Update GA

.github/workflows/R_CMD_check_Hades.yaml

@@ -20,29 +20,49 @@ 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 }}
+ CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
  R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
  RSPM: ${{ matrix.config.rspm }}
- CDM5_ORACLE_CDM_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM_SCHEMA }}
+ CDM5_ORACLE_CDM54_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM54_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_CDM54_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_CDM54_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_CDM54_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_CDM54_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_CDM54_SCHEMA: ${{ secrets.CDM5_REDSHIFT_CDM54_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 }}
+ CDM_SNOWFLAKE_CDM53_SCHEMA: ${{ secrets.CDM_SNOWFLAKE_CDM53_SCHEMA }}
+ CDM_SNOWFLAKE_OHDSI_SCHEMA: ${{ secrets.CDM_SNOWFLAKE_OHDSI_SCHEMA }}
+ CDM_SNOWFLAKE_PASSWORD: ${{ secrets.CDM_SNOWFLAKE_PASSWORD }}
+ CDM_SNOWFLAKE_CONNECTION_STRING: ${{ secrets.CDM_SNOWFLAKE_CONNECTION_STRING }}
+ CDM_SNOWFLAKE_USER: ${{ secrets.CDM_SNOWFLAKE_USER }} 
+ CDM5_SPARK_USER: ${{ secrets.CDM5_SPARK_USER }}
+ CDM5_SPARK_PASSWORD: ${{ secrets.CDM5_SPARK_PASSWORD }}
+ CDM5_SPARK_CONNECTION_STRING: ${{ secrets.CDM5_SPARK_CONNECTION_STRING }}
+ CDM5_SPARK_CDM_SCHEMA: ${{ secrets.CDM5_SPARK_CDM_SCHEMA }}
+ CDM5_SPARK_OHDSI_SCHEMA: ${{ secrets.CDM5_SPARK_OHDSI_SCHEMA }}
+ CDM_BIG_QUERY_CONNECTION_STRING: ${{ secrets.CDM_BIG_QUERY_CONNECTION_STRING }}
+ CDM_BIG_QUERY_KEY_FILE: ${{ secrets.CDM_BIG_QUERY_KEY_FILE }}
+ CDM_BIG_QUERY_CDM_SCHEMA: ${{ secrets.CDM_BIG_QUERY_CDM_SCHEMA }}
+ CDM_BIG_QUERY_OHDSI_SCHEMA: ${{ secrets.CDM_BIG_QUERY_OHDSI_SCHEMA }}
 
  steps:
  - uses: actions/checkout@v3
@@ -55,111 +75,109 @@ 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@v3
- 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@v3
+ - 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")'
+ 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@v3
+ 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}
-
- - uses: actions/checkout@v3
- with:
- fetch-depth: 0 
 
  - name: Remove any tarballs that already exists
+ if: ${{ env.new_version != '' }}
  run: |
  rm -f *.tar.gz
- 
+
  - name: Download package tarball
- uses: actions/download-artifact@v3
+ if: ${{ env.new_version != '' }}
+ uses: actions/download-artifact@v2
  with:
- name: package_tarball 
-
- - name: Tag and push to drat and BroadSea
+ name: package_tarball
+
+ - name: Push to drat
+ if: ${{ env.new_version != '' }}
+ run: |
+ bash deploy.sh
+
+ - name: Push to BroadSea
+ if: ${{ env.new_version != '' }}
  run: |
- perl compare_versions --tag && \
- bash deploy.sh && \
  curl --data "build=true" -X POST https://registry.hub.docker.com/u/ohdsi/broadsea-methodslibrary/trigger/f0b51cec-4027-4781-9383-4b38b42dd4f5/
-