Merge pull request #174 from davidycliao/dependabot/pip/contourpy-1.3.0 #1131
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| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | |
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | |
| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | |
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | |
| name: R-Python Integration and Test Coverage | |
| on: [push, pull_request] | |
| jobs: | |
| build-and-test: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v2 | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: '4.3.2' | |
| - name: Install R dependencies and Restore R environment | |
| run: | | |
| install.packages('renv') | |
| renv::restore() | |
| renv::install('covr') | |
| shell: Rscript {0} | |
| - name: Install testthat package | |
| run: Rscript -e 'install.packages("testthat")' | |
| shell: Rscript {0} | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.10.x' | |
| - name: Create Python virtual environment using venv | |
| run: python -m venv flair_env | |
| - name: Install Python dependencies in virtual environment | |
| run: | | |
| source flair_env/bin/activate | |
| pip install scipy==1.12.0 | |
| pip install flair | |
| pip install torch | |
| - name: Set Python Path for R reticulate | |
| run: | | |
| echo "RETICULATE_PYTHON=$(pwd)/flair_env/bin/python" >> $GITHUB_ENV | |
| shell: bash | |
| - name: Print RETICULATE_PYTHON value | |
| run: echo "RETICULATE_PYTHON=$RETICULATE_PYTHON" | |
| shell: bash | |
| - name: Check Python virtual environment structure | |
| run: | | |
| ls -l $(pwd)/flair_env/bin | |
| shell: bash | |
| - name: Run R tests with detailed logging | |
| run: | | |
| source flair_env/bin/activate | |
| Rscript -e 'reticulate::use_virtualenv("$(pwd)/flair_env", required = TRUE)' | |
| Rscript -e 'testthat::test_dir("tests/testthat")' | |
| shell: bash | |
| - name: Check renv status (debug step) | |
| run: Rscript -e 'renv::status()' | |
| shell: Rscript {0} | |
| - name: Run Test Coverage | |
| run: | | |
| source flair_env/bin/activate | |
| Rscript -e 'reticulate::use_virtualenv("$(pwd)/flair_env", required = TRUE)' | |
| Rscript -e 'covr::codecov(quiet = FALSE, clean = FALSE, install_path = file.path(Sys.getenv("RUNNER_TEMP"), "flaiR"))' | |
| shell: bash | |
| - name: Show testthat output | |
| if: always() | |
| run: | | |
| find /home/runner/work/_temp/package -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| env: | |
| R_LIBS_USER: /home/runner/work/_temp/Library | |
| TZ: UTC | |
| _R_CHECK_SYSTEM_CLOCK_: FALSE | |
| NOT_CRAN: true | |
| pythonLocation: /opt/hostedtoolcache/Python/3.10.15/x64 | |
| LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.10.15/x64/lib | |
| RETICULATE_PYTHON: /home/runner/work/flaiR/flaiR/flair_env/bin/python | |