sequence stringlengths 557 12.7k | docstring stringlengths 4 15.2k |
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(module
(function_definition
(function_name__run_nucmer) function_name__run_nucmer
(parameters
(identifier_self) identifier_self
(identifier_ref) identifier_ref
(identifier_qry) identifier_qry
(identifier_outfile) identifier_outfile
)parameters
(block
(expression_statemen... | Run nucmer of new assembly vs original assembly |
(module
(function_definition
(function_name_remove_listener) function_name_remove_listener
(parameters
(identifier_self) identifier_self
(identifier_registration_id) identifier_registration_id
)parameters
(block
(try_statement
(block
(expression_statement
... | Removes a lifecycle listener.
:param registration_id: (str), the id of the listener to be removed.
:return: (bool), ``true`` if the listener is removed successfully, ``false`` otherwise. |
(module
(function_definition
(function_name_first_order_score) function_name_first_order_score
(parameters
(identifier_y) identifier_y
(identifier_mean) identifier_mean
(identifier_scale) identifier_scale
(identifier_shape) identifier_shape
(identifier_skewness) identifier_skewne... | GAS Laplace Update term using gradient only - native Python function
Parameters
----------
y : float
datapoint for the time series
mean : float
location parameter for the Laplace distribution
scale : float
scale parameter for the Laplace dis... |
(module
(function_definition
(function_name_load) function_name_load
(parameters
(identifier_self) identifier_self
(identifier_filename) identifier_filename
)parameters
(block
(try_statement
(block
(with_statement
(with_clause
(with_item
... | Load counters to file |
(module
(function_definition
(function_name_get_port_bindings) function_name_get_port_bindings
(parameters
(identifier_container_config) identifier_container_config
(identifier_client_config) identifier_client_config
)parameters
(block
(expression_statement
(assignment
... | Generates the input dictionary contents for the ``port_bindings`` argument.
:param container_config: Container configuration.
:type container_config: dockermap.map.config.container.ContainerConfiguration
:param client_config: Client configuration.
:type client_config: dockermap.map.config.client.Client... |
(module
(function_definition
(function_name_get) function_name_get
(parameters
(identifier_self) identifier_self
(default_parameter
(identifier_transform) identifier_transform
(None) None
)default_parameter
)parameters
(block
(if_statement
(boolean_opera... | Return the JSON defined at the S3 location in the constructor.
The get method will reload the S3 object after the TTL has
expired.
Fetch the JSON object from cache or S3 if necessary |
(module
(function_definition
(function_name__rle) function_name__rle
(parameters
(identifier_self) identifier_self
(identifier_a) identifier_a
)parameters
(block
(expression_statement
(assignment
(identifier_ia) identifier_ia
(call
(attribute
... | rle implementation credit to Thomas Browne from his SOF post Sept 2015
Parameters
----------
a : array, shape[n,]
input vector
Returns
-------
z : array, shape[nt,]
run lengths
p : array, shape[nt,]
start positions of each run... |
(module
(function_definition
(function_name_rand_bivar) function_name_rand_bivar
(parameters
(identifier_X) identifier_X
(identifier_rho) identifier_rho
)parameters
(block
(import_statement
(aliased_import
(dotted_name
(identifier_numpy) identifier_numpy... | Transform two unrelated random variables into correlated bivariate data
X : ndarray
two univariate random variables
with N observations as <N x 2> matrix
rho : float
The Pearson correlations coefficient
as number between [-1, +1] |
(module
(function_definition
(function_name_highlight) function_name_highlight
(parameters
(identifier_str1) identifier_str1
(identifier_str2) identifier_str2
)parameters
(block
(expression_statement
(call
(identifier_print) identifier_print
(argument_list... | Highlight str1 with the contents of str2. |
(module
(function_definition
(function_name_validate) function_name_validate
(parameters
(identifier_self) identifier_self
(identifier_value) identifier_value
)parameters
(block
(for_statement
(identifier_v) identifier_v
(attribute
(identifier_self) identifi... | checks the validity of 'value' given the lits of validators |
(module
(function_definition
(function_name_get_type_name) function_name_get_type_name
(parameters
(identifier_type_name) identifier_type_name
(default_parameter
(identifier_sub_type) identifier_sub_type
(None) None
)default_parameter
)parameters
(block
(if_stat... | Returns a go type according to a spec type |
(module
(function_definition
(function_name_medium_integer) function_name_medium_integer
(parameters
(identifier_self) identifier_self
(identifier_column) identifier_column
(default_parameter
(identifier_auto_increment) identifier_auto_increment
(False) False
)default_p... | Create a new medium integer column on the table.
:param column: The column
:type column: str
:type auto_increment: bool
:type unsigned: bool
:rtype: Fluent |
(module
(function_definition
(function_name_closest_pair) function_name_closest_pair
(parameters
(identifier_arr) identifier_arr
(default_parameter
(identifier_give) identifier_give
(string_"indicies") string_"indicies"
)default_parameter
)parameters
(block
(exp... | Find the pair of indices corresponding to the closest elements in an array.
If multiple pairs are equally close, both pairs of indicies are returned.
Optionally returns the closest distance itself.
I am sure that this could be written as a cheaper operation. I
wrote this as a quick and dirty method be... |
(module
(function_definition
(function_name_get_app_guid) function_name_get_app_guid
(parameters
(identifier_self) identifier_self
(identifier_app_name) identifier_app_name
)parameters
(block
(expression_statement
(assignment
(identifier_summary) identifier_summary
... | Returns the GUID for the app instance with
the given name. |
(module
(function_definition
(function_name_bcc) function_name_bcc
(parameters
(identifier_self) identifier_self
(identifier_bcc_emails) identifier_bcc_emails
(default_parameter
(identifier_global_substitutions) identifier_global_substitutions
(None) None
)default_param... | Adds Bcc objects to the Personalization object
:param bcc_emails: An Bcc or list of Bcc objects
:type bcc_emails: Bcc, list(Bcc), tuple
:param global_substitutions: A dict of substitutions for all recipients
:type global_substitutions: dict
:param is_multiple: Create a new perso... |
(module
(function_definition
(function_name_is_python_interpreter) function_name_is_python_interpreter
(parameters
(identifier_filename) identifier_filename
)parameters
(block
(expression_statement
(assignment
(identifier_real_filename) identifier_real_filename
... | Evaluate wether a file is a python interpreter or not. |
(module
(function_definition
(function_name_read_option_value_from_nibble) function_name_read_option_value_from_nibble
(parameters
(identifier_nibble) identifier_nibble
(identifier_pos) identifier_pos
(identifier_values) identifier_values
)parameters
(block
(if_statement
... | Calculates the value used in the extended option fields.
:param nibble: the 4-bit option header value.
:return: the value calculated from the nibble and the extended option value. |
(module
(function_definition
(function_name__ReadPropertySet) function_name__ReadPropertySet
(parameters
(identifier_self) identifier_self
(identifier_property_set) identifier_property_set
)parameters
(block
(for_statement
(identifier_property_section) identifier_property_sec... | Reads properties from a property set.
Args:
property_set (pyolecf.property_set): OLECF property set. |
(module
(function_definition
(function_name_login) function_name_login
(parameters
(identifier_username) identifier_username
(identifier_password) identifier_password
(dictionary_splat_pattern
(identifier_kwargs) identifier_kwargs
)dictionary_splat_pattern
)parameters
(... | Login a user, returning a dict containing their user_id and session_id
This does the DB login to check the credentials, and then creates a session
so that requests from apps do not need to perform a login
args:
username (string): The user's username
password(string): Th... |
(module
(function_definition
(function_name_count) function_name_count
(parameters
(identifier_data) identifier_data
(default_parameter
(identifier_axis) identifier_axis
(None) None
)default_parameter
)parameters
(block
(return_statement
(call
... | Count the number of non-NA in this array along the given axis or axes |
(module
(function_definition
(function_name_get_el) function_name_get_el
(parameters
(identifier_el) identifier_el
)parameters
(block
(expression_statement
(assignment
(identifier_tag_name) identifier_tag_name
(call
(attribute
(attribut... | Get value of given `el` tag element.
Automatically choose proper method to set the `value` based on the type
of the `el`.
Args:
el (obj): Element reference to the input you want to convert to
typeahead.
Returns:
str: Value of the object. |
(module
(function_definition
(function_name_dK_dr_via_X) function_name_dK_dr_via_X
(parameters
(identifier_self) identifier_self
(identifier_X) identifier_X
(identifier_X2) identifier_X2
)parameters
(block
(return_statement
(call
(attribute
(identi... | compute the derivative of K wrt X going through X |
(module
(function_definition
(function_name_plot) function_name_plot
(parameters
(identifier_self) identifier_self
(default_parameter
(identifier_title) identifier_title
(identifier_LABEL_DEFAULT) identifier_LABEL_DEFAULT
)default_parameter
(default_parameter
(i... | Create a Plot object representing the SArray.
Notes
-----
- The plot will render either inline in a Jupyter Notebook, or in a
native GUI window, depending on the value provided in
`turicreate.visualization.set_target` (defaults to 'auto').
Parameters
-------... |
(module
(function_definition
(function_name_delete_thumbnails) function_name_delete_thumbnails
(parameters
(identifier_relative_source_path) identifier_relative_source_path
(default_parameter
(identifier_root) identifier_root
(None) None
)default_parameter
(default_para... | Delete all thumbnails for a source image. |
(module
(function_definition
(function_name_where) function_name_where
(parameters
(identifier_cmd) identifier_cmd
(default_parameter
(identifier_path) identifier_path
(None) None
)default_parameter
)parameters
(block
(expression_statement
(assignment
... | A function to wrap shutil.which for universal usage |
(module
(function_definition
(function_name_mean_curve) function_name_mean_curve
(parameters
(identifier_values) identifier_values
(default_parameter
(identifier_weights) identifier_weights
(None) None
)default_parameter
)parameters
(block
(if_statement
... | Compute the mean by using numpy.average on the first axis. |
(module
(function_definition
(function_name_urlsafe_b64decode) function_name_urlsafe_b64decode
(parameters
(identifier_data) identifier_data
)parameters
(block
(expression_statement
(assignment
(identifier_pad) identifier_pad
(binary_operator
(string... | urlsafe_b64decode without padding |
(module
(function_definition
(function_name_calculate_descriptors) function_name_calculate_descriptors
(parameters
(identifier_self) identifier_self
(identifier_mol) identifier_mol
)parameters
(block
(expression_statement
(assignment
(attribute
(identifi... | Calculates descriptors such as logP, charges and MR and saves that in a dictionary. |
(module
(function_definition
(function_name__writeFeatures) function_name__writeFeatures
(parameters
(identifier_self) identifier_self
(identifier_i) identifier_i
(identifier_image) identifier_image
)parameters
(block
(expression_statement
(assignment
(identif... | Write a text file containing the features as a table.
@param i: The number of the image in self._images.
@param image: A member of self._images.
@return: The C{str} features file name - just the base name, not
including the path to the file. |
(module
(function_definition
(function_name_parse_pseudo_open) function_name_parse_pseudo_open
(parameters
(identifier_self) identifier_self
(identifier_sel) identifier_sel
(identifier_name) identifier_name
(identifier_has_selector) identifier_has_selector
(identifier_iselector) ... | Parse pseudo with opening bracket. |
(module
(function_definition
(function_name_list_processed_parameter_groups) function_name_list_processed_parameter_groups
(parameters
(identifier_self) identifier_self
)parameters
(block
(expression_statement
(assignment
(identifier_path) identifier_path
(call
... | Returns the existing parameter groups.
:rtype: ~collections.Iterable[str] |
(module
(function_definition
(function_name_rename) function_name_rename
(parameters
(identifier_store) identifier_store
(identifier_src_path) identifier_src_path
(identifier_dst_path) identifier_dst_path
)parameters
(block
(expression_statement
(assignment
(i... | Rename all items under the given path. If `store` provides a `rename` method,
this will be called, otherwise will fall back to implementation via the
`MutableMapping` interface. |
(module
(function_definition
(function_name_cycle) function_name_cycle
(parameters
(identifier_self) identifier_self
(identifier_channel) identifier_channel
)parameters
(block
(if_statement
(not_operator
(call
(attribute
(identifier_self) i... | Rejoin channel. |
(module
(function_definition
(function_name__set_scores) function_name__set_scores
(parameters
(identifier_self) identifier_self
)parameters
(block
(expression_statement
(assignment
(identifier_anom_scores) identifier_anom_scores
(dictionary
)dictionar... | Compute anomaly scores for the time series by sliding both lagging window and future window. |
(module
(function_definition
(function_name_Equals) function_name_Equals
(parameters
(identifier_self) identifier_self
(identifier_other) identifier_other
)parameters
(block
(if_statement
(comparison_operator
(identifier_other) identifier_other
(None) None... | Test for equality.
Args:
other (obj):
Returns:
bool: True `other` equals self. |
(module
(function_definition
(function_name_delete_state_changes) function_name_delete_state_changes
(parameters
(identifier_self) identifier_self
(typed_parameter
(identifier_state_changes_to_delete) identifier_state_changes_to_delete
(type
(generic_type
(ide... | Delete state changes.
Args:
state_changes_to_delete: List of ids to delete. |
(module
(function_definition
(function_name_get_real_end_line) function_name_get_real_end_line
(parameters
(identifier_token) identifier_token
)parameters
(block
(expression_statement
(assignment
(identifier_end_line) identifier_end_line
(binary_operator
... | Finds the line on which the token really ends.
With pyyaml, scalar tokens often end on a next line. |
(module
(function_definition
(function_name_get_msg) function_name_get_msg
(parameters
(identifier_self) identifier_self
)parameters
(block
(expression_statement
(assignment
(identifier_width) identifier_width
(integer_72) integer_72
)assignment
)e... | This method is used to prepare the preamble text to display to
the user in non-batch mode. If your policy sets self.distro that
text will be substituted accordingly. You can also override this
method to do something more complicated. |
(module
(function_definition
(function_name_handle_dataframe) function_name_handle_dataframe
(parameters
(typed_parameter
(identifier_df) identifier_df
(type
(attribute
(identifier_pd) identifier_pd
(identifier_DataFrame) identifier_DataFrame
)... | Convert data frame on differential expression values as Gene objects.
:param df: Data frame with columns showing values on differential
expression.
:param cfp: An object that includes paths, cutoffs and other information.
:return list: A list of Gene objects. |
(module
(function_definition
(function_name_build_routes) function_name_build_routes
(parameters
(identifier_pfeed) identifier_pfeed
)parameters
(block
(expression_statement
(assignment
(identifier_f) identifier_f
(call
(attribute
(call... | Given a ProtoFeed, return a DataFrame representing ``routes.txt``. |
(module
(function_definition
(function_name_transitive_reduction) function_name_transitive_reduction
(parameters
(identifier_self) identifier_self
)parameters
(block
(expression_statement
(assignment
(identifier_combinations) identifier_combinations
(list
... | Performs a transitive reduction on the DAG. The transitive
reduction of a graph is a graph with as few edges as possible with the
same reachability as the original graph.
See https://en.wikipedia.org/wiki/Transitive_reduction |
(module
(function_definition
(function_name_arity_evaluation_checker) function_name_arity_evaluation_checker
(parameters
(identifier_function) identifier_function
)parameters
(block
(expression_statement
(assignment
(identifier_is_class) identifier_is_class
(cal... | Build an evaluation checker that will return True when it is
guaranteed that all positional arguments have been accounted for. |
(module
(function_definition
(function_name_update_config_value) function_name_update_config_value
(parameters
(identifier_self) identifier_self
(identifier_config_m) identifier_config_m
(identifier_config_key) identifier_config_key
)parameters
(block
(expression_statement
... | Updates the corresponding list store of a changed config value
:param ConfigModel config_m: The config model that has been changed
:param str config_key: The config key who's value has been changed |
(module
(function_definition
(function_name_verify_param) function_name_verify_param
(parameters
(identifier_self) identifier_self
(identifier_param) identifier_param
(default_parameter
(identifier_must) identifier_must
(list
)list
)default_parameter
(defa... | return Code.ARGUMENT_MISSING if every key in must not found in param |
(module
(function_definition
(function_name_write_csvs) function_name_write_csvs
(parameters
(identifier_self) identifier_self
(identifier_asset_map) identifier_asset_map
(default_parameter
(identifier_show_progress) identifier_show_progress
(False) False
)default_param... | Read CSVs as DataFrames from our asset map.
Parameters
----------
asset_map : dict[int -> str]
A mapping from asset id to file path with the CSV data for that
asset
show_progress : bool
Whether or not to show a progress bar while writing.
inva... |
(module
(function_definition
(function_name_decrypt) function_name_decrypt
(parameters
(identifier_self) identifier_self
(identifier_data) identifier_data
)parameters
(block
(expression_statement
(assignment
(identifier_decrypted_data) identifier_decrypted_data
... | DES decrypts the data based on the key it was initialised with.
:param data: The encrypted bytes string to decrypt
:return: The decrypted bytes string |
(module
(function_definition
(function_name_db) function_name_db
(parameters
(identifier_cls) identifier_cls
(default_parameter
(identifier_path) identifier_path
(None) None
)default_parameter
)parameters
(block
(if_statement
(boolean_operator
... | Returns a pymongo Collection object from the current database connection.
If the database connection is in test mode, collection will be in the
test database.
@param path: if is None, the PATH attribute of the current class is used;
if is not None, this is used instead
... |
(module
(function_definition
(function_name_recalibrate_quality) function_name_recalibrate_quality
(parameters
(identifier_bam_file) identifier_bam_file
(identifier_sam_ref) identifier_sam_ref
(identifier_dbsnp_file) identifier_dbsnp_file
(identifier_picard_dir) identifier_picard_dir
... | Recalibrate alignments with GATK and provide pdf summary. |
(module
(function_definition
(function_name_wait_for_task) function_name_wait_for_task
(parameters
(identifier_upid) identifier_upid
(default_parameter
(identifier_timeout) identifier_timeout
(integer_300) integer_300
)default_parameter
)parameters
(block
(expre... | Wait until a the task has been finished successfully |
(module
(function_definition
(function_name_sys_register_SDL_renderer) function_name_sys_register_SDL_renderer
(parameters
(typed_parameter
(identifier_callback) identifier_callback
(type
(generic_type
(identifier_Callable) identifier_Callable
(type_para... | Register a custom randering function with libtcod.
Note:
This callback will only be called by the SDL renderer.
The callack will receive a :any:`CData <ffi-cdata>` void* to an
SDL_Surface* struct.
The callback is called on every call to :any:`tcod.console_flush`.
Args:
callback C... |
(module
(function_definition
(function_name_bind_type) function_name_bind_type
(parameters
(identifier_python_value) identifier_python_value
)parameters
(block
(expression_statement
(assignment
(identifier_binding_table) identifier_binding_table
(dictionary
... | Return a Gibica type derived from a Python type. |
(module
(function_definition
(function_name_get_func_args) function_name_get_func_args
(parameters
(identifier_func) identifier_func
)parameters
(block
(if_statement
(call
(identifier_isinstance) identifier_isinstance
(argument_list
(identifier_func)... | Given a callable, return a tuple of argument names. Handles
`functools.partial` objects and class-based callables.
.. versionchanged:: 3.0.0a1
Do not return bound arguments, eg. ``self``. |
(module
(function_definition
(function_name_make_interval) function_name_make_interval
(parameters
(identifier_long_name) identifier_long_name
(identifier_short_name) identifier_short_name
)parameters
(block
(return_statement
(call
(attribute
(call
... | Create an interval segment |
(module
(function_definition
(function_name_samples) function_name_samples
(parameters
(identifier_self) identifier_self
)parameters
(block
(if_statement
(boolean_operator
(not_operator
(call
(identifier_hasattr) identifier_hasattr
... | Dataframe with samples drawn from isochrone according to posterior
Columns include both the sampling parameters from the MCMC
fit (mass, age, Fe/H, [distance, A_V]), and also evaluation
of the :class:`Isochrone` at each of these sample points---this
is how chains of physical/observable ... |
(module
(function_definition
(function_name__iter_keys) function_name__iter_keys
(parameters
(identifier_key) identifier_key
)parameters
(block
(for_statement
(identifier_i) identifier_i
(call
(identifier_range) identifier_range
(argument_list
... | ! Iterate over subkeys of a key |
(module
(function_definition
(function_name_primers) function_name_primers
(parameters
(identifier_self) identifier_self
(default_parameter
(identifier_tm) identifier_tm
(integer_60) integer_60
)default_parameter
)parameters
(block
(expression_statement
... | Design primers for amplifying the assembled sequence.
:param tm: melting temperature (lower than overlaps is best).
:type tm: float
:returns: Primer list (the output of coral.design.primers).
:rtype: list |
(module
(function_definition
(function_name_gborders) function_name_gborders
(parameters
(identifier_img) identifier_img
(default_parameter
(identifier_alpha) identifier_alpha
(float_1.0) float_1.0
)default_parameter
(default_parameter
(identifier_sigma) identif... | Stopping criterion for image borders. |
(module
(function_definition
(function_name_get_wsgi_request_object) function_name_get_wsgi_request_object
(parameters
(identifier_curr_request) identifier_curr_request
(identifier_method) identifier_method
(identifier_url) identifier_url
(identifier_headers) identifier_headers
(... | Based on the given request parameters, constructs and returns the WSGI request object. |
(module
(function_definition
(function_name_from_snl) function_name_from_snl
(parameters
(identifier_cls) identifier_cls
(identifier_snl) identifier_snl
)parameters
(block
(expression_statement
(assignment
(identifier_hist) identifier_hist
(list
... | Create TransformedStructure from SNL.
Args:
snl (StructureNL): Starting snl
Returns:
TransformedStructure |
(module
(function_definition
(function_name_get_tissue_in_references) function_name_get_tissue_in_references
(parameters
(identifier_self) identifier_self
(identifier_entry) identifier_entry
)parameters
(block
(expression_statement
(assignment
(identifier_tissue_in_... | get list of models.TissueInReference from XML node entry
:param entry: XML node entry
:return: list of :class:`pyuniprot.manager.models.TissueInReference` objects |
(module
(function_definition
(function_name_stream_members) function_name_stream_members
(parameters
(identifier_self) identifier_self
(identifier_stream_id) identifier_stream_id
)parameters
(block
(expression_statement
(assignment
(pattern_list
(identif... | get stream members |
(module
(function_definition
(function_name_process_binding_statements) function_name_process_binding_statements
(parameters
(identifier_self) identifier_self
)parameters
(block
(expression_statement
(assignment
(identifier_G) identifier_G
(attribute
... | Looks for Binding events in the graph and extracts them into INDRA
statements.
In particular, looks for a Binding event node with outgoing edges
with relations Theme and Theme2 - the entities these edges point to
are the two constituents of the Complex INDRA statement. |
(module
(function_definition
(function_name__get_parameter_conversion_entry) function_name__get_parameter_conversion_entry
(parameters
(identifier_parameter_config) identifier_parameter_config
)parameters
(block
(expression_statement
(assignment
(identifier_entry) identif... | Get information needed to convert the given parameter to its API type.
Args:
parameter_config: The dictionary containing information specific to the
parameter in question. This is retrieved from request.parameters in the
method config.
Returns:
The entry from _PARAM_CONVERSION_MAP with functio... |
(module
(function_definition
(function_name__parse_deploy) function_name__parse_deploy
(parameters
(identifier_self) identifier_self
(typed_parameter
(identifier_deploy_values) identifier_deploy_values
(type
(identifier_dict) identifier_dict
)type
)typed_par... | Parse deploy key.
Args:
deploy_values (dict): deploy configuration values
service_config (dict): Service configuration |
(module
(function_definition
(function_name_supportsType) function_name_supportsType
(parameters
(identifier_self) identifier_self
(identifier_type_uri) identifier_type_uri
)parameters
(block
(return_statement
(parenthesized_expression
(boolean_operator
... | Does this endpoint support this type?
I consider C{/server} endpoints to implicitly support C{/signon}. |
(module
(function_definition
(function_name__RunSingleHook) function_name__RunSingleHook
(parameters
(identifier_self) identifier_self
(identifier_hook_cls) identifier_hook_cls
(identifier_executed_set) identifier_executed_set
(default_parameter
(identifier_required) identifier... | Run the single hook specified by resolving all its prerequisites. |
(module
(function_definition
(function_name_PyParseRangeCheck) function_name_PyParseRangeCheck
(parameters
(identifier_lower_bound) identifier_lower_bound
(identifier_upper_bound) identifier_upper_bound
)parameters
(block
(function_definition
(function_name_CheckRange) functi... | Verify that a number is within a defined range.
This is a callback method for pyparsing setParseAction
that verifies that a read number is within a certain range.
To use this method it needs to be defined as a callback method
in setParseAction with the upper and lower bound set as parameters.
Args:
low... |
(module
(function_definition
(function_name_read_hierarchy) function_name_read_hierarchy
(parameters
(identifier_self) identifier_self
(identifier_fid) identifier_fid
)parameters
(block
(expression_statement
(assignment
(identifier_lin) identifier_lin
(cal... | Read hierarchy information from acclaim skeleton file stream. |
(module
(function_definition
(function_name_show_gateway_device) function_name_show_gateway_device
(parameters
(identifier_self) identifier_self
(identifier_gateway_device_id) identifier_gateway_device_id
(dictionary_splat_pattern
(identifier__params) identifier__params
)dictio... | Fetch a gateway device. |
(module
(function_definition
(function_name_restore) function_name_restore
(parameters
(identifier_self) identifier_self
)parameters
(block
(expression_statement
(call
(attribute
(identifier_signal) identifier_signal
(identifier_signal) identifier_... | Restore signal handlers to their original settings. |
(module
(function_definition
(function_name_post) function_name_post
(parameters
(identifier_url) identifier_url
(default_parameter
(identifier_data) identifier_data
(None) None
)default_parameter
(default_parameter
(identifier_json) identifier_json
(Non... | A wrapper for ``requests.post``. |
(module
(function_definition
(function_name_all) function_name_all
(parameters
(identifier_self) identifier_self
)parameters
(block
(expression_statement
(call
(attribute
(identifier_self) identifier_self
(identifier__check_layout) identifier__chec... | Returns all layout objects of first level of depth |
(module
(function_definition
(function_name_get_one) function_name_get_one
(parameters
(identifier_self) identifier_self
(default_parameter
(identifier_fields) identifier_fields
(call
(identifier_list) identifier_list
(argument_list
)argument_list
... | Convenience function for queries returning only one result. Validates response before returning.
:param fields: List of fields to return in the result
:raise:
:MultipleResults: if more than one match is found
:return:
- Record content |
(module
(function_definition
(function_name_init_logging) function_name_init_logging
(parameters
)parameters
(block
(expression_statement
(assignment
(identifier_fmt) identifier_fmt
(concatenated_string
(string_'%(asctime)s.%(msecs)03d | %(name)-60s | %(le... | Initialise Python logging. |
(module
(function_definition
(function_name_frequencies_plot) function_name_frequencies_plot
(parameters
(identifier_self) identifier_self
(default_parameter
(identifier_xmin) identifier_xmin
(integer_0) integer_0
)default_parameter
(default_parameter
(identifie... | Generate the qualities plot |
(module
(function_definition
(function_name_get_shortcut) function_name_get_shortcut
(parameters
(identifier_self) identifier_self
(identifier_name) identifier_name
)parameters
(block
(expression_statement
(assignment
(identifier_name) identifier_name
(cal... | Returns given action shortcut.
:param name: Action to retrieve the shortcut.
:type name: unicode
:return: Action shortcut.
:rtype: unicode |
(module
(function_definition
(function_name_get_pins) function_name_get_pins
(parameters
(identifier_self) identifier_self
)parameters
(block
(expression_statement
(assignment
(identifier_result) identifier_result
(list
)list
)assignment
... | Get a list containing references to all 16 pins of the chip.
:Example:
>>> expander = MCP23017I2C(gw)
>>> pins = expander.get_pins()
>>> pprint.pprint(pins)
[<GPIOPin A0 on MCP23017I2C>,
<GPIOPin A1 on MCP23017I2C>,
<GPIOPin A2 on MCP23017I2C>,
<GPIOP... |
(module
(function_definition
(function_name_compose) function_name_compose
(parameters
(identifier_f) identifier_f
(list_splat_pattern
(identifier_fs) identifier_fs
)list_splat_pattern
)parameters
(block
(expression_statement
(assignment
(identifier_rf... | Compose functions right to left.
compose(f, g, h)(x) -> f(g(h(x)))
Args:
f, *fs: The head and rest of a sequence of callables. The
rightmost function passed can accept any arguments and
the returned function will have the same signature as
this last prov... |
(module
(function_definition
(function_name__inputcooker_store) function_name__inputcooker_store
(parameters
(identifier_self) identifier_self
(identifier_char) identifier_char
)parameters
(block
(if_statement
(attribute
(identifier_self) identifier_self
(... | Put the cooked data in the correct queue |
(module
(function_definition
(function_name__changeGroupImage) function_name__changeGroupImage
(parameters
(identifier_self) identifier_self
(identifier_image_id) identifier_image_id
(default_parameter
(identifier_thread_id) identifier_thread_id
(None) None
)default_par... | Changes a thread image from an image id
:param image_id: ID of uploaded image
:param thread_id: User/Group ID to change image. See :ref:`intro_threads`
:raises: FBchatException if request failed |
(module
(function_definition
(function_name__update_field) function_name__update_field
(parameters
(identifier_self) identifier_self
(identifier_action) identifier_action
(identifier_field) identifier_field
(identifier_value) identifier_value
(identifier_max_tries) identifier_max... | Private update_field method. Wrapped by Document.update_field.
Tracks a "tries" var to help limit recursion. |
(module
(function_definition
(function_name_document_quote) function_name_document_quote
(parameters
(identifier_document) identifier_document
)parameters
(block
(expression_statement
(assignment
(pattern_list
(identifier_doc) identifier_doc
(ident... | Quote given document. |
(module
(function_definition
(function_name_is_text_extractor_available) function_name_is_text_extractor_available
(parameters
(typed_parameter
(identifier_extension) identifier_extension
(type
(identifier_str) identifier_str
)type
)typed_parameter
)parameters... | Is a text extractor available for the specified extension? |
(module
(function_definition
(function_name_set_of_vars) function_name_set_of_vars
(parameters
(identifier_arg_plot) identifier_arg_plot
)parameters
(block
(return_statement
(call
(identifier_set) identifier_set
(generator_expression
(identifier_var)... | Build set of needed variables.
Args:
arg_plot (str): string with variable names separated with ``,``.
Returns:
set of str: set of variables. |
(module
(function_definition
(function_name_match_gpus) function_name_match_gpus
(parameters
(identifier_available_devices) identifier_available_devices
(identifier_requirements) identifier_requirements
)parameters
(block
(if_statement
(not_operator
(identifier_requ... | Determines sufficient GPUs for the given requirements and returns a list of GPUDevices.
If there aren't sufficient GPUs a InsufficientGPUException is thrown.
:param available_devices: A list of GPUDevices
:param requirements: A list of GPURequirements
:return: A list of sufficient devices |
(module
(function_definition
(function_name_viewport_to_screen_space) function_name_viewport_to_screen_space
(parameters
(typed_parameter
(identifier_framebuffer_size) identifier_framebuffer_size
(type
(identifier_vec2) identifier_vec2
)type
)typed_parameter
... | Transform point in viewport space to screen space. |
(module
(function_definition
(function_name_ols_covariance) function_name_ols_covariance
(parameters
(identifier_self) identifier_self
)parameters
(block
(expression_statement
(assignment
(identifier_Y) identifier_Y
(call
(attribute
(id... | Creates OLS estimate of the covariance matrix
Returns
----------
The OLS estimate of the covariance matrix |
(module
(function_definition
(function_name_load_device) function_name_load_device
(parameters
(identifier_self) identifier_self
(default_parameter
(identifier_serial) identifier_serial
(None) None
)default_parameter
)parameters
(block
(expression_statement
... | Creates an AndroidDevice for the given serial number.
If no serial is given, it will read from the ANDROID_SERIAL
environmental variable. If the environmental variable is not set, then
it will read from 'adb devices' if there is only one. |
(module
(function_definition
(function_name_exists) function_name_exists
(parameters
(identifier_self) identifier_self
(identifier_obj_id) identifier_obj_id
(default_parameter
(identifier_obj_type) identifier_obj_type
(None) None
)default_parameter
)parameters
(... | Return whether the given object exists in the search index.
:param obj_id: The object's unique identifier.
:param obj_type: The object's type. |
(module
(function_definition
(function_name_return_real_id) function_name_return_real_id
(parameters
(identifier_self) identifier_self
)parameters
(block
(if_statement
(comparison_operator
(attribute
(identifier_self) identifier_self
(identifier__p... | Returns a list of real_id's
Parameters
----------
Returns
-------
A list of real_id values for the dataset (a real_id is the filename minus the suffix and prefix) |
(module
(function_definition
(function_name_set_unobserved_before) function_name_set_unobserved_before
(parameters
(identifier_self) identifier_self
(identifier_tlen) identifier_tlen
(identifier_qlen) identifier_qlen
(identifier_nt) identifier_nt
(identifier_p) identifier_p
)... | Set the unobservable sequence data before this base
:param tlen: target homopolymer length
:param qlen: query homopolymer length
:param nt: nucleotide
:param p: p is the probability of attributing this base to the unobserved error
:type tlen: int
:type qlen: int
:type nt: char
:type p: ... |
(module
(function_definition
(function_name_model_deleted) function_name_model_deleted
(parameters
(identifier_sender) identifier_sender
(identifier_instance) identifier_instance
(identifier_using) identifier_using
(dictionary_splat_pattern
(identifier_kwargs) identifier_kwargs... | Automatically triggers "deleted" actions. |
(module
(function_definition
(function_name_Sign) function_name_Sign
(parameters
(identifier_verifiable) identifier_verifiable
(identifier_keypair) identifier_keypair
)parameters
(block
(expression_statement
(assignment
(identifier_prikey) identifier_prikey
... | Sign the `verifiable` object with the private key from `keypair`.
Args:
verifiable:
keypair (neocore.KeyPair):
Returns:
bool: True if successfully signed. False otherwise. |
(module
(function_definition
(function_name_load_vint) function_name_load_vint
(parameters
(identifier_buf) identifier_buf
(identifier_pos) identifier_pos
)parameters
(block
(expression_statement
(assignment
(identifier_limit) identifier_limit
(call
... | Load variable-size int. |
(module
(function_definition
(function_name_run) function_name_run
(parameters
(identifier_categories) identifier_categories
(identifier_param_file) identifier_param_file
(identifier_project_dir) identifier_project_dir
(identifier_plugin) identifier_plugin
(identifier_target) ide... | Generate code for this project and run it |
(module
(function_definition
(function_name_query) function_name_query
(parameters
(identifier_cls) identifier_cls
(list_splat_pattern
(identifier_criteria) identifier_criteria
)list_splat_pattern
(dictionary_splat_pattern
(identifier_filters) identifier_filters
)... | Wrap sqlalchemy query methods.
A wrapper for the filter and filter_by functions of sqlalchemy.
Define a dict with which columns should be filtered by which values.
.. codeblock:: python
WorkflowObject.query(id=123)
WorkflowObject.query(status=ObjectStatus.COMPLETED)
... |
(module
(function_definition
(function_name_allan_variance) function_name_allan_variance
(parameters
(identifier_data) identifier_data
(identifier_dt) identifier_dt
(default_parameter
(identifier_tmax) identifier_tmax
(integer_10) integer_10
)default_parameter
)para... | Calculate Allan variance.
Args:
data (np.ndarray): Input data.
dt (float): Time between each data.
tmax (float): Maximum time.
Returns:
vk (np.ndarray): Frequency.
allanvar (np.ndarray): Allan variance. |
(module
(function_definition
(function_name_to_type_with_default) function_name_to_type_with_default
(parameters
(identifier_value_type) identifier_value_type
(identifier_value) identifier_value
(identifier_default_value) identifier_default_value
)parameters
(block
(expression_... | Converts value into an object type specified by Type Code or returns default value when conversion is not possible.
:param value_type: the TypeCode for the data type into which 'value' is to be converted.
:param value: the value to convert.
:param default_value: the default value to return if... |
(module
(function_definition
(function_name_zSaveFile) function_name_zSaveFile
(parameters
(identifier_self) identifier_self
(identifier_fileName) identifier_fileName
)parameters
(block
(expression_statement
(assignment
(identifier_cmd) identifier_cmd
(cal... | Saves the lens currently loaded in the server to a Zemax file |
(module
(function_definition
(function_name_expect_dimensions) function_name_expect_dimensions
(parameters
(default_parameter
(identifier___funcname) identifier___funcname
(identifier__qualified_name) identifier__qualified_name
)default_parameter
(dictionary_splat_pattern
... | Preprocessing decorator that verifies inputs are numpy arrays with a
specific dimensionality.
Examples
--------
>>> from numpy import array
>>> @expect_dimensions(x=1, y=2)
... def foo(x, y):
... return x[0] + y[0, 0]
...
>>> foo(array([1, 1]), array([[1, 1], [2, 2]]))
2
... |
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