def test_assert_no_duplicates(self):
# Signature: name(lst, error_func=None)
# Check for duplicates in a sequence.
#
# This function checks that a list contains no duplicates, by casting the list
# to a set and comparing the lengths.
#
# It raises an `NineMLRuntimeError` if the lengths are not equal.
# Duplication
self.assertRaises(
NineMLRuntimeError,
assert_no_duplicates, [1, 2, 3, 4, 4],
)
self.assertRaises(
NineMLRuntimeError,
assert_no_duplicates, ['1', '2', '3', '4', '4'],
)
assert_no_duplicates([1, 2, 3, 4])
assert_no_duplicates(['1', '2', '3', '4'])
assert_no_duplicates([None])
assert_no_duplicates([True])
assert_no_duplicates([()])
def test_assert_no_duplicates(self):
# Signature: name(lst, error_func=None)
# Check for duplicates in a sequence.
#
# This function checks that a list contains no duplicates, by casting the list
# to a set and comparing the lengths.
#
# It raises an `NineMLUsageError` if the lengths are not equal.
# Duplication
self.assertRaises(
NineMLUsageError,
assert_no_duplicates,
[1, 2, 3, 4, 4],
)
self.assertRaises(
NineMLUsageError,
assert_no_duplicates,
['1', '2', '3', '4', '4'],
)
assert_no_duplicates([1, 2, 3, 4])
assert_no_duplicates(['1', '2', '3', '4'])
assert_no_duplicates([None])
assert_no_duplicates([True])
assert_no_duplicates([()])
def __init__(self, *args, **kwargs):
BaseALObject.__init__(self)
ContainerObject.__init__(self)
valid_kwargs = ('name', 'transitions', 'on_events', 'on_conditions',
'time_derivatives', 'aliases')
for arg in kwargs:
if arg not in valid_kwargs:
err = 'Unexpected Arg: %s' % arg
raise NineMLUsageError(err)
name = kwargs.get('name', None)
if name is None:
self._name = 'default'
else:
self._name = validate_identifier(name)
validate_identifier(self._name)
# Get Time derivatives from args or kwargs
kw_tds = normalise_parameter_as_list(
kwargs.get('time_derivatives', None))
time_derivatives = list(args) + kw_tds
# Un-named arguments are time_derivatives:
time_derivatives = normalise_parameter_as_list(time_derivatives)
# time_derivatives.extend( args )
td_types = (basestring, TimeDerivative)
td_type_dict = filter_discrete_types(time_derivatives, td_types)
td_from_str = [TimeDerivative.from_str(o)
for o in td_type_dict[basestring]]
time_derivatives = td_type_dict[TimeDerivative] + td_from_str
# Check for double definitions:
td_dep_vars = [td.variable for td in time_derivatives]
assert_no_duplicates(
td_dep_vars,
("Multiple time derivatives found for the same state variable "
"in regime '{}' (found '{}')".format(
self.name,
"', '".join(td.variable for td in time_derivatives))))
self.add(*time_derivatives)
# We support passing in 'transitions', which is a list of both OnEvents
# and OnConditions as well as separate on_conditions and on_events.
transitions = normalise_parameter_as_list(
kwargs.get('transitions', None))
self.add(*transitions)
on_conditions = normalise_parameter_as_list(
kwargs.get('on_conditions', None))
self.add(*on_conditions)
on_events = normalise_parameter_as_list(
kwargs.get('on_events', None))
self.add(*on_events)
# Add regime specific aliases
aliases = normalise_parameter_as_list(kwargs.get('aliases', None))
self.add(*aliases)
def _resolve_transition_regime_names(self):
# Check that the names of the regimes are unique:
names = [r.name for r in self.regimes]
assert_no_duplicates(names)
# Create a map of regime names to regimes:
regime_map = dict([(r.name, r) for r in self.regimes])
# We only worry about 'target' regimes, since source regimes are taken
# care of for us by the Regime objects they are attached to.
for trans in self.transitions:
if trans.target_regime_name not in regime_map:
raise NineMLRuntimeError(
"Can't find regime '{}'".format(trans.target_regime_name))
trans.set_target_regime(regime_map[trans.target_regime_name])
def _resolve_transition_regime_names(self):
# Check that the names of the regimes are unique:
names = [r.name for r in self.regimes]
assert_no_duplicates(names)
# Create a map of regime names to regimes:
regime_map = dict([(r.name, r) for r in self.regimes])
# We only worry about 'target' regimes, since source regimes are taken
# care of for us by the Regime objects they are attached to.
for trans in self.transitions:
if trans.target_regime_name not in regime_map:
raise NineMLRuntimeError("Can't find regime '{}'".format(
trans.target_regime_name))
trans.set_target_regime(regime_map[trans.target_regime_name])
def _resolve_transition_regimes(self):
# Check that the names of the regimes are unique:
assert_no_duplicates([r.name for r in self.regimes])
# We only worry about 'target' regimes, since source regimes are taken
# care of for us by the Regime objects they are attached to.
for regime in self.regimes:
for trans in regime.transitions:
trans.set_source_regime(regime)
target = trans.target_regime_name
if target is None:
target = regime # to same regime
else:
try:
target = self.regime(target) # Lookup by name
except KeyError:
self.regime(target)
raise NineMLUsageError(
"Can't find regime '{}' referenced from '{}' "
"transition".format(trans.target_regime,
trans.key))
trans.set_target_regime(target)
def _resolve_transition_regimes(self):
# Check that the names of the regimes are unique:
assert_no_duplicates([r.name for r in self.regimes])
# We only worry about 'target' regimes, since source regimes are taken
# care of for us by the Regime objects they are attached to.
for regime in self.regimes:
for trans in regime.transitions:
trans.set_source_regime(regime)
target = trans.target_regime_name
if target is None:
target = regime # to same regime
else:
try:
target = self.regime(target) # Lookup by name
except KeyError:
self.regime(target)
raise NineMLUsageError(
"Can't find regime '{}' referenced from '{}' "
"transition".format(trans.target_regime,
trans.key))
trans.set_target_regime(target)
def __init__(self, regimes=None, aliases=None, state_variables=None):
"""DynamicsBlock object constructor
:param aliases: A list of aliases, which must be either |Alias|
objects or ``string``s.
:param regimes: A list containing at least one |Regime| object.
:param state_variables: An optional list of the state variables,
which can either be |StateVariable| objects or `string` s. If
provided, it must match the inferred state-variables from the
regimes; if it is not provided it will be inferred
automatically.
"""
aliases = normalise_parameter_as_list(aliases)
regimes = normalise_parameter_as_list(regimes)
state_variables = normalise_parameter_as_list(state_variables)
# Load the aliases as objects or strings:
alias_td = filter_discrete_types(aliases, (basestring, Alias))
aliases_from_strs = [Alias.from_str(o) for o in alias_td[basestring]]
aliases = alias_td[Alias] + aliases_from_strs
# Load the state variables as objects or strings:
sv_types = (basestring, StateVariable)
sv_td = filter_discrete_types(state_variables, sv_types)
sv_from_strings = [
StateVariable(o, dimension=None) for o in sv_td[basestring]
]
state_variables = sv_td[StateVariable] + sv_from_strings
assert_no_duplicates(r.name for r in regimes)
assert_no_duplicates(a.lhs for a in aliases)
assert_no_duplicates(s.name for s in state_variables)
self._regimes = dict((r.name, r) for r in regimes)
self._aliases = dict((a.lhs, a) for a in aliases)
self._state_variables = dict((s.name, s) for s in state_variables)
def __init__(self, regimes=None, aliases=None, state_variables=None):
"""DynamicsBlock object constructor
:param aliases: A list of aliases, which must be either |Alias|
objects or ``string``s.
:param regimes: A list containing at least one |Regime| object.
:param state_variables: An optional list of the state variables,
which can either be |StateVariable| objects or `string` s. If
provided, it must match the inferred state-variables from the
regimes; if it is not provided it will be inferred
automatically.
"""
aliases = normalise_parameter_as_list(aliases)
regimes = normalise_parameter_as_list(regimes)
state_variables = normalise_parameter_as_list(state_variables)
# Load the aliases as objects or strings:
alias_td = filter_discrete_types(aliases, (basestring, Alias))
aliases_from_strs = [Alias.from_str(o) for o in alias_td[basestring]]
aliases = alias_td[Alias] + aliases_from_strs
# Load the state variables as objects or strings:
sv_types = (basestring, StateVariable)
sv_td = filter_discrete_types(state_variables, sv_types)
sv_from_strings = [StateVariable(o, dimension=None)
for o in sv_td[basestring]]
state_variables = sv_td[StateVariable] + sv_from_strings
assert_no_duplicates(r.name for r in regimes)
assert_no_duplicates(a.lhs for a in aliases)
assert_no_duplicates(s.name for s in state_variables)
self._regimes = dict((r.name, r) for r in regimes)
self._aliases = dict((a.lhs, a) for a in aliases)
self._state_variables = dict((s.name, s) for s in state_variables)
def __init__(self, name, parameters=None, analog_ports=[],
event_ports=[],
dynamicsblock=None, subnodes=None,
portconnections=None, regimes=None,
aliases=None, state_variables=None):
"""Constructs a DynamicsClass
:param name: The name of the componentclass.
:param parameters: A list containing either |Parameter| objects
or strings representing the parameter names. If ``None``, then the
parameters are automatically inferred from the |Dynamics| block.
:param analog_ports: A list of |AnalogPorts|, which will be the
local |AnalogPorts| for this object.
:param event_ports: A list of |EventPorts| objects, which will be the
local event-ports for this object. If this is ``None``, then they
will be automatically inferred from the dynamics block.
:param dynamicsblock: A |DynamicsBlock| object, defining the local
dynamicsblock of the componentclass.
:param subnodes: A dictionary mapping namespace-names to sub-
componentclass. [Type: ``{string:|DynamicsClass|,
string:|DynamicsClass|, string:|DynamicsClass|}`` ] describing the
namespace of subcomponents for this componentclass.
:param portconnections: A list of pairs, specifying the connections
between the ports of the subcomponents in this componentclass.
These can be `(|NamespaceAddress|, |NamespaceAddress|)' or
``(string, string)``.
:param interface: A shorthand way of specifying the **interface** for
this componentclass; |Parameters|, |AnalogPorts| and |EventPorts|.
``interface`` takes a list of these objects, and automatically
resolves them by type into the correct types.
Examples:
>>> a = DynamicsClass(name='MyComponent1')
.. todo::
Point this towards and example of constructing ComponentClasses.
This can't be here, because we also need to know about dynamics.
For examples
"""
# We can specify in the componentclass, and they will get forwarded to
# the dynamics class. We check that we do not specify half-and-half:
if dynamicsblock is not None:
if regimes or aliases or state_variables:
err = "Either specify a 'dynamicsblock' parameter, or "
err += "state_variables /regimes/aliases, but not both!"
raise NineMLRuntimeError(err)
else:
dynamicsblock = DynamicsBlock(regimes=regimes, aliases=aliases,
state_variables=state_variables)
ComponentClass.__init__(self, name, parameters,
main_block=dynamicsblock)
self._query = DynamicsQueryer(self)
# Ensure analog_ports is a list not an iterator
analog_ports = list(analog_ports)
event_ports = list(event_ports)
# Check there aren't any duplicates in the port and parameter names
assert_no_duplicates(p if isinstance(p, basestring) else p.name
for p in chain(parameters if parameters else [],
analog_ports, event_ports))
self._analog_send_ports = dict(
(p.name, p) for p in analog_ports if isinstance(p, AnalogSendPort))
self._analog_receive_ports = dict(
(p.name, p) for p in analog_ports if isinstance(p,
AnalogReceivePort))
self._analog_reduce_ports = dict(
(p.name, p) for p in analog_ports if isinstance(p,
AnalogReducePort))
# Create dummy event ports to keep the ActionVisitor base class of
# the interface inferrer happy
self._event_receive_ports = self._event_send_ports = self.subnodes = {}
# EventPort, StateVariable and Parameter Inference:
inferred_struct = DynamicsClassInterfaceInferer(self)
# Check any supplied parameters match:
if parameters is not None:
inf_check(self._parameters.keys(),
inferred_struct.parameter_names,
'Parameters')
else:
self._parameters = dict((n, Parameter(n))
for n in inferred_struct.parameter_names)
# Check any supplied state_variables match:
if self.dynamicsblock._state_variables:
state_var_names = [p.name
for p in self.dynamicsblock.state_variables]
inf_check(state_var_names,
inferred_struct.state_variable_names,
'StateVariables')
else:
state_vars = dict((n, StateVariable(n)) for n in
inferred_struct.state_variable_names)
self.dynamicsblock._state_variables = state_vars
# Set and check event receive ports match inferred
self._event_receive_ports = dict(
(p.name, p) for p in event_ports if isinstance(p,
EventReceivePort))
if len(self._event_receive_ports):
# FIXME: not all OutputEvents are necessarily exposed as Ports,
# so really we should just check that all declared output event
# ports are in the list of inferred ports, not that the declared
# list is identical to the inferred one.
inf_check(self._event_receive_ports.keys(),
inferred_struct.input_event_port_names,
'Event Ports In')
else:
# FIXME: TGC don't like this shorthand
# Event ports not supplied, so lets use the inferred ones.
for pname in inferred_struct.input_event_port_names:
self._event_receive_ports[pname] = EventReceivePort(name=pname)
# Set and check event send ports match inferred
self._event_send_ports = dict(
(p.name, p) for p in event_ports if isinstance(p, EventSendPort))
if len(self._event_send_ports):
inf_check(self._event_send_ports.keys(),
inferred_struct.event_out_port_names,
'Event Ports Out')
else:
# Event ports not supplied, so lets use the inferred ones.
for pname in inferred_struct.event_out_port_names:
self._event_send_ports[pname] = EventSendPort(name=pname)
# Call namespace mixin constructor
_NamespaceMixin.__init__(
self, subnodes=subnodes, portconnections=portconnections)
# Finalise initiation:
self._resolve_transition_regime_names()
# Store flattening Information:
self._flattener = None
# Is the finished componentclass valid?:
self._validate_self()
def __init__(self, *args, **kwargs):
"""Regime constructor
:param name: The name of the constructor. If none, then a name will
be automatically generated.
:param time_derivatives: A list of time derivatives, as
either ``string``s (e.g 'dg/dt = g/gtau') or as
|TimeDerivative| objects.
:param transitions: A list containing either |OnEvent| or
|OnCondition| objects, which will automatically be sorted into
the appropriate classes automatically.
:param *args: Any non-keyword arguments will be treated as
time_derivatives.
"""
valid_kwargs = ('name', 'transitions', 'time_derivatives')
for arg in kwargs:
if arg not in valid_kwargs:
err = 'Unexpected Arg: %s' % arg
raise NineMLRuntimeError(err)
transitions = kwargs.get('transitions', None)
name = kwargs.get('name', None)
kw_tds = normalise_parameter_as_list(kwargs.get('time_derivatives',
None))
time_derivatives = list(args) + kw_tds
self._name = name
if self.name is not None:
self._name = self._name.strip()
ensure_valid_identifier(self._name)
# Un-named arguments are time_derivatives:
time_derivatives = normalise_parameter_as_list(time_derivatives)
# time_derivatives.extend( args )
td_types = (basestring, TimeDerivative)
td_type_dict = filter_discrete_types(time_derivatives, td_types)
td_from_str = [TimeDerivative.from_str(o)
for o in td_type_dict[basestring]]
time_derivatives = td_type_dict[TimeDerivative] + td_from_str
# Check for double definitions:
td_dep_vars = [td.dependent_variable for td in time_derivatives]
assert_no_duplicates(td_dep_vars)
# Store as a dictionary
self._time_derivatives = dict((td.dependent_variable, td)
for td in time_derivatives)
# We support passing in 'transitions', which is a list of both OnEvents
# and OnConditions. So, lets filter this by type and add them
# appropriately:
transitions = normalise_parameter_as_list(transitions)
f_dict = filter_discrete_types(transitions, (OnEvent, OnCondition))
self._on_events = []
self._on_conditions = []
# Add all the OnEvents and OnConditions:
for event in f_dict[OnEvent]:
self.add_on_event(event)
for condition in f_dict[OnCondition]:
self.add_on_condition(condition)
# Sort for equality checking
self._on_events = sorted(self._on_events,
key=lambda x: x.src_port_name)
self._on_conditions = sorted(self._on_conditions,
key=lambda x: x.trigger)
def action_componentclass(self, componentclass,
namespace): # @UnusedVariable @IgnorePep8
regime_names = [r.name for r in componentclass.regimes]
assert_no_duplicates(regime_names)
def action_componentclass(self, componentclass, namespace): # @UnusedVariable @IgnorePep8
regime_names = [r.name for r in componentclass.regimes]
assert_no_duplicates(regime_names)
def action_regime(self, regime, namespace, **kwargs): # @UnusedVariable
event_triggers = [on_event.src_port_name
for on_event in regime.on_events]
assert_no_duplicates(event_triggers)
def __init__(self,
name,
parameters=None,
analog_ports=[],
event_ports=[],
dynamicsblock=None,
subnodes=None,
portconnections=None,
regimes=None,
aliases=None,
state_variables=None):
"""Constructs a DynamicsClass
:param name: The name of the componentclass.
:param parameters: A list containing either |Parameter| objects
or strings representing the parameter names. If ``None``, then the
parameters are automatically inferred from the |Dynamics| block.
:param analog_ports: A list of |AnalogPorts|, which will be the
local |AnalogPorts| for this object.
:param event_ports: A list of |EventPorts| objects, which will be the
local event-ports for this object. If this is ``None``, then they
will be automatically inferred from the dynamics block.
:param dynamicsblock: A |DynamicsBlock| object, defining the local
dynamicsblock of the componentclass.
:param subnodes: A dictionary mapping namespace-names to sub-
componentclass. [Type: ``{string:|DynamicsClass|,
string:|DynamicsClass|, string:|DynamicsClass|}`` ] describing the
namespace of subcomponents for this componentclass.
:param portconnections: A list of pairs, specifying the connections
between the ports of the subcomponents in this componentclass.
These can be `(|NamespaceAddress|, |NamespaceAddress|)' or
``(string, string)``.
:param interface: A shorthand way of specifying the **interface** for
this componentclass; |Parameters|, |AnalogPorts| and |EventPorts|.
``interface`` takes a list of these objects, and automatically
resolves them by type into the correct types.
Examples:
>>> a = DynamicsClass(name='MyComponent1')
.. todo::
Point this towards and example of constructing ComponentClasses.
This can't be here, because we also need to know about dynamics.
For examples
"""
# We can specify in the componentclass, and they will get forwarded to
# the dynamics class. We check that we do not specify half-and-half:
if dynamicsblock is not None:
if regimes or aliases or state_variables:
err = "Either specify a 'dynamicsblock' parameter, or "
err += "state_variables /regimes/aliases, but not both!"
raise NineMLRuntimeError(err)
else:
dynamicsblock = DynamicsBlock(regimes=regimes,
aliases=aliases,
state_variables=state_variables)
ComponentClass.__init__(self,
name,
parameters,
main_block=dynamicsblock)
self._query = DynamicsQueryer(self)
# Ensure analog_ports is a list not an iterator
analog_ports = list(analog_ports)
event_ports = list(event_ports)
# Check there aren't any duplicates in the port and parameter names
assert_no_duplicates(p if isinstance(p, basestring) else p.name
for p in chain(parameters if parameters else [],
analog_ports, event_ports))
self._analog_send_ports = dict(
(p.name, p) for p in analog_ports if isinstance(p, AnalogSendPort))
self._analog_receive_ports = dict((p.name, p) for p in analog_ports
if isinstance(p, AnalogReceivePort))
self._analog_reduce_ports = dict((p.name, p) for p in analog_ports
if isinstance(p, AnalogReducePort))
# Create dummy event ports to keep the ActionVisitor base class of
# the interface inferrer happy
self._event_receive_ports = self._event_send_ports = self.subnodes = {}
# EventPort, StateVariable and Parameter Inference:
inferred_struct = DynamicsClassInterfaceInferer(self)
# Check any supplied parameters match:
if parameters is not None:
inf_check(self._parameters.keys(), inferred_struct.parameter_names,
'Parameters')
else:
self._parameters = dict(
(n, Parameter(n)) for n in inferred_struct.parameter_names)
# Check any supplied state_variables match:
if self.dynamicsblock._state_variables:
state_var_names = [
p.name for p in self.dynamicsblock.state_variables
]
inf_check(state_var_names, inferred_struct.state_variable_names,
'StateVariables')
else:
state_vars = dict((n, StateVariable(n))
for n in inferred_struct.state_variable_names)
self.dynamicsblock._state_variables = state_vars
# Set and check event receive ports match inferred
self._event_receive_ports = dict((p.name, p) for p in event_ports
if isinstance(p, EventReceivePort))
if len(self._event_receive_ports):
# FIXME: not all OutputEvents are necessarily exposed as Ports,
# so really we should just check that all declared output event
# ports are in the list of inferred ports, not that the declared
# list is identical to the inferred one.
inf_check(self._event_receive_ports.keys(),
inferred_struct.input_event_port_names, 'Event Ports In')
else:
# FIXME: TGC don't like this shorthand
# Event ports not supplied, so lets use the inferred ones.
for pname in inferred_struct.input_event_port_names:
self._event_receive_ports[pname] = EventReceivePort(name=pname)
# Set and check event send ports match inferred
self._event_send_ports = dict(
(p.name, p) for p in event_ports if isinstance(p, EventSendPort))
if len(self._event_send_ports):
inf_check(self._event_send_ports.keys(),
inferred_struct.event_out_port_names, 'Event Ports Out')
else:
# Event ports not supplied, so lets use the inferred ones.
for pname in inferred_struct.event_out_port_names:
self._event_send_ports[pname] = EventSendPort(name=pname)
# Call namespace mixin constructor
_NamespaceMixin.__init__(self,
subnodes=subnodes,
portconnections=portconnections)
# Finalise initiation:
self._resolve_transition_regime_names()
# Store flattening Information:
self._flattener = None
# Is the finished componentclass valid?:
self._validate_self()
def action_regime(self, regime, namespace, **kwargs): # @UnusedVariable
event_triggers = [
on_event.src_port_name for on_event in regime.on_events
]
assert_no_duplicates(event_triggers)
def __init__(self, componentclass):
PerNamespaceComponentValidator.__init__(
self, require_explicit_overrides=True)
self.all_objects = list()
self.visit(componentclass)
assert_no_duplicates(self.all_objects)