Merge remote-tracking branch 'remotes/boutproject/next' into refactor…

…-coordinates-with-next-merged-in
tomc271 · Jan 28, 2025 · 4b5bee3 · 4b5bee3
2 parents e117fa5 + 1a002d2
commit 4b5bee3
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diff --git a/.ci_fedora.sh b/.ci_fedora.sh
@@ -40,6 +40,7 @@ then
     cat /etc/os-release
     # Ignore weak depencies
     echo "install_weak_deps=False" >> /etc/dnf/dnf.conf
+    echo "minrate=10M" >> /etc/dnf/dnf.conf
     time dnf -y install dnf5
     time dnf5 -y install dnf5-plugins cmake python3-zoidberg python3-natsort
     # Allow to override packages - see #2073
@@ -58,7 +59,11 @@ else
     export OMPI_MCA_rmaps_base_oversubscribe=yes
     export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe
     export TRAVIS=true
+    # Try limiting openmp threads
     export FLEXIBLAS=NETLIB
+    export MKL_NUM_THREADS=1
+    export NUMEXPR_NUM_THREADS=1
+    export OMP_NUM_THREADS=1
     cd
     cd BOUT-dev
     echo "starting configure"

diff --git a/.clang-tidy b/.clang-tidy
@@ -1,18 +1,10 @@
 ---
-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'
+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'
 WarningsAsErrors: ''
 HeaderFilterRegex: ''
 FormatStyle:     file
 CheckOptions:
 
-  # Allow some common short names
-  - key:             readability-identifier-length.IgnoredVariableNames
-    value:           '^[dn]?[xyz]$'
-  - key:             readability-identifier-length.IgnoredParameterNames
-    value:           '^[dfijknxyz][01xyz]?$'
-  - key:             readability-identifier-length.IgnoredLoopCounterNames
-    value:           '^[ijkxyz_]$'
-
   # Don't expand macros when simplifying boolean expressions,
   # otherwise this breaks `ASSERT` macros!
   - key:             readability-simplify-boolean-expr.IgnoreMacros
@@ -27,6 +19,7 @@ These are all basically unavoidable in HPC numeric code:
 -cppcoreguidelines-pro-bounds-pointer-arithmetic
 -readability-function-cognitive-complexity
 -bugprone-easily-swappable-parameters
+-readability-identifier-length
 
 This doesn't work very well:
 -clang-analyzer-optin.mpi*

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -3,7 +3,7 @@ version: 2
 updates:
   - package-ecosystem: "gitsubmodule"
     schedule:
-        interval: "daily"
+        interval: "weekly"
     directory: "/"
 
   - package-ecosystem: "pip"

diff --git a/.github/workflows/clang-tidy-review.yml b/.github/workflows/clang-tidy-review.yml
@@ -22,15 +22,17 @@ jobs:
           submodules: true
 
       - name: Run clang-tidy
-        uses: ZedThree/clang-tidy-review@v0.14.0
+        uses: ZedThree/clang-tidy-review@v0.19.0
         id: review
         with:
+          annotations: true
           build_dir: build
           apt_packages: "libfftw3-dev,libnetcdf-c++4-dev,libopenmpi-dev,petsc-dev,slepc-dev,liblapack-dev,libparpack2-dev,libsundials-dev,uuid-dev"
           config_file: ".clang-tidy"
           # Googletest triggers a _lot_ of clang-tidy warnings, so ignore all
           # the unit tests until they're fixed or ignored upstream
           exclude: "tests/unit/*cxx"
+          lgtm_comment_body: ''
           cmake_command: |
             pip install --break-system-packages cmake && \
             cmake --version && \
@@ -46,4 +48,4 @@ jobs:
                              -DBOUT_UPDATE_GIT_SUBMODULE=OFF
 
       - name: Upload clang-tidy fixes
-        uses: ZedThree/clang-tidy-review/upload@v0.14.0
+        uses: ZedThree/clang-tidy-review/upload@v0.19.0
diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
@@ -22,7 +22,7 @@ jobs:
         fetch-depth: 0
         submodules: true
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
     - name: Install dependencies
       run: python -m pip install --upgrade pip &&
            pip install --upgrade build &&
@@ -62,7 +62,7 @@ jobs:
         fetch-depth: 0
         submodules: true
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
     - name: Install dependencies
       run: python -m pip install --upgrade pip &&
            pip install --upgrade build &&
@@ -111,7 +111,7 @@ jobs:
         fetch-depth: 0
         submodules: true
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
     - name: Install dependencies
       run: python -m pip install --upgrade pip &&
            pip install --upgrade build &&

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -47,9 +47,10 @@ jobs:
                             -DBOUT_USE_PETSC=ON
                             -DBOUT_USE_SLEPC=ON
                             -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_USE_HYPRE=OFF
                             -DBOUT_USE_ADIOS2=ON
                             -DBOUT_ENABLE_PYTHON=ON
-                            -DADIOS2_ROOT=/home/runner/local/adios2
+                            -DADIOS2_ROOT=/home/runner/local
                             -DSUNDIALS_ROOT=/home/runner/local
                             -DPETSC_DIR=/home/runner/local/petsc
                             -DSLEPC_DIR=/home/runner/local/slepc"
@@ -74,18 +75,20 @@ jobs:
                             -DBOUT_USE_PETSC=ON
                             -DBOUT_USE_SLEPC=ON
                             -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_USE_HYPRE=ON
                             -DSUNDIALS_ROOT=/home/runner/local"
             on_cron: false
 
           - name: "Debug, shared"
             os: ubuntu-latest
-            cmake_options: "-DCHECK=3
+            cmake_options: "-DCHECK=4
                             -DCMAKE_BUILD_TYPE=Debug
                             -DBOUT_ENABLE_SIGNAL=ON
                             -DBOUT_ENABLE_TRACK=ON
                             -DBOUT_USE_PETSC=ON
                             -DBOUT_USE_SLEPC=ON
                             -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_USE_HYPRE=ON
                             -DSUNDIALS_ROOT=/home/runner/local"
             on_cron: false
 
@@ -97,6 +100,7 @@ jobs:
                             -DBOUT_USE_PETSC=ON
                             -DBOUT_USE_SLEPC=ON
                             -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_USE_HYPRE=ON
                             -DBOUT_BUILD_DOCS=OFF
                             -DSUNDIALS_ROOT=/home/runner/local"
             omp_num_threads: 2
@@ -110,6 +114,7 @@ jobs:
                             -DBOUT_USE_PETSC=ON
                             -DBOUT_USE_SLEPC=ON
                             -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_USE_HYPRE=OFF
                             -DBOUT_ENABLE_PYTHON=ON
                             -DSUNDIALS_ROOT=/home/runner/local"
             omp_num_threads: 2
@@ -123,32 +128,15 @@ jobs:
                             -DBOUT_USE_PETSC=ON
                             -DBOUT_USE_SLEPC=ON
                             -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_USE_HYPRE=OFF
                             -DBOUT_ENABLE_PYTHON=ON
                             -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-latest
-            cmake_options: "-DBUILD_SHARED_LIBS=ON
-                            -DCMAKE_BUILD_TYPE=Debug
-                            -DCHECK=3
-                            -DENABLE_COVERAGE=ON
-                            -DBOUT_USE_PETSC=ON
-                            -DBOUT_USE_SLEPC=ON
-                            -DBOUT_USE_HDF5=ON
-                            -DBOUT_USE_SUNDIALS=ON
-                            -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
@@ -178,12 +166,13 @@ jobs:
                  slepc-dev
                  liblapack-dev
                  libparpack2-dev
+                 libhypre-dev
 
       - uses: actions/checkout@v4
         with:
           submodules: true
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.x'
 
@@ -193,7 +182,7 @@ jobs:
           python -m pip install -r requirements.txt
 
       - name: Cache SUNDIALS build
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: /home/runner/local
           key: bout-sundials-${{ matrix.config.os }}${{ matrix.config.build_petsc }}
@@ -210,26 +199,10 @@ jobs:
       - name: Build BOUT++
         run: UNIT_ONLY=${{ matrix.config.unit_only }} ./.ci_with_cmake.sh ${{ matrix.config.cmake_options }}
 
-      - name: Capture coverage
-        if: ${{ matrix.config.name == 'Coverage' }}
-        # Explicitly run the coverage capture target, because
-        # ci_script.sh also does the upload, and we're going to do
-        # that ourselves in the next step
-        run: |
-          # Ensure that there is a corresponding .gcda file for every .gcno file
-          # This is to try and make the coverage report slightly more accurate
-          # It still won't include, e.g. any solvers we don't build with though
-          find . -name "*.gcno" -exec sh -c 'touch -a "${1%.gcno}.gcda"' _ {} \;
-          make -C build code-coverage-capture
-
-      - name: Upload coverage
-        if: ${{ matrix.config.name == 'Coverage' }}
-        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
+    timeout-minutes: 120
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4

diff --git a/.gitmodules b/.gitmodules
@@ -13,6 +13,3 @@
 [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
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,6 +16,67 @@
   confusing. Now, monitors are called with the current number of
   completed monitor-steps.
 
+## [v5.1.1](https://github.com/boutproject/BOUT-dev/tree/v5.1.1)
+[Full Changelog](https://github.com/boutproject/BOUT-dev/compare/v5.1.0...v5.1.1)
+
+- Fix compilation error due to check_c_source_runs [\#2967][https://github.com/boutproject/BOUT-dev/pull/2967] ([mikekryjak][https://github.com/mikekryjak])
+- Resolve merge conflict for v5.1.1-rc [\#2964][https://github.com/boutproject/BOUT-dev/pull/2964] ([dschwoerer][https://github.com/dschwoerer])
+- Update boutdata and boututils submodules [\#2959][https://github.com/boutproject/BOUT-dev/pull/2959] ([dschwoerer][https://github.com/dschwoerer])
+- Small clang-tidy fixes for sundials solvers [\#2953][https://github.com/boutproject/BOUT-dev/pull/2953] ([ZedThree][https://github.com/ZedThree])
+- mark fmt::format() const [\#2942][https://github.com/boutproject/BOUT-dev/pull/2942] ([tchaikov][https://github.com/tchaikov])
+- CI: Ensure we do not timeout due to slow mirrors [\#2940][https://github.com/boutproject/BOUT-dev/pull/2940] ([dschwoerer][https://github.com/dschwoerer])
+- Bump externalpackages/boutdata from `cd0bc40` to `d9b8187` [\#2939][https://github.com/boutproject/BOUT-dev/pull/2939] ([dependabot[bot]][https://github.com/dependabot%5Bbot%5D])
+- SUNDIALS v7 support (backport to v5) [\#2937][https://github.com/boutproject/BOUT-dev/pull/2937] ([ZedThree][https://github.com/ZedThree])
+- Bump externalpackages/googletest from `33af80a` to `0953a17` [\#2968][https://github.com/boutproject/BOUT-dev/pull/2968] ([dependabot[bot]][https://github.com/dependabot%5Bbot%5D])
+- Update netcdf4 requirement from ~=1.6.0 to ~=1.7.1 [\#2960][https://github.com/boutproject/BOUT-dev/pull/2960] ([dependabot[bot]][https://github.com/dependabot%5Bbot%5D])
+- Bump ZedThree/clang-tidy-review from 0.18.0 to 0.19.0 [\#2913][https://github.com/boutproject/BOUT-dev/pull/2913] ([dependabot[bot]][https://github.com/dependabot%5Bbot%5D])
+- Bump externalpackages/googletest from `5a37b51` to `33af80a` [\#2912][https://github.com/boutproject/BOUT-dev/pull/2912] ([dependabot[bot]][https://github.com/dependabot%5Bbot%5D])
+- Bump externalpackages/boututils from `433995f` to `6c22995` [\#2911][https://github.com/boutproject/BOUT-dev/pull/2911] ([dependabot[bot]][https://github.com/dependabot%5Bbot%5D])
+- Bump externalpackages/googletest from `b479e7a` to `5a37b51` [\#2906][https://github.com/boutproject/BOUT-dev/pull/2906] ([dependabot[bot]][https://github.com/dependabot%5Bbot%5D])
+- Fix name of PVODE Config file [\#2903][https://github.com/boutproject/BOUT-dev/pull/2903] ([dschwoerer][https://github.com/dschwoerer])
+- Bump ZedThree/clang-tidy-review from 0.17.0 to 0.18.0 [\#2897][https://github.com/boutproject/BOUT-dev/pull/2897] ([dependabot[bot]][https://github.com/dependabot%5Bbot%5D])
+- Bump externalpackages/googletest from `e4fdb87` to `b479e7a` [\#2880][https://github.com/boutproject/BOUT-dev/pull/2880] ([dependabot[bot]][https://github.com/dependabot%5Bbot%5D])
+- Bump externalpackages/boutdata from `9e603a2` to `cd0bc40` [\#2879][https://github.com/boutproject/BOUT-dev/pull/2879] ([dependabot[bot]][https://github.com/dependabot%5Bbot%5D])
+- Bump externalpackages/googletest from `b75ecf1` to `e4fdb87` [\#2877][https://github.com/boutproject/BOUT-dev/pull/2877] ([dependabot[bot]][https://github.com/dependabot%5Bbot%5D])
+- Bump externalpackages/boutdata from `a043a2b` to `9e603a2` [\#2866][https://github.com/boutproject/BOUT-dev/pull/2866] ([dependabot[bot]][https://github.com/dependabot%5Bbot%5D])
+- Bump externalpackages/googletest from `dddb219` to `b75ecf1` [\#2864][https://github.com/boutproject/BOUT-dev/pull/2864] ([dependabot[bot]][https://github.com/dependabot%5Bbot%5D])
+- Bump codecov/codecov-action from 3 to 4 [\#2860][https://github.com/boutproject/BOUT-dev/pull/2860] ([dependabot[bot]][https://github.com/dependabot%5Bbot%5D])
+- Bump ZedThree/clang-tidy-review from 0.14.0 to 0.17.0 [\#2846][https://github.com/boutproject/BOUT-dev/pull/2846] ([dependabot[bot]][https://github.com/dependabot%5Bbot%5D])
+- Bump actions/cache from 3 to 4 [\#2845][https://github.com/boutproject/BOUT-dev/pull/2845] ([dependabot[bot]][https://github.com/dependabot%5Bbot%5D])
+- Add warnings about SUNDIALS versions <4 [\#2840][https://github.com/boutproject/BOUT-dev/pull/2840] ([Steven-Roberts][https://github.com/Steven-Roberts])
+- Do not excessively bump googletest [\#2836][https://github.com/boutproject/BOUT-dev/pull/2836] ([dschwoerer][https://github.com/dschwoerer])
+- Remove propietary data (master) [\#2832][https://github.com/boutproject/BOUT-dev/pull/2832] ([dschwoerer][https://github.com/dschwoerer])
+- Bump externalpackages/googletest from `829c199` to `dddb219` [\#2830][https://github.com/boutproject/BOUT-dev/pull/2830] ([dependabot[bot]][https://github.com/dependabot%5Bbot%5D])
+- Bump externalpackages/boutdata from `908a4c2` to `a043a2b` [\#2827][https://github.com/boutproject/BOUT-dev/pull/2827] ([dependabot[bot]][https://github.com/dependabot%5Bbot%5D])
+- CI: Bump actions/setup-python from 4 to 5 [\#2819][https://github.com/boutproject/BOUT-dev/pull/2819] ([dependabot[bot]][https://github.com/dependabot%5Bbot%5D])
+- Set oversubscribe flags for openmpi 5 [\#2800][https://github.com/boutproject/BOUT-dev/pull/2800] ([dschwoerer][https://github.com/dschwoerer])
+- CI: Replace pip script with requirements.txt [\#2794][https://github.com/boutproject/BOUT-dev/pull/2794] ([ZedThree][https://github.com/ZedThree])
+- master branch will be 5.1.1 not 5.2.0 [\#2784][https://github.com/boutproject/BOUT-dev/pull/2784] ([dschwoerer][https://github.com/dschwoerer])
+- Bump externalpackages/googletest from `2dd1c13` to `829c199` [\#2782][https://github.com/boutproject/BOUT-dev/pull/2782] ([dependabot[bot]][https://github.com/dependabot%5Bbot%5D])
+- Fix test-laplace-petsc3d [\#2781][https://github.com/boutproject/BOUT-dev/pull/2781] ([dschwoerer][https://github.com/dschwoerer])
+- CI: user master branch for docker actions [\#2780][https://github.com/boutproject/BOUT-dev/pull/2780] ([dschwoerer][https://github.com/dschwoerer])
+- [RTD] add os to read the docs config [\#2779][https://github.com/boutproject/BOUT-dev/pull/2779] ([dschwoerer][https://github.com/dschwoerer])
+- CI: Increase shm size in container [\#2777][https://github.com/boutproject/BOUT-dev/pull/2777] ([dschwoerer][https://github.com/dschwoerer])
+- Bump externalpackages/fmt from `f0903ad` to `2ac6c5c` [\#2776][https://github.com/boutproject/BOUT-dev/pull/2776] ([dependabot[bot]][https://github.com/dependabot%5Bbot%5D])
+- Bump ZedThree/clang-tidy-review from 0.13.1 to 0.14.0 [\#2773][https://github.com/boutproject/BOUT-dev/pull/2773] ([dependabot[bot]][https://github.com/dependabot%5Bbot%5D])
+- Bump stefanzweifel/git-auto-commit-action from 4 to 5 [\#2772][https://github.com/boutproject/BOUT-dev/pull/2772] ([dependabot[bot]][https://github.com/dependabot%5Bbot%5D])
+- Bump actions/setup-python from 1 to 4 [\#2771][https://github.com/boutproject/BOUT-dev/pull/2771] ([dependabot[bot]][https://github.com/dependabot%5Bbot%5D])
+- CI: Run on PETSc developement branch [\#2765][https://github.com/boutproject/BOUT-dev/pull/2765] ([dschwoerer][https://github.com/dschwoerer])
+- Prefer dnf5 for fedora CI (master) [\#2764][https://github.com/boutproject/BOUT-dev/pull/2764] ([dschwoerer][https://github.com/dschwoerer])
+- Fix sphinx configuration [\#2762][https://github.com/boutproject/BOUT-dev/pull/2762] ([dschwoerer][https://github.com/dschwoerer])
+- Bump docker/build-push-action from f2a1d5e99d037542a71f64918e516c093c6f3fc4 to 0f847266c302569530c95bfa228489494c43b002 [\#2761][https://github.com/boutproject/BOUT-dev/pull/2761] ([dependabot[bot]][https://github.com/dependabot%5Bbot%5D])
+- Ensure also lower case is accepted [\#2759][https://github.com/boutproject/BOUT-dev/pull/2759] ([dschwoerer][https://github.com/dschwoerer])
+- Bump externalpackages/googletest from `6092810` to `2dd1c13` [\#2757][https://github.com/boutproject/BOUT-dev/pull/2757] ([dependabot[bot]][https://github.com/dependabot%5Bbot%5D])
+- Add fallback if the version has been bumped bot not tagged [\#2754][https://github.com/boutproject/BOUT-dev/pull/2754] ([dschwoerer][https://github.com/dschwoerer])
+
+## [v5.1.0](https://github.com/boutproject/BOUT-dev/tree/v5.1.0
+
+### Breaking changes
+
+- The autotools `./configure` build system has been removed
+- Parsing of booleans has changed [\#2828][https://github.com/boutproject/BOUT-dev/pull/2828] ([bendudson][https://github.com/bendudson]).
+  See the [manual page](https://bout-dev.readthedocs.io/en/stable/user_docs/bout_options.html#boolean-expressions) for details.
+
 
 ## [v5.1.0](https://github.com/boutproject/BOUT-dev/tree/v5.1.0)
 [Full Changelog](https://github.com/boutproject/BOUT-dev/compare/v5.0.0...v5.1.0)

diff --git a/CITATION.cff b/CITATION.cff
@@ -188,11 +188,20 @@ authors:
   - family-names: Chapman
     given-names: Tom
 
-version: 5.1.0
+  - family-names: Chai
+    given-names: Kefu
+  - family-names: Roberts
+    given-names: Steven
+  - family-names: Georgakoudis
+    given-names: Giorgis
+  - family-names: Kryjak
+    given-names: Mike
+
+version: 5.1.1
 date-released: 2023-04-10
 repository-code: https://github.com/boutproject/BOUT-dev
 url: http://boutproject.github.io/
-doi: 10.5281/zenodo.8369888
+doi: 10.5281/zenodo.13753882
 license: 'LGPL-3.0-or-later'
 references:
   - type: article