Update bess_base.py #442
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| name: Code Coverage | |
| on: | |
| push: | |
| paths: | |
| - "python/**" | |
| - "R-package/**" | |
| - "src/**" | |
| - ".github/workflows/code_coverage.yml" | |
| - "!R-package/.gitignore" | |
| - "!R-package/README.md" | |
| - "!R-package/LICENSE" | |
| - "!R-package/cran-comments.md" | |
| - "!R-package/pre-release.R" | |
| - "!R-package/data-raw/**" | |
| - "!python/.gitignore" | |
| - "!python/README.rst" | |
| - "!python/LICENSE" | |
| pull_request: | |
| paths: | |
| - "python/**" | |
| - "R-package/**" | |
| - "src/**" | |
| - ".github/workflows/code_coverage.yml" | |
| - "!R-package/.gitignore" | |
| - "!R-package/README.md" | |
| - "!R-package/LICENSE" | |
| - "!R-package/cran-comments.md" | |
| - "!R-package/pre-release.R" | |
| - "!R-package/data-raw/**" | |
| - "!python/.gitignore" | |
| - "!python/README.rst" | |
| - "!python/LICENSE" | |
| workflow_dispatch: | |
| jobs: | |
| codecovPy: | |
| name: Codecov workflow for Python-package | |
| runs-on: ubuntu-latest | |
| env: | |
| PYTHON: "3.9" | |
| steps: | |
| - uses: actions/checkout@master | |
| - name: Setup Python | |
| uses: actions/setup-python@master | |
| with: | |
| python-version: 3.9 | |
| - name: Install abess & dependencies | |
| run: | | |
| pip install "pandas<2.0.0" | |
| pip install lifelines | |
| pip install pybind11[global] | |
| # pip install codecov | |
| # pip install gcovr | |
| # export CFLAGS="--coverage" | |
| cd python | |
| pip install . | |
| ls * -al | |
| - name: Generate coverage report | |
| run: | | |
| pip install pytest | |
| pip install pytest-cov | |
| cd ./python/pytest | |
| pytest --cov=abess -v --cov-report=xml | |
| # gcovr ./python/src/ --xml | |
| ls * -al | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v2 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| files: ./python/pytest/coverage.xml | |
| fail_ci_if_error: true | |
| flags: Python | |
| verbose: true | |
| codecovR: | |
| name: Codecov for R-package | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| - uses: r-lib/actions/setup-pandoc@v1 | |
| - name: Ubuntu dependencies | |
| run: | | |
| sudo apt-get install libomp5 | |
| sudo apt-get install libomp-dev | |
| sudo apt-get install libxml2-dev | |
| sudo apt-get install libcurl4-openssl-dev | |
| sudo apt-get install python3 | |
| sudo apt-get install python3-pip | |
| - name: Query dependencies | |
| run: | | |
| install.packages('remotes') | |
| saveRDS(remotes::dev_package_deps("R-package", dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | |
| shell: Rscript {0} | |
| - name: Install dependencies | |
| run: | | |
| remotes::install_deps("R-package", dependencies = TRUE) | |
| install.packages("covr") | |
| install.packages("xml2") | |
| shell: Rscript {0} | |
| - name: Install package | |
| run: R CMD INSTALL R-package | |
| - name: Generate coverage report | |
| run: | | |
| Rscript -e 'library(covr); x <- package_coverage(path = "./R-package", quiet = FALSE, type = c("tests"), function_exclusions = "\\.onUnload"); to_cobertura(x, "rpackage.xml")' | |
| - name: Upload coverage report | |
| run: | | |
| pip install --upgrade pip | |
| pip3 install --user codecov | |
| codecov -F rpackage -f rpackage.xml |