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update GH actions
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msuchard committed Oct 30, 2023
1 parent 773c56c commit 6141974
Showing 1 changed file with 35 additions and 52 deletions.
87 changes: 35 additions & 52 deletions .github/workflows/R_CMD_check_Hades.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -20,12 +20,12 @@ jobs:
fail-fast: false
matrix:
config:
- {os: windows-latest, r: 'release'} # Does not appear to have Java 32-bit, hence the --no-multiarch
- {os: windows-latest, r: 'release'}
- {os: macOS-latest, r: 'release'}
- {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
# - {os: ubuntu-20.04, r: 'devel', 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 }}
Expand All @@ -43,6 +43,18 @@ jobs:
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
Expand All @@ -55,63 +67,27 @@ jobs:

- uses: r-lib/actions/setup-pandoc@v2

- name: Query dependencies
run: |
install.packages('remotes')
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
shell: Rscript {0}

- name: Cache R packages
if: runner.os != 'Windows'
uses: actions/cache@v2
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-

- name: Install system dependencies
- 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"))')
- name: Install libssh
if: runner.os == 'Linux'
run: |
sudo apt-get install libssh-dev
- name: Install dependencies
run: |
remotes::install_deps(dependencies = TRUE, INSTALL_opts=c("--no-multiarch"))
remotes::install_cran("rcmdcheck")
shell: Rscript {0}

- name: Install covr
if: runner.os == 'macOS'
run: |
remotes::install_cran("covr")
shell: Rscript {0}

- name: Remove check folder if exists
if: runner.os == 'macOS'
run: unlink("check", recursive = TRUE)
shell: Rscript {0}

- name: Check
env:
_R_CHECK_CRAN_INCOMING_REMOTE_: false
run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--no-multiarch"), error_on = "warning", check_dir = "check")
shell: Rscript {0}
- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: any::rcmdcheck
needs: check

- name: Upload check results
if: failure()
uses: actions/upload-artifact@v2
- uses: r-lib/actions/check-r-package@v2
with:
name: ${{ runner.os }}-r${{ matrix.config.r }}-results
path: check
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'
Expand All @@ -120,6 +96,12 @@ jobs:
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()
Expand All @@ -137,7 +119,7 @@ jobs:

steps:

- uses: actions/checkout@v2
- uses: actions/checkout@v3
with:
fetch-depth: 0

Expand All @@ -163,7 +145,7 @@ jobs:
draft: false
prerelease: false

- uses: r-lib/actions/setup-r@v1
- uses: r-lib/actions/setup-r@v2
if: ${{ env.new_version != '' }}

- name: Install drat
Expand Down Expand Up @@ -192,3 +174,4 @@ jobs:
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/

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