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Merge pull request OHDSI#1096 from OHDSI/develop
Release v3.3.0
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‎.github/workflows/R_CMD_check_Hades.yaml

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

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

‎.github/workflows/R_CMD_check_sqlite_only.yaml

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# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
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# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
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on:
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push:
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branches:
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- '**'
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- '!develop'
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- '!main'
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pull_request:
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branches:
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- "**"
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- '!main'
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- "!develop"
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name: R-CMD-check-sqlite-only
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jobs:
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R-CMD-check:
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.os }} (${{ matrix.config.r }})
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strategy:
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fail-fast: false
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matrix:
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config:
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- {os: windows-latest, r: 'release'}
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- {os: macOS-latest, r: 'release'}
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env:
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GITHUB_PAT: ${{ secrets.GH_TOKEN }}
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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RSPM: ${{ matrix.config.rspm }}
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SKIP_DB_TESTS: "TRUE"
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steps:
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- uses: actions/checkout@v3
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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- uses: r-lib/actions/setup-tinytex@v2
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- uses: r-lib/actions/setup-pandoc@v2
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- name: Install system requirements
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if: runner.os == 'Linux'
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run: |
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sudo apt-get install -y libssh-dev
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Rscript -e 'install.packages("remotes")'
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while read -r cmd
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do
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eval sudo $cmd
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done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::rcmdcheck
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needs: check
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- uses: r-lib/actions/check-r-package@v2
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with:
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args: 'c("--no-manual", "--as-cran")'
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build_args: 'c("--compact-vignettes=both")'
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error-on: '"warning"'
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check-dir: '"check"'
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- name: Upload source package
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if: success() && runner.os == 'macOS' && github.event_name != 'pull_request' && github.ref == 'refs/heads/main'
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uses: actions/upload-artifact@v4
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with:
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name: package_tarball
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path: check/*.tar.gz
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- name: Install covr
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if: runner.os == 'macOS'
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run: |
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install.packages("covr")
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shell: Rscript {0}
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- name: Test coverage
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if: runner.os == 'macOS'
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run: covr::codecov()
85+
shell: Rscript {0}
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Release:
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needs: R-CMD-Check
89+
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runs-on: macOS-latest
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env:
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GH_TOKEN: ${{ secrets.GH_TOKEN }}
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if: ${{ github.event_name != 'pull_request' && github.ref == 'refs/heads/main' }}
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steps:
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- uses: actions/checkout@v3
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with:
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fetch-depth: 0
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- name: Check if version has increased
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run: |
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echo "new_version="$(perl compare_versions --tag) >> $GITHUB_ENV
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- name: Display new version number
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if: ${{ env.new_version != '' }}
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run: |
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echo "${{ env.new_version }}"
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- name: Create release
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if: ${{ env.new_version != '' }}
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uses: actions/create-release@v1
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env:
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GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
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with:
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tag_name: ${{ env.new_version }}
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release_name: Release ${{ env.new_version }}
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body: |
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See NEWS.md for release notes.
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draft: false
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prerelease: false
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- uses: r-lib/actions/setup-r@v2
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if: ${{ env.new_version != '' }}
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- name: Install drat
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if: ${{ env.new_version != '' }}
130+
run: |
131+
install.packages('drat')
132+
shell: Rscript {0}
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- name: Remove any tarballs that already exists
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if: ${{ env.new_version != '' }}
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run: |
137+
rm -f *.tar.gz
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- name: Download package tarball
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if: ${{ env.new_version != '' }}
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uses: actions/download-artifact@v4.1.7
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with:
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name: package_tarball
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- name: Push to drat
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if: ${{ env.new_version != '' }}
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run: |
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bash deploy.sh
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- name: Push to BroadSea
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if: ${{ env.new_version != '' }}
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run: |
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curl --data "build=true" -X POST https://registry.hub.docker.com/u/ohdsi/broadsea-methodslibrary/trigger/f0b51cec-4027-4781-9383-4b38b42dd4f5/

‎DESCRIPTION

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Package: CohortDiagnostics
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Type: Package
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Title: Diagnostics for OHDSI Cohorts
4-
Version: 3.2.5
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Date: 2023-29-11
4+
Version: 3.3.0
5+
Date: 2024-22-10
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Authors@R: c(
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person("Jamie", "Gilbert", email = "gilbert@ohdsi.org", role = c("aut", "cre")),
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person("Gowtham", "Rao", role = c("aut")),
@@ -20,50 +20,45 @@ Description: CohortDiagnostics is an R utility package for the development and e
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Through the identification of errors, CohortDiagnostics enables the comparison of multiple candidate cohort
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definitions across one or more data sources, facilitating reproducible research.
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Depends:
23-
DatabaseConnector (>= 5.0.0),
24-
FeatureExtraction (>= 3.2.0),
25-
R (>= 4.1.0)
23+
DatabaseConnector (>= 5.0.0),
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FeatureExtraction (>= 3.7.1),
25+
R (>= 4.1.0)
2626
Imports:
27-
Andromeda (>= 0.6.0),
28-
ResultModelManager (>= 0.5.2),
29-
checkmate,
30-
clock,
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digest,
32-
dplyr (>= 1.0.0),
33-
methods,
34-
ParallelLogger (>= 3.0.0),
35-
readr (>= 2.1.0),
36-
RJSONIO,
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rlang,
38-
SqlRender (>= 1.9.0),
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stringr,
40-
tidyr (>= 1.2.0),
41-
CohortGenerator (>= 0.8.0),
42-
remotes
27+
Andromeda (>= 0.6.0),
28+
ResultModelManager (>= 0.5.2),
29+
checkmate,
30+
clock,
31+
digest,
32+
dplyr (>= 1.0.0),
33+
methods,
34+
ParallelLogger (>= 3.0.0),
35+
readr (>= 2.1.0),
36+
RJSONIO,
37+
rlang,
38+
SqlRender (>= 1.9.0),
39+
stringr,
40+
tidyr (>= 1.2.0),
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CohortGenerator (>= 0.10.0),
42+
remotes,
43+
scales
4344
Suggests:
44-
Eunomia,
45-
ROhdsiWebApi (>= 1.2.0),
46-
RSQLite (>= 2.2.1),
47-
scales,
48-
testthat,
49-
withr,
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zip,
51-
knitr,
52-
shiny,
53-
OhdsiShinyModules
45+
Eunomia,
46+
RSQLite (>= 2.2.1),
47+
testthat,
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withr,
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zip,
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knitr,
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shiny,
52+
OhdsiShinyModules,
53+
rsconnect,
54+
yaml
5455
Remotes:
55-
ohdsi/Eunomia,
56-
ohdsi/FeatureExtraction,
57-
ohdsi/ResultModelManager,
58-
ohdsi/ROhdsiWebApi,
59-
ohdsi/CirceR,
60-
ohdsi/CohortGenerator,
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ohdsi/OhdsiShinyModules
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License: Apache License
6358
VignetteBuilder: knitr
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URL: https://ohdsi.github.io/CohortDiagnostics, https://github.com/OHDSI/CohortDiagnostics
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BugReports: https://github.com/OHDSI/CohortDiagnostics/issues
66-
RoxygenNote: 7.2.3
61+
RoxygenNote: 7.3.2
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Encoding: UTF-8
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Language: en-US
6964
StagedInstall: no

‎NAMESPACE

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33
export(createDiagnosticsExplorerZip)
44
export(createMergedResultsFile)
55
export(createResultsDataModel)
6+
export(deployPositConnectApp)
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export(executeDiagnostics)
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export(getCdmDataSourceInformation)
89
export(getCohortCounts)

‎NEWS.md

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CohortDiagnostics 3.3.0
2+
=======================
3+
4+
Changes:
5+
6+
1. Added function to make deployment to posit connect servers easier
7+
8+
2. Added ability to use CohortGenerator sample functionality to executeDiagnostics which speeds up execution for very
9+
large cohort definitions
10+
11+
3. Requires use of FeatureExtraction 3.4.0 to support new API
12+
13+
4. Removed annotation tables from result schema script
14+
115
CohortDiagnostics 3.2.5
216
=======================
317
Bug Fixes:

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