release: v2026.6.8

[chaoming0625]

Release v2026.6.8

A maintenance + housekeeping release. Summary:

Dependencies

Refreshed pinned components to their latest compatible versions:

Package	New
brainpy	2.7.8
brainunit	0.3.2
brainstate	0.4.0
brainevent	0.1.0
braintools	0.1.9
braintrace	0.2.0
jax	upper bound raised to <=0.10.1

(braincell 0.0.8, brainpy-state 0.0.4, brainmass 0.0.5, pinnx 0.0.3 unchanged.)

Typing

• Added a PEP 561 py.typed marker and declared it as package data so it ships in the wheel — downstream type checkers now treat BrainX as typed.

Continuous Integration

• Merged CI.yml + CI-daily.yml into a single workflow:
  • Cross-platform suite (Linux/macOS/Windows) on push, PR, and manual dispatch.
  • JAX-version compatibility matrix (0.7.1, 0.8.0, 0.9.0, latest) on a daily schedule and manual dispatch.

Repository rename

• Completed the brain-modeling-ecosystem → brainx rename across all source, docs, and packaging URLs.

Documentation

• Fixed "Open in Colab/Kaggle" badges in every example notebook to point at their real paths on main.
• Removed unused static assets (legacy PWA manifest/service worker, stale images); logo/favicon now use hosted WebP.

README

• Fixed the BrainTrace link (was pointing at the renamed brainscale repo).
• Added PINNx to the component list.
• Replaced the broken Read the Docs badge with Documentation + License badges.

Changelog

• Added a professional v2026.6.8 entry.

🤖 Generated with Claude Code

Summary by Sourcery

Prepare the v2026.6.8 maintenance release with refreshed dependencies, improved typing and CI, a completed repository rename, and updated documentation and metadata.

Bug Fixes:

• Correct Colab/Kaggle notebook links and various GitHub/BrainTrace URLs to point at the renamed brainx repository and current documentation paths.

Enhancements:

• Ship inline typing information by adding a PEP 561 py.typed marker and including it as package data.
• Refresh core BrainX ecosystem dependency pins and raise the supported JAX upper bound.
• Complete the project rename from brain-modeling-ecosystem to brainx across code, packaging metadata, documentation, and badges.
• Tune documentation assets by switching to hosted WebP branding, removing unused static files, and updating the Sphinx configuration.
• Update the changelog and package version to record the v2026.6.8 release.

Build:

• Modernize documentation build settings for Read the Docs (Ubuntu 24.04, Python 3.14).

CI:

• Consolidate CI into a single workflow that runs a cross-platform test suite on push/PR and a scheduled JAX-version compatibility matrix.
• Update the publish pipeline to build releases using Python 3.13.

Documentation:

• Refresh the README badges, imagery, installation instructions, and citation/support links to reflect the new brainx repository and docs site.
• Update example notebooks’ Colab and Kaggle badges to target the correct brainx paths on the main branch.

Chores:

• Add repository-wide attributes configuration via .gitattributes.

[sourcery-ai]

Reviewer's Guide

Release v2026.6.8 performs a dependency refresh, completes the GitHub repo rename to brainx, adds PEP 561 typing metadata, consolidates CI into a single workflow with a JAX compatibility matrix, updates docs/README links and badges, and bumps the library version and changelog entry to 2026.6.8.

Flow diagram for consolidated CI workflow and JAX compatibility matrix

flowchart TD
  subgraph Triggers
    A_push[push to main]
    A_pr[pull_request]
    A_dispatch[workflow_dispatch]
    A_schedule["schedule (cron 0 0 * * *)"]
  end

  subgraph Jobs
    B_test[test job]
    C_jax[test_jax_compatibility job]
  end

  A_push --> B_test
  A_pr --> B_test
  A_dispatch --> B_test
  A_schedule --> C_jax
  A_dispatch --> C_jax

  subgraph Matrix_test
    B_os[os: ubuntu-latest, macos-latest, windows-latest]
    B_py[python-version: 3.13]
  end

  subgraph Matrix_jax
    C_py[python-version: 3.13]
    C_jax_versions[jax-version: 0.7.1, 0.8.0, 0.9.0, latest]
  end

  B_test --> B_os
  B_test --> B_py
  C_jax --> C_py
  C_jax --> C_jax_versions

Loading

File-Level Changes

Change	Details	Files
Consolidated CI workflows and added a scheduled JAX-version compatibility matrix.	Replaced separate Linux/macOS/Windows jobs with a single matrix-based test job running on all three OSes for pushes, PRs, and manual dispatch. Introduced a scheduled and manually-triggerable test_jax_compatibility job that runs the test suite against multiple pinned JAX versions and latest on Linux. Removed explicit cancel-workflow steps in favor of native concurrency settings and simplified dependency installation commands.	.github/workflows/CI.yml .github/workflows/CI-daily.yml
Completed repository rename from brain-modeling-ecosystem to brainx across packaging, docs, and support links.	Updated project URLs (homepage, source, bug tracker) in pyproject.toml to point to the chaobrain/brainx GitHub repo. Adjusted README badges, clone instructions, issue links, and header image URLs to reference the new brainx repository and hosted assets. Refreshed documentation links in notebooks, install docs, and security policy to use github.com/chaobrain/brainx paths and correct file locations/branches.	pyproject.toml README.md docs/conf.py docs/install.md docs/**/*.ipynb SECURITY.md
Refreshed core ecosystem dependencies and JAX version bounds.	Bumped brainunit, brainevent, and brainstate to their latest compatible versions in requirements.txt. Raised the upper JAX bound to <=0.10.1 and the lower bound to >=0.7.1 in requirements.txt to align with tested versions. Simplified CUDA extra dependencies by dropping ninja from cuda12 and cuda13 extras in pyproject.toml.	requirements.txt pyproject.toml
Marked the package as typed and ensured typing metadata is shipped.	Registered BrainX package data to include py.typed via tool.setuptools.package-data configuration. Documented the PEP 561 typing support in the changelog entry for v2026.6.8.	pyproject.toml CHANGELOG.md BrainX/py.typed
Improved documentation build configuration and cleaned static assets.	Updated Read the Docs build image and Python version to Ubuntu 24.04 / Python 3.14 in .readthedocs.yml. Adjusted Sphinx theme options to use the new brainx repository URL in the docs configuration. Removed unused PWA-related static assets (service worker and manifest) to slim the docs bundle.	.readthedocs.yml docs/conf.py docs/_static/js/service-worker.js docs/_static/manifest.json
Updated project versioning and release metadata for v2026.6.8.	Bumped the library version constant to 2026.6.8 in the package __init__. Documented the release in CHANGELOG.md with sections for dependencies, typing, CI, repo rename, docs, README, and badges. Aligned the publish workflow to build with Python 3.13 instead of 3.12.	BrainX/__init__.py CHANGELOG.md .github/workflows/Publish.yml

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[sourcery-ai]

Hey - I've left some high level feedback:

• The JAX version range in CHANGELOG.md (>=0.6.0) does not match the updated constraint in requirements.txt (>=0.7.1); consider aligning these so the changelog accurately reflects the current requirement.
• In SECURITY.md, the text still refers to reporting security bugs in "BrainPy" and links to brainmodeling; this should be updated to reference BrainX and the chaobrain/brainx repository to match the rename.
• In docs/conf.py, html_title is still set to "Brain Modeling Ecosystem" while the project branding is now "BrainX"; consider updating this title to keep the docs branding consistent with the repository rename.

Prompt for AI Agents

Please address the comments from this code review:

## Overall Comments
- The JAX version range in `CHANGELOG.md` (`>=0.6.0`) does not match the updated constraint in `requirements.txt` (`>=0.7.1`); consider aligning these so the changelog accurately reflects the current requirement.
- In `SECURITY.md`, the text still refers to reporting security bugs in "BrainPy" and links to `brainmodeling`; this should be updated to reference BrainX and the `chaobrain/brainx` repository to match the rename.
- In `docs/conf.py`, `html_title` is still set to "Brain Modeling Ecosystem" while the project branding is now "BrainX"; consider updating this title to keep the docs branding consistent with the repository rename.

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