptor/cache.py | LookupCache.match_to_string | def match_to_string(self, match, gids, values=None):
"""
Return the mapped string from match object. If a dictionary of
values is provided then use it to build the string.
"""
s = match.string
parts = []
k = 0
for gid in sorted(gids, key=lambda x: gids[x])... | python | def match_to_string(self, match, gids, values=None):
"""
Return the mapped string from match object. If a dictionary of
values is provided then use it to build the string.
"""
s = match.string
parts = []
k = 0
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brunato/lograptor | lograptor/cache.py | LookupCache.gethost | def gethost(self, ip_addr):
"""
Do reverse lookup on an ip address
"""
# Handle silly fake ipv6 addresses
try:
if ip_addr[:7] == '::ffff:':
ip_addr = ip_addr[7:]
except TypeError:
pass
if ip_addr[0] in string.letters:
... | python | def gethost(self, ip_addr):
"""
Do reverse lookup on an ip address
"""
# Handle silly fake ipv6 addresses
try:
if ip_addr[:7] == '::ffff:':
ip_addr = ip_addr[7:]
except TypeError:
pass
if ip_addr[0] in string.letters:
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brunato/lograptor | lograptor/cache.py | LookupCache.getuname | def getuname(self, uid):
"""
Get the username of a given uid.
"""
uid = int(uid)
try:
return self.uidsmap[uid]
except KeyError:
pass
try:
name = pwd.getpwuid(uid)[0]
except (KeyError, AttributeError):
name =... | python | def getuname(self, uid):
"""
Get the username of a given uid.
"""
uid = int(uid)
try:
return self.uidsmap[uid]
except KeyError:
pass
try:
name = pwd.getpwuid(uid)[0]
except (KeyError, AttributeError):
name =... | [
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mardix/Mocha | mocha/core.py | redirect | def redirect(endpoint, **kw):
"""
Redirect allow to redirect dynamically using the classes methods without
knowing the right endpoint.
Expecting all endpoint have GET as method, it will try to pick the first
match, based on the endpoint provided or the based on the Rule map_url
An endpoint can ... | python | def redirect(endpoint, **kw):
"""
Redirect allow to redirect dynamically using the classes methods without
knowing the right endpoint.
Expecting all endpoint have GET as method, it will try to pick the first
match, based on the endpoint provided or the based on the Rule map_url
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mardix/Mocha | mocha/core.py | get_true_argspec | def get_true_argspec(method):
"""Drills through layers of decorators attempting to locate the actual argspec for the method."""
argspec = inspect.getargspec(method)
args = argspec[0]
if args and args[0] == 'self':
return argspec
if hasattr(method, '__func__'):
method = method.__func... | python | def get_true_argspec(method):
"""Drills through layers of decorators attempting to locate the actual argspec for the method."""
argspec = inspect.getargspec(method)
args = argspec[0]
if args and args[0] == 'self':
return argspec
if hasattr(method, '__func__'):
method = method.__func... | [
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mardix/Mocha | mocha/core.py | Mocha.setup_installed_apps | def setup_installed_apps(cls):
"""
To import 3rd party applications along with associated properties
It is a list of dict or string.
When a dict, it contains the `app` key and the configuration,
if it's a string, it is just the app name
If you require dependencies from... | python | def setup_installed_apps(cls):
"""
To import 3rd party applications along with associated properties
It is a list of dict or string.
When a dict, it contains the `app` key and the configuration,
if it's a string, it is just the app name
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mardix/Mocha | mocha/core.py | Mocha._add_asset_bundle | def _add_asset_bundle(cls, path):
"""
Add a webassets bundle yml file
"""
f = "%s/assets.yml" % path
if os.path.isfile(f):
cls._asset_bundles.add(f) | python | def _add_asset_bundle(cls, path):
"""
Add a webassets bundle yml file
"""
f = "%s/assets.yml" % path
if os.path.isfile(f):
cls._asset_bundles.add(f) | [
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mardix/Mocha | mocha/core.py | Mocha._setup_db | def _setup_db(cls):
"""
Setup the DB connection if DB_URL is set
"""
uri = cls._app.config.get("DB_URL")
if uri:
db.connect__(uri, cls._app) | python | def _setup_db(cls):
"""
Setup the DB connection if DB_URL is set
"""
uri = cls._app.config.get("DB_URL")
if uri:
db.connect__(uri, cls._app) | [
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mardix/Mocha | mocha/core.py | Mocha.parse_options | def parse_options(cls, options):
"""Extracts subdomain and endpoint values from the options dict and returns
them along with a new dict without those values.
"""
options = options.copy()
subdomain = options.pop('subdomain', None)
endpoint = options.pop('endpoint', None... | python | def parse_options(cls, options):
"""Extracts subdomain and endpoint values from the options dict and returns
them along with a new dict without those values.
"""
options = options.copy()
subdomain = options.pop('subdomain', None)
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mardix/Mocha | mocha/core.py | Mocha.get_base_route | def get_base_route(cls):
"""Returns the route base to use for the current class."""
base_route = cls.__name__.lower()
if cls.base_route is not None:
base_route = cls.base_route
base_rule = parse_rule(base_route)
cls.base_args = [r[2] for r in base_rule]
... | python | def get_base_route(cls):
"""Returns the route base to use for the current class."""
base_route = cls.__name__.lower()
if cls.base_route is not None:
base_route = cls.base_route
base_rule = parse_rule(base_route)
cls.base_args = [r[2] for r in base_rule]
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clement-alexandre/TotemBionet | totembionet/src/discrete_model/influence_graph.py | InfluenceGraph.find_gene_by_name | def find_gene_by_name(self, gene_name: str) -> Gene:
"""
Find and return a gene in the influence graph with the given name.
Raise an AttributeError if there is no gene in the graph with the given name.
"""
for gene in self.genes:
if gene.name == gene_name:
... | python | def find_gene_by_name(self, gene_name: str) -> Gene:
"""
Find and return a gene in the influence graph with the given name.
Raise an AttributeError if there is no gene in the graph with the given name.
"""
for gene in self.genes:
if gene.name == gene_name:
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clement-alexandre/TotemBionet | totembionet/src/discrete_model/influence_graph.py | InfluenceGraph.find_multiplex_by_name | def find_multiplex_by_name(self, multiplex_name: str) -> Multiplex:
"""
Find and return a multiplex in the influence graph with the given name.
Raise an AttributeError if there is no multiplex in the graph with the given name.
"""
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i... | python | def find_multiplex_by_name(self, multiplex_name: str) -> Multiplex:
"""
Find and return a multiplex in the influence graph with the given name.
Raise an AttributeError if there is no multiplex in the graph with the given name.
"""
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clement-alexandre/TotemBionet | totembionet/src/discrete_model/influence_graph.py | InfluenceGraph.all_states | def all_states(self) -> Tuple[State, ...]:
""" Return all the possible states of this influence graph. """
return tuple(self._transform_list_of_states_to_state(states)
for states in self._cartesian_product_of_every_states_of_each_genes()) | python | def all_states(self) -> Tuple[State, ...]:
""" Return all the possible states of this influence graph. """
return tuple(self._transform_list_of_states_to_state(states)
for states in self._cartesian_product_of_every_states_of_each_genes()) | [
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clement-alexandre/TotemBionet | totembionet/src/discrete_model/influence_graph.py | InfluenceGraph._cartesian_product_of_every_states_of_each_genes | def _cartesian_product_of_every_states_of_each_genes(self) -> Tuple[Tuple[int, ...]]:
"""
Private method which return the cartesian product of the states
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Examples
--------
The model cont... | python | def _cartesian_product_of_every_states_of_each_genes(self) -> Tuple[Tuple[int, ...]]:
"""
Private method which return the cartesian product of the states
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Examples
--------
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clement-alexandre/TotemBionet | totembionet/src/discrete_model/influence_graph.py | InfluenceGraph._transform_list_of_states_to_state | def _transform_list_of_states_to_state(self, state: List[int]) -> State:
"""
Private method which transform a list which contains the state of the gene
in the models to a State object.
Examples
--------
The model contains 2 genes: operon = {0, 1, 2}
... | python | def _transform_list_of_states_to_state(self, state: List[int]) -> State:
"""
Private method which transform a list which contains the state of the gene
in the models to a State object.
Examples
--------
The model contains 2 genes: operon = {0, 1, 2}
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Kortemme-Lab/klab | klab/box_backup.py | read_sha1 | def read_sha1(
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buf_size = None,
start_byte = 0,
read_size = None,
extra_hashers = [], # update(data) will be called on all of these
):
'''
Determines the sha1 hash of a file in chunks, to prevent loading the entire file at once into memory
'''
read_size = read_size or os.s... | python | def read_sha1(
file_path,
buf_size = None,
start_byte = 0,
read_size = None,
extra_hashers = [], # update(data) will be called on all of these
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Determines the sha1 hash of a file in chunks, to prevent loading the entire file at once into memory
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Kortemme-Lab/klab | klab/box_backup.py | BoxAPI.verify_uploaded_file | def verify_uploaded_file(
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'''
Verifies the integrity of a file uploaded to Box
'''
source_file_size = os.stat(source_path).st_size
total_part_size = 0
file_po... | python | def verify_uploaded_file(
self,
destination_folder_id,
source_path,
verbose = True,
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Verifies the integrity of a file uploaded to Box
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uogbuji/versa | tools/py/reader/md.py | handle_resourcelist | def handle_resourcelist(ltext, **kwargs):
'''
A helper that converts lists of resources from a textual format such as Markdown, including absolutizing relative IRIs
'''
base=kwargs.get('base', VERSA_BASEIRI)
model=kwargs.get('model')
iris = ltext.strip().split()
newlist = model.generate_reso... | python | def handle_resourcelist(ltext, **kwargs):
'''
A helper that converts lists of resources from a textual format such as Markdown, including absolutizing relative IRIs
'''
base=kwargs.get('base', VERSA_BASEIRI)
model=kwargs.get('model')
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uogbuji/versa | tools/py/reader/md.py | handle_resourceset | def handle_resourceset(ltext, **kwargs):
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Alveo/pyalveo | pyalveo/cache.py | Cache.create_cache_database | def create_cache_database(self):
""" Create a new SQLite3 database for use with Cache objects
:raises: IOError if there is a problem creating the database file
"""
conn = sqlite3.connect(self.database)
conn.text_factory = str
c = conn.cursor()
c.execute("""CR... | python | def create_cache_database(self):
""" Create a new SQLite3 database for use with Cache objects
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"""
conn = sqlite3.connect(self.database)
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Alveo/pyalveo | pyalveo/cache.py | Cache.__exists_row_not_too_old | def __exists_row_not_too_old(self, row):
""" Check if the given row exists and is not too old """
if row is None:
return False
record_time = dateutil.parser.parse(row[2])
now = datetime.datetime.now(dateutil.tz.gettz())
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""" Check if the given row exists and is not too old """
if row is None:
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Alveo/pyalveo | pyalveo/cache.py | Cache.has_item | def has_item(self, item_url):
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Alveo/pyalveo | pyalveo/cache.py | Cache.get_primary_text | def get_primary_text(self, item_url):
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Alveo/pyalveo | pyalveo/cache.py | Cache.add_document | def add_document(self, doc_url, data):
""" Add the given document to the cache, updating
the existing content data if the document is already present
:type doc_url: String or Document
:param doc_url: the URL of the document, or a Document object
:type data: String
:param... | python | def add_document(self, doc_url, data):
""" Add the given document to the cache, updating
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Alveo/pyalveo | pyalveo/cache.py | Cache.add_primary_text | def add_primary_text(self, item_url, primary_text):
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cgrok/cr-async | examples/crcog.py | ClashCog.profile | async def profile(self, ctx, tag):
'''Example command for use inside a discord bot cog.'''
if not self.check_valid_tag(tag):
return await ctx.send('Invalid tag!')
profile = await self.cr.get_profile(tag)
em = discord.Embed(color=0x00FFFFF)
em.set_author(name=str(pro... | python | async def profile(self, ctx, tag):
'''Example command for use inside a discord bot cog.'''
if not self.check_valid_tag(tag):
return await ctx.send('Invalid tag!')
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TheGhouls/oct | oct/results/stats_handler.py | StatsHandler.write_remaining | def write_remaining(self):
"""Write the remaning stack content
"""
if not self.results:
return
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del self.results[:] | python | def write_remaining(self):
"""Write the remaning stack content
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TheGhouls/oct | oct/utilities/configuration.py | configure | def configure(project_path, config_file=None):
"""Get the configuration of the test and return it as a config object
:return: the configured config object
:rtype: Object
"""
if config_file is None:
config_file = os.path.join(project_path, 'config.json')
try:
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"""Get the configuration of the test and return it as a config object
:return: the configured config object
:rtype: Object
"""
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TheGhouls/oct | oct/utilities/configuration.py | get_db_uri | def get_db_uri(config, output_dir):
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:param dict config: project configuration dict
:param str output_dir: output directory for results
:return: string for db uri
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ethan92429/onshapepy | onshapepy/document.py | Document.update | def update(self):
"""All client calls to update this instance with Onshape."""
self.json = c.get_document(self.uri.did).json()
self.e_list = c.element_list(self.uri.as_dict()).json() | python | def update(self):
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ethan92429/onshapepy | onshapepy/document.py | Document.find_element | def find_element(self, name, type=ElementType.ANY):
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name: str
the name of the element.
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DsixTools/python-smeftrunner | smeftrunner/beta.py | beta_array | def beta_array(C, HIGHSCALE, *args, **kwargs):
"""Return the beta functions of all SM parameters and SMEFT Wilson
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beta_odict = beta(C, HIGHSCALE, *args, **kwargs)
return np.hstack([np.asarray(b).ravel() for b in beta_odict.values()]) | python | def beta_array(C, HIGHSCALE, *args, **kwargs):
"""Return the beta functions of all SM parameters and SMEFT Wilson
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beta_odict = beta(C, HIGHSCALE, *args, **kwargs)
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peergradeio/flask-mongo-profiler | flask_mongo_profiler/contrib/flask_admin/views/base.py | RelationalSearchMixin._search | def _search(self, query, search_term):
"""
Improved search between words.
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In this ref it's stated that there is a bug with complex Q queries preventing
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"""
Improved search between words.
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DavidDoukhan/py_sonicvisualiser | py_sonicvisualiser/SVDataset.py | SVDataset2D.set_data_from_iterable | def set_data_from_iterable(self, frames, values, labels=None):
"""
Initialize a dataset structure from iterable parameters
:param x: The temporal indices of the dataset
:param y: The values of the dataset
:type x: iterable
:type y: iterable
"""
if not isi... | python | def set_data_from_iterable(self, frames, values, labels=None):
"""
Initialize a dataset structure from iterable parameters
:param x: The temporal indices of the dataset
:param y: The values of the dataset
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DavidDoukhan/py_sonicvisualiser | py_sonicvisualiser/SVDataset.py | SVDataset2D.writexml | def writexml(self, writer, indent="", addindent="", newl=""):
"""
Write the continuous dataset using sonic visualiser xml conventions
"""
# dataset = self.data.appendChild(self.doc.createElement('dataset'))
# dataset.setAttribute('id', str(imodel))
# dataset.setAttribute... | python | def writexml(self, writer, indent="", addindent="", newl=""):
"""
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assamite/creamas | creamas/math.py | gaus_pdf | def gaus_pdf(x, mean, std):
'''Gaussian distribution's probability density function.
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:param x: point in x-axis
:type x: float or numpy.ndarray
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'''Gaussian distribution's probability density function.
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assamite/creamas | creamas/math.py | logistic | def logistic(x, x0, k, L):
'''Logistic function.
See, e.g `Wikipedia <https://en.wikipedia.org/wiki/Logistic_function>`_.
:param x: point in x-axis
:type x: float or numpy.ndarray
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'''Logistic function.
See, e.g `Wikipedia <https://en.wikipedia.org/wiki/Logistic_function>`_.
:param x: point in x-axis
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assamite/creamas | creamas/examples/grid/grid_node.py | populate_menv | def populate_menv(menv, agent_cls_name, log_folder):
'''Populate given multiprocessing grid environment with agents.
:param menv: Instance of :py:class:`GridMultiEnvironment`
:param str agent_cls_name: Name of the agent class, e.g. 'grip_mp:GridAgent'
:param str log_folder: Root logging folder for the ... | python | def populate_menv(menv, agent_cls_name, log_folder):
'''Populate given multiprocessing grid environment with agents.
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assamite/creamas | creamas/examples/grid/grid_node.py | get_slave_addrs | def get_slave_addrs(mgr_addr, N):
'''Get ports for the slave environments.
Currently the ports are not checked for availability.
'''
return [(HOST, p) for p in range(mgr_addr+1, mgr_addr+1+N)] | python | def get_slave_addrs(mgr_addr, N):
'''Get ports for the slave environments.
Currently the ports are not checked for availability.
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assamite/creamas | creamas/rules/rule.py | weighted_average | def weighted_average(rule, artifact):
"""Evaluate artifact's value to be weighted average of values returned by
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"""
e = 0
w = 0
for i in range(len(rule.R)):
r = rule.R[i](artifact)
if r is not None:
e += r * rule.W[i]
w += abs(rule.W[i])
... | python | def weighted_average(rule, artifact):
"""Evaluate artifact's value to be weighted average of values returned by
rule's subrules.
"""
e = 0
w = 0
for i in range(len(rule.R)):
r = rule.R[i](artifact)
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e += r * rule.W[i]
w += abs(rule.W[i])
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assamite/creamas | creamas/rules/rule.py | minimum | def minimum(rule, artifact):
"""Evaluate artifact's value to be minimum of values returned by rule's
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This evaluation function ignores subrule weights.
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"""Evaluate artifact's value to be minimum of values returned by rule's
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This evaluation function ignores subrule weights.
"""
m = 1.0
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assamite/creamas | creamas/rules/rule.py | Rule.add_subrule | def add_subrule(self, subrule, weight):
"""Add subrule to the rule.
:param subrule:
Subrule to add to this rule, an instance of :class:`Rule` or
:class:`RuleLeaf`.
:param float weight: Weight of the subrule
"""
if not issubclass(subrule.__class__, (Rule,... | python | def add_subrule(self, subrule, weight):
"""Add subrule to the rule.
:param subrule:
Subrule to add to this rule, an instance of :class:`Rule` or
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:param float weight: Weight of the subrule
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Kortemme-Lab/klab | klab/chainsequence.py | ChainSequences.parse_seqres | def parse_seqres(self, pdb):
"""Parse the SEQRES entries into the object"""
seqresre = re.compile("SEQRES")
seqreslines = [line for line in pdb.lines if seqresre.match(line)]
for line in seqreslines:
chain = line[11]
resnames = line[19:70].strip()
self.setdefault(chain, ... | python | def parse_seqres(self, pdb):
"""Parse the SEQRES entries into the object"""
seqresre = re.compile("SEQRES")
seqreslines = [line for line in pdb.lines if seqresre.match(line)]
for line in seqreslines:
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Kortemme-Lab/klab | klab/chainsequence.py | ChainSequences.parse_atoms | def parse_atoms(self, pdb):
"""Parse the ATOM entries into the object"""
atomre = re.compile("ATOM")
atomlines = [line for line in pdb.lines if atomre.match(line)]
chainresnums = {}
for line in atomlines:
chain = line[21]
resname = line[17:20]
resnum = line[22:2... | python | def parse_atoms(self, pdb):
"""Parse the ATOM entries into the object"""
atomre = re.compile("ATOM")
atomlines = [line for line in pdb.lines if atomre.match(line)]
chainresnums = {}
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Kortemme-Lab/klab | klab/chainsequence.py | ChainSequences.seqres_lines | def seqres_lines(self):
"""Generate SEQRES lines representing the contents"""
lines = []
for chain in self.keys():
seq = self[chain]
serNum = 1
startidx = 0
while startidx < len(seq):
endidx = min(startidx+13, len(seq))
lines += ["SEQRES %2i %s %4i %s\n" % (se... | python | def seqres_lines(self):
"""Generate SEQRES lines representing the contents"""
lines = []
for chain in self.keys():
seq = self[chain]
serNum = 1
startidx = 0
while startidx < len(seq):
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Kortemme-Lab/klab | klab/chainsequence.py | ChainSequences.replace_seqres | def replace_seqres(self, pdb, update_atoms = True):
"""Replace SEQRES lines with a new sequence, optionally removing
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newpdb = PDB()
inserted_seqres = False
entries_before_seqres = set(["HEADER", "OBSLTE", "TITLE", "CAVEAT", "COMPND", "SOURCE",
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"""Replace SEQRES lines with a new sequence, optionally removing
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newpdb = PDB()
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entries_before_seqres = set(["HEADER", "OBSLTE", "TITLE", "CAVEAT", "COMPND", "SOURCE",
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brunato/lograptor | lograptor/matcher.py | has_host_match | def has_host_match(log_data, hosts):
"""
Match the data with a list of hostname patterns. If the log line data
doesn't include host information considers the line as matched.
"""
hostname = getattr(log_data, 'host', None)
if hostname and hostname not in host_cache:
for host_pattern in ho... | python | def has_host_match(log_data, hosts):
"""
Match the data with a list of hostname patterns. If the log line data
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"""
hostname = getattr(log_data, 'host', None)
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aacanakin/glim | glim/commands.py | StartCommand.run | def run(self, app):
"""Function starts the web server given configuration."""
GlimLog.info('Glim server started on %s environment' % self.args.env)
try:
kwargs = Config.get('app.server.options')
run(app.wsgi,
host=Config.get('app.server.host'),
... | python | def run(self, app):
"""Function starts the web server given configuration."""
GlimLog.info('Glim server started on %s environment' % self.args.env)
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Kortemme-Lab/klab | klab/benchmarking/analysis/ssm.py | get_symmetrical_std_devs | def get_symmetrical_std_devs(values, ignore_zeros = True):
"""Takes a list of values and splits it into positive and negative values. For both of these subsets, a symmetrical
distribution is created by mirroring each value along the origin and the standard deviation for both subsets is returned.
:param ... | python | def get_symmetrical_std_devs(values, ignore_zeros = True):
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Kortemme-Lab/klab | klab/benchmarking/analysis/ssm.py | get_std_xy_dataset_statistics | def get_std_xy_dataset_statistics(x_values, y_values, expect_negative_correlation = False, STDev_cutoff = 1.0):
'''Calls parse_csv and returns the analysis in a format similar to get_xy_dataset_statistics in klab.stats.misc.'''
assert(len(x_values) == len(y_values))
csv_lines = ['ID,X,Y'] + [','.join(map(st... | python | def get_std_xy_dataset_statistics(x_values, y_values, expect_negative_correlation = False, STDev_cutoff = 1.0):
'''Calls parse_csv and returns the analysis in a format similar to get_xy_dataset_statistics in klab.stats.misc.'''
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clement-alexandre/TotemBionet | totembionet/src/discrete_model/gene.py | Gene.active_multiplex | def active_multiplex(self, state: 'State') -> Tuple['Multiplex']:
"""
Return a tuple of all the active multiplex in the given state.
"""
return tuple(multiplex for multiplex in self.multiplexes if multiplex.is_active(state)) | python | def active_multiplex(self, state: 'State') -> Tuple['Multiplex']:
"""
Return a tuple of all the active multiplex in the given state.
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assamite/creamas | creamas/core/agent.py | CreativeAgent.sanitized_name | def sanitized_name(self):
"""Sanitized name of the agent, used for file and directory creation.
"""
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return "_".join([i for i in a if len(i) > 0]) | python | def sanitized_name(self):
"""Sanitized name of the agent, used for file and directory creation.
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assamite/creamas | creamas/core/agent.py | CreativeAgent.get_connections | def get_connections(self, data=False):
"""Get agent's current connections.
:param bool data:
Also return the data dictionary for each connection.
:returns: A list of agent addresses or a dictionary
"""
if data:
return self._connections
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"""Get agent's current connections.
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"""
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assamite/creamas | creamas/core/agent.py | CreativeAgent.publish | def publish(self, artifact):
"""Publish artifact to agent's environment.
:param artifact: artifact to be published
:type artifact: :py:class:`~creamas.core.artifact.Artifact`
"""
self.env.add_artifact(artifact)
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"""Publish artifact to agent's environment.
:param artifact: artifact to be published
:type artifact: :py:class:`~creamas.core.artifact.Artifact`
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assamite/creamas | creamas/core/agent.py | CreativeAgent.ask_opinion | async def ask_opinion(self, addr, artifact):
"""Ask an agent's opinion about an artifact.
:param str addr: Address of the agent which opinion is asked
:type addr: :py:class:`~creamas.core.agent.CreativeAgent`
:param object artifact: artifact to be evaluated
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"""Ask an agent's opinion about an artifact.
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projectshift/shift-boiler | boiler/feature/localization.py | localization_feature | def localization_feature(app):
"""
Localization feature
This will initialize support for translations and localization of values
such as numbers, money, dates and formatting timezones.
"""
# apply app default to babel
app.config['BABEL_DEFAULT_LOCALE'] = app.config['DEFAULT_LOCALE']
app... | python | def localization_feature(app):
"""
Localization feature
This will initialize support for translations and localization of values
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"""
# apply app default to babel
app.config['BABEL_DEFAULT_LOCALE'] = app.config['DEFAULT_LOCALE']
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adaptive-learning/proso-apps | proso/django/enrichment.py | enrich_json_objects_by_object_type | def enrich_json_objects_by_object_type(request, value):
"""
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"""
Take the given value and start enrichment by object_type. The va
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adaptive-learning/proso-apps | proso/django/enrichment.py | enrich_by_predicate | def enrich_by_predicate(request, json, fun, predicate, skip_nested=False, **kwargs):
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from pprint import pprint
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adaptive-learning/proso-apps | proso/django/enrichment.py | enrich_by_object_type | def enrich_by_object_type(request, json, fun, object_type, skip_nested=False, **kwargs):
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adaptive-learning/proso-apps | proso_flashcards/models.py | change_parent | def change_parent(sender, instance, **kwargs):
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When the given flashcard has changed. Look at term and context and change
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"""
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return
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... | python | def change_parent(sender, instance, **kwargs):
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Kortemme-Lab/klab | klab/bio/bonsai.py | example | def example():
'''This section gives examples of how to use the module.'''
# 1a8d is an example from the loops benchmark
# 1lfa contains hydrogens
b = Bonsai.retrieve('1lfa', cache_dir='/tmp')
search_radius = 10.0
atom_of_interest = b.get_atom(1095)
nearby_atoms = b.find_atoms_near_atom(at... | python | def example():
'''This section gives examples of how to use the module.'''
# 1a8d is an example from the loops benchmark
# 1lfa contains hydrogens
b = Bonsai.retrieve('1lfa', cache_dir='/tmp')
search_radius = 10.0
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Kortemme-Lab/klab | klab/bio/bonsai.py | PDBSection.from_non_aligned_residue_IDs | def from_non_aligned_residue_IDs(Chain, StartResidueID, EndResidueID, Sequence = None):
'''A more forgiving method that does not care about the padding of the residue IDs.'''
return PDBSection(Chain, PDB.ResidueID2String(StartResidueID), PDB.ResidueID2String(EndResidueID), Sequence = Sequence) | python | def from_non_aligned_residue_IDs(Chain, StartResidueID, EndResidueID, Sequence = None):
'''A more forgiving method that does not care about the padding of the residue IDs.'''
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Kortemme-Lab/klab | klab/bio/bonsai.py | ResidueIndexedPDBFile.bin_atoms | def bin_atoms(self):
'''This function bins the Atoms into fixed-size sections of the protein space in 3D.'''
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low_point = numpy.array([self.min_x, self.min_y, self.min_z])
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'''This function bins the Atoms into fixed-size sections of the protein space in 3D.'''
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low_point = numpy.array([self.min_x, self.min_y, self.min_z])
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Kortemme-Lab/klab | klab/bio/bonsai.py | Bonsai.find_heavy_atoms_near_atom | def find_heavy_atoms_near_atom(self, source_atom, search_radius, atom_hit_cache = set(), restrict_to_CA = False):
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TUNE-Archive/freight_forwarder | freight_forwarder/config.py | Config.get | def get(self, attr_name, *args):
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TUNE-Archive/freight_forwarder | freight_forwarder/config.py | Config.service_references | def service_references(self):
""" returns a list of service names
"""
services_blue_print = self._scheme_references.get('services')
if services_blue_print is None:
raise LookupError('unable to find any services in the config.')
# TODO: this needs to be cleaned up and... | python | def service_references(self):
""" returns a list of service names
"""
services_blue_print = self._scheme_references.get('services')
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TUNE-Archive/freight_forwarder | freight_forwarder/config.py | Config.validate | def validate(self):
""" Validate the contents of the configuration file. Will return None if validation is successful or
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"""
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raise TypeError('freight forwarder configuration file must be a dict.')
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""" Validate the contents of the configuration file. Will return None if validation is successful or
raise an error if not.
"""
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TUNE-Archive/freight_forwarder | freight_forwarder/config.py | Config._load | def _load(self):
""" Load a configuration file. This method will be called when the Config class is instantiated. The
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"""
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TUNE-Archive/freight_forwarder | freight_forwarder/config.py | Config._load_yml_config | def _load_yml_config(self, config_file):
""" loads a yaml str, creates a few constructs for pyaml, serializes and normalized the config data. Then
assigns the config data to self._data.
:param config_file: A :string: loaded from a yaml file.
"""
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TUNE-Archive/freight_forwarder | freight_forwarder/config.py | Config._create_attr | def _create_attr(self, property_key, data, ancestors):
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:param property_key: A :string: configuration property name.
:param data: The adds the user supplied for this specific property.
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TUNE-Archive/freight_forwarder | freight_forwarder/config.py | Config._collect_unrecognized_values | def _collect_unrecognized_values(self, scheme, data, ancestors):
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TUNE-Archive/freight_forwarder | freight_forwarder/config.py | Config._update_scheme | def _update_scheme(self, scheme, ancestors):
""" Updates the current scheme based off special pre-defined keys and retruns a new updated scheme.
:param scheme: A :dict:, The scheme defining the validations.
:param ancestors: A :OrderedDict: that provides a history of its ancestors.
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""" Updates the current scheme based off special pre-defined keys and retruns a new updated scheme.
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TUNE-Archive/freight_forwarder | freight_forwarder/config.py | Config._walk_tree | def _walk_tree(self, data, scheme, ancestors=None, property_name=None, prefix=None):
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TUNE-Archive/freight_forwarder | freight_forwarder/config.py | Config._update_ancestors | def _update_ancestors(self, config_data, property_name, ancestors=None):
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:param ancestors: A :OrderedDict:, representing the ancestors of a property.
:param config_data: The data that needs to be validated agents the scheme.
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TUNE-Archive/freight_forwarder | freight_forwarder/config.py | Config._reference_keys | def _reference_keys(self, reference):
""" Returns a list of all of keys for a given reference.
:param reference: a :string:
:rtype: A :list: of reference keys.
"""
if not isinstance(reference, six.string_types):
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""" Returns a list of all of keys for a given reference.
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"""
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TUNE-Archive/freight_forwarder | freight_forwarder/config.py | Config.__execute_validations | def __execute_validations(self, validations, data, property_name, ancestors, negation=False, prefix=None):
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ZEDGR/pychal | challonge/tournaments.py | create | def create(name, url, tournament_type="single elimination", **params):
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params.update({
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"url": url,
"tournament_type": tournament_type,
})
return api.fetch_and_parse("POST", "tournaments", "tournament", **params) | python | def create(name, url, tournament_type="single elimination", **params):
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params.update({
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# check we have jwt secret configures
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ethan92429/onshapepy | onshapepy/core/client.py | Client.rename_document | def rename_document(self, did, name):
'''
Renames the specified document.
Args:
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- name (str): New document name
Returns:
- requests.Response: Onshape response data
'''
payload = {
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'''
Renames the specified document.
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ethan92429/onshapepy | onshapepy/core/client.py | Client.copy_workspace | def copy_workspace(self, uri, new_name):
'''
Copy the current workspace.
Args:
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- new_name (str): the new name of the copied workspace.
Returns:
- requests.Response:... | python | def copy_workspace(self, uri, new_name):
'''
Copy the current workspace.
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ethan92429/onshapepy | onshapepy/core/client.py | Client.create_workspace | def create_workspace(self, did, name, version_id=None):
'''
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ethan92429/onshapepy | onshapepy/core/client.py | Client.get_partstudio_tessellatededges | def get_partstudio_tessellatededges(self, did, wid, eid):
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- eid (str): Element ID
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'''
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ethan92429/onshapepy | onshapepy/core/client.py | Client.upload_blob | def upload_blob(self, did, wid, filepath='./blob.json'):
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Args:
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'''
Uploads a file to a new blob element in the specified doc.
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ethan92429/onshapepy | onshapepy/core/client.py | Client.part_studio_stl | def part_studio_stl(self, did, wid, eid):
'''
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Args:
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- eid (str): Element ID
Returns:
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'''
... | python | def part_studio_stl(self, did, wid, eid):
'''
Exports STL export from a part studio
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- eid (str): Element ID
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ethan92429/onshapepy | onshapepy/core/client.py | Client.create_assembly_instance | def create_assembly_instance(self, assembly_uri, part_uri, configuration):
'''
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Args:
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'''
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- part (dict): eid and did of the configurable part
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ethan92429/onshapepy | onshapepy/core/client.py | Client.encode_configuration | def encode_configuration(self, did, eid, parameters):
'''
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Returns:
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ethan92429/onshapepy | onshapepy/core/client.py | Client.get_configuration | def get_configuration(self, uri):
'''
get the configuration of a PartStudio
Args:
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Returns:
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'''
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'''
get the configuration of a PartStudio
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ethan92429/onshapepy | onshapepy/core/client.py | Client.update_configuration | def update_configuration(self, did, wid, eid, payload):
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aacanakin/glim | glim/command.py | CommandAdapter.retrieve_commands | def retrieve_commands(self, module):
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Kortemme-Lab/klab | klab/bio/fasta.py | FASTA.replace_sequence | def replace_sequence(self, pdb_ID, chain_id, replacement_sequence):
'''Replaces a sequence with another. Typically not useful but I use it in the ResidueRelatrix to make sure that the FASTA and SEQRES sequences match.'''
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Kortemme-Lab/klab | klab/bio/fasta.py | FASTA.retrieve | def retrieve(pdb_id, cache_dir = None, bio_cache = None):
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# Check ... | python | def retrieve(pdb_id, cache_dir = None, bio_cache = None):
'''Creates a FASTA object by using a cached copy of the file if it exists or by retrieving the file from the RCSB.'''
pdb_id = pdb_id.upper()
if bio_cache:
return FASTA(bio_cache.get_fasta_contents(pdb_id))
# Check ... | [
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] | 6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b | https://github.com/Kortemme-Lab/klab/blob/6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b/klab/bio/fasta.py#L91-L117 | train |
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