Merge branch 'development'

README.rst

@@ -15,22 +15,20 @@ Dendrify
         :alt: Contributor Covenant
 
 
-Although neuronal dendrites play a crucial role in shaping how individual 
-neurons process synaptic information, their contribution to network-level 
-functions has remained largely unexplored. Current spiking neural networks 
-(SNNs) often oversimplify dendritic properties or overlook their essential 
-functions. On the other hand, circuit models with morphologically detailed 
-neuron representations are computationally intensive, making them impractical 
-for simulating large networks.
-
-In an effort to bridge this gap, we present Dendrify—a freely available,
-open-source Python package that seamlessly integrates with the
-`Brian 2 simulator <https://brian2.readthedocs.io/en/stable/>`_. Dendrify,
-through simple commands, automatically generates reduced compartmental neuron
-models with simplified yet biologically relevant dendritic and synaptic
-integrative properties. These models offer a well-rounded compromise between
-flexibility, performance, and biological accuracy, enabling us to investigate
-the impact of dendrites on network-level functions.
+Neuronal dendrites play a crucial role in shaping how individual neurons process
+synaptic information, yet their contributions to network-level functions remain
+largely underexplored. While current spiking neural networks (SNNs) often
+oversimplify or neglect essential dendritic properties, circuit models with
+morphologically detailed neuron representations are computationally expensive,
+limiting their practicality for large-scale network simulations.
+
+To address these challenges, we introduce Dendrify, a free and open-source Python
+package designed to work seamlessly with the 
+`Brian 2 simulator <https://brian2.readthedocs.io/en/stable/>`_. Dendrify enables
+users to generate reduced compartmental neuron models with biologically relevant
+dendritic and synaptic properties using simple commands. These models strike a
+good balance between flexibility, performance, and accuracy, making it possible 
+to study the impact of dendrites on network-level functions.
 
 .. image:: https://github.com/Poirazi-Lab/dendrify/assets/30598350/b6db9876-6de4-458a-b27e-61d4edd360db
    :width: 70 %

dendrify/__init__.py

@@ -3,5 +3,5 @@
                               update_default_params)
 from .equations import library
 from .neuronmodel import NeuronModel, PointNeuronModel
-
+from .playground import Playground
 from .version import __version__

dendrify/compartment.py

@@ -104,7 +104,7 @@ def __init__(
         self._connections = None
         self._synapses = None
         # Add membrane equations:
-        self._add_equations(model)
+        self._create_equations(model)
         # Keep track of electrophysiological properties:
         self._ephys_object = EphysProperties(
             name=self.name,
@@ -130,7 +130,7 @@ def __str__(self):
                f"USER PARAMETERS\n{15*'-'}\n{user}")
         return txt
 
-    def _add_equations(self, model: str):
+    def _create_equations(self, model: str):
         """
         Adds equations to a compartment.
 
@@ -386,6 +386,51 @@ def noise(self, tau: Quantity = 20*ms, sigma: Quantity = 1*pA,
         self._params[f'tau_noise_{self.name}'] = tau
         self._params[f'sigma_noise_{self.name}'] = sigma
         self._params[f'mean_noise_{self.name}'] = mean
+
+    def add_equations(self, eqs: str):
+        """
+        Adds custom equations to a compartment.
+
+        Parameters
+        ----------
+        eqs : str
+            A string of Brian-compatible equations to be added to the compartment.
+        """
+        if eqs in self._equations:
+            logger.warning("The equations you are trying to add already exist in the compartment.")
+        else:
+            self._equations += '\n' + eqs
+
+    def replace_equations(self, eqs_old: str, eqs_new: str):
+        """
+        Replaces a set of equations with new ones.
+
+        Parameters
+        ----------
+        eqs_old : str
+            The equations to be replaced.
+        eqs_new : str
+            The new equations.
+        """
+        if eqs_old in self._equations:
+            self._equations = self._equations.replace(eqs_old, eqs_new)
+        else:
+            logger.warning(
+                "The equations to be replaced are not found in the compartment."
+                )
+
+    def add_params(self, params_dict: dict):
+        """
+        Adds custom parameters to a compartment.
+
+        Parameters
+        ----------
+        params_dict : dict
+            A dictionary of parameters to be added to the compartment.
+        """
+        if not self._params:
+            self._params = {}
+        self._params.update(params_dict)
 
     @property
     def parameters(self) -> dict:
@@ -517,12 +562,6 @@ class Soma(Compartment):
     and parameters needed to describe a somatic compartment and any currents
     (synaptic, dendritic, noise) passing through it.
 
-    .. seealso::
-
-       Soma acts as a wrapper for Compartment with slight changes to account for
-       certain somatic properties. For a full list of its methods and attributes,
-       please see: :class:`.Compartment`.
-
     Parameters
     ----------
     name : str
@@ -604,11 +643,6 @@ class Dendrite(Compartment):
     mechanisms, and any currents (synaptic, dendritic, ionic, noise) passing
     through it.
 
-    .. seealso::
-       Dendrite inherits all the methods and attributes of its parent class
-       :class:`.Compartment`. For a complete list, please
-       refer to the documentation of the latter.
-
     Parameters
     ----------
     name : str

dendrify/neuronmodel.py

@@ -373,14 +373,14 @@ def make_neurongroup(self,
             for comp in self._compartments:
                 if show:
                     print(
-                        f"Setting V_{comp.name} = {comp._ephys_object.v_rest}")
+                        f"V_{comp.name} = {repr(comp._ephys_object.v_rest)}")
                 setattr(group, f'V_{comp.name}', comp._ephys_object.v_rest)
 
         if init_events:
             if self.event_actions:
                 for event, action in self.event_actions.items():
                     if show:
-                        print(f"Setting run_on_event('{event}', '{action}')")
+                        print(f"run_on_event('{event}', '{action}')")
                     group.run_on_event(event, action, order='before_groups')
 
         ap_reset = None
@@ -406,7 +406,7 @@ def make_neurongroup(self,
 
     def add_params(self, params_dict: dict):
         """
-        Allows specifying extra/custom parameters.
+        Adds extra/custom parameters to a NeuronModel.
 
         Parameters
         ----------
@@ -429,7 +429,33 @@ def add_equations(self, eqs: str):
         if not self._extra_equations:
             self._extra_equations = f"{eqs}"
         else:
-            self._extra_equations += f"\n{eqs}"
+            if eqs not in self._extra_equations:
+                self._extra_equations += f"\n{eqs}"
+            else:
+                logger.warning(
+                    "The equations you are trying to add already exist in the model."
+                )
+
+    def replace_equations(self, eqs_old: str, eqs_new: str):
+        """
+        Replaces existing equations with custom ones.
+
+        Parameters
+        ----------
+        eqs_old : str
+            The existing equations to be replaced.
+        eqs_new : str
+            The custom equations.
+        """
+        eqs_found = False
+        for comp in self._compartments:
+            if eqs_old in comp._equations:
+                comp._equations = comp._equations.replace(eqs_old, eqs_new)
+                eqs_found = True
+        if not eqs_found:
+            logger.warning(
+                "The equations to be replaced are not found in the model."
+            )
 
     def as_graph(self, figsize: list = [6, 4], fontsize: int = 10, fontcolor: str = 'white',
                  scale_nodes: float = 1, color_soma: str = '#4C6C92',
@@ -622,7 +648,7 @@ def __init__(
         self._extra_equations = None
         self._extra_params = None
         # Add membrane equations:
-        self._add_equations(model)
+        self._create_equations(model)
         # Keep track of electrophysiological properties:
         self._ephys_object = EphysProperties(
             name=None,
@@ -645,7 +671,7 @@ def __str__(self):
                f"USER PARAMETERS\n{15*'-'}\n{user}")
         return txt
 
-    def _add_equations(self, model: str):
+    def _create_equations(self, model: str):
         """
         Adds equations to a compartment.