Release v0.1.4

.Rbuildignore

@@ -1,4 +1,5 @@
 ^renv$
+^\.[Rr]environ$
 ^renv\.lock$
 ^.*\.Rproj$
 ^\.Rproj\.user$
@@ -18,3 +19,4 @@
 ^doc$
 ^Meta$
 ^AGENTS\.md$
+^CRAN-SUBMISSION$

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

@@ -67,7 +67,6 @@ jobs:
         with:
           extra-packages: |
             any::rcmdcheck
-            github::OHDSI/ROhdsiWebApi
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2

.github/workflows/pkgdown.yaml

@@ -33,7 +33,6 @@ jobs:
         with:
           extra-packages: |
             any::pkgdown
-            github::OHDSI/ROhdsiWebApi
             local::.
           needs: website
 

.github/workflows/test-coverage.yaml

@@ -0,0 +1,64 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, develop]
+  pull_request:
+
+name: test-coverage.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      # Use the CI library for coverage and its test subprocesses.
+      RENV_CONFIG_AUTOLOADER_ENABLED: "false"
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::covr
+            any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        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@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7
+        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: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v7
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

@@ -2,6 +2,8 @@
 .Rhistory
 .RData
 .Ruserdata
+.Renviron
+.renviron
 .positai
 .DS_Store
 # Generated pkgdown site. The published copy is maintained on the gh-pages branch.

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: studyGenerics
 Type: Package
 Title: A Centralised Repository of Tested and Frequently Used Methods for OMOP-CDM Studies
-Version: 0.1.3
+Version: 0.1.4
 Authors@R: c(
     person(
       "Cesar", "Barboza",
@@ -21,12 +21,22 @@ Authors@R: c(
     person(
       "Erasmus MC",
       role = "cph"
+    ),
+    person("Gowtham", "Rao", role = "ctb",
+      comment = "ROhdsiWebApi retrieval helpers"),
+    person("Martijn", "Schuemie", role = "ctb",
+      comment = "ROhdsiWebApi retrieval helpers"),
+    person("Jamie", "Gilbert", role = "ctb",
+      comment = "ROhdsiWebApi retrieval helpers"),
+    person(
+      "Observational Health Data Sciences and Informatics",
+      role = "cph",
+      comment = "Bundled ROhdsiWebApi retrieval helpers (Apache-2.0)"
     )
   )
 Description: Provides generic functions for routine tasks required to run OMOP-CDM studies.
-  In addition to testing these recurring methods, studyGenerics aims to centralise
-  collaboration and speed up the development of these types of projects. The optional
-  ROhdsiWebApi package is available from <https://github.com/OHDSI/ROhdsiWebApi>.
+  In addition to testing these recurring methods, the package aims to centralise
+  collaboration and speed up the development of these types of projects.
 License: Apache License (>= 2)
 Encoding: UTF-8
 LazyData: true
@@ -49,13 +59,16 @@ Suggests:
     desc,
     gert,
     gh,
+    httr (>= 1.3.1),
     jsonvalidate,
     knitr,
+    lubridate,
     omopgenerics,
     purrr,
     rmarkdown,
-    ROhdsiWebApi,    
-    testthat (>= 3.0.0)
+    RJSONIO,
+    rlang,
+    testthat (>= 3.2.0)
 Config/testthat/edition: 3
 URL: https://mi-erasmusmc.github.io/studyGenerics/, https://github.com/mi-erasmusmc/studyGenerics
 VignetteBuilder: knitr

NAMESPACE

@@ -59,7 +59,7 @@ importFrom(stringr,
   str_replace_all,
   str_to_lower
 )
-importFrom(usethis,proj_set)
+importFrom(usethis,proj_get)
 importFrom(zip,
   unzip,
   zip

NEWS.md

@@ -1,3 +1,9 @@
+# studyGenerics 0.1.4
+
+* `pullConceptsAtlas()` now integrates required functions from ROhdsiWebApi in order to submit to CRAN. 
+
+* Dependency on R >= 4.2.0 added to DESCRIPTION.
+
 # studyGenerics 0.1.3
 
 * Initial CRAN release.