Rerunning analyses for vignettes. Regenerating documentation #146
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# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag. | |
# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions | |
on: | |
push: | |
branches: | |
- '**' | |
pull_request: | |
branches: | |
- '**' | |
name: R-CMD-check | |
jobs: | |
R-CMD-check: | |
runs-on: ${{ matrix.config.os }} | |
name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
strategy: | |
fail-fast: false | |
matrix: | |
config: | |
- {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | |
- {os: windows-latest, r: '4.2.3'} | |
- {os: macOS-latest, r: '4.2.3'} | |
- {os: ubuntu-20.04, r: '4.2.3', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | |
env: | |
GITHUB_PAT: ${{ secrets.GH_TOKEN }} | |
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
RSPM: ${{ matrix.config.rspm }} | |
CDM5_ORACLE_CDM_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM_SCHEMA }} | |
CDM5_ORACLE_OHDSI_SCHEMA: ${{ secrets.CDM5_ORACLE_OHDSI_SCHEMA }} | |
CDM5_ORACLE_PASSWORD: ${{ secrets.CDM5_ORACLE_PASSWORD }} | |
CDM5_ORACLE_SERVER: ${{ secrets.CDM5_ORACLE_SERVER }} | |
CDM5_ORACLE_USER: ${{ secrets.CDM5_ORACLE_USER }} | |
CDM5_POSTGRESQL_CDM_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_CDM_SCHEMA }} | |
CDM5_POSTGRESQL_OHDSI_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_OHDSI_SCHEMA }} | |
CDM5_POSTGRESQL_PASSWORD: ${{ secrets.CDM5_POSTGRESQL_PASSWORD }} | |
CDM5_POSTGRESQL_SERVER: ${{ secrets.CDM5_POSTGRESQL_SERVER }} | |
CDM5_POSTGRESQL_USER: ${{ secrets.CDM5_POSTGRESQL_USER }} | |
CDM5_SQL_SERVER_CDM_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_CDM_SCHEMA }} | |
CDM5_SQL_SERVER_OHDSI_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_OHDSI_SCHEMA }} | |
CDM5_SQL_SERVER_PASSWORD: ${{ secrets.CDM5_SQL_SERVER_PASSWORD }} | |
CDM5_SQL_SERVER_SERVER: ${{ secrets.CDM5_SQL_SERVER_SERVER }} | |
CDM5_SQL_SERVER_USER: ${{ secrets.CDM5_SQL_SERVER_USER }} | |
CDM5_REDSHIFT_CDM_SCHEMA: ${{ secrets.CDM5_REDSHIFT_CDM_SCHEMA }} | |
CDM5_REDSHIFT_OHDSI_SCHEMA: ${{ secrets.CDM5_REDSHIFT_OHDSI_SCHEMA }} | |
CDM5_REDSHIFT_PASSWORD: ${{ secrets.CDM5_REDSHIFT_PASSWORD }} | |
CDM5_REDSHIFT_SERVER: ${{ secrets.CDM5_REDSHIFT_SERVER }} | |
CDM5_REDSHIFT_USER: ${{ secrets.CDM5_REDSHIFT_USER }} | |
CDM5_SPARK_USER: ${{ secrets.CDM5_SPARK_USER }} | |
CDM5_SPARK_PASSWORD: ${{ secrets.CDM5_SPARK_PASSWORD }} | |
CDM5_SPARK_CONNECTION_STRING: ${{ secrets.CDM5_SPARK_CONNECTION_STRING }} | |
WEBAPI_TEST_WEBAPI_URL: ${{ secrets.WEBAPI_TEST_WEBAPI_URL }} | |
WEBAPI_TEST_SECURE_WEBAPI_URL: ${{ secrets.WEBAPI_TEST_SECURE_WEBAPI_URL }} | |
WEBAPI_TEST_ADMIN_USER_NAME: ${{ secrets.WEBAPI_TEST_ADMIN_USER_NAME }} | |
WEBAPI_TEST_ADMIN_USER_PASSWORD: ${{ secrets.WEBAPI_TEST_ADMIN_USER_PASSWORD }} | |
steps: | |
- uses: actions/checkout@v3 | |
- uses: r-lib/actions/setup-r@v2 | |
with: | |
r-version: ${{ matrix.config.r }} | |
- uses: r-lib/actions/setup-tinytex@v2 | |
- uses: r-lib/actions/setup-pandoc@v2 | |
- name: Install system requirements | |
if: runner.os == 'Linux' | |
run: | | |
sudo apt-get install -y libssh-dev | |
Rscript -e 'install.packages("remotes")' | |
while read -r cmd | |
do | |
eval sudo $cmd | |
done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') | |
- uses: r-lib/actions/setup-r-dependencies@v2 | |
with: | |
extra-packages: any::rcmdcheck | |
needs: check | |
- uses: r-lib/actions/check-r-package@v2 | |
with: | |
args: 'c("--no-manual", "--as-cran")' | |
build_args: 'c("--compact-vignettes=both")' | |
error-on: '"warning"' | |
check-dir: '"check"' | |
- name: Upload source package | |
if: success() && runner.os == 'macOS' && github.event_name != 'pull_request' && github.ref == 'refs/heads/main' | |
uses: actions/upload-artifact@v2 | |
with: | |
name: package_tarball | |
path: check/*.tar.gz | |
- name: Install covr | |
if: runner.os == 'macOS' | |
run: | | |
install.packages("covr") | |
shell: Rscript {0} | |
- name: Test coverage | |
if: runner.os == 'macOS' | |
run: covr::codecov() | |
shell: Rscript {0} | |
Release: | |
needs: R-CMD-Check | |
runs-on: macOS-latest | |
env: | |
GH_TOKEN: ${{ secrets.GH_TOKEN }} | |
if: ${{ github.event_name != 'pull_request' && github.ref == 'refs/heads/main' }} | |
steps: | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 0 | |
- name: Check if version has increased | |
run: | | |
echo "new_version="$(perl compare_versions --tag) >> $GITHUB_ENV | |
- name: Display new version number | |
if: ${{ env.new_version != '' }} | |
run: | | |
echo "${{ env.new_version }}" | |
- name: Create release | |
if: ${{ env.new_version != '' }} | |
uses: actions/create-release@v1 | |
env: | |
GITHUB_TOKEN: ${{ secrets.GH_TOKEN }} | |
with: | |
tag_name: ${{ env.new_version }} | |
release_name: Release ${{ env.new_version }} | |
body: | | |
See NEWS.md for release notes. | |
draft: false | |
prerelease: false | |
- uses: r-lib/actions/setup-r@v2 | |
if: ${{ env.new_version != '' }} | |
- name: Install drat | |
if: ${{ env.new_version != '' }} | |
run: | | |
install.packages('drat') | |
shell: Rscript {0} | |
- name: Remove any tarballs that already exists | |
if: ${{ env.new_version != '' }} | |
run: | | |
rm -f *.tar.gz | |
- name: Download package tarball | |
if: ${{ env.new_version != '' }} | |
uses: actions/download-artifact@v2 | |
with: | |
name: package_tarball | |
- name: Push to drat | |
if: ${{ env.new_version != '' }} | |
run: | | |
bash deploy.sh | |
- name: Push to BroadSea | |
if: ${{ env.new_version != '' }} | |
run: | | |
curl --data "build=true" -X POST https://registry.hub.docker.com/u/ohdsi/broadsea-methodslibrary/trigger/f0b51cec-4027-4781-9383-4b38b42dd4f5/ | |