CRAN submission changes (#189)

* Add cran-comments.md * Fix CRAN check errors * Additional checks for tests * Address CRAN submission feedback * Regenerate site documentation * Bump upload-artifact * Add CRAN badge & regenerate site documentation
OHDSI · Sep 16, 2024 · bf65599 · bf65599
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -10,3 +10,5 @@ deploy.sh
 docs
 extras
 man-roxygen
+^cran-comments\.md$
+^CRAN-SUBMISSION$
diff --git a/.github/workflows/R_CMD_check_Hades.yaml b/.github/workflows/R_CMD_check_Hades.yaml
@@ -140,14 +140,14 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: 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
+        uses: actions/upload-artifact@v4
         with:
           name: package_tarball
           path: check/*.tar.gz

diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -0,0 +1,3 @@
+Version: 0.11.0
+Date: 2024-09-09 13:18:20 UTC
+SHA: 39c45bae218f8ffd983b9bc9a6a5914ad4f7f9df
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: CohortGenerator
 Type: Package
-Title: An R Package for Cohort Generation Against the OMOP CDM
-Version: 0.11.0
-Date: 2024-08-31
+Title: Cohort Generation for the OMOP Common Data Model
+Version: 0.11.1
+Date: 2024-09-12
 Authors@R: c(
   person("Anthony", "Sena", email = "[email protected]", role = c("aut", "cre")),
   person("Jamie", "Gilbert", role = c("aut")),
@@ -11,7 +11,10 @@ Authors@R: c(
   person("Observational Health Data Science and Informatics", role = c("cph"))
   )
 Maintainer: Anthony Sena <[email protected]>
-Description: An R package for that encapsulates the functions for generating cohorts against the OMOP CDM.
+Description: Generate cohorts and subsets using an Observational 
+  Medical Outcomes Partnership (OMOP) Common Data Model (CDM) Database. 
+  Cohorts are  defined using 'CIRCE' (<https://github.com/ohdsi/circe-be>) or 
+  SQL compatible with 'SqlRender' (<https://github.com/OHDSI/SqlRender>).
 Depends:
   DatabaseConnector (>= 5.0.0),
   R (>= 3.6.0),

diff --git a/README.md b/README.md
@@ -1,6 +1,7 @@
 # CohortGenerator
 
-[![Build Status](https://github.com/OHDSI/CohortGenerator/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/CohortGenerator/actions?query=workflow%3AR-CMD-check) [![codecov.io](https://codecov.io/github/OHDSI/CohortGenerator/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/CohortGenerator?branch=main)
+[![CRAN status](https://www.r-pkg.org/badges/version/CohortGenerator)](https://CRAN.R-project.org/package=CohortGenerator)
+[![Build Status](https://github.com/OHDSI/CohortGenerator/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/CohortGenerator/actions?query=workflow%3AR-CMD-check) [![codecov.io](https://codecov.io/github/OHDSI/CohortGenerator/coverage.svg?branch=main)](https://app.codecov.io/github/OHDSI/CohortGenerator?branch=main)
 
 CohortGenerator is part of [HADES](https://ohdsi.github.io/Hades/).
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -0,0 +1,5 @@
+## R CMD check results
+
+0 errors | 0 warnings | 1 note
+
+* This is a new release.
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/articles/CreatingCohortSubsetDefinitions.html b/docs/articles/CreatingCohortSubsetDefinitions.html
diff --git a/docs/articles/GeneratingCohorts.html b/docs/articles/GeneratingCohorts.html
diff --git a/docs/articles/SamplingCohorts.html b/docs/articles/SamplingCohorts.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/deps/bootstrap-5.3.1/fonts/1Ptug8zYS_SKggPNyC0ITw.woff2 b/docs/deps/bootstrap-5.3.1/fonts/1Ptug8zYS_SKggPNyC0ITw.woff2
diff --git a/docs/deps/bootstrap-5.3.1/fonts/1Ptug8zYS_SKggPNyCAIT5lu.woff2 b/docs/deps/bootstrap-5.3.1/fonts/1Ptug8zYS_SKggPNyCAIT5lu.woff2
diff --git a/docs/deps/bootstrap-5.3.1/fonts/1Ptug8zYS_SKggPNyCIIT5lu.woff2 b/docs/deps/bootstrap-5.3.1/fonts/1Ptug8zYS_SKggPNyCIIT5lu.woff2
diff --git a/docs/deps/bootstrap-5.3.1/fonts/1Ptug8zYS_SKggPNyCMIT5lu.woff2 b/docs/deps/bootstrap-5.3.1/fonts/1Ptug8zYS_SKggPNyCMIT5lu.woff2
diff --git a/docs/deps/bootstrap-5.3.1/fonts/1Ptug8zYS_SKggPNyCkIT5lu.woff2 b/docs/deps/bootstrap-5.3.1/fonts/1Ptug8zYS_SKggPNyCkIT5lu.woff2
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -1,11 +1,11 @@
-pandoc: 3.1.1
+pandoc: 3.1.11
 pkgdown: 2.1.0
 pkgdown_sha: ~
 articles:
   CreatingCohortSubsetDefinitions: CreatingCohortSubsetDefinitions.html
   GeneratingCohorts: GeneratingCohorts.html
   SamplingCohorts: SamplingCohorts.html
-last_built: 2024-09-01T14:46Z
+last_built: 2024-09-16T13:44Z
 urls:
   reference: https://ohdsi.github.io/CohortGenerator/reference
   article: https://ohdsi.github.io/CohortGenerator/articles