WIP: Binary distributions via GitHub Releases.

.github/workflows/main.yml

@@ -2,6 +2,8 @@ on:
   push:
     branches:
       - main
+    tags:
+      - 'v*'  # Trigger on version tags
   pull_request:
     branches:
       - main
@@ -11,6 +13,11 @@ on:
   # run testing on the first of each month 5am ET / 9am UTC
   - cron: '0 9 1 * *'
 
+# Set minimal permissions for all jobs (read-only)
+permissions:
+  contents: read
+  actions: read
+
 jobs:
   R-build:
     strategy:
@@ -20,16 +27,15 @@ jobs:
         os: [ 'macos-15-intel', 'ubuntu-latest', 'windows-latest']
     runs-on: ${{ matrix.os }}
     name: ${{ matrix.R }} ${{ matrix.os }} build
-    env:
-      R_LIBS: ${{ github.workspace }}/Rlibs
 
     steps:
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
       with:
         fetch-depth: 0
         ref: ${{ github.event.pull_request.head.sha }}
-    - name: Setup R
-      uses: r-lib/actions/setup-r@v2
+
+    - name: Setup R (also sets the R_LIBS_USER environment variable)
+      uses: r-lib/actions/setup-r@a51a8012b0aab7c32ef9d19bf54da93f3254335e # v2.12.0
       with:
         r-version: ${{ matrix.R }}
     - name: System Dependencies
@@ -41,7 +47,6 @@ jobs:
     - name: Configuration Information
       shell: bash
       run: |
-        mkdir -p "$R_LIBS"
         cmake --version
         if [[ "$RUNNER_OS" == "Windows" ]]; then
           ls -d /c/rtools* 2>/dev/null || echo "No rtools found in /c/"
@@ -55,11 +60,109 @@ jobs:
     - name: Install R packages
       shell: bash
       run: |
-        R -e "install.packages(c('remotes'), lib=Sys.getenv('R_LIBS'), repos='https://cloud.r-project.org/')"
+        R -e "install.packages(c('remotes'), lib=Sys.getenv('R_LIBS_USER'), repos='https://cloud.r-project.org/')"
     - name: Build and test
       shell: bash
       env:
         ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS: 2
       run: |
-        R -e "Sys.setenv(MAKEJ=2); remotes::install_git(c('.'), lib=Sys.getenv('R_LIBS'))"
+        R -e "Sys.setenv(MAKEJ=2); remotes::install_git(c('.'), lib=Sys.getenv('R_LIBS_USER'))"
         R -e "library(SimpleITK); Version()"
+    - name: Create binary package from installed package
+      id: create_package
+      shell: bash
+      run: |
+        # Get the R version for naming
+        R_VERSION_SHORT=$(echo "${{ matrix.R }}" | cut -d'.' -f1,2)
+
+        # Get package version from DESCRIPTION
+        PKG_VERSION=$(Rscript -e "cat(read.dcf(file.path(Sys.getenv('R_LIBS_USER'), 'SimpleITK', 'DESCRIPTION'), 'Version')[1])")
+
+        # Create output directory for artifacts
+        mkdir -p artifacts
+
+        # Create binary package archive from installed package (no recompilation)
+        cd "${R_LIBS_USER}"
+        if [[ "$RUNNER_OS" == "macOS" ]]; then
+          PKG_NAME="SimpleITK_${PKG_VERSION}_R${R_VERSION_SHORT}_macos-x86_64.tgz"
+          tar czf "${GITHUB_WORKSPACE}/artifacts/${PKG_NAME}" SimpleITK
+        elif [[ "$RUNNER_OS" == "Linux" ]]; then
+          PKG_NAME="SimpleITK_${PKG_VERSION}_R${R_VERSION_SHORT}_linux-x86_64.tar.gz"
+          tar czf "${GITHUB_WORKSPACE}/artifacts/${PKG_NAME}" SimpleITK
+        elif [[ "$RUNNER_OS" == "Windows" ]]; then
+          PKG_NAME="SimpleITK_${PKG_VERSION}_R${R_VERSION_SHORT}_windows-x86_64.zip"
+          7z a -tzip "${GITHUB_WORKSPACE}/artifacts/${PKG_NAME}" SimpleITK
+        fi
+
+        cd "${GITHUB_WORKSPACE}"
+        ls -lh artifacts/
+
+        # Export PKG_NAME as output for use in upload step
+        echo "pkg_name=${PKG_NAME}" >> $GITHUB_OUTPUT
+    - name: Upload binary package
+      if: steps.create_package.outcome == 'success'
+      uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
+      with:
+        name: ${{ steps.create_package.outputs.pkg_name }}
+        path: artifacts/*
+        retention-days: 30
+
+  create-release:
+    name: Create GitHub Draft Release
+    # Only run this job for tag pushes after the R-build job completes
+    # successfully.
+    if: startsWith(github.ref, 'refs/tags/v')
+    needs: R-build
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+      with:
+        fetch-depth: 1
+
+    - name: Verify tag matches SITK_TARGET
+      id: verify_tag
+      run: |
+        SITK_TARGET=$(grep '^SITK_TARGET:' DESCRIPTION | awk '{print $2}')
+        TAG_NAME="${{ github.ref_name }}"
+        if [ "${TAG_NAME}" != "${SITK_TARGET}" ]; then
+          echo "Tag ${TAG_NAME} does not match SITK_TARGET ${SITK_TARGET}"
+          echo "Skipping draft release creation."
+          echo "draft_release=false" >> $GITHUB_OUTPUT
+        else
+          echo "draft_release=true" >> $GITHUB_OUTPUT
+        fi
+
+    - name: Download all artifacts
+      if: steps.verify_tag.outputs.draft_release == 'true'
+      uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1
+      with:
+        path: release-artifacts
+        pattern: SimpleITK_*
+        merge-multiple: true
+
+    - name: Display downloaded artifacts
+      if: steps.verify_tag.outputs.draft_release == 'true'
+      run: |
+        echo "Downloaded artifacts:"
+        ls -lhR release-artifacts/
+
+    # This action automatically creates the release if it doesn't exist,
+    # or updates it if it does.
+    - name: Create or Update Draft Release
+      if: steps.verify_tag.outputs.draft_release == 'true'
+      uses: softprops/action-gh-release@b4309332981a82ec1c5618f44dd2e27cc8bfbfda # v3.0.0
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      with:
+        draft: true
+        name: SimpleITK ${{ github.ref_name }} R Package Release
+        body: |
+          Please review and test the packages before publishing this release.
+          Then remove the "Draft" status to make it public and delete this message.
+        files: |
+          release-artifacts/*
+        fail_on_unmatched_files: true

.github/workflows/update_gh_cran.yml

@@ -0,0 +1,57 @@
+name: Update CRAN Repository
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: write
+
+concurrency:
+  group: update-cran-repository
+  cancel-in-progress: false
+
+jobs:
+  update-repo:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        with:
+          fetch-depth: 0
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@a51a8012b0aab7c32ef9d19bf54da93f3254335e # v2.12.0
+
+      - name: Download Release Assets
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          mkdir -p temp_packages
+          gh release download ${{ github.event.release.tag_name }} --dir temp_packages
+
+      - name: Route Assets and Build PACKAGES Files
+        shell: bash
+        run: |
+          # Run the R script and always do the cleanup of the temp_packages directory,
+          # step returns the exit code from the R script.
+          (
+            Rscript update_cran_repo.R \
+              --packages-dir temp_packages \
+              --docs-dir docs \
+              --repo-url https://github.com/${{ github.repository }} \
+              --tag ${{ github.event.release.tag_name }}
+            status=$?
+            rm -rf temp_packages
+            exit $status
+          )
+
+      - name: Commit and Push Changes
+        run: |
+          git config --global user.name "github-actions[bot]"
+          git config --global user.email "github-actions[bot]@users.noreply.github.com"
+          git add docs/
+          if ! git diff --cached --quiet; then
+            git commit -m "Update CRAN repository index for release ${{ github.event.release.tag_name }}"
+            git push
+          fi

DESCRIPTION

@@ -13,7 +13,7 @@ Authors@R: c(person("Richard", "Beare", role = c("aut", "cre"),
                      email = "blowekamp@mail.nih.gov"),
 		     person("Ziv", "Yaniv", role="aut",
 		     email = "zivyaniv@nih.gov"))
-Author: Richard Beare, Bradley Lowekamp, Ziv Yaniv plus loads of others
+Author: Richard Beare, Bradley Lowekamp, Ziv Yaniv, The Insight Software Consortium and the ITK user and developer communities.
 Depends: R (>= 4.0)
 Imports: methods,
          desc

configure

@@ -54,9 +54,14 @@ mkdir -p SITK
     mkdir -p Build &&
         cd Build &&
         cmake \
+        -D "CMAKE_CXX_FLAGS:STRING=-fvisibility=hidden -fvisibility-inlines-hidden ${CFLAGS}" \
+        -D "CMAKE_C_FLAGS:STRING=-fvisibility=hidden ${CFLAGS}" \
+        -DITK_C_OPTIMIZATION_FLAGS:STRING="" \
+        -DITK_CXX_OPTIMIZATION_FLAGS:STRING="" \
         -DWRAP_DEFAULT=OFF\
         -DWRAP_R=ON \
         -DSimpleITK_BUILD_DISTRIBUTE=ON \
+        -DSimpleITK_BUILD_STRIP:BOOL=ON \
         -DBUILD_EXAMPLES=OFF \
         -DBUILD_TESTING=OFF \
         -DCMAKE_BUILD_TYPE=MinSizeRel \

configure.win

@@ -83,9 +83,14 @@ export MAKEJ
 
   # Configure with Unix Makefiles (Rtools toolchain)
   cmake -G "Unix Makefiles" \
+    -D "CMAKE_CXX_FLAGS:STRING=-fvisibility=hidden -fvisibility-inlines-hidden ${CFLAGS}" \
+    -D "CMAKE_C_FLAGS:STRING=-fvisibility=hidden ${CFLAGS}" \
+    -DITK_C_OPTIMIZATION_FLAGS:STRING="" \
+    -DITK_CXX_OPTIMIZATION_FLAGS:STRING="" \
     -DWRAP_DEFAULT=OFF \
     -DWRAP_R=ON \
     -DSimpleITK_BUILD_DISTRIBUTE=ON \
+    -DSimpleITK_BUILD_STRIP:BOOL=ON \
     -DBUILD_EXAMPLES=OFF \
     -DBUILD_TESTING=OFF \
     -DITK_SKIP_PATH_LENGTH_CHECK=ON \