Merge pull request #44 from PKU-NIP-Lab/develop

Update docs
brainpy · Apr 28, 2021 · ec9e6dd · ec9e6dd
2 parents 1a2334a + 3491ec9
commit ec9e6dd
Show file tree

Hide file tree

Showing 22 changed files with 484 additions and 225 deletions.
diff --git a/.gitignore b/.gitignore
@@ -18,13 +18,12 @@ docs/quickstart/.ipynb_checkpoints
 
 docs/tutorials_advanced/_autosummary
 docs/tutorials_advanced/.ipynb_checkpoints
-develop/fast_synapse_computation.py
-develop/fast_synapse_computation2.py
-
-docs/apis/_autosummary
 docs/tutorials_advanced/usage_of_inputfactory.py
 docs/tutorials_advanced/usage_of_utils_connect.py
 
+docs/apis/_autosummary
+docs/apis/integrators/_autosummary
+
 develop/benchmark/COBA/brian2*
 develop/benchmark/COBA/annarchy*
 develop/benchmark/COBAHH/brian2*

diff --git a/README.md b/README.md
@@ -29,10 +29,15 @@ Moreover, `BrainPy` is designed to effectively satisfy your basic requirements:
 
 # Installation
 
+``BrainPy`` is based on Python (>=3.7), and the following packages are required to be installed to use ``BrainPy``:
+
+- NumPy >= 1.13
+- Matplotlib >= 3.3
+
 Install ``BrainPy`` by using ``pip``:
 
 ```bash
-> pip install brainpy-simulator>=1.0.0rc2
+> pip install -U brainpy-simulator
 ```
 
 Install ``BrainPy`` by using ``conda``:
@@ -48,15 +53,9 @@ Install ``BrainPy`` from source:
 > # or
 > pip install git+https://git.openi.org.cn/OpenI/BrainPy
 > # or
-> pip install -e git://github.com/PKU-NIP-Lab/BrainPy.git@V0.2.5
+> pip install -e git://github.com/PKU-NIP-Lab/BrainPy.git@V1.0.0
 ```
 
-``BrainPy`` is based on Python (>=3.7), and the following packages are required to be installed to use ``BrainPy``:
-
-- NumPy >= 1.13
-- Matplotlib >= 3.3
-
-
 
 # Let's start
 

diff --git a/brainpy/__init__.py b/brainpy/__init__.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = "1.0.0"
+__version__ = "1.0.1"
 
 # "backend" module
 from . import backend

diff --git a/brainpy/backend/drivers/__init__.py b/brainpy/backend/drivers/__init__.py
@@ -32,6 +32,12 @@ def switch_to(backend):
 
     elif backend in ['numba', 'numba-parallel']:
         from . import numba_cpu
+
+        if backend == 'numba':
+            numba_cpu.set_numba_profile(nogil=False, parallel=False)
+        else:
+            numba_cpu.set_numba_profile(nogil=True, parallel=True)
+
         NET_DRIVER = buffer.get('net', None) or GeneralNetDriver
         NODE_DRIVER = buffer.get('node', None) or numba_cpu.NumbaCPUNodeDriver
         DIFFINT_DRIVER = buffer.get('intg', None) or numba_cpu.NumbaCpuDiffIntDriver

diff --git a/brainpy/visualization/plots.py b/brainpy/visualization/plots.py
@@ -60,11 +60,10 @@ def line_plot(ts,
         plot_ids = [0]
     elif isinstance(plot_ids, int):
         plot_ids = [plot_ids]
-    try:
-        assert isinstance(plot_ids, (list, tuple))
-    except AssertionError:
-        raise ModelUseError('"plot_ids" specifies the value index to plot, '
-                            'it must be a list/tuple.')
+    if not isinstance(plot_ids, (list, tuple)) and \
+            not (isinstance(plot_ids, np.ndarray) and np.ndim(plot_ids) == 1):
+        raise ModelUseError(f'"plot_ids" specifies the value index to plot, it must '
+                            f'be a list/tuple/1D numpy.ndarray, not {type(plot_ids)}.')
 
     # get ax
     if ax is None:
@@ -184,7 +183,7 @@ def animate_2D(values,
                val_min=None,
                val_max=None,
                cmap=None,
-               frame_delay=1.,
+               frame_delay=10,
                frame_step=1,
                title_size=10,
                figsize=None,
@@ -231,8 +230,8 @@ def animate_2D(values,
 
     Returns
     -------
-    figure : plt.figure
-        The created figure instance.
+    anim : animation.FuncAnimation
+        The created animation function.
     """
     dt = backend.get_dt() if dt is None else dt
     num_step, num_neuron = values.shape
@@ -252,25 +251,29 @@ def frame(t):
         plt.pcolor(img, cmap=cmap, vmin=val_min, vmax=val_max)
         plt.colorbar()
         plt.axis('off')
-        fig.suptitle("Time: {:.2f} ms".format((t + 1) * dt),
-                     fontsize=title_size, fontweight='bold')
+        fig.suptitle(t="Time: {:.2f} ms".format((t + 1) * dt),
+                     fontsize=title_size,
+                     fontweight='bold')
         return [fig.gca()]
 
     values = values.reshape((num_step, height, width))
-    anim_result = animation.FuncAnimation(
-        fig, frame, frames=list(range(1, num_step, frame_step)),
-        init_func=None, interval=frame_delay, repeat_delay=3000)
+    anim = animation.FuncAnimation(fig=fig,
+                                   func=frame,
+                                   frames=list(range(1, num_step, frame_step)),
+                                   init_func=None,
+                                   interval=frame_delay,
+                                   repeat_delay=3000)
     if save_path is None:
         if show:
             plt.show()
     else:
         if save_path[-3:] == 'gif':
-            anim_result.save(save_path, dpi=gif_dpi, writer='imagemagick')
+            anim.save(save_path, dpi=gif_dpi, writer='imagemagick')
         elif save_path[-3:] == 'mp4':
-            anim_result.save(save_path, writer='ffmpeg', fps=video_fps, bitrate=3000)
+            anim.save(save_path, writer='ffmpeg', fps=video_fps, bitrate=3000)
         else:
-            anim_result.save(save_path + '.mp4', writer='ffmpeg', fps=video_fps, bitrate=3000)
-    return fig
+            anim.save(save_path + '.mp4', writer='ffmpeg', fps=video_fps, bitrate=3000)
+    return anim
 
 
 def animate_1D(dynamical_vars,

diff --git a/develop/conda-recipe/meta.yaml b/develop/conda-recipe/meta.yaml
@@ -1,6 +1,6 @@
 package:
     name: brainpy-simulator
-    version: "1.0.0"
+    version: "1.0.1"
 
 source:
     path: ../../

diff --git a/docs/apis/backend.rst b/docs/apis/backend.rst
@@ -11,6 +11,6 @@ brainpy.backend
     set_dt
     get_dt
     set_ops
-    get_backend
+    get_backend_name
     set_class_keywords
     set_ops_from_module
diff --git a/docs/apis/connectivity.rst b/docs/apis/connectivity.rst
@@ -1,5 +1,5 @@
-brainpy.connect
-===============
+``brainpy.connect`` module
+==========================
 
 .. currentmodule:: brainpy.simulation.connectivity
 .. automodule:: brainpy.simulation.connectivity
@@ -17,8 +17,8 @@ brainpy.connect
     post2pre
     pre2syn
     post2syn
-    pre_slice_syn
-    post_slice_syn
+    pre_slice
+    post_slice
 
 
 ``connector`` methods

diff --git a/docs/apis/integrators.rst b/docs/apis/integrators.rst
@@ -1,13 +1,14 @@
-brainpy.integrators
-===================
+``brainpy.integrators`` module
+==============================
 
 .. currentmodule:: brainpy.integrators
 .. automodule:: brainpy.integrators
 
-.. contents::
-    :local:
-    :depth: 1
+.. toctree::
+    :maxdepth: 3
 
+    integrators/ODE
+    integrators/SDE
 
 
 General functions
@@ -18,22 +19,51 @@ General functions
 
     odeint
     sdeint
-    ddeint
-    fdeint
     set_default_odeint
     get_default_odeint
     set_default_sdeint
     get_default_sdeint
 
-``ast_analysis`` module
------------------------
+
+
+.. rubric:: :doc:`integrators/ODE`
 
 .. autosummary::
-    :toctree: _autosummary
+    :nosignatures:
+
+    ode.euler
+    ode.midpoint
+    ode.heun2
+    ode.ralston2
+    ode.rk2
+    ode.rk3
+    ode.heun3
+    ode.ralston3
+    ode.ssprk3
+    ode.rk4
+    ode.ralston4
+    ode.rk4_38rule
+
+    ode.rkf45
+    ode.rkf12
+    ode.rkdp
+    ode.ck
+    ode.bs
+    ode.heun_euler
 
-    DiffEqReader
-    separate_variables
+    ode.exponential_euler
 
-.. autoclass:: DiffEqReader
-    :members:
 
+
+.. rubric:: :doc:`integrators/SDE`
+
+.. autosummary::
+    :nosignatures:
+
+    sde.euler
+    sde.heun
+    sde.milstein
+    sde.exponential_euler
+    sde.srk1w1_scalar
+    sde.srk2w1_scalar
+    sde.KlPl_scalar
diff --git a/docs/apis/integrators/ODE.rst b/docs/apis/integrators/ODE.rst
@@ -0,0 +1,47 @@
+Numerical Methods for ODEs
+==========================
+
+.. currentmodule:: brainpy.integrators.ode
+.. automodule:: brainpy.integrators.ode
+
+
+Explicit Runge-Kutta methods
+----------------------------
+
+.. autosummary::
+    :toctree: _autosummary
+
+    euler
+    midpoint
+    heun2
+    ralston2
+    rk2
+    rk3
+    heun3
+    ralston3
+    ssprk3
+    rk4
+    ralston4
+    rk4_38rule
+
+
+Adaptive Runge-Kutta methods
+----------------------------
+
+.. autosummary::
+    :toctree: _autosummary
+
+    rkf45
+    rkf12
+    rkdp
+    ck
+    bs
+    heun_euler
+
+Other methods
+-------------
+
+.. autosummary::
+    :toctree: _autosummary
+
+    exponential_euler
diff --git a/docs/apis/integrators/SDE.rst b/docs/apis/integrators/SDE.rst
@@ -0,0 +1,16 @@
+Numerical Methods for SDEs
+==========================
+
+.. currentmodule:: brainpy.integrators.sde
+.. automodule:: brainpy.integrators.sde
+
+.. autosummary::
+    :toctree: _autosummary
+
+    euler
+    heun
+    milstein
+    exponential_euler
+    srk1w1_scalar
+    srk2w1_scalar
+    KlPl_scalar
diff --git a/docs/index.rst b/docs/index.rst
@@ -19,15 +19,6 @@ Comprehensive examples of BrainPy please see
 `BrainModels <https://brainmodels.readthedocs.io/en/latest/>`_.
 
 
-.. Hint::
-
-    “Do you know calculus?”
-
-    “You had better learn it. It’s the language God talks.”
-
-    -- Richard Feynman
-
-
 .. toctree::
    :maxdepth: 2
    :caption: Quickstart
@@ -59,6 +50,8 @@ Comprehensive examples of BrainPy please see
    :maxdepth: 1
    :caption: API documentation
 
+   apis/integrators
+   apis/connectivity
    apis/inputs_module
    apis/changelog