Merge pull request #1096 from OHDSI/develop

Release v3.3.0

.github/workflows/R_CMD_check_Hades.yaml

@@ -3,10 +3,11 @@
 on:
   push:
     branches:
-      - '**'
+      - 'develop'
+      - 'main'
   pull_request:
     branches:
-      - '**'
+      - 'main'
 
 name: R-CMD-check
 
@@ -50,6 +51,7 @@ jobs:
       CDM5_SPARK_USER: ${{ secrets.CDM5_SPARK_USER }}
       CDM5_SPARK_PASSWORD: ${{ secrets.CDM5_SPARK_PASSWORD }}
       CDM5_SPARK_CONNECTION_STRING: ${{ secrets.CDM5_SPARK_CONNECTION_STRING }}
+      IS_GITHUB_ACTIONS: true
 
     steps:
       - uses: actions/checkout@v3
@@ -85,27 +87,27 @@ jobs:
           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@v2
+        if: success() && runner.os == 'Windows' && github.event_name != 'pull_request' && github.ref == 'refs/heads/main'
+        uses: actions/upload-artifact@v4
         with:
           name: package_tarball
           path: check/*.tar.gz
 
       - name: Install covr
-        if: runner.os == 'macOS'
+        if: runner.os == 'Windows'
         run: |
           install.packages("covr")
         shell: Rscript {0}
 
       - name: Test coverage
-        if: runner.os == 'macOS'
+        if: runner.os == 'Windows'
         run: covr::codecov()
         shell: Rscript {0}
 
   Release:
     needs: R-CMD-Check
 
-    runs-on: macOS-latest
+    runs-on: windows-latest
 
     env:
       GH_TOKEN: ${{ secrets.GH_TOKEN }}
@@ -156,7 +158,7 @@ jobs:
 
       - name: Download package tarball
         if: ${{ env.new_version != '' }}
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v4.1.7
         with:
           name: package_tarball
 

.github/workflows/R_CMD_check_main_weekly.yaml

@@ -14,7 +14,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest, r: 'release'}
+          - {os: windows-latest, r: 'release'}
 
     env:
       GITHUB_PAT: ${{ secrets.GH_TOKEN }}
@@ -43,6 +43,7 @@ jobs:
       CDM5_SPARK_USER: ${{ secrets.CDM5_SPARK_USER }}
       CDM5_SPARK_PASSWORD: ${{ secrets.CDM5_SPARK_PASSWORD }}
       CDM5_SPARK_CONNECTION_STRING: ${{ secrets.CDM5_SPARK_CONNECTION_STRING }}
+      IS_GITHUB_ACTIONS: true
 
     steps:
       - uses: actions/checkout@v3

.github/workflows/R_CMD_check_sqlite_only.yaml

@@ -0,0 +1,153 @@
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on:
+  push:
+    branches:
+      - '**'
+      - '!develop'
+      - '!main'
+  pull_request:
+    branches:
+      - "**"
+      - '!main'
+      - "!develop"
+
+name: R-CMD-check-sqlite-only
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release'}
+          - {os: macOS-latest, r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GH_TOKEN }}
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      SKIP_DB_TESTS: "TRUE"
+
+    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
+
+      - 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"))')
+
+      - 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"'
+
+      - name: Upload source package
+        if: success() && runner.os == 'macOS' && github.event_name != 'pull_request' && github.ref == 'refs/heads/main'
+        uses: actions/upload-artifact@v4
+        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}
+
+      - name: Remove any tarballs that already exists
+        if: ${{ env.new_version != '' }}
+        run: |
+          rm -f *.tar.gz
+
+      - name: Download package tarball
+        if: ${{ env.new_version != '' }}
+        uses: actions/download-artifact@v4.1.7
+        with:
+          name: package_tarball
+
+      - name: Push to drat
+        if: ${{ env.new_version != '' }}
+        run: |
+          bash deploy.sh
+
+      - name: Push to BroadSea
+        if: ${{ env.new_version != '' }}
+        run: |
+          curl --data "build=true" -X POST https://registry.hub.docker.com/u/ohdsi/broadsea-methodslibrary/trigger/f0b51cec-4027-4781-9383-4b38b42dd4f5/

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: CohortDiagnostics
 Type: Package
 Title: Diagnostics for OHDSI Cohorts
-Version: 3.2.5
-Date: 2023-29-11
+Version: 3.3.0
+Date: 2024-22-10
 Authors@R: c(
     person("Jamie", "Gilbert", email = "gilbert@ohdsi.org", role = c("aut", "cre")),
     person("Gowtham", "Rao", role = c("aut")),
@@ -20,50 +20,45 @@ Description: CohortDiagnostics is an R utility package for the development and e
     Through the identification of errors, CohortDiagnostics enables the comparison of multiple candidate cohort
     definitions across one or more data sources, facilitating reproducible research.
 Depends:
-	DatabaseConnector (>= 5.0.0),
-	FeatureExtraction (>= 3.2.0),
-	R (>= 4.1.0)
+    DatabaseConnector (>= 5.0.0),
+    FeatureExtraction (>= 3.7.1),
+    R (>= 4.1.0)
 Imports:
-  Andromeda (>= 0.6.0),
-  ResultModelManager (>= 0.5.2),
-  checkmate,
-  clock,
-  digest,
-  dplyr (>= 1.0.0),
-  methods,
-  ParallelLogger (>= 3.0.0),
-  readr (>= 2.1.0),
-  RJSONIO,
-  rlang,
-  SqlRender (>= 1.9.0),
-  stringr,
-  tidyr (>= 1.2.0),
-  CohortGenerator (>= 0.8.0),
-  remotes
+    Andromeda (>= 0.6.0),
+    ResultModelManager (>= 0.5.2),
+    checkmate,
+    clock,
+    digest,
+    dplyr (>= 1.0.0),
+    methods,
+    ParallelLogger (>= 3.0.0),
+    readr (>= 2.1.0),
+    RJSONIO,
+    rlang,
+    SqlRender (>= 1.9.0),
+    stringr,
+    tidyr (>= 1.2.0),
+    CohortGenerator (>= 0.10.0),
+    remotes,
+    scales
 Suggests:
-  Eunomia,
-  ROhdsiWebApi (>= 1.2.0),
-  RSQLite (>= 2.2.1),
-  scales,
-  testthat,
-  withr,
-  zip,
-  knitr,
-  shiny,
-  OhdsiShinyModules
+    Eunomia,
+    RSQLite (>= 2.2.1),
+    testthat,
+    withr,
+    zip,
+    knitr,
+    shiny,
+    OhdsiShinyModules,
+    rsconnect,
+    yaml
 Remotes:
-  ohdsi/Eunomia,
-  ohdsi/FeatureExtraction,
-  ohdsi/ResultModelManager,
-  ohdsi/ROhdsiWebApi,
-  ohdsi/CirceR,
-  ohdsi/CohortGenerator,
   ohdsi/OhdsiShinyModules
 License: Apache License
 VignetteBuilder: knitr
 URL: https://ohdsi.github.io/CohortDiagnostics, https://github.com/OHDSI/CohortDiagnostics
 BugReports: https://github.com/OHDSI/CohortDiagnostics/issues
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Encoding: UTF-8
 Language: en-US
 StagedInstall: no

NAMESPACE

@@ -3,6 +3,7 @@
 export(createDiagnosticsExplorerZip)
 export(createMergedResultsFile)
 export(createResultsDataModel)
+export(deployPositConnectApp)
 export(executeDiagnostics)
 export(getCdmDataSourceInformation)
 export(getCohortCounts)

NEWS.md

@@ -1,3 +1,17 @@
+CohortDiagnostics 3.3.0
+=======================
+
+Changes:
+
+1. Added function to make deployment to posit connect servers easier
+
+2. Added ability to use CohortGenerator sample functionality to executeDiagnostics which speeds up execution for very
+large cohort definitions
+
+3. Requires use of FeatureExtraction 3.4.0 to support new API
+
+4. Removed annotation tables from result schema script
+
 CohortDiagnostics 3.2.5
 =======================
 Bug Fixes: