Fixed issues with conda environments not building successfully #3
Workflow file for this run
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| # Run Tests | |
| name: Aviary Tests | |
| on: | |
| # Trigger on push or pull request events for the main branch | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| pre_commit: | |
| if: github.repository_owner == 'OpenMDAO' | |
| # run pre-commit checks | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v3 | |
| with: | |
| python-version: '3.11' | |
| - uses: pre-commit/[email protected] | |
| test_ubuntu: | |
| if: github.repository_owner == 'OpenMDAO' | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 90 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| # oldest versions of openmdao/dymos | |
| - NAME: oldest | |
| PY: '3.9' | |
| NUMPY: '1.20' | |
| SCIPY: '1.6' | |
| PYOPTSPARSE: 'v2.9.1' | |
| SNOPT: '7.7' | |
| OPENMDAO: '3.27' | |
| DYMOS: '1.8.0' | |
| extend: 0 | |
| # development versions of openmdao/dymos | |
| - NAME: dev | |
| PY: 3 | |
| NUMPY: 1 | |
| SCIPY: 1 | |
| PYOPTSPARSE: 'v2.9.1' | |
| SNOPT: '7.7' | |
| OPENMDAO: 'dev' | |
| DYMOS: 'dev' | |
| extend: 1 | |
| # latest versions of openmdao/dymos | |
| - NAME: latest | |
| PY: '3.10' | |
| NUMPY: 1 | |
| SCIPY: 1 | |
| PYOPTSPARSE: 'v2.9.1' | |
| SNOPT: '7.7' | |
| OPENMDAO: 'latest' | |
| DYMOS: 'latest' | |
| extend: 0 | |
| steps: | |
| - name: Display run details | |
| run: | | |
| echo "=============================================================" | |
| echo "Run #${GITHUB_RUN_NUMBER}" | |
| echo "Run ID: ${GITHUB_RUN_ID}" | |
| echo "Testing: ${GITHUB_REPOSITORY}" | |
| echo "Triggered by: ${GITHUB_EVENT_NAME}" | |
| echo "Initiated by: ${GITHUB_ACTOR}" | |
| echo "=============================================================" | |
| - name: Create SSH key | |
| shell: bash | |
| env: | |
| SSH_PRIVATE_KEY: ${{secrets.SSH_PRIVATE_KEY}} | |
| SSH_KNOWN_HOSTS: ${{secrets.SSH_KNOWN_HOSTS}} | |
| run: | | |
| mkdir -p ~/.ssh/ | |
| echo "$SSH_PRIVATE_KEY" > ~/.ssh/id_rsa | |
| sudo chmod 600 ~/.ssh/id_rsa | |
| echo "$SSH_KNOWN_HOSTS" > ~/.ssh/known_hosts | |
| - name: Setup miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.PY }} | |
| - name: Install dependencies | |
| shell: bash -l {0} | |
| run: | | |
| echo "=============================================================" | |
| echo "Install dependencies" | |
| echo "=============================================================" | |
| conda install numpy=${{ matrix.NUMPY }} scipy=${{ matrix.SCIPY }} -q -y | |
| conda install matplotlib pandas panel hvplot -q -y | |
| pip install testflo pyxdsm -q | |
| - name: Install pyOptSparse | |
| if: matrix.PYOPTSPARSE | |
| shell: bash -l {0} | |
| run: | | |
| echo "=============================================================" | |
| echo "Install pyoptsparse" | |
| echo "=============================================================" | |
| if [[ "${{ matrix.SNOPT }}" == "7.7" && "${{ secrets.SNOPT_LOCATION_77 }}" ]]; then | |
| mkdir SNOPT | |
| echo " > Secure copying SNOPT 7.7 over SSH" | |
| scp -qr ${{ secrets.SNOPT_LOCATION_77 }} SNOPT | |
| SNOPT="-s SNOPT/src" | |
| elif [[ "${{ matrix.SNOPT }}" ]]; then | |
| echo "SNOPT version ${{ matrix.SNOPT }} was requested but source is not available" | |
| fi | |
| conda config --add channels conda-forge | |
| pip install git+https://github.com/OpenMDAO/build_pyoptsparse | |
| build_pyoptsparse -v -b ${{ matrix.PYOPTSPARSE }} $SNOPT | |
| - name: Install TeX Live | |
| shell: bash | |
| run: | | |
| echo "=============================================================" | |
| echo "Install TeX Live (for pyXDSM)" | |
| echo "=============================================================" | |
| sudo apt-get update | |
| sudo apt-get install texlive-pictures texlive-latex-extra -y | |
| - name: Install OpenMDAO | |
| if: matrix.OPENMDAO | |
| shell: bash -l {0} | |
| run: | | |
| echo "=============================================================" | |
| echo "Install OpenMDAO" | |
| echo "=============================================================" | |
| if [[ "${{ matrix.OPENMDAO }}" == "dev" ]]; then | |
| pip install git+https://github.com/OpenMDAO/OpenMDAO | |
| elif [[ "${{ matrix.OPENMDAO }}" == "latest" ]]; then | |
| pip install openmdao | |
| else | |
| pip install openmdao==${{ matrix.OPENMDAO }} | |
| fi | |
| - name: Install Dymos | |
| if: matrix.DYMOS | |
| shell: bash -l {0} | |
| run: | | |
| echo "=============================================================" | |
| echo "Install Dymos" | |
| echo "=============================================================" | |
| if [[ "${{ matrix.DYMOS }}" == "dev" ]]; then | |
| pip install git+https://github.com/OpenMDAO/Dymos | |
| elif [[ "${{ matrix.DYMOS }}" == "latest" ]]; then | |
| pip install dymos | |
| else | |
| pip install dymos==${{ matrix.DYMOS }} | |
| fi | |
| - name: Checkout Aviary | |
| uses: actions/checkout@v2 | |
| - name: Install Aviary | |
| shell: bash -l {0} | |
| run: | | |
| echo "=============================================================" | |
| echo "Install Aviary" | |
| echo "=============================================================" | |
| pip install -e .[all] | |
| - name: Display conda environment info | |
| shell: bash -l {0} | |
| run: | | |
| conda info | |
| conda list | |
| conda env export --name ${{ matrix.NAME }}_env --file ${{ matrix.NAME }}_environment.yml | |
| - name: 'Upload environment artifact' | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: ${{ matrix.NAME }}_environment | |
| path: ${{ matrix.NAME }}_environment.yml | |
| retention-days: 5 | |
| - name: Generate specs | |
| shell: bash -l {0} | |
| run: | | |
| echo "=============================================================" | |
| echo "Generate specs" | |
| echo "=============================================================" | |
| cd aviary/xdsm | |
| python run_all.py | |
| cd ../.. | |
| - name: Run tests | |
| shell: bash -l {0} | |
| run: | | |
| echo "=============================================================" | |
| echo "Run Tests" | |
| echo "=============================================================" | |
| testflo . -n 1 --show_skipped --coverage --coverpkg aviary | |
| - name: Build docs | |
| if: matrix.extend | |
| shell: bash -l {0} | |
| run: | | |
| pip install -U jupyter-book | |
| cd aviary/docs | |
| echo "=============================================================" | |
| echo "Build the docs" | |
| echo "=============================================================" | |
| bash build_book.sh | |
| - name: Display doc build reports | |
| continue-on-error: True | |
| if: matrix.extend | |
| shell: bash -l {0} | |
| run: | | |
| cd $HOME/work/om-Aviary/om-Aviary/aviary/docs | |
| find _build/html/reports/ -type f -name '*.log' \ | |
| -exec echo "#################################################################" \; \ | |
| -exec echo {} \; \ | |
| -exec echo "#################################################################" \; \ | |
| -exec cat {} \; | |
| - name: Publish docs to github.io | |
| if: | | |
| github.event_name == 'push' && github.ref == 'refs/heads/main' && | |
| matrix.extend | |
| shell: bash -l {0} | |
| run: | | |
| echo "=============================================================" | |
| echo "Publishing Docs to github.io" | |
| echo "=============================================================" | |
| pip install ghp-import | |
| cd $HOME/work/om-Aviary/om-Aviary/aviary | |
| ghp-import -n -p -f docs/_build/html | |
| - name: Scan for security issues | |
| if: matrix.extend | |
| shell: bash -l {0} | |
| run: | | |
| python -m pip install bandit | |
| echo "=============================================================" | |
| echo "Run bandit scan for medium/high severity issues" | |
| echo "=============================================================" | |
| cd $GITHUB_WORKSPACE | |
| python -m bandit -r -ll aviary |