Release 1.4.0 to master

.github/bot-base.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+
+set -e
+
+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}" "$1"
+}
+
+api_post() {
+  curl -X POST -s -H "${AUTH_HEADER}" -H "${API_HEADER}" "$1" -d "$2"
+}
+
+api_patch() {
+  curl -X PATCH -s -H "${AUTH_HEADER}" -H "${API_HEADER}" "$1" -d "$2"
+}
+
+api_delete() {
+  curl -X DELETE -s -H "${AUTH_HEADER}" -H "${API_HEADER}" "$1"
+}

.github/bot-pr-base.sh

@@ -0,0 +1,100 @@
+#!/bin/bash
+
+source .github/bot-base.sh
+
+echo -n "Collecting information on triggering PR"
+PR_URL=$(jq -r .pull_request.url "$GITHUB_EVENT_PATH")
+if [[ "$PR_URL" == "null" ]]; then
+  # if this was triggered by an issue comment: get PR and commenter
+  echo -n .............
+  PR_URL=$(jq -er .issue.pull_request.url "$GITHUB_EVENT_PATH")
+  echo -n .
+  USER_LOGIN=$(jq -er ".comment.user.login" "$GITHUB_EVENT_PATH")
+  echo -n .
+  USER_URL=$(jq -er ".comment.user.url" "$GITHUB_EVENT_PATH")
+  echo -n .
+else
+  # else it was triggered by a PR sync: get PR creator
+  USER_LOGIN=$(jq -er ".pull_request.user.login" "$GITHUB_EVENT_PATH")
+  echo -n .
+  USER_URL=$(jq -er ".pull_request.user.url" "$GITHUB_EVENT_PATH")
+  echo -n .
+fi
+echo -n .
+PR_JSON=$(api_get $PR_URL)
+echo -n .
+PR_MERGED=$(echo "$PR_JSON" | jq -r .merged)
+echo -n .
+ISSUE_URL=$(echo "$PR_JSON" | jq -er ".issue_url")
+echo -n .
+BASE_REPO=$(echo "$PR_JSON" | jq -er .base.repo.full_name)
+echo -n .
+BASE_BRANCH=$(echo "$PR_JSON" | jq -er .base.ref)
+echo -n .
+HEAD_REPO=$(echo "$PR_JSON" | jq -er .head.repo.full_name)
+echo -n .
+HEAD_BRANCH=$(echo "$PR_JSON" | jq -er .head.ref)
+echo .
+
+BASE_URL="https://${GITHUB_ACTOR}:${GITHUB_TOKEN}@github.com/$BASE_REPO"
+HEAD_URL="https://${GITHUB_ACTOR}:${GITHUB_TOKEN}@github.com/$HEAD_REPO"
+
+JOB_URL="https://github.com/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID"
+
+bot_delete_comments_matching() {
+  local search_matching="$1"
+  COMMENTS=$(api_get "$ISSUE_URL/comments" | jq -r '.[] | select((.user.login == "ginkgo-bot") and (.body | startswith('"\"$search_matching\""'))) | .url')
+  for URL in $COMMENTS; do
+    api_delete "$URL" > /dev/null
+  done
+}
+
+bot_comment() {
+  api_post "$ISSUE_URL/comments" "{\"body\":\"$1\"}" > /dev/null
+}
+
+bot_error() {
+  echo "$1"
+  bot_comment "Error: $1"
+  exit 1
+}
+
+bot_get_all_changed_files() {
+  local pr_url="$1"
+  local pr_files=""
+  local page="1"
+  while true; do
+    # this api allows 100 items per page
+    # github action uses `bash -e`. The last empty page will leads jq error, use `|| :` to ignore the error.
+    local pr_page_files=$(api_get "$pr_url/files?&per_page=100&page=${page}" | jq -er '.[] | select(.status != "removed") | .filename' || :)
+    if [ "${pr_page_files}" = "" ]; then
+      break
+    fi
+    if [ ! "${pr_files}" = "" ]; then
+      # add the same new line format as jq output
+      pr_files="${pr_files}"$'\n'
+    fi
+    pr_files="${pr_files}${pr_page_files}"
+    page=$(( page + 1 ))
+  done
+  echo "${pr_files}"
+}
+
+# collect info on the user that invoked the bot
+echo -n "Collecting information on triggering user"
+USER_JSON=$(api_get $USER_URL)
+echo .
+
+USER_NAME=$(echo "$USER_JSON" | jq -r ".name")
+if [[ "$USER_NAME" == "null" ]]; then
+	USER_NAME=$USER_LOGIN
+fi
+USER_EMAIL=$(echo "$USER_JSON" | jq -r ".email")
+if [[ "$USER_EMAIL" == "null" ]]; then
+	USER_EMAIL="$USER_LOGIN@users.noreply.github.com"
+fi
+USER_COMBINED="$USER_NAME <$USER_EMAIL>"
+
+if [[ "$PR_MERGED" == "true" ]]; then
+  bot_error "PR already merged!"
+fi

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

@@ -0,0 +1,44 @@
+#!/bin/bash
+
+source .github/bot-pr-base.sh
+
+EXTENSION_REGEX='\.(cuh?|hpp|hpp\.inc?|cpp)$'
+FORMAT_HEADER_REGEX='^(benchmark|core|cuda|hip|include/ginkgo/core|omp|reference|dpcpp)/'
+FORMAT_REGEX='^(common|examples|test)/'
+
+echo "Retrieving PR file list"
+PR_FILES=$(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 $EXTENSION_REGEX || true)"
+
+git remote add fork "$HEAD_URL"
+git fetch fork "$HEAD_BRANCH"
+
+git config user.email "ginkgo.library@gmail.com"
+git config user.name "ginkgo-bot"
+
+# save scripts from develop
+pushd dev_tools/scripts
+cp add_license.sh format_header.sh update_ginkgo_header.sh /tmp
+popd
+
+# checkout current PR head
+LOCAL_BRANCH=format-tmp-$HEAD_BRANCH
+git checkout -b $LOCAL_BRANCH fork/$HEAD_BRANCH
+
+# restore files from develop
+cp /tmp/add_license.sh dev_tools/scripts/
+cp /tmp/format_header.sh dev_tools/scripts/
+cp /tmp/update_ginkgo_header.sh dev_tools/scripts/
+
+# format files
+CLANG_FORMAT=clang-format-9
+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

.github/check-format.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+cp .github/bot-pr-format-base.sh /tmp
+source /tmp/bot-pr-format-base.sh
+
+# check for changed files, replace newlines by \n
+LIST_FILES=$(git diff --name-only | sed '$!s/$/\\n/' | tr -d '\n')
+
+git diff > /tmp/format.patch
+mv /tmp/format.patch .
+
+bot_delete_comments_matching "Error: The following files need to be formatted"
+
+if [[ "$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

.github/format.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+cp .github/bot-pr-format-base.sh /tmp
+source /tmp/bot-pr-format-base.sh
+
+# check for changed files, replace newlines by \n
+LIST_FILES=$(git diff --name-only | sed '$!s/$/\\n/' | tr -d '\n')
+
+# commit changes if necessary
+if [[ "$LIST_FILES" != "" ]]; then
+  git commit -a -m "Format files
+
+Co-authored-by: $USER_COMBINED"
+  git push fork $LOCAL_BRANCH:$HEAD_BRANCH 2>&1 || bot_error "Cannot push formatted branch, are edits for maintainers allowed?"
+fi

.github/label.sh

@@ -0,0 +1,46 @@
+#!/bin/bash
+
+source .github/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 ${NUM} changed files"
+
+echo "Retrieving PR label list"
+OLD_LABELS=$(api_get "$ISSUE_URL" | jq -er '[.labels | .[] | .name]')
+
+
+label_match() {
+  if echo "$PR_FILES" | grep -qE "$2"; then
+    echo "+[\"$1\"]"
+  fi
+}
+
+LABELS="[]"
+LABELS=$LABELS$(label_match mod:core '(^core/|^include/)')
+LABELS=$LABELS$(label_match mod:reference '^reference/')
+LABELS=$LABELS$(label_match mod:openmp '^omp/')
+LABELS=$LABELS$(label_match mod:cuda '(^cuda/|^common/)')
+LABELS=$LABELS$(label_match mod:hip '(^hip/|^common/)')
+LABELS=$LABELS$(label_match mod:dpcpp '^dpcpp/')
+LABELS=$LABELS$(label_match reg:benchmarking '^benchmark/')
+LABELS=$LABELS$(label_match reg:example '^examples/')
+LABELS=$LABELS$(label_match reg:build '(cm|CM)ake')
+LABELS=$LABELS$(label_match reg:ci-cd '(^\.github/|\.yml$)')
+LABELS=$LABELS$(label_match reg:documentation '^doc/|\.md$')
+LABELS=$LABELS$(label_match reg:testing /test/)
+LABELS=$LABELS$(label_match reg:helper-scripts '^dev_tools/')
+LABELS=$LABELS$(label_match type:factorization /factorization/)
+LABELS=$LABELS$(label_match type:matrix-format /matrix/)
+LABELS=$LABELS$(label_match type:multigrid /multigrid/)
+LABELS=$LABELS$(label_match type:preconditioner /preconditioner/)
+LABELS=$LABELS$(label_match type:reordering /reorder/)
+LABELS=$LABELS$(label_match type:solver /solver/)
+LABELS=$LABELS$(label_match type:stopping-criteria /stop/)
+
+# if all mod: labels present: replace by mod:all
+LABELS=$(echo "$LABELS" | sed 's/.*mod:.*mod:.*mod:.*mod:.*mod:.*mod:[^"]*"\]/[]+["mod:all"]/')
+
+PATCH_BODY=$(jq -rn "{labels:($OLD_LABELS + $LABELS | unique)}")
+api_patch "$ISSUE_URL" "$PATCH_BODY" > /dev/null

.github/rebase.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+
+source .github/bot-pr-base.sh
+
+git remote add base "$BASE_URL"
+git remote add fork "$HEAD_URL"
+
+git fetch base $BASE_BRANCH
+git fetch fork $HEAD_BRANCH
+
+git config user.email "$USER_EMAIL"
+git config user.name "$USER_NAME"
+
+LOCAL_BRANCH=rebase-tmp-$HEAD_BRANCH
+git checkout -b $LOCAL_BRANCH fork/$HEAD_BRANCH
+
+bot_delete_comments_matching "Error: Rebase failed"
+
+# do the rebase
+git rebase base/$BASE_BRANCH 2>&1 || bot_error "Rebase failed, see the related [Action]($JOB_URL) for details"
+
+# push back
+git push --force-with-lease fork $LOCAL_BRANCH:$HEAD_BRANCH 2>&1 || bot_error "Cannot push rebased branch, are edits for maintainers allowed?"

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

@@ -0,0 +1,65 @@
+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@v2
+      with:
+        ref: develop
+    - name: Add appropriate labels
+      env:
+        GITHUB_TOKEN: ${{ secrets.BOT_TOKEN }}
+      run: cp .github/label.sh /tmp && /tmp/label.sh
+  check_format:
+    name: check-format
+    runs-on: ubuntu-18.04
+    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@v2
+      with:
+        ref: develop
+    - name: Check for formatting changes
+      env:
+        GITHUB_TOKEN: ${{ secrets.BOT_TOKEN }}
+      run: cp .github/check-format.sh /tmp && /tmp/check-format.sh
+    - name: Upload code formatting patch
+      if: failure()
+      uses: actions/upload-artifact@v2
+      with:
+          name: patch
+          path: format.patch
+  format:
+    name: format
+    runs-on: ubuntu-18.04
+    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@v2
+      with:
+        ref: develop
+        persist-credentials: false
+    - name: Commit formatting changes
+      env:
+        GITHUB_TOKEN: ${{ secrets.BOT_TOKEN }}
+      run: cp .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@v2
+      with:
+        ref: develop
+        fetch-depth: 0
+        persist-credentials: false
+    - name: Automatic Rebase
+      env:
+        GITHUB_TOKEN: ${{ secrets.BOT_TOKEN }}
+      run: cp .github/rebase.sh /tmp && /tmp/rebase.sh

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

@@ -0,0 +1,18 @@
+on:
+  pull_request_target:
+    types: [opened]
+
+name: OnNewPR
+jobs:
+  label:
+    runs-on: ubuntu-latest
+    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@v2
+        with:
+          ref: develop
+      - name: Add appropriate labels
+        env:
+          GITHUB_TOKEN: ${{ secrets.BOT_TOKEN }}
+        run: .github/label.sh

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

@@ -0,0 +1,24 @@
+on:
+  pull_request_target:
+    types: [opened,synchronize]
+
+name: OnSyncPR
+jobs:
+  check-format:
+    runs-on: ubuntu-18.04
+    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@v2
+        with:
+          ref: develop
+      - name: Check for formatting changes
+        env:
+          GITHUB_TOKEN: ${{ secrets.BOT_TOKEN }}
+        run: cp .github/check-format.sh /tmp && /tmp/check-format.sh
+      - name: Upload code formatting patch
+        if: failure()
+        uses: actions/upload-artifact@v2
+        with:
+          name: patch
+          path: format.patch

.github/workflows/joss.yml

@@ -11,7 +11,9 @@ jobs:
     runs-on: [ubuntu-latest] 
 
     steps:
-    - uses: actions/checkout@v2
+    - name: Checkout the latest code (shallow clone)
+      uses: actions/checkout@v2
+
     - name: setup
       run: sudo apt-get install texlive-xetex pandoc pandoc-citeproc
     - name: info