sequence stringlengths 557 12.7k | docstring stringlengths 4 15.2k |
|---|---|
(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_statement
(assignment
(identifier_n) identifier_n
(call
(attribute
(attribute
(identifier_pymummer) identifier_pymummer
(identifier_nucmer) identifier_nucmer
)attribute
(identifier_Runner) identifier_Runner
)attribute
(argument_list
(identifier_ref) identifier_ref
(identifier_qry) identifier_qry
(identifier_outfile) identifier_outfile
(keyword_argument
(identifier_min_id) identifier_min_id
(attribute
(identifier_self) identifier_self
(identifier_nucmer_min_id) identifier_nucmer_min_id
)attribute
)keyword_argument
(keyword_argument
(identifier_min_length) identifier_min_length
(attribute
(identifier_self) identifier_self
(identifier_nucmer_min_length) identifier_nucmer_min_length
)attribute
)keyword_argument
(keyword_argument
(identifier_diagdiff) identifier_diagdiff
(attribute
(identifier_self) identifier_self
(identifier_nucmer_diagdiff) identifier_nucmer_diagdiff
)attribute
)keyword_argument
(keyword_argument
(identifier_maxmatch) identifier_maxmatch
(True) True
)keyword_argument
(keyword_argument
(identifier_breaklen) identifier_breaklen
(attribute
(identifier_self) identifier_self
(identifier_nucmer_breaklen) identifier_nucmer_breaklen
)attribute
)keyword_argument
(keyword_argument
(identifier_simplify) identifier_simplify
(True) True
)keyword_argument
(keyword_argument
(identifier_verbose) identifier_verbose
(attribute
(identifier_self) identifier_self
(identifier_verbose) identifier_verbose
)attribute
)keyword_argument
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(call
(attribute
(identifier_n) identifier_n
(identifier_run) identifier_run
)attribute
(argument_list
)argument_list
)call
)expression_statement
)block
)function_definition
)module | 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
(call
(attribute
(attribute
(identifier_self) identifier_self
(identifier__listeners) identifier__listeners
)attribute
(identifier_pop) identifier_pop
)attribute
(argument_list
(identifier_registration_id) identifier_registration_id
)argument_list
)call
)expression_statement
(return_statement
(True) True
)return_statement
)block
(except_clause
(identifier_KeyError) identifier_KeyError
(block
(return_statement
(False) False
)return_statement
)block
)except_clause
)try_statement
)block
)function_definition
)module | 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_skewness
)parameters
(block
(return_statement
(binary_operator
(parenthesized_expression
(binary_operator
(identifier_y) identifier_y
(identifier_mean) identifier_mean
)binary_operator
)parenthesized_expression
(call
(identifier_float) identifier_float
(argument_list
(binary_operator
(identifier_scale) identifier_scale
(call
(attribute
(identifier_np) identifier_np
(identifier_abs) identifier_abs
)attribute
(argument_list
(binary_operator
(identifier_y) identifier_y
(identifier_mean) identifier_mean
)binary_operator
)argument_list
)call
)binary_operator
)argument_list
)call
)binary_operator
)return_statement
)block
)function_definition
)module | 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 distribution
shape : float
tail thickness parameter for the Laplace distribution
skewness : float
skewness parameter for the Laplace distribution
Returns
----------
- Score of the Laplace family |
(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
(as_pattern
(call
(identifier_open) identifier_open
(argument_list
(identifier_filename) identifier_filename
(string_'rb') string_'rb'
)argument_list
)call
(as_pattern_target
(identifier_fp) identifier_fp
)as_pattern_target
)as_pattern
)with_item
)with_clause
(block
(expression_statement
(assignment
(attribute
(identifier_self) identifier_self
(identifier_counters) identifier_counters
)attribute
(call
(attribute
(identifier_cPickle) identifier_cPickle
(identifier_load) identifier_load
)attribute
(argument_list
(identifier_fp) identifier_fp
)argument_list
)call
)assignment
)expression_statement
)block
)with_statement
)block
(except_clause
(block
(expression_statement
(call
(attribute
(identifier_logging) identifier_logging
(identifier_debug) identifier_debug
)attribute
(argument_list
(string_"can't load counter from file: %s") string_"can't load counter from file: %s"
(identifier_filename) identifier_filename
)argument_list
)call
)expression_statement
(return_statement
(False) False
)return_statement
)block
)except_clause
)try_statement
(return_statement
(True) True
)return_statement
)block
)function_definition
)module | 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
(identifier_port_bindings) identifier_port_bindings
(dictionary
)dictionary
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_if_ipv4) identifier_if_ipv4
(attribute
(identifier_client_config) identifier_client_config
(identifier_interfaces) identifier_interfaces
)attribute
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_if_ipv6) identifier_if_ipv6
(attribute
(identifier_client_config) identifier_client_config
(identifier_interfaces_ipv6) identifier_interfaces_ipv6
)attribute
)assignment
)expression_statement
(for_statement
(pattern_list
(identifier_exposed_port) identifier_exposed_port
(identifier_ex_port_bindings) identifier_ex_port_bindings
)pattern_list
(call
(attribute
(identifier_itertools) identifier_itertools
(identifier_groupby) identifier_groupby
)attribute
(argument_list
(call
(identifier_sorted) identifier_sorted
(argument_list
(attribute
(identifier_container_config) identifier_container_config
(identifier_exposes) identifier_exposes
)attribute
(keyword_argument
(identifier_key) identifier_key
(identifier__get_ex_port) identifier__get_ex_port
)keyword_argument
)argument_list
)call
(identifier__get_ex_port) identifier__get_ex_port
)argument_list
)call
(block
(expression_statement
(assignment
(identifier_bind_list) identifier_bind_list
(call
(identifier_list) identifier_list
(argument_list
(call
(identifier__get_port_bindings) identifier__get_port_bindings
(argument_list
(identifier_ex_port_bindings) identifier_ex_port_bindings
(identifier_if_ipv4) identifier_if_ipv4
(identifier_if_ipv6) identifier_if_ipv6
)argument_list
)call
)argument_list
)call
)assignment
)expression_statement
(if_statement
(identifier_bind_list) identifier_bind_list
(block
(expression_statement
(assignment
(subscript
(identifier_port_bindings) identifier_port_bindings
(identifier_exposed_port) identifier_exposed_port
)subscript
(identifier_bind_list) identifier_bind_list
)assignment
)expression_statement
)block
)if_statement
)block
)for_statement
(return_statement
(identifier_port_bindings) identifier_port_bindings
)return_statement
)block
)function_definition
)module | 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.ClientConfiguration
:return: Dictionary of ports with mapped port, and if applicable, with bind address
:rtype: dict[unicode | str, list[unicode | str | int | tuple]] |
(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_operator
(not_operator
(call
(attribute
(identifier_self) identifier_self
(identifier_has_expired) identifier_has_expired
)attribute
(argument_list
)argument_list
)call
)not_operator
(comparison_operator
(attribute
(identifier_self) identifier_self
(identifier__cached_copy) identifier__cached_copy
)attribute
(None) None
)comparison_operator
)boolean_operator
(block
(return_statement
(expression_list
(attribute
(identifier_self) identifier_self
(identifier__cached_copy) identifier__cached_copy
)attribute
(False) False
)expression_list
)return_statement
)block
)if_statement
(return_statement
(expression_list
(call
(attribute
(identifier_self) identifier_self
(identifier__refresh_cache) identifier__refresh_cache
)attribute
(argument_list
(identifier_transform) identifier_transform
)argument_list
)call
(True) True
)expression_list
)return_statement
)block
)function_definition
)module | 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
(identifier_np) identifier_np
(identifier_asarray) identifier_asarray
)attribute
(argument_list
(identifier_a) identifier_a
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_n) identifier_n
(call
(identifier_len) identifier_len
(argument_list
(identifier_ia) identifier_ia
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_y) identifier_y
(call
(attribute
(identifier_np) identifier_np
(identifier_array) identifier_array
)attribute
(argument_list
(comparison_operator
(subscript
(identifier_ia) identifier_ia
(slice
(integer_1) integer_1
(colon) colon
)slice
)subscript
(subscript
(identifier_ia) identifier_ia
(slice
(colon) colon
(unary_operator
(integer_1) integer_1
)unary_operator
)slice
)subscript
)comparison_operator
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_i) identifier_i
(call
(attribute
(identifier_np) identifier_np
(identifier_append) identifier_append
)attribute
(argument_list
(call
(attribute
(identifier_np) identifier_np
(identifier_where) identifier_where
)attribute
(argument_list
(identifier_y) identifier_y
)argument_list
)call
(binary_operator
(identifier_n) identifier_n
(integer_1) integer_1
)binary_operator
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_z) identifier_z
(call
(attribute
(identifier_np) identifier_np
(identifier_diff) identifier_diff
)attribute
(argument_list
(call
(attribute
(identifier_np) identifier_np
(identifier_append) identifier_append
)attribute
(argument_list
(unary_operator
(integer_1) integer_1
)unary_operator
(identifier_i) identifier_i
)argument_list
)call
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_p) identifier_p
(subscript
(call
(attribute
(identifier_np) identifier_np
(identifier_cumsum) identifier_cumsum
)attribute
(argument_list
(call
(attribute
(identifier_np) identifier_np
(identifier_append) identifier_append
)attribute
(argument_list
(integer_0) integer_0
(identifier_z) identifier_z
)argument_list
)call
)argument_list
)call
(slice
(colon) colon
(unary_operator
(integer_1) integer_1
)unary_operator
)slice
)subscript
)assignment
)expression_statement
(return_statement
(tuple
(identifier_z) identifier_z
(identifier_p) identifier_p
(subscript
(identifier_ia) identifier_ia
(identifier_i) identifier_i
)subscript
)tuple
)return_statement
)block
)function_definition
)module | 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
ar : array, shape[nt,]
values for 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
)dotted_name
(identifier_np) identifier_np
)aliased_import
)import_statement
(expression_statement
(assignment
(identifier_Y) identifier_Y
(call
(attribute
(identifier_np) identifier_np
(identifier_empty) identifier_empty
)attribute
(argument_list
(attribute
(identifier_X) identifier_X
(identifier_shape) identifier_shape
)attribute
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(subscript
(identifier_Y) identifier_Y
(slice
(colon) colon
)slice
(integer_0) integer_0
)subscript
(subscript
(identifier_X) identifier_X
(slice
(colon) colon
)slice
(integer_0) integer_0
)subscript
)assignment
)expression_statement
(expression_statement
(assignment
(subscript
(identifier_Y) identifier_Y
(slice
(colon) colon
)slice
(integer_1) integer_1
)subscript
(binary_operator
(binary_operator
(identifier_rho) identifier_rho
(subscript
(identifier_X) identifier_X
(slice
(colon) colon
)slice
(integer_0) integer_0
)subscript
)binary_operator
(binary_operator
(call
(attribute
(identifier_np) identifier_np
(identifier_sqrt) identifier_sqrt
)attribute
(argument_list
(binary_operator
(float_1.0) float_1.0
(binary_operator
(identifier_rho) identifier_rho
(integer_2) integer_2
)binary_operator
)binary_operator
)argument_list
)call
(subscript
(identifier_X) identifier_X
(slice
(colon) colon
)slice
(integer_1) integer_1
)subscript
)binary_operator
)binary_operator
)assignment
)expression_statement
(return_statement
(identifier_Y) identifier_Y
)return_statement
)block
)function_definition
)module | 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
(string_'------------------------------') string_'------------------------------'
)argument_list
)call
)expression_statement
(try_statement
(block
(expression_statement
(assignment
(identifier_str2) identifier_str2
(subscript
(identifier_str2) identifier_str2
(integer_0) integer_0
)subscript
)assignment
)expression_statement
)block
(except_clause
(identifier_IndexError) identifier_IndexError
(block
(expression_statement
(assignment
(identifier_str2) identifier_str2
(None) None
)assignment
)expression_statement
)block
)except_clause
)try_statement
(if_statement
(boolean_operator
(identifier_str1) identifier_str1
(identifier_str2) identifier_str2
)boolean_operator
(block
(return_statement
(call
(attribute
(identifier_str1) identifier_str1
(identifier_replace) identifier_replace
)attribute
(argument_list
(identifier_str2) identifier_str2
(call
(attribute
(string_"<b>{}</b>") string_"<b>{}</b>"
(identifier_format) identifier_format
)attribute
(argument_list
(identifier_str2) identifier_str2
)argument_list
)call
)argument_list
)call
)return_statement
)block
(else_clause
(block
(return_statement
(identifier_str1) identifier_str1
)return_statement
)block
)else_clause
)if_statement
)block
)function_definition
)module | 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) identifier_self
(identifier_validators) identifier_validators
)attribute
(block
(expression_statement
(call
(attribute
(identifier_v) identifier_v
(identifier_validate) identifier_validate
)attribute
(argument_list
(identifier_value) identifier_value
)argument_list
)call
)expression_statement
)block
)for_statement
(return_statement
(True) True
)return_statement
)block
)function_definition
)module | 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_statement
(comparison_operator
(identifier_type_name) identifier_type_name
(tuple
(string_"string") string_"string"
(string_"enum") string_"enum"
)tuple
)comparison_operator
(block
(return_statement
(string_"string") string_"string"
)return_statement
)block
)if_statement
(if_statement
(comparison_operator
(identifier_type_name) identifier_type_name
(string_"float") string_"float"
)comparison_operator
(block
(return_statement
(string_"float64") string_"float64"
)return_statement
)block
)if_statement
(if_statement
(comparison_operator
(identifier_type_name) identifier_type_name
(string_"boolean") string_"boolean"
)comparison_operator
(block
(return_statement
(string_"bool") string_"bool"
)return_statement
)block
)if_statement
(if_statement
(comparison_operator
(identifier_type_name) identifier_type_name
(string_"list") string_"list"
)comparison_operator
(block
(expression_statement
(assignment
(identifier_st) identifier_st
(conditional_expression
(call
(identifier_get_type_name) identifier_get_type_name
(argument_list
(keyword_argument
(identifier_type_name) identifier_type_name
(identifier_sub_type) identifier_sub_type
)keyword_argument
(keyword_argument
(identifier_sub_type) identifier_sub_type
(None) None
)keyword_argument
)argument_list
)call
(identifier_sub_type) identifier_sub_type
(string_"interface{}") string_"interface{}"
)conditional_expression
)assignment
)expression_statement
(return_statement
(binary_operator
(string_"[]%s") string_"[]%s"
(identifier_st) identifier_st
)binary_operator
)return_statement
)block
)if_statement
(if_statement
(comparison_operator
(identifier_type_name) identifier_type_name
(string_"integer") string_"integer"
)comparison_operator
(block
(return_statement
(string_"int") string_"int"
)return_statement
)block
)if_statement
(if_statement
(comparison_operator
(identifier_type_name) identifier_type_name
(string_"time") string_"time"
)comparison_operator
(block
(return_statement
(string_"float64") string_"float64"
)return_statement
)block
)if_statement
(return_statement
(string_"interface{}") string_"interface{}"
)return_statement
)block
)function_definition
)module | 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_parameter
(default_parameter
(identifier_unsigned) identifier_unsigned
(False) False
)default_parameter
)parameters
(block
(return_statement
(call
(attribute
(identifier_self) identifier_self
(identifier__add_column) identifier__add_column
)attribute
(argument_list
(string_'medium_integer') string_'medium_integer'
(identifier_column) identifier_column
(keyword_argument
(identifier_auto_increment) identifier_auto_increment
(identifier_auto_increment) identifier_auto_increment
)keyword_argument
(keyword_argument
(identifier_unsigned) identifier_unsigned
(identifier_unsigned) identifier_unsigned
)keyword_argument
)argument_list
)call
)return_statement
)block
)function_definition
)module | 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
(expression_statement
(assignment
(identifier_idxs) identifier_idxs
(list_comprehension
(identifier_idx) identifier_idx
(for_in_clause
(identifier_idx) identifier_idx
(call
(attribute
(identifier_np) identifier_np
(identifier_ndindex) identifier_ndindex
)attribute
(argument_list
(attribute
(identifier_arr) identifier_arr
(identifier_shape) identifier_shape
)attribute
)argument_list
)call
)for_in_clause
)list_comprehension
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_outs) identifier_outs
(list
)list
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_min_dist) identifier_min_dist
(binary_operator
(call
(attribute
(identifier_arr) identifier_arr
(identifier_max) identifier_max
)attribute
(argument_list
)argument_list
)call
(call
(attribute
(identifier_arr) identifier_arr
(identifier_min) identifier_min
)attribute
(argument_list
)argument_list
)call
)binary_operator
)assignment
)expression_statement
(for_statement
(identifier_idxa) identifier_idxa
(identifier_idxs) identifier_idxs
(block
(for_statement
(identifier_idxb) identifier_idxb
(identifier_idxs) identifier_idxs
(block
(if_statement
(comparison_operator
(identifier_idxa) identifier_idxa
(identifier_idxb) identifier_idxb
)comparison_operator
(block
(continue_statement
)continue_statement
)block
)if_statement
(expression_statement
(assignment
(identifier_dist) identifier_dist
(call
(identifier_abs) identifier_abs
(argument_list
(binary_operator
(subscript
(identifier_arr) identifier_arr
(identifier_idxa) identifier_idxa
)subscript
(subscript
(identifier_arr) identifier_arr
(identifier_idxb) identifier_idxb
)subscript
)binary_operator
)argument_list
)call
)assignment
)expression_statement
(if_statement
(comparison_operator
(identifier_dist) identifier_dist
(identifier_min_dist) identifier_min_dist
)comparison_operator
(block
(if_statement
(not_operator
(comparison_operator
(list
(identifier_idxb) identifier_idxb
(identifier_idxa) identifier_idxa
)list
(identifier_outs) identifier_outs
)comparison_operator
)not_operator
(block
(expression_statement
(call
(attribute
(identifier_outs) identifier_outs
(identifier_append) identifier_append
)attribute
(argument_list
(list
(identifier_idxa) identifier_idxa
(identifier_idxb) identifier_idxb
)list
)argument_list
)call
)expression_statement
)block
)if_statement
)block
(elif_clause
(comparison_operator
(identifier_dist) identifier_dist
(identifier_min_dist) identifier_min_dist
)comparison_operator
(block
(expression_statement
(assignment
(identifier_min_dist) identifier_min_dist
(identifier_dist) identifier_dist
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_outs) identifier_outs
(list
(list
(identifier_idxa) identifier_idxa
(identifier_idxb) identifier_idxb
)list
)list
)assignment
)expression_statement
)block
)elif_clause
)if_statement
)block
)for_statement
)block
)for_statement
(if_statement
(comparison_operator
(identifier_give) identifier_give
(string_"indicies") string_"indicies"
)comparison_operator
(block
(return_statement
(identifier_outs) identifier_outs
)return_statement
)block
(elif_clause
(comparison_operator
(identifier_give) identifier_give
(string_"distance") string_"distance"
)comparison_operator
(block
(return_statement
(identifier_min_dist) identifier_min_dist
)return_statement
)block
)elif_clause
(else_clause
(block
(raise_statement
(call
(identifier_KeyError) identifier_KeyError
(argument_list
(string_"give not recognized in closest_pair") string_"give not recognized in closest_pair"
)argument_list
)call
)raise_statement
)block
)else_clause
)if_statement
)block
)function_definition
)module | 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 because I need it now to use on some
relatively small arrays. Feel free to refactor if you need this operation
done as fast as possible. - Blaise 2016-02-07
Parameters
----------
arr : numpy.ndarray
The array to search.
give : {'indicies', 'distance'} (optional)
Toggle return behavior. If 'distance', returns a single float - the
closest distance itself. Default is indicies.
Returns
-------
list of lists of two tuples
List containing lists of two tuples: indicies the nearest pair in the
array.
>>> arr = np.array([0, 1, 2, 3, 3, 4, 5, 6, 1])
>>> closest_pair(arr)
[[(1,), (8,)], [(3,), (4,)]] |
(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
(call
(attribute
(attribute
(identifier_self) identifier_self
(identifier_space) identifier_space
)attribute
(identifier_get_space_summary) identifier_get_space_summary
)attribute
(argument_list
)argument_list
)call
)assignment
)expression_statement
(for_statement
(identifier_app) identifier_app
(subscript
(identifier_summary) identifier_summary
(string_'apps') string_'apps'
)subscript
(block
(if_statement
(comparison_operator
(subscript
(identifier_app) identifier_app
(string_'name') string_'name'
)subscript
(identifier_app_name) identifier_app_name
)comparison_operator
(block
(return_statement
(subscript
(identifier_app) identifier_app
(string_'guid') string_'guid'
)subscript
)return_statement
)block
)if_statement
)block
)for_statement
)block
)function_definition
)module | 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_parameter
(default_parameter
(identifier_is_multiple) identifier_is_multiple
(False) False
)default_parameter
(default_parameter
(identifier_p) identifier_p
(integer_0) integer_0
)default_parameter
)parameters
(block
(if_statement
(call
(identifier_isinstance) identifier_isinstance
(argument_list
(identifier_bcc_emails) identifier_bcc_emails
(identifier_list) identifier_list
)argument_list
)call
(block
(for_statement
(identifier_email) identifier_email
(identifier_bcc_emails) identifier_bcc_emails
(block
(if_statement
(call
(identifier_isinstance) identifier_isinstance
(argument_list
(identifier_email) identifier_email
(identifier_str) identifier_str
)argument_list
)call
(block
(expression_statement
(assignment
(identifier_email) identifier_email
(call
(identifier_Bcc) identifier_Bcc
(argument_list
(identifier_email) identifier_email
(None) None
)argument_list
)call
)assignment
)expression_statement
)block
)if_statement
(if_statement
(call
(identifier_isinstance) identifier_isinstance
(argument_list
(identifier_email) identifier_email
(identifier_tuple) identifier_tuple
)argument_list
)call
(block
(expression_statement
(assignment
(identifier_email) identifier_email
(call
(identifier_Bcc) identifier_Bcc
(argument_list
(subscript
(identifier_email) identifier_email
(integer_0) integer_0
)subscript
(subscript
(identifier_email) identifier_email
(integer_1) integer_1
)subscript
)argument_list
)call
)assignment
)expression_statement
)block
)if_statement
(expression_statement
(call
(attribute
(identifier_self) identifier_self
(identifier_add_bcc) identifier_add_bcc
)attribute
(argument_list
(identifier_email) identifier_email
(identifier_global_substitutions) identifier_global_substitutions
(identifier_is_multiple) identifier_is_multiple
(identifier_p) identifier_p
)argument_list
)call
)expression_statement
)block
)for_statement
)block
(else_clause
(block
(if_statement
(call
(identifier_isinstance) identifier_isinstance
(argument_list
(identifier_bcc_emails) identifier_bcc_emails
(identifier_str) identifier_str
)argument_list
)call
(block
(expression_statement
(assignment
(identifier_bcc_emails) identifier_bcc_emails
(call
(identifier_Bcc) identifier_Bcc
(argument_list
(identifier_bcc_emails) identifier_bcc_emails
(None) None
)argument_list
)call
)assignment
)expression_statement
)block
)if_statement
(if_statement
(call
(identifier_isinstance) identifier_isinstance
(argument_list
(identifier_bcc_emails) identifier_bcc_emails
(identifier_tuple) identifier_tuple
)argument_list
)call
(block
(expression_statement
(assignment
(identifier_bcc_emails) identifier_bcc_emails
(call
(identifier_Bcc) identifier_Bcc
(argument_list
(subscript
(identifier_bcc_emails) identifier_bcc_emails
(integer_0) integer_0
)subscript
(subscript
(identifier_bcc_emails) identifier_bcc_emails
(integer_1) integer_1
)subscript
)argument_list
)call
)assignment
)expression_statement
)block
)if_statement
(expression_statement
(call
(attribute
(identifier_self) identifier_self
(identifier_add_bcc) identifier_add_bcc
)attribute
(argument_list
(identifier_bcc_emails) identifier_bcc_emails
(identifier_global_substitutions) identifier_global_substitutions
(identifier_is_multiple) identifier_is_multiple
(identifier_p) identifier_p
)argument_list
)call
)expression_statement
)block
)else_clause
)if_statement
)block
)function_definition
)module | 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 personilization for each recipient
:type is_multiple: bool
:param p: p is the Personalization object or Personalization object
index
:type p: Personalization, integer, optional |
(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
(call
(attribute
(attribute
(identifier_os) identifier_os
(identifier_path) identifier_path
)attribute
(identifier_realpath) identifier_realpath
)attribute
(argument_list
(identifier_filename) identifier_filename
)argument_list
)call
)assignment
)expression_statement
(if_statement
(parenthesized_expression
(boolean_operator
(not_operator
(call
(attribute
(identifier_osp) identifier_osp
(identifier_isfile) identifier_isfile
)attribute
(argument_list
(identifier_real_filename) identifier_real_filename
)argument_list
)call
)not_operator
(not_operator
(call
(identifier_is_python_interpreter_valid_name) identifier_is_python_interpreter_valid_name
(argument_list
(identifier_filename) identifier_filename
)argument_list
)call
)not_operator
)boolean_operator
)parenthesized_expression
(block
(return_statement
(False) False
)return_statement
)block
(elif_clause
(call
(identifier_is_pythonw) identifier_is_pythonw
(argument_list
(identifier_filename) identifier_filename
)argument_list
)call
(block
(if_statement
(comparison_operator
(attribute
(identifier_os) identifier_os
(identifier_name) identifier_name
)attribute
(string_'nt') string_'nt'
)comparison_operator
(block
(if_statement
(not_operator
(call
(attribute
(identifier_encoding) identifier_encoding
(identifier_is_text_file) identifier_is_text_file
)attribute
(argument_list
(identifier_real_filename) identifier_real_filename
)argument_list
)call
)not_operator
(block
(return_statement
(True) True
)return_statement
)block
(else_clause
(block
(return_statement
(False) False
)return_statement
)block
)else_clause
)if_statement
)block
(elif_clause
(comparison_operator
(attribute
(identifier_sys) identifier_sys
(identifier_platform) identifier_platform
)attribute
(string_'darwin') string_'darwin'
)comparison_operator
(block
(if_statement
(boolean_operator
(call
(identifier_is_anaconda) identifier_is_anaconda
(argument_list
)argument_list
)call
(call
(attribute
(identifier_encoding) identifier_encoding
(identifier_is_text_file) identifier_is_text_file
)attribute
(argument_list
(identifier_real_filename) identifier_real_filename
)argument_list
)call
)boolean_operator
(block
(return_statement
(True) True
)return_statement
)block
(elif_clause
(not_operator
(call
(attribute
(identifier_encoding) identifier_encoding
(identifier_is_text_file) identifier_is_text_file
)attribute
(argument_list
(identifier_real_filename) identifier_real_filename
)argument_list
)call
)not_operator
(block
(return_statement
(True) True
)return_statement
)block
)elif_clause
(else_clause
(block
(return_statement
(False) False
)return_statement
)block
)else_clause
)if_statement
)block
)elif_clause
(else_clause
(block
(return_statement
(False) False
)return_statement
)block
)else_clause
)if_statement
)block
)elif_clause
(elif_clause
(call
(attribute
(identifier_encoding) identifier_encoding
(identifier_is_text_file) identifier_is_text_file
)attribute
(argument_list
(identifier_real_filename) identifier_real_filename
)argument_list
)call
(block
(return_statement
(False) False
)return_statement
)block
)elif_clause
(else_clause
(block
(return_statement
(call
(identifier_check_python_help) identifier_check_python_help
(argument_list
(identifier_filename) identifier_filename
)argument_list
)call
)return_statement
)block
)else_clause
)if_statement
)block
)function_definition
)module | 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
(comparison_operator
(identifier_nibble) identifier_nibble
(integer_12) integer_12
)comparison_operator
(block
(return_statement
(expression_list
(identifier_nibble) identifier_nibble
(identifier_pos) identifier_pos
)expression_list
)return_statement
)block
(elif_clause
(comparison_operator
(identifier_nibble) identifier_nibble
(integer_13) integer_13
)comparison_operator
(block
(expression_statement
(assignment
(identifier_tmp) identifier_tmp
(binary_operator
(subscript
(call
(attribute
(identifier_struct) identifier_struct
(identifier_unpack) identifier_unpack
)attribute
(argument_list
(string_"!B") string_"!B"
(call
(attribute
(subscript
(identifier_values) identifier_values
(identifier_pos) identifier_pos
)subscript
(identifier_to_bytes) identifier_to_bytes
)attribute
(argument_list
(integer_1) integer_1
(string_"big") string_"big"
)argument_list
)call
)argument_list
)call
(integer_0) integer_0
)subscript
(integer_13) integer_13
)binary_operator
)assignment
)expression_statement
(expression_statement
(augmented_assignment
(identifier_pos) identifier_pos
(integer_1) integer_1
)augmented_assignment
)expression_statement
(return_statement
(expression_list
(identifier_tmp) identifier_tmp
(identifier_pos) identifier_pos
)expression_list
)return_statement
)block
)elif_clause
(elif_clause
(comparison_operator
(identifier_nibble) identifier_nibble
(integer_14) integer_14
)comparison_operator
(block
(expression_statement
(assignment
(identifier_s) identifier_s
(call
(attribute
(identifier_struct) identifier_struct
(identifier_Struct) identifier_Struct
)attribute
(argument_list
(string_"!H") string_"!H"
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_tmp) identifier_tmp
(binary_operator
(subscript
(call
(attribute
(identifier_s) identifier_s
(identifier_unpack_from) identifier_unpack_from
)attribute
(argument_list
(call
(attribute
(subscript
(identifier_values) identifier_values
(slice
(identifier_pos) identifier_pos
(colon) colon
)slice
)subscript
(identifier_to_bytes) identifier_to_bytes
)attribute
(argument_list
(integer_2) integer_2
(string_"big") string_"big"
)argument_list
)call
)argument_list
)call
(integer_0) integer_0
)subscript
(integer_269) integer_269
)binary_operator
)assignment
)expression_statement
(expression_statement
(augmented_assignment
(identifier_pos) identifier_pos
(integer_2) integer_2
)augmented_assignment
)expression_statement
(return_statement
(expression_list
(identifier_tmp) identifier_tmp
(identifier_pos) identifier_pos
)expression_list
)return_statement
)block
)elif_clause
(else_clause
(block
(raise_statement
(call
(identifier_AttributeError) identifier_AttributeError
(argument_list
(binary_operator
(string_"Unsupported option nibble ") string_"Unsupported option nibble "
(call
(identifier_str) identifier_str
(argument_list
(identifier_nibble) identifier_nibble
)argument_list
)call
)binary_operator
)argument_list
)call
)raise_statement
)block
)else_clause
)if_statement
)block
)function_definition
)module | 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_section
(attribute
(identifier_property_set) identifier_property_set
(identifier_sections) identifier_sections
)attribute
(block
(if_statement
(comparison_operator
(attribute
(identifier_property_section) identifier_property_section
(identifier_class_identifier) identifier_class_identifier
)attribute
(attribute
(identifier_self) identifier_self
(identifier__CLASS_IDENTIFIER) identifier__CLASS_IDENTIFIER
)attribute
)comparison_operator
(block
(continue_statement
)continue_statement
)block
)if_statement
(for_statement
(identifier_property_value) identifier_property_value
(attribute
(identifier_property_section) identifier_property_section
(identifier_properties) identifier_properties
)attribute
(block
(expression_statement
(assignment
(identifier_property_name) identifier_property_name
(call
(attribute
(attribute
(identifier_self) identifier_self
(identifier__PROPERTY_NAMES) identifier__PROPERTY_NAMES
)attribute
(identifier_get) identifier_get
)attribute
(argument_list
(attribute
(identifier_property_value) identifier_property_value
(identifier_identifier) identifier_identifier
)attribute
(None) None
)argument_list
)call
)assignment
)expression_statement
(if_statement
(not_operator
(identifier_property_name) identifier_property_name
)not_operator
(block
(expression_statement
(assignment
(identifier_property_name) identifier_property_name
(call
(attribute
(string_'0x{0:04}') string_'0x{0:04}'
(identifier_format) identifier_format
)attribute
(argument_list
(attribute
(identifier_property_value) identifier_property_value
(identifier_identifier) identifier_identifier
)attribute
)argument_list
)call
)assignment
)expression_statement
)block
)if_statement
(expression_statement
(assignment
(identifier_value) identifier_value
(call
(attribute
(identifier_self) identifier_self
(identifier__GetValueAsObject) identifier__GetValueAsObject
)attribute
(argument_list
(identifier_property_value) identifier_property_value
)argument_list
)call
)assignment
)expression_statement
(if_statement
(attribute
(identifier_self) identifier_self
(identifier__PROPERTY_VALUE_MAPPINGS) identifier__PROPERTY_VALUE_MAPPINGS
)attribute
(block
(expression_statement
(assignment
(identifier_value_callback_name) identifier_value_callback_name
(call
(attribute
(attribute
(identifier_self) identifier_self
(identifier__PROPERTY_VALUE_MAPPINGS) identifier__PROPERTY_VALUE_MAPPINGS
)attribute
(identifier_get) identifier_get
)attribute
(argument_list
(identifier_property_name) identifier_property_name
(None) None
)argument_list
)call
)assignment
)expression_statement
(if_statement
(identifier_value_callback_name) identifier_value_callback_name
(block
(expression_statement
(assignment
(identifier_value_callback_method) identifier_value_callback_method
(call
(identifier_getattr) identifier_getattr
(argument_list
(identifier_self) identifier_self
(identifier_value_callback_name) identifier_value_callback_name
(None) None
)argument_list
)call
)assignment
)expression_statement
(if_statement
(identifier_value_callback_method) identifier_value_callback_method
(block
(expression_statement
(assignment
(identifier_value) identifier_value
(call
(identifier_value_callback_method) identifier_value_callback_method
(argument_list
(identifier_value) identifier_value
)argument_list
)call
)assignment
)expression_statement
)block
)if_statement
)block
)if_statement
)block
)if_statement
(if_statement
(comparison_operator
(identifier_property_name) identifier_property_name
(attribute
(identifier_self) identifier_self
(identifier__DATE_TIME_PROPERTIES) identifier__DATE_TIME_PROPERTIES
)attribute
)comparison_operator
(block
(expression_statement
(assignment
(identifier_properties_dict) identifier_properties_dict
(attribute
(identifier_self) identifier_self
(identifier_date_time_properties) identifier_date_time_properties
)attribute
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_value) identifier_value
(call
(attribute
(identifier_dfdatetime_filetime) identifier_dfdatetime_filetime
(identifier_Filetime) identifier_Filetime
)attribute
(argument_list
(keyword_argument
(identifier_timestamp) identifier_timestamp
(identifier_value) identifier_value
)keyword_argument
)argument_list
)call
)assignment
)expression_statement
)block
(else_clause
(block
(expression_statement
(assignment
(identifier_properties_dict) identifier_properties_dict
(attribute
(identifier_self) identifier_self
(identifier__properties) identifier__properties
)attribute
)assignment
)expression_statement
)block
)else_clause
)if_statement
(if_statement
(comparison_operator
(identifier_property_name) identifier_property_name
(identifier_properties_dict) identifier_properties_dict
)comparison_operator
(block
(expression_statement
(assignment
(subscript
(identifier_properties_dict) identifier_properties_dict
(identifier_property_name) identifier_property_name
)subscript
(identifier_value) identifier_value
)assignment
)expression_statement
)block
)if_statement
)block
)for_statement
)block
)for_statement
)block
)function_definition
)module | 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
(block
(expression_statement
(assignment
(identifier_user_id) identifier_user_id
(call
(attribute
(attribute
(identifier_util) identifier_util
(identifier_hdb) identifier_hdb
)attribute
(identifier_login_user) identifier_login_user
)attribute
(argument_list
(identifier_username) identifier_username
(identifier_password) identifier_password
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_hydra_session) identifier_hydra_session
(call
(attribute
(identifier_session) identifier_session
(identifier_Session) identifier_Session
)attribute
(argument_list
(dictionary
)dictionary
(keyword_argument
(identifier_validate_key) identifier_validate_key
(call
(attribute
(identifier_config) identifier_config
(identifier_get) identifier_get
)attribute
(argument_list
(string_'COOKIES') string_'COOKIES'
(string_'VALIDATE_KEY') string_'VALIDATE_KEY'
(string_'YxaDbzUUSo08b+') string_'YxaDbzUUSo08b+'
)argument_list
)call
)keyword_argument
(keyword_argument
(identifier_type) identifier_type
(string_'file') string_'file'
)keyword_argument
(keyword_argument
(identifier_cookie_expires) identifier_cookie_expires
(True) True
)keyword_argument
(keyword_argument
(identifier_data_dir) identifier_data_dir
(call
(attribute
(identifier_config) identifier_config
(identifier_get) identifier_get
)attribute
(argument_list
(string_'COOKIES') string_'COOKIES'
(string_'DATA_DIR') string_'DATA_DIR'
(string_'/tmp') string_'/tmp'
)argument_list
)call
)keyword_argument
(keyword_argument
(identifier_file_dir) identifier_file_dir
(call
(attribute
(identifier_config) identifier_config
(identifier_get) identifier_get
)attribute
(argument_list
(string_'COOKIES') string_'COOKIES'
(string_'FILE_DIR') string_'FILE_DIR'
(string_'/tmp/auth') string_'/tmp/auth'
)argument_list
)call
)keyword_argument
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(subscript
(identifier_hydra_session) identifier_hydra_session
(string_'user_id') string_'user_id'
)subscript
(identifier_user_id) identifier_user_id
)assignment
)expression_statement
(expression_statement
(assignment
(subscript
(identifier_hydra_session) identifier_hydra_session
(string_'username') string_'username'
)subscript
(identifier_username) identifier_username
)assignment
)expression_statement
(expression_statement
(call
(attribute
(identifier_hydra_session) identifier_hydra_session
(identifier_save) identifier_save
)attribute
(argument_list
)argument_list
)call
)expression_statement
(return_statement
(tuple
(identifier_user_id) identifier_user_id
(attribute
(identifier_hydra_session) identifier_hydra_session
(identifier_id) identifier_id
)attribute
)tuple
)return_statement
)block
)function_definition
)module | 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): The user's password (unencrypted)
returns:
A dict containing the user_id and session_id
raises:
HydraError if the login fails |
(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
(attribute
(identifier_np) identifier_np
(identifier_sum) identifier_sum
)attribute
(argument_list
(call
(attribute
(identifier_np) identifier_np
(identifier_logical_not) identifier_logical_not
)attribute
(argument_list
(call
(identifier_isnull) identifier_isnull
(argument_list
(identifier_data) identifier_data
)argument_list
)call
)argument_list
)call
(keyword_argument
(identifier_axis) identifier_axis
(identifier_axis) identifier_axis
)keyword_argument
)argument_list
)call
)return_statement
)block
)function_definition
)module | 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
(attribute
(attribute
(identifier_el) identifier_el
(identifier_elt) identifier_elt
)attribute
(identifier_tagName) identifier_tagName
)attribute
(identifier_lower) identifier_lower
)attribute
(argument_list
)argument_list
)call
)assignment
)expression_statement
(if_statement
(comparison_operator
(identifier_tag_name) identifier_tag_name
(set
(string_"input") string_"input"
(string_"textarea") string_"textarea"
(string_"select") string_"select"
)set
)comparison_operator
(block
(return_statement
(attribute
(identifier_el) identifier_el
(identifier_value) identifier_value
)attribute
)return_statement
)block
(else_clause
(block
(raise_statement
(call
(identifier_ValueError) identifier_ValueError
(argument_list
(binary_operator
(string_"Getter for %s (%s) not implemented!") string_"Getter for %s (%s) not implemented!"
(tuple
(identifier_tag_name) identifier_tag_name
(attribute
(identifier_el) identifier_el
(identifier_id) identifier_id
)attribute
)tuple
)binary_operator
)argument_list
)call
)raise_statement
)block
)else_clause
)if_statement
)block
)function_definition
)module | 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
(identifier_self) identifier_self
(identifier_dK_dr) identifier_dK_dr
)attribute
(argument_list
(call
(attribute
(identifier_self) identifier_self
(identifier__scaled_dist) identifier__scaled_dist
)attribute
(argument_list
(identifier_X) identifier_X
(identifier_X2) identifier_X2
)argument_list
)call
)argument_list
)call
)return_statement
)block
)function_definition
)module | 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
(identifier_xlabel) identifier_xlabel
(identifier_LABEL_DEFAULT) identifier_LABEL_DEFAULT
)default_parameter
(default_parameter
(identifier_ylabel) identifier_ylabel
(identifier_LABEL_DEFAULT) identifier_LABEL_DEFAULT
)default_parameter
)parameters
(block
(if_statement
(comparison_operator
(identifier_title) identifier_title
(string_"") string_""
)comparison_operator
(block
(expression_statement
(assignment
(identifier_title) identifier_title
(string_" ") string_" "
)assignment
)expression_statement
)block
)if_statement
(if_statement
(comparison_operator
(identifier_xlabel) identifier_xlabel
(string_"") string_""
)comparison_operator
(block
(expression_statement
(assignment
(identifier_xlabel) identifier_xlabel
(string_" ") string_" "
)assignment
)expression_statement
)block
)if_statement
(if_statement
(comparison_operator
(identifier_ylabel) identifier_ylabel
(string_"") string_""
)comparison_operator
(block
(expression_statement
(assignment
(identifier_ylabel) identifier_ylabel
(string_" ") string_" "
)assignment
)expression_statement
)block
)if_statement
(if_statement
(comparison_operator
(identifier_title) identifier_title
(None) None
)comparison_operator
(block
(expression_statement
(assignment
(identifier_title) identifier_title
(string_"") string_""
)assignment
)expression_statement
)block
)if_statement
(if_statement
(comparison_operator
(identifier_xlabel) identifier_xlabel
(None) None
)comparison_operator
(block
(expression_statement
(assignment
(identifier_xlabel) identifier_xlabel
(string_"") string_""
)assignment
)expression_statement
)block
)if_statement
(if_statement
(comparison_operator
(identifier_ylabel) identifier_ylabel
(None) None
)comparison_operator
(block
(expression_statement
(assignment
(identifier_ylabel) identifier_ylabel
(string_"") string_""
)assignment
)expression_statement
)block
)if_statement
(return_statement
(call
(identifier_Plot) identifier_Plot
(argument_list
(call
(attribute
(attribute
(identifier_self) identifier_self
(identifier___proxy__) identifier___proxy__
)attribute
(identifier_plot) identifier_plot
)attribute
(argument_list
(identifier_title) identifier_title
(identifier_xlabel) identifier_xlabel
(identifier_ylabel) identifier_ylabel
)argument_list
)call
)argument_list
)call
)return_statement
)block
)function_definition
)module | 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
----------
title : str
The plot title to show for the resulting visualization.
If the title is None, the title will be omitted.
xlabel : str
The X axis label to show for the resulting visualization.
If the xlabel is None, the X axis label will be omitted.
ylabel : str
The Y axis label to show for the resulting visualization.
If the ylabel is None, the Y axis label will be omitted.
Returns
-------
out : Plot
A :class: Plot object that is the visualization of the SArray.
Examples
--------
Suppose 'sa' is an SArray, we can create a plot of it using:
>>> plt = sa.plot()
To override the default plot title and axis labels:
>>> plt = sa.plot(title="My Plot Title", xlabel="My X Axis", ylabel="My Y Axis")
We can then visualize the plot using:
>>> plt.show() |
(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_parameter
(identifier_basedir) identifier_basedir
(None) None
)default_parameter
(default_parameter
(identifier_subdir) identifier_subdir
(None) None
)default_parameter
(default_parameter
(identifier_prefix) identifier_prefix
(None) None
)default_parameter
)parameters
(block
(expression_statement
(assignment
(identifier_thumbs) identifier_thumbs
(call
(identifier_thumbnails_for_file) identifier_thumbnails_for_file
(argument_list
(identifier_relative_source_path) identifier_relative_source_path
(identifier_root) identifier_root
(identifier_basedir) identifier_basedir
(identifier_subdir) identifier_subdir
(identifier_prefix) identifier_prefix
)argument_list
)call
)assignment
)expression_statement
(return_statement
(call
(identifier__delete_using_thumbs_list) identifier__delete_using_thumbs_list
(argument_list
(identifier_thumbs) identifier_thumbs
)argument_list
)call
)return_statement
)block
)function_definition
)module | 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
(identifier_raw_result) identifier_raw_result
(call
(attribute
(identifier_shutil) identifier_shutil
(identifier_which) identifier_which
)attribute
(argument_list
(identifier_cmd) identifier_cmd
(attribute
(identifier_os) identifier_os
(identifier_X_OK) identifier_X_OK
)attribute
(identifier_path) identifier_path
)argument_list
)call
)assignment
)expression_statement
(if_statement
(identifier_raw_result) identifier_raw_result
(block
(return_statement
(call
(attribute
(attribute
(identifier_os) identifier_os
(identifier_path) identifier_path
)attribute
(identifier_abspath) identifier_abspath
)attribute
(argument_list
(identifier_raw_result) identifier_raw_result
)argument_list
)call
)return_statement
)block
(else_clause
(block
(raise_statement
(call
(identifier_ValueError) identifier_ValueError
(argument_list
(call
(attribute
(string_"Could not find '{}' in the path") string_"Could not find '{}' in the path"
(identifier_format) identifier_format
)attribute
(argument_list
(identifier_cmd) identifier_cmd
)argument_list
)call
)argument_list
)call
)raise_statement
)block
)else_clause
)if_statement
)block
)function_definition
)module | 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
(comparison_operator
(identifier_weights) identifier_weights
(None) None
)comparison_operator
(block
(expression_statement
(assignment
(identifier_weights) identifier_weights
(binary_operator
(list
(binary_operator
(float_1.) float_1.
(call
(identifier_len) identifier_len
(argument_list
(identifier_values) identifier_values
)argument_list
)call
)binary_operator
)list
(call
(identifier_len) identifier_len
(argument_list
(identifier_values) identifier_values
)argument_list
)call
)binary_operator
)assignment
)expression_statement
)block
)if_statement
(if_statement
(not_operator
(call
(identifier_isinstance) identifier_isinstance
(argument_list
(identifier_values) identifier_values
(attribute
(identifier_numpy) identifier_numpy
(identifier_ndarray) identifier_ndarray
)attribute
)argument_list
)call
)not_operator
(block
(expression_statement
(assignment
(identifier_values) identifier_values
(call
(attribute
(identifier_numpy) identifier_numpy
(identifier_array) identifier_array
)attribute
(argument_list
(identifier_values) identifier_values
)argument_list
)call
)assignment
)expression_statement
)block
)if_statement
(return_statement
(call
(attribute
(identifier_numpy) identifier_numpy
(identifier_average) identifier_average
)attribute
(argument_list
(identifier_values) identifier_values
(keyword_argument
(identifier_axis) identifier_axis
(integer_0) integer_0
)keyword_argument
(keyword_argument
(identifier_weights) identifier_weights
(identifier_weights) identifier_weights
)keyword_argument
)argument_list
)call
)return_statement
)block
)function_definition
)module | 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_b'=') string_b'='
(parenthesized_expression
(binary_operator
(integer_4) integer_4
(parenthesized_expression
(binary_operator
(call
(identifier_len) identifier_len
(argument_list
(identifier_data) identifier_data
)argument_list
)call
(integer_3) integer_3
)binary_operator
)parenthesized_expression
)binary_operator
)parenthesized_expression
)binary_operator
)assignment
)expression_statement
(return_statement
(call
(attribute
(identifier_base64) identifier_base64
(identifier_urlsafe_b64decode) identifier_urlsafe_b64decode
)attribute
(argument_list
(binary_operator
(identifier_data) identifier_data
(identifier_pad) identifier_pad
)binary_operator
)argument_list
)call
)return_statement
)block
)function_definition
)module | 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
(identifier_self) identifier_self
(identifier_ligand_atoms) identifier_ligand_atoms
)attribute
(dictionary_comprehension
(pair
(identifier_index) identifier_index
(dictionary
(pair
(string_"name") string_"name"
(attribute
(identifier_x) identifier_x
(identifier_name) identifier_name
)attribute
)pair
)dictionary
)pair
(for_in_clause
(pattern_list
(identifier_index) identifier_index
(identifier_x) identifier_x
)pattern_list
(call
(identifier_enumerate) identifier_enumerate
(argument_list
(attribute
(attribute
(attribute
(attribute
(identifier_self) identifier_self
(identifier_topology_data) identifier_topology_data
)attribute
(identifier_universe) identifier_universe
)attribute
(identifier_ligand_noH) identifier_ligand_noH
)attribute
(identifier_atoms) identifier_atoms
)attribute
)argument_list
)call
)for_in_clause
)dictionary_comprehension
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_contribs) identifier_contribs
(call
(attribute
(identifier_self) identifier_self
(identifier_calculate_logP) identifier_calculate_logP
)attribute
(argument_list
(identifier_mol) identifier_mol
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(call
(attribute
(identifier_self) identifier_self
(identifier_calculate_Gasteiger_charges) identifier_calculate_Gasteiger_charges
)attribute
(argument_list
(identifier_mol) identifier_mol
)argument_list
)call
)expression_statement
(expression_statement
(assignment
(identifier_fcharges) identifier_fcharges
(call
(attribute
(identifier_self) identifier_self
(identifier_calculate_formal_charge) identifier_calculate_formal_charge
)attribute
(argument_list
(identifier_mol) identifier_mol
)argument_list
)call
)assignment
)expression_statement
(for_statement
(identifier_atom) identifier_atom
(call
(attribute
(attribute
(identifier_self) identifier_self
(identifier_ligand_atoms) identifier_ligand_atoms
)attribute
(identifier_keys) identifier_keys
)attribute
(argument_list
)argument_list
)call
(block
(expression_statement
(assignment
(subscript
(subscript
(attribute
(identifier_self) identifier_self
(identifier_ligand_atoms) identifier_ligand_atoms
)attribute
(identifier_atom) identifier_atom
)subscript
(string_"logP") string_"logP"
)subscript
(subscript
(subscript
(identifier_contribs) identifier_contribs
(identifier_atom) identifier_atom
)subscript
(integer_0) integer_0
)subscript
)assignment
)expression_statement
(expression_statement
(assignment
(subscript
(subscript
(attribute
(identifier_self) identifier_self
(identifier_ligand_atoms) identifier_ligand_atoms
)attribute
(identifier_atom) identifier_atom
)subscript
(string_"MR") string_"MR"
)subscript
(subscript
(subscript
(identifier_contribs) identifier_contribs
(identifier_atom) identifier_atom
)subscript
(integer_1) integer_1
)subscript
)assignment
)expression_statement
(expression_statement
(assignment
(subscript
(subscript
(attribute
(identifier_self) identifier_self
(identifier_ligand_atoms) identifier_ligand_atoms
)attribute
(identifier_atom) identifier_atom
)subscript
(string_"Gasteiger_ch") string_"Gasteiger_ch"
)subscript
(call
(attribute
(call
(attribute
(identifier_mol) identifier_mol
(identifier_GetAtomWithIdx) identifier_GetAtomWithIdx
)attribute
(argument_list
(identifier_atom) identifier_atom
)argument_list
)call
(identifier_GetProp) identifier_GetProp
)attribute
(argument_list
(string_"_GasteigerCharge") string_"_GasteigerCharge"
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(subscript
(subscript
(attribute
(identifier_self) identifier_self
(identifier_ligand_atoms) identifier_ligand_atoms
)attribute
(identifier_atom) identifier_atom
)subscript
(string_"Formal charges") string_"Formal charges"
)subscript
(subscript
(identifier_fcharges) identifier_fcharges
(identifier_atom) identifier_atom
)subscript
)assignment
)expression_statement
)block
)for_statement
(expression_statement
(assignment
(attribute
(identifier_self) identifier_self
(identifier_rot_bonds) identifier_rot_bonds
)attribute
(call
(attribute
(identifier_self) identifier_self
(identifier_get_rotatable_bonds) identifier_get_rotatable_bonds
)attribute
(argument_list
(identifier_mol) identifier_mol
)argument_list
)call
)assignment
)expression_statement
)block
)function_definition
)module | 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
(identifier_basename) identifier_basename
(binary_operator
(string_'features-%d.txt') string_'features-%d.txt'
(identifier_i) identifier_i
)binary_operator
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_filename) identifier_filename
(binary_operator
(string_'%s/%s') string_'%s/%s'
(tuple
(attribute
(identifier_self) identifier_self
(identifier__outputDir) identifier__outputDir
)attribute
(identifier_basename) identifier_basename
)tuple
)binary_operator
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_featureList) identifier_featureList
(subscript
(subscript
(identifier_image) identifier_image
(string_'graphInfo') string_'graphInfo'
)subscript
(string_'features') string_'features'
)subscript
)assignment
)expression_statement
(with_statement
(with_clause
(with_item
(as_pattern
(call
(identifier_open) identifier_open
(argument_list
(identifier_filename) identifier_filename
(string_'w') string_'w'
)argument_list
)call
(as_pattern_target
(identifier_fp) identifier_fp
)as_pattern_target
)as_pattern
)with_item
)with_clause
(block
(for_statement
(identifier_feature) identifier_feature
(identifier_featureList) identifier_featureList
(block
(expression_statement
(call
(attribute
(identifier_fp) identifier_fp
(identifier_write) identifier_write
)attribute
(argument_list
(binary_operator
(string_'%s\n\n') string_'%s\n\n'
(attribute
(identifier_feature) identifier_feature
(identifier_feature) identifier_feature
)attribute
)binary_operator
)argument_list
)call
)expression_statement
)block
)for_statement
)block
)with_statement
(return_statement
(identifier_basename) identifier_basename
)return_statement
)block
)function_definition
)module | 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) identifier_iselector
(identifier_index) identifier_index
)parameters
(block
(expression_statement
(assignment
(identifier_flags) identifier_flags
(binary_operator
(identifier_FLG_PSEUDO) identifier_FLG_PSEUDO
(identifier_FLG_OPEN) identifier_FLG_OPEN
)binary_operator
)assignment
)expression_statement
(if_statement
(comparison_operator
(identifier_name) identifier_name
(string_':not') string_':not'
)comparison_operator
(block
(expression_statement
(augmented_assignment
(identifier_flags) identifier_flags
(identifier_FLG_NOT) identifier_FLG_NOT
)augmented_assignment
)expression_statement
)block
)if_statement
(if_statement
(comparison_operator
(identifier_name) identifier_name
(string_':has') string_':has'
)comparison_operator
(block
(expression_statement
(augmented_assignment
(identifier_flags) identifier_flags
(identifier_FLG_RELATIVE) identifier_FLG_RELATIVE
)augmented_assignment
)expression_statement
)block
)if_statement
(expression_statement
(call
(attribute
(attribute
(identifier_sel) identifier_sel
(identifier_selectors) identifier_selectors
)attribute
(identifier_append) identifier_append
)attribute
(argument_list
(call
(attribute
(identifier_self) identifier_self
(identifier_parse_selectors) identifier_parse_selectors
)attribute
(argument_list
(identifier_iselector) identifier_iselector
(identifier_index) identifier_index
(identifier_flags) identifier_flags
)argument_list
)call
)argument_list
)call
)expression_statement
(expression_statement
(assignment
(identifier_has_selector) identifier_has_selector
(True) True
)assignment
)expression_statement
(return_statement
(identifier_has_selector) identifier_has_selector
)return_statement
)block
)function_definition
)module | 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
(attribute
(string_'/archive/{}/parameter-groups') string_'/archive/{}/parameter-groups'
(identifier_format) identifier_format
)attribute
(argument_list
(attribute
(identifier_self) identifier_self
(identifier__instance) identifier__instance
)attribute
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_response) identifier_response
(call
(attribute
(attribute
(identifier_self) identifier_self
(identifier__client) identifier__client
)attribute
(identifier_get_proto) identifier_get_proto
)attribute
(argument_list
(keyword_argument
(identifier_path) identifier_path
(identifier_path) identifier_path
)keyword_argument
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_message) identifier_message
(call
(attribute
(identifier_archive_pb2) identifier_archive_pb2
(identifier_ParameterGroupInfo) identifier_ParameterGroupInfo
)attribute
(argument_list
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(call
(attribute
(identifier_message) identifier_message
(identifier_ParseFromString) identifier_ParseFromString
)attribute
(argument_list
(attribute
(identifier_response) identifier_response
(identifier_content) identifier_content
)attribute
)argument_list
)call
)expression_statement
(expression_statement
(assignment
(identifier_groups) identifier_groups
(call
(identifier_getattr) identifier_getattr
(argument_list
(identifier_message) identifier_message
(string_'group') string_'group'
)argument_list
)call
)assignment
)expression_statement
(return_statement
(call
(identifier_iter) identifier_iter
(argument_list
(identifier_groups) identifier_groups
)argument_list
)call
)return_statement
)block
)function_definition
)module | 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
(identifier_src_path) identifier_src_path
(call
(identifier_normalize_storage_path) identifier_normalize_storage_path
(argument_list
(identifier_src_path) identifier_src_path
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_dst_path) identifier_dst_path
(call
(identifier_normalize_storage_path) identifier_normalize_storage_path
(argument_list
(identifier_dst_path) identifier_dst_path
)argument_list
)call
)assignment
)expression_statement
(if_statement
(call
(identifier_hasattr) identifier_hasattr
(argument_list
(identifier_store) identifier_store
(string_'rename') string_'rename'
)argument_list
)call
(block
(expression_statement
(call
(attribute
(identifier_store) identifier_store
(identifier_rename) identifier_rename
)attribute
(argument_list
(identifier_src_path) identifier_src_path
(identifier_dst_path) identifier_dst_path
)argument_list
)call
)expression_statement
)block
(else_clause
(block
(expression_statement
(call
(identifier__rename_from_keys) identifier__rename_from_keys
(argument_list
(identifier_store) identifier_store
(identifier_src_path) identifier_src_path
(identifier_dst_path) identifier_dst_path
)argument_list
)call
)expression_statement
)block
)else_clause
)if_statement
)block
)function_definition
)module | 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) identifier_self
(identifier_in_channel) identifier_in_channel
)attribute
(argument_list
(identifier_channel) identifier_channel
)argument_list
)call
)not_operator
(block
(raise_statement
(call
(identifier_NotInChannel) identifier_NotInChannel
(argument_list
(identifier_channel) identifier_channel
)argument_list
)call
)raise_statement
)block
)if_statement
(expression_statement
(assignment
(identifier_password) identifier_password
(subscript
(subscript
(attribute
(identifier_self) identifier_self
(identifier_channels) identifier_channels
)attribute
(identifier_channel) identifier_channel
)subscript
(string_'password') string_'password'
)subscript
)assignment
)expression_statement
(expression_statement
(await
(call
(attribute
(identifier_self) identifier_self
(identifier_part) identifier_part
)attribute
(argument_list
(identifier_channel) identifier_channel
)argument_list
)call
)await
)expression_statement
(expression_statement
(await
(call
(attribute
(identifier_self) identifier_self
(identifier_join) identifier_join
)attribute
(argument_list
(identifier_channel) identifier_channel
(identifier_password) identifier_password
)argument_list
)call
)await
)expression_statement
)block
)function_definition
)module | 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
)dictionary
)assignment
)expression_statement
(expression_statement
(call
(attribute
(identifier_self) identifier_self
(identifier__generate_SAX) identifier__generate_SAX
)attribute
(argument_list
)argument_list
)call
)expression_statement
(expression_statement
(call
(attribute
(identifier_self) identifier_self
(identifier__construct_all_SAX_chunk_dict) identifier__construct_all_SAX_chunk_dict
)attribute
(argument_list
)argument_list
)call
)expression_statement
(expression_statement
(assignment
(identifier_length) identifier_length
(attribute
(identifier_self) identifier_self
(identifier_time_series_length) identifier_time_series_length
)attribute
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_lws) identifier_lws
(attribute
(identifier_self) identifier_self
(identifier_lag_window_size) identifier_lag_window_size
)attribute
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_fws) identifier_fws
(attribute
(identifier_self) identifier_self
(identifier_future_window_size) identifier_future_window_size
)attribute
)assignment
)expression_statement
(for_statement
(pattern_list
(identifier_i) identifier_i
(identifier_timestamp) identifier_timestamp
)pattern_list
(call
(identifier_enumerate) identifier_enumerate
(argument_list
(attribute
(attribute
(identifier_self) identifier_self
(identifier_time_series) identifier_time_series
)attribute
(identifier_timestamps) identifier_timestamps
)attribute
)argument_list
)call
(block
(if_statement
(boolean_operator
(comparison_operator
(identifier_i) identifier_i
(identifier_lws) identifier_lws
)comparison_operator
(comparison_operator
(identifier_i) identifier_i
(binary_operator
(identifier_length) identifier_length
(identifier_fws) identifier_fws
)binary_operator
)comparison_operator
)boolean_operator
(block
(expression_statement
(assignment
(subscript
(identifier_anom_scores) identifier_anom_scores
(identifier_timestamp) identifier_timestamp
)subscript
(integer_0) integer_0
)assignment
)expression_statement
)block
(else_clause
(block
(expression_statement
(assignment
(subscript
(identifier_anom_scores) identifier_anom_scores
(identifier_timestamp) identifier_timestamp
)subscript
(call
(attribute
(identifier_self) identifier_self
(identifier__compute_anom_score_between_two_windows) identifier__compute_anom_score_between_two_windows
)attribute
(argument_list
(identifier_i) identifier_i
)argument_list
)call
)assignment
)expression_statement
)block
)else_clause
)if_statement
)block
)for_statement
(expression_statement
(assignment
(attribute
(identifier_self) identifier_self
(identifier_anom_scores) identifier_anom_scores
)attribute
(call
(identifier_TimeSeries) identifier_TimeSeries
(argument_list
(call
(attribute
(identifier_self) identifier_self
(identifier__denoise_scores) identifier__denoise_scores
)attribute
(argument_list
(identifier_anom_scores) identifier_anom_scores
)argument_list
)call
)argument_list
)call
)assignment
)expression_statement
)block
)function_definition
)module | 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
)comparison_operator
(block
(return_statement
(False) False
)return_statement
)block
)if_statement
(if_statement
(boolean_operator
(comparison_operator
(call
(attribute
(attribute
(identifier_other) identifier_other
(identifier_PrevHash) identifier_PrevHash
)attribute
(identifier_ToBytes) identifier_ToBytes
)attribute
(argument_list
)argument_list
)call
(call
(attribute
(attribute
(identifier_self) identifier_self
(identifier_PrevHash) identifier_PrevHash
)attribute
(identifier_ToBytes) identifier_ToBytes
)attribute
(argument_list
)argument_list
)call
)comparison_operator
(comparison_operator
(attribute
(identifier_other) identifier_other
(identifier_PrevIndex) identifier_PrevIndex
)attribute
(attribute
(identifier_self) identifier_self
(identifier_PrevIndex) identifier_PrevIndex
)attribute
)comparison_operator
)boolean_operator
(block
(return_statement
(True) True
)return_statement
)block
)if_statement
(return_statement
(False) False
)return_statement
)block
)function_definition
)module | 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
(identifier_List) identifier_List
(type_parameter
(type
(identifier_int) identifier_int
)type
)type_parameter
)generic_type
)type
)typed_parameter
)parameters
(type
(None) None
)type
(block
(with_statement
(with_clause
(with_item
(attribute
(identifier_self) identifier_self
(identifier_write_lock) identifier_write_lock
)attribute
)with_item
(with_item
(attribute
(identifier_self) identifier_self
(identifier_conn) identifier_conn
)attribute
)with_item
)with_clause
(block
(expression_statement
(call
(attribute
(attribute
(identifier_self) identifier_self
(identifier_conn) identifier_conn
)attribute
(identifier_executemany) identifier_executemany
)attribute
(argument_list
(string_'DELETE FROM state_events WHERE identifier = ?') string_'DELETE FROM state_events WHERE identifier = ?'
(identifier_state_changes_to_delete) identifier_state_changes_to_delete
)argument_list
)call
)expression_statement
)block
)with_statement
)block
)function_definition
)module | 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
(attribute
(attribute
(identifier_token) identifier_token
(identifier_end_mark) identifier_end_mark
)attribute
(identifier_line) identifier_line
)attribute
(integer_1) integer_1
)binary_operator
)assignment
)expression_statement
(if_statement
(not_operator
(call
(identifier_isinstance) identifier_isinstance
(argument_list
(identifier_token) identifier_token
(attribute
(identifier_yaml) identifier_yaml
(identifier_ScalarToken) identifier_ScalarToken
)attribute
)argument_list
)call
)not_operator
(block
(return_statement
(identifier_end_line) identifier_end_line
)return_statement
)block
)if_statement
(expression_statement
(assignment
(identifier_pos) identifier_pos
(binary_operator
(attribute
(attribute
(identifier_token) identifier_token
(identifier_end_mark) identifier_end_mark
)attribute
(identifier_pointer) identifier_pointer
)attribute
(integer_1) integer_1
)binary_operator
)assignment
)expression_statement
(while_statement
(parenthesized_expression
(boolean_operator
(comparison_operator
(identifier_pos) identifier_pos
(binary_operator
(attribute
(attribute
(identifier_token) identifier_token
(identifier_start_mark) identifier_start_mark
)attribute
(identifier_pointer) identifier_pointer
)attribute
(integer_1) integer_1
)binary_operator
)comparison_operator
(comparison_operator
(subscript
(attribute
(attribute
(identifier_token) identifier_token
(identifier_end_mark) identifier_end_mark
)attribute
(identifier_buffer) identifier_buffer
)attribute
(identifier_pos) identifier_pos
)subscript
(attribute
(identifier_string) identifier_string
(identifier_whitespace) identifier_whitespace
)attribute
)comparison_operator
)boolean_operator
)parenthesized_expression
(block
(if_statement
(comparison_operator
(subscript
(attribute
(attribute
(identifier_token) identifier_token
(identifier_end_mark) identifier_end_mark
)attribute
(identifier_buffer) identifier_buffer
)attribute
(identifier_pos) identifier_pos
)subscript
(string_'\n') string_'\n'
)comparison_operator
(block
(expression_statement
(augmented_assignment
(identifier_end_line) identifier_end_line
(integer_1) integer_1
)augmented_assignment
)expression_statement
)block
)if_statement
(expression_statement
(augmented_assignment
(identifier_pos) identifier_pos
(integer_1) integer_1
)augmented_assignment
)expression_statement
)block
)while_statement
(return_statement
(identifier_end_line) identifier_end_line
)return_statement
)block
)function_definition
)module | 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
)expression_statement
(expression_statement
(assignment
(identifier__msg) identifier__msg
(binary_operator
(attribute
(identifier_self) identifier_self
(identifier_msg) identifier_msg
)attribute
(dictionary
(pair
(string_'distro') string_'distro'
(attribute
(identifier_self) identifier_self
(identifier_distro) identifier_distro
)attribute
)pair
(pair
(string_'vendor') string_'vendor'
(attribute
(identifier_self) identifier_self
(identifier_vendor) identifier_vendor
)attribute
)pair
(pair
(string_'vendor_url') string_'vendor_url'
(attribute
(identifier_self) identifier_self
(identifier_vendor_url) identifier_vendor_url
)attribute
)pair
(pair
(string_'vendor_text') string_'vendor_text'
(attribute
(identifier_self) identifier_self
(identifier_vendor_text) identifier_vendor_text
)attribute
)pair
(pair
(string_'tmpdir') string_'tmpdir'
(subscript
(attribute
(identifier_self) identifier_self
(identifier_commons) identifier_commons
)attribute
(string_'tmpdir') string_'tmpdir'
)subscript
)pair
)dictionary
)binary_operator
)assignment
)expression_statement
(expression_statement
(assignment
(identifier__fmt) identifier__fmt
(string_"") string_""
)assignment
)expression_statement
(for_statement
(identifier_line) identifier_line
(call
(attribute
(identifier__msg) identifier__msg
(identifier_splitlines) identifier_splitlines
)attribute
(argument_list
)argument_list
)call
(block
(expression_statement
(assignment
(identifier__fmt) identifier__fmt
(binary_operator
(binary_operator
(identifier__fmt) identifier__fmt
(call
(identifier_fill) identifier_fill
(argument_list
(identifier_line) identifier_line
(identifier_width) identifier_width
(keyword_argument
(identifier_replace_whitespace) identifier_replace_whitespace
(False) False
)keyword_argument
)argument_list
)call
)binary_operator
(string_'\n') string_'\n'
)binary_operator
)assignment
)expression_statement
)block
)for_statement
(return_statement
(identifier__fmt) identifier__fmt
)return_statement
)block
)function_definition
)module | 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
)attribute
)type
)typed_parameter
(identifier_entrez_id_name) identifier_entrez_id_name
(identifier_log2_fold_change_name) identifier_log2_fold_change_name
(identifier_adjusted_p_value_name) identifier_adjusted_p_value_name
(identifier_entrez_delimiter) identifier_entrez_delimiter
(default_parameter
(identifier_base_mean) identifier_base_mean
(None) None
)default_parameter
)parameters
(type
(generic_type
(identifier_List) identifier_List
(type_parameter
(type
(identifier_Gene) identifier_Gene
)type
)type_parameter
)generic_type
)type
(block
(expression_statement
(call
(attribute
(identifier_logger) identifier_logger
(identifier_info) identifier_info
)attribute
(argument_list
(string_"In _handle_df()") string_"In _handle_df()"
)argument_list
)call
)expression_statement
(if_statement
(boolean_operator
(comparison_operator
(identifier_base_mean) identifier_base_mean
(None) None
)comparison_operator
(comparison_operator
(identifier_base_mean) identifier_base_mean
(attribute
(identifier_df) identifier_df
(identifier_columns) identifier_columns
)attribute
)comparison_operator
)boolean_operator
(block
(expression_statement
(assignment
(identifier_df) identifier_df
(subscript
(identifier_df) identifier_df
(call
(attribute
(identifier_pd) identifier_pd
(identifier_notnull) identifier_notnull
)attribute
(argument_list
(subscript
(identifier_df) identifier_df
(identifier_base_mean) identifier_base_mean
)subscript
)argument_list
)call
)subscript
)assignment
)expression_statement
)block
)if_statement
(expression_statement
(assignment
(identifier_df) identifier_df
(subscript
(identifier_df) identifier_df
(call
(attribute
(identifier_pd) identifier_pd
(identifier_notnull) identifier_notnull
)attribute
(argument_list
(subscript
(identifier_df) identifier_df
(identifier_entrez_id_name) identifier_entrez_id_name
)subscript
)argument_list
)call
)subscript
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_df) identifier_df
(subscript
(identifier_df) identifier_df
(call
(attribute
(identifier_pd) identifier_pd
(identifier_notnull) identifier_notnull
)attribute
(argument_list
(subscript
(identifier_df) identifier_df
(identifier_log2_fold_change_name) identifier_log2_fold_change_name
)subscript
)argument_list
)call
)subscript
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_df) identifier_df
(subscript
(identifier_df) identifier_df
(call
(attribute
(identifier_pd) identifier_pd
(identifier_notnull) identifier_notnull
)attribute
(argument_list
(subscript
(identifier_df) identifier_df
(identifier_adjusted_p_value_name) identifier_adjusted_p_value_name
)subscript
)argument_list
)call
)subscript
)assignment
)expression_statement
(return_statement
(list_comprehension
(call
(identifier_Gene) identifier_Gene
(argument_list
(keyword_argument
(identifier_entrez_id) identifier_entrez_id
(identifier_entrez_id) identifier_entrez_id
)keyword_argument
(keyword_argument
(identifier_log2_fold_change) identifier_log2_fold_change
(subscript
(identifier_data) identifier_data
(identifier_log2_fold_change_name) identifier_log2_fold_change_name
)subscript
)keyword_argument
(keyword_argument
(identifier_padj) identifier_padj
(subscript
(identifier_data) identifier_data
(identifier_adjusted_p_value_name) identifier_adjusted_p_value_name
)subscript
)keyword_argument
)argument_list
)call
(for_in_clause
(pattern_list
(identifier__) identifier__
(identifier_data) identifier_data
)pattern_list
(call
(attribute
(identifier_df) identifier_df
(identifier_iterrows) identifier_iterrows
)attribute
(argument_list
)argument_list
)call
)for_in_clause
(for_in_clause
(identifier_entrez_id) identifier_entrez_id
(call
(attribute
(call
(identifier_str) identifier_str
(argument_list
(subscript
(identifier_data) identifier_data
(identifier_entrez_id_name) identifier_entrez_id_name
)subscript
)argument_list
)call
(identifier_split) identifier_split
)attribute
(argument_list
(identifier_entrez_delimiter) identifier_entrez_delimiter
)argument_list
)call
)for_in_clause
)list_comprehension
)return_statement
)block
)function_definition
)module | 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
(attribute
(subscript
(attribute
(identifier_pfeed) identifier_pfeed
(identifier_frequencies) identifier_frequencies
)attribute
(list
(string_'route_short_name') string_'route_short_name'
(string_'route_long_name') string_'route_long_name'
(string_'route_type') string_'route_type'
(string_'shape_id') string_'shape_id'
)list
)subscript
(identifier_drop_duplicates) identifier_drop_duplicates
)attribute
(argument_list
)argument_list
)call
(identifier_copy) identifier_copy
)attribute
(argument_list
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(subscript
(identifier_f) identifier_f
(string_'route_id') string_'route_id'
)subscript
(binary_operator
(string_'r') string_'r'
(call
(attribute
(subscript
(identifier_f) identifier_f
(string_'route_short_name') string_'route_short_name'
)subscript
(identifier_map) identifier_map
)attribute
(argument_list
(identifier_str) identifier_str
)argument_list
)call
)binary_operator
)assignment
)expression_statement
(delete_statement
(subscript
(identifier_f) identifier_f
(string_'shape_id') string_'shape_id'
)subscript
)delete_statement
(return_statement
(identifier_f) identifier_f
)return_statement
)block
)function_definition
)module | 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
)list
)assignment
)expression_statement
(for_statement
(pattern_list
(identifier_node) identifier_node
(identifier_edges) identifier_edges
)pattern_list
(call
(attribute
(attribute
(identifier_self) identifier_self
(identifier_graph) identifier_graph
)attribute
(identifier_items) identifier_items
)attribute
(argument_list
)argument_list
)call
(block
(expression_statement
(augmented_assignment
(identifier_combinations) identifier_combinations
(list_comprehension
(list
(identifier_node) identifier_node
(identifier_edge) identifier_edge
)list
(for_in_clause
(identifier_edge) identifier_edge
(identifier_edges) identifier_edges
)for_in_clause
)list_comprehension
)augmented_assignment
)expression_statement
)block
)for_statement
(while_statement
(True) True
(block
(expression_statement
(assignment
(identifier_new_combinations) identifier_new_combinations
(list
)list
)assignment
)expression_statement
(for_statement
(identifier_comb1) identifier_comb1
(identifier_combinations) identifier_combinations
(block
(for_statement
(identifier_comb2) identifier_comb2
(identifier_combinations) identifier_combinations
(block
(if_statement
(not_operator
(comparison_operator
(subscript
(identifier_comb1) identifier_comb1
(unary_operator
(integer_1) integer_1
)unary_operator
)subscript
(subscript
(identifier_comb2) identifier_comb2
(integer_0) integer_0
)subscript
)comparison_operator
)not_operator
(block
(continue_statement
)continue_statement
)block
)if_statement
(expression_statement
(assignment
(identifier_new_entry) identifier_new_entry
(binary_operator
(identifier_comb1) identifier_comb1
(subscript
(identifier_comb2) identifier_comb2
(slice
(integer_1) integer_1
(colon) colon
)slice
)subscript
)binary_operator
)assignment
)expression_statement
(if_statement
(comparison_operator
(identifier_new_entry) identifier_new_entry
(identifier_combinations) identifier_combinations
)comparison_operator
(block
(expression_statement
(call
(attribute
(identifier_new_combinations) identifier_new_combinations
(identifier_append) identifier_append
)attribute
(argument_list
(identifier_new_entry) identifier_new_entry
)argument_list
)call
)expression_statement
)block
)if_statement
)block
)for_statement
)block
)for_statement
(if_statement
(not_operator
(identifier_new_combinations) identifier_new_combinations
)not_operator
(block
(break_statement
)break_statement
)block
)if_statement
(expression_statement
(augmented_assignment
(identifier_combinations) identifier_combinations
(identifier_new_combinations) identifier_new_combinations
)augmented_assignment
)expression_statement
)block
)while_statement
(expression_statement
(assignment
(identifier_constructed) identifier_constructed
(set_comprehension
(tuple
(subscript
(identifier_c) identifier_c
(integer_0) integer_0
)subscript
(subscript
(identifier_c) identifier_c
(unary_operator
(integer_1) integer_1
)unary_operator
)subscript
)tuple
(for_in_clause
(identifier_c) identifier_c
(identifier_combinations) identifier_combinations
)for_in_clause
(if_clause
(comparison_operator
(call
(identifier_len) identifier_len
(argument_list
(identifier_c) identifier_c
)argument_list
)call
(integer_2) integer_2
)comparison_operator
)if_clause
)set_comprehension
)assignment
)expression_statement
(for_statement
(pattern_list
(identifier_node) identifier_node
(identifier_edges) identifier_edges
)pattern_list
(call
(attribute
(attribute
(identifier_self) identifier_self
(identifier_graph) identifier_graph
)attribute
(identifier_items) identifier_items
)attribute
(argument_list
)argument_list
)call
(block
(expression_statement
(assignment
(identifier_bad_nodes) identifier_bad_nodes
(set_comprehension
(identifier_e) identifier_e
(for_in_clause
(pattern_list
(identifier_n) identifier_n
(identifier_e) identifier_e
)pattern_list
(identifier_constructed) identifier_constructed
)for_in_clause
(if_clause
(comparison_operator
(identifier_node) identifier_node
(identifier_n) identifier_n
)comparison_operator
)if_clause
)set_comprehension
)assignment
)expression_statement
(expression_statement
(assignment
(subscript
(attribute
(identifier_self) identifier_self
(identifier_graph) identifier_graph
)attribute
(identifier_node) identifier_node
)subscript
(binary_operator
(identifier_edges) identifier_edges
(identifier_bad_nodes) identifier_bad_nodes
)binary_operator
)assignment
)expression_statement
)block
)for_statement
)block
)function_definition
)module | 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
(call
(attribute
(identifier_inspect) identifier_inspect
(identifier_isclass) identifier_isclass
)attribute
(argument_list
(identifier_function) identifier_function
)argument_list
)call
)assignment
)expression_statement
(if_statement
(identifier_is_class) identifier_is_class
(block
(expression_statement
(assignment
(identifier_function) identifier_function
(attribute
(identifier_function) identifier_function
(identifier___init__) identifier___init__
)attribute
)assignment
)expression_statement
)block
)if_statement
(expression_statement
(assignment
(identifier_function_info) identifier_function_info
(call
(attribute
(identifier_inspect) identifier_inspect
(identifier_getargspec) identifier_getargspec
)attribute
(argument_list
(identifier_function) identifier_function
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_function_args) identifier_function_args
(attribute
(identifier_function_info) identifier_function_info
(identifier_args) identifier_args
)attribute
)assignment
)expression_statement
(if_statement
(identifier_is_class) identifier_is_class
(block
(expression_statement
(assignment
(identifier_function_args) identifier_function_args
(subscript
(identifier_function_args) identifier_function_args
(slice
(integer_1) integer_1
(colon) colon
)slice
)subscript
)assignment
)expression_statement
)block
)if_statement
(function_definition
(function_name_evaluation_checker) function_name_evaluation_checker
(parameters
(list_splat_pattern
(identifier_args) identifier_args
)list_splat_pattern
(dictionary_splat_pattern
(identifier_kwargs) identifier_kwargs
)dictionary_splat_pattern
)parameters
(block
(expression_statement
(assignment
(identifier_kwarg_keys) identifier_kwarg_keys
(call
(identifier_set) identifier_set
(argument_list
(call
(attribute
(identifier_kwargs) identifier_kwargs
(identifier_keys) identifier_keys
)attribute
(argument_list
)argument_list
)call
)argument_list
)call
)assignment
)expression_statement
(if_statement
(comparison_operator
(attribute
(identifier_function_info) identifier_function_info
(identifier_keywords) identifier_keywords
)attribute
(None) None
)comparison_operator
(block
(expression_statement
(assignment
(identifier_acceptable_kwargs) identifier_acceptable_kwargs
(subscript
(identifier_function_args) identifier_function_args
(slice
(call
(identifier_len) identifier_len
(argument_list
(identifier_args) identifier_args
)argument_list
)call
(colon) colon
)slice
)subscript
)assignment
)expression_statement
(if_statement
(not_operator
(call
(attribute
(identifier_kwarg_keys) identifier_kwarg_keys
(identifier_issubset) identifier_issubset
)attribute
(argument_list
(identifier_acceptable_kwargs) identifier_acceptable_kwargs
)argument_list
)call
)not_operator
(block
(expression_statement
(call
(identifier_TypeError) identifier_TypeError
(argument_list
(call
(attribute
(string_"Unrecognized Arguments: {0}") string_"Unrecognized Arguments: {0}"
(identifier_format) identifier_format
)attribute
(argument_list
(list_comprehension
(identifier_key) identifier_key
(for_in_clause
(identifier_key) identifier_key
(identifier_kwarg_keys) identifier_kwarg_keys
)for_in_clause
(if_clause
(comparison_operator
(identifier_key) identifier_key
(identifier_acceptable_kwargs) identifier_acceptable_kwargs
)comparison_operator
)if_clause
)list_comprehension
)argument_list
)call
)argument_list
)call
)expression_statement
)block
)if_statement
)block
)if_statement
(expression_statement
(assignment
(identifier_needed_args) identifier_needed_args
(subscript
(identifier_function_args) identifier_function_args
(slice
(call
(identifier_len) identifier_len
(argument_list
(identifier_args) identifier_args
)argument_list
)call
(colon) colon
)slice
)subscript
)assignment
)expression_statement
(if_statement
(attribute
(identifier_function_info) identifier_function_info
(identifier_defaults) identifier_defaults
)attribute
(block
(expression_statement
(assignment
(identifier_needed_args) identifier_needed_args
(subscript
(identifier_needed_args) identifier_needed_args
(slice
(colon) colon
(unary_operator
(call
(identifier_len) identifier_len
(argument_list
(attribute
(identifier_function_info) identifier_function_info
(identifier_defaults) identifier_defaults
)attribute
)argument_list
)call
)unary_operator
)slice
)subscript
)assignment
)expression_statement
)block
)if_statement
(return_statement
(boolean_operator
(not_operator
(identifier_needed_args) identifier_needed_args
)not_operator
(call
(attribute
(identifier_kwarg_keys) identifier_kwarg_keys
(identifier_issuperset) identifier_issuperset
)attribute
(argument_list
(identifier_needed_args) identifier_needed_args
)argument_list
)call
)boolean_operator
)return_statement
)block
)function_definition
(return_statement
(identifier_evaluation_checker) identifier_evaluation_checker
)return_statement
)block
)function_definition
)module | 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
(assignment
(identifier_config_value) identifier_config_value
(call
(attribute
(identifier_config_m) identifier_config_m
(identifier_get_current_config_value) identifier_get_current_config_value
)attribute
(argument_list
(identifier_config_key) identifier_config_key
)argument_list
)call
)assignment
)expression_statement
(if_statement
(comparison_operator
(identifier_config_m) identifier_config_m
(attribute
(identifier_self) identifier_self
(identifier_core_config_model) identifier_core_config_model
)attribute
)comparison_operator
(block
(expression_statement
(assignment
(identifier_list_store) identifier_list_store
(attribute
(identifier_self) identifier_self
(identifier_core_list_store) identifier_core_list_store
)attribute
)assignment
)expression_statement
)block
(elif_clause
(comparison_operator
(identifier_config_m) identifier_config_m
(attribute
(identifier_self) identifier_self
(identifier_gui_config_model) identifier_gui_config_model
)attribute
)comparison_operator
(block
(expression_statement
(assignment
(identifier_list_store) identifier_list_store
(attribute
(identifier_self) identifier_self
(identifier_gui_list_store) identifier_gui_list_store
)attribute
)assignment
)expression_statement
)block
)elif_clause
(else_clause
(block
(return_statement
)return_statement
)block
)else_clause
)if_statement
(expression_statement
(call
(attribute
(identifier_self) identifier_self
(identifier__update_list_store_entry) identifier__update_list_store_entry
)attribute
(argument_list
(identifier_list_store) identifier_list_store
(identifier_config_key) identifier_config_key
(identifier_config_value) identifier_config_value
)argument_list
)call
)expression_statement
)block
)function_definition
)module | 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
(default_parameter
(identifier_r) identifier_r
(None) None
)default_parameter
)parameters
(block
(if_statement
(comparison_operator
(identifier_APIKEY) identifier_APIKEY
(identifier_param) identifier_param
)comparison_operator
(block
(expression_statement
(assignment
(subscript
(identifier_param) identifier_param
(identifier_APIKEY) identifier_APIKEY
)subscript
(call
(attribute
(identifier_self) identifier_self
(identifier_apikey) identifier_apikey
)attribute
(argument_list
)argument_list
)call
)assignment
)expression_statement
)block
)if_statement
(expression_statement
(assignment
(identifier_r) identifier_r
(conditional_expression
(call
(identifier_Result) identifier_Result
(argument_list
)argument_list
)call
(comparison_operator
(identifier_r) identifier_r
(None) None
)comparison_operator
(identifier_r) identifier_r
)conditional_expression
)assignment
)expression_statement
(for_statement
(identifier_p) identifier_p
(identifier_must) identifier_must
(block
(if_statement
(comparison_operator
(identifier_p) identifier_p
(identifier_param) identifier_param
)comparison_operator
(block
(expression_statement
(call
(attribute
(call
(attribute
(identifier_r) identifier_r
(identifier_code) identifier_code
)attribute
(argument_list
(attribute
(identifier_Code) identifier_Code
(identifier_ARGUMENT_MISSING) identifier_ARGUMENT_MISSING
)attribute
)argument_list
)call
(identifier_detail) identifier_detail
)attribute
(argument_list
(binary_operator
(string_'missing-') string_'missing-'
(identifier_p) identifier_p
)binary_operator
)argument_list
)call
)expression_statement
(break_statement
)break_statement
)block
)if_statement
)block
)for_statement
(return_statement
(identifier_r) identifier_r
)return_statement
)block
)function_definition
)module | 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_parameter
(default_parameter
(identifier_invalid_data_behavior) identifier_invalid_data_behavior
(string_'warn') string_'warn'
)default_parameter
)parameters
(block
(expression_statement
(assignment
(identifier_read) identifier_read
(call
(identifier_partial) identifier_partial
(argument_list
(identifier_read_csv) identifier_read_csv
(keyword_argument
(identifier_parse_dates) identifier_parse_dates
(list
(string_'day') string_'day'
)list
)keyword_argument
(keyword_argument
(identifier_index_col) identifier_index_col
(string_'day') string_'day'
)keyword_argument
(keyword_argument
(identifier_dtype) identifier_dtype
(attribute
(identifier_self) identifier_self
(identifier__csv_dtypes) identifier__csv_dtypes
)attribute
)keyword_argument
)argument_list
)call
)assignment
)expression_statement
(return_statement
(call
(attribute
(identifier_self) identifier_self
(identifier_write) identifier_write
)attribute
(argument_list
(generator_expression
(tuple
(identifier_asset) identifier_asset
(call
(identifier_read) identifier_read
(argument_list
(identifier_path) identifier_path
)argument_list
)call
)tuple
(for_in_clause
(pattern_list
(identifier_asset) identifier_asset
(identifier_path) identifier_path
)pattern_list
(call
(identifier_iteritems) identifier_iteritems
(argument_list
(identifier_asset_map) identifier_asset_map
)argument_list
)call
)for_in_clause
)generator_expression
(keyword_argument
(identifier_assets) identifier_assets
(call
(identifier_viewkeys) identifier_viewkeys
(argument_list
(identifier_asset_map) identifier_asset_map
)argument_list
)call
)keyword_argument
(keyword_argument
(identifier_show_progress) identifier_show_progress
(identifier_show_progress) identifier_show_progress
)keyword_argument
(keyword_argument
(identifier_invalid_data_behavior) identifier_invalid_data_behavior
(identifier_invalid_data_behavior) identifier_invalid_data_behavior
)keyword_argument
)argument_list
)call
)return_statement
)block
)function_definition
)module | 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.
invalid_data_behavior : {'warn', 'raise', 'ignore'}
What to do when data is encountered that is outside the range of
a uint32. |
(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
(string_b"") string_b""
)assignment
)expression_statement
(for_statement
(identifier_i) identifier_i
(call
(identifier_range) identifier_range
(argument_list
(integer_0) integer_0
(call
(identifier_len) identifier_len
(argument_list
(identifier_data) identifier_data
)argument_list
)call
(integer_8) integer_8
)argument_list
)call
(block
(expression_statement
(assignment
(identifier_block) identifier_block
(subscript
(identifier_data) identifier_data
(slice
(identifier_i) identifier_i
(colon) colon
(binary_operator
(identifier_i) identifier_i
(integer_8) integer_8
)binary_operator
)slice
)subscript
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_block_length) identifier_block_length
(call
(identifier_len) identifier_len
(argument_list
(identifier_block) identifier_block
)argument_list
)call
)assignment
)expression_statement
(if_statement
(comparison_operator
(identifier_block_length) identifier_block_length
(integer_8) integer_8
)comparison_operator
(block
(raise_statement
(call
(identifier_ValueError) identifier_ValueError
(argument_list
(concatenated_string
(string_"DES decryption must be a multiple of 8 ") string_"DES decryption must be a multiple of 8 "
(string_"bytes") string_"bytes"
)concatenated_string
)argument_list
)call
)raise_statement
)block
)if_statement
(expression_statement
(augmented_assignment
(identifier_decrypted_data) identifier_decrypted_data
(call
(attribute
(identifier_self) identifier_self
(identifier__decode_block) identifier__decode_block
)attribute
(argument_list
(identifier_block) identifier_block
)argument_list
)call
)augmented_assignment
)expression_statement
)block
)for_statement
(return_statement
(identifier_decrypted_data) identifier_decrypted_data
)return_statement
)block
)function_definition
)module | 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
(comparison_operator
(attribute
(identifier_cls) identifier_cls
(identifier_PATH) identifier_PATH
)attribute
(None) None
)comparison_operator
(comparison_operator
(identifier_path) identifier_path
(None) None
)comparison_operator
)boolean_operator
(block
(raise_statement
(call
(identifier_Exception) identifier_Exception
(argument_list
(string_"No database specified") string_"No database specified"
)argument_list
)call
)raise_statement
)block
)if_statement
(if_statement
(comparison_operator
(identifier_path) identifier_path
(None) None
)comparison_operator
(block
(expression_statement
(assignment
(identifier_path) identifier_path
(attribute
(identifier_cls) identifier_cls
(identifier_PATH) identifier_PATH
)attribute
)assignment
)expression_statement
)block
)if_statement
(if_statement
(comparison_operator
(string_".") string_"."
(identifier_path) identifier_path
)comparison_operator
(block
(raise_statement
(call
(identifier_Exception) identifier_Exception
(argument_list
(binary_operator
(parenthesized_expression
(binary_operator
(string_'invalid path "%s"; database paths must be ') string_'invalid path "%s"; database paths must be '
(string_'of the form "database.collection"') string_'of the form "database.collection"'
)binary_operator
)parenthesized_expression
(tuple
(identifier_path) identifier_path
)tuple
)binary_operator
)argument_list
)call
)raise_statement
)block
)if_statement
(if_statement
(attribute
(identifier_CONNECTION) identifier_CONNECTION
(identifier_test_mode) identifier_test_mode
)attribute
(block
(return_statement
(subscript
(subscript
(call
(attribute
(identifier_CONNECTION) identifier_CONNECTION
(identifier_get_connection) identifier_get_connection
)attribute
(argument_list
)argument_list
)call
(identifier_TEST_DATABASE_NAME) identifier_TEST_DATABASE_NAME
)subscript
(identifier_path) identifier_path
)subscript
)return_statement
)block
)if_statement
(expression_statement
(assignment
(tuple_pattern
(identifier_db) identifier_db
(identifier_coll) identifier_coll
)tuple_pattern
(call
(attribute
(identifier_path) identifier_path
(identifier_split) identifier_split
)attribute
(argument_list
(string_'.') string_'.'
(integer_1) integer_1
)argument_list
)call
)assignment
)expression_statement
(return_statement
(subscript
(subscript
(call
(attribute
(identifier_CONNECTION) identifier_CONNECTION
(identifier_get_connection) identifier_get_connection
)attribute
(argument_list
)argument_list
)call
(identifier_db) identifier_db
)subscript
(identifier_coll) identifier_coll
)subscript
)return_statement
)block
)function_definition
)module | 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
@raise Exception: if neither cls.PATH or path are valid |
(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
)parameters
(block
(expression_statement
(assignment
(identifier_cl) identifier_cl
(list
(string_"picard_gatk_recalibrate.py") string_"picard_gatk_recalibrate.py"
(identifier_picard_dir) identifier_picard_dir
(identifier_sam_ref) identifier_sam_ref
(identifier_bam_file) identifier_bam_file
)list
)assignment
)expression_statement
(if_statement
(identifier_dbsnp_file) identifier_dbsnp_file
(block
(expression_statement
(call
(attribute
(identifier_cl) identifier_cl
(identifier_append) identifier_append
)attribute
(argument_list
(identifier_dbsnp_file) identifier_dbsnp_file
)argument_list
)call
)expression_statement
)block
)if_statement
(expression_statement
(call
(attribute
(identifier_subprocess) identifier_subprocess
(identifier_check_call) identifier_check_call
)attribute
(argument_list
(identifier_cl) identifier_cl
)argument_list
)call
)expression_statement
(expression_statement
(assignment
(identifier_out_file) identifier_out_file
(subscript
(call
(attribute
(identifier_glob) identifier_glob
(identifier_glob) identifier_glob
)attribute
(argument_list
(binary_operator
(string_"%s*gatkrecal.bam") string_"%s*gatkrecal.bam"
(subscript
(call
(attribute
(attribute
(identifier_os) identifier_os
(identifier_path) identifier_path
)attribute
(identifier_splitext) identifier_splitext
)attribute
(argument_list
(identifier_bam_file) identifier_bam_file
)argument_list
)call
(integer_0) integer_0
)subscript
)binary_operator
)argument_list
)call
(integer_0) integer_0
)subscript
)assignment
)expression_statement
(return_statement
(identifier_out_file) identifier_out_file
)return_statement
)block
)function_definition
)module | 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
(expression_statement
(assignment
(identifier_start_time) identifier_start_time
(call
(attribute
(identifier_time) identifier_time
(identifier_time) identifier_time
)attribute
(argument_list
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_info) identifier_info
(call
(identifier__lookup_proxmox_task) identifier__lookup_proxmox_task
(argument_list
(identifier_upid) identifier_upid
)argument_list
)call
)assignment
)expression_statement
(if_statement
(not_operator
(identifier_info) identifier_info
)not_operator
(block
(expression_statement
(call
(attribute
(identifier_log) identifier_log
(identifier_error) identifier_error
)attribute
(argument_list
(concatenated_string
(string_'wait_for_task: No task information ') string_'wait_for_task: No task information '
(string_'retrieved based on given criteria.') string_'retrieved based on given criteria.'
)concatenated_string
)argument_list
)call
)expression_statement
(raise_statement
(identifier_SaltCloudExecutionFailure) identifier_SaltCloudExecutionFailure
)raise_statement
)block
)if_statement
(while_statement
(True) True
(block
(if_statement
(boolean_operator
(comparison_operator
(string_'status') string_'status'
(identifier_info) identifier_info
)comparison_operator
(comparison_operator
(subscript
(identifier_info) identifier_info
(string_'status') string_'status'
)subscript
(string_'OK') string_'OK'
)comparison_operator
)boolean_operator
(block
(expression_statement
(call
(attribute
(identifier_log) identifier_log
(identifier_debug) identifier_debug
)attribute
(argument_list
(string_'Task has been finished!') string_'Task has been finished!'
)argument_list
)call
)expression_statement
(return_statement
(True) True
)return_statement
)block
)if_statement
(expression_statement
(call
(attribute
(identifier_time) identifier_time
(identifier_sleep) identifier_sleep
)attribute
(argument_list
(integer_3) integer_3
)argument_list
)call
)expression_statement
(if_statement
(comparison_operator
(binary_operator
(call
(attribute
(identifier_time) identifier_time
(identifier_time) identifier_time
)attribute
(argument_list
)argument_list
)call
(identifier_start_time) identifier_start_time
)binary_operator
(identifier_timeout) identifier_timeout
)comparison_operator
(block
(expression_statement
(call
(attribute
(identifier_log) identifier_log
(identifier_debug) identifier_debug
)attribute
(argument_list
(string_'Timeout reached while waiting for task to be finished') string_'Timeout reached while waiting for task to be finished'
)argument_list
)call
)expression_statement
(return_statement
(False) False
)return_statement
)block
)if_statement
(expression_statement
(assignment
(identifier_info) identifier_info
(call
(identifier__lookup_proxmox_task) identifier__lookup_proxmox_task
(argument_list
(identifier_upid) identifier_upid
)argument_list
)call
)assignment
)expression_statement
)block
)while_statement
)block
)function_definition
)module | 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_parameter
(type
(list
(identifier_Any) identifier_Any
)list
)type
(type
(None) None
)type
)type_parameter
)generic_type
)type
)typed_parameter
)parameters
(type
(None) None
)type
(block
(with_statement
(with_clause
(with_item
(as_pattern
(call
(identifier__PropagateException) identifier__PropagateException
(argument_list
)argument_list
)call
(as_pattern_target
(identifier_propagate) identifier_propagate
)as_pattern_target
)as_pattern
)with_item
)with_clause
(block
(decorated_definition
(decorator
(call
(attribute
(identifier_ffi) identifier_ffi
(identifier_def_extern) identifier_def_extern
)attribute
(argument_list
(keyword_argument
(identifier_onerror) identifier_onerror
(identifier_propagate) identifier_propagate
)keyword_argument
)argument_list
)call
)decorator
(function_definition
(function_name__pycall_sdl_hook) function_name__pycall_sdl_hook
(parameters
(typed_parameter
(identifier_sdl_surface) identifier_sdl_surface
(type
(identifier_Any) identifier_Any
)type
)typed_parameter
)parameters
(type
(None) None
)type
(block
(expression_statement
(call
(identifier_callback) identifier_callback
(argument_list
(identifier_sdl_surface) identifier_sdl_surface
)argument_list
)call
)expression_statement
)block
)function_definition
)decorated_definition
(expression_statement
(call
(attribute
(identifier_lib) identifier_lib
(identifier_TCOD_sys_register_SDL_renderer) identifier_TCOD_sys_register_SDL_renderer
)attribute
(argument_list
(attribute
(identifier_lib) identifier_lib
(identifier__pycall_sdl_hook) identifier__pycall_sdl_hook
)attribute
)argument_list
)call
)expression_statement
)block
)with_statement
)block
)function_definition
)module | 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 Callable[[CData], None]:
A function which takes a single argument. |
(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
(pair
(string_'bool') string_'bool'
(identifier_Bool) identifier_Bool
)pair
(pair
(string_'int') string_'int'
(identifier_Int) identifier_Int
)pair
(pair
(string_'float') string_'float'
(identifier_Float) identifier_Float
)pair
)dictionary
)assignment
)expression_statement
(if_statement
(comparison_operator
(identifier_python_value) identifier_python_value
(None) None
)comparison_operator
(block
(return_statement
(call
(identifier_NoneType) identifier_NoneType
(argument_list
)argument_list
)call
)return_statement
)block
)if_statement
(expression_statement
(assignment
(identifier_python_type) identifier_python_type
(call
(identifier_type) identifier_type
(argument_list
(identifier_python_value) identifier_python_value
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_gibica_type) identifier_gibica_type
(call
(attribute
(identifier_binding_table) identifier_binding_table
(identifier_get) identifier_get
)attribute
(argument_list
(attribute
(identifier_python_type) identifier_python_type
(identifier___name__) identifier___name__
)attribute
)argument_list
)call
)assignment
)expression_statement
(if_statement
(comparison_operator
(identifier_gibica_type) identifier_gibica_type
(None) None
)comparison_operator
(block
(raise_statement
(call
(identifier_TypeError) identifier_TypeError
(argument_list
(string_'Impossible to recognize underlying type.') string_'Impossible to recognize underlying type.'
)argument_list
)call
)raise_statement
)block
)if_statement
(return_statement
(call
(identifier_gibica_type) identifier_gibica_type
(argument_list
(identifier_python_value) identifier_python_value
)argument_list
)call
)return_statement
)block
)function_definition
)module | 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) identifier_func
(attribute
(identifier_functools) identifier_functools
(identifier_partial) identifier_partial
)attribute
)argument_list
)call
(block
(return_statement
(call
(identifier__signature) identifier__signature
(argument_list
(attribute
(identifier_func) identifier_func
(identifier_func) identifier_func
)attribute
)argument_list
)call
)return_statement
)block
)if_statement
(if_statement
(boolean_operator
(call
(attribute
(identifier_inspect) identifier_inspect
(identifier_isfunction) identifier_isfunction
)attribute
(argument_list
(identifier_func) identifier_func
)argument_list
)call
(call
(attribute
(identifier_inspect) identifier_inspect
(identifier_ismethod) identifier_ismethod
)attribute
(argument_list
(identifier_func) identifier_func
)argument_list
)call
)boolean_operator
(block
(return_statement
(call
(identifier__signature) identifier__signature
(argument_list
(identifier_func) identifier_func
)argument_list
)call
)return_statement
)block
)if_statement
(return_statement
(call
(identifier__signature) identifier__signature
(argument_list
(attribute
(identifier_func) identifier_func
(identifier___call__) identifier___call__
)attribute
)argument_list
)call
)return_statement
)block
)function_definition
)module | 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
(identifier_Group) identifier_Group
(argument_list
(binary_operator
(call
(identifier_Regex) identifier_Regex
(argument_list
(string_"(-+)?[0-9]+") string_"(-+)?[0-9]+"
)argument_list
)call
(parenthesized_expression
(binary_operator
(binary_operator
(binary_operator
(binary_operator
(binary_operator
(call
(identifier_upkey) identifier_upkey
(argument_list
(binary_operator
(identifier_long_name) identifier_long_name
(string_"s") string_"s"
)binary_operator
)argument_list
)call
(call
(attribute
(call
(identifier_Regex) identifier_Regex
(argument_list
(binary_operator
(identifier_long_name) identifier_long_name
(string_"s") string_"s"
)binary_operator
)argument_list
)call
(identifier_setParseAction) identifier_setParseAction
)attribute
(argument_list
(identifier_upcaseTokens) identifier_upcaseTokens
)argument_list
)call
)binary_operator
(call
(identifier_upkey) identifier_upkey
(argument_list
(identifier_long_name) identifier_long_name
)argument_list
)call
)binary_operator
(call
(attribute
(call
(identifier_Regex) identifier_Regex
(argument_list
(identifier_long_name) identifier_long_name
)argument_list
)call
(identifier_setParseAction) identifier_setParseAction
)attribute
(argument_list
(identifier_upcaseTokens) identifier_upcaseTokens
)argument_list
)call
)binary_operator
(call
(identifier_upkey) identifier_upkey
(argument_list
(identifier_short_name) identifier_short_name
)argument_list
)call
)binary_operator
(call
(attribute
(call
(identifier_Regex) identifier_Regex
(argument_list
(identifier_short_name) identifier_short_name
)argument_list
)call
(identifier_setParseAction) identifier_setParseAction
)attribute
(argument_list
(identifier_upcaseTokens) identifier_upcaseTokens
)argument_list
)call
)binary_operator
)parenthesized_expression
)binary_operator
)argument_list
)call
(identifier_setResultsName) identifier_setResultsName
)attribute
(argument_list
(identifier_long_name) identifier_long_name
)argument_list
)call
)return_statement
)block
)function_definition
)module | 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
(argument_list
(identifier_self) identifier_self
(string_'sampler') string_'sampler'
)argument_list
)call
)not_operator
(comparison_operator
(attribute
(identifier_self) identifier_self
(identifier__samples) identifier__samples
)attribute
(None) None
)comparison_operator
)boolean_operator
(block
(raise_statement
(call
(identifier_AttributeError) identifier_AttributeError
(argument_list
(binary_operator
(string_'Must run MCMC (or load from file) ') string_'Must run MCMC (or load from file) '
(string_'before accessing samples') string_'before accessing samples'
)binary_operator
)argument_list
)call
)raise_statement
)block
)if_statement
(if_statement
(comparison_operator
(attribute
(identifier_self) identifier_self
(identifier__samples) identifier__samples
)attribute
(None) None
)comparison_operator
(block
(expression_statement
(assignment
(identifier_df) identifier_df
(attribute
(identifier_self) identifier_self
(identifier__samples) identifier__samples
)attribute
)assignment
)expression_statement
)block
(else_clause
(block
(expression_statement
(call
(attribute
(identifier_self) identifier_self
(identifier__make_samples) identifier__make_samples
)attribute
(argument_list
)argument_list
)call
)expression_statement
(expression_statement
(assignment
(identifier_df) identifier_df
(attribute
(identifier_self) identifier_self
(identifier__samples) identifier__samples
)attribute
)assignment
)expression_statement
)block
)else_clause
)if_statement
(return_statement
(identifier_df) identifier_df
)return_statement
)block
)function_definition
)module | 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 parameters get produced. |
(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
(subscript
(call
(attribute
(identifier_winreg) identifier_winreg
(identifier_QueryInfoKey) identifier_QueryInfoKey
)attribute
(argument_list
(identifier_key) identifier_key
)argument_list
)call
(integer_0) integer_0
)subscript
)argument_list
)call
(block
(expression_statement
(yield
(call
(attribute
(identifier_winreg) identifier_winreg
(identifier_OpenKey) identifier_OpenKey
)attribute
(argument_list
(identifier_key) identifier_key
(call
(attribute
(identifier_winreg) identifier_winreg
(identifier_EnumKey) identifier_EnumKey
)attribute
(argument_list
(identifier_key) identifier_key
(identifier_i) identifier_i
)argument_list
)call
)argument_list
)call
)yield
)expression_statement
)block
)for_statement
)block
)function_definition
)module | ! 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
(assignment
(attribute
(identifier_self) identifier_self
(identifier_primers) identifier_primers
)attribute
(call
(attribute
(attribute
(identifier_coral) identifier_coral
(identifier_design) identifier_design
)attribute
(identifier_primers) identifier_primers
)attribute
(argument_list
(attribute
(identifier_self) identifier_self
(identifier_template) identifier_template
)attribute
(keyword_argument
(identifier_tm) identifier_tm
(identifier_tm) identifier_tm
)keyword_argument
)argument_list
)call
)assignment
)expression_statement
(return_statement
(attribute
(identifier_self) identifier_self
(identifier_primers) identifier_primers
)attribute
)return_statement
)block
)function_definition
)module | 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) identifier_sigma
(float_1.0) float_1.0
)default_parameter
)parameters
(block
(expression_statement
(assignment
(identifier_gradnorm) identifier_gradnorm
(call
(identifier_gaussian_gradient_magnitude) identifier_gaussian_gradient_magnitude
(argument_list
(identifier_img) identifier_img
(identifier_sigma) identifier_sigma
(keyword_argument
(identifier_mode) identifier_mode
(string_'constant') string_'constant'
)keyword_argument
)argument_list
)call
)assignment
)expression_statement
(return_statement
(binary_operator
(float_1.0) float_1.0
(call
(attribute
(identifier_np) identifier_np
(identifier_sqrt) identifier_sqrt
)attribute
(argument_list
(binary_operator
(float_1.0) float_1.0
(binary_operator
(identifier_alpha) identifier_alpha
(identifier_gradnorm) identifier_gradnorm
)binary_operator
)binary_operator
)argument_list
)call
)binary_operator
)return_statement
)block
)function_definition
)module | 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
(identifier_body) identifier_body
)parameters
(block
(expression_statement
(assignment
(identifier_x_headers) identifier_x_headers
(call
(identifier_headers_to_include_from_request) identifier_headers_to_include_from_request
(argument_list
(identifier_curr_request) identifier_curr_request
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(pattern_list
(identifier_method) identifier_method
(identifier_t_headers) identifier_t_headers
)pattern_list
(call
(identifier_pre_process_method_headers) identifier_pre_process_method_headers
(argument_list
(identifier_method) identifier_method
(identifier_headers) identifier_headers
)argument_list
)call
)assignment
)expression_statement
(if_statement
(comparison_operator
(string_"CONTENT_TYPE") string_"CONTENT_TYPE"
(identifier_t_headers) identifier_t_headers
)comparison_operator
(block
(expression_statement
(call
(attribute
(identifier_t_headers) identifier_t_headers
(identifier_update) identifier_update
)attribute
(argument_list
(dictionary
(pair
(string_"CONTENT_TYPE") string_"CONTENT_TYPE"
(attribute
(identifier__settings) identifier__settings
(identifier_DEFAULT_CONTENT_TYPE) identifier_DEFAULT_CONTENT_TYPE
)attribute
)pair
)dictionary
)argument_list
)call
)expression_statement
)block
)if_statement
(expression_statement
(call
(attribute
(identifier_x_headers) identifier_x_headers
(identifier_update) identifier_update
)attribute
(argument_list
(identifier_t_headers) identifier_t_headers
)argument_list
)call
)expression_statement
(expression_statement
(assignment
(identifier_content_type) identifier_content_type
(call
(attribute
(identifier_x_headers) identifier_x_headers
(identifier_get) identifier_get
)attribute
(argument_list
(string_"CONTENT_TYPE") string_"CONTENT_TYPE"
(attribute
(identifier__settings) identifier__settings
(identifier_DEFAULT_CONTENT_TYPE) identifier_DEFAULT_CONTENT_TYPE
)attribute
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(identifier__request_factory) identifier__request_factory
(call
(identifier_BatchRequestFactory) identifier_BatchRequestFactory
(argument_list
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(identifier__request_provider) identifier__request_provider
(call
(identifier_getattr) identifier_getattr
(argument_list
(identifier__request_factory) identifier__request_factory
(identifier_method) identifier_method
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_secure) identifier_secure
(attribute
(identifier__settings) identifier__settings
(identifier_USE_HTTPS) identifier_USE_HTTPS
)attribute
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_request) identifier_request
(call
(identifier__request_provider) identifier__request_provider
(argument_list
(identifier_url) identifier_url
(keyword_argument
(identifier_data) identifier_data
(identifier_body) identifier_body
)keyword_argument
(keyword_argument
(identifier_secure) identifier_secure
(identifier_secure) identifier_secure
)keyword_argument
(keyword_argument
(identifier_content_type) identifier_content_type
(identifier_content_type) identifier_content_type
)keyword_argument
(dictionary_splat
(identifier_x_headers) identifier_x_headers
)dictionary_splat
)argument_list
)call
)assignment
)expression_statement
(return_statement
(identifier_request) identifier_request
)return_statement
)block
)function_definition
)module | 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
)list
)assignment
)expression_statement
(for_statement
(identifier_h) identifier_h
(attribute
(identifier_snl) identifier_snl
(identifier_history) identifier_history
)attribute
(block
(expression_statement
(assignment
(identifier_d) identifier_d
(attribute
(identifier_h) identifier_h
(identifier_description) identifier_description
)attribute
)assignment
)expression_statement
(expression_statement
(assignment
(subscript
(identifier_d) identifier_d
(string_'_snl') string_'_snl'
)subscript
(dictionary
(pair
(string_'url') string_'url'
(attribute
(identifier_h) identifier_h
(identifier_url) identifier_url
)attribute
)pair
(pair
(string_'name') string_'name'
(attribute
(identifier_h) identifier_h
(identifier_name) identifier_name
)attribute
)pair
)dictionary
)assignment
)expression_statement
(expression_statement
(call
(attribute
(identifier_hist) identifier_hist
(identifier_append) identifier_append
)attribute
(argument_list
(identifier_d) identifier_d
)argument_list
)call
)expression_statement
)block
)for_statement
(return_statement
(call
(identifier_cls) identifier_cls
(argument_list
(attribute
(identifier_snl) identifier_snl
(identifier_structure) identifier_structure
)attribute
(keyword_argument
(identifier_history) identifier_history
(identifier_hist) identifier_hist
)keyword_argument
)argument_list
)call
)return_statement
)block
)function_definition
)module | 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_references) identifier_tissue_in_references
(list
)list
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_query) identifier_query
(string_"./reference/source/tissue") string_"./reference/source/tissue"
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_tissues) identifier_tissues
(set_comprehension
(attribute
(identifier_x) identifier_x
(identifier_text) identifier_text
)attribute
(for_in_clause
(identifier_x) identifier_x
(call
(attribute
(identifier_entry) identifier_entry
(identifier_iterfind) identifier_iterfind
)attribute
(argument_list
(identifier_query) identifier_query
)argument_list
)call
)for_in_clause
)set_comprehension
)assignment
)expression_statement
(for_statement
(identifier_tissue) identifier_tissue
(identifier_tissues) identifier_tissues
(block
(if_statement
(comparison_operator
(identifier_tissue) identifier_tissue
(attribute
(identifier_self) identifier_self
(identifier_tissues) identifier_tissues
)attribute
)comparison_operator
(block
(expression_statement
(assignment
(subscript
(attribute
(identifier_self) identifier_self
(identifier_tissues) identifier_tissues
)attribute
(identifier_tissue) identifier_tissue
)subscript
(call
(attribute
(identifier_models) identifier_models
(identifier_TissueInReference) identifier_TissueInReference
)attribute
(argument_list
(keyword_argument
(identifier_tissue) identifier_tissue
(identifier_tissue) identifier_tissue
)keyword_argument
)argument_list
)call
)assignment
)expression_statement
)block
)if_statement
(expression_statement
(call
(attribute
(identifier_tissue_in_references) identifier_tissue_in_references
(identifier_append) identifier_append
)attribute
(argument_list
(subscript
(attribute
(identifier_self) identifier_self
(identifier_tissues) identifier_tissues
)attribute
(identifier_tissue) identifier_tissue
)subscript
)argument_list
)call
)expression_statement
)block
)for_statement
(return_statement
(identifier_tissue_in_references) identifier_tissue_in_references
)return_statement
)block
)function_definition
)module | 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
(identifier_response) identifier_response
(identifier_status_code) identifier_status_code
)pattern_list
(call
(attribute
(call
(attribute
(attribute
(attribute
(identifier_self) identifier_self
(identifier___pod__) identifier___pod__
)attribute
(identifier_Streams) identifier_Streams
)attribute
(identifier_get_v1_admin_stream_id_membership_list) identifier_get_v1_admin_stream_id_membership_list
)attribute
(argument_list
(keyword_argument
(identifier_sessionToken) identifier_sessionToken
(attribute
(identifier_self) identifier_self
(identifier___session__) identifier___session__
)attribute
)keyword_argument
(keyword_argument
(identifier_id) identifier_id
(identifier_stream_id) identifier_stream_id
)keyword_argument
)argument_list
)call
(identifier_result) identifier_result
)attribute
(argument_list
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(call
(attribute
(attribute
(identifier_self) identifier_self
(identifier_logger) identifier_logger
)attribute
(identifier_debug) identifier_debug
)attribute
(argument_list
(binary_operator
(string_'%s: %s') string_'%s: %s'
(tuple
(identifier_status_code) identifier_status_code
(identifier_response) identifier_response
)tuple
)binary_operator
)argument_list
)call
)expression_statement
(return_statement
(expression_list
(identifier_status_code) identifier_status_code
(identifier_response) identifier_response
)expression_list
)return_statement
)block
)function_definition
)module | 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
(identifier_self) identifier_self
(identifier_G) identifier_G
)attribute
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_statements) identifier_statements
(list
)list
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_binding_nodes) identifier_binding_nodes
(call
(attribute
(identifier_self) identifier_self
(identifier_find_event_with_outgoing_edges) identifier_find_event_with_outgoing_edges
)attribute
(argument_list
(string_'Binding') string_'Binding'
(list
(string_'Theme') string_'Theme'
(string_'Theme2') string_'Theme2'
)list
)argument_list
)call
)assignment
)expression_statement
(for_statement
(identifier_node) identifier_node
(identifier_binding_nodes) identifier_binding_nodes
(block
(expression_statement
(assignment
(identifier_theme1) identifier_theme1
(call
(attribute
(identifier_self) identifier_self
(identifier_get_entity_text_for_relation) identifier_get_entity_text_for_relation
)attribute
(argument_list
(identifier_node) identifier_node
(string_'Theme') string_'Theme'
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_theme1_node) identifier_theme1_node
(call
(attribute
(identifier_self) identifier_self
(identifier_get_related_node) identifier_get_related_node
)attribute
(argument_list
(identifier_node) identifier_node
(string_'Theme') string_'Theme'
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_theme2) identifier_theme2
(call
(attribute
(identifier_self) identifier_self
(identifier_get_entity_text_for_relation) identifier_get_entity_text_for_relation
)attribute
(argument_list
(identifier_node) identifier_node
(string_'Theme2') string_'Theme2'
)argument_list
)call
)assignment
)expression_statement
(assert_statement
(parenthesized_expression
(comparison_operator
(identifier_theme1) identifier_theme1
(None) None
)comparison_operator
)parenthesized_expression
)assert_statement
(assert_statement
(parenthesized_expression
(comparison_operator
(identifier_theme2) identifier_theme2
(None) None
)comparison_operator
)parenthesized_expression
)assert_statement
(expression_statement
(assignment
(identifier_evidence) identifier_evidence
(call
(attribute
(identifier_self) identifier_self
(identifier_node_to_evidence) identifier_node_to_evidence
)attribute
(argument_list
(identifier_theme1_node) identifier_theme1_node
(keyword_argument
(identifier_is_direct) identifier_is_direct
(True) True
)keyword_argument
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(call
(attribute
(identifier_statements) identifier_statements
(identifier_append) identifier_append
)attribute
(argument_list
(call
(identifier_Complex) identifier_Complex
(argument_list
(list
(call
(identifier_s2a) identifier_s2a
(argument_list
(identifier_theme1) identifier_theme1
)argument_list
)call
(call
(identifier_s2a) identifier_s2a
(argument_list
(identifier_theme2) identifier_theme2
)argument_list
)call
)list
(keyword_argument
(identifier_evidence) identifier_evidence
(identifier_evidence) identifier_evidence
)keyword_argument
)argument_list
)call
)argument_list
)call
)expression_statement
)block
)for_statement
(return_statement
(identifier_statements) identifier_statements
)return_statement
)block
)function_definition
)module | 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) identifier_entry
(call
(attribute
(identifier__PARAM_CONVERSION_MAP) identifier__PARAM_CONVERSION_MAP
(identifier_get) identifier_get
)attribute
(argument_list
(call
(attribute
(identifier_parameter_config) identifier_parameter_config
(identifier_get) identifier_get
)attribute
(argument_list
(string_'type') string_'type'
)argument_list
)call
)argument_list
)call
)assignment
)expression_statement
(if_statement
(boolean_operator
(comparison_operator
(identifier_entry) identifier_entry
(None) None
)comparison_operator
(comparison_operator
(string_'enum') string_'enum'
(identifier_parameter_config) identifier_parameter_config
)comparison_operator
)boolean_operator
(block
(expression_statement
(assignment
(identifier_entry) identifier_entry
(subscript
(identifier__PARAM_CONVERSION_MAP) identifier__PARAM_CONVERSION_MAP
(string_'enum') string_'enum'
)subscript
)assignment
)expression_statement
)block
)if_statement
(return_statement
(identifier_entry) identifier_entry
)return_statement
)block
)function_definition
)module | 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 functions/information needed to
validate and convert the given parameter from a string to the type expected
by the API. |
(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_parameter
(typed_parameter
(identifier_service_config) identifier_service_config
(type
(identifier_dict) identifier_dict
)type
)typed_parameter
)parameters
(block
(expression_statement
(assignment
(identifier_mode) identifier_mode
(dictionary
)dictionary
)assignment
)expression_statement
(for_statement
(identifier_d_value) identifier_d_value
(identifier_deploy_values) identifier_deploy_values
(block
(if_statement
(comparison_operator
(string_'restart_policy') string_'restart_policy'
(identifier_d_value) identifier_d_value
)comparison_operator
(block
(expression_statement
(assignment
(identifier_restart_spec) identifier_restart_spec
(call
(attribute
(attribute
(identifier_docker) identifier_docker
(identifier_types) identifier_types
)attribute
(identifier_RestartPolicy) identifier_RestartPolicy
)attribute
(argument_list
(dictionary_splat
(subscript
(identifier_deploy_values) identifier_deploy_values
(identifier_d_value) identifier_d_value
)subscript
)dictionary_splat
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(subscript
(identifier_service_config) identifier_service_config
(string_'restart_policy') string_'restart_policy'
)subscript
(identifier_restart_spec) identifier_restart_spec
)assignment
)expression_statement
)block
)if_statement
(if_statement
(comparison_operator
(string_'placement') string_'placement'
(identifier_d_value) identifier_d_value
)comparison_operator
(block
(for_statement
(pattern_list
(identifier_constraints_key) identifier_constraints_key
(identifier_constraints_value) identifier_constraints_value
)pattern_list
(line_continuation_\) line_continuation_\
(call
(attribute
(subscript
(identifier_deploy_values) identifier_deploy_values
(identifier_d_value) identifier_d_value
)subscript
(identifier_items) identifier_items
)attribute
(argument_list
)argument_list
)call
(block
(expression_statement
(assignment
(subscript
(identifier_service_config) identifier_service_config
(identifier_constraints_key) identifier_constraints_key
)subscript
(identifier_constraints_value) identifier_constraints_value
)assignment
)expression_statement
)block
)for_statement
)block
)if_statement
(if_statement
(comparison_operator
(string_'mode') string_'mode'
(identifier_d_value) identifier_d_value
)comparison_operator
(block
(expression_statement
(assignment
(subscript
(identifier_mode) identifier_mode
(identifier_d_value) identifier_d_value
)subscript
(subscript
(identifier_deploy_values) identifier_deploy_values
(identifier_d_value) identifier_d_value
)subscript
)assignment
)expression_statement
)block
)if_statement
(if_statement
(comparison_operator
(string_'replicas') string_'replicas'
(identifier_d_value) identifier_d_value
)comparison_operator
(block
(expression_statement
(assignment
(subscript
(identifier_mode) identifier_mode
(identifier_d_value) identifier_d_value
)subscript
(subscript
(identifier_deploy_values) identifier_deploy_values
(identifier_d_value) identifier_d_value
)subscript
)assignment
)expression_statement
)block
)if_statement
(if_statement
(comparison_operator
(string_'resources') string_'resources'
(identifier_d_value) identifier_d_value
)comparison_operator
(block
(expression_statement
(assignment
(identifier_resource_spec) identifier_resource_spec
(call
(attribute
(identifier_self) identifier_self
(identifier__parse_resources) identifier__parse_resources
)attribute
(argument_list
(identifier_deploy_values) identifier_deploy_values
(identifier_d_value) identifier_d_value
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(subscript
(identifier_service_config) identifier_service_config
(string_'resources') string_'resources'
)subscript
(identifier_resource_spec) identifier_resource_spec
)assignment
)expression_statement
)block
)if_statement
)block
)for_statement
(expression_statement
(assignment
(identifier_mode_spec) identifier_mode_spec
(call
(attribute
(attribute
(identifier_docker) identifier_docker
(identifier_types) identifier_types
)attribute
(identifier_ServiceMode) identifier_ServiceMode
)attribute
(argument_list
(dictionary_splat
(identifier_mode) identifier_mode
)dictionary_splat
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(subscript
(identifier_service_config) identifier_service_config
(string_'mode') string_'mode'
)subscript
(identifier_mode_spec) identifier_mode_spec
)assignment
)expression_statement
)block
)function_definition
)module | 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
(parenthesized_expression
(comparison_operator
(identifier_type_uri) identifier_type_uri
(attribute
(identifier_self) identifier_self
(identifier_type_uris) identifier_type_uris
)attribute
)comparison_operator
)parenthesized_expression
(parenthesized_expression
(boolean_operator
(comparison_operator
(identifier_type_uri) identifier_type_uri
(identifier_OPENID_2_0_TYPE) identifier_OPENID_2_0_TYPE
)comparison_operator
(call
(attribute
(identifier_self) identifier_self
(identifier_isOPIdentifier) identifier_isOPIdentifier
)attribute
(argument_list
)argument_list
)call
)boolean_operator
)parenthesized_expression
)boolean_operator
)parenthesized_expression
)return_statement
)block
)function_definition
)module | 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_required
(None) None
)default_parameter
)parameters
(block
(if_statement
(comparison_operator
(identifier_hook_cls) identifier_hook_cls
(identifier_executed_set) identifier_executed_set
)comparison_operator
(block
(return_statement
)return_statement
)block
)if_statement
(for_statement
(identifier_pre_hook) identifier_pre_hook
(attribute
(identifier_hook_cls) identifier_hook_cls
(identifier_pre) identifier_pre
)attribute
(block
(expression_statement
(call
(attribute
(identifier_self) identifier_self
(identifier__RunSingleHook) identifier__RunSingleHook
)attribute
(argument_list
(identifier_pre_hook) identifier_pre_hook
(identifier_executed_set) identifier_executed_set
(keyword_argument
(identifier_required) identifier_required
(attribute
(identifier_hook_cls) identifier_hook_cls
(identifier___name__) identifier___name__
)attribute
)keyword_argument
)argument_list
)call
)expression_statement
)block
)for_statement
(expression_statement
(assignment
(identifier_cls_instance) identifier_cls_instance
(call
(identifier_hook_cls) identifier_hook_cls
(argument_list
)argument_list
)call
)assignment
)expression_statement
(if_statement
(identifier_required) identifier_required
(block
(expression_statement
(call
(attribute
(identifier_logging) identifier_logging
(identifier_debug) identifier_debug
)attribute
(argument_list
(string_"Initializing %s, required by %s") string_"Initializing %s, required by %s"
(attribute
(identifier_hook_cls) identifier_hook_cls
(identifier___name__) identifier___name__
)attribute
(identifier_required) identifier_required
)argument_list
)call
)expression_statement
)block
(else_clause
(block
(expression_statement
(call
(attribute
(identifier_logging) identifier_logging
(identifier_debug) identifier_debug
)attribute
(argument_list
(string_"Initializing %s") string_"Initializing %s"
(attribute
(identifier_hook_cls) identifier_hook_cls
(identifier___name__) identifier___name__
)attribute
)argument_list
)call
)expression_statement
)block
)else_clause
)if_statement
(expression_statement
(call
(attribute
(identifier_cls_instance) identifier_cls_instance
(identifier_Run) identifier_Run
)attribute
(argument_list
)argument_list
)call
)expression_statement
(expression_statement
(call
(attribute
(identifier_executed_set) identifier_executed_set
(identifier_add) identifier_add
)attribute
(argument_list
(identifier_hook_cls) identifier_hook_cls
)argument_list
)call
)expression_statement
(if_statement
(comparison_operator
(identifier_hook_cls) identifier_hook_cls
(attribute
(identifier_self) identifier_self
(identifier_already_run_once) identifier_already_run_once
)attribute
)comparison_operator
(block
(expression_statement
(call
(attribute
(identifier_cls_instance) identifier_cls_instance
(identifier_RunOnce) identifier_RunOnce
)attribute
(argument_list
)argument_list
)call
)expression_statement
(expression_statement
(call
(attribute
(attribute
(identifier_self) identifier_self
(identifier_already_run_once) identifier_already_run_once
)attribute
(identifier_add) identifier_add
)attribute
(argument_list
(identifier_hook_cls) identifier_hook_cls
)argument_list
)call
)expression_statement
)block
)if_statement
)block
)function_definition
)module | 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) function_name_CheckRange
(parameters
(identifier_string) identifier_string
(identifier_location) identifier_location
(identifier_tokens) identifier_tokens
)parameters
(block
(try_statement
(block
(expression_statement
(assignment
(identifier_check_number) identifier_check_number
(subscript
(identifier_tokens) identifier_tokens
(integer_0) integer_0
)subscript
)assignment
)expression_statement
)block
(except_clause
(identifier_IndexError) identifier_IndexError
(block
(expression_statement
(assignment
(identifier_check_number) identifier_check_number
(unary_operator
(integer_1) integer_1
)unary_operator
)assignment
)expression_statement
)block
)except_clause
)try_statement
(if_statement
(comparison_operator
(identifier_check_number) identifier_check_number
(identifier_lower_bound) identifier_lower_bound
)comparison_operator
(block
(raise_statement
(call
(attribute
(identifier_pyparsing) identifier_pyparsing
(identifier_ParseException) identifier_ParseException
)attribute
(argument_list
(call
(attribute
(string_'Value: {0:d} precedes lower bound: {1:d}') string_'Value: {0:d} precedes lower bound: {1:d}'
(identifier_format) identifier_format
)attribute
(argument_list
(identifier_check_number) identifier_check_number
(identifier_lower_bound) identifier_lower_bound
)argument_list
)call
)argument_list
)call
)raise_statement
)block
)if_statement
(if_statement
(comparison_operator
(identifier_check_number) identifier_check_number
(identifier_upper_bound) identifier_upper_bound
)comparison_operator
(block
(raise_statement
(call
(attribute
(identifier_pyparsing) identifier_pyparsing
(identifier_ParseException) identifier_ParseException
)attribute
(argument_list
(call
(attribute
(string_'Value: {0:d} exceeds upper bound: {1:d}') string_'Value: {0:d} exceeds upper bound: {1:d}'
(identifier_format) identifier_format
)attribute
(argument_list
(identifier_check_number) identifier_check_number
(identifier_upper_bound) identifier_upper_bound
)argument_list
)call
)argument_list
)call
)raise_statement
)block
)if_statement
)block
)function_definition
(return_statement
(identifier_CheckRange) identifier_CheckRange
)return_statement
)block
)function_definition
)module | 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:
lower_bound (int): lower bound of the range.
upper_bound (int): upper bound of the range.
Returns:
Function: callback method that can be used by pyparsing setParseAction. |
(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
(call
(attribute
(identifier_self) identifier_self
(identifier_read_line) identifier_read_line
)attribute
(argument_list
(identifier_fid) identifier_fid
)argument_list
)call
)assignment
)expression_statement
(while_statement
(comparison_operator
(identifier_lin) identifier_lin
(string_'end') string_'end'
)comparison_operator
(block
(expression_statement
(assignment
(identifier_parts) identifier_parts
(call
(attribute
(identifier_lin) identifier_lin
(identifier_split) identifier_split
)attribute
(argument_list
)argument_list
)call
)assignment
)expression_statement
(if_statement
(comparison_operator
(identifier_lin) identifier_lin
(string_'begin') string_'begin'
)comparison_operator
(block
(expression_statement
(assignment
(identifier_ind) identifier_ind
(call
(attribute
(identifier_self) identifier_self
(identifier_get_index_by_name) identifier_get_index_by_name
)attribute
(argument_list
(subscript
(identifier_parts) identifier_parts
(integer_0) integer_0
)subscript
)argument_list
)call
)assignment
)expression_statement
(for_statement
(identifier_i) identifier_i
(call
(identifier_range) identifier_range
(argument_list
(integer_1) integer_1
(call
(identifier_len) identifier_len
(argument_list
(identifier_parts) identifier_parts
)argument_list
)call
)argument_list
)call
(block
(expression_statement
(call
(attribute
(attribute
(subscript
(attribute
(identifier_self) identifier_self
(identifier_vertices) identifier_vertices
)attribute
(identifier_ind) identifier_ind
)subscript
(identifier_children) identifier_children
)attribute
(identifier_append) identifier_append
)attribute
(argument_list
(call
(attribute
(identifier_self) identifier_self
(identifier_get_index_by_name) identifier_get_index_by_name
)attribute
(argument_list
(subscript
(identifier_parts) identifier_parts
(identifier_i) identifier_i
)subscript
)argument_list
)call
)argument_list
)call
)expression_statement
)block
)for_statement
)block
)if_statement
(expression_statement
(assignment
(identifier_lin) identifier_lin
(call
(attribute
(identifier_self) identifier_self
(identifier_read_line) identifier_read_line
)attribute
(argument_list
(identifier_fid) identifier_fid
)argument_list
)call
)assignment
)expression_statement
)block
)while_statement
(expression_statement
(assignment
(identifier_lin) identifier_lin
(call
(attribute
(identifier_self) identifier_self
(identifier_read_line) identifier_read_line
)attribute
(argument_list
(identifier_fid) identifier_fid
)argument_list
)call
)assignment
)expression_statement
(return_statement
(identifier_lin) identifier_lin
)return_statement
)block
)function_definition
)module | 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
)dictionary_splat_pattern
)parameters
(block
(return_statement
(call
(attribute
(identifier_self) identifier_self
(identifier_get) identifier_get
)attribute
(argument_list
(binary_operator
(attribute
(identifier_self) identifier_self
(identifier_gateway_device_path) identifier_gateway_device_path
)attribute
(identifier_gateway_device_id) identifier_gateway_device_id
)binary_operator
(keyword_argument
(identifier_params) identifier_params
(identifier__params) identifier__params
)keyword_argument
)argument_list
)call
)return_statement
)block
)function_definition
)module | 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_signal
)attribute
(argument_list
(attribute
(identifier_signal) identifier_signal
(identifier_SIGINT) identifier_SIGINT
)attribute
(attribute
(identifier_self) identifier_self
(identifier_original_sigint) identifier_original_sigint
)attribute
)argument_list
)call
)expression_statement
(expression_statement
(call
(attribute
(identifier_signal) identifier_signal
(identifier_signal) identifier_signal
)attribute
(argument_list
(attribute
(identifier_signal) identifier_signal
(identifier_SIGTERM) identifier_SIGTERM
)attribute
(attribute
(identifier_self) identifier_self
(identifier_original_sigterm) identifier_original_sigterm
)attribute
)argument_list
)call
)expression_statement
(if_statement
(comparison_operator
(attribute
(identifier_os) identifier_os
(identifier_name) identifier_name
)attribute
(string_'nt') string_'nt'
)comparison_operator
(block
(expression_statement
(call
(attribute
(identifier_signal) identifier_signal
(identifier_signal) identifier_signal
)attribute
(argument_list
(attribute
(identifier_signal) identifier_signal
(identifier_SIGBREAK) identifier_SIGBREAK
)attribute
(attribute
(identifier_self) identifier_self
(identifier_original_sigbreak) identifier_original_sigbreak
)attribute
)argument_list
)call
)expression_statement
)block
)if_statement
)block
)function_definition
)module | 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
(None) None
)default_parameter
(dictionary_splat_pattern
(identifier_kwargs) identifier_kwargs
)dictionary_splat_pattern
)parameters
(block
(expression_statement
(call
(identifier__set_content_type) identifier__set_content_type
(argument_list
(identifier_kwargs) identifier_kwargs
)argument_list
)call
)expression_statement
(if_statement
(boolean_operator
(call
(identifier__content_type_is_json) identifier__content_type_is_json
(argument_list
(identifier_kwargs) identifier_kwargs
)argument_list
)call
(comparison_operator
(identifier_data) identifier_data
(None) None
)comparison_operator
)boolean_operator
(block
(expression_statement
(assignment
(identifier_data) identifier_data
(call
(identifier_dumps) identifier_dumps
(argument_list
(identifier_data) identifier_data
)argument_list
)call
)assignment
)expression_statement
)block
)if_statement
(expression_statement
(call
(identifier__log_request) identifier__log_request
(argument_list
(string_'POST') string_'POST'
(identifier_url) identifier_url
(identifier_kwargs) identifier_kwargs
(identifier_data) identifier_data
)argument_list
)call
)expression_statement
(expression_statement
(assignment
(identifier_response) identifier_response
(call
(attribute
(identifier_requests) identifier_requests
(identifier_post) identifier_post
)attribute
(argument_list
(identifier_url) identifier_url
(identifier_data) identifier_data
(identifier_json) identifier_json
(dictionary_splat
(identifier_kwargs) identifier_kwargs
)dictionary_splat
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(call
(identifier__log_response) identifier__log_response
(argument_list
(identifier_response) identifier_response
)argument_list
)call
)expression_statement
(return_statement
(identifier_response) identifier_response
)return_statement
)block
)function_definition
)module | 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__check_layout
)attribute
(argument_list
)argument_list
)call
)expression_statement
(return_statement
(call
(identifier_LayoutSlice) identifier_LayoutSlice
(argument_list
(attribute
(identifier_self) identifier_self
(identifier_layout) identifier_layout
)attribute
(call
(identifier_slice) identifier_slice
(argument_list
(integer_0) integer_0
(call
(identifier_len) identifier_len
(argument_list
(attribute
(attribute
(identifier_self) identifier_self
(identifier_layout) identifier_layout
)attribute
(identifier_fields) identifier_fields
)attribute
)argument_list
)call
(integer_1) integer_1
)argument_list
)call
)argument_list
)call
)return_statement
)block
)function_definition
)module | 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
)call
)default_parameter
)parameters
(block
(expression_statement
(assignment
(identifier_response) identifier_response
(call
(attribute
(attribute
(identifier_self) identifier_self
(identifier_session) identifier_session
)attribute
(identifier_get) identifier_get
)attribute
(argument_list
(call
(attribute
(identifier_self) identifier_self
(identifier__get_table_url) identifier__get_table_url
)attribute
(argument_list
)argument_list
)call
(keyword_argument
(identifier_params) identifier_params
(call
(attribute
(identifier_self) identifier_self
(identifier__get_formatted_query) identifier__get_formatted_query
)attribute
(argument_list
(identifier_fields) identifier_fields
(keyword_argument
(identifier_limit) identifier_limit
(None) None
)keyword_argument
(keyword_argument
(identifier_order_by) identifier_order_by
(call
(identifier_list) identifier_list
(argument_list
)argument_list
)call
)keyword_argument
(keyword_argument
(identifier_offset) identifier_offset
(None) None
)keyword_argument
)argument_list
)call
)keyword_argument
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_content) identifier_content
(call
(attribute
(identifier_self) identifier_self
(identifier__get_content) identifier__get_content
)attribute
(argument_list
(identifier_response) identifier_response
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_l) identifier_l
(call
(identifier_len) identifier_len
(argument_list
(identifier_content) identifier_content
)argument_list
)call
)assignment
)expression_statement
(if_statement
(comparison_operator
(identifier_l) identifier_l
(integer_1) integer_1
)comparison_operator
(block
(raise_statement
(call
(identifier_MultipleResults) identifier_MultipleResults
(argument_list
(string_'Multiple results for get_one()') string_'Multiple results for get_one()'
)argument_list
)call
)raise_statement
)block
)if_statement
(if_statement
(comparison_operator
(call
(identifier_len) identifier_len
(argument_list
(identifier_content) identifier_content
)argument_list
)call
(integer_0) integer_0
)comparison_operator
(block
(return_statement
(dictionary
)dictionary
)return_statement
)block
)if_statement
(return_statement
(subscript
(identifier_content) identifier_content
(integer_0) integer_0
)subscript
)return_statement
)block
)function_definition
)module | 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 | %(levelname)-7s ') string_'%(asctime)s.%(msecs)03d | %(name)-60s | %(levelname)-7s '
(string_'| %(message)s') string_'| %(message)s'
)concatenated_string
)assignment
)expression_statement
(expression_statement
(call
(attribute
(identifier_logging) identifier_logging
(identifier_basicConfig) identifier_basicConfig
)attribute
(argument_list
(keyword_argument
(identifier_format) identifier_format
(identifier_fmt) identifier_fmt
)keyword_argument
(keyword_argument
(identifier_datefmt) identifier_datefmt
(string_'%H:%M:%S') string_'%H:%M:%S'
)keyword_argument
(keyword_argument
(identifier_level) identifier_level
(attribute
(identifier_logging) identifier_logging
(identifier_DEBUG) identifier_DEBUG
)attribute
)keyword_argument
)argument_list
)call
)expression_statement
)block
)function_definition
)module | 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
(identifier_xmax) identifier_xmax
(integer_200) integer_200
)default_parameter
)parameters
(block
(expression_statement
(assignment
(identifier_helptext) identifier_helptext
(assignment
(identifier_pconfig) identifier_pconfig
(dictionary
(pair
(string_'id') string_'id'
(string_'Jellyfish_kmer_plot') string_'Jellyfish_kmer_plot'
)pair
(pair
(string_'title') string_'title'
(string_'Jellyfish: K-mer plot') string_'Jellyfish: K-mer plot'
)pair
(pair
(string_'ylab') string_'ylab'
(string_'Counts') string_'Counts'
)pair
(pair
(string_'xlab') string_'xlab'
(string_'k-mer frequency') string_'k-mer frequency'
)pair
(pair
(string_'xDecimals') string_'xDecimals'
(False) False
)pair
(pair
(string_'xmin') string_'xmin'
(identifier_xmin) identifier_xmin
)pair
(pair
(string_'xmax') string_'xmax'
(identifier_xmax) identifier_xmax
)pair
)dictionary
)assignment
)assignment
)expression_statement
(expression_statement
(call
(attribute
(identifier_self) identifier_self
(identifier_add_section) identifier_add_section
)attribute
(argument_list
(keyword_argument
(identifier_anchor) identifier_anchor
(string_'jellyfish_kmer_plot') string_'jellyfish_kmer_plot'
)keyword_argument
(keyword_argument
(identifier_description) identifier_description
(string_'The K-mer plot lets you estimate library complexity and coverage from k-mer content.') string_'The K-mer plot lets you estimate library complexity and coverage from k-mer content.'
)keyword_argument
(keyword_argument
(identifier_helptext) identifier_helptext
(identifier_helptext) identifier_helptext
)keyword_argument
(keyword_argument
(identifier_plot) identifier_plot
(call
(attribute
(identifier_linegraph) identifier_linegraph
(identifier_plot) identifier_plot
)attribute
(argument_list
(attribute
(identifier_self) identifier_self
(identifier_jellyfish_data) identifier_jellyfish_data
)attribute
(identifier_pconfig) identifier_pconfig
)argument_list
)call
)keyword_argument
)argument_list
)call
)expression_statement
)block
)function_definition
)module | 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
(call
(attribute
(identifier_self) identifier_self
(identifier___normalize_name) identifier___normalize_name
)attribute
(argument_list
(identifier_name) identifier_name
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_action) identifier_action
(call
(attribute
(identifier_self) identifier_self
(identifier_get_action) identifier_get_action
)attribute
(argument_list
(identifier_name) identifier_name
)argument_list
)call
)assignment
)expression_statement
(if_statement
(not_operator
(identifier_action) identifier_action
)not_operator
(block
(return_statement
(string_"") string_""
)return_statement
)block
)if_statement
(return_statement
(call
(attribute
(call
(attribute
(identifier_action) identifier_action
(identifier_shortcut) identifier_shortcut
)attribute
(argument_list
)argument_list
)call
(identifier_toString) identifier_toString
)attribute
(argument_list
)argument_list
)call
)return_statement
)block
)function_definition
)module | 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
)expression_statement
(for_statement
(identifier_a) identifier_a
(call
(identifier_range) identifier_range
(argument_list
(integer_0) integer_0
(integer_7) integer_7
)argument_list
)call
(block
(expression_statement
(call
(attribute
(identifier_result) identifier_result
(identifier_append) identifier_append
)attribute
(argument_list
(call
(identifier_GPIOPin) identifier_GPIOPin
(argument_list
(identifier_self) identifier_self
(string_'_action') string_'_action'
(dictionary
(pair
(string_'pin') string_'pin'
(call
(attribute
(string_'A{}') string_'A{}'
(identifier_format) identifier_format
)attribute
(argument_list
(identifier_a) identifier_a
)argument_list
)call
)pair
)dictionary
(keyword_argument
(identifier_name) identifier_name
(call
(attribute
(string_'A{}') string_'A{}'
(identifier_format) identifier_format
)attribute
(argument_list
(identifier_a) identifier_a
)argument_list
)call
)keyword_argument
)argument_list
)call
)argument_list
)call
)expression_statement
)block
)for_statement
(for_statement
(identifier_b) identifier_b
(call
(identifier_range) identifier_range
(argument_list
(integer_0) integer_0
(integer_7) integer_7
)argument_list
)call
(block
(expression_statement
(call
(attribute
(identifier_result) identifier_result
(identifier_append) identifier_append
)attribute
(argument_list
(call
(identifier_GPIOPin) identifier_GPIOPin
(argument_list
(identifier_self) identifier_self
(string_'_action') string_'_action'
(dictionary
(pair
(string_'pin') string_'pin'
(call
(attribute
(string_'B{}') string_'B{}'
(identifier_format) identifier_format
)attribute
(argument_list
(identifier_b) identifier_b
)argument_list
)call
)pair
)dictionary
(keyword_argument
(identifier_name) identifier_name
(call
(attribute
(string_'B{}') string_'B{}'
(identifier_format) identifier_format
)attribute
(argument_list
(identifier_b) identifier_b
)argument_list
)call
)keyword_argument
)argument_list
)call
)argument_list
)call
)expression_statement
)block
)for_statement
(return_statement
(identifier_result) identifier_result
)return_statement
)block
)function_definition
)module | 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>,
<GPIOPin A3 on MCP23017I2C>,
<GPIOPin A4 on MCP23017I2C>,
<GPIOPin A5 on MCP23017I2C>,
<GPIOPin A6 on MCP23017I2C>,
<GPIOPin B0 on MCP23017I2C>,
<GPIOPin B1 on MCP23017I2C>,
<GPIOPin B2 on MCP23017I2C>,
<GPIOPin B3 on MCP23017I2C>,
<GPIOPin B4 on MCP23017I2C>,
<GPIOPin B5 on MCP23017I2C>,
<GPIOPin B6 on MCP23017I2C>] |
(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_rfs) identifier_rfs
(call
(identifier_list) identifier_list
(argument_list
(call
(identifier_chain) identifier_chain
(argument_list
(list
(identifier_f) identifier_f
)list
(identifier_fs) identifier_fs
)argument_list
)call
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(call
(attribute
(identifier_rfs) identifier_rfs
(identifier_reverse) identifier_reverse
)attribute
(argument_list
)argument_list
)call
)expression_statement
(function_definition
(function_name_composed) function_name_composed
(parameters
(list_splat_pattern
(identifier_args) identifier_args
)list_splat_pattern
(dictionary_splat_pattern
(identifier_kwargs) identifier_kwargs
)dictionary_splat_pattern
)parameters
(block
(return_statement
(call
(identifier_reduce) identifier_reduce
(argument_list
(lambda
(lambda_parameters
(identifier_result) identifier_result
(identifier_fn) identifier_fn
)lambda_parameters
(call
(identifier_fn) identifier_fn
(argument_list
(identifier_result) identifier_result
)argument_list
)call
)lambda
(subscript
(identifier_rfs) identifier_rfs
(slice
(integer_1) integer_1
(colon) colon
)slice
)subscript
(call
(subscript
(identifier_rfs) identifier_rfs
(integer_0) integer_0
)subscript
(argument_list
(list_splat
(identifier_args) identifier_args
)list_splat
(dictionary_splat
(identifier_kwargs) identifier_kwargs
)dictionary_splat
)argument_list
)call
)argument_list
)call
)return_statement
)block
)function_definition
(return_statement
(identifier_composed) identifier_composed
)return_statement
)block
)function_definition
)module | 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 provided function. All preceding functions
must be unary.
Returns:
The composition of the argument functions. The returned
function will accept the same arguments as the rightmost
passed in function. |
(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
(identifier_sb) identifier_sb
)attribute
(block
(expression_statement
(assignment
(attribute
(identifier_self) identifier_self
(identifier_sbdataq) identifier_sbdataq
)attribute
(binary_operator
(attribute
(identifier_self) identifier_self
(identifier_sbdataq) identifier_sbdataq
)attribute
(identifier_char) identifier_char
)binary_operator
)assignment
)expression_statement
)block
(else_clause
(block
(expression_statement
(call
(attribute
(identifier_self) identifier_self
(identifier_inputcooker_store_queue) identifier_inputcooker_store_queue
)attribute
(argument_list
(identifier_char) identifier_char
)argument_list
)call
)expression_statement
)block
)else_clause
)if_statement
)block
)function_definition
)module | 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_parameter
)parameters
(block
(expression_statement
(assignment
(pattern_list
(identifier_thread_id) identifier_thread_id
(identifier_thread_type) identifier_thread_type
)pattern_list
(call
(attribute
(identifier_self) identifier_self
(identifier__getThread) identifier__getThread
)attribute
(argument_list
(identifier_thread_id) identifier_thread_id
(None) None
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_data) identifier_data
(dictionary
(pair
(string_"thread_image_id") string_"thread_image_id"
(identifier_image_id) identifier_image_id
)pair
(pair
(string_"thread_id") string_"thread_id"
(identifier_thread_id) identifier_thread_id
)pair
)dictionary
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_j) identifier_j
(call
(attribute
(identifier_self) identifier_self
(identifier__post) identifier__post
)attribute
(argument_list
(attribute
(attribute
(identifier_self) identifier_self
(identifier_req_url) identifier_req_url
)attribute
(identifier_THREAD_IMAGE) identifier_THREAD_IMAGE
)attribute
(identifier_data) identifier_data
(keyword_argument
(identifier_fix_request) identifier_fix_request
(True) True
)keyword_argument
(keyword_argument
(identifier_as_json) identifier_as_json
(True) True
)keyword_argument
)argument_list
)call
)assignment
)expression_statement
(return_statement
(identifier_image_id) identifier_image_id
)return_statement
)block
)function_definition
)module | 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_tries
(default_parameter
(identifier_tries) identifier_tries
(integer_0) integer_0
)default_parameter
)parameters
(block
(expression_statement
(call
(attribute
(identifier_self) identifier_self
(identifier_fetch) identifier_fetch
)attribute
(argument_list
)argument_list
)call
)expression_statement
(expression_statement
(call
(identifier_action) identifier_action
(argument_list
(identifier_self) identifier_self
(identifier_field) identifier_field
(identifier_value) identifier_value
)argument_list
)call
)expression_statement
(try_statement
(block
(expression_statement
(call
(attribute
(identifier_self) identifier_self
(identifier_save) identifier_save
)attribute
(argument_list
)argument_list
)call
)expression_statement
)block
(except_clause
(as_pattern
(attribute
(identifier_requests) identifier_requests
(identifier_HTTPError) identifier_HTTPError
)attribute
(as_pattern_target
(identifier_ex) identifier_ex
)as_pattern_target
)as_pattern
(block
(if_statement
(boolean_operator
(comparison_operator
(identifier_tries) identifier_tries
(identifier_max_tries) identifier_max_tries
)comparison_operator
(comparison_operator
(attribute
(attribute
(identifier_ex) identifier_ex
(identifier_response) identifier_response
)attribute
(identifier_status_code) identifier_status_code
)attribute
(integer_409) integer_409
)comparison_operator
)boolean_operator
(block
(expression_statement
(call
(attribute
(identifier_self) identifier_self
(identifier__update_field) identifier__update_field
)attribute
(argument_list
(identifier_action) identifier_action
(identifier_field) identifier_field
(identifier_value) identifier_value
(identifier_max_tries) identifier_max_tries
(keyword_argument
(identifier_tries) identifier_tries
(binary_operator
(identifier_tries) identifier_tries
(integer_1) integer_1
)binary_operator
)keyword_argument
)argument_list
)call
)expression_statement
)block
(else_clause
(block
(raise_statement
)raise_statement
)block
)else_clause
)if_statement
)block
)except_clause
)try_statement
)block
)function_definition
)module | 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
(identifier_query) identifier_query
)pattern_list
(call
(attribute
(identifier_urllib) identifier_urllib
(identifier_splitquery) identifier_splitquery
)attribute
(argument_list
(identifier_document) identifier_document
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_doc) identifier_doc
(call
(identifier_url_quote_part) identifier_url_quote_part
(argument_list
(identifier_doc) identifier_doc
(string_'/=,') string_'/=,'
)argument_list
)call
)assignment
)expression_statement
(if_statement
(identifier_query) identifier_query
(block
(return_statement
(binary_operator
(string_"%s?%s") string_"%s?%s"
(tuple
(identifier_doc) identifier_doc
(identifier_query) identifier_query
)tuple
)binary_operator
)return_statement
)block
)if_statement
(return_statement
(identifier_doc) identifier_doc
)return_statement
)block
)function_definition
)module | 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
(type
(identifier_bool) identifier_bool
)type
(block
(if_statement
(comparison_operator
(identifier_extension) identifier_extension
(None) None
)comparison_operator
(block
(expression_statement
(assignment
(identifier_extension) identifier_extension
(call
(attribute
(identifier_extension) identifier_extension
(identifier_lower) identifier_lower
)attribute
(argument_list
)argument_list
)call
)assignment
)expression_statement
)block
)if_statement
(expression_statement
(assignment
(identifier_info) identifier_info
(call
(attribute
(identifier_ext_map) identifier_ext_map
(identifier_get) identifier_get
)attribute
(argument_list
(identifier_extension) identifier_extension
)argument_list
)call
)assignment
)expression_statement
(if_statement
(comparison_operator
(identifier_info) identifier_info
(None) None
)comparison_operator
(block
(return_statement
(False) False
)return_statement
)block
)if_statement
(expression_statement
(assignment
(identifier_availability) identifier_availability
(subscript
(identifier_info) identifier_info
(identifier_AVAILABILITY) identifier_AVAILABILITY
)subscript
)assignment
)expression_statement
(if_statement
(comparison_operator
(call
(identifier_type) identifier_type
(argument_list
(identifier_availability) identifier_availability
)argument_list
)call
(identifier_bool) identifier_bool
)comparison_operator
(block
(return_statement
(identifier_availability) identifier_availability
)return_statement
)block
(elif_clause
(call
(identifier_callable) identifier_callable
(argument_list
(identifier_availability) identifier_availability
)argument_list
)call
(block
(return_statement
(call
(identifier_availability) identifier_availability
(argument_list
)argument_list
)call
)return_statement
)block
)elif_clause
(else_clause
(block
(raise_statement
(call
(identifier_ValueError) identifier_ValueError
(argument_list
(call
(attribute
(string_"Bad information object for extension: {}") string_"Bad information object for extension: {}"
(identifier_format) identifier_format
)attribute
(argument_list
(identifier_extension) identifier_extension
)argument_list
)call
)argument_list
)call
)raise_statement
)block
)else_clause
)if_statement
)block
)function_definition
)module | 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) identifier_var
(for_in_clause
(identifier_var) identifier_var
(call
(attribute
(identifier_arg_plot) identifier_arg_plot
(identifier_split) identifier_split
)attribute
(argument_list
(string_',') string_','
)argument_list
)call
)for_in_clause
(if_clause
(comparison_operator
(identifier_var) identifier_var
(attribute
(identifier_phyvars) identifier_phyvars
(identifier_PLATES) identifier_PLATES
)attribute
)comparison_operator
)if_clause
)generator_expression
)call
)return_statement
)block
)function_definition
)module | 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_requirements) identifier_requirements
)not_operator
(block
(return_statement
(list
)list
)return_statement
)block
)if_statement
(if_statement
(not_operator
(identifier_available_devices) identifier_available_devices
)not_operator
(block
(raise_statement
(call
(identifier_InsufficientGPUError) identifier_InsufficientGPUError
(argument_list
(call
(attribute
(string_"No GPU devices available, but {} devices required.") string_"No GPU devices available, but {} devices required."
(identifier_format) identifier_format
)attribute
(argument_list
(call
(identifier_len) identifier_len
(argument_list
(identifier_requirements) identifier_requirements
)argument_list
)call
)argument_list
)call
)argument_list
)call
)raise_statement
)block
)if_statement
(expression_statement
(assignment
(identifier_available_devices) identifier_available_devices
(call
(attribute
(identifier_available_devices) identifier_available_devices
(identifier_copy) identifier_copy
)attribute
(argument_list
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_used_devices) identifier_used_devices
(list
)list
)assignment
)expression_statement
(for_statement
(identifier_req) identifier_req
(identifier_requirements) identifier_requirements
(block
(expression_statement
(assignment
(identifier_dev) identifier_dev
(call
(identifier_search_device) identifier_search_device
(argument_list
(identifier_req) identifier_req
(identifier_available_devices) identifier_available_devices
)argument_list
)call
)assignment
)expression_statement
(if_statement
(identifier_dev) identifier_dev
(block
(expression_statement
(call
(attribute
(identifier_used_devices) identifier_used_devices
(identifier_append) identifier_append
)attribute
(argument_list
(identifier_dev) identifier_dev
)argument_list
)call
)expression_statement
(expression_statement
(call
(attribute
(identifier_available_devices) identifier_available_devices
(identifier_remove) identifier_remove
)attribute
(argument_list
(identifier_dev) identifier_dev
)argument_list
)call
)expression_statement
)block
(else_clause
(block
(raise_statement
(call
(identifier_InsufficientGPUError) identifier_InsufficientGPUError
(argument_list
(string_"Not all GPU requirements could be fulfilled.") string_"Not all GPU requirements could be fulfilled."
)argument_list
)call
)raise_statement
)block
)else_clause
)if_statement
)block
)for_statement
(return_statement
(identifier_used_devices) identifier_used_devices
)return_statement
)block
)function_definition
)module | 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
(typed_parameter
(identifier_point) identifier_point
(type
(identifier_vec4) identifier_vec4
)type
)typed_parameter
)parameters
(type
(identifier_vec2) identifier_vec2
)type
(block
(return_statement
(binary_operator
(parenthesized_expression
(binary_operator
(identifier_framebuffer_size) identifier_framebuffer_size
(attribute
(identifier_point) identifier_point
(identifier_xy) identifier_xy
)attribute
)binary_operator
)parenthesized_expression
(attribute
(identifier_point) identifier_point
(identifier_w) identifier_w
)attribute
)binary_operator
)return_statement
)block
)function_definition
)module | 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
(identifier_np) identifier_np
(identifier_array) identifier_array
)attribute
(argument_list
(list_comprehension
(subscript
(identifier_reg) identifier_reg
(slice
(attribute
(identifier_self) identifier_self
(identifier_lags) identifier_lags
)attribute
(colon) colon
(subscript
(attribute
(identifier_reg) identifier_reg
(identifier_shape) identifier_shape
)attribute
(integer_0) integer_0
)subscript
)slice
)subscript
(for_in_clause
(identifier_reg) identifier_reg
(attribute
(identifier_self) identifier_self
(identifier_data) identifier_data
)attribute
)for_in_clause
)list_comprehension
)argument_list
)call
)assignment
)expression_statement
(return_statement
(binary_operator
(parenthesized_expression
(binary_operator
(float_1.0) float_1.0
(parenthesized_expression
(subscript
(attribute
(subscript
(identifier_Y) identifier_Y
(integer_0) integer_0
)subscript
(identifier_shape) identifier_shape
)attribute
(integer_0) integer_0
)subscript
)parenthesized_expression
)binary_operator
)parenthesized_expression
(call
(attribute
(identifier_np) identifier_np
(identifier_dot) identifier_dot
)attribute
(argument_list
(call
(attribute
(identifier_self) identifier_self
(identifier_residuals) identifier_residuals
)attribute
(argument_list
(identifier_Y) identifier_Y
)argument_list
)call
(call
(attribute
(identifier_np) identifier_np
(identifier_transpose) identifier_transpose
)attribute
(argument_list
(call
(attribute
(identifier_self) identifier_self
(identifier_residuals) identifier_residuals
)attribute
(argument_list
(identifier_Y) identifier_Y
)argument_list
)call
)argument_list
)call
)argument_list
)call
)binary_operator
)return_statement
)block
)function_definition
)module | 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
(assignment
(identifier_serials) identifier_serials
(call
(attribute
(identifier_android_device) identifier_android_device
(identifier_list_adb_devices) identifier_list_adb_devices
)attribute
(argument_list
)argument_list
)call
)assignment
)expression_statement
(if_statement
(not_operator
(identifier_serials) identifier_serials
)not_operator
(block
(raise_statement
(call
(identifier_Error) identifier_Error
(argument_list
(string_'No adb device found!') string_'No adb device found!'
)argument_list
)call
)raise_statement
)block
)if_statement
(if_statement
(not_operator
(identifier_serial) identifier_serial
)not_operator
(block
(expression_statement
(assignment
(identifier_env_serial) identifier_env_serial
(call
(attribute
(attribute
(identifier_os) identifier_os
(identifier_environ) identifier_environ
)attribute
(identifier_get) identifier_get
)attribute
(argument_list
(string_'ANDROID_SERIAL') string_'ANDROID_SERIAL'
(None) None
)argument_list
)call
)assignment
)expression_statement
(if_statement
(comparison_operator
(identifier_env_serial) identifier_env_serial
(None) None
)comparison_operator
(block
(expression_statement
(assignment
(identifier_serial) identifier_serial
(identifier_env_serial) identifier_env_serial
)assignment
)expression_statement
)block
(elif_clause
(comparison_operator
(call
(identifier_len) identifier_len
(argument_list
(identifier_serials) identifier_serials
)argument_list
)call
(integer_1) integer_1
)comparison_operator
(block
(expression_statement
(assignment
(identifier_serial) identifier_serial
(subscript
(identifier_serials) identifier_serials
(integer_0) integer_0
)subscript
)assignment
)expression_statement
)block
)elif_clause
(else_clause
(block
(raise_statement
(call
(identifier_Error) identifier_Error
(argument_list
(binary_operator
(concatenated_string
(string_'Expected one phone, but %d found. Use the -s flag or ') string_'Expected one phone, but %d found. Use the -s flag or '
(string_'specify ANDROID_SERIAL.') string_'specify ANDROID_SERIAL.'
)concatenated_string
(call
(identifier_len) identifier_len
(argument_list
(identifier_serials) identifier_serials
)argument_list
)call
)binary_operator
)argument_list
)call
)raise_statement
)block
)else_clause
)if_statement
)block
)if_statement
(if_statement
(comparison_operator
(identifier_serial) identifier_serial
(identifier_serials) identifier_serials
)comparison_operator
(block
(raise_statement
(call
(identifier_Error) identifier_Error
(argument_list
(binary_operator
(string_'Device "%s" is not found by adb.') string_'Device "%s" is not found by adb.'
(identifier_serial) identifier_serial
)binary_operator
)argument_list
)call
)raise_statement
)block
)if_statement
(expression_statement
(assignment
(identifier_ads) identifier_ads
(call
(attribute
(identifier_android_device) identifier_android_device
(identifier_get_instances) identifier_get_instances
)attribute
(argument_list
(list
(identifier_serial) identifier_serial
)list
)argument_list
)call
)assignment
)expression_statement
(assert_statement
(comparison_operator
(call
(identifier_len) identifier_len
(argument_list
(identifier_ads) identifier_ads
)argument_list
)call
(integer_1) integer_1
)comparison_operator
)assert_statement
(expression_statement
(assignment
(attribute
(identifier_self) identifier_self
(identifier__ad) identifier__ad
)attribute
(subscript
(identifier_ads) identifier_ads
(integer_0) integer_0
)subscript
)assignment
)expression_statement
)block
)function_definition
)module | 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
(block
(return_statement
(comparison_operator
(call
(attribute
(identifier_self) identifier_self
(identifier_object_key) identifier_object_key
)attribute
(argument_list
(identifier_obj_id) identifier_obj_id
(identifier_obj_type) identifier_obj_type
)argument_list
)call
(attribute
(identifier_self) identifier_self
(identifier__data) identifier__data
)attribute
)comparison_operator
)return_statement
)block
)function_definition
)module | 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__prepopulated) identifier__prepopulated
)attribute
(False) False
)comparison_operator
(block
(raise_statement
(call
(attribute
(identifier_errors) identifier_errors
(identifier_EmptyDatabase) identifier_EmptyDatabase
)attribute
(argument_list
(attribute
(identifier_self) identifier_self
(identifier_dbpath) identifier_dbpath
)attribute
)argument_list
)call
)raise_statement
)block
(else_clause
(block
(return_statement
(call
(identifier_return_real_id_base) identifier_return_real_id_base
(argument_list
(attribute
(identifier_self) identifier_self
(identifier_dbpath) identifier_dbpath
)attribute
(attribute
(identifier_self) identifier_self
(identifier__set_object) identifier__set_object
)attribute
)argument_list
)call
)return_statement
)block
)else_clause
)if_statement
)block
)function_definition
)module | 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
)parameters
(block
(expression_statement
(call
(attribute
(attribute
(identifier_self) identifier_self
(identifier__unobservable) identifier__unobservable
)attribute
(identifier_set_before) identifier_set_before
)attribute
(argument_list
(identifier_tlen) identifier_tlen
(identifier_qlen) identifier_qlen
(identifier_nt) identifier_nt
(identifier_p) identifier_p
)argument_list
)call
)expression_statement
)block
)function_definition
)module | 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: float |
(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
)dictionary_splat_pattern
)parameters
(block
(expression_statement
(assignment
(identifier_opts) identifier_opts
(call
(identifier_get_opts) identifier_get_opts
(argument_list
(identifier_instance) identifier_instance
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_model) identifier_model
(call
(attribute
(string_'.') string_'.'
(identifier_join) identifier_join
)attribute
(argument_list
(list
(attribute
(identifier_opts) identifier_opts
(identifier_app_label) identifier_app_label
)attribute
(attribute
(identifier_opts) identifier_opts
(identifier_object_name) identifier_object_name
)attribute
)list
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(call
(identifier_distill_model_event) identifier_distill_model_event
(argument_list
(identifier_instance) identifier_instance
(identifier_model) identifier_model
(string_'deleted') string_'deleted'
)argument_list
)call
)expression_statement
)block
)function_definition
)module | 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
(call
(identifier_bytes) identifier_bytes
(argument_list
(attribute
(identifier_keypair) identifier_keypair
(identifier_PrivateKey) identifier_PrivateKey
)attribute
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_hashdata) identifier_hashdata
(call
(attribute
(identifier_verifiable) identifier_verifiable
(identifier_GetHashData) identifier_GetHashData
)attribute
(argument_list
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_res) identifier_res
(call
(attribute
(call
(attribute
(identifier_Crypto) identifier_Crypto
(identifier_Default) identifier_Default
)attribute
(argument_list
)argument_list
)call
(identifier_Sign) identifier_Sign
)attribute
(argument_list
(identifier_hashdata) identifier_hashdata
(identifier_prikey) identifier_prikey
)argument_list
)call
)assignment
)expression_statement
(return_statement
(identifier_res) identifier_res
)return_statement
)block
)function_definition
)module | 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
(identifier_min) identifier_min
(argument_list
(binary_operator
(identifier_pos) identifier_pos
(integer_11) integer_11
)binary_operator
(call
(identifier_len) identifier_len
(argument_list
(identifier_buf) identifier_buf
)argument_list
)call
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_res) identifier_res
(assignment
(identifier_ofs) identifier_ofs
(integer_0) integer_0
)assignment
)assignment
)expression_statement
(while_statement
(comparison_operator
(identifier_pos) identifier_pos
(identifier_limit) identifier_limit
)comparison_operator
(block
(expression_statement
(assignment
(identifier_b) identifier_b
(call
(identifier__byte_code) identifier__byte_code
(argument_list
(subscript
(identifier_buf) identifier_buf
(identifier_pos) identifier_pos
)subscript
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(augmented_assignment
(identifier_res) identifier_res
(parenthesized_expression
(binary_operator
(parenthesized_expression
(binary_operator
(identifier_b) identifier_b
(integer_0x7F) integer_0x7F
)binary_operator
)parenthesized_expression
(identifier_ofs) identifier_ofs
)binary_operator
)parenthesized_expression
)augmented_assignment
)expression_statement
(expression_statement
(augmented_assignment
(identifier_pos) identifier_pos
(integer_1) integer_1
)augmented_assignment
)expression_statement
(expression_statement
(augmented_assignment
(identifier_ofs) identifier_ofs
(integer_7) integer_7
)augmented_assignment
)expression_statement
(if_statement
(comparison_operator
(identifier_b) identifier_b
(integer_0x80) integer_0x80
)comparison_operator
(block
(return_statement
(expression_list
(identifier_res) identifier_res
(identifier_pos) identifier_pos
)expression_list
)return_statement
)block
)if_statement
)block
)while_statement
(raise_statement
(call
(identifier_BadRarFile) identifier_BadRarFile
(argument_list
(string_'cannot load vint') string_'cannot load vint'
)argument_list
)call
)raise_statement
)block
)function_definition
)module | 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) identifier_target
(identifier_status_update_interval) identifier_status_update_interval
)parameters
(block
(return_statement
(call
(identifier__run) identifier__run
(argument_list
(identifier_categories) identifier_categories
(identifier_param_file) identifier_param_file
(identifier_project_dir) identifier_project_dir
(identifier_plugin) identifier_plugin
(identifier_target) identifier_target
(identifier_status_update_interval) identifier_status_update_interval
)argument_list
)call
)return_statement
)block
)function_definition
)module | 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
)dictionary_splat_pattern
)parameters
(block
(expression_statement
(assignment
(identifier_query) identifier_query
(call
(attribute
(call
(attribute
(attribute
(attribute
(identifier_cls) identifier_cls
(identifier_dbmodel) identifier_dbmodel
)attribute
(identifier_query) identifier_query
)attribute
(identifier_filter) identifier_filter
)attribute
(argument_list
(list_splat
(identifier_criteria) identifier_criteria
)list_splat
)argument_list
)call
(identifier_filter_by) identifier_filter_by
)attribute
(argument_list
(dictionary_splat
(identifier_filters) identifier_filters
)dictionary_splat
)argument_list
)call
)assignment
)expression_statement
(return_statement
(list_comprehension
(call
(identifier_cls) identifier_cls
(argument_list
(identifier_obj) identifier_obj
)argument_list
)call
(for_in_clause
(identifier_obj) identifier_obj
(call
(attribute
(identifier_query) identifier_query
(identifier_all) identifier_all
)attribute
(argument_list
)argument_list
)call
)for_in_clause
)list_comprehension
)return_statement
)block
)function_definition
)module | 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)
The function supports also "hybrid" arguments using WorkflowObjectModel
indirectly.
.. codeblock:: python
WorkflowObject.query(
WorkflowObject.dbmodel.status == ObjectStatus.COMPLETED,
user_id=user_id
)
See also SQLAlchemy BaseQuery's filter and filter_by documentation. |
(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
)parameters
(block
(expression_statement
(assignment
(identifier_allanvar) identifier_allanvar
(list
)list
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_nmax) identifier_nmax
(conditional_expression
(call
(identifier_len) identifier_len
(argument_list
(identifier_data) identifier_data
)argument_list
)call
(comparison_operator
(call
(identifier_len) identifier_len
(argument_list
(identifier_data) identifier_data
)argument_list
)call
(binary_operator
(identifier_tmax) identifier_tmax
(identifier_dt) identifier_dt
)binary_operator
)comparison_operator
(call
(identifier_int) identifier_int
(argument_list
(binary_operator
(identifier_tmax) identifier_tmax
(identifier_dt) identifier_dt
)binary_operator
)argument_list
)call
)conditional_expression
)assignment
)expression_statement
(for_statement
(identifier_i) identifier_i
(call
(identifier_range) identifier_range
(argument_list
(integer_1) integer_1
(binary_operator
(identifier_nmax) identifier_nmax
(integer_1) integer_1
)binary_operator
)argument_list
)call
(block
(expression_statement
(assignment
(identifier_databis) identifier_databis
(subscript
(identifier_data) identifier_data
(slice
(binary_operator
(call
(identifier_len) identifier_len
(argument_list
(identifier_data) identifier_data
)argument_list
)call
(identifier_i) identifier_i
)binary_operator
(colon) colon
)slice
)subscript
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_y) identifier_y
(call
(attribute
(call
(attribute
(identifier_databis) identifier_databis
(identifier_reshape) identifier_reshape
)attribute
(argument_list
(binary_operator
(call
(identifier_len) identifier_len
(argument_list
(identifier_data) identifier_data
)argument_list
)call
(identifier_i) identifier_i
)binary_operator
(identifier_i) identifier_i
)argument_list
)call
(identifier_mean) identifier_mean
)attribute
(argument_list
(keyword_argument
(identifier_axis) identifier_axis
(integer_1) integer_1
)keyword_argument
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(call
(attribute
(identifier_allanvar) identifier_allanvar
(identifier_append) identifier_append
)attribute
(argument_list
(binary_operator
(call
(attribute
(parenthesized_expression
(binary_operator
(parenthesized_expression
(binary_operator
(subscript
(identifier_y) identifier_y
(slice
(integer_1) integer_1
(colon) colon
)slice
)subscript
(subscript
(identifier_y) identifier_y
(slice
(colon) colon
(unary_operator
(integer_1) integer_1
)unary_operator
)slice
)subscript
)binary_operator
)parenthesized_expression
(integer_2) integer_2
)binary_operator
)parenthesized_expression
(identifier_mean) identifier_mean
)attribute
(argument_list
)argument_list
)call
(integer_2) integer_2
)binary_operator
)argument_list
)call
)expression_statement
)block
)for_statement
(return_statement
(expression_list
(binary_operator
(identifier_dt) identifier_dt
(call
(attribute
(identifier_np) identifier_np
(identifier_arange) identifier_arange
)attribute
(argument_list
(integer_1) integer_1
(binary_operator
(identifier_nmax) identifier_nmax
(integer_1) integer_1
)binary_operator
)argument_list
)call
)binary_operator
(call
(attribute
(identifier_np) identifier_np
(identifier_array) identifier_array
)attribute
(argument_list
(identifier_allanvar) identifier_allanvar
)argument_list
)call
)expression_list
)return_statement
)block
)function_definition
)module | 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_statement
(assignment
(identifier_result) identifier_result
(call
(attribute
(identifier_TypeConverter) identifier_TypeConverter
(identifier_to_nullable_type) identifier_to_nullable_type
)attribute
(argument_list
(identifier_value_type) identifier_value_type
(identifier_value) identifier_value
)argument_list
)call
)assignment
)expression_statement
(return_statement
(conditional_expression
(identifier_result) identifier_result
(comparison_operator
(identifier_result) identifier_result
(None) None
)comparison_operator
(identifier_default_value) identifier_default_value
)conditional_expression
)return_statement
)block
)function_definition
)module | 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 conversion is not possible (returns None).
:return: object value of type corresponding to TypeCode, or default value when conversion is not supported. |
(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
(call
(attribute
(string_"SaveFile,{}") string_"SaveFile,{}"
(identifier_format) identifier_format
)attribute
(argument_list
(identifier_fileName) identifier_fileName
)argument_list
)call
)assignment
)expression_statement
(expression_statement
(assignment
(identifier_reply) identifier_reply
(call
(attribute
(identifier_self) identifier_self
(identifier__sendDDEcommand) identifier__sendDDEcommand
)attribute
(argument_list
(identifier_cmd) identifier_cmd
)argument_list
)call
)assignment
)expression_statement
(return_statement
(call
(identifier_int) identifier_int
(argument_list
(call
(identifier_float) identifier_float
(argument_list
(call
(attribute
(identifier_reply) identifier_reply
(identifier_rstrip) identifier_rstrip
)attribute
(argument_list
)argument_list
)call
)argument_list
)call
)argument_list
)call
)return_statement
)block
)function_definition
)module | 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
(identifier_dimensions) identifier_dimensions
)dictionary_splat_pattern
)parameters
(block
(if_statement
(call
(identifier_isinstance) identifier_isinstance
(argument_list
(identifier___funcname) identifier___funcname
(identifier_str) identifier_str
)argument_list
)call
(block
(function_definition
(function_name_get_funcname) function_name_get_funcname
(parameters
(identifier__) identifier__
)parameters
(block
(return_statement
(identifier___funcname) identifier___funcname
)return_statement
)block
)function_definition
)block
(else_clause
(block
(expression_statement
(assignment
(identifier_get_funcname) identifier_get_funcname
(identifier___funcname) identifier___funcname
)assignment
)expression_statement
)block
)else_clause
)if_statement
(function_definition
(function_name__expect_dimension) function_name__expect_dimension
(parameters
(identifier_expected_ndim) identifier_expected_ndim
)parameters
(block
(function_definition
(function_name__check) function_name__check
(parameters
(identifier_func) identifier_func
(identifier_argname) identifier_argname
(identifier_argvalue) identifier_argvalue
)parameters
(block
(expression_statement
(assignment
(identifier_actual_ndim) identifier_actual_ndim
(attribute
(identifier_argvalue) identifier_argvalue
(identifier_ndim) identifier_ndim
)attribute
)assignment
)expression_statement
(if_statement
(comparison_operator
(identifier_actual_ndim) identifier_actual_ndim
(identifier_expected_ndim) identifier_expected_ndim
)comparison_operator
(block
(if_statement
(comparison_operator
(identifier_actual_ndim) identifier_actual_ndim
(integer_0) integer_0
)comparison_operator
(block
(expression_statement
(assignment
(identifier_actual_repr) identifier_actual_repr
(string_'scalar') string_'scalar'
)assignment
)expression_statement
)block
(else_clause
(block
(expression_statement
(assignment
(identifier_actual_repr) identifier_actual_repr
(binary_operator
(string_"%d-D array") string_"%d-D array"
(identifier_actual_ndim) identifier_actual_ndim
)binary_operator
)assignment
)expression_statement
)block
)else_clause
)if_statement
(raise_statement
(call
(identifier_ValueError) identifier_ValueError
(argument_list
(call
(attribute
(concatenated_string
(string_"{func}() expected a {expected:d}-D array") string_"{func}() expected a {expected:d}-D array"
(string_" for argument {argname!r}, but got a {actual}") string_" for argument {argname!r}, but got a {actual}"
(string_" instead.") string_" instead."
)concatenated_string
(identifier_format) identifier_format
)attribute
(argument_list
(keyword_argument
(identifier_func) identifier_func
(call
(identifier_get_funcname) identifier_get_funcname
(argument_list
(identifier_func) identifier_func
)argument_list
)call
)keyword_argument
(keyword_argument
(identifier_expected) identifier_expected
(identifier_expected_ndim) identifier_expected_ndim
)keyword_argument
(keyword_argument
(identifier_argname) identifier_argname
(identifier_argname) identifier_argname
)keyword_argument
(keyword_argument
(identifier_actual) identifier_actual
(identifier_actual_repr) identifier_actual_repr
)keyword_argument
)argument_list
)call
)argument_list
)call
)raise_statement
)block
)if_statement
(return_statement
(identifier_argvalue) identifier_argvalue
)return_statement
)block
)function_definition
(return_statement
(identifier__check) identifier__check
)return_statement
)block
)function_definition
(return_statement
(call
(identifier_preprocess) identifier_preprocess
(argument_list
(dictionary_splat
(call
(identifier_valmap) identifier_valmap
(argument_list
(identifier__expect_dimension) identifier__expect_dimension
(identifier_dimensions) identifier_dimensions
)argument_list
)call
)dictionary_splat
)argument_list
)call
)return_statement
)block
)function_definition
)module | 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
>>> foo(array([1, 1]), array([1, 1])) # doctest: +NORMALIZE_WHITESPACE
... # doctest: +ELLIPSIS
Traceback (most recent call last):
...
ValueError: ...foo() expected a 2-D array for argument 'y',
but got a 1-D array instead. |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.