Merge branch 'brainpy:master' into master

.github/workflows/CI.yml

@@ -51,7 +51,7 @@ jobs:
       - name: Test with pytest
         run: |
           cd brainpy
-          pytest _src/
+          export IS_GITHUB_ACTIONS=1 && pytest _src/
 
 
   test_macos:
@@ -79,10 +79,12 @@ jobs:
           if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
           pip uninstall brainpy -y
           python setup.py install
+          pip install jax==0.4.30
+          pip install jaxlib==0.4.30
       - name: Test with pytest
         run: |
           cd brainpy
-          pytest _src/
+          export IS_GITHUB_ACTIONS=1 && pytest _src/
 
 
   test_windows:
@@ -113,4 +115,4 @@ jobs:
       - name: Test with pytest
         run: |
           cd brainpy
-          pytest _src/ -p no:faulthandler
+          set IS_GITHUB_ACTIONS=1 && pytest _src/

.github/workflows/docker.yml

@@ -41,7 +41,7 @@ jobs:
         password: ${{ secrets.DOCKERHUB_TOKEN }}
 
     - name: Docker Build & Push (version tag)
-      uses: docker/build-push-action@v5
+      uses: docker/build-push-action@v6
       with:
         context: ${{ matrix.context }}
         tags: ${{ matrix.base }}:${{ env.DOCKER_TAG_NAME }}
@@ -51,7 +51,7 @@ jobs:
     - name: Docker Build & Push (latest tag)
       if: |
           (github.event_name == 'release' && ! github.event.release.prerelease)
-      uses: docker/build-push-action@v5
+      uses: docker/build-push-action@v6
       with:
         context: ${{ matrix.context }}
         tags: ${{ matrix.base }}:latest

README.md

@@ -22,6 +22,21 @@ BrainPy is a flexible, efficient, and extensible framework for computational neu
 - **Source on OpenI**: https://git.openi.org.cn/OpenI/BrainPy
 
 
+---
+**NOTE**
+
+Starting from our experimental BrainPy package, a better and mature ecosystem for brain dynamics programming is emerging.
+Please see the [Brain Dynamics Programming Ecosystem](https://ecosystem-for-brain-dynamics.readthedocs.io/) for more details.
+
+
+If you are heavily using BrainPy, please consider using [brainstate](https://brainstate.readthedocs.io) for a more stable, efficient, concise, and powerful experience.
+
+
+[brainstate](https://github.com/chaobrain/brainstate) is and will be active maintained and developed by our team. We highly recommend transferring your code to [brainstate](https://brainstate.readthedocs.io) for a better performance.
+
+---
+
+
 
 ## Installation
 
@@ -50,8 +65,12 @@ We provide a Binder environment for BrainPy. You can use the following button to
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/brainpy/BrainPy-binder/main)
 
 
+
+
 ## Ecosystem
 
+
+- **[Brain Dynamics Programming Ecosystem](https://ecosystem-for-brain-dynamics.readthedocs.io/)**: An emerging and mature ecosystem for brain dynamics programming.
 - **[BrainPy](https://github.com/brainpy/BrainPy)**: The solution for the general-purpose brain dynamics programming. 
 - **[brainpy-examples](https://github.com/brainpy/examples)**: Comprehensive examples of BrainPy computation. 
 - **[brainpy-datasets](https://github.com/brainpy/datasets)**: Neuromorphic and Cognitive Datasets for Brain Dynamics Modeling.
@@ -67,21 +86,3 @@ Our team is committed to the long-term maintenance and development of the projec
 
 If you are using ``brainpy``, please consider citing [the corresponding papers](https://brainpy.readthedocs.io/en/latest/tutorial_FAQs/citing_and_publication.html). 
 
-
-
-## Ongoing development plans
-
-We highlight the key features and functionalities that are currently under active development. 
-
-We also welcome your contributions 
-(see [Contributing to BrainPy](https://brainpy.readthedocs.io/en/latest/tutorial_advanced/contributing.html)). 
-
-- [x] model and data parallelization on multiple devices for dense connection models
-- [ ] model parallelization on multiple devices for sparse spiking network models
-- [ ] data parallelization on multiple devices for sparse spiking network models
-- [ ] pipeline parallelization on multiple devices for sparse spiking network models
-- [ ] multi-compartment modeling
-- [ ] measurements, analysis, and visualization methods for large-scale spiking data
-- [ ] Online learning methods for large-scale spiking network models
-- [ ] Classical plasticity rules for large-scale spiking network models
-

brainpy-changelog.md

@@ -2,6 +2,80 @@
 
 
 ## brainpy>2.3.x
+### Version 2.6.1
+#### Breaking Changes
+- Fixing compatibility issues between `numpy` and `jax`
+
+#### What's Changed
+* [doc] Add Chinese version of `operator_custom_with_cupy.ipynb` and Rename it's title by @Routhleck in https://github.com/brainpy/BrainPy/pull/659
+* Fix "amsgrad" is used before being defined when initializing the AdamW optimizer by @CloudyDory in https://github.com/brainpy/BrainPy/pull/660
+* fix issue #661 by @chaoming0625 in https://github.com/brainpy/BrainPy/pull/662
+* fix flax RNN interoperation, fix #663 by @chaoming0625 in https://github.com/brainpy/BrainPy/pull/665
+* [fix] Replace jax.experimental.host_callback with jax.pure_callback by @Routhleck in https://github.com/brainpy/BrainPy/pull/670
+* [math] Update `CustomOpByNumba` to support JAX version >= 0.4.24 by @Routhleck in https://github.com/brainpy/BrainPy/pull/669
+* [math] Fix `CustomOpByNumba` on `multiple_results=True` by @Routhleck in https://github.com/brainpy/BrainPy/pull/671
+* [math] Implementing event-driven sparse matrix @ matrix operators  by @Routhleck in https://github.com/brainpy/BrainPy/pull/613
+* [math] Add getting JIT connect matrix method for `brainpy.dnn.linear` by @Routhleck in https://github.com/brainpy/BrainPy/pull/672
+* [math] Add get JIT weight matrix methods(Uniform & Normal) for `brainpy.dnn.linear` by @Routhleck in https://github.com/brainpy/BrainPy/pull/673
+* support `Integrator.to_math_expr()` by @chaoming0625 in https://github.com/brainpy/BrainPy/pull/674
+* [bug] Replace `collections.Iterable` with `collections.abc.Iterable` by @Routhleck in https://github.com/brainpy/BrainPy/pull/677
+* Fix surrogate gradient function and numpy 2.0 compatibility by @chaoming0625 in https://github.com/brainpy/BrainPy/pull/679
+* :arrow_up: Bump docker/build-push-action from 5 to 6 by @dependabot in https://github.com/brainpy/BrainPy/pull/678
+* fix the incorrect verbose of `clear_name_cache()` by @chaoming0625 in https://github.com/brainpy/BrainPy/pull/681
+* [bug] Fix prograss bar is not displayed and updated as expected by @Routhleck in https://github.com/brainpy/BrainPy/pull/683
+* Fix autograd by @chaoming0625 in https://github.com/brainpy/BrainPy/pull/687
+
+
+**Full Changelog**: https://github.com/brainpy/BrainPy/compare/V2.6.0...V2.6.1
+
+### Version 2.6.0
+
+#### New Features
+
+This release provides several new features, including:
+
+- ``MLIR`` registered operator customization interface in ``brainpy.math.XLACustomOp``.
+- Operator customization with CuPy JIT interface.
+- Bug fixes.
+
+
+
+#### What's Changed
+* [doc] Fix the wrong path of more examples of `operator customized with taichi.ipynb` by @Routhleck in https://github.com/brainpy/BrainPy/pull/612
+* [docs] Add colab link for documentation notebooks by @Routhleck in https://github.com/brainpy/BrainPy/pull/614
+* Update requirements-doc.txt to fix doc building temporally by @chaoming0625 in https://github.com/brainpy/BrainPy/pull/617
+* [math] Rebase operator customization using MLIR registration interface by @chaoming0625 in https://github.com/brainpy/BrainPy/pull/618
+* [docs] Add kaggle link for documentation notebooks by @Routhleck in https://github.com/brainpy/BrainPy/pull/619
+* update requirements by @chaoming0625 in https://github.com/brainpy/BrainPy/pull/620
+* require `brainpylib>=0.2.6` for `jax>=0.4.24` by @chaoming0625 in https://github.com/brainpy/BrainPy/pull/622
+* [tools] add `brainpy.tools.compose` and `brainpy.tools.pipe` by @chaoming0625 in https://github.com/brainpy/BrainPy/pull/624
+* doc hierarchy update by @chaoming0625 in https://github.com/brainpy/BrainPy/pull/630
+* Standardizing and generalizing object-oriented transformations by @chaoming0625 in https://github.com/brainpy/BrainPy/pull/628
+* fix #626 by @chaoming0625 in https://github.com/brainpy/BrainPy/pull/631
+* Fix delayvar not correct in concat mode by @CloudyDory in https://github.com/brainpy/BrainPy/pull/632
+* [dependency] remove hard dependency of `taichi` and `numba` by @Routhleck in https://github.com/brainpy/BrainPy/pull/635
+* `clear_buffer_memory()` support clearing `array`, `compilation`, and `names` by @chaoming0625 in https://github.com/brainpy/BrainPy/pull/639
+* add `brainpy.math.surrogate..Surrogate` by @chaoming0625 in https://github.com/brainpy/BrainPy/pull/638
+* Enable brainpy object as pytree so that it can be applied with ``jax.jit`` etc. directly by @chaoming0625 in https://github.com/brainpy/BrainPy/pull/625
+* Fix ci by @chaoming0625 in https://github.com/brainpy/BrainPy/pull/640
+* Clean taichi AOT caches by @chaoming0625 in https://github.com/brainpy/BrainPy/pull/643
+* [ci] Fix windows pytest fatal exception by @Routhleck in https://github.com/brainpy/BrainPy/pull/644
+* [math] Support more than 8 parameters of taichi gpu custom operator definition by @Routhleck in https://github.com/brainpy/BrainPy/pull/642
+* Doc for ``brainpylib>=0.3.0`` by @chaoming0625 in https://github.com/brainpy/BrainPy/pull/645
+* Find back updates by @chaoming0625 in https://github.com/brainpy/BrainPy/pull/646
+* Update installation instruction by @chaoming0625 in https://github.com/brainpy/BrainPy/pull/651
+* Fix delay bug by @chaoming0625 in https://github.com/brainpy/BrainPy/pull/650
+* update doc by @chaoming0625 in https://github.com/brainpy/BrainPy/pull/652
+* [math] Add new customize operators with `cupy` by @Routhleck in https://github.com/brainpy/BrainPy/pull/653
+* [math] Fix taichi custom operator on gpu backend by @Routhleck in https://github.com/brainpy/BrainPy/pull/655
+* update cupy operator custom doc by @chaoming0625 in https://github.com/brainpy/BrainPy/pull/656
+* version 2.6.0 by @chaoming0625 in https://github.com/brainpy/BrainPy/pull/657
+* Upgrade CI by @chaoming0625 in https://github.com/brainpy/BrainPy/pull/658
+
+## New Contributors
+* @CloudyDory made their first contribution in https://github.com/brainpy/BrainPy/pull/632
+
+**Full Changelog**: https://github.com/brainpy/BrainPy/compare/V2.5.0...V2.6.0
 
 
 ### Version 2.5.0

brainpy/__init__.py

@@ -153,3 +153,8 @@
 
 del deprecation_getattr2
 
+# jax config
+import os
+os.environ['XLA_FLAGS'] = '--xla_cpu_use_thunk_runtime=false'
+import jax
+jax.config.update('jax_cpu_enable_async_dispatch', False)

brainpy/_src/analysis/highdim/slow_points.py

@@ -329,7 +329,7 @@ def find_fps_with_gd_method(
     """
     # optimization settings
     if optimizer is None:
-      optimizer = optim.Adam(lr=optim.ExponentialDecay(0.2, 1, 0.9999),
+      optimizer = optim.Adam(lr=optim.ExponentialDecayLR(0.2, 1, 0.9999),
                              beta1=0.9, beta2=0.999, eps=1e-8)
     else:
       if not isinstance(optimizer, optim.Optimizer):