version 2.2.0 (#248)

version 2.2.0

Author: chaoming0625

.github/PULL_REQUEST_TEMPLATE.md

@@ -14,10 +14,6 @@
 <!--- For example, markdown files should pass markdownlint locally according to the rules -->
 <!--- See how your change affects other areas of the code, etc. -->
 
-## Screenshots(optional)
-<!--- If Screenshots is not necessary or not available in this pull request, you can delete this section -->
-<!--- Changes including html and css are required to have screenshots -->
-
 ## Types of changes
 <!--- What types of changes does your code introduce? -->
 <!--- Only left the line that best describes this pull request -->

.github/workflows/Linux_CI.yml

@@ -28,14 +28,15 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest
+        # python -m pip install https://github.com/google/jax/archive/refs/tags/jax-v0.3.14.tar.gz
         if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
         python setup.py install
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
         pytest brainpy/

.github/workflows/MacOS_CI.yml

@@ -28,14 +28,16 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest
+        python -m pip install jax==0.3.14
+        python -m pip install jaxlib==0.3.14
         if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
         python setup.py install
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
         pytest brainpy/

.github/workflows/Sync_branches.yml

@@ -9,10 +9,10 @@ jobs:
     steps:
       - uses: actions/checkout@master
 
-      - name: Merge master -> brainpy-2.x
+      - name: Merge master -> brainpy-2.2.x
         uses: devmasx/merge-branch@master
         with:
           type: now
           from_branch: master
-          target_branch: brainpy-2.x
+          target_branch: brainpy-2.2.x
           github_token: ${{ github.token }}

.github/workflows/Windows_CI.yml

@@ -28,8 +28,9 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest
-        python -m pip install numpy==1.21.0
-        python -m pip install "jax[cpu]==0.3.2" -f https://whls.blob.core.windows.net/unstable/index.html --use-deprecated legacy-resolver
+        python -m pip install numpy>=1.21.0
+        python -m pip install "jaxlib==0.3.14" -f https://whls.blob.core.windows.net/unstable/index.html --use-deprecated legacy-resolver
+        python -m pip install https://github.com/google/jax/archive/refs/tags/jax-v0.3.14.tar.gz
         python -m pip install -r requirements-win.txt
         python -m pip install tqdm brainpylib
         python setup.py install
@@ -38,7 +39,7 @@ jobs:
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
         pytest brainpy/

.gitignore

@@ -7,7 +7,9 @@ brainpy/base/tests/io_test_tmp*
 
 development
 
+brainpy/dyn/tests/data
 examples/simulation/data
+examples/simulation/results
 examples/analysis/data
 extensions/.idea
 extensions/wheelhouse
@@ -211,3 +213,4 @@ dmypy.json
 cython_debug/
 
 /docs/apis/simulation/generated/
+!/brainpy/dyn/tests/data/

brainpy/__init__.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = "2.1.12"
+__version__ = "2.2.0"
 
 
 try:
@@ -15,7 +15,7 @@
 
 
 # fundamental modules
-from . import errors, tools, check
+from . import errors, tools, check, modes
 
 
 # "base" module
@@ -29,7 +29,15 @@
 
 
 # toolboxes
-from . import connect, initialize, optimizers, measure, losses, datasets, inputs
+from . import (connect,  # synaptic connection
+               initialize,  # weight initialization
+               optimizers,  # gradient descent optimizers
+               losses,  # loss functions
+               measure,  # methods for data analysis
+               datasets,  # methods for generating data
+               inputs,  # methods for generating input currents
+               algorithms,  # online or offline training algorithms
+               )
 
 
 # numerical integrators
@@ -45,26 +53,32 @@
 
 # dynamics simulation
 from . import dyn
+from .dyn import (channels,  # channel models
+                  layers,  # ANN layers
+                  networks,  # network models
+                  neurons,  # neuron groups
+                  rates,  # rate models
+                  synapses,  # synaptic dynamics
+                  synouts,   # synaptic output
+                  synplast,  # synaptic plasticity
+                  )
+from .dyn.runners import *
 
 
-# neural networks modeling
-from . import nn
-
-
-# running
-from . import running
+# dynamics training
+from . import train
 
 
 # automatic dynamics analysis
 from . import analysis
 
 
-# "visualization" module, will be removed soon
-from .visualization import visualize
+# running
+from . import running
 
 
-# compatible interface
-from .compat import *  # compat
+# "visualization" module, will be removed soon
+from .visualization import visualize
 
 
 # convenient access

brainpy/nn/algorithms/__init__.py renamed to brainpy/algorithms/__init__.py

@@ -2,3 +2,4 @@
 
 from .offline import *
 from .online import *
+from . import utils