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multi_mst v2 on fast_hdbscan update
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‎.github/workflows/Docs.yml‎

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name: Documentation
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concurrency:
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group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
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cancel-in-progress: true
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on:
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push:
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branches:
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- main
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paths:
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- 'doc/**'
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- 'multi_mst/*.py'
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- '.github/workflows/Docs.yml'
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workflow_dispatch:
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jobs:
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pages:
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runs-on: ubuntu-20.04
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environment:
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name: github-pages
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url: ${{ steps.deployment.outputs.page_url }}
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permissions:
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pages: write
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id-token: write
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- uses: actions/setup-python@v5
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name: Install python
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with:
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python-version: 3.9
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cache: 'pip'
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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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sudo apt-get install -y pandoc
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pip install -e .
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- name: Prepare Examples
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run: |
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cd notebooks
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for FILE in *.ipynb; do
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cp $FILE ../doc
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done
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cd ..
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- id: deployment
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uses: sphinx-notes/pages@v3
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with:
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cache: True
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checkout: False
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documentation_path: ./doc
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requirements_path: ./doc/requirements.txt

‎.github/workflows/Publish.yml‎

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name: Publish Python Package
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concurrency:
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group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
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cancel-in-progress: false
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on:
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push:
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tags:
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- v*
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workflow_dispatch:
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jobs:
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publish_pypi:
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name: Publish to PyPi
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runs-on: ubuntu-20.04
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permissions:
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# IMPORTANT: this permission is mandatory for trusted publishing
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id-token: write
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contents: write
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environment:
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name: pypi
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url: https://pypi.org/p/multi_mst
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steps:
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- name: Extract version
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id: version
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run: |
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TAG=${{ github.ref }}
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VERSION=${TAG#refs/tags/v}
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echo "version=$VERSION" >> $GITHUB_OUTPUT
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echo "tag=v$VERSION" >> $GITHUB_OUTPUT
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- name: Download sdist
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uses: dawidd6/action-download-artifact@v7
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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workflow: Tests.yml
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workflow_conclusion: success
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branch: main
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path: .
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- name: Move files to dist
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run: |
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mkdir dist
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mv dists/* dist/
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if [[ ! -f dist/multi_mst-${{ steps.version.outputs.version }}.tar.gz ]] ; then exit 1; fi
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- name: Create Github Release
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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run: |
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gh release create -R vda-lab/multi_mst -t "Version ${{ steps.version.outputs.version }}" -n "**Full Changelog**: https://github.com/vda-lab/multi_mst/commits/${{ steps.version.outputs.tag }}" "${{ steps.version.outputs.tag }}" dist/*.whl dist/*.tar.gz
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- name: Publish package to (Test)PyPI
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uses: pypa/[email protected]
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# Comment lines below to publish to PyPi instead of test PyPi
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# with:
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# repository-url: https://test.pypi.org/legacy/

‎.github/workflows/Tests.yml‎

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name: Tests
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concurrency:
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group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
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cancel-in-progress: true
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on:
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push:
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branches:
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- main
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paths-ignore:
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- 'doc/**'
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- 'notebooks/**'
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- 'README.md'
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- '.gitignore'
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- '.github/workflows/Docs.yml'
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- '.github/workflows/Publish.yml'
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pull_request:
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branches:
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- main
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paths-ignore:
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- 'doc/**'
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- 'notebooks/**'
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- 'README.md'
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- '.gitignore'
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- '.github/workflows/Docs.yml'
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- '.github/workflows/Publish.yml'
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workflow_dispatch:
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jobs:
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build_dists:
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name: Build dists
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runs-on: ubuntu-20.04
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outputs:
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WHEEL_NAME: ${{ steps.dists.outputs.WHEEL_NAME }}
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- uses: actions/setup-python@v5
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name: Install python
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with:
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python-version: 3.9
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cache: 'pip'
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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 -r requirements.txt
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pip install twine flake8 build
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- name: Lint with flake8
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run: |
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# stop the build if there are Python syntax errors or undefined names
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flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
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- name: Build dists
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id: dists
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run: |
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python -m build --sdist --wheel
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python ci/export_name.py
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- name: Check README rendering for PyPI
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run: twine check dist/*
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- name: Upload sdist result
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uses: actions/upload-artifact@v4
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with:
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name: dists
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path: dist/*
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if-no-files-found: error
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test_sdist:
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name: Test dist for cp${{ matrix.python }}-${{ matrix.platform_id }}-${{ matrix.manylinux_image }}
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needs: build_dists
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: true
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matrix:
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include:
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- os: windows-latest
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python: "3.9"
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platform_id: win_amd64
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- os: windows-latest
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python: "3.10"
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platform_id: win_amd64
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- os: windows-latest
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python: "3.11"
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platform_id: win_amd64
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# Linux 64 bit manylinux2014
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- os: ubuntu-latest
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python: "3.9"
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platform_id: manylinux_x86_64
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manylinux_image: manylinux2014
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- os: ubuntu-latest
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python: "3.10"
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platform_id: manylinux_x86_64
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manylinux_image: manylinux2014
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- os: ubuntu-latest
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python: "3.11"
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platform_id: manylinux_x86_64
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manylinux_image: manylinux2014
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# MacOS x86_64
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- os: macos-latest
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python: "3.9"
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platform_id: macosx_x86_64
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- os: macos-latest
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python: "3.10"
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platform_id: macosx_x86_64
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- os: macos-latest
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python: "3.11"
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platform_id: macosx_x86_64
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steps:
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- name: Download sdist
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uses: actions/download-artifact@v4
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with:
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name: dists
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path: dist/
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- name: Setup Python
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install pytest
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- name: Run tests
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run: |
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pip install dist/${{ needs.build_dists.outputs.WHEEL_NAME }}
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python -c "from multi_mst.tests import run_tests; run_tests()"
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‎.gitignore‎

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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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build/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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*.egg
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MANIFEST
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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*.py,cover
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.hypothesis/
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.pytest_cache/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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db.sqlite3-journal
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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target/
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doc/_build/
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# Jupyter Notebook
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.ipynb_checkpoints
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!notebooks/lib/
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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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.python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow
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__pypackages__/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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.venv
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env.bak/
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venv.bak/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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*.code-workspace

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