Merge pull request #2604 from boutproject/v5.0.0-rc

BOUT++ v5.0.0 release candidate

.ci_fedora.sh

@@ -0,0 +1,64 @@
+#!/bin/sh
+## Copied script from arpack-ng. Please submit fixes also to
+## arpack-ng (if applicable)
+## -e : Make sure all errors cause the script to fail
+## -x be verbose; write what we are doing, as we do it
+set -ex
+## Should we init a container?
+if [ ".$1" = .setup ] || [ ".$1" = .podman ]
+then
+  # fedora
+  #   note: when you PR, docker-cp provides, in the container, the branch associated with the PR (not master where there's nothing new)
+  #         1. docker create --name mobydick IMAGE CMD        <=> create a container (= instance of image) but container is NOT yet started
+  #         2. docker cp -a ${TRAVIS_BUILD_DIR} mobydick:/tmp <=> copy git repository (CI worker, checkout-ed on PR branch) into the container
+  #                                                               note: docker-cp works only if copy from/to containers (not images)
+  #         3. docker start -a mobydick                       <=> start to run the container (initialized with docker-cp)
+    if test $1 = podman ; then
+	cmd=podman
+    else
+	cmd="sudo docker"
+    fi
+    test . != ".$2" && mpi="$2" || mpi=openmpi
+    test . != ".$3" && version="$3" || version=latest
+    time $cmd pull registry.fedoraproject.org/fedora:$version
+    time $cmd create --cap-add=SYS_PTRACE --security-opt seccomp=unconfined \
+         --name mobydick registry.fedoraproject.org/fedora:$version \
+	     /tmp/BOUT-dev/.ci_fedora.sh $mpi
+    time $cmd cp ${TRAVIS_BUILD_DIR} mobydick:/tmp
+    time $cmd start -a mobydick
+    exit 0
+fi
+
+test . != ".$1" && mpi="$1" || mpi=openmpi
+
+## If we are called as root, setup everything
+if [ $UID -eq 0 ]
+then
+    cat /etc/os-release
+    # Ignore weak depencies
+    echo "install_weak_deps=False" >> /etc/dnf/dnf.conf
+    time dnf -y install dnf-plugins-core python3-pip cmake
+    # Allow to override packages - see #2073
+    time dnf copr enable -y davidsch/fixes4bout || :
+    time dnf -y upgrade
+    time dnf -y builddep bout++
+    useradd test
+    cp -a /tmp/BOUT-dev /home/test/
+    chown -R test /home/test
+    chmod u+rwX /home/test -R
+    sudo -u test ${0/\/tmp/\/home\/test} $mpi
+## If we are called as normal user, run test
+else
+    pip install --user zoidberg
+    . /etc/profile.d/modules.sh
+    module load mpi/${1}-x86_64
+    export OMPI_MCA_rmaps_base_oversubscribe=yes
+    export TRAVIS=true
+    export FLEXIBLAS=NETLIB
+    cd
+    cd BOUT-dev
+    echo "starting configure"
+    time cmake -DBOUT_USE_PETSC=ON -S . -B build
+    time make -C build build-check -j 2
+    time make -C build check
+fi

.travis_script.sh → .ci_script.sh

@@ -10,6 +10,7 @@ MMS=0
 TESTS=0
 MAIN_TARGET=
 UPDATE_SCRIPT=0
+CONFIGURE_SHELL=
 
 usage() {
     echo "$0 options are: "
@@ -19,7 +20,7 @@ usage() {
 }
 
 #Handle input flags
-while getopts "cuimt:5" arg;
+while getopts "cuimt:5s:" arg;
 do
     case $arg in
 	c) ### Run the coverage-post job tasks
@@ -43,13 +44,16 @@ do
         5) ### Run the update to version 5 script
             UPDATE_SCRIPT=1
             ;;
+	s) ### Use specific shell to configure
+	    CONFIGURE_SHELL="$OPTARG"
+	    ;;
         *) ### Show usage message
 	    usage
 	    ;;
     esac
 done
 
-./.build_sundials_for_travis.sh
+./.build_sundials_for_ci.sh
 
 if test $UPDATE_SCRIPT -gt 0
 then
@@ -71,7 +75,7 @@ echo "****************************************"
 echo "Configuring with $CONFIGURE_OPTIONS"
 echo "****************************************"
 conf=0
-time ./configure $CONFIGURE_OPTIONS MAKEFLAGS="$MAKEFLAGS" || conf=$?
+time $CONFIGURE_SHELL ./configure $CONFIGURE_OPTIONS MAKEFLAGS="$MAKEFLAGS" || conf=$?
 if test $conf -gt 0
 then
     RED_FG="\033[031m"
@@ -113,11 +117,6 @@ do
     fi
 done
 
-if [[ ${TESTS} == 1 ]]
-then
-    time make build-check
-fi
-
 if [[ ${UNIT} == 1 ]]
 then
     time make check-unit-tests

.ci_with_cmake.sh

@@ -13,8 +13,23 @@ cd ../examples/make-script
 PATH=../../build/bin:$PATH make
 ./test --help
 cd -
-make install -j 2
+# Test bout++Config.cmake
+cd ../examples/conduction
+cmake . -B build -DCMAKE_PREFIX_PATH=../../build
+cmake --build build
+./build/conduction
 cd -
+
+make install -j 2
+rm -rf build
+# Test installation with plain `make`
+cd ../examples/make-script
 rm test
 PATH=../../installed/bin:$PATH make
 ./test --help
+cd -
+# Test installation with CMake
+cd ../examples/conduction
+cmake . -B build -DCMAKE_PREFIX_PATH=../../installed
+cmake --build build
+./build/conduction

.clang-format

@@ -76,6 +76,8 @@ IndentCaseLabels: false
 # IndentPPDirectives: None
 IndentWidth:     2
 IndentWrappedFunctionNames: false
+# requires clang-format 15+
+# InsertBraces: true
 KeepEmptyLinesAtTheStartOfBlocks: true
 MacroBlockBegin: ''
 MacroBlockEnd:   ''
@@ -91,7 +93,7 @@ PenaltyBreakString: 1000
 PenaltyExcessCharacter: 1000000
 PenaltyReturnTypeOnItsOwnLine: 60
 PointerAlignment: Left
-ReflowComments:  true
+ReflowComments:  false
 SortIncludes:    true
 # SortUsingDeclarations: true
 SpaceAfterCStyleCast: false
@@ -105,7 +107,8 @@ SpacesInContainerLiterals: true
 SpacesInCStyleCastParentheses: false
 SpacesInParentheses: false
 SpacesInSquareBrackets: false
-Standard:        Cpp11
+StatementMacros:
+  - BOUT_OMP
+Standard:        c++14
 TabWidth:        8
 UseTab:          Never
-...

.git-blame-ignore-revs

@@ -0,0 +1,3 @@
+# Clang-format whole repo
+d8f14fdddb5ca0fbb32d8e2bf5ac2960d6ac5ce6
+ed2117e6d6826a98b6988e2f18c0c34e408563b6

.github/workflows/black-fix.yml

@@ -0,0 +1,46 @@
+name: black
+
+on:
+  push:
+    paths:
+      - '**.py'
+      - 'bin/**'
+      - '**/runtest'
+      - '**/run'
+      - 'tests/integrated/test_suite'
+      - 'tests/requirements/*'
+      - 'tools/tokamak_grids/**'
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  black:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        ref: ${{ github.head_ref }}
+
+    - name: Install black
+      run: |
+        sudo apt update -y
+        sudo apt -y install python3-pip python3-setuptools python3-wheel
+        pip3 install black
+
+    - name: Version
+      run: |
+        python3 --version
+        $HOME/.local/bin/black --version
+
+    - name: Run black
+      run: |
+        pwd
+        ls
+        $HOME/.local/bin/black tests/ tools/ $(grep -EIlr '^#!.*python.*$' bin/ tests/ tools/ src/ | grep -v _boutpp_build)
+
+    - uses: stefanzweifel/git-auto-commit-action@v4
+      with:
+        commit_message: "Apply black changes"

.github/workflows/clang-format.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Checkout the pull request branch, also include all history
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           ref: ${{ github.head_ref }}
           fetch-depth: 0

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

@@ -5,6 +5,9 @@ on:
     paths:
       - '**.cxx'
       - '**.hxx'
+    branches-ignore:
+      # Release candidate branches tend to have big PRs which causes all sorts of problems
+      - 'v*rc'
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -14,7 +17,7 @@ jobs:
   review:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           submodules: true
 
@@ -29,13 +32,15 @@ jobs:
           # the unit tests until they're fixed or ignored upstream
           exclude: "tests/unit/*cxx"
           cmake_command: |
-            git config --global --add safe.directory '*' &&
+            pip install cmake && \
+            cmake --version && \
+            git config --global --add safe.directory "$GITHUB_WORKSPACE" && \
             cmake . -B build -DBUILD_SHARED_LIBS=ON \
-                             -DBOUT_ENABLE_OPENMP=ON \
                              -DBOUT_USE_PETSC=ON \
                              -DBOUT_USE_SLEPC=ON \
                              -DBOUT_USE_SUNDIALS=ON \
                              -DBOUT_BUILD_EXAMPLES=ON \
                              -DBOUT_BUILD_DOCS=OFF \
                              -DBOUT_ENABLE_PYTHON=OFF \
-                             -DCMAKE_EXPORT_COMPILE_COMMANDS=On
+                             -DCMAKE_EXPORT_COMPILE_COMMANDS=On \
+                             -DBOUT_UPDATE_GIT_SUBMODULE=OFF