Merge branch 'brainpy:master' into master

Author: PraPaudel

.github/workflows/CI-models.yml

@@ -22,7 +22,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ "3.9", "3.10", "3.11"]
+        python-version: [ "3.9", "3.10", "3.11", "3.12"]
 
     steps:
       - uses: actions/checkout@v4
@@ -70,7 +70,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ "3.9", "3.10", "3.11"]
+        python-version: [ "3.9", "3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v4
@@ -119,7 +119,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v4
@@ -132,7 +132,7 @@ jobs:
         python -m pip install --upgrade pip
         python -m pip install numpy>=1.21.0
         python -m pip install -r requirements-dev.txt
-        python -m pip install tqdm brainpylib
+        python -m pip install tqdm
         pip uninstall brainpy -y
         python setup.py install
     - name: Test with pytest

.github/workflows/CI.yml

@@ -28,7 +28,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ "3.9", "3.10", "3.11" ]
+        python-version: [ "3.9", "3.10", "3.11", "3.12" ]
 
     steps:
       - name: Cancel Previous Runs
@@ -59,7 +59,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ "3.9", "3.10", "3.11" ]
+        python-version: [ "3.9", "3.10", "3.11", "3.12" ]
 
     steps:
       - name: Cancel Previous Runs
@@ -92,7 +92,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ "3.9", "3.10", "3.11" ]
+        python-version: [ "3.9", "3.10", "3.11", "3.12" ]
 
     steps:
       - name: Cancel Previous Runs

README.md

@@ -22,21 +22,6 @@ 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
 
@@ -70,7 +55,6 @@ We provide a Binder environment for BrainPy. You can use the following button to
 ## 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.

brainpy/_src/dnn/linear.py

@@ -12,7 +12,7 @@
 from brainpy import math as bm
 from brainpy._src import connect, initialize as init
 from brainpy._src.context import share
-from brainpy._src.dependency_check import import_taichi, import_braintaichi
+from brainpy._src.dependency_check import import_taichi, import_braintaichi, raise_braintaichi_not_found
 from brainpy._src.dnn.base import Layer
 from brainpy._src.mixin import SupportOnline, SupportOffline, SupportSTDP
 from brainpy.check import is_initializer
@@ -241,7 +241,7 @@ def update(self, x):
         return x
 
 
-if ti is not None:
+if ti is not None and bti is not None:
 
     # @numba.njit(nogil=True, fastmath=True, parallel=False)
     # def _cpu_dense_on_post(weight, spike, trace, w_min, w_max, out_w):
@@ -321,7 +321,7 @@ def _dense_on_pre(
 
 def dense_on_pre(weight, spike, trace, w_min, w_max):
     if dense_on_pre_prim is None:
-        raise PackageMissingError.by_purpose('taichi', 'custom operators')
+        raise_braintaichi_not_found()
 
     if w_min is None:
         w_min = -np.inf
@@ -341,7 +341,7 @@ def dense_on_pre(weight, spike, trace, w_min, w_max):
 
 def dense_on_post(weight, spike, trace, w_min, w_max):
     if dense_on_post_prim is None:
-        raise PackageMissingError.by_purpose('taichi', 'custom operators')
+        raise_braintaichi_not_found()
 
     if w_min is None:
         w_min = -np.inf
@@ -728,7 +728,7 @@ def _batch_csrmv(self, x):
                               transpose=self.transpose)
 
 
-if ti is not None:
+if ti is not None and bti is not None:
     @ti.kernel
     def _csr_on_pre_update(
         old_w: ti.types.ndarray(ndim=1),  # vector with shape of (num_syn)
@@ -852,7 +852,7 @@ def _csc_on_post_update(
 
 def csr_on_pre_update(w, indices, indptr, spike, trace, w_min=None, w_max=None):
     if csr_on_pre_update_prim is None:
-        raise PackageMissingError.by_purpose('taichi', 'customized operators')
+        raise_braintaichi_not_found()
 
     if w_min is None:
         w_min = -np.inf
@@ -874,7 +874,7 @@ def csr_on_pre_update(w, indices, indptr, spike, trace, w_min=None, w_max=None):
 
 def coo_on_pre_update(w, pre_ids, post_ids, spike, trace, w_min=None, w_max=None):
     if coo_on_pre_update_prim is None:
-        raise PackageMissingError.by_purpose('taichi', 'customized operators')
+        raise_braintaichi_not_found()
 
     if w_min is None:
         w_min = -np.inf
@@ -897,7 +897,7 @@ def coo_on_pre_update(w, pre_ids, post_ids, spike, trace, w_min=None, w_max=None
 
 def csc_on_post_update(w, post_ids, indptr, w_ids, post_spike, pre_trace, w_min=None, w_max=None):
     if csc_on_post_update_prim is None:
-        raise PackageMissingError.by_purpose('taichi', 'customized operators')
+        raise_braintaichi_not_found()
 
     if w_min is None:
         w_min = -np.inf

brainpy/_src/math/ndarray.py

@@ -98,7 +98,7 @@ def _check_tracer(self):
     self_value = self.value
     if hasattr(self_value, '_trace') and hasattr(self_value._trace.main, 'jaxpr_stack'):
       if len(self_value._trace.main.jaxpr_stack) == 0:
-        raise RuntimeError('This Array is modified during the transformation. '
+        raise jax.errors.UnexpectedTracerError('This Array is modified during the transformation. '
                            'BrainPy only supports transformations for Variable. '
                            'Please declare it as a Variable.') from jax.core.escaped_tracer_error(self_value, None)
     return self_value

brainpy/_src/math/tests/test_ndarray.py

@@ -62,7 +62,7 @@ def _f(self, b):
 
   def test_tracing(self):
     print(self.f(1.))
-    with self.assertRaises(RuntimeError):
+    with self.assertRaises(jax.errors.UnexpectedTracerError):
       print(self.f(bm.ones(10)))
 
 

docker/requirements.txt

@@ -6,10 +6,10 @@ jax
 jaxlib
 scipy>=1.1.0
 brainpy
-brainpylib
 brainpy_datasets
 h5py
 pathos
+braintaichi
 
 # test requirements
 pytest

docs/index.rst

@@ -20,13 +20,7 @@ Installation
           # python 3.9-3.11
           pip install -U brainpy[cpu]  # windows, linux, macos
 
-    .. tab-item:: GPU (CUDA 11.0)
-
-       .. code-block:: bash
-
-          pip install -U brainpy[cuda11] -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
-
-    .. tab-item:: GPU (CUDA 12.0)
+    .. tab-item:: GPU (CUDA 12)
 
        .. code-block:: bash
 
@@ -110,15 +104,6 @@ Learn more
    APIs may be changed over time. Please always keeps
    in mind what BrainPy version you are using.
 
-.. 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 for a better performance.
-
 
 
 ----

docs/quickstart/installation.rst

@@ -36,7 +36,6 @@ To install brainpy with minimum requirements (only depends on ``jax``), you can
 
     # or
 
-    pip install brainpy[cuda11_mini] -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html  # for CUDA 11.0
     pip install brainpy[cuda12_mini] -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html  # for CUDA 12.0
 
     # or
@@ -64,7 +63,6 @@ To install a GPU-only version of BrainPy, you can run
 .. code-block:: bash
 
     pip install brainpy[cuda12] -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html  # for CUDA 12.0
-    pip install brainpy[cuda11] -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html  # for CUDA 11.0
 
 
 
@@ -79,25 +77,3 @@ you can run the following in your cloud TPU VM:
     pip install brainpy[tpu] -f https://storage.googleapis.com/jax-releases/libtpu_releases.html  # for google TPU
 
 
-
-``brainpylib``
---------------
-
-
-``brainpylib`` defines a set of useful operators for building and simulating spiking neural networks.
-
-
-To install the ``brainpylib`` package on CPU devices, you can run
-
-.. code-block:: bash
-
-    pip install brainpylib
-
-
-To install the ``brainpylib`` package on CUDA (Linux only), you can run
-
-
-.. code-block:: bash
-
-    pip install brainpylib
-

requirements-dev.txt

@@ -9,6 +9,7 @@ braintaichi
 numba
 brainstate
 braintools
+setuptools
 
 
 # test requirements