Swtich from HDF5 to NetCDF #284
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| name: CI | |
| concurrency: | |
| group: ${{ github.head_ref || github.run_id }} | |
| cancel-in-progress: true | |
| on: | |
| push: | |
| branches: | |
| - main | |
| tags: | |
| - 'v*' | |
| pull_request: | |
| workflow_dispatch: | |
| jobs: | |
| pipeline-tests: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| julia-version: | |
| - '1.8' | |
| - '1' | |
| os: | |
| - ubuntu-latest | |
| - macOS-latest | |
| - windows-latest | |
| arch: | |
| - x64 | |
| experimental: | |
| - false | |
| fail-fast: false | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| - name: Set up julia | |
| uses: julia-actions/setup-julia@v1 | |
| with: | |
| version: ${{ matrix.julia-version }} | |
| arch: ${{ matrix.arch }} | |
| - name: Build package | |
| uses: julia-actions/julia-buildpkg@v1 | |
| - name: Fix manifest for active Julia version | |
| run: | | |
| using Pkg | |
| Pkg.activate("examples/SEIRS") | |
| Pkg.resolve() | |
| shell: julia --color=yes {0} | |
| - name: Set up python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.x' | |
| architecture: 'x64' | |
| - name: Install graphviz and venv | |
| run: | | |
| # You may need to install python: https://python.org | |
| # Create venv | |
| # If not installed: pip3 install venv | |
| python3 -m venv .venv | |
| if [ "$RUNNER_OS" == "Linux" ]; then | |
| # If your Linux installation doesn't use apt, then use your package manager | |
| sudo apt-get install graphviz | |
| elif [ "$RUNNER_OS" == "Windows" ]; then | |
| # If choco is not installed: Install from https://chocolatey.org | |
| choco install graphviz | |
| elif [ "$RUNNER_OS" == "Darwin" ]; then | |
| # If brew not installed: Install from https://brew.sh | |
| brew install graphviz | |
| fi | |
| shell: bash | |
| - name: Install and start remote registry on Windows | |
| if: ${{ runner.os == 'Windows' }} | |
| run: | | |
| # Activate venv | |
| .venv\Scripts\activate | |
| # Install fair-cli | |
| pip3 install fair-cli | |
| # Install remote registry | |
| mkdir ${{ github.workspace }}\.registry | |
| $script1 = "${{ github.workspace }}",".registry\remoteregistry.ps1" -join "\" | |
| Write-Host "Download script: " $script1 | |
| curl https://data.fairdatapipeline.org/static/remoteregistry.ps1 > $script1 | |
| dir $script1 | |
| # Temporary fix for downloading old registry | |
| & $script1 -d ${{ github.workspace }}\.registry\registry-rem -s drams.test-remote-settings -u admin -p admin | |
| # Start the remote registry | |
| $script2 = "${{ github.workspace }}",".registry\registry-rem\scripts\start_fair_registry_windows.ps1" -join "\" | |
| Write-Host "Start registry script: " $script2 | |
| dir $script2 | |
| & $script2 -p 8001 -s drams.test-remote-settings -b | |
| # Copy the remote token | |
| $token = "${{ github.workspace }}",".registry\registry-rem\token" -join "\" | |
| Write-Host "Token location: " $token | |
| dir $token | |
| cp $token token | |
| deactivate | |
| - name: Install and start remote registry on Linux / macOS | |
| if: ${{ runner.os != 'Windows' }} | |
| run: | | |
| # Activate venv | |
| source .venv/bin/activate | |
| # Install fair-cli | |
| pip3 install fair-cli | |
| # Install remote registry | |
| mkdir ${{ github.workspace }}/.registry | |
| curl -fsSL https://data.fairdatapipeline.org/static/remoteregistry.sh | /bin/bash -s -- -d ${{ github.workspace }}/.registry/registry-rem -s drams.test-remote-settings -u admin -p admin | |
| # Start the remote registry | |
| script=${{ github.workspace }}/.registry/registry-rem/scripts/start_fair_registry | |
| echo $script | |
| $script -p 8001 -s drams.test-remote-settings | |
| # Copy the remote token | |
| cp ${{ github.workspace }}/.registry/registry-rem/token $PWD/token | |
| deactivate | |
| - name: Initialise and run fair-cli | |
| run: | | |
| source .venv/${ACTIVATE_DIR}/activate | |
| fair registry install | |
| fair registry start | |
| fair init --ci | |
| fair pull --debug examples/SEIRS/full_config.yaml | |
| fair run --debug --dirty examples/SEIRS/full_config.yaml | |
| exit $? | |
| deactivate | |
| shell: bash | |
| env: | |
| ACTIVATE_DIR: ${{ runner.os == 'Windows' && 'Scripts' || 'bin' }} | |
| # working-directory: julia_example # Use the julia_example Directory | |
| - name: Run tests on Windows | |
| if: ${{ runner.os == 'Windows' }} | |
| uses: julia-actions/julia-runtest@v1 | |
| env: | |
| WORKSPACE: . | |
| ACTIVATE_DIR: 'Scripts' | |
| with: | |
| prefix: ./test/runtests.sh | |
| - name: Run tests on Linux / macOS | |
| if: ${{ runner.os != 'Windows' }} | |
| uses: julia-actions/julia-runtest@v1 | |
| env: | |
| WORKSPACE: ${{ github.workspace }} | |
| ACTIVATE_DIR: 'bin' | |
| with: | |
| prefix: ${{ github.workspace }}/test/runtests.sh | |
| - name: Process coverage | |
| uses: julia-actions/julia-processcoverage@v1 | |
| - name: Coveralls | |
| uses: coverallsapp/github-action@v2 | |
| with: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| file: ./lcov.info | |
| - name: Codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| files: lcov.info |