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Move old functionalities into brainpy.version2 and add new modules in brainpy module (#778)
* Fix spike return values and update file paths in simulation scripts * Refactor code for improved readability by consolidating parameters in simulation scripts * Refactor decision making network and delay handling for improved clarity and functionality * Refactor module structure by renaming files and updating imports for improved organization * Add __init__.py files and implement module imports for improved package structure * Add __init__.py file and update imports for version2 migration * Update dependencies and improve package structure for version 3.0.0 * Update changelog for version 3.0.0 release * Update CI configuration to limit Python versions to 3.13 * Enhance issue templates and CI configurations for better usability and automation * Add tests for readout and synapse models, and update acknowledgments * Add tests for readout and synapse models, and update acknowledgments * Refactor error handling and rename neuron module to LIF * Add comprehensive tests for Neuron and Synapse base classes * Add projection modules and update imports for synaptic dynamics * Update imports to use brainpy.version2 across multiple modules * Update imports to use brainpy._errors and adjust version2 references * Update imports to use brainpy.version2 across multiple modules * Refactor imports and update usage of brainpy.version2 across multiple modules * Refactor imports and enhance usage of brainpy.version2 across multiple modules * Refactor imports to enhance usage of brainpy.version2 and streamline module references * Update CI configuration to run tests on the brainpy module instead of brainpy/_src * Refactor documentation structure to use docs_version2 and update related paths * Update documentation links to use docs_version2 and adjust version references * Refactor imports to utilize brainpy.version2 and streamline module references * Update module references to brainpy.version2 across documentation and code * Add Read the Docs configuration and update module references to brainpy.version2 * Update Read the Docs configuration and adjust requirements path --------- Co-authored-by: oujago <oujago@gmail.com>
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‎.github/CODEOWNERS‎

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# Code Owners for BrainPy
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# These owners will be requested for review when someone opens a pull request
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# that modifies code in specific paths or files.
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#
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# Learn more about CODEOWNERS:
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# https://docs.github.com/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-code-owners
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# Default owners for everything in the repo
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* @brainpy/core-team
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# Documentation
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/docs/ @brainpy/docs-team
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*.md @brainpy/docs-team
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*.rst @brainpy/docs-team
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# CI/CD and GitHub workflows
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/.github/ @brainpy/maintainers
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/.github/workflows/ @brainpy/maintainers
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# Core library
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/brainpy/_src/ @brainpy/core-team
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# Build and packaging
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/pyproject.toml @brainpy/maintainers
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/requirements*.txt @brainpy/maintainers
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# Tests
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/tests/ @brainpy/core-team
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# Examples
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/examples/ @brainpy/docs-team

‎.github/ISSUE_TEMPLATE/bug_report.md‎

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---
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name: 'Bug Report'
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about: 'Report a bug or unexpected behavior to help us improve the package'
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labels: 'bug'
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name: Bug Report
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about: Report a bug or unexpected behavior to help us improve BrainPy
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title: '[BUG] '
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labels: bug
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assignees: ''
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---
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Please:
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## Bug Description
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- [ ] Check for duplicate issues.
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- [ ] Provide a complete example of how to reproduce the bug, wrapped in triple backticks like this:
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**Describe the bug**
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A clear and concise description of what the bug is.
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## To Reproduce
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**Minimal code example to reproduce the issue:**
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```python
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import brainpy as bp
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# Your code here that demonstrates the bug
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```
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**Steps to reproduce:**
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1.
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3.
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## Expected Behavior
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What you expected to happen.
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## Actual Behavior
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What actually happened. Include the full error message and traceback if applicable.
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```
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Paste error message/traceback here
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```
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## Environment
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Please provide the following information:
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- **BrainPy Version:** [e.g., 2.4.0]
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- **Python Version:** [e.g., 3.10.5]
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- **JAX Version:** [e.g., 0.4.30]
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- **Operating System:** [e.g., Ubuntu 22.04, macOS 13.0, Windows 11]
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- **Hardware:** [e.g., CPU only, CUDA GPU, TPU]
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- **Installation method:** [e.g., pip, conda, from source]
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**Additional context:**
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```python
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import brainpy.math as bm
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print(bm.asarray([1, 2, 3]))
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# Array([1, 2, 3], dtype=int32)
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import brainpy as bp
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print(bp.__version__)
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# Add any other relevant version info
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```
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- [ ] If applicable, include full error messages/tracebacks.
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## Additional Context
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Add any other context about the problem here (e.g., related issues, potential causes, attempted solutions).
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## Checklist
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- [ ] I have checked for duplicate issues
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- [ ] I have provided a minimal code example to reproduce the bug
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- [ ] I have included the full error message/traceback
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- [ ] I have provided environment information

‎.github/ISSUE_TEMPLATE/config.yml‎

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blank_issues_enabled: true
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contact_links:
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- name: 📚 Documentation
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url: https://brainpy.readthedocs.io/
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about: Check the documentation for guides, tutorials, and API reference
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- name: 💬 GitHub Discussions
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url: https://github.com/brainpy/BrainPy/discussions
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about: Ask questions and discuss ideas with the community
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- name: 🔒 Security Vulnerability
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url: https://github.com/brainpy/BrainPy/security/advisories/new
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about: Report security vulnerabilities privately (do not create public issues)

‎.github/ISSUE_TEMPLATE/feature_request.md‎

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---
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name: 'Feature Request'
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about: 'Suggest a new idea or improvement for BrainPy'
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labels: 'enhancement'
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name: Feature Request
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about: Suggest a new idea or improvement for BrainPy
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title: '[FEATURE] '
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labels: enhancement
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assignees: ''
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---
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Please:
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## Feature Description
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- [ ] Check for duplicate requests.
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- [ ] Describe your goal, and if possible provide a code snippet with a motivating example.
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**Is your feature request related to a problem? Please describe.**
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A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
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**Describe the solution you'd like**
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A clear and concise description of what you want to happen.
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## Motivation and Use Case
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**Why is this feature important?**
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Explain the motivation for this feature and who would benefit from it.
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**Example use case:**
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```python
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import brainpy as bp
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# Example code showing how you would like to use this feature
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# This helps us understand your vision
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```
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## Proposed Implementation (Optional)
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**How do you envision this working?**
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If you have ideas about how this could be implemented, share them here.
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**API design (if applicable):**
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```python
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# Proposed API or interface
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```
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## Alternatives Considered
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**What alternatives have you considered?**
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Describe alternative solutions or features you've considered and why they don't fully address your needs.
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## Additional Context
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Add any other context, screenshots, references to related work, or examples from other libraries.
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**Related issues/PRs:**
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- #issue_number
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## Checklist
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- [ ] I have checked for duplicate feature requests
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- [ ] I have provided a clear use case and motivation
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- [ ] I have described the desired behavior
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- [ ] I have considered and described alternatives

‎.github/PULL_REQUEST_TEMPLATE.md‎

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<!--- Provide a general summary of your changes in the Title above -->
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<!--- Please do remember to follow the contributing guidelines -->
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<!--
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Thank you for contributing to BrainPy!
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Please fill out this template to help us review your pull request.
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See CONTRIBUTING.md for guidelines.
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-->
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## Summary
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<!-- Provide a clear, concise summary of your changes -->
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**Fixes #(issue number)** <!-- If this PR closes an issue, link it here -->
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## Type of Change
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<!-- Mark the appropriate option with an "x" -->
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- [ ] Bug fix (non-breaking change which fixes an issue)
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- [ ] New feature (non-breaking change which adds functionality)
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- [ ] Breaking change (fix or feature that would cause existing functionality to change)
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- [ ] Documentation update
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- [ ] Code refactoring (no functional changes)
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- [ ] Performance improvement
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- [ ] Test coverage improvement
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- [ ] Other (please describe):
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## Description
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<!--- Why is this change required? What problem does it solve? -->
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<!--- Describe your changes in detail here to communicate to the maintainers why this pull request should be accepted -->
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<!--- Describe your technology stack here if not a documentation update -->
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<!--- Tasklist format is recommended for all pull requests and is required for all draft pull requests. You can couple your description with the tasklist -->
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<!--- If it fixes an open issue, please link to the issue here in the last line. -->
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## How Has This Been Tested
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<!--- Please describe in detail how you tested your changes locally -->
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<!--- Include details of your testing environment, and the tests you ran to -->
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<!--- For example, markdown files should pass markdownlint locally according to the rules -->
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<!--- See how your change affects other areas of the code, etc. -->
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## Types of changes
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<!--- What types of changes does your code introduce? -->
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<!--- Only left the line that best describes this pull request -->
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- Bug fix (non-breaking change which fixes an issue)
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- New feature (non-breaking change which adds functionality)
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- Documentation (non-breaking change which updates documentation)
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- Breaking change (fix or feature that would cause existing functionality to change)
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- Code style (formatting, renaming)
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- Refactoring (no functional changes, no api changes)
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- Other (please describe here):
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**What does this PR do?**
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<!-- Describe your changes in detail -->
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**Why is this change needed?**
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<!-- Explain the motivation for this change -->
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**How does it work?**
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<!-- Provide technical details about your implementation -->
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## Changes Made
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<!-- List the main changes in this PR -->
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-
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-
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-
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## Testing
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**How has this been tested?**
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<!-- Describe the tests you ran to verify your changes -->
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```python
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# Example test code or commands used
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```
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**Test environment:**
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- Python version:
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- BrainPy version:
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- JAX version:
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- OS:
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**Test coverage:**
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- [ ] Added new tests for this change
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- [ ] All existing tests pass
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- [ ] Manual testing performed
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## Performance Impact
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<!-- If applicable, describe any performance implications -->
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- [ ] No performance impact
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- [ ] Performance improved (provide benchmarks)
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- [ ] Performance may be affected (explain why and how much)
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## Documentation
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- [ ] Docstrings added/updated
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- [ ] Documentation updated (if needed)
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- [ ] Examples added/updated (if applicable)
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- [ ] CHANGELOG entry added (for notable changes)
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## Screenshots (if applicable)
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<!-- Add screenshots to help explain your changes -->
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## Breaking Changes
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<!-- If this is a breaking change, describe the impact and migration path -->
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**Breaking change details:**
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<!-- What breaks? How should users update their code? -->
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**Migration guide:**
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```python
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# Before (old way)
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# After (new way)
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```
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## Checklist
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<!--- Go over all the following points, and put an `x` in all the boxes that apply. -->
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<!--- If you're unsure about any of these, don't hesitate to ask. We're here to help! -->
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- [ ] Code follows the code style of this project.
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- [ ] Changes follow the **CONTRIBUTING** guidelines.
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- [ ] Update necessary documentation accordingly.
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- [ ] Lint and tests pass locally with the changes.
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- [ ] Check issues and pull requests first. You don't want to duplicate effort.
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## Other information
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<!-- Ensure all items are complete before submitting -->
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- [ ] My code follows the project's style guidelines
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- [ ] I have performed a self-review of my code
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- [ ] I have commented my code, particularly in hard-to-understand areas
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- [ ] I have made corresponding changes to the documentation
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- [ ] My changes generate no new warnings
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- [ ] I have added tests that prove my fix is effective or that my feature works
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- [ ] New and existing unit tests pass locally with my changes
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- [ ] Any dependent changes have been merged and published
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- [ ] I have checked for duplicate PRs/issues
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- [ ] I have read and followed the [CONTRIBUTING](../CONTRIBUTING.md) guidelines
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## Additional Notes
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<!-- Any additional information that reviewers should know -->
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## Related Issues/PRs
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<!-- Link to related issues or pull requests -->
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- Related to #
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- Depends on #
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- Blocks #

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