From 25e25a7a5b912f94369cec09a18757d924a6037b Mon Sep 17 00:00:00 2001
From: Chaoming Wang <adaduo@outlook.com>
Date: Tue, 9 Jul 2024 20:20:50 +0100
Subject: [PATCH] update doc

---
 dendritex/_base.py              | 23 +++++++++++++++++++++--
 docs/apis/dendritex.neurons.rst | 15 +++++++++++++++
 docs/apis/dendritex.rst         | 16 +++-------------
 3 files changed, 39 insertions(+), 15 deletions(-)
 create mode 100644 docs/apis/dendritex.neurons.rst

diff --git a/dendritex/_base.py b/dendritex/_base.py
index a210e5a..7b47f22 100644
--- a/dendritex/_base.py
+++ b/dendritex/_base.py
@@ -288,6 +288,22 @@ def add_elem(self, *elems, **elements):
 
 
 class IonChannel(DendriticDynamics, TreeNode):
+  """
+  The base class for ion channel modeling.
+
+  :py:class:`IonChannel` can be used to model the dynamics of an ion (instance of :py:class:`Ion`), or
+  a mixture of ions (instance of :py:class:`MixIons`), or a channel (instance of :py:class:`Channel`).
+
+  Particularly, an implementation of a :py:class:`IonChannel` should implement the following methods:
+
+  - :py:meth:`current`: Calculate the current of the ion channel.
+  - :py:meth:`before_integral`: Calculate the state variables before the integral.
+  - :py:meth:`compute_derivative`: Calculate the derivative of the state variables.
+  - :py:meth:`after_integral`: Calculate the state variables after the integral.
+  - :py:meth:`init_state`: Initialize the state variables.
+  - :py:meth:`reset_state`: Reset the state variables.
+
+  """
   __module__ = 'dentritex'
 
   def current(self, *args, **kwargs):
@@ -315,7 +331,8 @@ class IonInfo(NamedTuple):
 
 
 class Ion(IonChannel, Container):
-  """The brainpy_object calcium dynamics.
+  """
+  The base class for modeling the Ion dynamics.
 
   Args:
     size: The size of the simulation target.
@@ -577,5 +594,7 @@ def mix_ions(*ions) -> MixIons:
 
 
 class Channel(IonChannel):
-  """Base class for ion channels."""
+  """
+  The base class for modeling channel dynamics.
+  """
   __module__ = 'dentritex'
diff --git a/docs/apis/dendritex.neurons.rst b/docs/apis/dendritex.neurons.rst
new file mode 100644
index 0000000..e117d33
--- /dev/null
+++ b/docs/apis/dendritex.neurons.rst
@@ -0,0 +1,15 @@
+``dendritex.neurons`` module
+============================
+
+.. currentmodule:: dendritex.neurons
+.. automodule:: dendritex.neurons
+
+
+.. autosummary::
+   :toctree: generated/
+   :nosignatures:
+   :template: classtemplate.rst
+
+   SingleCompartment
+   MultiCompartment
+
diff --git a/docs/apis/dendritex.rst b/docs/apis/dendritex.rst
index d5ccf7d..1945788 100644
--- a/docs/apis/dendritex.rst
+++ b/docs/apis/dendritex.rst
@@ -15,24 +15,15 @@ Base Classes
    :template: classtemplate.rst
 
     HHTypedNeuron
+    State4Integral
     IonChannel
     Ion
+    IonInfo
     MixIons
     Channel
 
 
-Helper Classes
---------------
-
-.. autosummary::
-   :toctree: generated/
-   :nosignatures:
-   :template: classtemplate.rst
-
-    IonInfo
-
-
-Integrator Methods
+Integration Methods
 --------------------
 
 .. autosummary::
@@ -40,7 +31,6 @@ Integrator Methods
    :nosignatures:
    :template: classtemplate.rst
 
-    State4Integral
     euler_step
     rk2_step
     rk3_step