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Merge pull request #2604 from boutproject/v5.0.0-rc
BOUT++ v5.0.0 release candidate
2 parents ea1f962 + 779ed3c commit d935fa1

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.build_sundials_for_travis.sh renamed to .build_sundials_for_ci.sh

File renamed without changes.

‎.ci_fedora.sh‎

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#!/bin/sh
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## Copied script from arpack-ng. Please submit fixes also to
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## arpack-ng (if applicable)
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## -e : Make sure all errors cause the script to fail
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## -x be verbose; write what we are doing, as we do it
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set -ex
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## Should we init a container?
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if [ ".$1" = .setup ] || [ ".$1" = .podman ]
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then
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# fedora
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# note: when you PR, docker-cp provides, in the container, the branch associated with the PR (not master where there's nothing new)
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# 1. docker create --name mobydick IMAGE CMD <=> create a container (= instance of image) but container is NOT yet started
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# 2. docker cp -a ${TRAVIS_BUILD_DIR} mobydick:/tmp <=> copy git repository (CI worker, checkout-ed on PR branch) into the container
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# note: docker-cp works only if copy from/to containers (not images)
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# 3. docker start -a mobydick <=> start to run the container (initialized with docker-cp)
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if test $1 = podman ; then
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cmd=podman
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else
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cmd="sudo docker"
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fi
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test . != ".$2" && mpi="$2" || mpi=openmpi
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test . != ".$3" && version="$3" || version=latest
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time $cmd pull registry.fedoraproject.org/fedora:$version
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time $cmd create --cap-add=SYS_PTRACE --security-opt seccomp=unconfined \
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--name mobydick registry.fedoraproject.org/fedora:$version \
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/tmp/BOUT-dev/.ci_fedora.sh $mpi
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time $cmd cp ${TRAVIS_BUILD_DIR} mobydick:/tmp
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time $cmd start -a mobydick
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exit 0
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fi
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test . != ".$1" && mpi="$1" || mpi=openmpi
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## If we are called as root, setup everything
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if [ $UID -eq 0 ]
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then
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cat /etc/os-release
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# Ignore weak depencies
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echo "install_weak_deps=False" >> /etc/dnf/dnf.conf
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time dnf -y install dnf-plugins-core python3-pip cmake
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# Allow to override packages - see #2073
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time dnf copr enable -y davidsch/fixes4bout || :
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time dnf -y upgrade
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time dnf -y builddep bout++
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useradd test
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cp -a /tmp/BOUT-dev /home/test/
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chown -R test /home/test
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chmod u+rwX /home/test -R
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sudo -u test ${0/\/tmp/\/home\/test} $mpi
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## If we are called as normal user, run test
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else
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pip install --user zoidberg
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. /etc/profile.d/modules.sh
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module load mpi/${1}-x86_64
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export OMPI_MCA_rmaps_base_oversubscribe=yes
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export TRAVIS=true
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export FLEXIBLAS=NETLIB
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cd
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cd BOUT-dev
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echo "starting configure"
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time cmake -DBOUT_USE_PETSC=ON -S . -B build
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time make -C build build-check -j 2
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time make -C build check
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fi

.travis_script.sh renamed to .ci_script.sh

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TESTS=0
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MAIN_TARGET=
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UPDATE_SCRIPT=0
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CONFIGURE_SHELL=
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usage() {
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echo "$0 options are: "
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}
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#Handle input flags
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while getopts "cuimt:5" arg;
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while getopts "cuimt:5s:" arg;
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do
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case $arg in
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c) ### Run the coverage-post job tasks
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5) ### Run the update to version 5 script
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UPDATE_SCRIPT=1
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;;
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s) ### Use specific shell to configure
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CONFIGURE_SHELL="$OPTARG"
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;;
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*) ### Show usage message
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usage
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;;
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esac
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done
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./.build_sundials_for_travis.sh
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./.build_sundials_for_ci.sh
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if test $UPDATE_SCRIPT -gt 0
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then
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echo "Configuring with $CONFIGURE_OPTIONS"
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echo "****************************************"
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conf=0
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time ./configure $CONFIGURE_OPTIONS MAKEFLAGS="$MAKEFLAGS" || conf=$?
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time $CONFIGURE_SHELL ./configure $CONFIGURE_OPTIONS MAKEFLAGS="$MAKEFLAGS" || conf=$?
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if test $conf -gt 0
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then
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RED_FG="\033[031m"
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fi
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done
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if [[ ${TESTS} == 1 ]]
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then
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time make build-check
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fi
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if [[ ${UNIT} == 1 ]]
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then
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time make check-unit-tests

‎.ci_with_cmake.sh‎

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PATH=../../build/bin:$PATH make
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./test --help
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cd -
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make install -j 2
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# Test bout++Config.cmake
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cd ../examples/conduction
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cmake . -B build -DCMAKE_PREFIX_PATH=../../build
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cmake --build build
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./build/conduction
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cd -
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make install -j 2
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rm -rf build
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# Test installation with plain `make`
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cd ../examples/make-script
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rm test
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PATH=../../installed/bin:$PATH make
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./test --help
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cd -
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# Test installation with CMake
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cd ../examples/conduction
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cmake . -B build -DCMAKE_PREFIX_PATH=../../installed
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cmake --build build
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./build/conduction

‎.clang-format‎

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# IndentPPDirectives: None
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IndentWidth: 2
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IndentWrappedFunctionNames: false
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# requires clang-format 15+
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# InsertBraces: true
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KeepEmptyLinesAtTheStartOfBlocks: true
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MacroBlockBegin: ''
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MacroBlockEnd: ''
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PenaltyExcessCharacter: 1000000
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PenaltyReturnTypeOnItsOwnLine: 60
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PointerAlignment: Left
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ReflowComments: true
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ReflowComments: false
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SortIncludes: true
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# SortUsingDeclarations: true
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SpaceAfterCStyleCast: false
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SpacesInCStyleCastParentheses: false
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SpacesInParentheses: false
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SpacesInSquareBrackets: false
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Standard: Cpp11
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StatementMacros:
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- BOUT_OMP
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Standard: c++14
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TabWidth: 8
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UseTab: Never
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...

‎.git-blame-ignore-revs‎

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# Clang-format whole repo
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d8f14fdddb5ca0fbb32d8e2bf5ac2960d6ac5ce6
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ed2117e6d6826a98b6988e2f18c0c34e408563b6

‎.github/workflows/black-fix.yml‎

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name: black
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on:
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push:
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paths:
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- '**.py'
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- 'bin/**'
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- '**/runtest'
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- '**/run'
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- 'tests/integrated/test_suite'
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- 'tests/requirements/*'
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- 'tools/tokamak_grids/**'
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defaults:
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run:
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shell: bash
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jobs:
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black:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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with:
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ref: ${{ github.head_ref }}
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- name: Install black
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run: |
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sudo apt update -y
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sudo apt -y install python3-pip python3-setuptools python3-wheel
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pip3 install black
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- name: Version
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run: |
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python3 --version
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$HOME/.local/bin/black --version
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- name: Run black
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run: |
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pwd
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ls
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$HOME/.local/bin/black tests/ tools/ $(grep -EIlr '^#!.*python.*$' bin/ tests/ tools/ src/ | grep -v _boutpp_build)
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- uses: stefanzweifel/git-auto-commit-action@v4
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with:
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commit_message: "Apply black changes"

‎.github/workflows/clang-format.yml‎

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runs-on: ubuntu-latest
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steps:
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# Checkout the pull request branch, also include all history
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- uses: actions/checkout@v2
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- uses: actions/checkout@v3
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with:
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ref: ${{ github.head_ref }}
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fetch-depth: 0

‎.github/workflows/clang-tidy-review.yml‎

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paths:
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- '**.cxx'
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- '**.hxx'
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branches-ignore:
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# Release candidate branches tend to have big PRs which causes all sorts of problems
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- 'v*rc'
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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review:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v3
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with:
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submodules: true
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# the unit tests until they're fixed or ignored upstream
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exclude: "tests/unit/*cxx"
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cmake_command: |
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git config --global --add safe.directory '*' &&
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pip install cmake && \
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cmake --version && \
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git config --global --add safe.directory "$GITHUB_WORKSPACE" && \
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cmake . -B build -DBUILD_SHARED_LIBS=ON \
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-DBOUT_ENABLE_OPENMP=ON \
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-DBOUT_USE_PETSC=ON \
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-DBOUT_USE_SLEPC=ON \
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-DBOUT_USE_SUNDIALS=ON \
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-DBOUT_BUILD_EXAMPLES=ON \
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-DBOUT_BUILD_DOCS=OFF \
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-DBOUT_ENABLE_PYTHON=OFF \
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-DCMAKE_EXPORT_COMPILE_COMMANDS=On
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-DCMAKE_EXPORT_COMPILE_COMMANDS=On \
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-DBOUT_UPDATE_GIT_SUBMODULE=OFF

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