Update README.md #875
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| # The purpose of this action is to calculate the code coverage and add the results on codecov.io | |
| # codecov.io provides a badge showing the current coverage and generates coverage reports for each pull requests. | |
| # | |
| # 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 | |
| on: | |
| push: | |
| branches: [main, master] | |
| pull_request: | |
| branches: [main, master] | |
| name: test-coverage | |
| jobs: | |
| test-coverage: | |
| runs-on: self-hosted # ubuntu-22.04 | |
| env: | |
| GITHUB_PAT: ${{ secrets.TOKEN }} | |
| CIBERSORTX_EMAIL: ${{ secrets.CIBERSORTX_EMAIL }} | |
| CIBERSORTX_TOKEN: ${{ secrets.CIBERSORTX_TOKEN }} | |
| CODECOV_TOKEN: ${{secrets.CODECOV_TOKEN}} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Update system dependencies | |
| # due to recent versions of GLIBC missing | |
| run: | | |
| sudo apt-get update && sudo apt-get install cmake libstdc++6 \ | |
| libcurl4-openssl-dev libssl-dev libxml2-dev libfontconfig1-dev \ | |
| libharfbuzz-dev libfribidi-dev \ | |
| libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev -y | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - name: Install pak | |
| run: Rscript -e "install.packages('pak', repos='https://cran.rstudio.com/')" | |
| # - name: Install SpatialExperiment | |
| # run: Rscript -e "pak::pkg_install('drighelli/SpatialExperiment')" | |
| - name: Install Devtools | |
| run: Rscript -e "pak::pkg_install('devtools')" | |
| - name: Install SpatialExperiment | |
| run: Rscript -e "devtools::install_github('drighelli/SpatialExperiment')" | |
| - name: Install Immunedeconv | |
| run: Rscript -e "pak::pkg_install('omnideconv/immunedeconv')" | |
| - name: Install Omnideconv | |
| run: Rscript -e "pak::pkg_install('omnideconv/omnideconv')" | |
| - name: Install OmnipathR | |
| run: Rscript -e "pak::pkg_install('OmnipathR')" | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| dependencies: '"hard"' # do not install suggests | |
| extra-packages: any::covr, any::devtools | |
| needs: coverage | |
| - name: Test coverage | |
| run: covr::codecov(quiet = FALSE) | |
| shell: Rscript {0} |