Merge branch 'next' into next-run-id

* next: (310 commits)
  Note removing support for HDF5 in changelog
  Better notation for indexing zShift
  Update note on zShift in grid-files section of manual
  Print error for HDF5 macros when running bout-v5-macro-upgrader.py
  Support macros being removed in bout-v5-macro-upgrader.py
  Remove HDF5 support
  Removed bout_runners from repo, and redirected to project site
  Allow test-options-netcdf on Fedora
  Add missing brackets in test-options-netcdf
  Skip test-io when using legacy netCDF interface
  clang-format FCIMap constructor
  Add braces around conditional body
  Pass dy by reference
  Guard OptionsNetCDF test against legacy netcdf
  Cache index offsets in FCI boundary loop
  Invert conditional in FCI boundary calculation
  Convert nested-loop to BOUT_FOR in FCI
  Make local variables const
  Pass dy down into FCIMap
  Remove some unused code from FCI
  ...

.github/workflows/clang-format-command.yml

@@ -0,0 +1,50 @@
+name: clang-format-command
+on:
+  repository_dispatch:
+    types: [clang-format-command]
+jobs:
+  clang-format:
+    runs-on: ubuntu-latest
+    steps:
+      # Checkout the pull request branch
+      - uses: actions/checkout@v2
+        with:
+          token: ${{ secrets.REPO_ACCESS_TOKEN }}
+          repository: ${{ github.event.client_payload.pull_request.head.repo.full_name }}
+          ref: ${{ github.event.client_payload.pull_request.head.ref }}
+      # Fetch the merge base too, or git clang-format won't have anything to compare to!
+      - run: |
+          git fetch --no-tags --prune --depth=1 origin ${{ github.event.client_payload.pull_request.base.sha }}
+
+      # This also installs git-clang-format
+      - name: Install clang-format
+        run: sudo apt install clang-format
+
+      # git-clang-format is a bit annoying and doesn't have a proper "quiet" or "check" mode
+      # So we have to hope that the "nothing to do" message doesn't change ever
+      - name: Run clang-format
+        id: format
+        run: |
+          if [[ $(git clang-format-9 --quiet --diff ${{ github.event.client_payload.pull_request.base.sha }}) != "no modified files to format" ]]; then
+              echo "::set-output name=format::true"
+          else
+              echo "::set-output name=format::false"
+          fi
+
+      # Execute clang-format and commit the change to the PR branch
+      - name: Commit to the PR branch
+        if: steps.format.outputs.format == 'true'
+        run: |
+          git clang-format-9 ${{ github.event.client_payload.pull_request.base.sha }}
+          git config --global user.name 'github-actions[bot]'
+          git config --global user.email '41898282+github-actions[bot]@users.noreply.github.com'
+          git commit -am "[clang-format-command] fixes"
+          git push
+
+      - name: Add reaction
+        uses: peter-evans/create-or-update-comment@v1
+        with:
+          token: ${{ secrets.REPO_ACCESS_TOKEN }}
+          repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
+          comment-id: ${{ github.event.client_payload.github.payload.comment.id }}
+          reaction-type: hooray

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

@@ -0,0 +1,51 @@
+name: clang-tidy-review
+
+on: [pull_request]
+
+jobs:
+  review:
+    runs-on: ubuntu-20.04
+    env:
+      PETSC_DIR: /usr/lib/petscdir/3.7.7/x86_64-linux-gnu-real
+      PETSC_ARCH: ""
+      SLEPC_DIR: /usr/lib/slepcdir/3.7.4/x86_64-linux-gnu-real
+      SLEPC_ARCH: ""
+    steps:
+      - name: Install dependencies
+        run: sudo apt update &&
+             sudo apt install -y
+                 libfftw3-dev
+                 libnetcdf-dev
+                 libnetcdf-c++4-dev
+                 netcdf-bin
+                 openmpi-bin
+                 libopenmpi-dev
+                 petsc-dev
+                 slepc-dev
+                 liblapack-dev
+                 libparpack2-dev
+                 libsundials-dev
+
+      - uses: actions/checkout@v2
+        with:
+          submodules: true
+
+      - name: Create compile_commands.json
+        run: |
+          cmake --version
+          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 \
+                           -DCMAKE_EXPORT_COMPILE_COMMANDS=On
+
+      - name: Run clang-tidy
+        uses: ZedThree/[email protected]
+        id: review
+        with:
+          build_dir: build
+          apt_packages: "libfftw3-dev,libnetcdf-c++4-dev,libopenmpi-dev,petsc-dev,slepc-dev,liblapack-dev,libparpack2-dev,libsundials-dev"
+          clang_tidy_checks: '-*,performance-*,readability-*,bugprone-*,clang-analyzer-*,cppcoreguidelines-*,mpi-*,misc-*,-readability-magic-numbers,-cppcoreguidelines-avoid-magic-numbers'
+

.github/workflows/slash-command-dispatch.yml

@@ -0,0 +1,16 @@
+name: Slash Command Dispatch
+on:
+  issue_comment:
+    types: [created]
+jobs:
+  slashCommandDispatch:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Slash Command Dispatch
+        uses: peter-evans/slash-command-dispatch@v1
+        with:
+          token: ${{ secrets.REPO_ACCESS_TOKEN }}
+          reaction-token: ${{ secrets.GITHUB_TOKEN }}
+          commands: clang-format
+          issue-type: pull-request

.github/workflows/tests.yml

@@ -0,0 +1,187 @@
+name: Tests
+on: [push, pull_request]
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  standard_tests:
+    name: ${{ matrix.config.name }}
+    runs-on: ${{ matrix.config.os }}
+    env:
+      BOUT_TEST_TIMEOUT: "6m"
+      PETSC_DIR: /usr/lib/petscdir/3.7.7/x86_64-linux-gnu-real
+      PETSC_ARCH: ""
+      SLEPC_DIR: /usr/lib/slepcdir/3.7.4/x86_64-linux-gnu-real
+      SLEPC_ARCH: ""
+      OMP_NUM_THREADS: ${{ matrix.config.omp_num_threads }}
+      PYTHONPATH: ${{ github.workspace }}/tools/pylib
+      OMPI_MCA_rmaps_base_oversubscribe: yes
+      MPIRUN: mpiexec -np
+    strategy:
+      fail-fast: false
+      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' }}
+        config:
+          - name: "Default options"
+            os: ubuntu-18.04
+            configure_options: "--with-petsc
+                                --with-slepc
+                                --with-sundials=/home/runner/local"
+            script_flags: "-uim"
+
+          - name: "Optimised, shared, Python"
+            os: ubuntu-18.04
+            configure_options: "--enable-shared
+                                --enable-checks=no
+                                --enable-optimize=3
+                                --disable-signal
+                                --disable-track
+                                --disable-backtrace
+                                --with-petsc
+                                --with-slepc
+                                --with-sundials=/home/runner/local"
+            script_flags: "-uim -t shared -t python"
+
+          - name: "Debug, shared"
+            os: ubuntu-18.04
+            configure_options: "--enable-shared
+                                --enable-sigfpe
+                                --enable-debug
+                                --enable-track
+                                --with-petsc
+                                --with-slepc
+                                --with-sundials=/home/runner/local"
+            script_flags: "-uim"
+
+          - name: "OpenMP, shared"
+            os: ubuntu-18.04
+            configure_options: "--enable-shared
+                                --enable-openmp
+                                --with-petsc
+                                --with-slepc
+                                --with-sundials=/home/runner/local"
+            script_flags: "-uim"
+            omp_num_threads: 2
+
+          - name: "CMake, shared, Ubuntu 20.04"
+            os: ubuntu-20.04
+            cmake_options: "-DBUILD_SHARED_LIBS=ON
+                            -DBOUT_ENABLE_OPENMP=ON
+                            -DBOUT_USE_PETSC=ON
+                            -DBOUT_USE_SLEPC=ON
+                            -DBOUT_USE_SUNDIALS=ON
+                            -DSUNDIALS_ROOT=/home/runner/local"
+            omp_num_threads: 2
+
+          - name: "Coverage"
+            os: ubuntu-18.04
+            configure_options: "--enable-shared
+                                --enable-code-coverage
+                                --enable-debug
+                                --enable-track
+                                --with-lapack
+                                --with-petsc
+                                --with-slepc
+                                --with-sundials=/home/runner/local"
+            script_flags: "-u"
+        exclude:
+          # Don't run the coverage tests if the branch isn't master or next
+          - is_master_or_next: false
+            config:
+              name: "Coverage"
+
+    steps:
+      - name: Job information
+        run: |
+          echo Build: ${{ matrix.config.name }}, ${{ matrix.config.os }}
+          echo Configure options: ${{ matrix.config.configure_options }}
+          echo CMake options: ${{ matrix.config.cmake_options }}
+
+      - name: Install dependencies
+        run: sudo apt update &&
+             sudo apt install -y
+                 libfftw3-dev
+                 libnetcdf-dev
+                 libnetcdf-c++4-dev
+                 netcdf-bin
+                 python3
+                 python3-pip
+                 python3-pytest
+                 python3-numpy
+                 python3-scipy
+                 lcov
+                 openmpi-bin
+                 libopenmpi-dev
+                 petsc-dev
+                 slepc-dev
+                 liblapack-dev
+                 libparpack2-dev
+
+      - uses: actions/checkout@v2
+        with:
+          submodules: true
+
+      - name: Install pip packages
+        run: |
+          ./.pip_install_for_travis.sh 'cython~=0.29' 'netcdf4~=1.5' 'sympy~=1.5' 'gcovr' 'cmake' 'h5py'
+          # Add the pip install location to the runner's PATH
+          echo ~/.local/bin >> $GITHUB_PATH
+
+      - name: Cache SUNDIALS build
+        uses: actions/cache@v2
+        with:
+          path: /home/runner/local
+          key: bout-sundials-${{ matrix.config.os }}
+
+      - name: Build SUNDIALS
+        run: ./.build_sundials_for_travis.sh
+
+      - name: Build (configure)
+        if: ${{ ! contains(matrix.config.name, 'CMake') }}
+        run: ./.travis_script.sh ${{ matrix.config.script_flags }}
+        env:
+          LD_LIBRARY_PATH: /home/runner/local/lib:$LD_LIBRARY_PATH
+          CONFIGURE_OPTIONS: ${{ matrix.config.configure_options }}
+
+      - name: Build (CMake)
+        if: ${{ contains(matrix.config.name, 'CMake') }}
+        run: |
+          cmake --version
+          cmake . -B build ${{ matrix.config.cmake_options }}
+          cmake --build build --target build-check -j 2
+          cd build
+          ctest --output-on-failure --timeout 300
+
+      - name: Capture coverage
+        if: ${{ matrix.config.name == 'Coverage' }}
+        # Explicitly run the coverage capture target, because
+        # travis_script.sh also does the upload, and we're going to do
+        # that ourselves in the next step
+        run: |
+          # Ensure that there is a corresponding .gcda file for every .gcno file
+          # This is to try and make the coverage report slightly more accurate
+          # It still won't include, e.g. any solvers we don't build with though
+          find . -name "*.gcno" -exec sh -c 'touch -a "${1%.gcno}.gcda"' _ {} \;
+          make code-coverage-capture
+
+      - name: Upload coverage
+        if: ${{ matrix.config.name == 'Coverage' }}
+        uses: codecov/codecov-action@v1
+
+  Fedora:
+    # This is its own job as it doesn't use most of the steps of the
+    # standard_tests
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: true
+      - name: Build Fedora rawhide
+        run: ./.travis_fedora.sh setup mpich rawhide
+        shell: bash
+        env:
+          TRAVIS_BUILD_DIR: ${{ github.workspace }}

.gitmodules

@@ -10,3 +10,9 @@
 [submodule "externalpackages/fmt"]
 	path = externalpackages/fmt
 	url = https://github.com/fmtlib/fmt.git
+[submodule "externalpackages/boutdata"]
+	path = externalpackages/boutdata
+	url = https://github.com/boutproject/boutdata.git
+[submodule "externalpackages/boututils"]
+	path = externalpackages/boututils
+	url = https://github.com/boutproject/boututils.git