Merge branch 'next' into adios-io-next-rebase

* next:
  Set oversubscribe flags for openmpi 5
  CI: Replace pip script with requirements.txt
  Add BOUT_HOST_DEVICE to accessor operators for GPU
  hypre3d: Replace finite() with std::isfinite()
  hypre3d: Remove reference to datafile
  Use latest python in CI
  Bump externalpackages/boutdata from `ab59ef9` to `908a4c2`
  Bump externalpackages/googletest from `2dd1c13` to `829c199`
  Bump externalpackages/fmt from `f0903ad` to `2ac6c5c`
  Bump externalpackages/mpark.variant from `3c7fc82` to `23cb94f`
  CI: run only once per week
  Increase shm size in container
  CI: Also build slepc from devel branch
  CI: Run on PETSc developement branch
  Fix test-laplace-petsc3d
  CI: user master branch for OCI workflow
  [RTD] specify tool
  [RTD] add os too read the docs config
  Bump ZedThree/clang-tidy-review from 0.13.1 to 0.14.0
  Bump stefanzweifel/git-auto-commit-action from 4 to 5
  Bump actions/setup-python from 1 to 4
  Increase MG levels for Petsc3DAMG test
  Don't include headers for petsc interface if we're not building it
  Apply clang-format changes
  Fix a whole bunch of clang-tidy issues in petsc interface/AMG solver
  Apply clang-format
  Add defaulted move ctor/assignment for `PetscMatrix::Element`
  Fix getting correct parallel slice for `getWeightsForYApproximation`
  Stop clang-tidy complaining about some short names
  Change some variable names to keep clang-tidy happy
  Apply clang-format changes
  Delete unneeded PetscVectorElement test
  Refactor setting boundary conditions in LaplacePetsc3dAmg
  Set LaplacePetsc3damg options in initialiser list
  Print error in laplace-petsc3d test
  Add a utility function for checking flags in bitsets
  Make sure guard cells in PetscVector buffer are -1
  Fix some clang-tidy issues, mostly multiple declarations on one line
  Replace direct calls to `VecSetValue` with buffered calls
  Make `Field2D::data` private
  Collect all test failures for petsc3d
  Add `size()` method to Fields to get total number of points
  Simplify getting parallel slice interpolation weights
  Use `BoutException` formatted message instead of `std::cout`
  Use default constructor for `Vec/Mat` deleters
  WIP convert petscvector
  Fix lots of clang-tidy issues in PETSc interface
  Docs: Note removal of `./configure` build system
  Remove all autoconf files
  Docs: Remove remaining references to `./configure` from docs
  Fix sphinx configuration
  Bump docker/build-push-action
  Ensure also lower case is accepted
  Bump externalpackages/googletest from `6092810` to `2dd1c13`
  Apply clang-format changes
  Cast reason to int for formatting
  Do not try to print KSPConvergedReason
  CI: Use more system packages
  CI: Reenable petsc
  Try disabeling PETSc
  Bump actions/cache from 2 to 3
  Bump docker/metadata-action
  Bump actions/checkout from 2 to 4
  Bump codecov/codecov-action from 1 to 3
  Bump externalpackages/boututils from `c2e97a2` to `433995f`
  Also give a backtrace if we are hitting a bus error
  Switch back to openmpi
  CI: switch to mpich to workaround openmpi issue
  Switch to fedora packes
  Default to current working directory
  Ensure submodules are present for local testing
  Change default to rawhide
  Prefer dnf5
  Bump required C++ standard to 17

.build_petsc_for_ci.sh

@@ -3,12 +3,13 @@
 set -e
 
 if test $BUILD_PETSC ; then
-    if [[ ! -d $HOME/local/petsc/include/petsc ]]; then
+    if [[ ! -d $HOME/local/petsc/include/petsc ]] || test $1 ; then
 	echo "****************************************"
 	echo "Building PETSc"
 	echo "****************************************"
 
-	git clone -b release https://gitlab.com/petsc/petsc.git petsc --depth=1
+	branch=${1:-release}
+	git clone -b $branch https://gitlab.com/petsc/petsc.git petsc --depth=1
 
 	unset PETSC_DIR
 	unset PETSC_ARCH
@@ -34,7 +35,7 @@ if test $BUILD_PETSC ; then
 	echo "Building SLEPc"
 	echo "****************************************"
 
-    git clone -b release https://gitlab.com/slepc/slepc.git slepc --depth=1
+    git clone -b $branch https://gitlab.com/slepc/slepc.git slepc --depth=1
 
     pushd slepc
 	unset SLEPC_DIR

.ci_fedora.sh

@@ -15,16 +15,19 @@ then
   #         3. docker start -a mobydick                       <=> start to run the container (initialized with docker-cp)
     if test $1 = podman ; then
 	cmd=podman
+	# For the use of testing
+	git submodule update --init # --recursive
     else
 	cmd="sudo docker"
     fi
     test . != ".$2" && mpi="$2" || mpi=openmpi
-    test . != ".$3" && version="$3" || version=latest
+    test . != ".$3" && version="$3" || version=rawhide
     time $cmd pull registry.fedoraproject.org/fedora:$version
     time $cmd create --cap-add=SYS_PTRACE --security-opt seccomp=unconfined \
+	 --shm-size 256M \
          --name mobydick registry.fedoraproject.org/fedora:$version \
 	     /tmp/BOUT-dev/.ci_fedora.sh $mpi
-    time $cmd cp ${TRAVIS_BUILD_DIR} mobydick:/tmp
+    time $cmd cp ${TRAVIS_BUILD_DIR:-$(pwd)} mobydick:/tmp/BOUT-dev
     time $cmd start -a mobydick
     exit 0
 fi
@@ -37,28 +40,34 @@ then
     cat /etc/os-release
     # Ignore weak depencies
     echo "install_weak_deps=False" >> /etc/dnf/dnf.conf
-    time dnf -y install dnf5-plugins python3-pip cmake
+    time dnf -y install dnf5
+    time dnf5 -y install dnf5-plugins cmake python3-zoidberg python3-natsort
     # Allow to override packages - see #2073
-    time dnf copr enable -y davidsch/fixes4bout || :
-    time dnf -y upgrade
-    time dnf -y builddep bout++
+    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
     sudo -u test ${0/\/tmp/\/home\/test} $mpi
 ## If we are called as normal user, run test
 else
-    pip install --user zoidberg natsort
     . /etc/profile.d/modules.sh
     module load mpi/${1}-x86_64
     export OMPI_MCA_rmaps_base_oversubscribe=yes
+    export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe
     export TRAVIS=true
     export FLEXIBLAS=NETLIB
     cd
     cd BOUT-dev
     echo "starting configure"
-    time cmake -S . -B build -DBOUT_USE_PETSC=ON
+    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
+
     time make -C build build-check -j 2
     time make -C build check
 fi

.clang-tidy

@@ -359,5 +359,11 @@ CheckOptions:
     value:           'false'
   - key:             readability-simplify-subscript-expr.Types
     value:           '::std::basic_string;::std::basic_string_view;::std::vector;::std::array'
+  - key:             readability-identifier-length.IgnoredVariableNames
+    value:           '^n?[xyz]$'
+  - key:             readability-identifier-length.IgnoredParameterNames
+    value:           '^[ijkxyz][01]?$'
+  - key:             readability-identifier-length.IgnoredLoopCounterNames
+    value:           '^[ijkxyz_]$'
 ...
 

.github/workflows/black-fix.yml

@@ -20,7 +20,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         ref: ${{ github.head_ref }}
 
@@ -41,6 +41,6 @@ jobs:
         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
+    - uses: stefanzweifel/git-auto-commit-action@v5
       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@v3
+      - uses: actions/checkout@v4
         with:
           ref: ${{ github.head_ref }}
           fetch-depth: 0
@@ -25,6 +25,6 @@ jobs:
         run: git clang-format origin/${{ github.base_ref }}
 
       - name: Commit to the PR branch
-        uses: stefanzweifel/git-auto-commit-action@v4
+        uses: stefanzweifel/git-auto-commit-action@v5
         with:
           commit_message: "Apply clang-format changes"

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

@@ -17,12 +17,12 @@ jobs:
   review:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
 
       - name: Run clang-tidy
-        uses: ZedThree/clang-tidy-review@v0.13.1
+        uses: ZedThree/clang-tidy-review@v0.14.0
         id: review
         with:
           build_dir: build
@@ -46,4 +46,4 @@ jobs:
                              -DBOUT_UPDATE_GIT_SUBMODULE=OFF
 
       - name: Upload clang-tidy fixes
-        uses: ZedThree/clang-tidy-review/upload@v0.13.1
+        uses: ZedThree/clang-tidy-review/upload@v0.14.0

.github/workflows/docker.yml

@@ -52,25 +52,25 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Log in to the Container registry
-        uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1
+        uses: docker/login-action@master
         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
+        uses: docker/metadata-action@master
         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
+        uses: docker/build-push-action@master
         with:
           build-args: |
             BASE=${{ matrix.mpi }}-${{ matrix.metric3d.base_prefix }}${{ matrix.config.base_postfix }}-main

.github/workflows/python-package.yml

@@ -17,12 +17,12 @@ jobs:
     if: always()
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
         submodules: true
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
     - name: Install dependencies
       run: python -m pip install --upgrade pip &&
            pip install --upgrade build &&
@@ -57,12 +57,12 @@ jobs:
     if: always()
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
         submodules: true
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
     - name: Install dependencies
       run: python -m pip install --upgrade pip &&
            pip install --upgrade build &&
@@ -106,12 +106,12 @@ jobs:
     if: always()
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
         submodules: true
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
     - name: Install dependencies
       run: python -m pip install --upgrade pip &&
            pip install --upgrade build &&

.github/workflows/tests.yml

@@ -1,5 +1,10 @@
 name: Tests
-on: [push, pull_request]
+on:
+  push:
+  pull_request:
+  schedule:
+    # run sunday moring
+    - cron: '30 6 * * 0'
 
 defaults:
   run:
@@ -23,17 +28,37 @@ jobs:
       OMP_NUM_THREADS: ${{ matrix.config.omp_num_threads }}
       PYTHONPATH: ${{ github.workspace }}/tools/pylib
       OMPI_MCA_rmaps_base_oversubscribe: yes
+      PRTE_MCA_rmaps_default_mapping_policy: ":oversubscribe"
       MPIRUN: mpiexec -np
     strategy:
       fail-fast: true
       matrix:
         # Need this to be able to exclude the coverage job
         is_master_or_next:
           - ${{ github.ref ==  'refs/heads/master' || github.ref == 'refs/heads/next'  || github.base_ref ==  'master' || github.base_ref == 'next' }}
+        is_cron:
+          - ${{ github.event_name == 'cron' }}
         config:
+          - name: "CMake, PETSc unreleased"
+            os: ubuntu-20.04
+            cmake_options: "-DBUILD_SHARED_LIBS=ON
+                            -DBOUT_ENABLE_METRIC_3D=ON
+                            -DBOUT_ENABLE_OPENMP=ON
+                            -DBOUT_USE_PETSC=ON
+                            -DBOUT_USE_SLEPC=ON
+                            -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_ENABLE_PYTHON=ON
+                            -DSUNDIALS_ROOT=/home/runner/local
+                            -DPETSC_DIR=/home/runner/local/petsc
+                            -DSLEPC_DIR=/home/runner/local/slepc"
+            build_petsc: -petsc-main
+            build_petsc_branch: main
+            on_cron: true
+
           - name: "Default options, Ubuntu 20.04"
             os: ubuntu-20.04
             cmake_options: ""
+            on_cron: false
 
           - name: "Optimised, static"
             os: ubuntu-20.04
@@ -47,6 +72,7 @@ jobs:
                             -DBOUT_USE_SLEPC=ON
                             -DBOUT_USE_SUNDIALS=ON
                             -DSUNDIALS_ROOT=/home/runner/local"
+            on_cron: false
 
           - name: "Debug, shared"
             os: ubuntu-20.04
@@ -58,6 +84,7 @@ jobs:
                             -DBOUT_USE_SLEPC=ON
                             -DBOUT_USE_SUNDIALS=ON
                             -DSUNDIALS_ROOT=/home/runner/local"
+            on_cron: false
 
           - name: "Shared, release, Ubuntu 20.04"
             os: ubuntu-20.04
@@ -70,6 +97,7 @@ jobs:
                             -DBOUT_BUILD_DOCS=OFF
                             -DSUNDIALS_ROOT=/home/runner/local"
             omp_num_threads: 2
+            on_cron: false
 
           - name: "Shared, OpenMP, 3D metrics"
             os: ubuntu-latest
@@ -82,6 +110,7 @@ jobs:
                             -DBOUT_ENABLE_PYTHON=ON
                             -DSUNDIALS_ROOT=/home/runner/local"
             omp_num_threads: 2
+            on_cron: false
 
           - name: "CMake, new PETSc"
             os: ubuntu-20.04
@@ -95,8 +124,8 @@ jobs:
                             -DSUNDIALS_ROOT=/home/runner/local
                             -DPETSC_DIR=/home/runner/local/petsc
                             -DSLEPC_DIR=/home/runner/local/slepc"
-
             build_petsc: -petsc
+            on_cron: false
 
           - name: "Coverage"
             os: ubuntu-20.04
@@ -111,11 +140,15 @@ jobs:
                             -DBOUT_ENABLE_PYTHON=ON
                             -DSUNDIALS_ROOT=/home/runner/local"
             unit_only: YES
+            on_cron: false
         exclude:
           # Don't run the coverage tests if the branch isn't master or next
           - is_master_or_next: false
             config:
               name: "Coverage"
+          - is_cron: true
+            config:
+              on_cron: false
 
     steps:
       - name: Job information
@@ -143,18 +176,21 @@ jobs:
                  liblapack-dev
                  libparpack2-dev
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
 
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.x'
+
       - name: Install pip packages
         run: |
-          ./.pip_install_for_ci.sh 'cython~=0.29' 'netcdf4~=1.5' 'sympy~=1.5' 'gcovr' 'cmake' zoidberg fastcov
-          # Add the pip install location to the runner's PATH
-          echo ~/.local/bin >> $GITHUB_PATH
+          python -m pip install --upgrade pip setuptools
+          python -m pip install -r requirements.txt
 
       - name: Cache SUNDIALS build
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: /home/runner/local
           key: bout-sundials-${{ matrix.config.os }}${{ matrix.config.build_petsc }}
@@ -163,7 +199,7 @@ jobs:
         run: ./.build_sundials_for_ci.sh
 
       - name: Build PETSc
-        run: BUILD_PETSC=${{ matrix.config.build_petsc }} ./.build_petsc_for_ci.sh
+        run: BUILD_PETSC=${{ matrix.config.build_petsc }} ./.build_petsc_for_ci.sh ${{ matrix.config.build_petsc_branch }}
 
       - name: Build BOUT++
         run: UNIT_ONLY=${{ matrix.config.unit_only }} ./.ci_with_cmake.sh ${{ matrix.config.cmake_options }}
@@ -182,15 +218,15 @@ jobs:
 
       - name: Upload coverage
         if: ${{ matrix.config.name == 'Coverage' }}
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v3
 
   Fedora:
     # This is its own job as it doesn't use most of the steps of the
     # standard_tests
     timeout-minutes: 60
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           submodules: true
       - name: Build Fedora rawhide