Modified the LIONESS R code to disallow PANDA inference unless either a PPI or motif are provided #692
Workflow file for this run
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| # This workflow uses actions that are not certified by GitHub. | |
| # They are provided by a third-party and are governed by | |
| # separate terms of service, privacy policy, and support | |
| # documentation. | |
| # | |
| # See https://github.com/r-lib/actions/tree/master/examples#readme for | |
| # additional example workflows available for the R community. | |
| name: netZooR | |
| env: | |
| ACTIONS_ALLOW_UNSECURE_COMMANDS: 'true' | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - devel | |
| pull_request: | |
| branches: | |
| - master | |
| - devel | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| timeout-minutes: 300 | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest] | |
| r-version: [4.3] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| - uses: r-lib/actions/setup-pandoc@v2.9.0 | |
| - name: Set up R ${{ matrix.r-version }} | |
| uses: r-lib/actions/setup-r@v2.9.0 | |
| with: | |
| r-version: ${{ matrix.r-version }} | |
| - name: install dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2.9.0 | |
| with: | |
| cache-version: 2 | |
| extra-packages: | | |
| any::reticulate | |
| any::rcmdcheck | |
| any::covr | |
| needs: | | |
| website | |
| coverage | |
| - name: Install blas/lapack | |
| run: | | |
| La_library() | |
| extSoftVersion()["BLAS"] | |
| shell: Rscript {0} | |
| - if: matrix.os == 'ubuntu-latest' | |
| run: | | |
| sudo apt-get install python3-venv | |
| pip install --upgrade pip | |
| python3 -m venv env | |
| source env/bin/activate | |
| echo "VIRTUAL ENV:" $VIRTUAL_ENV | |
| - name: Install reticulate | |
| run: | | |
| library("reticulate") | |
| py_config() | |
| py_install("numpy") | |
| py_install("scipy") | |
| py_install("pandas") | |
| py_install("joblib") | |
| shell: Rscript {0} | |
| - name: Check | |
| uses: r-lib/actions/check-r-package@v2.9.0 | |
| with: | |
| args: 'c("--no-manual", "--ignore-vignettes")' | |
| build_args: 'c("--no-build-vignettes")' | |
| error-on: '"error"' | |
| - name: Report coverage | |
| run: | | |
| covr::codecov() | |
| shell: Rscript {0} |