ANNarchy 5.0.1__tar.gz → 5.0.2__tar.gz

{annarchy-5.0.1 → annarchy-5.0.2}/ANNarchy/__init__.py

@@ -7,20 +7,54 @@ from .core.Global import *
 from .core.Simulate import *
 from .core.Constant import Constant
 from .core.Neuron import Neuron
-from .core.Parameters import Parameter, Variable, Creating, Pruning
+from .core.Attributes import Parameter, Variable, Creating, Pruning
 from .core.Synapse import Synapse
 from .core.Population import Population
 from .core.Projection import Projection
 from .inputs import *
 from .core.Dendrite import Dendrite
-from .core.Random import Uniform, DiscreteUniform, Normal, LogNormal, Gamma, Exponential, Binomial
-from .core.IO import save, load, load_parameter, load_parameters, save_parameters, MonitorList
+from .core.Random import (
+    Uniform,
+    DiscreteUniform,
+    Normal,
+    LogNormal,
+    Gamma,
+    Exponential,
+    Binomial,
+)
+from .core.IO import (
+    save,
+    load,
+    load_parameter,
+    load_parameters,
+    save_parameters,
+    MonitorList,
+)
 from .core.Utils import sparse_random_matrix, sparse_delays_from_weights, timeit
 from .core.Monitor import Monitor
 from .core.Network import Network
 from .parser.report.Report import report
-from .models.Neurons import *
-from .models.Synapses import *
+from .models.Neurons import (
+    LeakyIntegrator,
+    EIF_cond_alpha_isfa_ista,
+    EIF_cond_exp_isfa_ista,
+    GIF_curr,
+    GIF_curr_exp,
+    HH_cond_exp,
+    IF_cond_alpha,
+    IF_cond_exp,
+    IF_curr_alpha,
+    IF_curr_exp,
+    Izhikevich
+)
+from .models.Synapses import (
+    Hebb,
+    IBCM,
+    Oja,
+    STDP,
+    STP,
+    Synapse
+)
 from .extensions import *
 from .intern.ConfigManagement import setup
 from .intern import Messages
@@ -43,60 +77,108 @@ from .generator import compile
 
 # several setup() arguments can be set on command-line
 from ANNarchy.generator.CmdLineArgParser import CmdLineArgParser
+
 _arg_parser = CmdLineArgParser()
 _arg_parser.parse_arguments_for_setup()
 
 # Automatically call ANNarchy.core.Global.clear()
 # if the script terminates
 import atexit
+
 atexit.register(clear)
 
 # Version
-__version__ = '5.0'
-__release__ = '5.0.1'
+__version__ = "5.0"
+__release__ = "5.0.2"
 
 # Deprecated imports from this module:
 _deprecated = {
-    "Population", "Projection", "Monitor", "compile", "setup", "simulate", "simulate_until",
-    "reset", "get_population", "get_projection", "populations", "projections", "monitors",
-    "enable_learning", "disable_learning", "get_time", "set_time", "get_current_step",
-    "set_current_step", "dt", "set_seed", "step", "callbacks_enabled", "disable_callbacks",
-    "enable_callbacks", "clear_all_callbacks", "save", "load", "save_parameters", "load_parameters",
+    "Population",
+    "Projection",
+    "Monitor",
+    "compile",
+    "setup",
+    "simulate",
+    "simulate_until",
+    "reset",
+    "get_population",
+    "get_projection",
+    "populations",
+    "projections",
+    "monitors",
+    "enable_learning",
+    "disable_learning",
+    "get_time",
+    "set_time",
+    "get_current_step",
+    "set_current_step",
+    "dt",
+    "set_seed",
+    "step",
+    "callbacks_enabled",
+    "disable_callbacks",
+    "enable_callbacks",
+    "clear_all_callbacks",
+    "save",
+    "load",
+    "save_parameters",
+    "load_parameters",
 }
+
+
 def _deprecated_wrapper(obj, name, message=None):
     if isinstance(obj, types.FunctionType):
+
         def wrapper(*args, **kwargs):
-            Messages._warning(message or f"{name} is deprecated. Please use ann.Network().{name}() instead.")
+            Messages.warning(
+                message
+                or f"{name} is deprecated. Please use ann.Network().{name}() instead."
+            )
             return obj(*args, **kwargs)
+
         wrapper.__name__ = name
         wrapper.__doc__ = obj.__doc__
         return wrapper
     elif isinstance(obj, type):  # class
+
         class DeprecatedClass(obj):
             def __new__(cls, *args, **kwargs):
-                Messages._warning(message or f"{name} is deprecated. Please use ann.Network().{name}() instead.")
+                Messages.warning(
+                    message
+                    or f"{name} is deprecated. Please use ann.Network().{name}() instead."
+                )
                 return super().__new__(cls)
+
         DeprecatedClass.__name__ = name
         DeprecatedClass.__doc__ = obj.__doc__
         return DeprecatedClass
     else:
         return obj
 
+
 for name in _deprecated:
     obj = globals().get(name)
     if obj is not None:
         if name == "Population":
-            message = "Population is deprecated. Please use ann.Network().create() instead."
+            message = (
+                "Population is deprecated. Please use ann.Network().create() instead."
+            )
         elif name == "Projection":
-            message = "Projection is deprecated. Please use ann.Network().connect() instead."
+            message = (
+                "Projection is deprecated. Please use ann.Network().connect() instead."
+            )
         elif name == "Monitor":
-            message = "Monitor is deprecated. Please use ann.Network().monitor() instead."
+            message = (
+                "Monitor is deprecated. Please use ann.Network().monitor() instead."
+            )
         elif name == "compile":
             message = "compile is deprecated. Please use ann.Network().compile() instead.\n\t Since ANNarchy 5.0 the compilation of shadow networks is not supported anymore\n\t and using them possibly could generate errorneous simulation results or crash.\n\t You need to construct a Network object, please refer to the documentation."
         elif name == "set_seed":
             message = "set_seed is deprecated. Please use ann.Network().seed() instead."
         elif name == "save_parameters":
-            message = "save_parameters is deprecated and will be removed in future releases."
+            message = (
+                "save_parameters is deprecated and will be removed in future releases."
+            )
         elif name == "load_parameters":
             message = "load_parameters is deprecated. Parameters can be directly loaded and used as dictionaries in Neuron and Synapse definitions."
         else:
@@ -104,6 +186,14 @@ for name in _deprecated:
         globals()[name] = _deprecated_wrapper(obj, name, message)
 
 
-
-print( 'ANNarchy ' + __version__ + ' (' + __release__ + \
-                    ') on ' + sys.platform + ' (' + os.name + ').' )
+print(
+    "ANNarchy "
+    + __version__
+    + " ("
+    + __release__
+    + ") on "
+    + sys.platform
+    + " ("
+    + os.name
+    + ")."
+)

annarchy-5.0.1/ANNarchy/core/Parameters.py → annarchy-5.0.2/ANNarchy/core/Attributes.py

@@ -8,6 +8,7 @@ from ANNarchy.core.Random import RandomDistribution
 
 # Parameters
 
+
 @dataclass
 class Parameter:
     """
@@ -17,11 +18,11 @@ class Parameter:
     neuron = ann.Neuron(
         parameters = dict(
 
-            # Global parameter
-            tau = 10.0 # or ann.Parameter(value=10.0, locality='global')
+            # Global parameter (default)
+            tau = 10.0 # or ann.Parameter(value=10.0),
 
             # Local parameter
-            baseline = ann.Parameter(value=ann.Uniform(-1., 1.)),
+            baseline = ann.Parameter(value=ann.Uniform(-1., 1.), locality='local'),
 
             # Boolean global parameter
             activated = ann.Parameter(value=True, locality='global', type=bool),
@@ -29,11 +30,11 @@ class Parameter:
     )
     ```
 
-    In a neuron or synapse model, parameters are global and use the float type if the `Parameter` class is not used.
+    In a neuron or synapse model, parameters defined as direct assignment are by default `global` and use the float type.
 
-    If you need a local parameter (one value per neuron or synapse), the `Parameter` class allows to specify it. Note that you can also define global parameters by passing `locality='global'`.
+    If you need a local parameter (one value per neuron or synapse), the `Parameter` class allows to specify it using `locality='local'`.
 
-    Semi-global synaptic parameters (one value per post-synaptic neuron) can be defined using `locality='semiglobalglobal'`.
+    Semi-global synaptic parameters (one value per post-synaptic neuron) can be defined using `locality='semiglobal'`.
 
     If the parameter is an int or a bool, pass it to the `type` attribute.
 
@@ -43,8 +44,8 @@ class Parameter:
     """
 
     value: float | int | bool | RandomDistribution
-    locality: str = 'local'
-    type: str = 'float'
+    locality: str = "global"
+    type: str = "float"
 
 
 # Variables
@@ -79,10 +80,10 @@ class Variable:
     min: float = None
     max: float = None
     method: str = None
-    locality: str = 'local'
-    type: str = 'float'
+    locality: str = "local"
+    type: str = "float"
 
-    def _to_string(self, object_type:str) -> str:
+    def _to_string(self, object_type: str) -> str:
         "Returns a one-liner string with the flags. object_type is either 'neuron' or 'synapse'. to decide between population and projection"
 
         representation = self.equation
@@ -92,7 +93,9 @@ class Variable:
         flags = []
 
         if self.init is not None:
-            if not has_flag: has_flag = True ; representation += " : "
+            if not has_flag:
+                has_flag = True
+                representation += " : "
             if isinstance(self.init, (RandomDistribution,)):
                 init = repr(self.init)
             else:
@@ -100,33 +103,47 @@ class Variable:
             flags.append(f"init={init}")
 
         if self.min is not None:
-            if not has_flag: has_flag = True ; representation += " : "
+            if not has_flag:
+                has_flag = True
+                representation += " : "
             flags.append(f"min={self.min}")
 
         if self.max is not None:
-            if not has_flag: has_flag = True ; representation += " : "
+            if not has_flag:
+                has_flag = True
+                representation += " : "
             flags.append(f"max={self.max}")
 
         if self.method is not None:
-            if not has_flag: has_flag = True ; representation += " : "
+            if not has_flag:
+                has_flag = True
+                representation += " : "
             flags.append(f"{self.method}")
 
-        if self.type != 'float':
-            if not has_flag: has_flag = True ; representation += " : "
+        if self.type != "float":
+            if not has_flag:
+                has_flag = True
+                representation += " : "
             flags.append(f"{self.type}")
 
-        if self.locality != 'local':
-            if not has_flag: has_flag = True ; representation += " : "
-            if object_type == 'neuron':
-                val = 'population' # 'global' and 'population' would work
-            elif object_type == 'synapse':
-                if self.locality in ['global', 'projection']: # both are OK
-                    val = 'projection'
-                else: val = 'postsynaptic'
-            flags.append(f"{val}")
+        if self.locality != "local":
+            if not has_flag:
+                has_flag = True
+                representation += " : "
+
+            if object_type == "neuron":
+                val = "population"  # 'global' and 'population' would work
+            elif object_type == "synapse":
+                if self.locality in ["global", "projection"]:  # both are OK
+                    val = "projection"
+                else:
+                    val = "postsynaptic"
+            else:
+                raise ValueError("No default flag for object_type =", object_type)
 
+            flags.append(f"{val}")
 
-        return representation + ', '.join(flags)
+        return representation + ", ".join(flags)
 
 
 # Structural plasticity
@@ -153,11 +170,13 @@ class Creating:
     :param w: weight when the synapse is created.
     :param d: delay when the synapse is created.
     """
+
     equation: str
     proba: float = 1.0
     w: float = 0.0
     d: float = None
 
+
 @dataclass
 class Pruning:
     """
@@ -182,5 +201,6 @@ class Pruning:
     :param proba: probability of pruning of the synapse.
 
     """
+
     equation: str
     proba: float = 1.0