boutproject · tbody-cfs · Oct 18, 2023 · Oct 20, 2023 · Oct 30, 2023 · Nov 6, 2023
diff --git a/.ci_fedora.sh b/.ci_fedora.sh
@@ -56,6 +56,7 @@ else
     . /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

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
@@ -22,7 +22,7 @@ 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:
           build_dir: build
@@ -46,4 +46,4 @@ jobs:
                              -DBOUT_UPDATE_GIT_SUBMODULE=OFF
 
       - name: Upload clang-tidy fixes
-        uses: ZedThree/clang-tidy-review/upload@v0.14.0
+        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
@@ -28,6 +28,7 @@ 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
@@ -179,18 +180,17 @@ jobs:
         with:
           submodules: true
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         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@v3
+        uses: actions/cache@v4
         with:
           path: /home/runner/local
           key: bout-sundials-${{ matrix.config.os }}${{ matrix.config.build_petsc }}
@@ -218,7 +218,7 @@ 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

diff --git a/.pip_install_for_ci.sh b/.pip_install_for_ci.sh
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -26,7 +26,7 @@ endif()
 # 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_next_version "5.2.0")
+set(_bout_next_version "5.1.1")
 execute_process(
   COMMAND "git" describe --tags --match=v${_bout_previous_version}
   COMMAND sed -e s/${_bout_previous_version}-/${_bout_next_version}.dev/ -e s/-/+/

diff --git a/cmake/FindSUNDIALS.cmake b/cmake/FindSUNDIALS.cmake
@@ -121,6 +121,10 @@ if (SUNDIALS_INCLUDE_DIR)
   set(SUNDIALS_VERSION "${SUNDIALS_VERSION_MAJOR}.${SUNDIALS_VERSION_MINOR}.${SUNDIALS_VERSION_PATCH}" CACHE STRING "SUNDIALS version")
 endif()
 
+if("${SUNDIALS_VERSION_MAJOR}" LESS 4)
+  message(WARNING "SUNDIALS versions <4 are depricated and will not be supported in the next release")
+endif()
+
 if (SUNDIALS_DEBUG)
   message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
     " SUNDIALS_VERSION = ${SUNDIALS_VERSION}")

diff --git a/examples/shear-alfven-wave/orig_test.idl.dat b/examples/shear-alfven-wave/orig_test.idl.dat
diff --git a/examples/uedge-benchmark/result_080917.idl b/examples/uedge-benchmark/result_080917.idl
diff --git a/examples/uedge-benchmark/ue_bmk.idl b/examples/uedge-benchmark/ue_bmk.idl
diff --git a/externalpackages/PVODE/CMakeLists.txt b/externalpackages/PVODE/CMakeLists.txt
@@ -82,7 +82,7 @@ write_basic_package_version_file(
   )
 
 install(EXPORT PVODETargets
-  FILE PVODETargets.cmake
+  FILE PVODEConfig.cmake
   NAMESPACE PVODE::
   DESTINATION "${CMAKE_INSTALL_LIBDIR}/cmake/PVODE"
   )

diff --git a/externalpackages/boutdata b/externalpackages/boutdata
diff --git a/externalpackages/boututils b/externalpackages/boututils
diff --git a/externalpackages/googletest b/externalpackages/googletest
diff --git a/manual/sphinx/user_docs/advanced_install.rst b/manual/sphinx/user_docs/advanced_install.rst
@@ -430,9 +430,10 @@ solver. Currently, BOUT++ also supports the SUNDIALS solvers CVODE, IDA
 and ARKODE which are available from
 https://computation.llnl.gov/casc/sundials/main.html.
 
-.. note:: BOUT++ currently supports SUNDIALS > 2.6, up to 5.4.0 as of
-          September 2020. It is advisable to use the highest possible
-          version
+.. note:: BOUT++ currently supports SUNDIALS > 2.6, up to 6.7.0 as of
+          January 2024. It is advisable to use the highest possible
+          version. Support for SUNDIALS versions < 4 will be removed
+          in the next release.
 
 The full installation guide is found in the downloaded ``.tar.gz``,
 but we will provide a step-by-step guide to install it and make it

diff --git a/manual/sphinx/user_docs/variable_init.rst b/manual/sphinx/user_docs/variable_init.rst
@@ -328,22 +328,20 @@ to ``generate`` in the ``Context`` object.
 
   Field3D shear = ...; // Value calculated in BOUT++
 
-  FieldFactory factory(mesh);
-  auto gen = factory->parse("model:viscosity");
+  Options& model_options = options["model"];
+  auto str = model_options["viscosity"].doc("Viscosity").as<std::string()>;
+
+  auto gen = FieldFactory::get()->parse(str, &model_options);
 
   Field3D viscosity;
   viscosity.allocate();
-
-  BOUT_FOR(i, viscosity.region("RGN_ALL")) {
-    viscosity[i] = gen->generate(bout::generator::Context(i, CELL_CENTRE, mesh, 0.0)
-                                   .set("shear", shear[i]));
+
+  BOUT_FOR(i, viscosity.getRegion("RGN_ALL")) {
+    viscosity[i] = gen->generate(bout::generator::Context().set("shear", shear[i]));
   }
 
-Note that the ``Context`` constructor takes the index, the cell
-location (e.g. staggered), a mesh, and then the time (set to 0.0
-here). Additional variables can be ``set``, "shear" in this case.  In
-the input options file (or command line) the viscosity could now be a
-function of ``{shear}``
+In the input options file (or command line) the viscosity can now be written as
+a function of ``{shear}``
 
 .. code-block:: cfg
 

diff --git a/requirements.txt b/requirements.txt
@@ -1,6 +1,8 @@
 Jinja2>=2.11.3
 numpy>=1.14.1
 scipy>=1.0.0
-netcdf4>=1.3.1
+netcdf4~=1.6.0
 matplotlib>=2.0.0
-Cython>=0.29.0
+Cython~=3.0.0
+boututils~=0.2.1
+boutdata~=0.2.1
diff --git a/tests/integrated/test-interchange-instability/orig_test.idl.dat b/tests/integrated/test-interchange-instability/orig_test.idl.dat
diff --git a/tools/pylib/_boutpp_build/backend.py b/tools/pylib/_boutpp_build/backend.py
@@ -34,7 +34,7 @@ def getversion():
             return version
 
         _bout_previous_version = "v5.1.0"
-        _bout_next_version = "v5.2.0"
+        _bout_next_version = "v5.1.1"
 
         try:
             try:
+3 −3		boutdata/data.py
+1 −0		boutdata/gen_surface.py
+20 −12		boutdata/restart.py
+6 −0		boutdata/squashoutput.py
+2 −7		README.md
+0 −1		boututils/analyse_equil_2.py
+0 −1		boututils/anim.py
+0 −1		boututils/calculus.py
+1 −2		boututils/datafile.py
+0 −1		boututils/showdata.py
+0 −1		boututils/spectrogram.py
+0 −1		boututils/surface_average.py
+0 −1		boututils/volume_integral.py
+0 −43		.github/workflows/gtest-ci.yml
+1 −0		.gitignore
+17 −0		BUILD.bazel
+9 −0		CMakeLists.txt
+1 −0		CONTRIBUTORS
+61 −0		MODULE.bazel
+14 −12		WORKSPACE
+35 −0		WORKSPACE.bzlmod
+6 −4		ci/linux-presubmit.sh
+2 −1		ci/macos-presubmit.sh
+2 −2		ci/windows-presubmit.bat
+15 −5		docs/advanced.md
+32 −3		docs/gmock_cook_book.md
+2 −0		docs/gmock_for_dummies.md
+17 −18		docs/primer.md
+7 −3		docs/reference/testing.md
+33 −0		fake_fuchsia_sdk.bzl
+4 −3		googlemock/CMakeLists.txt
+27 −9		googlemock/include/gmock/gmock-actions.h
+90 −89		googlemock/include/gmock/gmock-matchers.h
+4 −3		googlemock/include/gmock/gmock-more-actions.h
+1 −0		googlemock/include/gmock/gmock.h
+8 −6		googlemock/include/gmock/internal/gmock-internal-utils.h
+4 −4		googlemock/include/gmock/internal/gmock-port.h
+3 −2		googlemock/src/gmock-internal-utils.cc
+2 −1		googlemock/src/gmock-spec-builders.cc
+9 −0		googlemock/test/gmock-matchers-comparisons_test.cc
+39 −1		googlemock/test/gmock-more-actions_test.cc
+9 −0		googlemock/test/gmock_link_test.h
+1 −1		googletest/CMakeLists.txt
+4 −0		googletest/cmake/Config.cmake.in
+3 −1		googletest/cmake/internal_utils.cmake
+1 −1		googletest/include/gtest/gtest-assertion-result.h
+4 −4		googletest/include/gtest/gtest-death-test.h
+4 −4		googletest/include/gtest/gtest-param-test.h
+35 −21		googletest/include/gtest/gtest-printers.h
+65 −61		googletest/include/gtest/gtest-typed-test.h
+32 −14		googletest/include/gtest/gtest.h
+24 −23		googletest/include/gtest/internal/gtest-death-test-internal.h
+7 −1		googletest/include/gtest/internal/gtest-filepath.h
+25 −63		googletest/include/gtest/internal/gtest-internal.h
+78 −76		googletest/include/gtest/internal/gtest-param-util.h
+2 −0		googletest/include/gtest/internal/gtest-port-arch.h
+51 −20		googletest/include/gtest/internal/gtest-port.h
+18 −16		googletest/src/gtest-death-test.cc
+28 −16		googletest/src/gtest-internal-inl.h
+34 −19		googletest/src/gtest-port.cc
+159 −109		googletest/src/gtest.cc
+1 −0		googletest/test/googletest-color-test.py
+39 −37		googletest/test/googletest-death-test-test.cc
+15 −0		googletest/test/googletest-json-output-unittest.py
+4 −1		googletest/test/googletest-options-test.cc
+0 −5		googletest/test/googletest-output-test-golden-lin.txt
+52 −44		googletest/test/gtest_environment_test.cc
+3 −0		googletest/test/gtest_json_test_utils.py
+1 −3		googletest/test/gtest_repeat_test.cc
+18 −26		googletest/test/gtest_unittest.cc
+9 −6		googletest/test/gtest_xml_output_unittest.py
+14 −8		googletest_deps.bzl