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DEV: Simplify Workflows (iqtree#112)
* DEV: move iq-tree building into composite action * DEV: correctly specify composite action * DEV: specify shell to use * DEV: merge python setup and libiqtree fetching into composite action * DEV: ensure dependabot updates composite actions
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‎.github/actions/build-iqtree/action.yml

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name: Fetch or Build IQ-TREE 2 Static Library
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description: "Checks if the IQ-TREE 2 static library exists, if not then building it."
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inputs:
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os:
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description: "Runner OS Name."
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required: true
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outputs:
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iqtree2-sha:
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description: "SHA for commit of IQ-TREE 2 static library."
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value: ${{ steps.iqtree2-sha.outputs.iqtree2-sha }}
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runs:
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using: "composite"
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steps:
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- id: iqtree2-sha
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name: Get IQ-TREE 2 SHA
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shell: bash
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run: |
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cd iqtree2
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IQ_TREE_2_SHA=$(git rev-parse HEAD)
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echo "iqtree2-sha=${IQ_TREE_2_SHA}" >> "$GITHUB_OUTPUT"
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- uses: actions/cache@v4
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id: cache
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with:
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key: libiqtree-${{ inputs.os }}-${{ steps.iqtree2-sha.outputs.iqtree2-sha }}
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path: src/piqtree2/_libiqtree/libiqtree2.a
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lookup-only: true
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- name: Build IQ-TREE
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shell: bash
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if: steps.cache.outputs.cache-hit != 'true'
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run: |
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if [[ "${{ inputs.os }}" == "ubuntu-latest" ]]; then
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sudo ./build_tools/before_all_linux.sh
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else
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./build_tools/before_all_mac.sh
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fi

‎.github/actions/setup-piqtree/action.yml

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name: Setup piqtree
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description: "Setup Python and Fetch Static Library."
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inputs:
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python-version:
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description: "Python version."
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required: true
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cache-key:
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description: "Key for static library cache."
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required: true
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runs:
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using: "composite"
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steps:
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- uses: "actions/setup-python@v5"
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with:
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python-version: ${{ inputs.python-version }}
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- uses: actions/cache/restore@v4
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with:
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key: ${{ inputs.cache-key }}
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path: src/piqtree2/_libiqtree/libiqtree2.a
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fail-on-cache-miss: true

‎.github/dependabot.yml

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schedule:
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interval: "weekly"
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open-pull-requests-limit: 10
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- package-ecosystem: "github-actions"
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directory: "/.github/actions/build-iqtree/"
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schedule:
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interval: "weekly"
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open-pull-requests-limit: 10
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- package-ecosystem: "github-actions"
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directory: "/.github/actions/setup-piqtree/"
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schedule:
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interval: "weekly"
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open-pull-requests-limit: 10
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- package-ecosystem: "gitsubmodule"
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directory: "/"

‎.github/workflows/build_docs.yml

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name: Build docs
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name: Build Docs
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on: [workflow_dispatch]
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@@ -12,23 +12,13 @@ jobs:
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fetch-depth: 0
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submodules: recursive
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- name: Get IQ-TREE 2 SHA
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run: |
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cd iqtree2
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IQ_TREE_2_SHA=$(git rev-parse HEAD)
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echo "IQ_TREE_2_SHA=${IQ_TREE_2_SHA}" >> $GITHUB_ENV
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- uses: actions/cache@v4
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id: cache
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- id: build
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uses: ./.github/actions/build-iqtree
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with:
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key: libiqtree-${{ matrix.os }}-${{ env.IQ_TREE_2_SHA }}
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path: src/piqtree2/_libiqtree/libiqtree2.a
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lookup-only: true
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- name: Build IQ-TREE
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if: steps.cache.outputs.cache-hit != 'true'
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run: |
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sudo ./build_tools/before_all_linux.sh
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os: ubuntu-latest
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outputs:
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iqtree2-sha: ${{steps.build.outputs.iqtree2-sha}}
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build-docs:
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runs-on: ubuntu-latest
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fetch-depth: 0
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submodules: recursive
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- uses: actions/cache/restore@v4
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with:
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key: libiqtree-ubuntu-latest-${{ env.IQ_TREE_2_SHA }}
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path: src/piqtree2/_libiqtree/libiqtree2.a
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fail-on-cache-miss: true
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- name: Set up Python
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uses: actions/setup-python@v5
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- uses: ./.github/actions/setup-piqtree
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with:
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python-version: "3.12"
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cache-key: libiqtree-ubuntu-latest-${{ needs.build-iqtree.outputs.iqtree2-sha }}
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- name: Install Docs Dependencies
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run: |

‎.github/workflows/ci.yml

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fetch-depth: 0
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submodules: recursive
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- name: Get IQ-TREE 2 SHA
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run: |
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cd iqtree2
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IQ_TREE_2_SHA=$(git rev-parse HEAD)
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echo "IQ_TREE_2_SHA=${IQ_TREE_2_SHA}" >> $GITHUB_ENV
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- uses: actions/cache@v4
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id: cache
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- id: build
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uses: ./.github/actions/build-iqtree
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with:
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key: libiqtree-${{ matrix.os }}-${{ env.IQ_TREE_2_SHA }}
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path: src/piqtree2/_libiqtree/libiqtree2.a
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lookup-only: true
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- name: Build IQ-TREE
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if: steps.cache.outputs.cache-hit != 'true'
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run: |
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if [[ "${{ matrix.os }}" == "ubuntu-latest" ]]; then
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sudo ./build_tools/before_all_linux.sh
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else
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./build_tools/before_all_mac.sh
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fi
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os: ${{ matrix.os }}
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outputs:
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iqtree2-sha: ${{steps.build.outputs.iqtree2-sha}}
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tests:
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name: Run Tests with Python ${{matrix.python-version}} on ${{matrix.os}}
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fetch-depth: 0
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submodules: recursive
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- uses: "actions/setup-python@v5"
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with:
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python-version: "${{ matrix.python-version }}"
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- uses: actions/cache/restore@v4
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- uses: ./.github/actions/setup-piqtree
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with:
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key: libiqtree-${{ matrix.os }}-${{ env.IQ_TREE_2_SHA }}
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path: src/piqtree2/_libiqtree/libiqtree2.a
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fail-on-cache-miss: true
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python-version: ${{ matrix.python-version }}
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cache-key: libiqtree-${{ matrix.os }}-${{ needs.build-iqtree.outputs.iqtree2-sha }}
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- name: Run Nox Testing
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run: |
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with:
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fetch-depth: 0
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- uses: "actions/setup-python@v5"
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- uses: ./.github/actions/setup-piqtree
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with:
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python-version: "${{ matrix.python-version }}"
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- uses: actions/cache/restore@v4
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with:
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key: libiqtree-${{ matrix.os }}-${{ env.IQ_TREE_2_SHA }}
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path: src/piqtree2/_libiqtree/libiqtree2.a
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fail-on-cache-miss: true
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python-version: ${{ matrix.python-version }}
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cache-key: libiqtree-${{ matrix.os }}-${{ needs.build-iqtree.outputs.iqtree2-sha }}
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- name: "Run Type Checking for ${{ matrix.python-version }}"
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run: |
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pip install nox
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nox -s type_check-${{ matrix.python-version }}
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pip install nox
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nox -s type_check-${{ matrix.python-version }}
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lint:
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name: "Linting"
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with:
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fetch-depth: 0
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- uses: "actions/setup-python@v5"
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- uses: ./.github/actions/setup-piqtree
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with:
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python-version: "${{ matrix.python-version }}"
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- uses: actions/cache/restore@v4
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with:
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key: libiqtree-${{ matrix.os }}-${{ env.IQ_TREE_2_SHA }}
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path: src/piqtree2/_libiqtree/libiqtree2.a
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fail-on-cache-miss: true
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python-version: ${{ matrix.python-version }}
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cache-key: libiqtree-${{ matrix.os }}-${{ needs.build-iqtree.outputs.iqtree2-sha }}
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- name: "Run Type Checking for ${{ matrix.python-version }}"
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run: |
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pip install nox
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nox -s ruff-${{ matrix.python-version }}
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pip install nox
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nox -s ruff-${{ matrix.python-version }}

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