Search is not available for this dataset
identifier stringlengths 1 155 | parameters stringlengths 2 6.09k | docstring stringlengths 11 63.4k | docstring_summary stringlengths 0 63.4k | function stringlengths 29 99.8k | function_tokens list | start_point list | end_point list | language stringclasses 1
value | docstring_language stringlengths 2 7 | docstring_language_predictions stringlengths 18 23 | is_langid_reliable stringclasses 2
values |
|---|---|---|---|---|---|---|---|---|---|---|---|
pp_options_list | (keys, width=80, _print=False) | Builds a concise listing of available options, grouped by prefix | Builds a concise listing of available options, grouped by prefix | def pp_options_list(keys, width=80, _print=False):
""" Builds a concise listing of available options, grouped by prefix """
from textwrap import wrap
from itertools import groupby
def pp(name, ks):
pfx = ('- ' + name + '.[' if name else '')
ls = wrap(', '.join(ks), width, initial_inden... | [
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"'-... | [
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config_prefix | (prefix) | contextmanager for multiple invocations of API with a common prefix
supported API functions: (register / get / set )__option
Warning: This is not thread - safe, and won't work properly if you import
the API functions into your module using the "from x import y" construct.
Example:
import ibis.confi... | contextmanager for multiple invocations of API with a common prefix
supported API functions: (register / get / set )__option
Warning: This is not thread - safe, and won't work properly if you import
the API functions into your module using the "from x import y" construct.
Example:
import ibis.confi... | def config_prefix(prefix):
"""contextmanager for multiple invocations of API with a common prefix
supported API functions: (register / get / set )__option
Warning: This is not thread - safe, and won't work properly if you import
the API functions into your module using the "from x import y" construct.
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is_type_factory | (_type) |
Parameters
----------
`_type` - a type to be compared against (e.g. type(x) == `_type`)
Returns
-------
validator - a function of a single argument x , which returns the
True if type(x) is equal to `_type`
|
Parameters
----------
`_type` - a type to be compared against (e.g. type(x) == `_type`)
Returns
-------
validator - a function of a single argument x , which returns the
True if type(x) is equal to `_type`
| def is_type_factory(_type):
"""
Parameters
----------
`_type` - a type to be compared against (e.g. type(x) == `_type`)
Returns
-------
validator - a function of a single argument x , which returns the
True if type(x) is equal to `_type`
"""
def inner(x):
if ... | [
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is_instance_factory | (_type) |
Parameters
----------
`_type` - the type to be checked against
Returns
-------
validator - a function of a single argument x , which returns the
True if x is an instance of `_type`
|
Parameters
----------
`_type` - the type to be checked against
Returns
-------
validator - a function of a single argument x , which returns the
True if x is an instance of `_type`
| def is_instance_factory(_type):
"""
Parameters
----------
`_type` - the type to be checked against
Returns
-------
validator - a function of a single argument x , which returns the
True if x is an instance of `_type`
"""
if isinstance(_type, (tuple, list)):
_t... | [
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Get_License.getHwAddr | (self, ifname) |
获取主机物理地址
|
获取主机物理地址
| def getHwAddr(self, ifname):
"""
获取主机物理地址
"""
s = socket.socket(socket.AF_INET, socket.SOCK_DGRAM)
info = fcntl.ioctl(s.fileno(), 0x8927, struct.pack('256s', ifname[:15]))
return ''.join(['%02x' % ord(char) for char in info[18:24]]) | [
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Get_License.decrypt | (self, text) |
从.lic中解密出主机地址
|
从.lic中解密出主机地址
| def decrypt(self, text):
"""
从.lic中解密出主机地址
"""
try:
cryptor = AES.new(self.aesKey, self.aesMode, self.aesIv)
plain_text = cryptor.decrypt(a2b_hex(text))
return plain_text.rstrip('\0')
except:
return "" | [
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simple_get | (url) |
Attempts to get the content at `url` by making an HTTP GET request.
If the content-type of response is some kind of HTML/XML, return the
text content, otherwise return None.
|
Attempts to get the content at `url` by making an HTTP GET request.
If the content-type of response is some kind of HTML/XML, return the
text content, otherwise return None.
| def simple_get(url):
"""
Attempts to get the content at `url` by making an HTTP GET request.
If the content-type of response is some kind of HTML/XML, return the
text content, otherwise return None.
"""
try:
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is_good_response | (resp) |
Returns True if the response seems to be HTML, False otherwise.
|
Returns True if the response seems to be HTML, False otherwise.
| def is_good_response(resp):
"""
Returns True if the response seems to be HTML, False otherwise.
"""
content_type = resp.headers['Content-Type'].lower()
return (resp.status_code == 200
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create_udf_node | (name, fields) | Create a new UDF node type.
Parameters
----------
name : str
Then name of the UDF node
fields : OrderedDict
Mapping of class member name to definition
Returns
-------
result : type
A new BigQueryUDFNode subclass
| Create a new UDF node type. | def create_udf_node(name, fields):
"""Create a new UDF node type.
Parameters
----------
name : str
Then name of the UDF node
fields : OrderedDict
Mapping of class member name to definition
Returns
-------
result : type
A new BigQueryUDFNode subclass
"""
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udf | (input_type, output_type, strict=True, libraries=None) | Define a UDF for BigQuery
Parameters
----------
input_type : List[DataType]
output_type : DataType
strict : bool
Whether or not to put a ``'use strict';`` string at the beginning of
the UDF. Setting to ``False`` is probably a bad idea.
libraries : List[str]
A list of Goo... | Define a UDF for BigQuery | def udf(input_type, output_type, strict=True, libraries=None):
'''Define a UDF for BigQuery
Parameters
----------
input_type : List[DataType]
output_type : DataType
strict : bool
Whether or not to put a ``'use strict';`` string at the beginning of
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test_limited_fetches | (started_cluster) |
Test checks that that we utilize all available threads for fetches
|
Test checks that that we utilize all available threads for fetches
| def test_limited_fetches(started_cluster):
"""
Test checks that that we utilize all available threads for fetches
"""
node1.query("CREATE TABLE t (key UInt64, data String) ENGINE = ReplicatedMergeTree('/clickhouse/test/t', '1') ORDER BY tuple() PARTITION BY key")
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FileSock.readline | (self) | may be optimized... | may be optimized... | def readline(self):
# print("readline!")
"""may be optimized..."""
s=bytes()
while True:
c=self.read(1)
s+=c
if len(c)==0 or chr(c[0])=='\n':
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Server.one_function | (self) |
Executes a single function with associated I/O.
Protocol:
- the arguments and results are serialized with the pickle protocol
- client sends : (fname,args)
fname = method name to call
args = tuple of arguments
- server sends result: (rid,st,ret)
... |
Executes a single function with associated I/O.
Protocol:
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fname = method name to call
args = tuple of arguments
- server sends result: (rid,st,ret)
... | def one_function(self):
"""
Executes a single function with associated I/O.
Protocol:
- the arguments and results are serialized with the pickle protocol
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fname = method name to call
args = tuple of arguments
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Server.exec_loop | (self) | main execution loop. Loops and handles exit states | main execution loop. Loops and handles exit states | def exec_loop(self):
""" main execution loop. Loops and handles exit states"""
self.log("in exec_loop")
try:
while True:
self.one_function()
except ClientExit as e:
self.log("ClientExit %s"%e)
except socket.error as e:
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get_env | (env_id, **kwargs) |
Get environment
Parameters
----------
env_id: str
Environment identifier.
kwargs: dict
Parameters of the environment
|
Get environment | def get_env(env_id, **kwargs):
"""
Get environment
Parameters
----------
env_id: str
Environment identifier.
kwargs: dict
Parameters of the environment
"""
env = gym.make(env_id, **kwargs)
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check_inputs | (in1, in2, flags) |
Perform checking on the user provided inputs and diagnose any abnormalities
|
Perform checking on the user provided inputs and diagnose any abnormalities
| def check_inputs(in1, in2, flags):
"""
Perform checking on the user provided inputs and diagnose any abnormalities
"""
in1_kind, in1_err = classify_input_file(in1)
in2_kind, in2_err = classify_input_file(in2)
output_file = find_benchmark_flag('--benchmark_out=', flags)
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psql_server | (psql_client) | Return PostgreSQL container when it is healthy. | Return PostgreSQL container when it is healthy. | def psql_server(psql_client):
"""Return PostgreSQL container when it is healthy."""
retries = 30
for i in range(retries):
info = psql_client.client.api.inspect_container(psql_client.name)
if info['State']['Health']['Status'] == 'healthy':
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NSGAII.__init__ | (self, env, params) |
NSGA-II Algorithm based on the implementation in the Pymoo library.
Parameters
----------
env: BaseEnv
The learning environment.
params: dict
All experiment params
Attributes
----------
layers: tuple of ints
Describe... |
NSGA-II Algorithm based on the implementation in the Pymoo library. | def __init__(self, env, params):
"""
NSGA-II Algorithm based on the implementation in the Pymoo library.
Parameters
----------
env: BaseEnv
The learning environment.
params: dict
All experiment params
Attributes
----------
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NSGAII.act | (self, state, deterministic=False) |
Policy that uses the learned critics.
Parameters
----------
state: 1D nd.array
Current state.
deterministic: bool
Whether the policy should be deterministic (e.g. in evaluation mode).
Returns
-------
action: nd.array
... |
Policy that uses the learned critics. | def act(self, state, deterministic=False):
"""
Policy that uses the learned critics.
Parameters
----------
state: 1D nd.array
Current state.
deterministic: bool
Whether the policy should be deterministic (e.g. in evaluation mode).
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NSGAII.learn | (self, num_train_steps) |
Main training loop.
Parameters
----------
num_train_steps: int
Number of training steps (environment steps)
Returns
-------
|
Main training loop. | def learn(self, num_train_steps):
"""
Main training loop.
Parameters
----------
num_train_steps: int
Number of training steps (environment steps)
Returns
-------
"""
self.res_run = minimize(problem=self.nsga_problem,
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load_courses_into_db | (apps, schema_editor) | Saves all courses in AVAIL_COURSES to the database. | Saves all courses in AVAIL_COURSES to the database. | def load_courses_into_db(apps, schema_editor):
'''Saves all courses in AVAIL_COURSES to the database.'''
# We can't import the Course model directly as it may be a newer
# version than this migration expects. We use the historical version.
Course = apps.get_model('coursetracker', 'Course')
print(''... | [
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load_data_files | () | Loads the data files into global variables. | Loads the data files into global variables. | def load_data_files():
'''Loads the data files into global variables.'''
return (_load_json(AVAILABLE_COURSES_FN), _load_json(COURSE_INFORMATION_FN),
_load_json(COURSE_STATISTICS_FN), _load_json(GRADE_DISTRIBUTIONS_FN),
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_load_json | (filename) | Returns the objects stored in a json file. | Returns the objects stored in a json file. | def _load_json(filename):
'''Returns the objects stored in a json file.'''
with open(os.path.join(DATA_DIR_PATH, filename), 'r') as json_file:
return json.load(json_file) | [
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save_course_instance | (Course, course_name, course_info, course_stats, grade_distrs, prof_info, teaching_team) | Creates and save a Course object to the database.
Inputs:
- Course (model)
- course_name (str): all caps, may have a detail (i.e., APSC 496D), or not (i.e., MATH 210)
- course_info, course_stats, grade_distrs, prof_info, teaching_team: read from json files; see the data
repository... | Creates and save a Course object to the database. | def save_course_instance(Course, course_name, course_info, course_stats, grade_distrs, prof_info, teaching_team):
'''Creates and save a Course object to the database.
Inputs:
- Course (model)
- course_name (str): all caps, may have a detail (i.e., APSC 496D), or not (i.e., MATH 210)
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_get_grades_str | (distribution_dict) | Returns a json string of the grade distribution list. There are 11 elements, in the following order:
[<50%, 50-54%, 55-59%, 60-63%, 64-67%, 68-71%, 72-75%, 76-79%, 80-84%, 85-89%, 90-100%]
| Returns a json string of the grade distribution list. There are 11 elements, in the following order:
[<50%, 50-54%, 55-59%, 60-63%, 64-67%, 68-71%, 72-75%, 76-79%, 80-84%, 85-89%, 90-100%]
| def _get_grades_str(distribution_dict):
'''Returns a json string of the grade distribution list. There are 11 elements, in the following order:
[<50%, 50-54%, 55-59%, 60-63%, 64-67%, 68-71%, 72-75%, 76-79%, 80-84%, 85-89%, 90-100%]
'''
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_get_prof_ratings | (sections_teaching_team, prof_info) | Returns the professor ratings list. See _append_prof_rating() for the format of each element in
this list.
| Returns the professor ratings list. See _append_prof_rating() for the format of each element in
this list.
| def _get_prof_ratings(sections_teaching_team, prof_info):
'''Returns the professor ratings list. See _append_prof_rating() for the format of each element in
this list.
'''
teaching_team_list = _get_teaching_team_list(sections_teaching_team)
prof_ratings = []
for full_name in teaching_team_list:
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_get_teaching_team_list | (sections_teaching_team) | Returns an alphabetical list of all teaching team members in sections_teaching_team.
Inputs:
- sections_teaching_team (dict): {section number: teaching team for that section (list)}
| Returns an alphabetical list of all teaching team members in sections_teaching_team. | def _get_teaching_team_list(sections_teaching_team):
'''Returns an alphabetical list of all teaching team members in sections_teaching_team.
Inputs:
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teaching_team_list = []
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_append_prof_rating | (prof_ratings, prof_name, prof_name_info, is_same_name=False) | Appends a dictionary with the keys: name, rating, number of ratings, and link of a professor to prof_ratings.
- If is_same_name == True, adds the professor's department to their name
- This is required because there may be multiple prof_name_info sections for a name
- Either the prof... | Appends a dictionary with the keys: name, rating, number of ratings, and link of a professor to prof_ratings.
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- This is required because there may be multiple prof_name_info sections for a name
- Either the prof... | def _append_prof_rating(prof_ratings, prof_name, prof_name_info, is_same_name=False):
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_create_preq_tree | (course_name, course_info) |
Receives a Course module and course_info dictionary as parameters, and returns a prerequisite tree dictionary
This includes not only the immediate prequisites of the paramater, but also all prerequisites
for all courses connected.
For example, MATH 200 requires MATH 150, and MATH 101.
- Additi... |
Receives a Course module and course_info dictionary as parameters, and returns a prerequisite tree dictionary
This includes not only the immediate prequisites of the paramater, but also all prerequisites
for all courses connected. | def _create_preq_tree(course_name, course_info):
'''
Receives a Course module and course_info dictionary as parameters, and returns a prerequisite tree dictionary
This includes not only the immediate prequisites of the paramater, but also all prerequisites
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privilege_granted_directly_or_via_role | (self, table_type, node=None) | Check that user is only able to execute OPTIMIZE when they have required privilege, either directly or via role.
| Check that user is only able to execute OPTIMIZE when they have required privilege, either directly or via role.
| def privilege_granted_directly_or_via_role(self, table_type, node=None):
"""Check that user is only able to execute OPTIMIZE when they have required privilege, either directly or via role.
"""
role_name = f"role_{getuid()}"
user_name = f"user_{getuid()}"
if node is None:
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privilege_check | (grant_target_name, user_name, table_type, node=None) | Run scenarios to check the user's access with different privileges.
| Run scenarios to check the user's access with different privileges.
| def privilege_check(grant_target_name, user_name, table_type, node=None):
"""Run scenarios to check the user's access with different privileges.
"""
exitcode, message = errors.not_enough_privileges(name=f"{user_name}")
with Scenario("user without privilege"):
table_name = f"merge_tree_{getuid()... | [
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feature | (self, node="clickhouse1", stress=None, parallel=None) | Check the RBAC functionality of OPTIMIZE.
| Check the RBAC functionality of OPTIMIZE.
| def feature(self, node="clickhouse1", stress=None, parallel=None):
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self.context.node = self.context.cluster.node(node)
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Question.validate_question_type | (cls, value: str) | Checks if question type in currently allowed types list. | Checks if question type in currently allowed types list. | def validate_question_type(cls, value: str) -> t.Optional[str]:
"""Checks if question type in currently allowed types list."""
value = value.lower()
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Question.validate_question_data | (
cls,
value: dict[str, t.Any]
) | Check does required data exists for question type and remove other data. | Check does required data exists for question type and remove other data. | def validate_question_data(
cls,
value: dict[str, t.Any]
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checkSketchlibVersion | () | Checks that sketchlib can be run, and returns version
Returns:
version (str)
Version string
| Checks that sketchlib can be run, and returns version | def checkSketchlibVersion():
"""Checks that sketchlib can be run, and returns version
Returns:
version (str)
Version string
"""
try:
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# Older versions didn't export attributes
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checkSketchlibLibrary | () | Gets the location of the sketchlib library
Returns:
lib (str)
Location of sketchlib .so/.dyld
| Gets the location of the sketchlib library | def checkSketchlibLibrary():
"""Gets the location of the sketchlib library
Returns:
lib (str)
Location of sketchlib .so/.dyld
"""
sketchlib_loc = pp_sketchlib.__file__
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createDatabaseDir | (outPrefix, kmers) | Creates the directory to write sketches to, removing old files if unnecessary
Args:
outPrefix (str)
output db prefix
kmers (list)
k-mer sizes in db
| Creates the directory to write sketches to, removing old files if unnecessary | def createDatabaseDir(outPrefix, kmers):
"""Creates the directory to write sketches to, removing old files if unnecessary
Args:
outPrefix (str)
output db prefix
kmers (list)
k-mer sizes in db
"""
# check for writing
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# remo... | [
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getSketchSize | (dbPrefix) | Determine sketch size, and ensures consistent in whole database
``sys.exit(1)`` is called if DBs have different sketch sizes
Args:
dbprefix (str)
Prefix for mash databases
Returns:
sketchSize (int)
sketch size (64x C++ definition)
codonPhased (bool)
... | Determine sketch size, and ensures consistent in whole database | def getSketchSize(dbPrefix):
"""Determine sketch size, and ensures consistent in whole database
``sys.exit(1)`` is called if DBs have different sketch sizes
Args:
dbprefix (str)
Prefix for mash databases
Returns:
sketchSize (int)
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getKmersFromReferenceDatabase | (dbPrefix) | Get kmers lengths from existing database
Args:
dbPrefix (str)
Prefix for sketch DB files
Returns:
kmers (list)
List of k-mer lengths used in database
| Get kmers lengths from existing database | def getKmersFromReferenceDatabase(dbPrefix):
"""Get kmers lengths from existing database
Args:
dbPrefix (str)
Prefix for sketch DB files
Returns:
kmers (list)
List of k-mer lengths used in database
"""
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readDBParams | (dbPrefix) | Get kmers lengths and sketch sizes from existing database
Calls :func:`~getKmersFromReferenceDatabase` and :func:`~getSketchSize`
Uses passed values if db missing
Args:
dbPrefix (str)
Prefix for sketch DB files
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Calls :func:`~getKmersFromReferenceDatabase` and :func:`~getSketchSize`
Uses passed values if db missing
Args:
dbPrefix (str)
Prefix for sketch DB files
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kmers (list)
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getSeqsInDb | (dbname) | Return an array with the sequences in the passed database
Args:
dbname (str)
Sketches database filename
Returns:
seqs (list)
List of sequence names in sketch DB
| Return an array with the sequences in the passed database | def getSeqsInDb(dbname):
"""Return an array with the sequences in the passed database
Args:
dbname (str)
Sketches database filename
Returns:
seqs (list)
List of sequence names in sketch DB
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joinDBs | (db1, db2, output, update_random = None) | Join two sketch databases with the low-level HDF5 copy interface
Args:
db1 (str)
Prefix for db1
db2 (str)
Prefix for db2
output (str)
Prefix for joined output
update_random (dict)
Whether to re-calculate the random object. May contain
... | Join two sketch databases with the low-level HDF5 copy interface | def joinDBs(db1, db2, output, update_random = None):
"""Join two sketch databases with the low-level HDF5 copy interface
Args:
db1 (str)
Prefix for db1
db2 (str)
Prefix for db2
output (str)
Prefix for joined output
update_random (dict)
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removeFromDB | (db_name, out_name, removeSeqs, full_names = False) | Remove sketches from the DB the low-level HDF5 copy interface
Args:
db_name (str)
Prefix for hdf database
out_name (str)
Prefix for output (pruned) database
removeSeqs (list)
Names of sequences to remove from database
full_names (bool)
... | Remove sketches from the DB the low-level HDF5 copy interface | def removeFromDB(db_name, out_name, removeSeqs, full_names = False):
"""Remove sketches from the DB the low-level HDF5 copy interface
Args:
db_name (str)
Prefix for hdf database
out_name (str)
Prefix for output (pruned) database
removeSeqs (list)
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constructDatabase | (assemblyList, klist, sketch_size, oPrefix,
threads, overwrite,
strand_preserved, min_count,
use_exact, qc_dict, calc_random = True,
codon_phased = False,
use_gpu = False, deviceid = 0) | Sketch the input assemblies at the requested k-mer lengths
A multithread wrapper around :func:`~runSketch`. Threads are used to either run multiple sketch
processes for each klist value, or increase the threads used by each ``mash sketch`` process
if len(klist) > threads.
Also calculates random match ... | Sketch the input assemblies at the requested k-mer lengths | def constructDatabase(assemblyList, klist, sketch_size, oPrefix,
threads, overwrite,
strand_preserved, min_count,
use_exact, qc_dict, calc_random = True,
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addRandom | (oPrefix, sequence_names, klist,
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Args:
oPrefix (str)
Sketch database prefix
sequence_names (list)
Names of sequences to include in calculation
klist (list)
List of k-mer sizes to sketch
strand_preserved (bool)
Set true to... | Add chance of random match to a HDF5 sketch DB | def addRandom(oPrefix, sequence_names, klist,
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Sketch database prefix
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queryDatabase | (rNames, qNames, dbPrefix, queryPrefix, klist, self = True, number_plot_fits = 0,
threads = 1, use_gpu = False, deviceid = 0) | Calculate core and accessory distances between query sequences and a sketched database
For a reference database, runs the query against itself to find all pairwise
core and accessory distances.
Uses the relation :math:`pr(a, b) = (1-a)(1-c)^k`
To get the ref and query name for each row of the returne... | Calculate core and accessory distances between query sequences and a sketched database | def queryDatabase(rNames, qNames, dbPrefix, queryPrefix, klist, self = True, number_plot_fits = 0,
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pickTypeIsolate | (prefix, names) | Selects a type isolate as that with a minimal proportion
of missing data.
Args:
prefix (str)
Prefix of output files
names (list)
Names of samples to QC
Returns:
type_isolate (str)
Name of isolate selected as reference
| Selects a type isolate as that with a minimal proportion
of missing data. | def pickTypeIsolate(prefix, names):
"""Selects a type isolate as that with a minimal proportion
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Args:
prefix (str)
Prefix of output files
names (list)
Names of samples to QC
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type_isolate (str)
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sketchlibAssemblyQC | (prefix, names, klist, qc_dict, strand_preserved, threads) | Calculates random match probability based on means of genomes
in assemblyList, and looks for length outliers.
Args:
prefix (str)
Prefix of output files
names (list)
Names of samples to QC
klist (list)
List of k-mer sizes to sketch
qc_dict (dic... | Calculates random match probability based on means of genomes
in assemblyList, and looks for length outliers. | def sketchlibAssemblyQC(prefix, names, klist, qc_dict, strand_preserved, threads):
"""Calculates random match probability based on means of genomes
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Names of samples... | [
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fitKmerCurve | (pairwise, klist, jacobian) | Fit the function :math:`pr = (1-a)(1-c)^k`
Supply ``jacobian = -np.hstack((np.ones((klist.shape[0], 1)), klist.reshape(-1, 1)))``
Args:
pairwise (numpy.array)
Proportion of shared k-mers at k-mer values in klist
klist (list)
k-mer sizes used
jacobian (numpy.arra... | Fit the function :math:`pr = (1-a)(1-c)^k` | def fitKmerCurve(pairwise, klist, jacobian):
"""Fit the function :math:`pr = (1-a)(1-c)^k`
Supply ``jacobian = -np.hstack((np.ones((klist.shape[0], 1)), klist.reshape(-1, 1)))``
Args:
pairwise (numpy.array)
Proportion of shared k-mers at k-mer values in klist
klist (list)
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TestCallbacks.test_transfer_pipe | (self) | transfer an index through a Unix pipe | transfer an index through a Unix pipe | def test_transfer_pipe(self):
""" transfer an index through a Unix pipe """
d, n = 32, 1000
x = np.random.uniform(size=(n, d)).astype('float32')
index = faiss.IndexFlatL2(d)
index.add(x)
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clear_events | (win) | clear all keys from psychopy
I've been having issues with keys remaining in psychopy's buffer,
being pulled in at a later time (thus, pressing the spacebar once
gets parsed as pressing it twice, in rapid succession). This takes a
brief pause, .1 seconds, to rapidly flip the window several times
(sh... | clear all keys from psychopy | def clear_events(win):
"""clear all keys from psychopy
I've been having issues with keys remaining in psychopy's buffer,
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calc_pct_correct | (raw_behavioral_path, idx, stim_df) | Calculate percent correct, grouped by scaling.
This is only intended for use during the training sessions, to give
participant a sense of how well they did.
Parameters
----------
raw_behavioral_path : str
The str to the hdf5 file that contains the behavioral results,
as saved by th... | Calculate percent correct, grouped by scaling. | def calc_pct_correct(raw_behavioral_path, idx, stim_df):
"""Calculate percent correct, grouped by scaling.
This is only intended for use during the training sessions, to give
participant a sense of how well they did.
Parameters
----------
raw_behavioral_path : str
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_convert_str | (list_of_strs) | convert strs to hdf5-savable format
python 3 strings are more complicated than python 2, see
http://docs.h5py.org/en/latest/strings.html and https://github.com/h5py/h5py/issues/892
| convert strs to hdf5-savable format | def _convert_str(list_of_strs):
"""convert strs to hdf5-savable format
python 3 strings are more complicated than python 2, see
http://docs.h5py.org/en/latest/strings.html and https://github.com/h5py/h5py/issues/892
"""
list_of_strs = np.array(list_of_strs)
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_insert_into_hdf5 | (f, key, value) | insert value into hdf5 file with given key
if you try to set a dataset that already exists, it raises an
exception, so this tries to create a dataset and, if it raises that
exception, pop off the corresponding key and set it anew
| insert value into hdf5 file with given key | def _insert_into_hdf5(f, key, value):
"""insert value into hdf5 file with given key
if you try to set a dataset that already exists, it raises an
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_set_params | (stimuli_path, idx_path, size=[1920, 1080], monitor='CBI-prisma-projector',
units='pix', fullscr=True, screen=[0], color=128, colorSpace='rgb255',
allowGUI=False, downsampled=False, **monitor_kwargs) | set the various experiment parameters
| set the various experiment parameters
| def _set_params(stimuli_path, idx_path, size=[1920, 1080], monitor='CBI-prisma-projector',
units='pix', fullscr=True, screen=[0], color=128, colorSpace='rgb255',
allowGUI=False, downsampled=False, **monitor_kwargs):
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_create_bar_mask | (bar_height, bar_width=200, fringe_proportion=.5) | Create central bar with raised-cosine edges.
| Create central bar with raised-cosine edges. | def _create_bar_mask(bar_height, bar_width=200, fringe_proportion=.5):
"""Create central bar with raised-cosine edges.
"""
x = np.linspace(-bar_width//2, bar_width//2, bar_width)
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_setup_run | (stimuli_path, idx_path, fix_deg_size=.25, screen_size_deg=73.45,
take_break=True, timings=[], start_from_stim=0, ecc_mask=False,
downsampled=False, **monitor_kwargs) | Setup the run.
Does the thigns that are constant across different tasks.
| Setup the run. | def _setup_run(stimuli_path, idx_path, fix_deg_size=.25, screen_size_deg=73.45,
take_break=True, timings=[], start_from_stim=0, ecc_mask=False,
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_explain_task | (win, expt_clock, comparison, fixation, text_height=50,
train_flag=False) | Draw some text explaining the task
| Draw some text explaining the task
| def _explain_task(win, expt_clock, comparison, fixation, text_height=50,
train_flag=False):
"""Draw some text explaining the task
"""
if comparison == 'met':
comp_text = "On this run, you'll be comparing two synthesized images."
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_end_run | (win, timings, text_height, expt_clock, train_flag=False) | End the run.
Do the things that are shared across task types.
| End the run. | def _end_run(win, timings, text_height, expt_clock, train_flag=False):
"""End the run.
Do the things that are shared across task types.
"""
if not train_flag:
visual.TextStim(win, "Run over.", height=text_height,
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run_split | (stimuli_path, idx_path, save_path, comparison,
on_msec_length=200, off_msec_length=(500, 500),
fix_deg_size=.25, screen_size_deg=73.45,
take_break=True, keys_pressed=[], timings=[],
start_from_stim=0, text_height=50, bar_deg_size=2,
train_flag=False... | r"""Run one run of the split task.
stimuli_path specifies the path of the unshuffled experiment stimuli, while
idx_path specifies the path of the shuffled indices to use for this run.
This function will load in the stimuli at stimuli_path and rearrange them
using the indices found at idx_path, then sim... | r"""Run one run of the split task. | def run_split(stimuli_path, idx_path, save_path, comparison,
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fix_deg_size=.25, screen_size_deg=73.45,
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expt | (stimuli_path, subj_name, sess_num, run_num, comparison,
output_dir="data/raw_behavioral", screen_size_pix=[3840, 2160],
screen_size_deg=73.45, take_break=True, text_height=50, screen=[0],
train_flag=False, ecc_mask=False, **kwargs) | run a full experiment
this just sets up the various paths, calls ``run``, and then saves
the output
| run a full experiment | def expt(stimuli_path, subj_name, sess_num, run_num, comparison,
output_dir="data/raw_behavioral", screen_size_pix=[3840, 2160],
screen_size_deg=73.45, take_break=True, text_height=50, screen=[0],
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valid_bind_dn | (self) | Check that LDAP users can login when `bind_dn` is valid.
| Check that LDAP users can login when `bind_dn` is valid.
| def valid_bind_dn(self):
"""Check that LDAP users can login when `bind_dn` is valid.
"""
servers = {
"openldap1": {
"host": "openldap1", "port": "389", "enable_tls": "no",
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invalid_bind_dn | (self) | Check that LDAP users can't login when `bind_dn` is invalid.
| Check that LDAP users can't login when `bind_dn` is invalid.
| def invalid_bind_dn(self):
"""Check that LDAP users can't login when `bind_dn` is invalid.
"""
servers = {
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"host": "openldap1", "port": "389", "enable_tls": "no",
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bind_dn_conflict_with_auth_dn | (self, timeout=60) | Check that an error is returned with both `bind_dn` and
`auth_dn_prefix` and `auth_dn_suffix` are specified at the same time.
| Check that an error is returned with both `bind_dn` and
`auth_dn_prefix` and `auth_dn_suffix` are specified at the same time.
| def bind_dn_conflict_with_auth_dn(self, timeout=60):
"""Check that an error is returned with both `bind_dn` and
`auth_dn_prefix` and `auth_dn_suffix` are specified at the same time.
"""
message = "DB::Exception: Deprecated 'auth_dn_prefix' and 'auth_dn_suffix' entries cannot be used with 'bind_dn' entry... | [
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"=",
"{",
"\"openldap1\"",
":",
"{",
"\"host\"... | [
53,
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67,
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feature | (self, node="clickhouse1") | Check LDAP server configuration.
| Check LDAP server configuration.
| def feature(self, node="clickhouse1"):
"""Check LDAP server configuration.
"""
self.context.node = self.context.cluster.node(node)
for scenario in loads(current_module(), Scenario):
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mapd_to_ibis_dtype | (mapd_dtype) |
Register MapD Data Types
mapd_dtype:
:return:
|
Register MapD Data Types | def mapd_to_ibis_dtype(mapd_dtype):
"""
Register MapD Data Types
mapd_dtype:
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MapDTable.metadata | (self) |
Return parsed results of DESCRIBE FORMATTED statement
Returns
-------
meta : TableMetadata
|
Return parsed results of DESCRIBE FORMATTED statement | def metadata(self):
"""
Return parsed results of DESCRIBE FORMATTED statement
Returns
-------
meta : TableMetadata
"""
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MapDTable.drop | (self) |
Drop the table from the database
|
Drop the table from the database
| def drop(self):
"""
Drop the table from the database
"""
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MapDTable.load_data | (self, df) |
Wraps the LOAD DATA DDL statement. Loads data into an MapD table from
pandas.DataFrame or pyarrow.Table
Parameters
----------
df: pandas.DataFrame or pyarrow.Table
Returns
-------
query : MapDQuery
|
Wraps the LOAD DATA DDL statement. Loads data into an MapD table from
pandas.DataFrame or pyarrow.Table | def load_data(self, df):
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Wraps the LOAD DATA DDL statement. Loads data into an MapD table from
pandas.DataFrame or pyarrow.Table
Parameters
----------
df: pandas.DataFrame or pyarrow.Table
Returns
-------
query : MapDQuery
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MapDTable.rename | (self, new_name, database=None) |
Rename table inside MapD. References to the old table are no longer
valid.
Parameters
----------
new_name : string
database : string
Returns
-------
renamed : MapDTable
|
Rename table inside MapD. References to the old table are no longer
valid. | def rename(self, new_name, database=None):
"""
Rename table inside MapD. References to the old table are no longer
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Parameters
----------
new_name : string
database : string
Returns
-------
renamed : MapDTable
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MapDTable.alter | (self, tbl_properties=None) |
Change setting and parameters of the table.
Parameters
----------
tbl_properties : dict, optional
Returns
-------
None (for now)
|
Change setting and parameters of the table. | def alter(self, tbl_properties=None):
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Change setting and parameters of the table.
Parameters
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tbl_properties : dict, optional
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None (for now)
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MapDClient.__init__ | (self, uri=None, user=None, password=None, host=None,
port=9091, database=None, protocol='binary',
execution_type=EXECUTION_TYPE_CURSOR) |
Parameters
----------
uri : str
user : str
password : str
host : str
port : int
database : str
protocol : {'binary', 'http', 'https'}
execution_type : {
EXECUTION_TYPE_ICP, EXECUTION_TYPE_ICP_GPU, EXECUTION_TYPE_CURSOR
}... | def __init__(self, uri=None, user=None, password=None, host=None,
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execution_type=EXECUTION_TYPE_CURSOR):
"""
Parameters
----------
uri : str
user : str
password : str
host : str
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MapDClient.close | (self) | Close MapD connection and drop any temporary objects | Close MapD connection and drop any temporary objects | def close(self):
"""Close MapD connection and drop any temporary objects"""
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MapDClient._build_ast | (self, expr, context) |
Required.
expr:
context:
:return:
|
Required. | def _build_ast(self, expr, context):
"""
Required.
expr:
context:
:return:
"""
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MapDClient._get_table_schema | (self, table_name, database=None) |
Parameters
----------
table_name : str
database : str
Returns
-------
schema : ibis Schema
| def _get_table_schema(self, table_name, database=None):
"""
Parameters
----------
table_name : str
database : str
Returns
-------
schema : ibis Schema
"""
table_name_ = table_name.split('.')
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MapDClient._execute | (self, query, results=True) |
query:
:return:
| def _execute(self, query, results=True):
"""
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MapDClient.create_database | (self, name, owner=None) |
Create a new MapD database
Parameters
----------
name : string
Database name
|
Create a new MapD database | def create_database(self, name, owner=None):
"""
Create a new MapD database
Parameters
----------
name : string
Database name
"""
statement = ddl.CreateDatabase(name, owner=owner)
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MapDClient.drop_database | (self, name, force=False) |
Drop an MapD database
Parameters
----------
name : string
Database name
force : boolean, default False
If False and there are any tables in this database, raises an
IntegrityError
|
Drop an MapD database | def drop_database(self, name, force=False):
"""
Drop an MapD database
Parameters
----------
name : string
Database name
force : boolean, default False
If False and there are any tables in this database, raises an
IntegrityError
"""
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MapDClient.create_user | (self, name, password, is_super=False) |
Create a new MapD user
Parameters
----------
name : string
User name
password : string
Password
is_super : bool
if user is a superuser
|
Create a new MapD user | def create_user(self, name, password, is_super=False):
"""
Create a new MapD user
Parameters
----------
name : string
User name
password : string
Password
is_super : bool
if user is a superuser
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MapDClient.alter_user | (self, name, password=None, is_super=None,
insert_access=None) |
Alter MapD user parameters
Parameters
----------
name : string
User name
password : string
Password
is_super : bool
If user is a superuser
insert_access : string
If users need to insert records to a database they do not ow... |
Alter MapD user parameters | def alter_user(self, name, password=None, is_super=None,
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Alter MapD user parameters
Parameters
----------
name : string
User name
password : string
Password
is_super : bool
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MapDClient.drop_user | (self, name) |
Drop an MapD user
Parameters
----------
name : string
Database name
|
Drop an MapD user | def drop_user(self, name):
"""
Drop an MapD user
Parameters
----------
name : string
Database name
"""
statement = ddl.DropUser(name)
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MapDClient.create_view | (self, name, expr, database=None) |
Create an MapD view from a table expression
Parameters
----------
name : string
expr : ibis TableExpr
database : string, default None
|
Create an MapD view from a table expression | def create_view(self, name, expr, database=None):
"""
Create an MapD view from a table expression
Parameters
----------
name : string
expr : ibis TableExpr
database : string, default None
"""
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MapDClient.drop_view | (self, name, database=None) |
Drop an MapD view
Parameters
----------
name : string
database : string, default None
|
Drop an MapD view | def drop_view(self, name, database=None):
"""
Drop an MapD view
Parameters
----------
name : string
database : string, default None
"""
statement = ddl.DropView(name, database=database)
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MapDClient.create_table | (self, table_name, obj=None, schema=None, database=None,
fragment_size=None, max_rows=None, page_size=None,
partitions=None, shard_count=None) |
Create a new table in MapD using an Ibis table expression.
Parameters
----------
table_name : string
obj : TableExpr or pandas.DataFrame, optional
If passed, creates table from select statement results
schema : ibis.Schema, optional
Mutually exclusiv... |
Create a new table in MapD using an Ibis table expression. | def create_table(self, table_name, obj=None, schema=None, database=None,
fragment_size=None, max_rows=None, page_size=None,
partitions=None, shard_count=None):
"""
Create a new table in MapD using an Ibis table expression.
Parameters
----------
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MapDClient.drop_table | (self, table_name, database=None, force=False) |
Drop an MapD table
Parameters
----------
table_name : string
database : string, default None (optional)
force : boolean, default False
Database may throw exception if table does not exist
Examples
--------
>>> table = 'my_table'
... |
Drop an MapD table | def drop_table(self, table_name, database=None, force=False):
"""
Drop an MapD table
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----------
table_name : string
database : string, default None (optional)
force : boolean, default False
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MapDClient.truncate_table | (self, table_name, database=None) |
Delete all rows from, but do not drop, an existing table
Parameters
----------
table_name : string
database : string, default None (optional)
|
Delete all rows from, but do not drop, an existing table | def truncate_table(self, table_name, database=None):
"""
Delete all rows from, but do not drop, an existing table
Parameters
----------
table_name : string
database : string, default None (optional)
"""
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MapDClient.drop_table_or_view | (self, name, database=None, force=False) |
Attempt to drop a relation that may be a view or table
|
Attempt to drop a relation that may be a view or table
| def drop_table_or_view(self, name, database=None, force=False):
"""
Attempt to drop a relation that may be a view or table
"""
try:
self.drop_table(name, database=database)
except Exception as e:
try:
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MapDClient.database | (self, name=None) | Connect to a database called `name`.
Parameters
----------
name : str, optional
The name of the database to connect to. If ``None``, return
the database named ``self.current_database``.
Returns
-------
db : Database
An :class:`ibis.cl... | Connect to a database called `name`. | def database(self, name=None):
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Parameters
----------
name : str, optional
The name of the database to connect to. If ``None``, return
the database named ``self.current_database``.
Returns
-------
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MapDClient.load_data | (self, table_name, obj, database=None, **kwargs) |
Wraps the LOAD DATA DDL statement. Loads data into an MapD table by
physically moving data files.
Parameters
----------
table_name : string
obj: pandas.DataFrame or pyarrow.Table
database : string, default None (optional)
|
Wraps the LOAD DATA DDL statement. Loads data into an MapD table by
physically moving data files. | def load_data(self, table_name, obj, database=None, **kwargs):
"""
Wraps the LOAD DATA DDL statement. Loads data into an MapD table by
physically moving data files.
Parameters
----------
table_name : string
obj: pandas.DataFrame or pyarrow.Table
database ... | [
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MapDClient.exists_table | (self, name, database=None) |
Determine if the indicated table or view exists
Parameters
----------
name : string
database : string, default None
Returns
-------
if_exists : boolean
|
Determine if the indicated table or view exists | def exists_table(self, name, database=None):
"""
Determine if the indicated table or view exists
Parameters
----------
name : string
database : string, default None
Returns
-------
if_exists : boolean
"""
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MapDClient.get_schema | (self, table_name, database=None) |
Return a Schema object for the indicated table and database
Parameters
----------
table_name : string
May be fully qualified
database : string, default None
Returns
-------
schema : ibis Schema
|
Return a Schema object for the indicated table and database | def get_schema(self, table_name, database=None):
"""
Return a Schema object for the indicated table and database
Parameters
----------
table_name : string
May be fully qualified
database : string, default None
Returns
-------
schema : i... | [
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fitDbScan | (X, min_samples, min_cluster_size, cache_out) | Function to fit DBSCAN model as an alternative to the Gaussian
Fits the DBSCAN model to the distances using hdbscan
Args:
X (np.array)
n x 2 array of core and accessory distances for n samples
min_samples (int)
Parameter for DBSCAN clustering 'conservativeness'
... | Function to fit DBSCAN model as an alternative to the Gaussian | def fitDbScan(X, min_samples, min_cluster_size, cache_out):
"""Function to fit DBSCAN model as an alternative to the Gaussian
Fits the DBSCAN model to the distances using hdbscan
Args:
X (np.array)
n x 2 array of core and accessory distances for n samples
min_samples (int)
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47,
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evaluate_dbscan_clusters | (model) | Evaluate whether fitted dbscan model contains non-overlapping clusters
Args:
model (DBSCANFit)
Fitted model from :func:`~PopPUNK.models.DBSCANFit.fit`
Returns:
indistinct (bool)
Boolean indicating whether putative within- and
between-strain clusters of point... | Evaluate whether fitted dbscan model contains non-overlapping clusters | def evaluate_dbscan_clusters(model):
"""Evaluate whether fitted dbscan model contains non-overlapping clusters
Args:
model (DBSCANFit)
Fitted model from :func:`~PopPUNK.models.DBSCANFit.fit`
Returns:
indistinct (bool)
Boolean indicating whether putative within- and
... | [
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findBetweenLabel | (assignments, within_cluster) | Identify between-strain links from a DBSCAN model
Finds the component containing the largest number of between-strain
links, excluding the cluster identified as containing within-strain
links.
Args:
assignments (numpy.array)
Sample cluster assignments
within_cluster (int)
... | Identify between-strain links from a DBSCAN model | def findBetweenLabel(assignments, within_cluster):
"""Identify between-strain links from a DBSCAN model
Finds the component containing the largest number of between-strain
links, excluding the cluster identified as containing within-strain
links.
Args:
assignments (numpy.array)
... | [
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hdfs_connect | (host='localhost', port=50070, protocol='webhdfs',
use_https='default', auth_mechanism='NOSASL',
verify=True, **kwds) |
Connect to HDFS
Parameters
----------
host : string, Host name of the HDFS NameNode
port : int, NameNode's WebHDFS port (default 50070)
protocol : {'webhdfs'}
use_https : boolean, default 'default'
Connect to WebHDFS with HTTPS, otherwise plain HTTP. For secure
authenticati... |
Connect to HDFS | def hdfs_connect(host='localhost', port=50070, protocol='webhdfs',
use_https='default', auth_mechanism='NOSASL',
verify=True, **kwds):
"""
Connect to HDFS
Parameters
----------
host : string, Host name of the HDFS NameNode
port : int, NameNode's WebHDFS port (d... | [
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feature | (self, node="clickhouse1") | Check grant privilege syntax.
```sql
GRANT [ON CLUSTER cluster_name]
privilege {SELECT | SELECT(columns) | INSERT | ALTER | CREATE | DROP | TRUNCATE | OPTIMIZE | SHOW | KILL QUERY | ACCESS MANAGEMENT | SYSTEM | INTROSPECTION | SOURCES | dictGet | NONE |ALL [PRIVILEGES]} [, ...]
ON {*.* | database.*... | Check grant privilege syntax. | def feature(self, node="clickhouse1"):
"""Check grant privilege syntax.
```sql
GRANT [ON CLUSTER cluster_name]
privilege {SELECT | SELECT(columns) | INSERT | ALTER | CREATE | DROP | TRUNCATE | OPTIMIZE | SHOW | KILL QUERY | ACCESS MANAGEMENT | SYSTEM | INTROSPECTION | SOURCES | dictGet | NONE |ALL ... | [
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133,
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] | python | en | ['en', 'it', 'en'] | True |
ParseNolintSuppressions | (filename, raw_line, linenum, error) | Updates the global list of line error-suppressions.
Parses any NOLINT comments on the current line, updating the global
error_suppressions store. Reports an error if the NOLINT comment
was malformed.
Args:
filename: str, the name of the input file.
raw_line: str, the line of input text, with comments... | Updates the global list of line error-suppressions. | def ParseNolintSuppressions(filename, raw_line, linenum, error):
"""Updates the global list of line error-suppressions.
Parses any NOLINT comments on the current line, updating the global
error_suppressions store. Reports an error if the NOLINT comment
was malformed.
Args:
filename: str, the name of th... | [
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"(",... | [
713,
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] | [
742,
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] | python | en | ['en', 'en', 'en'] | True |
ProcessGlobalSuppresions | (lines) | Updates the list of global error suppressions.
Parses any lint directives in the file that have global effect.
Args:
lines: An array of strings, each representing a line of the file, with the
last element being empty if the file is terminated with a newline.
| Updates the list of global error suppressions. | def ProcessGlobalSuppresions(lines):
"""Updates the list of global error suppressions.
Parses any lint directives in the file that have global effect.
Args:
lines: An array of strings, each representing a line of the file, with the
last element being empty if the file is terminated with a newline... | [
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760,
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ResetNolintSuppressions | () | Resets the set of NOLINT suppressions to empty. | Resets the set of NOLINT suppressions to empty. | def ResetNolintSuppressions():
"""Resets the set of NOLINT suppressions to empty."""
_error_suppressions.clear()
_global_error_suppressions.clear() | [
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763,
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766,
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IsErrorSuppressedByNolint | (category, linenum) | Returns true if the specified error category is suppressed on this line.
Consults the global error_suppressions map populated by
ParseNolintSuppressions/ProcessGlobalSuppresions/ResetNolintSuppressions.
Args:
category: str, the category of the error.
linenum: int, the current line number.
Returns:
... | Returns true if the specified error category is suppressed on this line. | def IsErrorSuppressedByNolint(category, linenum):
"""Returns true if the specified error category is suppressed on this line.
Consults the global error_suppressions map populated by
ParseNolintSuppressions/ProcessGlobalSuppresions/ResetNolintSuppressions.
Args:
category: str, the category of the error.
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