Merge remote-tracking branch 'origin/next' into fci-auto-with-debug

.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 wget
     # Allow to override packages - see #2073

.ci_with_cmake.sh

@@ -17,12 +17,6 @@ ctest --output-on-failure --timeout 300
 
 export LD_LIBRARY_PATH=/home/runner/local/lib:$LD_LIBRARY_PATH
 
-# Test bout-config basic functionallity
-cd ../examples/make-script
-PATH=../../build/bin:$PATH bout-config --all
-PATH=../../build/bin:$PATH make
-./test --help
-cd -
 # Test bout++Config.cmake
 cd ../examples/conduction
 cmake . -B build -DCMAKE_PREFIX_PATH=../../build
@@ -32,13 +26,6 @@ cd -
 
 make install -j 2
 rm -rf build
-# Test installation with plain `make`
-cd ../examples/make-script
-rm test
-PATH=../../installed/bin:$PATH bout-config --all
-PATH=../../installed/bin:$PATH make
-./test --help
-cd -
 # Test installation with CMake
 cd ../examples/conduction
 cmake . -B build -DCMAKE_PREFIX_PATH=../../installed

.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*

.github/dependabot.yml

@@ -3,7 +3,7 @@ version: 2
 updates:
   - package-ecosystem: "gitsubmodule"
     schedule:
-        interval: "daily"
+        interval: "weekly"
     directory: "/"
 
   - package-ecosystem: "pip"

.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

.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 &&

.github/workflows/tests.yml

@@ -40,7 +40,7 @@ jobs:
           - ${{ github.event_name == 'cron' }}
         config:
           - name: "CMake, PETSc unreleased, ADIOS2"
-            os: ubuntu-20.04
+            os: ubuntu-24.04
             cmake_options: "-DBUILD_SHARED_LIBS=ON
                             -DBOUT_ENABLE_METRIC_3D=ON
                             -DBOUT_ENABLE_OPENMP=ON
@@ -58,13 +58,13 @@ jobs:
             build_adios2: true
             on_cron: true
 
-          - name: "Default options, Ubuntu 20.04"
-            os: ubuntu-20.04
+          - name: "Default options, Ubuntu 22.04"
+            os: ubuntu-22.04
             cmake_options: ""
             on_cron: false
 
           - name: "Optimised, static"
-            os: ubuntu-20.04
+            os: ubuntu-latest
             cmake_options: "-DCHECK=0
                             -DBUILD_SHARED_LIBS=OFF
                             -DCMAKE_CXX_FLAGS=-Ofast
@@ -78,7 +78,7 @@ jobs:
             on_cron: false
 
           - name: "Debug, shared"
-            os: ubuntu-20.04
+            os: ubuntu-latest
             cmake_options: "-DCHECK=3
                             -DCMAKE_BUILD_TYPE=Debug
                             -DBOUT_ENABLE_SIGNAL=ON
@@ -89,8 +89,8 @@ jobs:
                             -DSUNDIALS_ROOT=/home/runner/local"
             on_cron: false
 
-          - name: "Shared, release, Ubuntu 20.04"
-            os: ubuntu-20.04
+          - name: "Shared, release"
+            os: ubuntu-latest
             cmake_options: "-DBUILD_SHARED_LIBS=ON
                             -DBOUT_ENABLE_OPENMP=ON
                             -DCMAKE_BUILD_TYPE=Release
@@ -116,7 +116,7 @@ jobs:
             on_cron: false
 
           - name: "CMake, new PETSc"
-            os: ubuntu-20.04
+            os: ubuntu-latest
             cmake_options: "-DBUILD_SHARED_LIBS=ON
                             -DBOUT_ENABLE_METRIC_3D=ON
                             -DBOUT_ENABLE_OPENMP=ON
@@ -131,7 +131,7 @@ jobs:
             on_cron: false
 
           - name: "Coverage"
-            os: ubuntu-20.04
+            os: ubuntu-latest
             cmake_options: "-DBUILD_SHARED_LIBS=ON
                             -DCMAKE_BUILD_TYPE=Debug
                             -DCHECK=3
@@ -183,7 +183,7 @@ jobs:
         with:
           submodules: true
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.x'
 
@@ -193,7 +193,7 @@ 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 }}
@@ -224,7 +224,7 @@ jobs:
 
       - name: Upload coverage
         if: ${{ matrix.config.name == 'Coverage' }}
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
 
   Fedora:
     # This is its own job as it doesn't use most of the steps of the

.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

CHANGELOG.md

@@ -5,6 +5,74 @@
 
 ### 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.
+- Previously, the `Solver` implementations passed the loop counter to
+  the `iter` argument of `call_monitors`, but since the iteration has
+  already been completed when the monitors are called, this results in
+  iter always being one less than the number of completed
+  monitor-steps at the point when the moniters are called, which is
+  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.

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

CMakeLists.txt

@@ -25,7 +25,7 @@ endif()
 # CMake currently doesn't support proper semver
 # Set the version here, strip any extra tags to use in `project`
 # We try to use git to get a full description, inspired by setuptools_scm
-set(_bout_previous_version "5.1.0")
+set(_bout_previous_version "5.1.1")
 set(_bout_next_version "5.2.0")
 execute_process(
   COMMAND "git" describe --tags --match=v${_bout_previous_version}
@@ -797,8 +797,15 @@ foreach (flag ${CONFIG_LDFLAGS_LIST})
       # message("${flag} is a file")
       set(_CONFIG_LDFLAGS "${_CONFIG_LDFLAGS} ${flag}")
     else()
-      message("Fixing ${flag} to -l${flag}")
-      set(_CONFIG_LDFLAGS "${_CONFIG_LDFLAGS} -l${flag}")
+      string(FIND "${flag}" "::" hascolcol)
+      if (${hascolcol} EQUAL -1)
+	message("Fixing ${flag} to -l${flag}")
+	set(_CONFIG_LDFLAGS "${_CONFIG_LDFLAGS} -l${flag}")
+      else()
+	string(REGEX MATCH "[^:]*$" flag2 "${flag}")
+	message("Fixing ${flag} to -l${flag2}")
+	set(_CONFIG_LDFLAGS "${_CONFIG_LDFLAGS} -l${flag2}")
+      endif()
     endif()
   endif()
 endforeach()

README.md

@@ -4,7 +4,7 @@
 [![Build Status](https://github.com/boutproject/BOUT-dev/actions/workflows/tests.yml/badge.svg?branch=next)](https://github.com/boutproject/BOUT-dev/actions)
 [![License](https://img.shields.io/badge/license-LGPL-blue.svg)](https://www.gnu.org/licenses/lgpl-3.0.en.html)
 [![py3comp](https://img.shields.io/badge/py3-compatible-brightgreen.svg)](https://img.shields.io/badge/py3-compatible-brightgreen.svg)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8369888.svg)](https://doi.org/10.5281/zenodo.8369888)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13753882.svg)](https://doi.org/10.5281/zenodo.8369888)
 
 ```
 .______     ______    __    __  .___________.