Workflow file (#24)

* Compute risk window in permanent tables (#19)

* Changes to store computed risk windows and intermediate reults in non-temporary table for later or additional processing.

* Fixed doc errors

* Moved computation of stats to new function

* Day diff no longer +1

* Day diff no longer +1

* Missing doc file

* Standardised output columns

* modified how results are exported

* Sql Bug fix

* Table name bug fix

* Including exposure start date in risk windows because it is not always the same as the risk window start.

* Incorrect exposure schema computing risk windows

* removed check on building manuals

* Added Eunomia from remotes

* Updated build script

* Fixed dev tools test helper

* Support use of Eunomia, new oracel temp schema, sql server fix

* Docs updated

* Docs updated

* Docs updated

* removed unused code, tidy of docs

* Improved tests, fixed failing code and added tests on redshift with default sqlite testing

- Allow calls to run with a DatabaseConnector `connection` object
- No longer supports undocumented use of `connectionDetails$conn` for storing connections
  when calling `runSelfControlledCohort`
  - Added tests on sqlite for faster unit testing while working on development
- Added tests on redshift dbms

* pull request template

* Batch read with DatabaseConnector::renderTranslateQueryApplyBatched (#20)

* Handling of query processes in batches

* Copyright year and date in DESCRIPTION. Re-added usage doc

* Package html documentation

* Added example on risk windows to docsumentation

* Fix hades logo

* Improved test coverage for scc risk window stats functions

* Create R_CMD_check_main_weekly.yaml (#23)

.github/workflows/R_CMD_check_main_weekly.yaml

@@ -0,0 +1,72 @@
+on:
+  schedule:
+    - cron: '0 10 * * 6'
+
+name: 'R check'
+
+jobs:
+  R-CMD-check-main:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest, r: 'release'}
+
+    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
+
+      - 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"'