Merge branch 'next' into options-array-ints-rebase

.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
@@ -37,19 +40,19 @@ 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
@@ -58,7 +61,12 @@ else
     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:
@@ -30,10 +35,29 @@ jobs:
         # 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 +71,7 @@ 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 +83,7 @@ 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 +96,7 @@ 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 +109,7 @@ 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 +123,8 @@ 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 +139,15 @@ 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 +175,22 @@ 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
 
       - 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

.readthedocs.yaml

@@ -15,12 +15,14 @@ sphinx:
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-   version: 3.8
    install:
    - requirements: manual/sphinx/requirements.txt
 
 
 build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.8"
   apt_packages:
     - mpich
     - libmpich-dev