From b8cce576d53e764ae30bba64cdf220fdfdc74332 Mon Sep 17 00:00:00 2001
From: Ziv Yaniv <zivyaniv@nih.gov>
Date: Sun, 12 Apr 2026 14:14:14 -0400
Subject: [PATCH] Streamline GH workflow and harmonize instructions across OSs.

Use bash as the shell for all OS instead of bash for macos/linux and
pwsh for windows.

Instead of passing environment variables via configure.vars
to remotes::install_git, set them via Sys.setenv() in R before
calling install_git. This works across all OSs. For some reason
configure.vars set the environment variables on linux/mac but not
on windows.
---
 .github/workflows/main.yml | 42 ++++++++++----------------------------
 README.md                  |  9 ++++----
 2 files changed, 16 insertions(+), 35 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 5d3a51c..a65bccc 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -42,44 +42,24 @@ jobs:
         sudo apt-get install -y libcurl4-openssl-dev libssh2-1-dev libharfbuzz-dev libfribidi-dev gh &&
         sudo rm -rf /var/lib/apt/lists/*
     - name: Configuration Information
-      if: runner.os == 'Linux' || runner.os == 'macOS'
+      shell: bash
       run: |
-        mkdir ${R_LIBS}
-        c++ --version
+        mkdir -p "$R_LIBS"
         cmake --version
+        if [[ "$RUNNER_OS" == "Windows" ]]; then
+          g++ --version
+        else
+          c++ --version
+        fi
         which R
         R --version
-    - name: Configuration Information (Windows)
-      if: startsWith(matrix.os, 'windows')
-      shell: pwsh
-      run: |
-        New-Item -ItemType Directory -Force -Path "$env:R_LIBS" | Out-Null
-        g++ --version
-        cmake --version
-        Get-Command R.exe
-        R.exe --version
     - name: Install R packages
-      if: runner.os == 'Linux' || runner.os == 'macOS'
-      run: |
-        R -e "install.packages(c('remotes'), lib=c('${R_LIBS}'), repos='https://cloud.r-project.org/')"
-    - name: Install R packages (Windows)
-      if: startsWith(matrix.os, 'windows')
-      shell: pwsh
+      shell: bash
       run: |
-        Rscript -e "lib <- Sys.getenv('R_LIBS'); lib <- normalizePath(lib, winslash='/', mustWork=FALSE); dir.create(lib, recursive=TRUE, showWarnings=FALSE); install.packages('remotes', lib=lib, repos='https://cloud.r-project.org/')"
-        Rscript.exe -e "install.packages(c('remotes', 'desc'), repos='https://cloud.r-project.org/')"
+        R -e "install.packages(c('remotes'), lib=Sys.getenv('R_LIBS'), repos='https://cloud.r-project.org/')"
     - name: Build and test
-      if: runner.os == 'Linux' || runner.os == 'macOS'
-      run: |
-        set -x
-        R -e "remotes::install_git(c('.'), lib=c('${R_LIBS}'), configure.vars=c('"MAKEJ=2"'))"
-      env:
-        ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS: 2
-    - name: Build and test (Windows)
-      if: startsWith(matrix.os, 'windows')
-      shell: pwsh
+      shell: bash
       env:
         ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS: 2
       run: |
-        $env:MAKEJ="3"
-        Rcmd.exe INSTALL --build .
+        R -e "Sys.setenv(MAKEJ=2); remotes::install_git(c('.'), lib=Sys.getenv('R_LIBS'))"
diff --git a/README.md b/README.md
index 97fcade..98f4b75 100644
--- a/README.md
+++ b/README.md
@@ -15,15 +15,16 @@ remotes::install_github("SimpleITK/SimpleITKRInstaller")
 Turn on mutlicore compilation, six cores in this example
 
 ```R
-remotes::install_github("SimpleITK/SimpleITKRInstaller", configure.vars=c("MAKEJ=6"))
+Sys.setenv(MAKEJ=6)
+remotes::install_github("SimpleITK/SimpleITKRInstaller")
 ```
 
 Use multicore compilation and build additional modules not included in the default build setup such as SimpleElastix (registration) and DCMTK (additional DICOM IO option beyond the default GDCM).
 
-**Note**: We need to use backslashes to escape the spaces in the `ADDITIONAL_SITK_MODULES` otherwise the `remotes::install` does not pass the string correctly to the shell (separates it using the spaces instead of passing as one string).
-
 ```R
-remotes::install_github("SimpleITK/SimpleITKRInstaller", configure.vars=c("MAKEJ=6", "ADDITIONAL_SITK_MODULES=-DSimpleITK_USE_ELASTIX=ON\\  -DModule_ITKIODCMTK:BOOL=ON"))
+Sys.setenv(MAKEJ=6)
+Sys.setenv(ADDITIONAL_SITK_MODULES="-DSimpleITK_USE_ELASTIX=ON -DModule_ITKIODCMTK:BOOL=ON")
+remotes::install_github("SimpleITK/SimpleITKRInstaller")
 ```
 
 Note: