Merge Release 1.8.0

Release 1.8.0

The Ginkgo team is proud to announce the new Ginkgo minor release 1.8.0. This
release brings new features such as:
- A brand new file-based configuration for Ginkgo objects: you can now construct
  Ginkgo objects (solvers, preconditioners, ...) from a JSON configuration file.
  This simplifies interfacing to Ginkgo as well as exploring different settings
  to solve a problem.
- Expand the batched feature set with: the Batched CSR Matrix format, batched CG
  solver, batched (Block-)Jacobi preconditioner, usage example and other
  features such as scaling,
- New Distributed Multigrid and the PGM coarsening method,
- New CUDA and HIP kernels for Reverse Cuthill McKee (RCM) reordering
- Better Ginkgo and Kokkos interaction thanks to a mapping from simple Ginkgo
  types to native Kokkos types

and more!

If you face an issue, please first check our [known issues page](https://github.com/ginkgo-project/ginkgo/wiki/Known-Issues) and the [open issues list](https://github.com/ginkgo-project/ginkgo/issues) and if you do not find a solution, feel free to [open a new issue](https://github.com/ginkgo-project/ginkgo/issues/new/choose) or ask a question using the [github discussions](https://github.com/ginkgo-project/ginkgo/discussions).

For detailed changes, please check our [CHANGELOG.md](./CHANGELOG.md) file.

Related PR: #1622

.clang-format

@@ -3,26 +3,26 @@ Language:        Cpp
 # BasedOnStyle:  Google
 AccessModifierOffset: -4
 AlignAfterOpenBracket: Align
-AlignConsecutiveAssignments: false
-AlignConsecutiveDeclarations: false
+AlignConsecutiveAssignments: None
+AlignConsecutiveDeclarations: None
 AlignEscapedNewlines: Left
 AlignOperands:   true
 AlignTrailingComments: true
 AllowAllParametersOfDeclarationOnNextLine: true
-AllowShortBlocksOnASingleLine: false
+AllowShortBlocksOnASingleLine: Never
 AllowShortCaseLabelsOnASingleLine: false
 AllowShortFunctionsOnASingleLine: All
 AllowShortIfStatementsOnASingleLine: true
 AllowShortLoopsOnASingleLine: true
 AlwaysBreakAfterDefinitionReturnType: None
 AlwaysBreakAfterReturnType: None
 AlwaysBreakBeforeMultilineStrings: true
-AlwaysBreakTemplateDeclarations: true
+AlwaysBreakTemplateDeclarations: Yes
 BinPackArguments: true
 BinPackParameters: true
 BraceWrapping:
   AfterClass:      false
-  AfterControlStatement: false
+  AfterControlStatement: Never
   AfterEnum:       false
   AfterFunction:   true
   AfterNamespace:  false
@@ -58,13 +58,6 @@ ForEachMacros:
   - foreach
   - Q_FOREACH
   - BOOST_FOREACH
-IncludeCategories:
-  - Regex:           '^<.*\.h>'
-    Priority:        1
-  - Regex:           '^<.*'
-    Priority:        2
-  - Regex:           '.*'
-    Priority:        3
 IncludeIsMainRegex: '([-_](test|unittest))?$'
 IndentCaseLabels: false
 IndentWidth:     4
@@ -88,7 +81,7 @@ PenaltyExcessCharacter: 1000000
 PenaltyReturnTypeOnItsOwnLine: 200
 PointerAlignment: Left
 ReflowComments:  true
-SortIncludes:    true
+SortIncludes:    CaseInsensitive
 SortUsingDeclarations: true
 SpaceAfterCStyleCast: false
 SpaceAfterTemplateKeyword: true
@@ -101,7 +94,7 @@ SpacesInContainerLiterals: true
 SpacesInCStyleCastParentheses: false
 SpacesInParentheses: false
 SpacesInSquareBrackets: false
-Standard:        Cpp11
+Standard:        c++14
 TabWidth:        8
 UseTab:          Never
 ...

.github/_typos.toml

@@ -4,7 +4,10 @@ extend-exclude = ["third_party/*", "*.svg"]
 [default.extend-words]
 dout = "dout"
 nd = "nd"
+ans = "ans"
 tht = "tht"
+thr = "thr"
+iy = "iy"
 automatical = "automatical"
 strat = "strat"
 entrie = "entrie"

.github/bot-base.sh

@@ -6,7 +6,11 @@ API_HEADER="Accept: application/vnd.github.v3+json"
 AUTH_HEADER="Authorization: token $GITHUB_TOKEN"
 
 api_get() {
-  curl -X GET -s -H "${AUTH_HEADER}" -H "${API_HEADER}" "$1"
+  curl -X GET -s -H "${AUTH_HEADER}" -H "${API_HEADER}" "$1" > $RUNNER_TEMP/output.json
+  cat $RUNNER_TEMP/output.json 
+  if [[ "$RUNNER_DEBUG" == "1" ]]; then
+    cat $RUNNER_TEMP/output.json 1>&2
+  fi
 }
 
 api_post() {

.github/bot-pr-format-base.sh

@@ -1,39 +1,32 @@
 #!/usr/bin/env bash
 
-source .github/bot-pr-base.sh
+cp .github/bot-pr-base.sh /tmp
+source /tmp/bot-pr-base.sh
 
-echo "Retrieving PR file list"
-PR_FILES=$(bot_get_all_changed_files ${PR_URL})
-NUM=$(echo "${PR_FILES}" | wc -l)
-echo "PR has ${NUM} changed files"
-
-TO_FORMAT="$(echo "$PR_FILES" | grep -E $EXTENSION_REGEX || true)"
+echo "Set-up working tree"
 
 git remote add fork "$HEAD_URL"
 git fetch fork "$HEAD_BRANCH"
+git fetch origin "$BASE_BRANCH"
 
 git config user.email "[email protected]"
 git config user.name "ginkgo-bot"
 
 # save scripts from develop
-pushd dev_tools/scripts
-cp add_license.sh format_header.sh update_ginkgo_header.sh /tmp
-popd
+cp .clang-format .pre-commit-config.yaml /tmp
+pushd dev_tools/scripts || exit 1
+cp format_header.sh update_ginkgo_header.sh /tmp
+popd || exit 1
 
 # checkout current PR head
 LOCAL_BRANCH=format-tmp-$HEAD_BRANCH
 git checkout -b $LOCAL_BRANCH fork/$HEAD_BRANCH
 
 # restore files from develop
-cp /tmp/add_license.sh dev_tools/scripts/
+cp /tmp/.clang-format .
+cp /tmp/.pre-commit-config.yaml .
 cp /tmp/format_header.sh dev_tools/scripts/
 cp /tmp/update_ginkgo_header.sh dev_tools/scripts/
 
-# format files
-dev_tools/scripts/add_license.sh
-dev_tools/scripts/update_ginkgo_header.sh
-for f in $(echo "$TO_FORMAT" | grep -E $FORMAT_HEADER_REGEX); do dev_tools/scripts/format_header.sh "$f"; done
-for f in $(echo "$TO_FORMAT" | grep -E $FORMAT_REGEX); do "$CLANG_FORMAT" -i -style=file "$f"; done
-
-# restore formatting scripts so they don't appear in the diff
-git checkout -- dev_tools/scripts/*.sh
+# make base pre-commit config available
+git add .pre-commit-config.yaml

.github/check-format.sh

@@ -3,17 +3,30 @@
 cp .github/bot-pr-format-base.sh /tmp
 source /tmp/bot-pr-format-base.sh
 
+echo "Run Pre-Commit checks"
+
+pipx run pre-commit run --show-diff-on-failure --color=always --from-ref "origin/$BASE_BRANCH" --to-ref HEAD || true
+
+echo -n "Collecting information on changed files"
+
+git restore --staged .pre-commit-config.yaml
+git checkout -- dev_tools/scripts/*.sh .pre-commit-config.yaml .clang-format
+
 # check for changed files, replace newlines by \n
 LIST_FILES=$(git diff --name-only | sed '$!s/$/\\n/' | tr -d '\n')
+echo -n .
 
 git diff > /tmp/format.patch
 mv /tmp/format.patch .
+echo -n .
 
 bot_delete_comments_matching "Error: The following files need to be formatted"
+echo -n .
 
 if [[ "$LIST_FILES" != "" ]]; then
   MESSAGE="The following files need to be formatted:\n"'```'"\n$LIST_FILES\n"'```'
   MESSAGE="$MESSAGE\nYou can find a formatting patch under **Artifacts** [here]"
   MESSAGE="$MESSAGE($JOB_URL) or run "'`format!` if you have write access to Ginkgo'
   bot_error "$MESSAGE"
 fi
+echo .

.github/format.sh

@@ -3,11 +3,22 @@
 cp .github/bot-pr-format-base.sh /tmp
 source /tmp/bot-pr-format-base.sh
 
+# format files
+echo "Formatting files"
+
+pipx run pre-commit run --from-ref "origin/$BASE_BRANCH" --to-ref HEAD || true
+
+# restore formatting scripts so they don't appear in the diff
+git restore --staged .pre-commit-config.yaml
+git checkout -- dev_tools/scripts/*.sh .pre-commit-config.yaml .clang-format
+
 # check for changed files, replace newlines by \n
-LIST_FILES=$(git diff --name-only | sed '$!s/$/\\n/' | tr -d '\n')
+CHANGES=$(git diff --name-only | sed '$!s/$/\\n/' | tr -d '\n')
+
+echo "$CHANGES"
 
 # commit changes if necessary
-if [[ "$LIST_FILES" != "" ]]; then
+if [[ "$CHANGES" != "" ]]; then
   git commit -a -m "Format files
 
 Co-authored-by: $USER_COMBINED"

.github/mirror.sh

@@ -1,7 +1,5 @@
 #!/usr/bin/env bash
 
-BRANCH_NAME=${BRANCH_NAME##*/}
-
 git remote add fork "[email protected]:${GITHUB_REPO}.git"
 git remote add gitlab "[email protected]:ginkgo-project/ginkgo-public-ci.git"
 

.github/workflows/bot-pr-comment.yml

@@ -1,86 +1,40 @@
+name: OnCommentPR
+
 on:
   issue_comment:
     types: [created]
-name: OnCommentPR
+
 jobs:
   label:
     runs-on: ubuntu-latest
     if: github.event.issue.pull_request != '' && github.event.comment.body == 'label!' && (github.event.comment.author_association == 'COLLABORATOR' || github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER')
     steps:
     - name: Checkout the latest code (shallow clone)
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         ref: develop
     - name: Add appropriate labels
       env:
         GITHUB_TOKEN: ${{ secrets.BOT_TOKEN }}
       run: cp --preserve .github/label.sh /tmp && /tmp/label.sh
+
   check_format:
     name: check-format
-    runs-on: ubuntu-22.04
     if: github.event.issue.pull_request != '' && github.event.comment.body == 'check-format!' && (github.event.comment.author_association == 'COLLABORATOR' || github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER')
-    steps:
-    - name: Checkout the latest code (shallow clone)
-      uses: actions/checkout@v3
-      with:
-        ref: develop
-    - name: Check for formatting changes
-      env:
-        GITHUB_TOKEN: ${{ secrets.BOT_TOKEN }}
-      run: cp --preserve .github/check-format.sh /tmp && /tmp/check-format.sh
-    - name: Upload code formatting patch
-      if: failure()
-      uses: actions/upload-artifact@v3
-      with:
-          name: patch
-          path: format.patch
+    uses: ./.github/workflows/check-formatting.yml
+    secrets: inherit
+
   format:
     name: format
     runs-on: ubuntu-22.04
     if: github.event.issue.pull_request != '' && github.event.comment.body == 'format!' && (github.event.comment.author_association == 'COLLABORATOR' || github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER')
     steps:
     - name: Checkout the latest code (shallow clone)
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         ref: develop
         persist-credentials: false
     - name: Commit formatting changes
       env:
         GITHUB_TOKEN: ${{ secrets.BOT_TOKEN }}
       run: cp --preserve .github/format.sh /tmp && /tmp/format.sh
-  rebase:
-    name: rebase
-    if: github.event.issue.pull_request != '' && github.event.comment.body == 'rebase!' && (github.event.comment.author_association == 'COLLABORATOR' || github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER')
-    runs-on: ubuntu-latest
-    steps:
-    - name: Checkout the latest code
-      uses: actions/checkout@v3
-      with:
-        ref: develop
-        fetch-depth: 0
-        persist-credentials: false
-    - name: Automatic Rebase
-      env:
-        GITHUB_TOKEN: ${{ secrets.BOT_TOKEN }}
-      run: cp --preserve .github/rebase.sh /tmp && /tmp/rebase.sh
-  format-rebase:
-    name: format-rebase
-    if: github.event.issue.pull_request != '' && github.event.comment.body == 'format-rebase!' && (github.event.comment.author_association == 'COLLABORATOR' || github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER')
-    runs-on: ubuntu-22.04
-    steps:
-    - name: Checkout the latest code
-      uses: actions/checkout@v3
-      with:
-        ref: develop
-        fetch-depth: 0
-        persist-credentials: false
-    - name: Automatic Formatting Rebase
-      env:
-        GITHUB_TOKEN: ${{ secrets.BOT_TOKEN }}
-      run: cp --preserve .github/format-rebase.sh /tmp && /tmp/format-rebase.sh
-    - name: Upload code formatting diffs
-      if: success()
-      uses: actions/upload-artifact@v3
-      with:
-          name: patch
-          path: diff.patch

.github/workflows/bot-pr-created.yml

@@ -8,7 +8,7 @@ jobs:
     if: github.event.pull_request.author_association == 'COLLABORATOR' || github.event.pull_request.author_association == 'MEMBER' || github.event.pull_request.author_association == 'OWNER'
     steps:
       - name: Checkout the latest code (shallow clone)
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: develop
       - name: Add appropriate labels