5.1 release candidate

.build_petsc_for_ci.sh

@@ -20,7 +20,7 @@ if test $BUILD_PETSC ; then
 	    --with-scalar-type=real \
 	    --with-shared-libraries=1 \
 	    --with-debugging=0 \
-	    {C,CXX,F}OPTFLAGS="-O3 -march=native" \
+	    {C,CXX,F}OPTFLAGS="-O3" \
 	    --prefix=$HOME/local/petsc
 
 	make && make install

.ci_fedora.sh

@@ -37,7 +37,7 @@ 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
+    time dnf -y install dnf5-plugins python3-pip cmake
     # Allow to override packages - see #2073
     time dnf copr enable -y davidsch/fixes4bout || :
     time dnf -y upgrade
@@ -58,7 +58,7 @@ else
     cd
     cd BOUT-dev
     echo "starting configure"
-    time cmake -DBOUT_USE_PETSC=ON -S . -B build
+    time cmake -S . -B build -DBOUT_USE_PETSC=ON
     time make -C build build-check -j 2
     time make -C build check
 fi

.ci_with_cmake.sh

@@ -3,13 +3,23 @@
 set -ex
 
 cmake --version
-cmake . -B build $@ -DCMAKE_INSTALL_PREFIX=$(pwd)/installed
+cmake -S . -B build $@ -DCMAKE_INSTALL_PREFIX=$(pwd)/installed
+
+if test ".$UNIT_ONLY" = ".YES" ; then
+    make -C build build-check-unit-tests
+    make -C build check-unit-tests
+    exit 0
+fi
+
 cmake --build build --target build-check -j 2
 cd build
 ctest --output-on-failure --timeout 300
 
+export LD_LIBRARY_PATH=/home/runner/local/lib:$LD_LIBRARY_PATH
+
 # Test bout-config basic functionallity
 cd ../examples/make-script
+PATH=../../build/bin:$PATH bout-config --all
 PATH=../../build/bin:$PATH make
 ./test --help
 cd -
@@ -25,6 +35,7 @@ rm -rf build
 # Test installation with plain `make`
 cd ../examples/make-script
 rm test
+PATH=../../installed/bin:$PATH bout-config --all
 PATH=../../installed/bin:$PATH make
 ./test --help
 cd -

.clang-tidy

@@ -1,5 +1,5 @@
 ---
-Checks:          'clang-diagnostic-*,clang-analyzer-*,-*,performance-*,readability-*,bugprone-*,clang-analyzer-*,cppcoreguidelines-*,mpi-*,misc-*,-readability-magic-numbers,-cppcoreguidelines-avoid-magic-numbers,-misc-non-private-member-variables-in-classes,-cppcoreguidelines-pro-bounds-array-to-pointer-decay,-cppcoreguidelines-pro-type-vararg,-clang-analyzer-optin.mpi*,-bugprone-exception-escape,-cppcoreguidelines-pro-bounds-pointer-arithmetic'
+Checks:          'clang-diagnostic-*,clang-analyzer-*,-*,performance-*,readability-*,bugprone-*,clang-analyzer-*,cppcoreguidelines-*,mpi-*,misc-*,-readability-magic-numbers,-cppcoreguidelines-avoid-magic-numbers,-misc-non-private-member-variables-in-classes,-cppcoreguidelines-pro-bounds-array-to-pointer-decay,-cppcoreguidelines-pro-type-vararg,-clang-analyzer-optin.mpi*,-bugprone-exception-escape,-cppcoreguidelines-pro-bounds-pointer-arithmetic,-readability-function-cognitive-complexity'
 WarningsAsErrors: ''
 HeaderFilterRegex: ''
 AnalyzeTemporaryDtors: false

.docker/build.sh

@@ -0,0 +1,29 @@
+set -ex
+
+if which docker &> /dev/null ; then
+    cmd="time sudo docker"
+else
+    cmd="time podman"
+fi
+
+file=$1
+(test $file && test -f $file) || file=.docker/fedora/Dockerfile
+test $# -gt 0 && shift
+
+if test -x $file
+then
+    COMMIT=$(git rev-parse HEAD) $file $@ > Dockerfile
+else
+    cp $file Dockerfile
+fi
+
+$cmd login -p $DOCKER_TOKEN -u $DOCKER_USER
+
+cat Dockerfile
+
+$cmd build -t mobydick . --build-arg=COMMIT=$(git rev-parse HEAD) --build-arg=MPI=$MPI --build-arg=CMAKE_OPTIONS="$CMAKE_OPTIONS" --build-arg=BASE=$BASE
+for tag in $TAGS
+do
+    $cmd tag mobydick $tag
+    $cmd push $tag
+done

.docker/fedora/Dockerfile

@@ -0,0 +1,39 @@
+ARG BASE
+FROM ghcr.io/dschwoerer/bout-container-base:$BASE
+
+# ----------------------------------------------------------------
+# Build and install BOUT++
+# ----------------------------------------------------------------
+# user: boutuser
+# password: boutforever
+
+ARG MPI
+ARG URL
+ARG COMMIT
+ARG CMAKE_OPTIONS
+
+RUN sudo ls
+
+# Checkout submodules now so configure later is fast, and iterating on
+# it less painful
+RUN git clone $URL \
+ && chown -R boutuser /home/boutuser/BOUT-dev \
+ && cd BOUT-dev \
+ && git checkout $COMMIT \
+ && git submodule update --init --recursive
+
+
+WORKDIR /home/boutuser/BOUT-dev
+
+RUN cmake -S . -B build -DCMAKE_INSTALL_PREFIX=/opt/bout++/ \
+          -DBOUT_GENERATE_FIELDOPS=OFF \
+          -DBOUT_USE_PETSC=ON -DPETSc_ROOT=/opt/petsc \
+          -DBOUT_ENABLE_PYTHON=ON \
+          -DBOUT_USE_SUNDIALS=ON -DSUNDIALS_ROOT=/usr/lib64/$MPI/ -DSUNDIALS_INCLUDE_DIR=/usr/include/$MPI-x86_64/sundials/ \
+	  $CMAKE_OPTIONS || (cat /home/boutuser/BOUT-dev/build/CMakeFiles/CMake{Output,Error}.log  ; exit 1)
+
+
+RUN make -C build -j 2
+RUN sudo make -C build install
+
+RUN find /opt/bout++

.github/dependabot.yml

@@ -0,0 +1,17 @@
+version: 2
+
+updates:
+  - package-ecosystem: "gitsubmodule"
+    schedule:
+        interval: "daily"
+    directory: "/"
+
+  - package-ecosystem: "pip"
+    schedule:
+        interval: "daily"
+    directory: "/"
+
+  - package-ecosystem: "github-actions"
+    schedule:
+      interval: "weekly"
+    directory: "/"

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

@@ -22,7 +22,7 @@ jobs:
           submodules: true
 
       - name: Run clang-tidy
-        uses: ZedThree/clang-tidy-review@v0.8.4
+        uses: ZedThree/clang-tidy-review@v0.13.1
         id: review
         with:
           build_dir: build
@@ -44,3 +44,6 @@ jobs:
                              -DBOUT_ENABLE_PYTHON=OFF \
                              -DCMAKE_EXPORT_COMPILE_COMMANDS=On \
                              -DBOUT_UPDATE_GIT_SUBMODULE=OFF
+
+      - name: Upload clang-tidy fixes
+        uses: ZedThree/clang-tidy-review/[email protected]

.github/workflows/docker.yml

@@ -0,0 +1,84 @@
+name: Docker
+
+on:
+  push:
+    branches:
+      - master
+      - next
+      # Add your branch here if you want containers for it
+      - db-WIP
+      - docker-ci
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build:
+    name: Build ${{ matrix.config.name }} Container (${{ matrix.metric3d.name }} ; ${{matrix.mpi}})
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        mpi: [mpich]
+        metric3d:
+          - name: "With OpenMP"
+            cmake: ON
+            base_prefix: "openmp-"
+            tag_prefix: "3d-"
+          - name: "Without OpenMP"
+            cmake: OFF
+            base_prefix: ""
+            tag_prefix: ""
+        config:
+          - name: "Debug"
+            tag_postfix: "debug"
+            options: "-DCHECK=3"
+            base_postfix: "mini"
+
+          - name: "Optimised"
+            tag_postfix: "opt"
+            options: "-DCHECK=0"
+            base_postfix: "mini"
+
+          - name: "Full"
+            tag_postfix: "full"
+            options: "-DCHECK=3"
+            base_postfix: "full"
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          flavor: |
+            prefix=${{ matrix.mpi }}-${{matrix.metric3d.tag_prefix}}${{ matrix.config.tag_postfix }}-
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@f2a1d5e99d037542a71f64918e516c093c6f3fc4
+        with:
+          build-args: |
+            BASE=${{ matrix.mpi }}-${{ matrix.metric3d.base_prefix }}${{ matrix.config.base_postfix }}-main
+            MPI=${{ matrix.mpi }}
+            CMAKE_OPTIONS=${{ matrix.config.options }} -DBOUT_ENABLE_METRIC_3D=${{ matrix.metric3d.cmake }} -DBOUT_ENABLE_OPENMP=${{ matrix.metric3d.cmake }}
+            COMMIT=${{ github.sha }}
+            URL=${{ github.server_url }}/${{ github.repository }}
+          context: .docker/fedora/
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}