feat/textual enrichment #32
Workflow file for this run
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| # This is a basic workflow to help you get started with GitHub Actions | |
| name: TESTS Talk2KnowledgeGraphs | |
| # Controls when the workflow will run | |
| on: | |
| # Triggers the workflow on push or pull request events | |
| pull_request: | |
| branches: [ main ] | |
| paths: | |
| - 'aiagents4pharma/talk2knowledgegraphs/**' | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| env: | |
| OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }} | |
| # This workflow contains jobs covering linting and code coverage (along with testing). | |
| jobs: | |
| # pylint job for windows, ubuntu, and macos | |
| pylint-windows-ubuntu-macos: | |
| # The type of runner that the job will run on | |
| name: pylint | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [windows-latest, ubuntu-latest, macos-13] | |
| # Steps represent a sequence of tasks that will be executed as part of the job | |
| steps: | |
| # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.12 | |
| - name: Cache files | |
| uses: actions/cache@v4 | |
| id: cache | |
| with: | |
| path: | | |
| ${{ github.workspace }}/venv/* | |
| key: ${{ runner.os }}-pip-pylint | |
| # install requirements for ubuntu and macos | |
| - name: Install the requirements (ubuntu and macos) | |
| if: steps.cache.outputs.cache-hit != 'true' && matrix.os != 'windows-latest' | |
| working-directory: ${{ github.workspace }} | |
| run: | | |
| python3 -m venv venv | |
| source venv/bin/activate | |
| pip install --upgrade pip | |
| pip3 install --break-system-packages -r requirements.txt | |
| # install requirements for windows | |
| - name: Install the requirements (windows) | |
| if: steps.cache.outputs.cache-hit != 'true' && matrix.os == 'windows-latest' | |
| working-directory: ${{ github.workspace }} | |
| run: | | |
| python3 -m venv venv | |
| venv\Scripts\activate | |
| pip install --upgrade pip | |
| pip3 install --break-system-packages -r requirements.txt | |
| # pylint for ubuntu and macos | |
| - name: Run pylint (ubuntu and macos) | |
| if: matrix.os != 'windows-latest' | |
| working-directory: ${{ github.workspace }} | |
| run: | | |
| source venv/bin/activate | |
| pylint --disable=R0801,R0902,W0221,W0122 aiagents4pharma/talk2knowledgegraphs | |
| # pylint for windows | |
| - name: Run pylint (windows) | |
| if: matrix.os == 'windows-latest' | |
| working-directory: ${{ github.workspace }} | |
| run: | | |
| venv\Scripts\activate | |
| pylint --disable=R0801,R0902,W0221,W0122 aiagents4pharma/talk2knowledgegraphs | |
| # code coverage job for macos | |
| code-cov-macos: | |
| name: code-coverage | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [macos-13] | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.12 | |
| - name: Cache files | |
| uses: actions/cache@v4 | |
| id: cache | |
| with: | |
| path: | | |
| ${{ github.workspace }}/ollama_models/* | |
| ${{ github.workspace }}/venv/* | |
| key: ${{ runner.os }}-pip-code-cov | |
| - name: Install dependencies | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| working-directory: ${{ github.workspace }} | |
| run: | | |
| python3 -m venv venv | |
| source venv/bin/activate | |
| pip install --upgrade pip | |
| pip3 install -r requirements.txt | |
| brew install ollama | |
| mkdir ${{ github.workspace }}/ollama_models | |
| export OLLAMA_MODELS=${{ github.workspace }}/ollama_models | |
| ollama serve & | |
| sleep 10 | |
| ollama pull llama3.2 | |
| - name: Reading cached Ollama models | |
| working-directory: ${{ github.workspace }} | |
| run: | | |
| echo "Cache Hit Status - ${{ steps.cache.outputs.cache-hit }}" | |
| source venv/bin/activate | |
| brew install ollama | |
| export OLLAMA_MODELS=${{ github.workspace }}/ollama_models | |
| ollama serve & | |
| sleep 10 | |
| ollama list | |
| - name: Run tests with coverage | |
| working-directory: ${{ github.workspace }} | |
| run: | | |
| source venv/bin/activate | |
| coverage run --include=aiagents4pharma/talk2knowledgegraphs/* -m pytest --cache-clear aiagents4pharma/talk2knowledgegraphs/tests/ | |
| - name: Check coverage | |
| working-directory: ${{ github.workspace }} | |
| run: | | |
| source venv/bin/activate | |
| coverage report -m | |
| TOTAL_COVERAGE=$(coverage report -m | awk 'END {print int($NF)}') | |
| if [[ $TOTAL_COVERAGE -ne 100 ]]; then | |
| echo "Code coverage is not 100%. Please check the coverage report." | |
| exit 1 | |
| fi | |
| env: | |
| COVERAGE_FILE: './.coverage' | |
| # code coverage job for ubuntu | |
| code-cov-ubuntu: | |
| name: code-coverage | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest] | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.12 | |
| - name: Cache files | |
| uses: actions/cache@v4 | |
| id: cache | |
| with: | |
| path: | | |
| ${{ github.workspace }}/ollama_models/* | |
| ${{ github.workspace }}/venv/* | |
| key: ${{ runner.os }}-pip-code-cov | |
| - name: Install dependencies | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| working-directory: ${{ github.workspace }} | |
| run: | | |
| python3 -m venv venv | |
| source venv/bin/activate | |
| pip install --upgrade pip | |
| pip3 install -r requirements.txt | |
| curl -fsSL https://ollama.com/install.sh | sh | |
| mkdir ${{ github.workspace }}/ollama_models | |
| export OLLAMA_MODELS=${{ github.workspace }}/ollama_models | |
| ollama serve & | |
| sleep 10 | |
| ollama pull llama3.2 | |
| - name: Reading cached Ollama models | |
| working-directory: ${{ github.workspace }} | |
| run: | | |
| echo "Cache Hit Status - ${{ steps.cache.outputs.cache-hit }}" | |
| source venv/bin/activate | |
| curl -fsSL https://ollama.com/install.sh | sh | |
| export OLLAMA_MODELS=${{ github.workspace }}/ollama_models | |
| ollama serve & | |
| sleep 10 | |
| ollama list | |
| - name: Run tests with coverage | |
| working-directory: ${{ github.workspace }} | |
| run: | | |
| source venv/bin/activate | |
| coverage run --include=aiagents4pharma/talk2knowledgegraphs/* -m pytest --cache-clear aiagents4pharma/talk2knowledgegraphs/tests/ | |
| - name: Check coverage | |
| working-directory: ${{ github.workspace }} | |
| run: | | |
| source venv/bin/activate | |
| coverage report -m | |
| TOTAL_COVERAGE=$(coverage report -m | awk 'END {print int($NF)}') | |
| if [[ $TOTAL_COVERAGE -ne 100 ]]; then | |
| echo "Code coverage is not 100%. Please check the coverage report." | |
| exit 1 | |
| fi | |
| env: | |
| COVERAGE_FILE: './.coverage' | |
| # code coverage job for windows | |
| code-cov-windows: | |
| name: code-coverage | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [windows-latest] | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.12 | |
| - name: Cache files | |
| uses: actions/cache@v4 | |
| id: cache | |
| with: | |
| path: | | |
| ${{ github.workspace }}\ollama_models\* | |
| ${{ github.workspace }}\venv\* | |
| key: ${{ runner.os }}-pip-code-cov | |
| - name: Install dependencies | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| working-directory: ${{ github.workspace }} | |
| run: | | |
| python3 -m venv venv | |
| venv\Scripts\activate | |
| pip install --upgrade pip | |
| pip3 install -r requirements.txt | |
| curl -L https://ollama.com/download/ollama-windows-amd64.zip -o ollama-windows-amd64.zip | |
| tar -xzf .\ollama-windows-amd64.zip | |
| mkdir ${{ github.workspace }}\ollama_models | |
| set OLLAMA_MODELS=${{ github.workspace }}\ollama_models | |
| start ollama serve | |
| sleep 10 | |
| cmd /k ollama pull llama3.2 | |
| - name: Reading cached Ollama models | |
| working-directory: ${{ github.workspace }} | |
| run: | | |
| echo "Cache Hit Status - ${{ steps.cache.outputs.cache-hit }}" | |
| venv\Scripts\activate | |
| curl -L https://ollama.com/download/ollama-windows-amd64.zip -o ollama-windows-amd64.zip | |
| tar -xzf .\ollama-windows-amd64.zip | |
| set OLLAMA_MODELS=${{ github.workspace }}\ollama_models | |
| start ollama serve | |
| sleep 10 | |
| cmd /k ollama list | |
| - name: Run tests with coverage | |
| working-directory: ${{ github.workspace }} | |
| run: | | |
| venv\Scripts\activate | |
| coverage run --include=aiagents4pharma/talk2knowledgegraphs/* -m pytest --cache-clear aiagents4pharma/talk2knowledgegraphs/tests/ | |
| - name: Check coverage | |
| working-directory: ${{ github.workspace }} | |
| run: | | |
| venv\Scripts\activate | |
| coverage report -m | |
| # $TOTAL_COVERAGE=(& coverage report -m | Select-Object -Last 1) -replace "[^\d]" # Extract the last line and remove non-numeric characters | |
| $TOTAL_COVERAGE=(& coverage report -m | Select-Object -Last 1) | |
| # split and extract the last element | |
| $TOTAL_COVERAGE=($TOTAL_COVERAGE -split " ")[-1] | |
| # remove non-numeric characters | |
| $TOTAL_COVERAGE=($TOTAL_COVERAGE -replace "[^\d]") | |
| # convert to int | |
| $TOTAL_COVERAGE=[int]$TOTAL_COVERAGE | |
| echo "Total coverage: $TOTAL_COVERAGE" | |
| if ($TOTAL_COVERAGE -ne 100) { | |
| Write-Host "Code coverage is not 100%. Please check the coverage report." | |
| exit 1 | |
| } | |
| env: | |
| COVERAGE_FILE: './.coverage' |