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Donglai Wei
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codebase cleanup
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‎.github/workflows/build-wheels.yml‎

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name: Build Wheels
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on:
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push:
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tags:
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- 'v*'
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workflow_dispatch:
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jobs:
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build_wheels:
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name: Build wheels on ${{ matrix.os }}
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [ubuntu-20.04, macos-11, windows-2019]
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python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install build wheel setuptools
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- name: Build wheel
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run: python -m build --wheel
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- name: Upload wheels
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uses: actions/upload-artifact@v3
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with:
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name: wheels
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path: dist/*.whl
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build_sdist:
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name: Build source distribution
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: '3.10'
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install build
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- name: Build sdist
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run: python -m build --sdist
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- name: Upload sdist
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uses: actions/upload-artifact@v3
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with:
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name: sdist
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path: dist/*.tar.gz
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upload_pypi:
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name: Upload to PyPI
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needs: [build_wheels, build_sdist]
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runs-on: ubuntu-latest
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if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
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steps:
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- uses: actions/download-artifact@v3
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with:
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name: wheels
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path: dist
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- uses: actions/download-artifact@v3
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with:
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name: sdist
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path: dist
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- name: Publish to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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user: __token__
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password: ${{ secrets.PYPI_API_TOKEN }}

‎.github/workflows/docs.yml‎

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name: Documentation
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on:
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push:
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branches: [ main, master, v2.0 ]
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pull_request:
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branches: [ main, master, v2.0 ]
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jobs:
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build-docs:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: '3.10'
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -e .[docs]
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- name: Build documentation
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run: |
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cd docs
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make html
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- name: Deploy to GitHub Pages
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if: github.event_name == 'push' && github.ref == 'refs/heads/master'
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uses: peaceiris/actions-gh-pages@v3
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: ./docs/build/html

‎.github/workflows/tests.yml‎

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name: Tests
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on:
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push:
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branches: [ main, master, v2.0 ]
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pull_request:
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branches: [ main, master, v2.0 ]
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jobs:
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test:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [ubuntu-latest, macos-latest, windows-latest]
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python-version: ['3.8', '3.9', '3.10', '3.11']
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install pytest pytest-cov
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pip install -e .
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- name: Run tests
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run: |
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pytest tests/ -v --cov=connectomics --cov-report=xml
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v3
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with:
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file: ./coverage.xml
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flags: unittests
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name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
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lint:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: '3.10'
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- name: Install linters
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run: |
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python -m pip install --upgrade pip
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pip install black flake8 isort mypy
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- name: Run black
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run: black --check connectomics/
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- name: Run flake8
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run: flake8 connectomics/ --max-line-length=100
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- name: Run isort
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run: isort --check connectomics/
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- name: Run mypy
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run: mypy connectomics/ --ignore-missing-imports

‎MANIFEST.in‎

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# Include documentation files
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include README.md
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include QUICKSTART.md
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include TROUBLESHOOTING.md
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include INSTALLATION.md
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include LICENSE
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include CONTRIBUTING.md
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include RELEASE_NOTES.md
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# Include configuration examples
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recursive-include tutorials *.yaml *.yml
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# Include notebooks
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recursive-include notebooks *.ipynb
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# Exclude unnecessary files
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global-exclude *.py[cod] __pycache__ *.so *.dylib
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exclude .gitignore
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exclude .gitattributes
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# Exclude development and CI files
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exclude .github
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recursive-exclude .github *
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exclude .claude
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recursive-exclude .claude *
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exclude docker
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recursive-exclude docker *
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exclude scripts
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recursive-exclude scripts *
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# Exclude outputs and temporary files
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exclude outputs
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recursive-exclude outputs *
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exclude datasets
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recursive-exclude datasets *
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prune tests

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