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lsst-sqre/documenteer | documenteer/sphinxext/utils.py | make_python_xref_nodes | def make_python_xref_nodes(py_typestr, state, hide_namespace=False):
"""Make docutils nodes containing a cross-reference to a Python object.
Parameters
----------
py_typestr : `str`
Name of the Python object. For example
``'mypackage.mymodule.MyClass'``. If you have the object itself, o... | python | def make_python_xref_nodes(py_typestr, state, hide_namespace=False):
"""Make docutils nodes containing a cross-reference to a Python object.
Parameters
----------
py_typestr : `str`
Name of the Python object. For example
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lsst-sqre/documenteer | documenteer/sphinxext/utils.py | make_python_xref_nodes_for_type | def make_python_xref_nodes_for_type(py_type, state, hide_namespace=False):
"""Make docutils nodes containing a cross-reference to a Python object,
given the object's type.
Parameters
----------
py_type : `obj`
Type of an object. For example ``mypackage.mymodule.MyClass``. If you
hav... | python | def make_python_xref_nodes_for_type(py_type, state, hide_namespace=False):
"""Make docutils nodes containing a cross-reference to a Python object,
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Parameters
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py_type : `obj`
Type of an object. For example ``mypackage.mymodule.MyClass``. If you
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lsst-sqre/documenteer | documenteer/sphinxext/utils.py | make_section | def make_section(section_id=None, contents=None):
"""Make a docutils section node.
Parameters
----------
section_id : `str`
Section identifier, which is appended to both the ``ids`` and ``names``
attributes.
contents : `list` of ``docutils.nodes``
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"""Make a docutils section node.
Parameters
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section_id : `str`
Section identifier, which is appended to both the ``ids`` and ``names``
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lsst-sqre/documenteer | documenteer/sphinxext/utils.py | split_role_content | def split_role_content(role_rawsource):
"""Split the ``rawsource`` of a role into standard components.
Parameters
----------
role_rawsource : `str`
The content of the role: its ``rawsource`` attribute.
Returns
-------
parts : `dict`
Dictionary with keys:
``last_com... | python | def split_role_content(role_rawsource):
"""Split the ``rawsource`` of a role into standard components.
Parameters
----------
role_rawsource : `str`
The content of the role: its ``rawsource`` attribute.
Returns
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parts : `dict`
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mojaie/chorus | chorus/molutil.py | largest_graph | def largest_graph(mol):
"""Return a molecule which has largest graph in the compound
Passing single molecule object will results as same as molutil.clone
"""
mol.require("Valence")
mol.require("Topology")
m = clone(mol) # Avoid modification of original object
if m.isolated:
for k in... | python | def largest_graph(mol):
"""Return a molecule which has largest graph in the compound
Passing single molecule object will results as same as molutil.clone
"""
mol.require("Valence")
mol.require("Topology")
m = clone(mol) # Avoid modification of original object
if m.isolated:
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mojaie/chorus | chorus/molutil.py | H_donor_count | def H_donor_count(mol):
"""Hydrogen bond donor count """
mol.require("Valence")
return sum(1 for _, a in mol.atoms_iter() if a.H_donor) | python | def H_donor_count(mol):
"""Hydrogen bond donor count """
mol.require("Valence")
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mojaie/chorus | chorus/molutil.py | H_acceptor_count | def H_acceptor_count(mol):
"""Hydrogen bond acceptor count """
mol.require("Valence")
return sum(1 for _, a in mol.atoms_iter() if a.H_acceptor) | python | def H_acceptor_count(mol):
"""Hydrogen bond acceptor count """
mol.require("Valence")
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mojaie/chorus | chorus/molutil.py | rotatable_count | def rotatable_count(mol):
"""Rotatable bond count """
mol.require("Rotatable")
return sum(1 for _, _, b in mol.bonds_iter() if b.rotatable) | python | def rotatable_count(mol):
"""Rotatable bond count """
mol.require("Rotatable")
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mojaie/chorus | chorus/molutil.py | rule_of_five_violation | def rule_of_five_violation(mol):
"""Lipinski's rule of five violation count """
v = 0
if mw(mol) > 500:
v += 1
if H_donor_count(mol) > 5:
v += 1
if H_acceptor_count(mol) > 10:
v += 1
try:
if wclogp.wclogp(mol) > 5:
v += 1
except TypeError: # N/A
... | python | def rule_of_five_violation(mol):
"""Lipinski's rule of five violation count """
v = 0
if mw(mol) > 500:
v += 1
if H_donor_count(mol) > 5:
v += 1
if H_acceptor_count(mol) > 10:
v += 1
try:
if wclogp.wclogp(mol) > 5:
v += 1
except TypeError: # N/A
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mojaie/chorus | chorus/molutil.py | formula | def formula(mol):
"""Chemical formula.
Atoms should be arranged in order of C, H and other atoms.
Molecules should be arranged in order of length of formula text.
"""
mol.require("Valence")
mol.require("Topology")
total_cntr = Counter()
for m in sorted(mols_iter(mol), key=len, reverse=Tr... | python | def formula(mol):
"""Chemical formula.
Atoms should be arranged in order of C, H and other atoms.
Molecules should be arranged in order of length of formula text.
"""
mol.require("Valence")
mol.require("Topology")
total_cntr = Counter()
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zsimic/runez | src/runez/click.py | debug | def debug(*args, **attrs):
"""Show debugging information."""
attrs.setdefault("is_flag", True)
attrs.setdefault("default", None)
return option(debug, *args, **attrs) | python | def debug(*args, **attrs):
"""Show debugging information."""
attrs.setdefault("is_flag", True)
attrs.setdefault("default", None)
return option(debug, *args, **attrs) | [
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zsimic/runez | src/runez/click.py | dryrun | def dryrun(*args, **attrs):
"""Perform a dryrun."""
attrs.setdefault("is_flag", True)
attrs.setdefault("default", None)
return option(dryrun, *args, **attrs) | python | def dryrun(*args, **attrs):
"""Perform a dryrun."""
attrs.setdefault("is_flag", True)
attrs.setdefault("default", None)
return option(dryrun, *args, **attrs) | [
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zsimic/runez | src/runez/click.py | log | def log(*args, **attrs):
"""Override log file location."""
attrs.setdefault("metavar", "PATH")
attrs.setdefault("show_default", False)
return option(log, *args, **attrs) | python | def log(*args, **attrs):
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zsimic/runez | src/runez/click.py | version | def version(*args, **attrs):
"""Show the version and exit."""
if hasattr(sys, "_getframe"):
package = attrs.pop("package", sys._getframe(1).f_globals.get("__package__"))
if package:
attrs.setdefault("version", get_version(package))
return click.version_option(*args, **attrs) | python | def version(*args, **attrs):
"""Show the version and exit."""
if hasattr(sys, "_getframe"):
package = attrs.pop("package", sys._getframe(1).f_globals.get("__package__"))
if package:
attrs.setdefault("version", get_version(package))
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mojaie/chorus | chorus/rdkit.py | to_rdmol | def to_rdmol(mol):
"""Convert molecule to RDMol"""
rwmol = Chem.RWMol(Chem.MolFromSmiles(''))
key_to_idx = {}
bond_type = {1: Chem.BondType.SINGLE,
2: Chem.BondType.DOUBLE,
3: Chem.BondType.TRIPLE}
conf = Chem.Conformer(rwmol.GetNumAtoms())
for k, a in mol.atoms... | python | def to_rdmol(mol):
"""Convert molecule to RDMol"""
rwmol = Chem.RWMol(Chem.MolFromSmiles(''))
key_to_idx = {}
bond_type = {1: Chem.BondType.SINGLE,
2: Chem.BondType.DOUBLE,
3: Chem.BondType.TRIPLE}
conf = Chem.Conformer(rwmol.GetNumAtoms())
for k, a in mol.atoms... | [
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mojaie/chorus | chorus/rdkit.py | morgan_sim | def morgan_sim(mol1, mol2, radius=2, digit=3):
"""Calculate morgan fingerprint similarity by using RDKit
radius=2 roughly equivalent to ECFP4
"""
rdmol1 = to_rdmol(mol1)
rdmol2 = to_rdmol(mol2)
fp1 = AllChem.GetMorganFingerprint(rdmol1, radius)
fp2 = AllChem.GetMorganFingerprint(rdmol2, radi... | python | def morgan_sim(mol1, mol2, radius=2, digit=3):
"""Calculate morgan fingerprint similarity by using RDKit
radius=2 roughly equivalent to ECFP4
"""
rdmol1 = to_rdmol(mol1)
rdmol2 = to_rdmol(mol2)
fp1 = AllChem.GetMorganFingerprint(rdmol1, radius)
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maljovec/topopy | topopy/MergeTree.py | MergeTree.build_for_contour_tree | def build_for_contour_tree(self, contour_tree, negate=False):
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tree_type = "Join"
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zsimic/runez | src/runez/context.py | verify_abort | def verify_abort(func, *args, **kwargs):
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zsimic/runez | src/runez/context.py | CapturedStream.pop | def pop(self, strip=False):
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self.clear()
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r = r.strip()
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mojaie/chorus | chorus/draw/svg.py | SVG.contents | def contents(self):
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c.append(' font-weight="{}"'.format(self.font_weight))
c.append(' font-family="{}"'.format(self.font_family))
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"""Get svg string
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# remove #svg from dataframe
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Returns the standard logger
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lsst-sqre/documenteer | documenteer/sphinxext/packagetoctree.py | _build_toctree_node | def _build_toctree_node(parent=None, entries=None, includefiles=None,
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lsst-sqre/documenteer | documenteer/sphinxext/packagetoctree.py | ModuleTocTree._parse_skip_option | def _parse_skip_option(self):
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mastro35/flows | flows/FlowsManager.py | FlowsManager._set_command_line_arguments | def _set_command_line_arguments(self, args):
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Start all the processes
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Global.LOGGER.info("starting the flow manager")
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Start all the processes
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Global.LOGGER.info("starting the flow manager")
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Stop all the processes
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mastro35/flows | flows/FlowsManager.py | FlowsManager._start_actions | def _start_actions(self):
"""
Start all the actions for the recipes
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Global.LOGGER.info("starting actions")
for recipe in Global.CONFIG_MANAGER.recipes:
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list(map(lambda section: self._start_action_for_section(
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"""
Start all the actions for the recipes
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Global.LOGGER.info("starting actions")
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mastro35/flows | flows/FlowsManager.py | FlowsManager._start_action_for_section | def _start_action_for_section(self, section):
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mastro35/flows | flows/FlowsManager.py | FlowsManager._stop_actions | def _stop_actions(self):
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Stop all the actions
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mastro35/flows | flows/FlowsManager.py | FlowsManager._deliver_message | def _deliver_message(self, msg):
"""
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Deliver the message to the subscripted actions
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mastro35/flows | flows/FlowsManager.py | FlowsManager._fetch_messages | def _fetch_messages(self):
"""
Get an input message from the socket
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try:
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"""
Get an input message from the socket
"""
try:
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mastro35/flows | flows/FlowsManager.py | FlowsManager.message_fetcher_coroutine | async def message_fetcher_coroutine(self, loop):
"""
Register callback for message fetcher coroutines
"""
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"""
Register callback for message fetcher coroutines
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mastro35/flows | flows/FlowsManager.py | FlowsManager._adapt_sleep_interval | def _adapt_sleep_interval(self, sent, received, queue, now):
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"""
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mastro35/flows | flows/FlowsManager.py | FlowsManager._parse_input_parameters | def _parse_input_parameters(self):
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Set the configuration for the Logger
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mesbahamin/chronophore | scripts/chronophore_migrate.py | migrate_050_to_051 | def migrate_050_to_051(session):
"""Set time_out field of all flagged
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ehansis/ozelot | ozelot/etl/tasks.py | get_task_param_string | def get_task_param_string(task):
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str: task parameter string
"""
# get dict str -> str from luigi
param_dict = task.to_str_params()
# sort keys, serialize
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str: task parameter string
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task (derived from luigi.Task): Task to check completion for; check everything 'downstream'
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ehansis/ozelot | ozelot/etl/tasks.py | TaskBase.build | def build(cls, local_scheduler=True, **task_params):
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Args:
local_scheduler (bool): use a local scheduler (True, default) or a remote scheduler
task_params: parameters to pass to task for instantiation
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"""Instantiate the task and build it with luigi
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ehansis/ozelot | ozelot/etl/tasks.py | ORMObjectCreatorMixin.clear | def clear(
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"""Delete all objects created by this task.
Iterate over `self.object_classes` and delete all objects of the listed classes.
"""
# mark this task as incomplete
self.mark_incomplete()
# delete objects
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ehansis/ozelot | ozelot/etl/tasks.py | ORMWrapperTask.complete | def complete(self):
"""Task is complete if completion marker is set and all requirements are complete
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is_complete = super(ORMWrapperTask, self).complete()
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is_complete &= req.complete()
return is_complete | python | def complete(self):
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maljovec/topopy | topopy/MorseSmaleComplex.py | MorseSmaleComplex.save | def save(self, filename=None):
""" Saves a constructed Morse-Smale Complex in json file
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if filename is None:
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maljovec/topopy | topopy/MorseSmaleComplex.py | MorseSmaleComplex.get_label | def get_label(self, indices=None):
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maljovec/topopy | topopy/MorseSmaleComplex.py | MorseSmaleComplex.get_sample_size | def get_sample_size(self, key=None):
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yymao/generic-catalog-reader | GCR/utils.py | dict_to_numpy_array | def dict_to_numpy_array(d):
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redhat-cip/python-dciclient | dciclient/v1/api/jobs_events.py | iter | def iter(context, sequence, limit=10):
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DheerendraRathor/django-auth-ldap-ng | django_auth_ldap/config.py | _LDAPConfig.get_ldap | def get_ldap(cls, global_options=None):
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DheerendraRathor/django-auth-ldap-ng | django_auth_ldap/config.py | LDAPSearch._begin | def _begin(self, connection, filterargs=(), escape=True):
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DheerendraRathor/django-auth-ldap-ng | django_auth_ldap/config.py | LDAPSearch._results | def _results(self, connection, msgid):
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DheerendraRathor/django-auth-ldap-ng | django_auth_ldap/config.py | LDAPSearch._escape_filterargs | def _escape_filterargs(self, filterargs):
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Escapes values in filterargs.
filterargs is a value suitable for Django's string formatting operator
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"""
Escapes values in filterargs.
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DheerendraRathor/django-auth-ldap-ng | django_auth_ldap/config.py | LDAPSearch._process_results | def _process_results(self, results):
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Returns a sanitized copy of raw LDAP results. This scrubs out
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"""
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"""
Returns a sanitized copy of raw LDAP results. This scrubs out
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ehansis/ozelot | ozelot/client.py | Client.get_connection_string | def get_connection_string(params, hide_password=True):
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params (dict): database configuration, as defined in :mod:`ozelot.config`
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"""Get a database connection string
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params (dict): database configuration, as defined in :mod:`ozelot.config`
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geminipy/geminipy | geminipy/__init__.py | Geminipy.pubticker | def pubticker(self, symbol='btcusd'):
"""Send a request for latest ticker info, return the response."""
url = self.base_url + '/v1/pubticker/' + symbol
return requests.get(url) | python | def pubticker(self, symbol='btcusd'):
"""Send a request for latest ticker info, return the response."""
url = self.base_url + '/v1/pubticker/' + symbol
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geminipy/geminipy | geminipy/__init__.py | Geminipy.book | def book(self, symbol='btcusd', limit_bids=0, limit_asks=0):
"""
Send a request to get the public order book, return the response.
Arguments:
symbol -- currency symbol (default 'btcusd')
limit_bids -- limit the number of bids returned (default 0)
limit_asks -- limit the ... | python | def book(self, symbol='btcusd', limit_bids=0, limit_asks=0):
"""
Send a request to get the public order book, return the response.
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symbol -- currency symbol (default 'btcusd')
limit_bids -- limit the number of bids returned (default 0)
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geminipy/geminipy | geminipy/__init__.py | Geminipy.trades | def trades(self, symbol='btcusd', since=0, limit_trades=50,
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"""
Send a request to get all public trades, return the response.
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symbol -- currency symbol (default 'btcusd')
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include_breaks=0):
"""
Send a request to get all public trades, return the response.
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geminipy/geminipy | geminipy/__init__.py | Geminipy.auction | def auction(self, symbol='btcusd'):
"""Send a request for latest auction info, return the response."""
url = self.base_url + '/v1/auction/' + symbol
return requests.get(url) | python | def auction(self, symbol='btcusd'):
"""Send a request for latest auction info, return the response."""
url = self.base_url + '/v1/auction/' + symbol
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geminipy/geminipy | geminipy/__init__.py | Geminipy.auction_history | def auction_history(self, symbol='btcusd', since=0,
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"""
Send a request for auction history info, return the response.
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symbol -- currency symbol (default 'btcusd')
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geminipy/geminipy | geminipy/__init__.py | Geminipy.new_order | def new_order(self, amount, price, side, client_order_id=None,
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"""
Send a request to place an order, return the response.
Arguments:
amount -- quoted decimal amount of BTC to purchase
price -- quoted decima... | python | def new_order(self, amount, price, side, client_order_id=None,
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geminipy/geminipy | geminipy/__init__.py | Geminipy.cancel_order | def cancel_order(self, order_id):
"""
Send a request to cancel an order, return the response.
Arguments:
order_id - the order id to cancel
"""
request = '/v1/order/cancel'
url = self.base_url + request
params = {
'request': request,
... | python | def cancel_order(self, order_id):
"""
Send a request to cancel an order, return the response.
Arguments:
order_id - the order id to cancel
"""
request = '/v1/order/cancel'
url = self.base_url + request
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geminipy/geminipy | geminipy/__init__.py | Geminipy.past_trades | def past_trades(self, symbol='btcusd', limit_trades=50, timestamp=0):
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geminipy/geminipy | geminipy/__init__.py | Geminipy.tradevolume | def tradevolume(self):
"""Send a request to get your trade volume, return the response."""
request = '/v1/tradevolume'
url = self.base_url + request
params = {
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'nonce': self.get_nonce()
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return requests.post(url, headers=self.... | python | def tradevolume(self):
"""Send a request to get your trade volume, return the response."""
request = '/v1/tradevolume'
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geminipy/geminipy | geminipy/__init__.py | Geminipy.newAddress | def newAddress(self, currency='btc', label=''):
"""
Send a request for a new cryptocurrency deposit address
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currency -- a Gemini supported cryptocurrency (btc, eth)
label -- optional label for the deposit address
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currency -- a Gemini supported cryptocurrency (btc, eth)
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geminipy/geminipy | geminipy/__init__.py | Geminipy.prepare | def prepare(self, params):
"""
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Arguments:
params -- a dictionary of parameters
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params -- a dictionary of parameters
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kataev/flake8-rst | flake8_rst/sourceblock.py | SourceBlock.merge | def merge(cls, source_blocks):
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ehansis/ozelot | examples/superheroes/superheroes/analysis.py | character_summary_table | def character_summary_table():
"""Export a table listing all characters and their data
Output is a CSV file and an Excel file, saved as 'characters.csv/.xlsx' in the output directory.
"""
# a database client/session to run queries in
cl = client.get_client()
session = cl.create_session()
#... | python | def character_summary_table():
"""Export a table listing all characters and their data
Output is a CSV file and an Excel file, saved as 'characters.csv/.xlsx' in the output directory.
"""
# a database client/session to run queries in
cl = client.get_client()
session = cl.create_session()
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Returns:
str: figure as SVG string
"""
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fig.savefig(buf, format='svg')
buf.seek(0)
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Returns:
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ehansis/ozelot | examples/superheroes/superheroes/analysis.py | movie_network | def movie_network():
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Output is an html page, rendered to 'movie_network.html' in the output directory.
"""
# page template
template = jenv.get_template("movie_network.html")
# container for template context
context = dict()
# ... | python | def movie_network():
"""Generate interactive network graph of movie appearances
Output is an html page, rendered to 'movie_network.html' in the output directory.
"""
# page template
template = jenv.get_template("movie_network.html")
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Helper function for splitting 2D data into x and y component to make
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y = _x[:, 1]
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Some heuristics to figure out whether this is called at a stage where the Python interpreter is shutting down.
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Replacement for sys.excepthook.
:param etype: exception type
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"""
Replacement for sys.excepthook.
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Prints the traceback of all threads.
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Prints the traceback of all threads.
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albertz/py_better_exchook | better_exchook.py | _main | def _main():
"""
Some demo.
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"""
Some demo.
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thorgate/django-esteid | esteid/signature.py | verify_mid_signature | def verify_mid_signature(certificate_data, sp_challenge, response_challenge, signature):
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:param sp_challenge: binary challenge sent via 'SPChallenge' field
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Used to dispatch events.
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Used to dispatch events.
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potash/drain | drain/step.py | _simplify_arguments | def _simplify_arguments(arguments):
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potash/drain | drain/aggregate.py | ColumnFunction.apply_and_name | def apply_and_name(self, aggregator):
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aggregator (Aggregator)
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pd.DataFrame: The dataframe has columns with names self.names
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... | python | def apply_and_name(self, aggregator):
"""Fetches the row-aggregated input columns for this ColumnFunction.
Args:
aggregator (Aggregator)
Returns:
pd.DataFrame: The dataframe has columns with names self.names
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potash/drain | drain/aggregate.py | Aggregator.aggregate | def aggregate(self, index):
"""Performs a groupby of the unique Columns by index, as constructed from self.df.
Args:
index (str, or pd.Index): Index or column name of self.df.
Returns:
pd.DataFrame: A dataframe, aggregated by index, that contains the result
... | python | def aggregate(self, index):
"""Performs a groupby of the unique Columns by index, as constructed from self.df.
Args:
index (str, or pd.Index): Index or column name of self.df.
Returns:
pd.DataFrame: A dataframe, aggregated by index, that contains the result
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potash/drain | drain/aggregate.py | Fraction._apply | def _apply(self, aggregator):
"""Returns a dataframe with the requested ColumnReductions.
"""
reduced_dfs = []
if self.include_fraction:
n_df = self.numerator.apply_and_name(aggregator)
d_df = self.denominator.apply_and_name(aggregator)
reduced_dfs.ex... | python | def _apply(self, aggregator):
"""Returns a dataframe with the requested ColumnReductions.
"""
reduced_dfs = []
if self.include_fraction:
n_df = self.numerator.apply_and_name(aggregator)
d_df = self.denominator.apply_and_name(aggregator)
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fkarb/xltable | xltable/table.py | Table.clone | def clone(self, **kwargs):
"""Create a clone of the Table, optionally with some properties changed"""
init_kwargs = {
"name": self.__name,
"dataframe": self.__df,
"include_columns": self.__include_columns,
"include_index": self.__include_index,
... | python | def clone(self, **kwargs):
"""Create a clone of the Table, optionally with some properties changed"""
init_kwargs = {
"name": self.__name,
"dataframe": self.__df,
"include_columns": self.__include_columns,
"include_index": self.__include_index,
... | [
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mojaie/chorus | chorus/v2000reader.py | inspect | def inspect(lines):
"""Inspect SDFile list of string
Returns:
tuple: (data label list, number of records)
"""
labels = set()
count = 0
exp = re.compile(r">.*?<([\w ]+)>") # Space should be accepted
valid = False
for line in lines:
if line.startswith("M END\n"):
... | python | def inspect(lines):
"""Inspect SDFile list of string
Returns:
tuple: (data label list, number of records)
"""
labels = set()
count = 0
exp = re.compile(r">.*?<([\w ]+)>") # Space should be accepted
valid = False
for line in lines:
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mojaie/chorus | chorus/v2000reader.py | inspect_file | def inspect_file(path):
"""Inspect SDFile structure
Returns:
tuple: (data label list, number of records)
"""
with open(path, 'rb') as f:
labels, count = inspect(tx.decode(line) for line in f)
return labels, count | python | def inspect_file(path):
"""Inspect SDFile structure
Returns:
tuple: (data label list, number of records)
"""
with open(path, 'rb') as f:
labels, count = inspect(tx.decode(line) for line in f)
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mojaie/chorus | chorus/v2000reader.py | optional_data | def optional_data(lines):
"""Parse SDFile data part into dict"""
data = {}
exp = re.compile(r">.*?<([\w ]+)>") # Space should be accepted
for i, line in enumerate(lines):
result = exp.match(line)
if result:
data[result.group(1)] = lines[i + 1]
return data | python | def optional_data(lines):
"""Parse SDFile data part into dict"""
data = {}
exp = re.compile(r">.*?<([\w ]+)>") # Space should be accepted
for i, line in enumerate(lines):
result = exp.match(line)
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