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code coverage

code coverage #226

Workflow file for this run

name: code coverage
on:
push:
branches:
- 'suite'
- 'suite_dev'
# pull_request:
# types: closed
# branches: [ "main" ]
schedule:
- cron: '16 20 * * 2'
jobs:
test-coverage:
name: Code coverage
runs-on: ubuntu-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
- name: Checkout repo for workflow access
uses: actions/checkout@v4
- name: Set up R environment
uses: r-lib/actions/setup-r@v2
with:
use-public-rspm: true
- name: Set up dependencies (general)
uses: r-lib/actions/setup-r-dependencies@v2
env:
_R_CHECK_FORCE_SUGGESTS: false
_R_CHECK_RD_XREFS: false
with:
dependencies: '"hard"' # do not use suggested dependencies
install-pandoc: false
extra-packages: |
any::rcmdcheck
any::testthat
any::rlang
any::R.utils
any::covr
any::remotes
any::hdf5r
github::drieslab/GiottoData
needs: coverage
- name: Generate coverage report
run: |
covr::codecov(
quiet = FALSE,
clean = FALSE,
install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
)
shell: Rscript {0}
- name: Upload coverage reports to Codecov
uses: codecov/codecov-action@v3
with:
token: e6770448-c694-49d7-b83f-b6cb21c0e7ad
fail_ci_if_error: false
flags: unittests
verbose: true