Merge branch 'dev' of https://github.com/biometryhub/biometryassist i… #171
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on: | |
push: | |
branches: | |
- main | |
- dev | |
#pull_request: | |
# branches: | |
# - master | |
#schedule: | |
# * is a special character in YAML so we have to quote this string | |
# 3am Pacific = 11am UTC | |
# https://crontab.guru is your friend | |
# - cron: '0 17 * * *' | |
name: test-coverage | |
jobs: | |
test-coverage: | |
runs-on: ubuntu-22.04 | |
env: | |
RSPM: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" | |
vsni_LICENSE: ${{ secrets.vsni_LICENSE }} | |
steps: | |
- uses: actions/checkout@v3 | |
- uses: r-lib/actions/setup-r@v2 | |
- uses: r-lib/actions/setup-pandoc@v2 | |
- name: Set up RSPM | |
run: | | |
echo "options(repos = c(CRAN = 'https://packagemanager.rstudio.com/all/__linux__/focal/latest'))" >> ~/.Rprofile.site | |
echo "options(HTTPUserAgent = sprintf('R/%s R (%s)', getRversion(), paste(getRversion(), R.version['platform'], R.version['arch'], R.version['os'])))" >> ~/.Rprofile.site | |
shell: bash | |
- name: Query dependencies | |
run: | | |
install.packages('remotes') | |
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
shell: Rscript {0} | |
- name: Get R and OS version | |
id: get-version | |
run: | | |
cat("##[set-output name=os-version;]", sessionInfo()$running, "\n", sep = "") | |
cat("##[set-output name=r-version;]", R.Version()$version.string, sep = "") | |
shell: Rscript {0} | |
- name: Cache R packages | |
uses: actions/cache@v3 | |
with: | |
path: ${{ env.R_LIBS_USER }} | |
key: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{ inputs.cache-version }}-${{ hashFiles('.github/depends.Rds') }} | |
restore-keys: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{inputs.cache-version }}- | |
- name: Install dependencies | |
run: | | |
install.packages(c("remotes")) | |
remotes::install_deps(dependencies = TRUE) | |
remotes::install_cran("covr") | |
shell: Rscript {0} | |
- name: Create and populate .Renviron file | |
run: echo vsni_LICENSE="vsni_LICENSE" >> ~/.Renviron | |
# - name: Licence ASreml | |
# run: | | |
# remotes::install_github("") | |
# biometryassist::install_asreml() | |
# shell: Rscript {0} | |
- name: Test coverage | |
run: covr::codecov() | |
shell: Rscript {0} |