[doc] update docs

.gitignore

@@ -225,3 +225,4 @@ cython_debug/
 /docs/tutorial_advanced/data/
 /my_tests/
 /examples/dynamics_simulation/Joglekar_2018_data/
+/docs/apis/deprecated/generated/

docs/_templates/class_template.rst

@@ -5,7 +5,9 @@
 
 .. autoclass:: {{ objname }}
 
-   .. automethod:: __init__
+   {% for item in methods %}
+      .. automethod:: {{ item }}
+   {%- endfor %}
 
    {% block methods %}
 

docs/_templates/classtemplate.rst

@@ -0,0 +1,10 @@
+.. role:: hidden
+    :class: hidden-section
+.. currentmodule:: {{ module }}
+
+
+{{ name | underline}}
+
+.. autoclass:: {{ name }}
+    :members:
+

docs/advanced_tutorials.rst

@@ -8,8 +8,8 @@ This section contains tutorials that illustrate more advanced features of BrainP
    :maxdepth: 2
 
    tutorial_advanced/1_advanced_math.rst
-   tutorial_building/2_interoperation.rst
-   tutorial_building/3_dedicated_operators.rst
-   tutorial_building/4_developer_guides.rst
-   tutorial_building/5_others.rst
+   tutorial_advanced/2_interoperation.rst
+   tutorial_advanced/3_dedicated_operators.rst
+   tutorial_advanced/4_developer_guides.rst
+   tutorial_advanced/5_others.rst
 

docs/api.rst

@@ -5,31 +5,31 @@ API Documentation
    :maxdepth: 1
 
    apis/auto/changelog.rst
-   apis/auto/brainpy.rst
-   apis/auto/math.rst
-   apis/auto/dnn.rst
-   apis/auto/dyn.rst
-   apis/auto/integrators.rst
-   apis/auto/analysis.rst
-   apis/auto/connect.rst
-   apis/auto/encoding.rst
-   apis/auto/initialize.rst
-   apis/auto/inputs.rst
-   apis/auto/losses.rst
-   apis/auto/measure.rst
-   apis/auto/optim.rst
-   apis/auto/running.rst
-   apis/auto/mixin.rst
+   apis/brainpy.rst
+   apis/math.rst
+   apis/dnn.rst
+   apis/dyn.rst
+   apis/integrators.rst
+   apis/analysis.rst
+   apis/connect.rst
+   apis/encoding.rst
+   apis/initialize.rst
+   apis/inputs.rst
+   apis/losses.rst
+   apis/measure.rst
+   apis/optim.rst
+   apis/running.rst
+   apis/mixin.rst
 
 The following APIs will no longer be maintained in the future, but you can still use them normally.
 
 .. toctree::
    :maxdepth: 1
 
-   apis/channels.rst
-   apis/neurons.rst
-   apis/rates.rst
-   apis/synapses.rst
-   apis/synouts.rst
-   apis/synplast.rst
-   apis/layers.rst
+   apis/deprecated/channels.rst
+   apis/deprecated/neurons.rst
+   apis/deprecated/rates.rst
+   apis/deprecated/synapses.rst
+   apis/deprecated/synouts.rst
+   apis/deprecated/synplast.rst
+   apis/deprecated/layers.rst

docs/apis/analysis.rst

@@ -0,0 +1,37 @@
+``brainpy.analysis`` module
+===========================
+
+.. currentmodule:: brainpy.analysis 
+.. automodule:: brainpy.analysis 
+
+.. contents::
+   :local:
+   :depth: 1
+
+Low-dimensional Analyzers
+-------------------------
+
+.. autosummary::
+   :toctree: generated/
+   :nosignatures:
+   :template: classtemplate.rst
+
+   PhasePlane1D
+   PhasePlane2D
+   Bifurcation1D
+   Bifurcation2D
+   FastSlow1D
+   FastSlow2D
+
+
+High-dimensional Analyzers
+--------------------------
+
+.. autosummary::
+   :toctree: generated/
+   :nosignatures:
+   :template: classtemplate.rst
+
+   SlowPointFinder
+
+

docs/apis/brainpy.rst

@@ -0,0 +1,81 @@
+``brainpy`` module
+==================
+
+.. currentmodule:: brainpy 
+.. automodule:: brainpy 
+
+.. contents::
+   :local:
+   :depth: 1
+
+Numerical Differential Integration
+----------------------------------
+
+.. autosummary::
+   :toctree: generated/
+   :nosignatures:
+   :template: classtemplate.rst
+
+   Integrator
+   JointEq
+   IntegratorRunner
+   odeint
+   sdeint
+   fdeint
+
+
+Building Dynamical System
+-------------------------
+
+.. autosummary::
+   :toctree: generated/
+   :nosignatures:
+   :template: classtemplate.rst
+
+   DynamicalSystem
+   DynSysGroup
+   Sequential
+   Network
+   Dynamic
+   Projection
+
+
+Simulating Dynamical System
+---------------------------
+
+.. autosummary::
+   :toctree: generated/
+   :nosignatures:
+   :template: classtemplate.rst
+
+   DSRunner
+
+
+Training Dynamical System
+-------------------------
+
+.. autosummary::
+   :toctree: generated/
+   :nosignatures:
+   :template: classtemplate.rst
+
+   DSTrainer
+   BPTT
+   BPFF
+   OnlineTrainer
+   ForceTrainer
+   OfflineTrainer
+   RidgeTrainer
+
+
+Dynamical System Helpers
+------------------------
+
+.. autosummary::
+   :toctree: generated/
+   :nosignatures:
+   :template: classtemplate.rst
+
+   LoopOverTime
+
+

docs/apis/connect.rst

@@ -0,0 +1,100 @@
+``brainpy.connect`` module
+==========================
+
+.. currentmodule:: brainpy.connect 
+.. automodule:: brainpy.connect 
+
+.. contents::
+   :local:
+   :depth: 1
+
+Base Connection Classes and Tools
+---------------------------------
+
+.. autosummary::
+   :toctree: generated/
+   :nosignatures:
+   :template: classtemplate.rst
+
+   set_default_dtype
+   get_idx_type
+   mat2coo
+   mat2csc
+   mat2csr
+   csr2csc
+   csr2mat
+   csr2coo
+   coo2csr
+   coo2csc
+   coo2mat
+   coo2mat_num
+   mat2mat_num
+   visualizeMat
+   MAT_DTYPE
+   IDX_DTYPE
+   Connector
+   TwoEndConnector
+   OneEndConnector
+   CONN_MAT
+   PRE_IDS
+   POST_IDS
+   PRE2POST
+   POST2PRE
+   PRE2SYN
+   POST2SYN
+   SUPPORTED_SYN_STRUCTURE
+
+
+Custom Connections
+------------------
+
+.. autosummary::
+   :toctree: generated/
+   :nosignatures:
+   :template: classtemplate.rst
+
+   MatConn
+   IJConn
+   CSRConn
+   SparseMatConn
+
+
+Random Connections
+------------------
+
+.. autosummary::
+   :toctree: generated/
+   :nosignatures:
+   :template: classtemplate.rst
+
+   FixedProb
+   FixedPreNum
+   FixedPostNum
+   FixedTotalNum
+   GaussianProb
+   ProbDist
+   SmallWorld
+   ScaleFreeBA
+   ScaleFreeBADual
+   PowerLaw
+
+
+Regular Connections
+-------------------
+
+.. autosummary::
+   :toctree: generated/
+   :nosignatures:
+   :template: classtemplate.rst
+
+   One2One
+   All2All
+   GridFour
+   GridEight
+   GridN
+   one2one
+   all2all
+   grid_four
+   grid_eight
+
+