Release v1.1.1

.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/
+

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 = "[email protected]", role = c("aut", "cre")),
 	person("Martijn", "Schuemie", email = "[email protected]", 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,

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)

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
 =======