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simonbesnard1simonbesnard1
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fix gedidb-contrib/ci-trigger@v1 action
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‎.github/workflows/ci.yaml‎

Lines changed: 113 additions & 35 deletions
Original file line numberDiff line numberDiff line change
@@ -1,29 +1,29 @@
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name: CI Pipeline
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name: CI
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on:
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push:
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branches:
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- "main"
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- "staging"
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- "documentation"
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pull_request:
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branches:
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- "main"
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- "staging"
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- "documentation"
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workflow_dispatch: # Allows manual triggering
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workflow_dispatch: # allows you to trigger manually
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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env:
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FORCE_COLOR: 3 # Enables colored output
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FORCE_COLOR: 3
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jobs:
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detect-ci-trigger:
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name: Detect CI Trigger
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name: detect ci trigger
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runs-on: ubuntu-latest
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if: |
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github.repository == 'gedidb'
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&& (github.event_name == 'push' || github.event_name == 'pull_request')
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outputs:
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triggered: ${{ steps.detect-trigger.outputs.trigger-found }}
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steps:
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- uses: actions/checkout@v4
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with:
@@ -32,55 +32,132 @@ jobs:
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id: detect-trigger
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with:
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keyword: "[skip-ci]"
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outputs:
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triggered: ${{ steps.detect-trigger.outputs.trigger-found }}
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test:
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name: ${{ matrix.os }} | py${{ matrix.python-version }}
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name: ${{ matrix.os }} py${{ matrix.python-version }} ${{ matrix.env }}
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runs-on: ${{ matrix.os }}
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needs: detect-ci-trigger
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if: needs.detect-ci-trigger.outputs.triggered == 'false'
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env:
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ZARR_V3_EXPERIMENTAL_API: 1
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defaults:
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run:
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shell: bash -l {0}
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strategy:
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fail-fast: false
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matrix:
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os: ["ubuntu-latest", "macos-latest", "windows-latest"]
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python-version: ["3.8", "3.10", "3.12"]
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# Bookend python versions
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python-version: ["3.10", "3.13"]
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env: [""]
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include:
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# Minimum python version:
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- env: "bare-minimum"
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python-version: "3.10"
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os: ubuntu-latest
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- env: "min-all-deps"
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python-version: "3.10"
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os: ubuntu-latest
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# Latest python version:
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- env: "all-but-numba"
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python-version: "3.13"
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os: ubuntu-latest
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- env: "all-but-dask"
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python-version: "3.12"
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os: ubuntu-latest
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- env: "flaky"
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python-version: "3.13"
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os: ubuntu-latest
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steps:
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- name: Checkout Code
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uses: actions/checkout@v4
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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fetch-depth: 0 # Fetch all history for all branches and tags.
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- name: Set environment variables
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run: |
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echo "TODAY=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
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- name: Setup Python Environment
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uses: actions/setup-python@v5
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if [[ ${{ matrix.os }} == windows* ]] ;
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then
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if [[ ${{ matrix.python-version }} != "3.14" ]]; then
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echo "CONDA_ENV_FILE=ci/requirements/environment-windows.yml" >> $GITHUB_ENV
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else
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echo "CONDA_ENV_FILE=ci/requirements/environment-windows-3.14.yml" >> $GITHUB_ENV
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fi
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elif [[ "${{ matrix.env }}" != "" ]] ;
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then
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if [[ "${{ matrix.env }}" == "flaky" ]] ;
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then
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echo "CONDA_ENV_FILE=ci/requirements/environment.yml" >> $GITHUB_ENV
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echo "PYTEST_ADDOPTS=-m 'flaky or network' --run-flaky --run-network-tests -W default" >> $GITHUB_ENV
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else
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echo "CONDA_ENV_FILE=ci/requirements/${{ matrix.env }}.yml" >> $GITHUB_ENV
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fi
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if [[ "${{ matrix.env }}" == "min-all-deps" ]] ;
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then
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# Don't raise on warnings
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echo "PYTEST_ADDOPTS=-W default" >> $GITHUB_ENV
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fi
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else
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if [[ ${{ matrix.python-version }} != "3.14" ]]; then
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echo "CONDA_ENV_FILE=ci/requirements/environment.yml" >> $GITHUB_ENV
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else
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echo "CONDA_ENV_FILE=ci/requirements/environment-3.14.yml" >> $GITHUB_ENV
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fi
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fi
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echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
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- name: Setup micromamba
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uses: mamba-org/setup-micromamba@v2
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with:
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python-version: ${{ matrix.python-version }}
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cache: "pip"
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environment-file: ${{ env.CONDA_ENV_FILE }}
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environment-name: gedidb-tests
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cache-environment: true
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cache-environment-key: "${{runner.os}}-${{runner.arch}}-py${{matrix.python-version}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
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create-args: >-
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python=${{matrix.python-version}}
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# We only want to install this on one run, because otherwise we'll have
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# duplicate annotations.
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- name: Install error reporter
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if: ${{ matrix.os }} == 'ubuntu-latest' and ${{ matrix.python-version }} == '3.12'
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run: |
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python -m pip install pytest-github-actions-annotate-failures
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- name: Install Dependencies
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- name: Install gedidb
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run: |
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python -m pip install --upgrade pip
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python -m pip install --no-cache-dir -e .
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python -m pip install pytest pytest-cov flake8 pytest-xdist
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python -m pip install --no-deps -e .
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- name: Run Linting (Flake8)
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run: flake8 gedidb
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- name: Version info
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run: |
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python gedidb/utils/print_versions.py
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- name: Run Tests
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- name: Import gedidb
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run: |
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pytest -n 4 --timeout=180 \
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--cov=gedidb --cov-branch --cov-report=xml --cov-report=term \
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python -c "import gedidb"
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- name: Restore cached hypothesis directory
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uses: actions/cache@v4
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with:
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path: .hypothesis/
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key: cache-hypothesis
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enableCrossOsArchive: true
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save-always: true
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- name: Run tests
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run: python -m pytest -n 4
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--timeout 180
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--cov=gedidb
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--cov-report=xml
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--junitxml=pytest.xml
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- name: Upload Test Results
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- name: Upload test results
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if: always()
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uses: actions/upload-artifact@v4
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with:
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name: Test Results (${{ matrix.os }} - py${{ matrix.python-version }})
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name: Test results for ${{ runner.os }}-${{ matrix.python-version }} ${{ matrix.env }}
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path: pytest.xml
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- name: Upload Code Coverage to Codecov
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- name: Upload code coverage to Codecov
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uses: codecov/codecov-action@v5.3.1
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env:
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
@@ -94,8 +171,9 @@ jobs:
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event_file:
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name: "Event File"
96173
runs-on: ubuntu-latest
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if: github.repository == 'gedidb'
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steps:
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- name: Upload GitHub Event File
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- name: Upload
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uses: actions/upload-artifact@v4
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with:
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name: Event File

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