Index

_

__init__() (nineml.abstraction_layer.component.Alias method) (nineml.abstraction_layer.component.AnalogPort method) (nineml.abstraction_layer.component.ComponentClass method) (nineml.abstraction_layer.component.ComponentClassMixinFlatStructure method) (nineml.abstraction_layer.component.ComponentClassMixinNamespaceStructure method) (nineml.abstraction_layer.component.ComponentQueryer method) (nineml.abstraction_layer.component.Condition method) (nineml.abstraction_layer.component.Dynamics method) (nineml.abstraction_layer.component.Equation method) (nineml.abstraction_layer.component.EventPort method) (nineml.abstraction_layer.component.Expression method) (nineml.abstraction_layer.component.ExpressionWithLHS method) (nineml.abstraction_layer.component.ExpressionWithSimpleLHS method) (nineml.abstraction_layer.component.NamespaceAddress method) (nineml.abstraction_layer.component.OnCondition method) (nineml.abstraction_layer.component.OnEvent method) (nineml.abstraction_layer.component.OutputEvent method) (nineml.abstraction_layer.component.Parameter method) (nineml.abstraction_layer.component.Port method) (nineml.abstraction_layer.component.Regime method) (nineml.abstraction_layer.component.RegimeElement method) (nineml.abstraction_layer.component.StateAssignment method) (nineml.abstraction_layer.component.StateVariable method) (nineml.abstraction_layer.component.TimeDerivative method) (nineml.abstraction_layer.component.Transition method) (nineml.abstraction_layer.component_modifiers.ComponentModifier method) (nineml.abstraction_layer.readers.XMLReader method) (nineml.abstraction_layer.writers.DotWriter method) (nineml.abstraction_layer.writers.TextWriter method) (nineml.abstraction_layer.writers.XMLWriter method) (nineml.utility.LocationMgr method)

A

accept_visitor() (nineml.abstraction_layer.component.Alias method) (nineml.abstraction_layer.component.AnalogPort method) (nineml.abstraction_layer.component.ComponentClass method) (nineml.abstraction_layer.component.Condition method) (nineml.abstraction_layer.component.Dynamics method) (nineml.abstraction_layer.component.EventPort method) (nineml.abstraction_layer.component.OnCondition method) (nineml.abstraction_layer.component.OnEvent method) (nineml.abstraction_layer.component.OutputEvent method) (nineml.abstraction_layer.component.Parameter method) (nineml.abstraction_layer.component.Regime method) (nineml.abstraction_layer.component.StateAssignment method) (nineml.abstraction_layer.component.StateVariable method) (nineml.abstraction_layer.component.TimeDerivative method) add_on_condition() (nineml.abstraction_layer.component.Regime method) add_on_event() (nineml.abstraction_layer.component.Regime method) Alias (class in nineml.abstraction_layer.component) aliases (nineml.abstraction_layer.component.ComponentClass attribute) (nineml.abstraction_layer.component.ComponentClassMixinFlatStructure attribute) (nineml.abstraction_layer.component.Dynamics attribute) aliases_map (nineml.abstraction_layer.component.ComponentClass attribute) (nineml.abstraction_layer.component.ComponentClassMixinFlatStructure attribute) (nineml.abstraction_layer.component.Dynamics attribute) analog_ports (nineml.abstraction_layer.component.ComponentClass attribute) (nineml.abstraction_layer.component.ComponentClassMixinFlatStructure attribute) analog_ports_map (nineml.abstraction_layer.component.ComponentQueryer attribute)

analog_recv_ports (nineml.abstraction_layer.component.ComponentQueryer attribute) analog_reduce_ports (nineml.abstraction_layer.component.ComponentQueryer attribute) analog_send_ports (nineml.abstraction_layer.component.ComponentQueryer attribute) AnalogPort (class in nineml.abstraction_layer.component) args (nineml.abstraction_layer.component.NineMLMathParseError attribute) assert_no_duplicates() (in module nineml.utility) atoms (nineml.abstraction_layer.component.Alias attribute) (nineml.abstraction_layer.component.ExpressionWithLHS attribute) (nineml.abstraction_layer.component.ExpressionWithSimpleLHS attribute) (nineml.abstraction_layer.component.StateAssignment attribute) (nineml.abstraction_layer.component.TimeDerivative attribute)

B

backsub_all() (nineml.abstraction_layer.component.ComponentClass method) (nineml.abstraction_layer.component.ComponentClassMixinFlatStructure method)

build() (nineml.abstraction_layer.writers.DotWriter class method)

C

close_all_reduce_ports() (nineml.abstraction_layer.component_modifiers.ComponentModifier class method) close_analog_port() (nineml.abstraction_layer.component_modifiers.ComponentModifier class method) ComponentClass (class in nineml.abstraction_layer.component) ComponentClassMixinFlatStructure (class in nineml.abstraction_layer.component) ComponentClassMixinNamespaceStructure (class in nineml.abstraction_layer.component) ComponentModifier (class in nineml.abstraction_layer.component_modifiers)

ComponentQueryer (class in nineml.abstraction_layer.component) concat() (nineml.abstraction_layer.component.NamespaceAddress class method) Condition (class in nineml.abstraction_layer.component) connect_ports() (nineml.abstraction_layer.component.ComponentClass method) (nineml.abstraction_layer.component.ComponentClassMixinNamespaceStructure method) create_root() (nineml.abstraction_layer.component.NamespaceAddress class method)

D

dependent_variable (nineml.abstraction_layer.component.TimeDerivative attribute) DotWriter (class in nineml.abstraction_layer.writers)

Dynamics (class in nineml.abstraction_layer.component) dynamics (nineml.abstraction_layer.component.ComponentClass attribute) (nineml.abstraction_layer.component.ComponentClassMixinFlatStructure attribute)

E

Equation (class in nineml.abstraction_layer.component) event_outputs (nineml.abstraction_layer.component.OnCondition attribute) (nineml.abstraction_layer.component.OnEvent attribute) (nineml.abstraction_layer.component.Transition attribute) event_ports (nineml.abstraction_layer.component.ComponentClass attribute) (nineml.abstraction_layer.component.ComponentClassMixinFlatStructure attribute) event_ports_map (nineml.abstraction_layer.component.ComponentQueryer attribute) event_recv_ports (nineml.abstraction_layer.component.ComponentQueryer attribute) event_send_ports (nineml.abstraction_layer.component.ComponentQueryer attribute)

EventPort (class in nineml.abstraction_layer.component) expect_single() (in module nineml.utility) Expression (class in nineml.abstraction_layer.component) ExpressionWithLHS (class in nineml.abstraction_layer.component) ExpressionWithSimpleLHS (class in nineml.abstraction_layer.component)

F

filter_by_type() (in module nineml.utility) filter_discrete_types() (in module nineml.utility) filter_expect_single() (in module nineml.utility)

flatten_first_level() (in module nineml.utility) flattener (nineml.abstraction_layer.component.ComponentClass attribute)

G

get_fully_qualified_port_connections() (nineml.abstraction_layer.component.ComponentQueryer method) get_local_name() (nineml.abstraction_layer.component.NamespaceAddress method) get_next_name() (nineml.abstraction_layer.component.Regime class method) get_node_addr() (nineml.abstraction_layer.component.ComponentClass method) (nineml.abstraction_layer.component.ComponentClassMixinNamespaceStructure method) get_parent_addr() (nineml.abstraction_layer.component.NamespaceAddress method) get_parent_model() (nineml.abstraction_layer.component.ComponentClass method) (nineml.abstraction_layer.component.ComponentClassMixinNamespaceStructure method) get_str_prefix() (nineml.abstraction_layer.component.NamespaceAddress method)

get_subnode() (nineml.abstraction_layer.component.ComponentClass method) (nineml.abstraction_layer.component.ComponentClassMixinNamespaceStructure method) get_subns_addr() (nineml.abstraction_layer.component.NamespaceAddress method) getCatalogDir() (nineml.utility.LocationMgr class method) getComponentDir() (nineml.utility.LocationMgr class method) getRootDir() (nineml.utility.LocationMgr class method) getstr() (nineml.abstraction_layer.component.NamespaceAddress method) getTmpDir() (nineml.utility.LocationMgr class method)

I

independent_variable (nineml.abstraction_layer.component.TimeDerivative attribute) insert_subnode() (nineml.abstraction_layer.component.ComponentClass method) (nineml.abstraction_layer.component.ComponentClassMixinNamespaceStructure method) invert_dictionary() (in module nineml.utility) is_flat() (nineml.abstraction_layer.component.ComponentClass method)

is_incoming() (nineml.abstraction_layer.component.AnalogPort method) (nineml.abstraction_layer.component.EventPort method) (nineml.abstraction_layer.component.Port method) is_outgoing() (nineml.abstraction_layer.component.AnalogPort method) (nineml.abstraction_layer.component.EventPort method) (nineml.abstraction_layer.component.Port method) is_root_namespace() (nineml.abstraction_layer.component.NamespaceAddress method)

L

lhs (nineml.abstraction_layer.component.Alias attribute) (nineml.abstraction_layer.component.ExpressionWithSimpleLHS attribute) (nineml.abstraction_layer.component.StateAssignment attribute) (nineml.abstraction_layer.component.TimeDerivative attribute) lhs_atoms (nineml.abstraction_layer.component.Alias attribute) (nineml.abstraction_layer.component.ExpressionWithLHS attribute) (nineml.abstraction_layer.component.ExpressionWithSimpleLHS attribute) (nineml.abstraction_layer.component.StateAssignment attribute) (nineml.abstraction_layer.component.TimeDerivative attribute)

lhs_name_transform_inplace() (nineml.abstraction_layer.component.Alias method) (nineml.abstraction_layer.component.ExpressionWithLHS method) (nineml.abstraction_layer.component.ExpressionWithSimpleLHS method) (nineml.abstraction_layer.component.StateAssignment method) (nineml.abstraction_layer.component.TimeDerivative method) LocationMgr (class in nineml.utility)

M

message (nineml.abstraction_layer.component.NineMLMathParseError attribute)

mode (nineml.abstraction_layer.component.AnalogPort attribute) (nineml.abstraction_layer.component.EventPort attribute) (nineml.abstraction_layer.component.Port attribute)

N

name (nineml.abstraction_layer.component.AnalogPort attribute) (nineml.abstraction_layer.component.ComponentClass attribute) (nineml.abstraction_layer.component.ComponentClassMixinFlatStructure attribute) (nineml.abstraction_layer.component.EventPort attribute) (nineml.abstraction_layer.component.Parameter attribute) (nineml.abstraction_layer.component.Port attribute) (nineml.abstraction_layer.component.Regime attribute) (nineml.abstraction_layer.component.StateVariable attribute) name_transform_inplace() (nineml.abstraction_layer.component.Alias method) (nineml.abstraction_layer.component.ExpressionWithLHS method) (nineml.abstraction_layer.component.ExpressionWithSimpleLHS method) (nineml.abstraction_layer.component.StateAssignment method) (nineml.abstraction_layer.component.TimeDerivative method)

NamespaceAddress (class in nineml.abstraction_layer.component) NineMLMathParseError

O

on_conditions (nineml.abstraction_layer.component.Regime attribute) on_events (nineml.abstraction_layer.component.Regime attribute) OnCondition (class in nineml.abstraction_layer.component)

OnEvent (class in nineml.abstraction_layer.component) OutputEvent (class in nineml.abstraction_layer.component)

P

Parameter (class in nineml.abstraction_layer.component) parameters (nineml.abstraction_layer.component.ComponentClass attribute) (nineml.abstraction_layer.component.ComponentClassMixinFlatStructure attribute) parameters_map (nineml.abstraction_layer.component.ComponentQueryer attribute) Port (class in nineml.abstraction_layer.component)

port_name (nineml.abstraction_layer.component.OutputEvent attribute) portconnections (nineml.abstraction_layer.component.ComponentClass attribute) (nineml.abstraction_layer.component.ComponentClassMixinNamespaceStructure attribute) ports (nineml.abstraction_layer.component.ComponentQueryer attribute)

Q

query (nineml.abstraction_layer.component.ComponentClass attribute)

R

read() (nineml.abstraction_layer.readers.XMLReader class method) read_component() (nineml.abstraction_layer.readers.XMLReader class method) read_components() (nineml.abstraction_layer.readers.XMLReader class method) recurse_all_components (nineml.abstraction_layer.component.ComponentQueryer attribute) reduce_op (nineml.abstraction_layer.component.AnalogPort attribute) (nineml.abstraction_layer.component.EventPort attribute) (nineml.abstraction_layer.component.Port attribute) Regime (class in nineml.abstraction_layer.component) regime() (nineml.abstraction_layer.component.ComponentQueryer method) RegimeElement (class in nineml.abstraction_layer.component) regimes (nineml.abstraction_layer.component.ComponentClass attribute) (nineml.abstraction_layer.component.ComponentClassMixinFlatStructure attribute) (nineml.abstraction_layer.component.Dynamics attribute) regimes_map (nineml.abstraction_layer.component.ComponentClass attribute) (nineml.abstraction_layer.component.ComponentClassMixinFlatStructure attribute) (nineml.abstraction_layer.component.Dynamics attribute)

rename_port() (nineml.abstraction_layer.component_modifiers.ComponentModifier class method) rhs (nineml.abstraction_layer.component.Alias attribute) (nineml.abstraction_layer.component.Condition attribute) (nineml.abstraction_layer.component.Equation attribute) (nineml.abstraction_layer.component.Expression attribute) (nineml.abstraction_layer.component.ExpressionWithLHS attribute) (nineml.abstraction_layer.component.ExpressionWithSimpleLHS attribute) (nineml.abstraction_layer.component.StateAssignment attribute) (nineml.abstraction_layer.component.TimeDerivative attribute) rhs_as_python_func() (nineml.abstraction_layer.component.Alias method) (nineml.abstraction_layer.component.Condition method) (nineml.abstraction_layer.component.Equation method) (nineml.abstraction_layer.component.Expression method) (nineml.abstraction_layer.component.ExpressionWithLHS method) (nineml.abstraction_layer.component.ExpressionWithSimpleLHS method) (nineml.abstraction_layer.component.StateAssignment method) (nineml.abstraction_layer.component.TimeDerivative method) rhs_atoms (nineml.abstraction_layer.component.Alias attribute) (nineml.abstraction_layer.component.Condition attribute) (nineml.abstraction_layer.component.Equation attribute) (nineml.abstraction_layer.component.Expression attribute) (nineml.abstraction_layer.component.ExpressionWithLHS attribute) (nineml.abstraction_layer.component.ExpressionWithSimpleLHS attribute) (nineml.abstraction_layer.component.StateAssignment attribute) (nineml.abstraction_layer.component.TimeDerivative attribute) rhs_funcs (nineml.abstraction_layer.component.Alias attribute) (nineml.abstraction_layer.component.Condition attribute) (nineml.abstraction_layer.component.Equation attribute) (nineml.abstraction_layer.component.Expression attribute) (nineml.abstraction_layer.component.ExpressionWithLHS attribute) (nineml.abstraction_layer.component.ExpressionWithSimpleLHS attribute) (nineml.abstraction_layer.component.StateAssignment attribute) (nineml.abstraction_layer.component.TimeDerivative attribute) rhs_has_missing_functions() (nineml.abstraction_layer.component.Alias method) (nineml.abstraction_layer.component.Condition method) (nineml.abstraction_layer.component.Equation method) (nineml.abstraction_layer.component.Expression method) (nineml.abstraction_layer.component.ExpressionWithLHS method) (nineml.abstraction_layer.component.ExpressionWithSimpleLHS method) (nineml.abstraction_layer.component.StateAssignment method) (nineml.abstraction_layer.component.TimeDerivative method) rhs_missing_functions (nineml.abstraction_layer.component.Alias attribute) (nineml.abstraction_layer.component.Condition attribute) (nineml.abstraction_layer.component.Equation attribute) (nineml.abstraction_layer.component.Expression attribute) (nineml.abstraction_layer.component.ExpressionWithLHS attribute) (nineml.abstraction_layer.component.ExpressionWithSimpleLHS attribute) (nineml.abstraction_layer.component.StateAssignment attribute) (nineml.abstraction_layer.component.TimeDerivative attribute) rhs_name_transform_inplace() (nineml.abstraction_layer.component.Alias method) (nineml.abstraction_layer.component.Condition method) (nineml.abstraction_layer.component.Equation method) (nineml.abstraction_layer.component.Expression method) (nineml.abstraction_layer.component.ExpressionWithLHS method) (nineml.abstraction_layer.component.ExpressionWithSimpleLHS method) (nineml.abstraction_layer.component.StateAssignment method) (nineml.abstraction_layer.component.TimeDerivative method) rhs_names (nineml.abstraction_layer.component.Alias attribute) (nineml.abstraction_layer.component.Condition attribute) (nineml.abstraction_layer.component.Equation attribute) (nineml.abstraction_layer.component.Expression attribute) (nineml.abstraction_layer.component.ExpressionWithLHS attribute) (nineml.abstraction_layer.component.ExpressionWithSimpleLHS attribute) (nineml.abstraction_layer.component.StateAssignment attribute) (nineml.abstraction_layer.component.TimeDerivative attribute)

S

safe_dictionary_merge() (in module nineml.utility) set_flattener() (nineml.abstraction_layer.component.ComponentClass method) set_parent_model() (nineml.abstraction_layer.component.ComponentClass method) (nineml.abstraction_layer.component.ComponentClassMixinNamespaceStructure method) set_source_regime() (nineml.abstraction_layer.component.OnCondition method) (nineml.abstraction_layer.component.OnEvent method) (nineml.abstraction_layer.component.Transition method) set_target_regime() (nineml.abstraction_layer.component.OnCondition method) (nineml.abstraction_layer.component.OnEvent method) (nineml.abstraction_layer.component.Transition method) source_regime (nineml.abstraction_layer.component.OnCondition attribute) (nineml.abstraction_layer.component.OnEvent attribute) (nineml.abstraction_layer.component.Transition attribute) source_regime_name (nineml.abstraction_layer.component.OnCondition attribute) (nineml.abstraction_layer.component.OnEvent attribute) (nineml.abstraction_layer.component.Transition attribute) src_port_name (nineml.abstraction_layer.component.OnEvent attribute)

state_assignments (nineml.abstraction_layer.component.OnCondition attribute) (nineml.abstraction_layer.component.OnEvent attribute) (nineml.abstraction_layer.component.Transition attribute) state_variables (nineml.abstraction_layer.component.ComponentClass attribute) (nineml.abstraction_layer.component.ComponentClassMixinFlatStructure attribute) (nineml.abstraction_layer.component.Dynamics attribute) state_variables_map (nineml.abstraction_layer.component.ComponentClass attribute) (nineml.abstraction_layer.component.ComponentClassMixinFlatStructure attribute) (nineml.abstraction_layer.component.Dynamics attribute) StateAssignment (class in nineml.abstraction_layer.component) StateVariable (class in nineml.abstraction_layer.component) std_append_to_path_called (nineml.utility.LocationMgr attribute) StdAppendToPath() (nineml.utility.LocationMgr class method)

T

target_regime (nineml.abstraction_layer.component.OnCondition attribute) (nineml.abstraction_layer.component.OnEvent attribute) (nineml.abstraction_layer.component.Transition attribute) target_regime_name (nineml.abstraction_layer.component.OnCondition attribute) (nineml.abstraction_layer.component.OnEvent attribute) (nineml.abstraction_layer.component.Transition attribute) temp_dir (nineml.utility.LocationMgr attribute) TextWriter (class in nineml.abstraction_layer.writers) time_derivatives (nineml.abstraction_layer.component.Regime attribute)

TimeDerivative (class in nineml.abstraction_layer.component) Transition (class in nineml.abstraction_layer.component) transitions (nineml.abstraction_layer.component.ComponentClass attribute) (nineml.abstraction_layer.component.ComponentClassMixinFlatStructure attribute) (nineml.abstraction_layer.component.Dynamics attribute) (nineml.abstraction_layer.component.Regime attribute) trigger (nineml.abstraction_layer.component.OnCondition attribute)

V

visit() (nineml.abstraction_layer.writers.XMLWriter method) visit_alias() (nineml.abstraction_layer.writers.XMLWriter method) visit_analogport() (nineml.abstraction_layer.writers.XMLWriter method) visit_assignment() (nineml.abstraction_layer.writers.XMLWriter method) visit_componentclass() (nineml.abstraction_layer.writers.XMLWriter method) visit_condition() (nineml.abstraction_layer.writers.XMLWriter method) visit_dynamics() (nineml.abstraction_layer.writers.XMLWriter method) visit_eventport() (nineml.abstraction_layer.writers.XMLWriter method)

visit_oncondition() (nineml.abstraction_layer.writers.XMLWriter method) visit_onevent() (nineml.abstraction_layer.writers.XMLWriter method) visit_outputevent() (nineml.abstraction_layer.writers.XMLWriter method) visit_parameter() (nineml.abstraction_layer.writers.XMLWriter method) visit_regime() (nineml.abstraction_layer.writers.XMLWriter method) visit_statevariable() (nineml.abstraction_layer.writers.XMLWriter method) visit_timederivative() (nineml.abstraction_layer.writers.XMLWriter method)

W

was_flattened() (nineml.abstraction_layer.component.ComponentClass method)

write() (nineml.abstraction_layer.component.ComponentClass method) (nineml.abstraction_layer.component.ComponentClassMixinFlatStructure method) (nineml.abstraction_layer.writers.DotWriter class method) (nineml.abstraction_layer.writers.TextWriter class method) (nineml.abstraction_layer.writers.XMLWriter class method)

X

XMLReader (class in nineml.abstraction_layer.readers)

XMLWriter (class in nineml.abstraction_layer.writers)