release: v2026.6.8

.gitattributes

@@ -0,0 +1,6 @@
+* text=auto eol=lf
+*.cu text eol=lf
+*.py text eol=lf
+*.md text eol=lf
+*.bat text eol=crlf
+*.cmd text eol=crlf

.github/workflows/CI.yml

@@ -1,4 +1,6 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# This workflow installs Python dependencies and runs the test suite across
+# operating systems on every push/PR, and additionally runs a JAX-version
+# compatibility matrix on a daily schedule.
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
 name: Continuous Integration
@@ -8,108 +10,80 @@ on:
     branches:
       - main
   pull_request:
+  schedule:
+    # Runs at 00:00 UTC every day. See https://crontab.guru for cron syntax.
+    - cron: '0 0 * * *'
+  workflow_dispatch:
 
 
 permissions:
   contents: read  # to fetch code
   actions: write  # to cancel previous workflows
 
-# This is what will cancel the workflow
+# Cancel in-progress runs for the same ref
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
 
 jobs:
-  test_linux:
-    runs-on: ubuntu-latest
+  # Cross-platform test suite on push, pull request, and manual runs.
+  test:
+    if: github.event_name != 'schedule'
+    name: Test (${{ matrix.os }}, Python ${{ matrix.python-version }})
+    runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
+        os: [ ubuntu-latest, macos-latest, windows-latest ]
         python-version: [ "3.13" ]
 
     steps:
-      - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.13.1
-        with:
-          access_token: ${{ github.token }}
       - uses: actions/checkout@v6
-      - name: Print concurrency group
-        run: echo '${{ github.workflow }}-${{ github.ref }}'
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
           python -m pip cache purge
-          python -m pip install --upgrade pip setuptools   --no-cache-dir
-          python -m pip install -r requirements.txt  --no-cache-dir
-          python -m pip install pytest  --no-cache-dir
-          pip install .  --no-cache-dir
+          python -m pip install --upgrade pip setuptools --no-cache-dir
+          python -m pip install -r requirements.txt --no-cache-dir
+          python -m pip install pytest --no-cache-dir
+          python -m pip install . --no-cache-dir
       - name: Test with pytest
         run: |
           pytest BrainX/
 
-
-  test_macos:
-    runs-on: macos-latest
+  # Daily / manual JAX-version compatibility matrix on Linux.
+  test_jax_compatibility:
+    if: github.event_name == 'schedule' || github.event_name == 'workflow_dispatch'
+    name: JAX compat (jax ${{ matrix.jax-version || 'latest' }})
+    runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
         python-version: [ "3.13" ]
+        jax-version: [ "0.7.1", "0.8.0", "0.9.0", "" ]
 
     steps:
-      - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.13.1
-        with:
-          access_token: ${{ github.token }}
       - uses: actions/checkout@v6
-      - name: Print concurrency group
-        run: echo '${{ github.workflow }}-${{ github.ref }}'
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
           python -m pip cache purge
-          python -m pip install --upgrade pip setuptools  --no-cache-dir
-          python -m pip install -r requirements.txt  --no-cache-dir
-          python -m pip install pytest  --no-cache-dir
-          pip install .  --no-cache-dir
+          python -m pip install --upgrade pip setuptools
+          python -m pip install -r requirements.txt
+          python -m pip install pytest
+          if [ "${{ matrix.jax-version }}" == "" ]; then
+            python -m pip install jax || exit 1
+          else
+            python -m pip install jax==${{ matrix.jax-version }} || exit 1
+          fi
+          python -m pip install . || exit 1
       - name: Test with pytest
         run: |
           pytest BrainX/
-
-
-  test_windows:
-    runs-on: windows-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        python-version: [ "3.13" ]
-
-    steps:
-      - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.13.1
-        with:
-          access_token: ${{ github.token }}
-      - uses: actions/checkout@v6
-      - name: Print concurrency group
-        run: echo '${{ github.workflow }}-${{ github.ref }}'
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v6
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
-        run: |
-          python -m pip cache purge
-          python -m pip install --upgrade pip setuptools  --no-cache-dir
-          python -m pip install -r requirements.txt  --no-cache-dir
-          python -m pip install pytest  --no-cache-dir
-          pip install .  --no-cache-dir
-      - name: Test with pytest
-        run: |
-          pytest BrainX/ 
-

.github/workflows/Publish.yml

@@ -25,7 +25,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v6
         with:
-          python-version: '3.12'
+          python-version: '3.13'
 
       - name: Install build tooling
         run: |

.readthedocs.yml

@@ -6,9 +6,9 @@
 version: 2
 
 build:
-  os: "ubuntu-20.04"
+  os: "ubuntu-24.04"
   tools:
-    python: "3.12"
+    python: "3.14"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

BrainX/__init__.py

@@ -16,5 +16,5 @@
 # -*- coding: utf-8 -*-
 
 
-__version__ = "2026.3.12"
+__version__ = "2026.6.8"
 __version_info__ = tuple(map(int, __version__.split(".")))

CHANGELOG.md

@@ -6,6 +6,58 @@
 
 
 
+## v2026.6.8
+
+This release ships inline type information (PEP 561), consolidates the continuous
+integration workflows, completes the repository rename to `brainx`, and refreshes
+the pinned component versions.
+
+- **Package Dependencies:**
+  - [`jax<=0.10.1,>=0.6.0`](https://pypi.org/project/jax/) ↗️ (raised upper bound)
+  - [`brainpy==2.7.8`](https://pypi.org/project/brainpy/2.7.8/) ↗️
+  - [`brainunit==0.3.2`](https://pypi.org/project/brainunit/0.3.2/) ↗️
+  - [`brainstate==0.4.0`](https://pypi.org/project/brainstate/0.4.0/) ↗️
+  - [`brainevent==0.1.0`](https://pypi.org/project/brainevent/0.1.0/) ↗️
+  - [`braintools==0.1.9`](https://pypi.org/project/braintools/0.1.9/) ↗️
+  - [`braintrace==0.2.0`](https://pypi.org/project/braintrace/0.2.0/) ↗️
+  - [`braincell==0.0.8`](https://pypi.org/project/braincell/0.0.8/)
+  - [`brainpy-state==0.0.4`](https://pypi.org/project/brainpy-state/0.0.4/)
+  - [`brainmass==0.0.5`](https://pypi.org/project/brainmass/0.0.5/)
+  - [`pinnx==0.0.3`](https://pypi.org/project/pinnx/0.0.3/)
+
+- **Typing:**
+  - Added a [PEP 561](https://peps.python.org/pep-0561/) `py.typed` marker so that
+    downstream type checkers (mypy, pyright) treat `BrainX` as a typed package
+  - Declared `py.typed` as package data in `pyproject.toml` so it ships in the wheel
+
+- **Continuous Integration:**
+  - Merged the push/pull-request workflow and the scheduled workflow into a single
+    `CI.yml`
+  - The cross-platform test suite (Linux, macOS, Windows) runs on push, pull
+    request, and manual dispatch
+  - A JAX-version compatibility matrix (`0.7.1`, `0.8.0`, `0.9.0`, and latest) runs
+    on a daily schedule and on manual dispatch
+
+- **Repository:**
+  - Renamed the GitHub repository from `brain-modeling-ecosystem` to `brainx`;
+    updated all source, documentation, and packaging URLs accordingly
+
+- **Documentation:**
+  - Corrected the "Open in Colab/Kaggle" badges in every example notebook to target
+    their actual paths on the `main` branch
+  - Replaced the logo and favicon with hosted WebP assets and removed the bundled
+    3.5 MB `plotly.js`
+  - Removed unused static assets (legacy PWA manifest, service worker, and stale
+    images)
+
+- **README:**
+  - Fixed the BrainTrace link, which previously pointed at the renamed `brainscale`
+    repository
+  - Added PINNx to the list of ecosystem components
+  - Replaced the broken Read the Docs badge with Documentation and License badges
+
+
+
 ## v2026.3.12
 
 This release updates package dependencies and drops Python 3.10 support.

README.md

@@ -1,17 +1,18 @@
 # Brain Simulation Ecosystem (BrainX)
 
 [![PyPI version](https://img.shields.io/pypi/v/brainx)](https://pypi.org/project/brainx/)
-![Read the Docs](https://img.shields.io/readthedocs/brainmodeling)
-[![Continuous Integration](https://github.com/chaobrain/brain-modeling-ecosystem/actions/workflows/CI.yml/badge.svg)](https://github.com/chaobrain/brain-modeling-ecosystem/actions/workflows/CI.yml)
+[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://github.com/chaobrain/brainx/blob/main/LICENSE)
+[![Documentation](https://img.shields.io/badge/docs-brainx.chaobrain.com-blue)](https://brainx.chaobrain.com)
+[![Continuous Integration](https://github.com/chaobrain/brainx/actions/workflows/CI.yml/badge.svg)](https://github.com/chaobrain/brainx/actions/workflows/CI.yml)
 
 
 <p align="center">
-  	<img alt="Header image of Brain Modeling Ecosystem." src="https://raw.githubusercontent.com/chaobrain/brain-modeling-ecosystem/main/docs/_static/bdp-ecosystem.png" width=50%>
+  	<img alt="Header image of Brain Modeling Ecosystem." src="https://brainx.chaobrain.com/images/brainx-ecosystem.webp" width=50%>
 </p> 
 
 ## Overview
 
-The BrainX ecosystem provides comprehensive framework for brain simulation and modeling.
+The BrainX ecosystem provides a comprehensive framework for brain simulation and modeling.
 It provides tools and libraries for researchers to model, simulate, train, and analyze neural systems at different
 scales.
 
@@ -36,12 +37,14 @@ scales.
 
 - [BrainEvent](https://github.com/chaobrain/brainevent): Enabling event-driven computations in brain dynamics.
 
-- [BrainTrace](https://github.com/chaobrain/brainscale): Enabling scalable online learning for brain dynamics: $O(N)$
-  complexity for SNNs, and $O(N^2)$ for RNN computations.
+- [BrainTrace](https://github.com/chaobrain/braintrace): Eligibility trace-based online learning for brain dynamics:
+  $O(N)$ complexity for SNNs and $O(N^2)$ for RNN computations.
 
 - [BrainTools](https://github.com/chaobrain/braintools): Commonly used tools for brain dynamics programming, for example
   checkpointing.
 
+- [PINNx](https://github.com/chaobrain/pinnx): Physics-informed neural networks for scientific machine learning in JAX.
+
 - More components may be added in the future.
 
 ## Installation
@@ -78,8 +81,8 @@ pip install BrainX[tpu] -U
 For development, you might want to clone the repository and install it in editable mode:
 
 ```bash
-git clone https://github.com/chaobrain/brain-modeling-ecosystem.git
-cd brain-modeling-ecosystem
+git clone https://github.com/chaobrain/brainx.git
+cd brainx
 pip install -e .
 ```
 
@@ -100,15 +103,15 @@ This project is licensed under the Apache License, Version 2.0. See the [LICENSE
 ## Citation
 
 If you use the BrainX Ecosystem in your research, please cite it appropriately. Refer to
-the [citation guide](https://brainx.chaobrain.com/citation.html) on our documentation portal.
+the [citation guide](https://brainx.chaobrain.com/research/papers-about-brainx/) on our documentation portal.
 
 ## Support
 
 If you have questions, encounter issues, or need support, please:
 
 * Check the [documentation](https://brainx.chaobrain.com).
-* Search the [existing issues](https://github.com/chaobrain/brain-modeling-ecosystem/issues).
-* [Open a new issue](https://github.com/chaobrain/brain-modeling-ecosystem/issues/new/choose) if your problem is not
+* Search the [existing issues](https://github.com/chaobrain/brainx/issues).
+* [Open a new issue](https://github.com/chaobrain/brainx/issues/new/choose) if your problem is not
   addressed.
 * Contact us via email: `chao.brain@qq.com`.
 

SECURITY.md

@@ -2,7 +2,7 @@
 
 ## Reporting a bug in Brain Modeling Ecosystem
 
-Report security bugs in BrainPy via [Github Issue](https://github.com/chaobrain/brainmodeling/issues).
+Report security bugs in BrainPy via [Github Issue](https://github.com/chaobrain/brainx/issues).
 
 Normally your report will be acknowledged within 5 days, and you'll receive a more detailed response 
 to your report within 10 days indicating the next steps in handling your submission. These timelines