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Merge release 1.4.0 to master
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Release 1.4.0 to master

The Ginkgo team is proud to announce the new Ginkgo minor release 1.4.0. This
release brings most of the Ginkgo functionality to the Intel DPC++ ecosystem
which enables Intel-GPU and CPU execution. The only Ginkgo features which have
not been ported yet are some preconditioners.

Ginkgo's mixed-precision support is greatly enhanced thanks to:
1. The new Accessor concept, which allows writing kernels featuring on-the-fly
memory compression, among other features. The accessor can be used as
header-only, see the [accessor BLAS benchmarks repository](https://github.com/ginkgo-project/accessor-BLAS/tree/develop) as a usage example.
2. All LinOps now transparently support mixed-precision execution. By default,
this is done through a temporary copy which may have a performance impact but
already allows mixed-precision research.

Native mixed-precision ELL kernels are implemented which do not see this cost.
The accessor is also leveraged in a new CB-GMRES solver which allows for
performance improvements by compressing the Krylov basis vectors. Many other
features have been added to Ginkgo, such as reordering support, a new IDR
solver, Incomplete Cholesky preconditioner, matrix assembly support (only CPU
for now), machine topology information, and more!

Supported systems and requirements:
+ For all platforms, cmake 3.13+
+ C++14 compliant compiler
+ Linux and MacOS
  + gcc: 5.3+, 6.3+, 7.3+, all versions after 8.1+
  + clang: 3.9+
  + Intel compiler: 2018+
  + Apple LLVM: 8.0+
  + CUDA module: CUDA 9.0+
  + HIP module: ROCm 3.5+
  + DPC++ module: Intel OneAPI 2021.3. Set the CXX compiler to `dpcpp`.
+ Windows
  + MinGW and Cygwin: gcc 5.3+, 6.3+, 7.3+, all versions after 8.1+
  + Microsoft Visual Studio: VS 2019
  + CUDA module: CUDA 9.0+, Microsoft Visual Studio
  + OpenMP module: MinGW or Cygwin.


Algorithm and important feature additions:
+ Add a new DPC++ Executor for SYCL execution and other base utilities
  [#648](#648), [#661](#661), [#757](#757), [#832](#832)
+ Port matrix formats, solvers and related kernels to DPC++. For some kernels,
  also make use of a shared kernel implementation for all executors (except
  Reference). [#710](#710), [#799](#799), [#779](#779), [#733](#733), [#844](#844), [#843](#843), [#789](#789), [#845](#845), [#849](#849), [#855](#855), [#856](#856)
+ Add accessors which allow multi-precision kernels, among other things.
  [#643](#643), [#708](#708)
+ Add support for mixed precision operations through apply in all LinOps. [#677](#677)
+ Add incomplete Cholesky factorizations and preconditioners as well as some
  improvements to ILU. [#672](#672), [#837](#837), [#846](#846)
+ Add an AMGX implementation and kernels on all devices but DPC++.
  [#528](#528), [#695](#695), [#860](#860)
+ Add a new mixed-precision capability solver, Compressed Basis GMRES
  (CB-GMRES). [#693](#693), [#763](#763)
+ Add the IDR(s) solver. [#620](#620)
+ Add a new fixed-size block CSR matrix format (for the Reference executor).
  [#671](#671), [#730](#730)
+ Add native mixed-precision support to the ELL format. [#717](#717), [#780](#780)
+ Add Reverse Cuthill-McKee reordering [#500](#500), [#649](#649)
+ Add matrix assembly support on CPUs. [#644](#644)
+ Extends ISAI from triangular to general and spd matrices. [#690](#690)

Other additions:
+ Add the possibility to apply real matrices to complex vectors.
  [#655](#655), [#658](#658)
+ Add functions to compute the absolute of a matrix format. [#636](#636)
+ Add symmetric permutation and improve existing permutations.
  [#684](#684), [#657](#657), [#663](#663)
+ Add a MachineTopology class with HWLOC support [#554](#554), [#697](#697)
+ Add an implicit residual norm criterion. [#702](#702), [#818](#818), [#850](#850)
+ Row-major accessor is generalized to more than 2 dimensions and a new
  "block column-major" accessor has been added. [#707](#707)
+ Add an heat equation example. [#698](#698), [#706](#706)
+ Add ccache support in CMake and CI. [#725](#725), [#739](#739)
+ Allow tuning and benchmarking variables non intrusively. [#692](#692)
+ Add triangular solver benchmark [#664](#664)
+ Add benchmarks for BLAS operations [#772](#772), [#829](#829)
+ Add support for different precisions and consistent index types in benchmarks.
  [#675](#675), [#828](#828)
+ Add a Github bot system to facilitate development and PR management.
  [#667](#667), [#674](#674), [#689](#689), [#853](#853)
+ Add Intel (DPC++) CI support and enable CI on HPC systems. [#736](#736), [#751](#751), [#781](#781)
+ Add ssh debugging for Github Actions CI. [#749](#749)
+ Add pipeline segmentation for better CI speed. [#737](#737)


Changes:
+ Add a Scalar Jacobi specialization and kernels. [#808](#808), [#834](#834), [#854](#854)
+ Add implicit residual log for solvers and benchmarks. [#714](#714)
+ Change handling of the conjugate in the dense dot product. [#755](#755)
+ Improved Dense stride handling. [#774](#774)
+ Multiple improvements to the OpenMP kernels performance, including COO,
an exclusive prefix sum, and more. [#703](#703), [#765](#765), [#740](#740)
+ Allow specialization of submatrix and other dense creation functions in solvers. [#718](#718)
+ Improved Identity constructor and treatment of rectangular matrices. [#646](#646)
+ Allow CUDA/HIP executors to select allocation mode. [#758](#758)
+ Check if executors share the same memory. [#670](#670)
+ Improve test install and smoke testing support. [#721](#721)
+ Update the JOSS paper citation and add publications in the documentation.
  [#629](#629), [#724](#724)
+ Improve the version output. [#806](#806)
+ Add some utilities for dim and span. [#821](#821)
+ Improved solver and preconditioner benchmarks. [#660](#660)
+ Improve benchmark timing and output. [#669](#669), [#791](#791), [#801](#801), [#812](#812)


Fixes:
+ Sorting fix for the Jacobi preconditioner. [#659](#659)
+ Also log the first residual norm in CGS [#735](#735)
+ Fix BiCG and HIP CSR to work with complex matrices. [#651](#651)
+ Fix Coo SpMV on strided vectors. [#807](#807)
+ Fix segfault of extract_diagonal, add short-and-fat test. [#769](#769)
+ Fix device_reset issue by moving counter/mutex to device. [#810](#810)
+ Fix `EnableLogging` superclass. [#841](#841)
+ Support ROCm 4.1.x and breaking HIP_PLATFORM changes. [#726](#726)
+ Decreased test size for a few device tests. [#742](#742)
+ Fix multiple issues with our CMake HIP and RPATH setup.
  [#712](#712), [#745](#745), [#709](#709)
+ Cleanup our CMake installation step. [#713](#713)
+ Various simplification and fixes to the Windows CMake setup. [#720](#720), [#785](#785)
+ Simplify third-party integration. [#786](#786)
+ Improve Ginkgo device arch flags management. [#696](#696)
+ Other fixes and improvements to the CMake setup.
  [#685](#685), [#792](#792), [#705](#705), [#836](#836)
+ Clarification of dense norm documentation [#784](#784)
+ Various development tools fixes and improvements [#738](#738), [#830](#830), [#840](#840)
+ Make multiple operators/constructors explicit. [#650](#650), [#761](#761)
+ Fix some issues, memory leaks and warnings found by MSVC.
  [#666](#666), [#731](#731)
+ Improved solver memory estimates and consistent iteration counts [#691](#691)
+ Various logger improvements and fixes [#728](#728), [#743](#743), [#754](#754)
+ Fix for ForwardIterator requirements in iterator_factory. [#665](#665)
+ Various benchmark fixes. [#647](#647), [#673](#673), [#722](#722)
+ Various CI fixes and improvements. [#642](#642), [#641](#641), [#795](#795), [#783](#783), [#793](#793), [#852](#852)

Related PR: #866
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tcojean authored Aug 23, 2021
2 parents 4678668 + 555f65e commit f811917
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22 changes: 22 additions & 0 deletions .github/bot-base.sh
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#!/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"
}
100 changes: 100 additions & 0 deletions .github/bot-pr-base.sh
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#!/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
44 changes: 44 additions & 0 deletions .github/bot-pr-format-base.sh
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#!/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 "[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

# 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
19 changes: 19 additions & 0 deletions .github/check-format.sh
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#!/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
15 changes: 15 additions & 0 deletions .github/format.sh
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@@ -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
46 changes: 46 additions & 0 deletions .github/label.sh
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@@ -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
23 changes: 23 additions & 0 deletions .github/rebase.sh
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#!/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?"
65 changes: 65 additions & 0 deletions .github/workflows/bot-pr-comment.yml
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@@ -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
18 changes: 18 additions & 0 deletions .github/workflows/bot-pr-created.yml
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@@ -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
24 changes: 24 additions & 0 deletions .github/workflows/bot-pr-updated.yml
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@@ -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
4 changes: 3 additions & 1 deletion .github/workflows/joss.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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
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