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242,800 | cdeboever3/cdpybio | cdpybio/star.py | _make_sj_out_dict | def _make_sj_out_dict(fns, jxns=None, define_sample_name=None):
"""Read multiple sj_outs, return dict with keys as sample names and values
as sj_out dataframes.
Parameters
----------
fns : list of strs of filenames or file handles
List of filename of the SJ.out.tab files to read in
jxn... | python | def _make_sj_out_dict(fns, jxns=None, define_sample_name=None):
"""Read multiple sj_outs, return dict with keys as sample names and values
as sj_out dataframes.
Parameters
----------
fns : list of strs of filenames or file handles
List of filename of the SJ.out.tab files to read in
jxn... | [
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242,801 | cdeboever3/cdpybio | cdpybio/star.py | _make_sj_out_panel | def _make_sj_out_panel(sj_outD, total_jxn_cov_cutoff=20):
"""Filter junctions from many sj_out files and make panel.
Parameters
----------
sj_outD : dict
Dict whose keys are sample names and values are sj_out dataframes
total_jxn_cov_cutoff : int
If the unique read coverage of a ju... | python | def _make_sj_out_panel(sj_outD, total_jxn_cov_cutoff=20):
"""Filter junctions from many sj_out files and make panel.
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----------
sj_outD : dict
Dict whose keys are sample names and values are sj_out dataframes
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242,802 | cdeboever3/cdpybio | cdpybio/star.py | read_external_annotation | def read_external_annotation(fn):
"""Read file with junctions from some database. This does not have to be the
same splice junction database used with STAR.
Parameters
----------
fn : filename str
File with splice junctions from annotation. The file should have a
header and contain ... | python | def read_external_annotation(fn):
"""Read file with junctions from some database. This does not have to be the
same splice junction database used with STAR.
Parameters
----------
fn : filename str
File with splice junctions from annotation. The file should have a
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242,803 | cdeboever3/cdpybio | cdpybio/star.py | combine_sj_out | def combine_sj_out(
fns,
external_db,
total_jxn_cov_cutoff=20,
define_sample_name=None,
verbose=False,
):
"""Combine SJ.out.tab files from STAR by filtering based on coverage and
comparing to an external annotation to discover novel junctions.
Parameters
----------
fns : list... | python | def combine_sj_out(
fns,
external_db,
total_jxn_cov_cutoff=20,
define_sample_name=None,
verbose=False,
):
"""Combine SJ.out.tab files from STAR by filtering based on coverage and
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----------
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242,804 | cdeboever3/cdpybio | cdpybio/star.py | _total_jxn_counts | def _total_jxn_counts(fns):
"""Count the total unique coverage junction for junctions in a set of
SJ.out.tab files."""
df = pd.read_table(fns[0], header=None, names=COLUMN_NAMES)
df.index = (df.chrom + ':' + df.start.astype(int).astype(str) + '-' +
df.end.astype(int).astype(str))
cou... | python | def _total_jxn_counts(fns):
"""Count the total unique coverage junction for junctions in a set of
SJ.out.tab files."""
df = pd.read_table(fns[0], header=None, names=COLUMN_NAMES)
df.index = (df.chrom + ':' + df.start.astype(int).astype(str) + '-' +
df.end.astype(int).astype(str))
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242,805 | cdeboever3/cdpybio | cdpybio/star.py | _make_splice_targets_dict | def _make_splice_targets_dict(df, feature, strand):
"""Make dict mapping each donor to the location of all acceptors it splices
to or each acceptor to all donors it splices from.
Parameters
----------
df : pandas.DataFrame
Dataframe with splice junction information from external database
... | python | def _make_splice_targets_dict(df, feature, strand):
"""Make dict mapping each donor to the location of all acceptors it splices
to or each acceptor to all donors it splices from.
Parameters
----------
df : pandas.DataFrame
Dataframe with splice junction information from external database
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242,806 | cdeboever3/cdpybio | cdpybio/star.py | _read_log | def _read_log(fn, define_sample_name=None):
"""Read STAR Log.final.out file.
Parameters
----------
fn : string
Path to Log.final.out file.
define_sample_name : function that takes string as input
Function mapping filename to sample name. For instance, you may have the
sampl... | python | def _read_log(fn, define_sample_name=None):
"""Read STAR Log.final.out file.
Parameters
----------
fn : string
Path to Log.final.out file.
define_sample_name : function that takes string as input
Function mapping filename to sample name. For instance, you may have the
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242,807 | cdeboever3/cdpybio | cdpybio/star.py | make_logs_df | def make_logs_df(fns, define_sample_name=None):
"""Make pandas DataFrame from multiple STAR Log.final.out files.
Parameters
----------
fns : string
List of paths to Log.final.out files.
define_sample_name : function that takes string as input
Function mapping filename to sample nam... | python | def make_logs_df(fns, define_sample_name=None):
"""Make pandas DataFrame from multiple STAR Log.final.out files.
Parameters
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fns : string
List of paths to Log.final.out files.
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242,808 | mariocesar/pengbot | examples/bob.py | uptime | def uptime():
"""Uptime of the host machine"""
from datetime import timedelta
with open('/proc/uptime', 'r') as f:
uptime_seconds = float(f.readline().split()[0])
uptime_string = str(timedelta(seconds=uptime_seconds))
bob.says(uptime_string) | python | def uptime():
"""Uptime of the host machine"""
from datetime import timedelta
with open('/proc/uptime', 'r') as f:
uptime_seconds = float(f.readline().split()[0])
uptime_string = str(timedelta(seconds=uptime_seconds))
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242,809 | firstprayer/monsql | monsql/query.py | value_to_sql_str | def value_to_sql_str(v):
"""
transform a python variable to the appropriate representation in SQL
"""
if v is None:
return 'null'
if type(v) in (types.IntType, types.FloatType, types.LongType):
return str(v)
if type(v) in (types.StringType, types.UnicodeType):
return "'... | python | def value_to_sql_str(v):
"""
transform a python variable to the appropriate representation in SQL
"""
if v is None:
return 'null'
if type(v) in (types.IntType, types.FloatType, types.LongType):
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242,810 | fr33jc/bang | bang/config.py | find_component_tarball | def find_component_tarball(bucket, comp_name, comp_config):
"""
Returns True if the component tarball is found in the bucket.
Otherwise, returns False.
"""
values = {
'name': comp_name,
'version': comp_config['version'],
'platform': comp_config['platform'],
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"""
Returns True if the component tarball is found in the bucket.
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"""
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242,811 | fr33jc/bang | bang/config.py | Config._prepare_servers | def _prepare_servers(self):
"""
Prepare the variables that are exposed to the servers.
Most attributes in the server config are used directly. However, due
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242,812 | fr33jc/bang | bang/config.py | Config._prepare_load_balancers | def _prepare_load_balancers(self):
"""
Prepare load balancer variables
"""
stack = {
A.NAME: self[A.NAME],
A.VERSION: self[A.VERSION],
}
for load_balancer in self.get(R.LOAD_BALANCERS, []):
svars = {A.STACK: stack}
... | python | def _prepare_load_balancers(self):
"""
Prepare load balancer variables
"""
stack = {
A.NAME: self[A.NAME],
A.VERSION: self[A.VERSION],
}
for load_balancer in self.get(R.LOAD_BALANCERS, []):
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242,813 | fr33jc/bang | bang/config.py | Config.prepare | def prepare(self):
"""
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- In order to minimize repetition, ... | python | def prepare(self):
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242,814 | fr33jc/bang | bang/config.py | Config.autoinc | def autoinc(self):
"""
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242,815 | Rafiot/PubSubLogger | pubsublogger/subscriber.py | setup | def setup(name, path='log', enable_debug=False):
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path_tmpl = os.path.join(path... | python | def setup(name, path='log', enable_debug=False):
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Prepare a NestedSetup.
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242,816 | Rafiot/PubSubLogger | pubsublogger/subscriber.py | mail_setup | def mail_setup(path):
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"""
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global smtp_server
global smtp_port
global src_server
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config.readfp(path)
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"""
Set the variables to be able to send emails.
:param path: path to the config file
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:param path: the path where the log files will be written
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"""
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242,818 | tylertrussell/flake8-docstrings-catnado | flake8_docstrings.py | pep257Checker.parse_options | def parse_options(cls, options):
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cls.ignore_decorators = options.ignore_decorators
cls.exclude_from_doctest = options.exclude_from_doctest
if not isinstance(cls.exclude_from_doctest, list):
cls.exclude_from_doctest = [cls.exclude_from_doctest] | python | def parse_options(cls, options):
"""Pass options through to this plugin."""
cls.ignore_decorators = options.ignore_decorators
cls.exclude_from_doctest = options.exclude_from_doctest
if not isinstance(cls.exclude_from_doctest, list):
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242,820 | GMadorell/abris | abris_transform/abris.py | Abris.prepare | def prepare(self, data_source):
"""
Called with the training data.
@param data_source: Either a pandas.DataFrame or a file-like object.
"""
dataframe = self.__get_dataframe(data_source, use_target=True)
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"""
Called with the training data.
@param data_source: Either a pandas.DataFrame or a file-like object.
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242,821 | jlesquembre/jlle | jlle/releaser/utils.py | fix_rst_heading | def fix_rst_heading(heading, below):
"""If the 'below' line looks like a reST line, give it the correct length.
This allows for different characters being used as header lines.
"""
if len(below) == 0:
return below
first = below[0]
if first not in '-=`~':
return below
if not ... | python | def fix_rst_heading(heading, below):
"""If the 'below' line looks like a reST line, give it the correct length.
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return below
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242,822 | jlesquembre/jlle | jlle/releaser/utils.py | sanity_check | def sanity_check(vcs):
"""Do sanity check before making changes
Check that we are not on a tag and/or do not have local changes.
Returns True when all is fine.
"""
if not vcs.is_clean_checkout():
q = ("This is NOT a clean checkout. You are on a tag or you have "
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"""Do sanity check before making changes
Check that we are not on a tag and/or do not have local changes.
Returns True when all is fine.
"""
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242,823 | jlesquembre/jlle | jlle/releaser/utils.py | check_recommended_files | def check_recommended_files(data, vcs):
"""Do check for recommended files.
Returns True when all is fine.
"""
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# Not a python package. We have no recommendations.
return Tr... | python | def check_recommended_files(data, vcs):
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Returns True when all is fine.
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242,824 | jlesquembre/jlle | jlle/releaser/utils.py | cleanup_version | def cleanup_version(version):
"""Check if the version looks like a development version."""
for w in WRONG_IN_VERSION:
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logger.debug("Version indicates development: %s.", version)
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242,825 | JNRowe/jnrbase | jnrbase/pager.py | pager | def pager(__text: str, *, pager: Optional[str] = 'less'):
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pager: Pager to use
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242,826 | zeromake/aiko | aiko/application.py | Application.listen | def listen(self, **kwargs: Any) -> Server:
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242,827 | armstrong/armstrong.hatband | armstrong/hatband/views/search.py | TypeAndModelQueryMixin.type_and_model_to_query | def type_and_model_to_query(self, request):
"""
Return JSON for an individual Model instance
If the required parameters are wrong, return 400 Bad Request
If the parameters are correct but there is no data, return empty JSON
"""
try:
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"""
Return JSON for an individual Model instance
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242,828 | vinu76jsr/pipsort | lib/pipsort/core/_config.py | _Config.load | def load(self, paths, params=None):
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242,829 | universalcore/unicore.distribute | unicore/distribute/utils.py | get_repositories | def get_repositories(path):
"""
Return an array of tuples with the name and path for
repositories found in a directory.
:param str path:
The path to find repositories in
:returns: tuple
"""
return [get_repository(os.path.join(path, subdir))
for subdir in os.listdir(path)... | python | def get_repositories(path):
"""
Return an array of tuples with the name and path for
repositories found in a directory.
:param str path:
The path to find repositories in
:returns: tuple
"""
return [get_repository(os.path.join(path, subdir))
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242,830 | universalcore/unicore.distribute | unicore/distribute/utils.py | get_repository_names | def get_repository_names(path):
"""
Return an array of the path name for
repositories found in a directory.
:param str path:
The path to find repositories in
:returns: array
"""
return [subdir
for subdir in os.listdir(path)
if os.path.isdir(os.path.join(path,... | python | def get_repository_names(path):
"""
Return an array of the path name for
repositories found in a directory.
:param str path:
The path to find repositories in
:returns: array
"""
return [subdir
for subdir in os.listdir(path)
if os.path.isdir(os.path.join(path,... | [
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242,831 | universalcore/unicore.distribute | unicore/distribute/utils.py | list_schemas | def list_schemas(repo):
"""
Return a list of parsed avro schemas as dictionaries.
:param Repo repo:
The git repository.
:returns: dict
"""
schema_files = glob.glob(
os.path.join(repo.working_dir, '_schemas', '*.avsc'))
schemas = {}
for schema_file in schema_files:
... | python | def list_schemas(repo):
"""
Return a list of parsed avro schemas as dictionaries.
:param Repo repo:
The git repository.
:returns: dict
"""
schema_files = glob.glob(
os.path.join(repo.working_dir, '_schemas', '*.avsc'))
schemas = {}
for schema_file in schema_files:
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242,832 | universalcore/unicore.distribute | unicore/distribute/utils.py | list_content_types | def list_content_types(repo):
"""
Return a list of content types in a repository.
:param Repo repo:
The git repository.
:returns: list
"""
schema_files = glob.glob(
os.path.join(repo.working_dir, '_schemas', '*.avsc'))
return [os.path.splitext(os.path.basename(schema_file))[... | python | def list_content_types(repo):
"""
Return a list of content types in a repository.
:param Repo repo:
The git repository.
:returns: list
"""
schema_files = glob.glob(
os.path.join(repo.working_dir, '_schemas', '*.avsc'))
return [os.path.splitext(os.path.basename(schema_file))[... | [
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242,833 | universalcore/unicore.distribute | unicore/distribute/utils.py | get_schema | def get_schema(repo, content_type):
"""
Return a schema for a content type in a repository.
:param Repo repo:
The git repository.
:returns: dict
"""
try:
with open(
os.path.join(repo.working_dir,
'_schemas',
... | python | def get_schema(repo, content_type):
"""
Return a schema for a content type in a repository.
:param Repo repo:
The git repository.
:returns: dict
"""
try:
with open(
os.path.join(repo.working_dir,
'_schemas',
... | [
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242,834 | universalcore/unicore.distribute | unicore/distribute/utils.py | get_mapping | def get_mapping(repo, content_type):
"""
Return an ES mapping for a content type in a repository.
:param Repo repo:
This git repository.
:returns: dict
"""
try:
with open(
os.path.join(repo.working_dir,
'_mappings',
'... | python | def get_mapping(repo, content_type):
"""
Return an ES mapping for a content type in a repository.
:param Repo repo:
This git repository.
:returns: dict
"""
try:
with open(
os.path.join(repo.working_dir,
'_mappings',
'... | [
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242,835 | universalcore/unicore.distribute | unicore/distribute/utils.py | format_repo | def format_repo(repo):
"""
Return a dictionary representing the repository
It returns ``None`` for things we do not support or are not
relevant.
:param str repo_name:
The name of the repository.
:param git.Repo repo:
The repository object.
:param str base_url:
The b... | python | def format_repo(repo):
"""
Return a dictionary representing the repository
It returns ``None`` for things we do not support or are not
relevant.
:param str repo_name:
The name of the repository.
:param git.Repo repo:
The repository object.
:param str base_url:
The b... | [
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242,836 | universalcore/unicore.distribute | unicore/distribute/utils.py | format_diffindex | def format_diffindex(diff_index):
"""
Return a JSON formattable representation of a DiffIndex.
Returns a generator that returns dictionaries representing the changes.
.. code::
[
{
'type': 'A',
'path': 'path/to/added/file.txt',
},
... | python | def format_diffindex(diff_index):
"""
Return a JSON formattable representation of a DiffIndex.
Returns a generator that returns dictionaries representing the changes.
.. code::
[
{
'type': 'A',
'path': 'path/to/added/file.txt',
},
... | [
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242,837 | universalcore/unicore.distribute | unicore/distribute/utils.py | format_content_type | def format_content_type(repo, content_type):
"""
Return a list of all content objects for a given content type
in a repository.
:param Repo repo:
The git repository.
:param str content_type:
The content type to list
:returns: list
"""
storage_manager = StorageManager(rep... | python | def format_content_type(repo, content_type):
"""
Return a list of all content objects for a given content type
in a repository.
:param Repo repo:
The git repository.
:param str content_type:
The content type to list
:returns: list
"""
storage_manager = StorageManager(rep... | [
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242,838 | universalcore/unicore.distribute | unicore/distribute/utils.py | format_content_type_object | def format_content_type_object(repo, content_type, uuid):
"""
Return a content object from a repository for a given content_type
and uuid
:param Repo repo:
The git repository.
:param str content_type:
The content type to list
:returns: dict
"""
try:
storage_manag... | python | def format_content_type_object(repo, content_type, uuid):
"""
Return a content object from a repository for a given content_type
and uuid
:param Repo repo:
The git repository.
:param str content_type:
The content type to list
:returns: dict
"""
try:
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242,839 | universalcore/unicore.distribute | unicore/distribute/utils.py | format_repo_status | def format_repo_status(repo):
"""
Return a dictionary representing the repository status
It returns ``None`` for things we do not support or are not
relevant.
:param str repo_name:
The name of the repository.
:returns: dict
"""
commit = repo.commit()
return {
'name... | python | def format_repo_status(repo):
"""
Return a dictionary representing the repository status
It returns ``None`` for things we do not support or are not
relevant.
:param str repo_name:
The name of the repository.
:returns: dict
"""
commit = repo.commit()
return {
'name... | [
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242,840 | universalcore/unicore.distribute | unicore/distribute/utils.py | save_content_type_object | def save_content_type_object(repo, schema, uuid, data):
"""
Save an object as a certain content type
"""
storage_manager = StorageManager(repo)
model_class = deserialize(schema,
module_name=schema['namespace'])
model = model_class(data)
commit = storage_manager.... | python | def save_content_type_object(repo, schema, uuid, data):
"""
Save an object as a certain content type
"""
storage_manager = StorageManager(repo)
model_class = deserialize(schema,
module_name=schema['namespace'])
model = model_class(data)
commit = storage_manager.... | [
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242,841 | universalcore/unicore.distribute | unicore/distribute/utils.py | delete_content_type_object | def delete_content_type_object(repo, content_type, uuid):
"""
Delete an object of a certain content type
"""
storage_manager = StorageManager(repo)
model_class = load_model_class(repo, content_type)
model = storage_manager.get(model_class, uuid)
commit = storage_manager.delete(model, 'Delete... | python | def delete_content_type_object(repo, content_type, uuid):
"""
Delete an object of a certain content type
"""
storage_manager = StorageManager(repo)
model_class = load_model_class(repo, content_type)
model = storage_manager.get(model_class, uuid)
commit = storage_manager.delete(model, 'Delete... | [
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242,842 | universalcore/unicore.distribute | unicore/distribute/utils.py | load_model_class | def load_model_class(repo, content_type):
"""
Return a model class for a content type in a repository.
:param Repo repo:
The git repository.
:param str content_type:
The content type to list
:returns: class
"""
schema = get_schema(repo, content_type).to_json()
return des... | python | def load_model_class(repo, content_type):
"""
Return a model class for a content type in a repository.
:param Repo repo:
The git repository.
:param str content_type:
The content type to list
:returns: class
"""
schema = get_schema(repo, content_type).to_json()
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242,843 | binilinlquad/bing-search-api | bing_search_api/api.py | BingSearchAPI.search_composite | def search_composite(self, query, source, payload=None):
'''Shortcut search with composite source'''
source = '+'.join(source)
if payload is None:
payload = dict(Sources=quote(source))
else:
payload['Sources'] = quote(source)
return self.search(query, 'C... | python | def search_composite(self, query, source, payload=None):
'''Shortcut search with composite source'''
source = '+'.join(source)
if payload is None:
payload = dict(Sources=quote(source))
else:
payload['Sources'] = quote(source)
return self.search(query, 'C... | [
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242,844 | pop/GrindStone | grindstone/lib.py | key_of | def key_of(d):
"""
Returns the key of a single element dict.
"""
if len(d) > 1 and not type(d) == dict():
raise ValueError('key_of(d) may only except single element dict')
else:
return keys_of(d)[0] | python | def key_of(d):
"""
Returns the key of a single element dict.
"""
if len(d) > 1 and not type(d) == dict():
raise ValueError('key_of(d) may only except single element dict')
else:
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242,845 | pop/GrindStone | grindstone/lib.py | GrindStone.open_grindstone | def open_grindstone(self):
"""
Opens a grindstone file and populates the grindstone with it's
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Returns an empty grindstone json object if a file does not exist.
"""
try:
with open(self.grindstone_path, 'r') as f:
# Try opening the file... | python | def open_grindstone(self):
"""
Opens a grindstone file and populates the grindstone with it's
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Returns an empty grindstone json object if a file does not exist.
"""
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242,846 | pop/GrindStone | grindstone/lib.py | GrindStone.delete_task | def delete_task(self, task=None):
"""
Deletes a given task by name.
"""
# Iterate over the list of tasks
for t in self.grindstone['tasks']:
# If they key of the task matches the task given
if key_of(t) == task:
# Remove that task
... | python | def delete_task(self, task=None):
"""
Deletes a given task by name.
"""
# Iterate over the list of tasks
for t in self.grindstone['tasks']:
# If they key of the task matches the task given
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242,847 | pop/GrindStone | grindstone/lib.py | GrindStone.write_grindstone | def write_grindstone(self):
"""
Writes self.gs to self.grindstone_path.
"""
with open(self.grindstone_path, 'w') as f:
# Write the JSON dump of the file
f.write(json.dumps(self.grindstone)) | python | def write_grindstone(self):
"""
Writes self.gs to self.grindstone_path.
"""
with open(self.grindstone_path, 'w') as f:
# Write the JSON dump of the file
f.write(json.dumps(self.grindstone)) | [
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242,848 | scivision/histutils | histutils/timedmc.py | datetime2unix | def datetime2unix(T):
"""
converts datetime to UT1 unix epoch time
"""
T = atleast_1d(T)
ut1_unix = empty(T.shape, dtype=float)
for i, t in enumerate(T):
if isinstance(t, (datetime, datetime64)):
pass
elif isinstance(t, str):
try:
ut1_unix... | python | def datetime2unix(T):
"""
converts datetime to UT1 unix epoch time
"""
T = atleast_1d(T)
ut1_unix = empty(T.shape, dtype=float)
for i, t in enumerate(T):
if isinstance(t, (datetime, datetime64)):
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elif isinstance(t, str):
try:
ut1_unix... | [
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242,849 | tshlabs/tunic | tunic/install.py | _is_iterable | def _is_iterable(val):
"""Ensure that a value is iterable and not some sort of string"""
try:
iter(val)
except (ValueError, TypeError):
return False
else:
return not isinstance(val, basestring) | python | def _is_iterable(val):
"""Ensure that a value is iterable and not some sort of string"""
try:
iter(val)
except (ValueError, TypeError):
return False
else:
return not isinstance(val, basestring) | [
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242,850 | tshlabs/tunic | tunic/install.py | download_url | def download_url(url, destination, retries=None, retry_delay=None, runner=None):
"""Download the given URL with wget to the provided path. The command is
run via Fabric on the current remote machine. Therefore, the destination
path should be for the remote machine.
:param str url: URL to download onto ... | python | def download_url(url, destination, retries=None, retry_delay=None, runner=None):
"""Download the given URL with wget to the provided path. The command is
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242,851 | tshlabs/tunic | tunic/install.py | VirtualEnvInstallation._get_install_sources | def _get_install_sources(self):
"""Construct arguments to use alternative package indexes if
there were sources supplied, empty string if there were not.
"""
if not self._sources:
return ''
parts = ['--no-index']
for source in self._sources:
parts.... | python | def _get_install_sources(self):
"""Construct arguments to use alternative package indexes if
there were sources supplied, empty string if there were not.
"""
if not self._sources:
return ''
parts = ['--no-index']
for source in self._sources:
parts.... | [
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242,852 | tshlabs/tunic | tunic/install.py | VirtualEnvInstallation.install | def install(self, release_id, upgrade=False):
"""Install target packages into a virtual environment.
If the virtual environment for the given release ID does not
exist on the remote system, it will be created. The virtual
environment will be created according to the standard Tunic
... | python | def install(self, release_id, upgrade=False):
"""Install target packages into a virtual environment.
If the virtual environment for the given release ID does not
exist on the remote system, it will be created. The virtual
environment will be created according to the standard Tunic
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242,853 | tshlabs/tunic | tunic/install.py | StaticFileInstallation.install | def install(self, release_id):
"""Install the contents of the local directory into a release directory.
If the directory for the given release ID does not exist on the remote
system, it will be created. The directory will be created according to
the standard Tunic directory structure (s... | python | def install(self, release_id):
"""Install the contents of the local directory into a release directory.
If the directory for the given release ID does not exist on the remote
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242,854 | tshlabs/tunic | tunic/install.py | LocalArtifactInstallation.install | def install(self, release_id):
"""Install the local artifact into the remote release directory, optionally
with a different name than the artifact had locally.
If the directory for the given release ID does not exist on the remote
system, it will be created. The directory will be create... | python | def install(self, release_id):
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242,855 | tshlabs/tunic | tunic/install.py | HttpArtifactInstallation._get_file_from_url | def _get_file_from_url(url):
"""Get the filename part of the path component from a URL."""
path = urlparse(url).path
if not path:
raise ValueError("Could not extract path from URL '{0}'".format(url))
name = os.path.basename(path)
if not name:
raise ValueEr... | python | def _get_file_from_url(url):
"""Get the filename part of the path component from a URL."""
path = urlparse(url).path
if not path:
raise ValueError("Could not extract path from URL '{0}'".format(url))
name = os.path.basename(path)
if not name:
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242,856 | tshlabs/tunic | tunic/install.py | HttpArtifactInstallation.install | def install(self, release_id):
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242,857 | mrstephenneal/dirutility | dirutility/walk/walk.py | pool_process | def pool_process(func, iterable, process_name='Pool processing', cpus=cpu_count()):
"""
Apply a function to each element in an iterable and return a result list.
:param func: A function that returns a value
:param iterable: A list or set of elements to be passed to the func as the singular parameter
... | python | def pool_process(func, iterable, process_name='Pool processing', cpus=cpu_count()):
"""
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242,858 | mrstephenneal/dirutility | dirutility/walk/walk.py | remover | def remover(file_path):
"""Delete a file or directory path only if it exists."""
if os.path.isfile(file_path):
os.remove(file_path)
return True
elif os.path.isdir(file_path):
shutil.rmtree(file_path)
return True
else:
return False | python | def remover(file_path):
"""Delete a file or directory path only if it exists."""
if os.path.isfile(file_path):
os.remove(file_path)
return True
elif os.path.isdir(file_path):
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242,859 | mrstephenneal/dirutility | dirutility/walk/walk.py | creation_date | def creation_date(path_to_file, return_datetime=True):
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242,860 | mrstephenneal/dirutility | dirutility/walk/walk.py | DirPaths._get_filepaths | def _get_filepaths(self):
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242,861 | mrstephenneal/dirutility | dirutility/walk/walk.py | DirPaths.files | def files(self):
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242,862 | mrstephenneal/dirutility | dirutility/walk/walk.py | DirPaths.folders | def folders(self):
"""Return list of folders in root directory"""
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for path in os.listdir(directory):
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if os.path.isdir(full_path):
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... | python | def folders(self):
"""Return list of folders in root directory"""
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242,863 | drongo-framework/drongo | drongo/app.py | Drongo.url | def url(self, pattern, method=None, name=None):
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Args:
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242,864 | shi-cong/PYSTUDY | PYSTUDY/image/pillib.py | GPS.get_exif_data | def get_exif_data(self, image):
"""Returns a dictionary from the exif data of an PIL Image item. Also converts the GPS Tags"""
exif_data = {}
info = image._getexif()
if info:
for tag, value in info.items():
decoded = TAGS.get(tag, tag)
if decod... | python | def get_exif_data(self, image):
"""Returns a dictionary from the exif data of an PIL Image item. Also converts the GPS Tags"""
exif_data = {}
info = image._getexif()
if info:
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242,865 | shi-cong/PYSTUDY | PYSTUDY/image/pillib.py | GPS._convert_to_degress | def _convert_to_degress(self, value):
"""Helper function to convert the GPS coordinates stored in the EXIF to degress in float format"""
d0 = value[0][0]
d1 = value[0][1]
d = float(d0) / float(d1)
m0 = value[1][0]
m1 = value[1][1]
m = float(m0) / float(m1)
... | python | def _convert_to_degress(self, value):
"""Helper function to convert the GPS coordinates stored in the EXIF to degress in float format"""
d0 = value[0][0]
d1 = value[0][1]
d = float(d0) / float(d1)
m0 = value[1][0]
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242,866 | asyncdef/interfaces | asyncdef/interfaces/engine/iselector.py | ISelector.add_reader | def add_reader(
self,
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) -> None:
"""Add a file descriptor to the processor and wait for READ.
Args:
fd (IFileLike): Any obect that exposes a 'fileno' method that
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fd: IFileLike,
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242,867 | robertchase/ergaleia | ergaleia/config.py | Config._load | def _load(self, path='config', filetype=None, relaxed=False, ignore=False):
""" load key value pairs from a file
Parameters:
path - path to configuration data (see Note 1)
filetype - type component of dot-delimited path
relaxed - if True, define ... | python | def _load(self, path='config', filetype=None, relaxed=False, ignore=False):
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path - path to configuration data (see Note 1)
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242,868 | robertchase/ergaleia | ergaleia/config.py | _item.load | def load(self, value):
""" enforce env > value when loading from file """
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242,869 | tBaxter/tango-shared-core | build/lib/tango_shared/models.py | set_img_path | def set_img_path(instance, filename):
"""
Sets upload_to dynamically
"""
upload_path = '/'.join(
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Sets upload_to dynamically
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upload_path = '/'.join(
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242,870 | tBaxter/tango-shared-core | build/lib/tango_shared/models.py | BaseUserContentModel.save | def save(self, *args, **kwargs):
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Clean text and save formatted version.
"""
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Clean text and save formatted version.
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242,871 | treystout/Agner | agner/queue.py | Queue.enqueue | def enqueue(self, job):
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"""Enqueue a job for later processing, returns the new length of the queue
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242,872 | treystout/Agner | agner/queue.py | Queue.next_job | def next_job(self, timeout_seconds=None):
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242,873 | maceoutliner/django-fiction-outlines | fiction_outlines/receivers.py | generate_headline_from_description | def generate_headline_from_description(sender, instance, *args, **kwargs):
'''
Auto generate the headline of the node from the first lines of the description.
'''
lines = instance.description.split('\n')
headline = truncatewords(lines[0], 20)
if headline[:-3] == '...':
headline = truncat... | python | def generate_headline_from_description(sender, instance, *args, **kwargs):
'''
Auto generate the headline of the node from the first lines of the description.
'''
lines = instance.description.split('\n')
headline = truncatewords(lines[0], 20)
if headline[:-3] == '...':
headline = truncat... | [
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242,874 | maceoutliner/django-fiction-outlines | fiction_outlines/receivers.py | story_root_for_new_outline | def story_root_for_new_outline(sender, instance, created, *args, **kwargs):
'''
If a new instance of a Outline is created, also create
the root node of the story tree.
'''
if created and isinstance(instance, Outline):
streeroot = StoryElementNode.add_root(outline=instance, story_element_type... | python | def story_root_for_new_outline(sender, instance, created, *args, **kwargs):
'''
If a new instance of a Outline is created, also create
the root node of the story tree.
'''
if created and isinstance(instance, Outline):
streeroot = StoryElementNode.add_root(outline=instance, story_element_type... | [
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242,875 | maceoutliner/django-fiction-outlines | fiction_outlines/receivers.py | story_node_add_arc_element_update_characters_locations | def story_node_add_arc_element_update_characters_locations(sender, instance, created, *args, **kwargs):
'''
If an arc element is added to a story element node, add any missing elements or locations.
'''
arc_node = ArcElementNode.objects.get(pk=instance.pk)
logger.debug('Scanning arc_node %s' % arc_n... | python | def story_node_add_arc_element_update_characters_locations(sender, instance, created, *args, **kwargs):
'''
If an arc element is added to a story element node, add any missing elements or locations.
'''
arc_node = ArcElementNode.objects.get(pk=instance.pk)
logger.debug('Scanning arc_node %s' % arc_n... | [
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242,876 | maceoutliner/django-fiction-outlines | fiction_outlines/receivers.py | validate_arc_links_same_outline | def validate_arc_links_same_outline(sender, instance, *args, **kwargs):
'''
Evaluates attempts to link an arc to a story node from another outline.
'''
if instance.story_element_node:
if instance.story_element_node.outline != instance.parent_outline:
raise IntegrityError(_('An arc ca... | python | def validate_arc_links_same_outline(sender, instance, *args, **kwargs):
'''
Evaluates attempts to link an arc to a story node from another outline.
'''
if instance.story_element_node:
if instance.story_element_node.outline != instance.parent_outline:
raise IntegrityError(_('An arc ca... | [
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242,877 | maceoutliner/django-fiction-outlines | fiction_outlines/receivers.py | validate_character_instance_valid_for_arc | def validate_character_instance_valid_for_arc(sender, instance, action, reverse, pk_set, *args, **kwargs):
'''
Evaluate attempts to assign a character instance to ensure it is from same
outline.
'''
if action == 'pre_add':
if reverse:
# Fetch arc definition through link.
... | python | def validate_character_instance_valid_for_arc(sender, instance, action, reverse, pk_set, *args, **kwargs):
'''
Evaluate attempts to assign a character instance to ensure it is from same
outline.
'''
if action == 'pre_add':
if reverse:
# Fetch arc definition through link.
... | [
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242,878 | maceoutliner/django-fiction-outlines | fiction_outlines/receivers.py | validate_location_instance_valid_for_arc | def validate_location_instance_valid_for_arc(sender, instance, action, reverse, pk_set, *args, **kwargs):
'''
Evaluates attempts to add location instances to arc, ensuring they are from same outline.
'''
if action == 'pre_add':
if reverse:
# Fetch arc definition through link.
... | python | def validate_location_instance_valid_for_arc(sender, instance, action, reverse, pk_set, *args, **kwargs):
'''
Evaluates attempts to add location instances to arc, ensuring they are from same outline.
'''
if action == 'pre_add':
if reverse:
# Fetch arc definition through link.
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242,879 | maceoutliner/django-fiction-outlines | fiction_outlines/receivers.py | validate_character_for_story_element | def validate_character_for_story_element(sender, instance, action, reverse, pk_set, *args, **kwargs):
'''
Validates that character is from the same outline as the story node.
'''
if action == 'pre_add':
if reverse:
for spk in pk_set:
story_node = StoryElementNode.obje... | python | def validate_character_for_story_element(sender, instance, action, reverse, pk_set, *args, **kwargs):
'''
Validates that character is from the same outline as the story node.
'''
if action == 'pre_add':
if reverse:
for spk in pk_set:
story_node = StoryElementNode.obje... | [
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242,880 | maceoutliner/django-fiction-outlines | fiction_outlines/receivers.py | validate_location_for_story_element | def validate_location_for_story_element(sender, instance, action, reverse, pk_set, *args, **kwargs):
'''
Validates that location is from same outline as story node.
'''
if action == 'pre_add':
if reverse:
for spk in pk_set:
story_node = StoryElementNode.objects.get(pk... | python | def validate_location_for_story_element(sender, instance, action, reverse, pk_set, *args, **kwargs):
'''
Validates that location is from same outline as story node.
'''
if action == 'pre_add':
if reverse:
for spk in pk_set:
story_node = StoryElementNode.objects.get(pk... | [
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242,881 | rsalmaso/django-fluo | fluo/views/base.py | View.options | def options(self, request, *args, **kwargs):
"""
Handles responding to requests for the OPTIONS HTTP verb
"""
response = HttpResponse()
response['Allow'] = ', '.join(self.allowed_methods)
response['Content-Length'] = 0
return response | python | def options(self, request, *args, **kwargs):
"""
Handles responding to requests for the OPTIONS HTTP verb
"""
response = HttpResponse()
response['Allow'] = ', '.join(self.allowed_methods)
response['Content-Length'] = 0
return response | [
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242,882 | DasIch/argvard | argvard/utils.py | is_python2_identifier | def is_python2_identifier(possible_identifier):
"""
Returns `True` if the given `possible_identifier` can be used as an
identifier in Python 2.
"""
match = _python2_identifier_re.match(possible_identifier)
return bool(match) and not iskeyword(possible_identifier) | python | def is_python2_identifier(possible_identifier):
"""
Returns `True` if the given `possible_identifier` can be used as an
identifier in Python 2.
"""
match = _python2_identifier_re.match(possible_identifier)
return bool(match) and not iskeyword(possible_identifier) | [
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242,883 | DasIch/argvard | argvard/utils.py | is_python3_identifier | def is_python3_identifier(possible_identifier):
"""
Returns `True` if the given `possible_identifier` can be used as an
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"""
possible_identifier = unicodedata.normalize('NFKC', possible_identifier)
return (
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"""
Returns `True` if the given `possible_identifier` can be used as an
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"""
possible_identifier = unicodedata.normalize('NFKC', possible_identifier)
return (
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242,884 | DasIch/argvard | argvard/utils.py | unique | def unique(iterable):
"""
Returns an iterator that yields the first occurence of a hashable item in
`iterable`.
"""
seen = set()
for obj in iterable:
if obj not in seen:
yield obj
seen.add(obj) | python | def unique(iterable):
"""
Returns an iterator that yields the first occurence of a hashable item in
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"""
seen = set()
for obj in iterable:
if obj not in seen:
yield obj
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242,885 | krinj/k-util | k_util/region.py | Region.contains | def contains(self, x, y) -> bool:
"""" Checks if the given x, y position is within the area of this region. """
if x < self._left or x > self._right or y < self._top or y > self._bottom:
return False
return True | python | def contains(self, x, y) -> bool:
"""" Checks if the given x, y position is within the area of this region. """
if x < self._left or x > self._right or y < self._top or y > self._bottom:
return False
return True | [
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242,886 | krinj/k-util | k_util/region.py | Region.is_in_bounds | def is_in_bounds(self, width, height) -> bool:
""" Check if this entire region is contained within the bounds of a given stage size."""
if self._top < 0 \
or self._bottom > height \
or self._left < 0 \
or self._right > width:
return False
... | python | def is_in_bounds(self, width, height) -> bool:
""" Check if this entire region is contained within the bounds of a given stage size."""
if self._top < 0 \
or self._bottom > height \
or self._left < 0 \
or self._right > width:
return False
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242,887 | krinj/k-util | k_util/region.py | Region.canvas_resize | def canvas_resize(self, scale):
""" Resize this region against the entire axis space. """
self._top *= scale
self._bottom *= scale
self._left *= scale
self._right *= scale
self._calibrate_to_rect() | python | def canvas_resize(self, scale):
""" Resize this region against the entire axis space. """
self._top *= scale
self._bottom *= scale
self._left *= scale
self._right *= scale
self._calibrate_to_rect() | [
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242,888 | krinj/k-util | k_util/region.py | Region.distance | def distance(r1: 'Region', r2: 'Region'):
""" Calculate distance between the x and y of the two regions."""
return math.sqrt((r2.x - r1.x) ** 2 + (r2.y - r1.y) ** 2) | python | def distance(r1: 'Region', r2: 'Region'):
""" Calculate distance between the x and y of the two regions."""
return math.sqrt((r2.x - r1.x) ** 2 + (r2.y - r1.y) ** 2) | [
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242,889 | krinj/k-util | k_util/region.py | Region.fast_distance | def fast_distance(r1: 'Region', r2: 'Region'):
""" A quicker way of calculating approximate distance. Lower accuracy but faster results."""
return abs(r1.x - r2.x) + abs(r1.y - r2.y) | python | def fast_distance(r1: 'Region', r2: 'Region'):
""" A quicker way of calculating approximate distance. Lower accuracy but faster results."""
return abs(r1.x - r2.x) + abs(r1.y - r2.y) | [
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242,890 | hobson/pug-invest | pug/invest/util.py | rms | def rms(x):
""""Root Mean Square"
Arguments:
x (seq of float): A sequence of numerical values
Returns:
The square root of the average of the squares of the values
math.sqrt(sum(x_i**2 for x_i in x) / len(x))
or
return (np.array(x) ** 2).mean() ** 0.5
>>> rms... | python | def rms(x):
""""Root Mean Square"
Arguments:
x (seq of float): A sequence of numerical values
Returns:
The square root of the average of the squares of the values
math.sqrt(sum(x_i**2 for x_i in x) / len(x))
or
return (np.array(x) ** 2).mean() ** 0.5
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242,891 | hobson/pug-invest | pug/invest/util.py | rmse | def rmse(target, prediction, relative=False, percent=False):
"""Root Mean Square Error
This seems like a simple formula that you'd never need to create a function for.
But my mistakes on coding challenges have convinced me that I do need it,
as a reminder of important tweaks, if nothing else.
>>> ... | python | def rmse(target, prediction, relative=False, percent=False):
"""Root Mean Square Error
This seems like a simple formula that you'd never need to create a function for.
But my mistakes on coding challenges have convinced me that I do need it,
as a reminder of important tweaks, if nothing else.
>>> ... | [
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>>> rmse([0, 1, 4, 3], [2, 1, 0, -1])
3.0
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242,892 | hobson/pug-invest | pug/invest/util.py | pandas_mesh | def pandas_mesh(df):
"""Create numpy 2-D "meshgrid" from 3+ columns in a Pandas DataFrame
Arguments:
df (DataFrame): Must have 3 or 4 columns of numerical data
Returns:
OrderedDict: column labels from the data frame are the keys, values are 2-D matrices
All matrices have shape NxM, whe... | python | def pandas_mesh(df):
"""Create numpy 2-D "meshgrid" from 3+ columns in a Pandas DataFrame
Arguments:
df (DataFrame): Must have 3 or 4 columns of numerical data
Returns:
OrderedDict: column labels from the data frame are the keys, values are 2-D matrices
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242,893 | hobson/pug-invest | pug/invest/util.py | get_integrator | def get_integrator(integrator):
"""Return the scipy.integrator indicated by an index, name, or integrator_function
>> get_integrator(0)
"""
integrator_types = set(['trapz', 'cumtrapz', 'simps', 'romb'])
integrator_funcs = [integrate.trapz, integrate.cumtrapz, integrate.simps, integrate.romb]
i... | python | def get_integrator(integrator):
"""Return the scipy.integrator indicated by an index, name, or integrator_function
>> get_integrator(0)
"""
integrator_types = set(['trapz', 'cumtrapz', 'simps', 'romb'])
integrator_funcs = [integrate.trapz, integrate.cumtrapz, integrate.simps, integrate.romb]
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242,894 | hobson/pug-invest | pug/invest/util.py | square_off | def square_off(series, time_delta=None, transition_seconds=1):
"""Insert samples in regularly sampled data to produce stairsteps from ramps when plotted.
New samples are 1 second (1e9 ns) before each existing samples, to facilitate plotting and sorting
>>> square_off(pd.Series(range(3), index=pd.date_rang... | python | def square_off(series, time_delta=None, transition_seconds=1):
"""Insert samples in regularly sampled data to produce stairsteps from ramps when plotted.
New samples are 1 second (1e9 ns) before each existing samples, to facilitate plotting and sorting
>>> square_off(pd.Series(range(3), index=pd.date_rang... | [
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... time_delta... | [
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242,895 | hobson/pug-invest | pug/invest/util.py | join_time_series | def join_time_series(serieses, ignore_year=False, T_s=None, aggregator='mean'):
"""Combine a dict of pd.Series objects into a single pd.DataFrame with optional downsampling
FIXME:
For ignore_year and multi-year data, the index (in seconds) is computed assuming
366 days per year (leap year). So 3 ou... | python | def join_time_series(serieses, ignore_year=False, T_s=None, aggregator='mean'):
"""Combine a dict of pd.Series objects into a single pd.DataFrame with optional downsampling
FIXME:
For ignore_year and multi-year data, the index (in seconds) is computed assuming
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242,896 | hobson/pug-invest | pug/invest/util.py | smooth | def smooth(x, window_len=11, window='hanning', fill='reflect'):
"""smooth the data using a window with requested size.
Convolve a normalized window with the signal.
input:
x: signal to be smoothed
window_len: the width of the smoothing window
window: the type of window from 'flat',... | python | def smooth(x, window_len=11, window='hanning', fill='reflect'):
"""smooth the data using a window with requested size.
Convolve a normalized window with the signal.
input:
x: signal to be smoothed
window_len: the width of the smoothing window
window: the type of window from 'flat',... | [
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242,897 | hobson/pug-invest | pug/invest/util.py | fuzzy_index_match | def fuzzy_index_match(possiblities, label, **kwargs):
"""Find the closest matching column label, key, or integer indexed value
Returns:
type(label): sequence of immutable objects corresponding to best matches to each object in label
if label is an int returns the object (value) in the list ... | python | def fuzzy_index_match(possiblities, label, **kwargs):
"""Find the closest matching column label, key, or integer indexed value
Returns:
type(label): sequence of immutable objects corresponding to best matches to each object in label
if label is an int returns the object (value) in the list ... | [
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242,898 | hobson/pug-invest | pug/invest/util.py | make_dataframe | def make_dataframe(obj, columns=None, exclude=None, limit=1e8):
"""Coerce an iterable, queryset, list or rows, dict of columns, etc into a Pandas DataFrame"""
try:
obj = obj.objects.all()[:limit]
except:
pass
if isinstance(obj, (pd.Series, list, tuple)):
return make_dataframe(pd.... | python | def make_dataframe(obj, columns=None, exclude=None, limit=1e8):
"""Coerce an iterable, queryset, list or rows, dict of columns, etc into a Pandas DataFrame"""
try:
obj = obj.objects.all()[:limit]
except:
pass
if isinstance(obj, (pd.Series, list, tuple)):
return make_dataframe(pd.... | [
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242,899 | armstrong/armstrong.apps.related_content | armstrong/apps/related_content/managers.py | RelatedContentQuerySet.filter | def filter(self, destination_object=None, source_object=None, **kwargs):
"""
See ``QuerySet.filter`` for full documentation
This adds support for ``destination_object`` and ``source_object``
as kwargs. This converts those objects into the values necessary
to handle the ``Generi... | python | def filter(self, destination_object=None, source_object=None, **kwargs):
"""
See ``QuerySet.filter`` for full documentation
This adds support for ``destination_object`` and ``source_object``
as kwargs. This converts those objects into the values necessary
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