Update Actions / Version #828
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| # Check latest release of all implementations still function with new changes | |
| name: FAIR CLI Implementation Testing | |
| on: [push, workflow_dispatch] | |
| jobs: | |
| Python: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 # Clone Fair CLI | |
| - name: Clone Python Implementation | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: FAIRDataPipeline/pyDataPipeline # Clone pyDataPipeline | |
| path: pyDataPipeline | |
| - name: Checkout pySimpleModel | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: FAIRDataPipeline/pySimpleModel # Clone pySimple Model | |
| path: pySimpleModel | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.9" | |
| architecture: "x64" | |
| - name: Install memcached | |
| run: sudo apt install -y libmemcached-dev | |
| - name: Setup fair | |
| run: | | |
| # Create venv | |
| python3 -m venv venv | |
| # Activate venv | |
| ./venv/bin/activate | |
| # Intall CLI | |
| pip3 install ../ | |
| # Install pyDataPipeline | |
| pip3 install ../pyDataPipeline | |
| # Install pySimple Model | |
| pip3 install . | |
| working-directory: pySimpleModel # Use the pySimpleModel Directory | |
| - name: Install remote registry | |
| run: | | |
| # Activate venv | |
| ./venv/bin/activate | |
| # Install the remote registry | |
| #fair registry install --directory ${GITHUB_WORKSPACE}/registry-rem | |
| curl -fsSL https://data.fairdatapipeline.org/static/remoteregistry.sh | /bin/bash -s -- -d ${GITHUB_WORKSPACE}/registry-rem -s drams.test-remote-settings -u admin -p admin | |
| # Start the remote registry | |
| ${GITHUB_WORKSPACE}/registry-rem/scripts/start_fair_registry -p 8001 -s drams.test-remote-settings | |
| # Copy the remote token | |
| cp ${GITHUB_WORKSPACE}/registry-rem/token $PWD/token | |
| export DJANGO_SETTINGS_MODULE=drams.test-remote-settings | |
| ${GITHUB_WORKSPACE}/registry-rem/venv/bin/python ${GITHUB_WORKSPACE}/registry-rem/manage.py createsuperuser --username FAIRDataPipeline --noinput | |
| working-directory: pySimpleModel | |
| - name: Install the registry and init | |
| run: | | |
| # Install the local registry | |
| fair registry install | |
| # Initialise Repository | |
| fair init --ci | |
| # Start the local registry | |
| fair registry start | |
| working-directory: pySimpleModel # Use the pySimpleModel Directory | |
| - name: Test Pull | |
| run: | | |
| # Activate venv | |
| ./venv/bin/activate | |
| # Pull (Register) the SEIRS Parameters | |
| fair pull --debug simpleModel/ext/SEIRSconfig.yaml | |
| working-directory: pySimpleModel # Use the pySimpleModel Directory | |
| - name: Test Run | |
| run: | | |
| # Activate venv | |
| ./venv/bin/activate | |
| # Run the Model | |
| fair run --debug simpleModel/ext/SEIRSconfig.yaml # Run the seirs model | |
| working-directory: pySimpleModel # Use the pySimpleModel Directory | |
| - name: Test Push | |
| run: | | |
| # Activate venv | |
| ./venv/bin/activate | |
| # Stage the SEIRS Parameters to be Pushed | |
| fair add PSU:SEIRS_model/[email protected] | |
| # Push the SEIRS parameters | |
| fair push | |
| working-directory: pySimpleModel # Use the pySimpleModel Directory | |
| Java: | |
| runs-on: ubuntu-latest | |
| #if: False | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Clone Java Implementation | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: FAIRDataPipeline/javaSimpleModel | |
| path: java_example | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.9" | |
| architecture: "x64" | |
| - name: Install memcached | |
| run: sudo apt install -y libmemcached-dev | |
| - name: Set up JDK 11 | |
| uses: actions/setup-java@v3 | |
| with: | |
| java-version: '11' | |
| distribution: 'adopt' | |
| server-id: github | |
| settings-path: ${{ github.workspace }} | |
| - name: Build with Gradle | |
| run: gradle build | |
| working-directory: java_example | |
| - name: Setup fair | |
| run: | | |
| # Create venv | |
| python3 -m venv venv | |
| # Activate venv | |
| ./venv/bin/activate | |
| # Intall CLI | |
| pip3 install ../ | |
| working-directory: java_example # Use the java_example Directory | |
| - name: Install remote registry | |
| run: | | |
| ./venv/bin/activate # Activate venv | |
| # Install the remote registry | |
| curl -fsSL https://data.fairdatapipeline.org/static/remoteregistry.sh | /bin/bash -s -- -d ${GITHUB_WORKSPACE}/registry-rem -s drams.test-remote-settings -u admin -p admin | |
| # Start the remote registry | |
| ${GITHUB_WORKSPACE}/registry-rem/scripts/start_fair_registry -p 8001 -s drams.test-remote-settings | |
| # Copy the remote token | |
| cp ${GITHUB_WORKSPACE}/registry-rem/token $PWD/token | |
| working-directory: java_example # Use the java_example Directory | |
| - name: run javaSimpleModel with fair cli | |
| run: | | |
| ./venv/bin/activate # Activate venv | |
| # Install local registry | |
| fair registry install | |
| # Start local registry | |
| fair registry start | |
| # Initialise repository | |
| fair init --ci | |
| # Pull (Register) SEIRS Parameters | |
| fair pull --debug src/main/resources/seirs-config.yaml # Pull SEIRS parameters | |
| # Run the model dirty as venv is not in .gitignore (to do) | |
| fair run --dirty --debug src/main/resources/seirs-config.yaml # Run the SEIRS Model | |
| working-directory: java_example # Use the java_example Directory | |
| R: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v3 # Clone FAIR CLI | |
| - name: Install memcached | |
| run: sudo apt install -y libmemcached-dev | |
| - name: Clone R Data Pipeline | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: FAIRDataPipeline/rDataPipeline | |
| path: r_data_pipeline | |
| ref: 'main' | |
| - name: Clone R Implementation | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: FAIRDataPipeline/rSimpleModel | |
| path: r_example | |
| ref: 'main' | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.9" | |
| architecture: "x64" | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: release | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| working-directory: r_data_pipeline | |
| extra-packages: | | |
| devtools | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| working-directory: r_example | |
| extra-packages: | | |
| devtools | |
| - name: Install implementation | |
| run: | | |
| devtools::install_github("FAIRDataPipeline/rDataPipeline") | |
| library(rDataPipeline) | |
| devtools::install_github("FAIRDataPipeline/rSimpleModel") | |
| library(rSimpleModel) | |
| shell: Rscript {0} | |
| - name: Setup fair | |
| run: | | |
| # Create venv | |
| python3 -m venv venv | |
| # Activate venv | |
| ./venv/bin/activate | |
| # Intall CLI | |
| pip3 install ../ # Install CLI | |
| working-directory: r_example # Use the r_example Directory | |
| - name: Install remote registry | |
| run: | | |
| # Activate venv | |
| ./venv/bin/activate # Activate venv | |
| # Install the remote registry | |
| curl -fsSL https://data.fairdatapipeline.org/static/remoteregistry.sh | /bin/bash -s -- -d ${GITHUB_WORKSPACE}/registry-rem -s drams.test-remote-settings -u admin -p admin | |
| # Start the remote registry | |
| ${GITHUB_WORKSPACE}/registry-rem/scripts/start_fair_registry -p 8001 -s drams.test-remote-settings | |
| # Copy the remote token | |
| cp ${GITHUB_WORKSPACE}/registry-rem/token $PWD/token | |
| working-directory: r_example # Use the r_example Directory | |
| - name: run rSimpleModel with fair cli | |
| run: | | |
| # Activate venv | |
| ./venv/bin/activate | |
| # Install local registry | |
| fair registry install | |
| # Start local registry | |
| fair registry start | |
| # Initialise repository | |
| fair init --ci | |
| # Pull (Register) SEIRS Parameters | |
| fair pull --debug inst/extdata/SEIRSconfig.yaml | |
| # Run the model dirty as venv is not in .gitignore (to do) | |
| fair run --dirty --debug inst/extdata/SEIRSconfig.yaml | |
| working-directory: r_example # Use the r_example Directory | |
| Julia: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Clone Julia Implementation | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: FAIRDataPipeline/DataPipeline.jl | |
| path: julia_example | |
| ref: 'main' | |
| - name: Install memcached | |
| run: sudo apt install -y libmemcached-dev | |
| - name: Set up julia | |
| uses: julia-actions/setup-julia@v1 | |
| with: | |
| version: "1.8.5" | |
| arch: 'x64' | |
| - name: Install Package | |
| run: julia -e 'using Pkg; Pkg.instantiate()' | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.9" | |
| architecture: "x64" | |
| - name: Setup fair | |
| run: | | |
| # Create venv | |
| python3 -m venv venv | |
| # Activate venv | |
| ./venv/bin/activate | |
| # Intall CLI | |
| pip3 install ../ # Install CLI | |
| working-directory: julia_example # Use the julia_example Directory | |
| - name: Install remote registry | |
| run: | | |
| # Activate venv | |
| ./venv/bin/activate # Activate venv | |
| # Install the remote registry | |
| curl -fsSL https://data.fairdatapipeline.org/static/remoteregistry.sh | /bin/bash -s -- -d ${GITHUB_WORKSPACE}/registry-rem -s drams.test-remote-settings -u admin -p admin | |
| # Start the remote registry | |
| ${GITHUB_WORKSPACE}/registry-rem/scripts/start_fair_registry -p 8001 -s drams.test-remote-settings | |
| # Copy the remote token | |
| cp ${GITHUB_WORKSPACE}/registry-rem/token $PWD/token | |
| working-directory: julia_example # Use the julia_example Directory | |
| - name: Run SEIRS Model with fair cli | |
| run: | | |
| # Activate venv | |
| ./venv/bin/activate | |
| # Install local registry | |
| fair registry install | |
| # Start local registry | |
| fair registry start | |
| # Initialise repository | |
| fair init --ci | |
| # Pull (Register) SEIRS Parameters | |
| fair pull --debug examples/fdp/SEIRSconfig.yaml | |
| # Run the model dirty as venv is not in .gitignore (to do) | |
| fair run --dirty --debug examples/fdp/SEIRSconfig.yaml | |
| working-directory: julia_example # Use the julia_example Directory | |
| CPlusPlus: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Clone CPlusPlus Model | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: FAIRDataPipeline/cppSimpleModel | |
| path: cpp_example | |
| ref: 'main' | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.9" | |
| architecture: "x64" | |
| - name: Install requirements | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get upgrade | |
| sudo apt install -y libmemcached-dev graphviz gnuplot --fix-missing | |
| sudo apt install -y libjsoncpp-dev curl libcurl4-openssl-dev --fix-missing | |
| sudo apt install -y libyaml-cpp-dev libhdf5-dev --fix-missing | |
| - name: Install Model | |
| run: | | |
| cmake -Bbuild | |
| cmake --build build | |
| working-directory: cpp_example | |
| - name: Setup fair | |
| run: | | |
| # Create venv | |
| python3 -m venv venv | |
| # Activate venv | |
| ./venv/bin/activate | |
| # Intall CLI | |
| pip3 install ../ # Install CLI | |
| working-directory: cpp_example # Use the cpp_example Directory | |
| - name: Install remote registry | |
| run: | | |
| # Activate venv | |
| ./venv/bin/activate # Activate venv | |
| # Install the remote registry | |
| curl -fsSL https://data.fairdatapipeline.org/static/remoteregistry.sh | /bin/bash -s -- -d ${GITHUB_WORKSPACE}/registry-rem -s drams.test-remote-settings -u admin -p admin | |
| # Start the remote registry | |
| ${GITHUB_WORKSPACE}/registry-rem/scripts/start_fair_registry -p 8001 -s drams.test-remote-settings | |
| # Copy the remote token | |
| cp ${GITHUB_WORKSPACE}/registry-rem/token $PWD/token | |
| working-directory: cpp_example # Use the cpp_example Directory | |
| - name: Run Example model with fair-cli | |
| run: | | |
| # Activate venv | |
| ./venv/bin/activate # Activate venv | |
| # Install local registry | |
| fair registry install | |
| # Start local registry | |
| fair registry start | |
| # Initialise repository | |
| fair init --ci | |
| # Pull (Register) SEIRS Parameters | |
| fair pull --debug data/seirs_config.yaml | |
| # Run the model dirty as venv is not in .gitignore (to do) | |
| fair run --dirty --debug data/seirs_config.yaml | |
| working-directory: cpp_example # Use the cpp_example Directory |