diff --git a/.github/workflows/R_CMD_check_Hades.yaml b/.github/workflows/R_CMD_check_Hades.yaml index 0047ccf9..c034d9e3 100644 --- a/.github/workflows/R_CMD_check_Hades.yaml +++ b/.github/workflows/R_CMD_check_Hades.yaml @@ -108,14 +108,14 @@ jobs: ) covr::to_cobertura(cov) shell: Rscript {0} - + - uses: codecov/codecov-action@v4 if: runner.os == 'Linux' with: file: ./cobertura.xml plugin: noop disable_search: true - token: ${{ secrets.CODECOV_TOKEN }} + token: ${{ secrets.CODECOV_TOKEN }} Release: needs: R-CMD-Check @@ -155,34 +155,33 @@ jobs: draft: false prerelease: false - # AGS: Commenting out until Strategus is in HADES - # - 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 - # 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/ - # + - 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 + 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/ + diff --git a/DESCRIPTION b/DESCRIPTION index 03ea3539..336fc993 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: Strategus Type: Package Title: Coordinate and Execute OHDSI HADES Modules -Version: 1.1.0 -Date: 2024-11-26 +Version: 1.1.1 +Date: 2024-12-03 Authors@R: c( person("Anthony", "Sena", email = "sena@ohdsi.org", role = c("aut", "cre")), person("Martijn", "Schuemie", email = "schuemie@ohdsi.org", role = c("aut")), @@ -26,7 +26,6 @@ Imports: methods, ParallelLogger (>= 3.1.0), purrr, - readr, ResultModelManager (>= 0.5.8), rlang, SqlRender (>= 1.18.0) @@ -43,6 +42,7 @@ Suggests: fs, knitr, PatientLevelPrediction, + readr, rmarkdown, RSQLite, SelfControlledCaseSeries, diff --git a/NEWS.md b/NEWS.md index d5ba77b0..4ff14823 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +Strategus 1.1.1 +=============== +- Fixes R CMD note and updates documentation for inclusion into HADES + Strategus 1.1.0 =============== - Inject cohort schema and table into `createCohortBasedCovariateSettings` (#181) diff --git a/README.md b/README.md index f83814fb..3a585c8d 100644 --- a/README.md +++ b/README.md @@ -4,6 +4,8 @@ Strategus [![Build Status](https://github.com/OHDSI/Strategus/actions/workflows/R_CMD_check_Hades.yaml/badge.svg?branch=main)](https://github.com/OHDSI/Strategus/actions/workflows/R_CMD_check_Hades.yaml/badge.svg?branch=main) [![codecov.io](https://codecov.io/github/OHDSI/Strategus/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/Strategus?branch=main) +Strategus is part of [HADES](https://ohdsi.github.io/Hades). + Introduction ============ Strategus is an R package for coordinating and executing analytics using [OHDSI HADES](https://ohdsi.github.io/Hades/) modules. Please see the [Introduction To Strategus](https://ohdsi.github.io/Strategus/articles/IntroductionToStrategus.html) for more details. @@ -20,7 +22,7 @@ Strategus is an R package. System Requirements ============ -Requires R (version 4.2.0 or higher). Installation on Windows requires [RTools](https://cran.r-project.org/bin/windows/Rtools/). Libraries used in Strategus require Java. Strategus requires you to setup your GitHub Personal Access Token as described [here](https://ohdsi.github.io/Hades/rSetup.html#GitHub_Personal_Access_Token) +Requires R (version 4.2.0 or higher). Installation on Windows requires [RTools](https://cran.r-project.org/bin/windows/Rtools/). Libraries used in Strategus require Java. Installation ============= @@ -38,7 +40,10 @@ Documentation can be found on the [package website](https://ohdsi.github.io/Stra PDF versions of the documentation are also available: - Package manual: [Strategus.pdf](https://raw.githubusercontent.com/OHDSI/Strategus/main/extras/Strategus.pdf) -- Vignette: [Creating HADES Modules](https://github.com/OHDSI/Strategus/raw/main/inst/doc/CreatingModules.pdf) +- Introduction to Strategus [IntroductionToStrategus.pdf](https://raw.githubusercontent.com/OHDSI/Strategus/main/inst/doc/IntroductionToStrategus.pdf) +- Creating analysis specification [CreatingAnalysisSpecification.pdf](https://raw.githubusercontent.com/OHDSI/Strategus/main/inst/doc/CreatingAnalysisSpecification.pdf) +- Execute Strategus [ExecuteStrategus.pdf](https://raw.githubusercontent.com/OHDSI/Strategus/main/inst/doc/ExecuteStrategus.pdf) +- Working with results [WorkingWithResults.pdf](https://raw.githubusercontent.com/OHDSI/Strategus/main/inst/doc/WorkingWithResults.pdf) Support ======= diff --git a/extras/Strategus.pdf b/extras/Strategus.pdf index ac63689b..654cbd46 100644 Binary files a/extras/Strategus.pdf and b/extras/Strategus.pdf differ diff --git a/inst/doc/CreatingAnalysisSpecification.pdf b/inst/doc/CreatingAnalysisSpecification.pdf index e88d651b..631f01f4 100644 Binary files a/inst/doc/CreatingAnalysisSpecification.pdf and b/inst/doc/CreatingAnalysisSpecification.pdf differ diff --git a/inst/doc/ExecuteStrategus.pdf b/inst/doc/ExecuteStrategus.pdf index c6f22e7c..67dcbcdc 100644 Binary files a/inst/doc/ExecuteStrategus.pdf and b/inst/doc/ExecuteStrategus.pdf differ diff --git a/inst/doc/IntroductionToStrategus.pdf b/inst/doc/IntroductionToStrategus.pdf index c38c5339..61c406bb 100644 Binary files a/inst/doc/IntroductionToStrategus.pdf and b/inst/doc/IntroductionToStrategus.pdf differ diff --git a/inst/doc/WorkingWithResults.pdf b/inst/doc/WorkingWithResults.pdf index 9eb93477..a25b1b1e 100644 Binary files a/inst/doc/WorkingWithResults.pdf and b/inst/doc/WorkingWithResults.pdf differ