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Update bess_base.py #443

Update bess_base.py

Update bess_base.py #443

Workflow file for this run

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