Merge branch 'develop' into feature/dirk-ext-prec

.github/actions/apply-style/checkout.sh

@@ -0,0 +1,45 @@
+#!/bin/bash
+
+###
+# Attempt to find the branch of the PR from the detached head state
+##
+
+echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+echo "Attempting to find branch that matches commit..."
+
+# Get the current commit SHA
+current_commit_sha=$(git rev-parse HEAD)
+# List all branches containing the current commit SHA
+branches=$(git branch -r --contains $current_commit_sha)
+
+echo "all branches:"
+echo "$(git branch -a)"
+echo "branches with SHA $current_commit_sha:"
+echo "$branches"
+
+# Loop over the string split by whitespace
+branch=""
+num_branches_found=0
+for _possible_branch in $branches; do
+  # Skip items that start with "pull/"
+  if [[ $_possible_branch == pull/* ]]; then
+    continue
+  fi
+  if [[ $_possible_branch == origin/* ]]; then
+    _possible_branch=$(echo "$_possible_branch" | sed 's/origin\///')
+  fi
+  echo "Possible Branch: $_possible_branch"
+  branch=$_possible_branch
+  num_branches_found=$((num_branches_found+1))
+done
+
+if [ "$num_branches_found" -ne 1 ]; then
+  echo "Error: Unable to find a single branch that matched git sha $current_commit_sha"
+  exit 1
+fi
+
+echo "Found branch: $branch"
+echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+
+git checkout $branch
+git submodule update --init --recursive

.github/dependabot.yml

@@ -6,3 +6,4 @@ updates:
     schedule:
       # Check for updates to GitHub Actions every week
       interval: "weekly"
+    target-branch: "develop"

.github/workflows/check-format.yml

@@ -3,9 +3,16 @@ name: Checks - formatting
 on:
   pull_request:
   workflow_dispatch:
+  issue_comment:
+    types: [created]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.ref_name }}
+  cancel-in-progress: true
 
 jobs:
   format_check:
+    if: ${{ github.event_name != 'issue_comment' || (github.event_name == 'issue_comment' && startsWith(github.event.comment.body, '/autofix')) }}
     runs-on: ubuntu-latest
     container:
       image: ghcr.io/llnl/sundials_spack_cache:llvm-17.0.4-h4lflucc3v2vage45opbo2didtcuigsn.spack
@@ -37,10 +44,18 @@ jobs:
         run: clang-format --version
 
       - name: Check out repository code
+        if: github.event_name != 'issue_comment'
         uses: actions/checkout@v4
         with:
           submodules: true
 
+      - name: Check out repository code
+        if: github.event_name == 'issue_comment'
+        uses: actions/checkout@v4
+        with:
+          ref: refs/pull/${{ github.event.issue.number }}/head
+          fetch-depth: 0
+
       - name: Add safe directory
         run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
 
@@ -56,9 +71,50 @@ jobs:
         run:  /usr/bin/git diff > format.patch
 
       - name: Archive diff as a patch if we failed
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: format.patch
           path: |
             ${{ github.workspace }}/format.patch
+
+  apply_format:
+    if: ${{ always() && contains(join(needs.*.result, ','), 'failure') && (github.event_name == 'issue_comment' && startsWith(github.event.comment.body, '/autofix')) }}
+    needs: format_check
+    runs-on: ubuntu-latest
+    steps:
+      # Checkout the GitHub created reference for the PR.
+      # The only way to do this is by using the "issue" number
+      # but that is really the PR number in this context.
+      # This is due to using an `issue_comment` event which
+      # is due to the GitHub Actions API that does not have
+      # a `pull_request_comment` event or something similar.
+      # This leaves us in a detached head state which is corrected
+      # in `apply-style/checkout.sh`
+      - name: Checkout repository code
+        uses: actions/checkout@v4
+        with:
+          ref: refs/pull/${{ github.event.issue.number }}/head
+          fetch-depth: 0
+
+      - name: Checkout the right git ref
+        run: ./.github/actions/apply-style/checkout.sh
+
+      - name: Download the git diff from format_check
+        uses: actions/download-artifact@v4
+        with:
+          name: format.patch
+
+      - name: Apply patch
+        run: |
+          git apply format.patch
+          rm format.patch
+
+      - name: Commit fixes
+        run: |
+          git config user.name "format-robot"
+          git config user.email "[email protected]"
+          if [ -n "$(git status --porcelain)" ]; then
+            git commit -am 'apply format updates'
+            git push
+          fi

.github/workflows/check-spelling.yml

@@ -3,9 +3,16 @@ name: Checks - spelling
 on:
   pull_request:
   workflow_dispatch:
+  issue_comment:
+    types: [created]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.ref_name }}
+  cancel-in-progress: true
 
 jobs:
   spelling_check:
+    if: ${{ github.event_name != 'issue_comment' || (github.event_name == 'issue_comment' && startsWith(github.event.comment.body, '/autofix')) }}
     runs-on: ubuntu-latest
     steps:
       - name: Install python3-pip
@@ -20,10 +27,18 @@ jobs:
         run: codespell --version
 
       - name: Check out repository code
+        if: github.event_name != 'issue_comment'
         uses: actions/checkout@v4
         with:
           submodules: true
 
+      - name: Check out repository code
+        if: github.event_name == 'issue_comment'
+        uses: actions/checkout@v4
+        with:
+          ref: refs/pull/${{ github.event.issue.number }}/head
+          fetch-depth: 0
+
       - name: Run codespell
         run: |
           ./scripts/spelling.sh
@@ -36,9 +51,50 @@ jobs:
         run: /usr/bin/git diff > spelling.patch
 
       - name: Archive diff as a patch if we failed
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: spelling.patch
           path: |
             ${{ github.workspace }}/spelling.patch
+
+  apply_spelling:
+    if: ${{ always() && contains(join(needs.*.result, ','), 'failure') && (github.event_name == 'issue_comment' && startsWith(github.event.comment.body, '/autofix')) }}
+    needs: spelling_check
+    runs-on: ubuntu-latest
+    steps:
+      # Checkout the GitHub created reference for the PR.
+      # The only way to do this is by using the "issue" number
+      # but that is really the PR number in this context.
+      # This is due to using an `issue_comment` event which
+      # is due to the GitHub Actions API that does not have
+      # a `pull_request_comment` event or something similar.
+      # This leaves us in a detached head state which is corrected
+      # in `apply-style/checkout.sh`
+      - name: Checkout repository code
+        uses: actions/checkout@v4
+        with:
+          ref: refs/pull/${{ github.event.issue.number }}/head
+          fetch-depth: 0
+
+      - name: Checkout the right git ref
+        run: ./.github/actions/apply-style/checkout.sh
+
+      - name: Download the git diff from spelling_check
+        uses: actions/download-artifact@v4
+        with:
+          name: spelling.patch
+
+      - name: Apply patch
+        run: |
+          git apply spelling.patch
+          rm spelling.patch
+
+      - name: Commit fixes
+        run: |
+          git config user.name "format-robot"
+          git config user.email "[email protected]"
+          if [ -n "$(git status --porcelain)" ]; then
+            git commit -am 'apply spelling updates'
+            git push
+          fi

.github/workflows/check-swig.yml

@@ -3,27 +3,41 @@ name: Checks - swig
 on:
   pull_request:
   workflow_dispatch:
+  issue_comment:
+    types: [created]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.ref_name }}
+  cancel-in-progress: true
 
 jobs:
-  swig:
+  swig_check:
+    if: ${{ github.event_name != 'issue_comment' || (github.event_name == 'issue_comment' && startsWith(github.event.comment.body, '/autofix')) }}
     runs-on: ubuntu-latest
-
     steps:
       - name: Install swig
         run: |
           git clone https://github.com/sundials-codes/swig
           cd swig
           ./autogen.sh
           ./configure --prefix=/usr/
-          make 
+          make
           sudo make install
           swig -version
 
       - name: Check out repository code
+        if: github.event_name != 'issue_comment'
         uses: actions/checkout@v4
         with:
           submodules: true
 
+      - name: Check out repository code
+        if: github.event_name == 'issue_comment'
+        uses: actions/checkout@v4
+        with:
+          ref: refs/pull/${{ github.event.issue.number }}/head
+          fetch-depth: 0
+
       - name: Add safe directory
         run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
 
@@ -41,9 +55,50 @@ jobs:
         run:  /usr/bin/git diff > swig.patch
 
       - name: Archive diff as a patch if we failed
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: swig.patch
           path: |
             ${{ github.workspace }}/swig.patch
+
+  apply_swig:
+    if: ${{ always() && contains(join(needs.*.result, ','), 'failure') && (github.event_name == 'issue_comment' && startsWith(github.event.comment.body, '/autofix')) }}
+    needs: swig_check
+    runs-on: ubuntu-latest
+    steps:
+      # Checkout the GitHub created reference for the PR.
+      # The only way to do this is by using the "issue" number
+      # but that is really the PR number in this context.
+      # This is due to using an `issue_comment` event which
+      # is due to the GitHub Actions API that does not have
+      # a `pull_request_comment` event or something similar.
+      # This leaves us in a detached head state which is corrected
+      # in `apply-style/checkout.sh`
+      - name: Checkout repository code
+        uses: actions/checkout@v4
+        with:
+          ref: refs/pull/${{ github.event.issue.number }}/head
+          fetch-depth: 0
+
+      - name: Checkout the right git ref
+        run: ./.github/actions/apply-style/checkout.sh
+
+      - name: Download the git diff from swig_check
+        uses: actions/download-artifact@v4
+        with:
+          name: swig.patch
+
+      - name: Apply patch
+        run: |
+          git apply swig.patch
+          rm swig.patch
+
+      - name: Commit fixes
+        run: |
+          git config user.name "format-robot"
+          git config user.email "[email protected]"
+          if [ -n "$(git status --porcelain)" ]; then
+            git commit -am 'apply swig updates'
+            git push
+          fi

.github/workflows/spack-develop.yml

@@ -33,15 +33,15 @@ jobs:
           indexsize: ${{ matrix.indexsize }}
           precision: ${{ matrix.precision }}
       - name: Archive build files from failed build
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: build_files
           path: |
             ${{ github.workspace }}/test/build_*
             !${{ github.workspace }}/test/build_*/Testing/output
       - name: Archive output files from failed build
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: output_files

.github/workflows/ubuntu-latest.yml

@@ -52,15 +52,15 @@ jobs:
         env:
           CMAKE_BUILD_TYPE: ${{ matrix.buildtype }}
       - name: Archive build files from failed build
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: build_files
           path: |
             ${{ github.workspace }}/test/build_*
             !${{ github.workspace }}/test/build_*/Testing/output
       - name: Archive output files from failed build
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: output_files

CHANGELOG.md

@@ -25,6 +25,10 @@ specific linker flags e.g., MKL.
 
 ### Bug Fixes
 
+Fixed a [bug](https://github.com/LLNL/sundials/issues/581) in the sparse matrix
+implementation of `SUNMatScaleAddI` which caused out of bounds writes unless
+`indexvals` were in ascending order for each row/column.
+
 Fixed `ARKodeResize` not using the default `hscale` when an argument of `0` was
 provided.
 
@@ -39,8 +43,14 @@ repeatedly.
 Fixed compilation errors when building the Trilinos Teptra NVector with CUDA
 support.
 
+Fixed a CMake configuration issue related to aliasing an `ALIAS` target when
+using `ENABLE_KLU=ON` in combination with a static-only build of SuiteSparse.
+
 ### Deprecation Notices
 
+The ARKODE stepper specific functions to retrieve the number of right-hand side
+function evaluations have been deprecated. Use `ARKodeGetNumRhsEvals` instead.
+
 ## Changes to SUNDIALS in release 7.1.1
 
 ### Bug Fixes