Fix docs warnings update

.ci_fedora.sh

@@ -21,11 +21,10 @@ then
 	cmd="sudo docker"
     fi
     test . != ".$2" && mpi="$2" || mpi=openmpi
-    test . != ".$3" && version="$3" || version=rawhide
-    time $cmd pull registry.fedoraproject.org/fedora:$version
+    time $cmd pull ghcr.io/boutproject/bout-container-base:main
     time $cmd create --cap-add=SYS_PTRACE --security-opt seccomp=unconfined \
 	 --shm-size 256M \
-         --name mobydick registry.fedoraproject.org/fedora:$version \
+         --name mobydick ghcr.io/boutproject/bout-container-base:main \
 	     /tmp/BOUT-dev/.ci_fedora.sh $mpi
     time $cmd cp ${TRAVIS_BUILD_DIR:-$(pwd)} mobydick:/tmp/BOUT-dev
     time $cmd start -a mobydick
@@ -34,27 +33,8 @@ fi
 
 test . != ".$1" && mpi="$1" || mpi=openmpi
 
-## If we are called as root, setup everything
-if [ $UID -eq 0 ]
-then
-    cat /etc/os-release
-    # Ignore weak depencies
-    echo "install_weak_deps=False" >> /etc/dnf/dnf.conf
-    echo "minrate=10M" >> /etc/dnf/dnf.conf
-    export FORCE_COLUMNS=200
-    time dnf -y install dnf5
-    time dnf5 -y install dnf5-plugins cmake python3-zoidberg python3-natsort
-    # Allow to override packages - see #2073
-    time dnf5 copr enable -y davidsch/fixes4bout || :
-    time dnf5 -y upgrade
-    time dnf5 -y builddep bout++
-    useradd test
-    cp -a /tmp/BOUT-dev /home/test/
-    chown -R test /home/test
-    chmod u+rwX /home/test -R
-    su - test -c "${0/\/tmp/\/home\/test} $mpi"
 ## If we are called as normal user, run test
-else
+    cp -a /tmp/BOUT-dev /home/test/
     . /etc/profile.d/modules.sh
     module load mpi/${1}-x86_64
     export OMPI_MCA_rmaps_base_oversubscribe=yes
@@ -67,13 +47,15 @@ else
     export OMP_NUM_THREADS=1
     cd
     cd BOUT-dev
+    python3 -m ensurepip
+    python3 -m pip install -r requirements.txt
     echo "starting configure"
     time cmake -S . -B build -DBOUT_USE_PETSC=ON \
 	 -DBOUT_UPDATE_GIT_SUBMODULE=OFF \
 	 -DBOUT_USE_SYSTEM_FMT=ON \
 	 -DBOUT_USE_SYSTEM_MPARK_VARIANT=ON \
-	 -DBOUT_USE_SUNDIALS=ON
+	 -DBOUT_USE_SUNDIALS=ON \
+	 -DBOUT_USE_SYSTEM_CPPTRACE=ON
 
     time make -C build build-check -j 2
     time make -C build check
-fi

.clang-format

@@ -93,6 +93,7 @@ PenaltyBreakString: 1000
 PenaltyExcessCharacter: 1000000
 PenaltyReturnTypeOnItsOwnLine: 60
 PointerAlignment: Left
+QualifierAlignment: Left
 ReflowComments:  false
 SortIncludes:    true
 # SortUsingDeclarations: true

.clang-format-ignore

@@ -0,0 +1,2 @@
+# ignore matlab files
+**/*.m

.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,-clang-analyzer-optin.mpi*,-bugprone-exception-escape,-cppcoreguidelines-pro-bounds-pointer-arithmetic,-readability-function-cognitive-complexity,-misc-no-recursion,-bugprone-easily-swappable-parameters,-readability-identifier-length'
+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,-clang-analyzer-optin.mpi*,-bugprone-exception-escape,-cppcoreguidelines-pro-bounds-pointer-arithmetic,-readability-function-cognitive-complexity,-misc-no-recursion,-bugprone-easily-swappable-parameters,-readability-identifier-length,-cppcoreguidelines-pro-bounds-avoid-unchecked-container-access'
 WarningsAsErrors: ''
 HeaderFilterRegex: ''
 FormatStyle:     file
@@ -9,6 +9,18 @@ CheckOptions:
   # otherwise this breaks `ASSERT` macros!
   - key:             readability-simplify-boolean-expr.IgnoreMacros
     value:           'true'
+
+  - key: misc-include-cleaner.IgnoreHeaders
+    value: 'petsc.*\.h;mpi\.h'
+
+  - key: readability-qualified-auto.IgnoreAliasing
+    value: 'false'
+
+  - key: readability-qualified-auto.AllowedTypes
+    value: 'MPI_Comm'
+
+  - key: misc-include-cleaner.IgnoreHeaders
+    value: 'adios2/.*;bits/.*;cpptrace/.*;petsc.*\.h'
 ---
 
 Disabled checks and reasons:
@@ -17,6 +29,7 @@ These are all basically unavoidable in HPC numeric code:
 -readability-magic-numbers
 -cppcoreguidelines-avoid-magic-numbers
 -cppcoreguidelines-pro-bounds-pointer-arithmetic
+-cppcoreguidelines-pro-bounds-avoid-unchecked-container-access
 -readability-function-cognitive-complexity
 -bugprone-easily-swappable-parameters
 -readability-identifier-length

.clangd

@@ -0,0 +1,6 @@
+Diagnostics:
+  MissingIncludes: Strict
+  ClangTidy:
+    FastCheckFilter: None
+  Includes:
+    IgnoreHeader: ["adios2/.*", "bits/.*", "cpptrace/.*", "petsc.*"]

.docker/fedora/Dockerfile

@@ -1,5 +1,5 @@
-ARG BASE
-FROM ghcr.io/dschwoerer/bout-container-base:$BASE
+ARG BASE=mpich-full-main
+FROM ghcr.io/boutproject/bout-container-base:$BASE
 
 # ----------------------------------------------------------------
 # Build and install BOUT++
@@ -22,18 +22,26 @@ RUN git clone $URL \
  && git checkout $COMMIT \
  && git submodule update --init --recursive
 
-
+ENV HOME=/home/boutuser
 WORKDIR /home/boutuser/BOUT-dev
 
-RUN cmake -S . -B build -DCMAKE_INSTALL_PREFIX=/opt/bout++/ \
+RUN cmake -S . -B build -DCMAKE_INSTALL_PREFIX=/usr/local/ \
+          -DCMAKE_BUILD_TYPE=RelWithDebInfo \
           -DBOUT_GENERATE_FIELDOPS=OFF \
-          -DBOUT_USE_PETSC=ON -DPETSc_ROOT=/opt/petsc \
+          -DBOUT_USE_PETSC=ON -DPETSc_ROOT=/usr/local \
           -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)
+	  $CMAKE_OPTIONS || (cat /home/boutuser/BOUT-dev/build/CMakeFiles/CMake{Output,Error}.log  ; exit 1); \
+    make -C build -j 2 VERBOSE=1; \
+    sudo make -C build install; \
+    rm -rf build
 
+# Add unversioned path for python
+RUN sudo ln -s /usr/local/lib/python3.* /usr/local/lib/python3.x
 
-RUN make -C build -j 2
-RUN sudo make -C build install
+ENV PATH=/usr/local/bin:$PATH \
+    LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH \
+    PYTHONPATH=/usr/local/lib/python3.x/site-packages/:$PYTHONPATH
 
-RUN find /opt/bout++
+# smoke test
+RUN python3 -c 'import boutpp'

.git-blame-ignore-revs

@@ -1,3 +1,22 @@
 # Clang-format whole repo
 d8f14fdddb5ca0fbb32d8e2bf5ac2960d6ac5ce6
 ed2117e6d6826a98b6988e2f18c0c34e408563b6
+# CMake formatting
+17ac13c28aa3b34a0e46dbe87bb3874f6b25e706
+# Added by the bot
+4b010b7634aee1045743be80c268d4644522cd29
+52301380586fdbf890f620c04f689b08d89a6c34
+a71cad2dd6ace5741a754e2ca7daacd4bb094e0e
+83cf77923a4c72e44303354923021acf932b4fd2
+2c2402ed59c91164eaff46dee0f79386b7347e9e
+05b7c571544c3bcb153fce67d12b9ac48947fc2d
+c8f38049359170a34c915e209276238ea66b9a1e
+65880e4af16cb95438437bf057c4b9fdb427b142
+d1cfb8abd6aa5c76e6c1a4d7ab20929c65f8afc2
+8d5cb39e03c2644715a50684f8cd0318b4e82676
+ec69e8838be2dde140a915e50506f8e1ce3cb534
+f2bc0488a298f136294c523bc5ab4086d090059b
+c59626a0498b0cfd1be46f84f0fa38b4855a43cc
+1b4707187a3a85126338303dc766280b8fb2dc56
+b2e2f3575e68f771be2a4341af5fd14e2870469e
+64e4285ec38569f66d31e589a4610cefd16d8076

.github/dependabot.yml

@@ -6,11 +6,6 @@ updates:
         interval: "weekly"
     directory: "/"
 
-  - package-ecosystem: "pip"
-    schedule:
-        interval: "daily"
-    directory: "/"
-
   - package-ecosystem: "github-actions"
     schedule:
       interval: "weekly"

.github/workflows/auto-formatting.yml

@@ -0,0 +1,33 @@
+name: format-command
+
+on:
+  pull_request:
+
+jobs:
+  clang-format:
+    # Release candidate branches tend to have big PRs which causes all sorts of problems
+    if: ${{ !endsWith(github.head_ref, '-rc') }}
+    runs-on: ubuntu-latest
+    steps:
+      # Checkout the pull request branch, also include all history
+      - uses: actions/checkout@v7
+        with:
+          ref: ${{ github.head_ref }}
+          fetch-depth: 0
+
+      - name: "Set up Python"
+        uses: actions/setup-python@v6
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          enable-cache: true
+
+      - name: Install dev tools
+        run: uv sync --only-dev
+
+      - name: Check prek versions are up-to-date
+        run: uv tool run sync-with-uv --check --diff
+
+      - name: Run everything
+        run: uv tool run prek run --show-diff-on-failure --from-ref origin/${{ github.base_ref }}

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

@@ -5,24 +5,23 @@ 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 }}
   cancel-in-progress: true
 
 jobs:
   review:
+    # Release candidate branches tend to have big PRs which causes all sorts of problems
+    if: ${{ !endsWith(github.head_ref, '-rc') }}
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
         with:
           submodules: true
 
       - name: Run clang-tidy
-        uses: ZedThree/clang-tidy-review@v0.20.1
+        uses: ZedThree/clang-tidy-review@v0.23.1
         id: review
         with:
           build_dir: build
@@ -47,4 +46,4 @@ jobs:
                              -DBOUT_UPDATE_GIT_SUBMODULE=OFF
 
       - name: Upload clang-tidy fixes
-        uses: ZedThree/clang-tidy-review/upload@v0.20.1
+        uses: ZedThree/clang-tidy-review/upload@v0.23.1

.github/workflows/docker.yml

@@ -6,7 +6,7 @@ on:
       - master
       - next
       # Add your branch here if you want containers for it
-      - db-WIP
+      - fix3121
       - docker-ci
 
 env:
@@ -26,18 +26,18 @@ jobs:
       matrix:
         mpi: [mpich]
         metric3d:
-          - name: "With OpenMP"
+          - name: "With 3D Metrics"
             cmake: ON
-            base_prefix: "openmp-"
+            base_prefix: ""
             tag_prefix: "3d-"
-          - name: "Without OpenMP"
+          - name: "With 2D Metrics"
             cmake: OFF
             base_prefix: ""
             tag_prefix: ""
         config:
           - name: "Debug"
             tag_postfix: "debug"
-            options: "-DCHECK=3"
+            options: "-DCHECK=4"
             base_postfix: "mini"
 
           - name: "Optimised"
@@ -47,12 +47,12 @@ jobs:
 
           - name: "Full"
             tag_postfix: "full"
-            options: "-DCHECK=3"
+            options: "-DCHECK=4"
             base_postfix: "full"
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
 
       - name: Log in to the Container registry
         uses: docker/login-action@master
@@ -75,7 +75,7 @@ jobs:
           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=${{ matrix.metric3d.cmake }}
+            CMAKE_OPTIONS=${{ matrix.config.options }} -DBOUT_ENABLE_METRIC_3D=${{ matrix.metric3d.cmake }}
             COMMIT=${{ github.sha }}
             URL=${{ github.server_url }}/${{ github.repository }}
           context: .docker/fedora/