Diff: dev vs main

.github/workflows/R-CMD-check.yaml

@@ -2,9 +2,10 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, dev]
+    branches: [main, dev, devex]
   pull_request:
-    branches: [main, dev]
+    branches: [main, dev, devex]
+  workflow_dispatch:
 
 name: R-CMD-check
 

.github/workflows/test-coverage.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, dev]
+    branches: [main, dev, devex]
   pull_request:
-    branches: [main, dev]
+    branches: [main, dev, devex]
   workflow_dispatch:
 
 name: test-coverage
@@ -15,7 +15,6 @@ jobs:
     env:
       RENV_PROFILE: "full"
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
       RENV_CONFIG_SANDBOX_ENABLED: false
 
     steps:
@@ -39,21 +38,28 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          packages: any::covr
+          packages: any::covr any::xml2
           needs: coverage 
-
-      - name: Install clinsight
-        shell: bash
-        run: R CMD INSTALL --preclean .
 
       - name: Test coverage
-        run: covr::codecov(
-           quiet = FALSE,
-           clean = FALSE,
-           install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package"),
-           token = Sys.getenv("CODECOV_TOKEN")
-           )
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          print(cov)
+          covr::to_cobertura(cov)
         shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v5
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          files: ./cobertura.xml
+          plugins: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
 
       - name: Show testthat output
         if: always()

.gitignore

@@ -2,6 +2,7 @@
 .Rhistory
 .RData
 .Ruserdata
+.Renviron
 *.html
 *.tmp
 ~$*

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: clinsight
 Title: ClinSight
-Version: 0.1.1
+Version: 0.1.1.9011
 Authors@R: c(
     person("Leonard Daniël", "Samson", , "lsamson@gcp-service.com", role = c("cre", "aut"),
            comment = c(ORCID = "0000-0002-6252-7639")),

NAMESPACE

@@ -2,6 +2,7 @@
 
 S3method(create_table,adverse_events)
 S3method(create_table,bm_cytology)
+S3method(create_table,common_forms)
 S3method(create_table,conc_procedures)
 S3method(create_table,continuous)
 S3method(create_table,default)
@@ -26,7 +27,6 @@ export(datatable_custom)
 export(date_cols_to_char)
 export(db_create)
 export(db_get_query)
-export(db_get_review)
 export(db_save)
 export(db_save_review)
 export(db_slice_rows)

NEWS.md

@@ -1,3 +1,20 @@
+# clinsight (development version)
+
+## Changed 
+
+- Generalized `merge_meta_with_data()` to allow user-defined processing functions.
+- Added a feature where, in applicable tables, a user can navigate to a form by double-clicking a table row.
+- Fixed warnings in `apply_edc_specific_changes` due to the use of a vector within `dplyr::select`.
+- Gave users ability to re-organized the column order in any table.
+- Added form type as a class to be used in `create_table()` to display tables.
+- Add a logging table to the DB for reviews.
+- Simplify pulling data from DB for reviews.
+- Review data by records IDs instead of subject & form
+
+## Bug fixes
+
+- The test-coverage GHA workflow is updated so that codecov uploads work again.
+
 # clinsight 0.1.1
 
 ## Changed 

R/app_server.R

@@ -58,7 +58,7 @@ app_server <- function(
   )
   # think of using the pool package, but functions such as row_update are not yet supported.
   r <- reactiveValues(
-    review_data       = db_slice_rows(user_db, db_table = "all_review_data"),
+    review_data       = db_get_table(user_db, db_table = "all_review_data"),
     query_data        = collect_query_data(user_db),
     filtered_subjects = app_vars$subject_id,
     filtered_data     = app_data,