Merge pull request #2383 from boutproject/v4.4.0-alpha

Release V4.4.0

.ci_with_cmake.sh

@@ -0,0 +1,20 @@
+#!/usr/bin/env bash
+
+set -ex
+
+cmake --version
+cmake . -B build $@ -DCMAKE_INSTALL_PREFIX=$(pwd)/installed
+cmake --build build --target build-check -j 2
+cd build
+ctest --output-on-failure --timeout 300
+
+# Test bout-config basic functionallity
+cd ../examples/make-script
+PATH=../../build/bin:$PATH make
+./test --help
+cd -
+make install -j 2
+cd -
+rm test
+PATH=../../installed/bin:$PATH make
+./test --help

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

@@ -42,12 +42,16 @@ jobs:
                            -DBOUT_USE_HDF5=ON \
                            -DBOUT_USE_SUNDIALS=ON \
                            -DBOUT_BUILD_EXAMPLES=ON \
+                           -DBOUT_BUILD_DOCS=OFF \
                            -DCMAKE_EXPORT_COMPILE_COMMANDS=On
 
       - name: Run clang-tidy
-        uses: ZedThree/clang-tidy-review@v0.3.0
+        uses: ZedThree/clang-tidy-review@v0.6.1
         id: review
         with:
           build_dir: build
-          apt_packages: "libfftw3-dev,libnetcdf-c++4-dev,libhdf5-mpi-dev,libopenmpi-dev,petsc-dev,slepc-dev,liblapack-dev,libparpack2-dev,libsundials-dev"
-
+          apt_packages: "libfftw3-dev,libnetcdf-c++4-dev,libopenmpi-dev,petsc-dev,slepc-dev,liblapack-dev,libparpack2-dev,libsundials-dev,uuid-dev"
+          clang_tidy_checks: '-*,performance-*,readability-*,bugprone-*,clang-analyzer-*,cppcoreguidelines-*,mpi-*,misc-*,-readability-magic-numbers,-cppcoreguidelines-avoid-magic-numbers,-misc-non-private-member-variables-in-classes,-cppcoreguidelines-pro-bounds-array-to-pointer-decay,-cppcoreguidelines-pro-type-vararg,-clang-analyzer-optin.mpi*'
+          # 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"

.github/workflows/tests.yml

@@ -74,11 +74,11 @@ jobs:
           - name: "CMake, shared, Ubuntu 20.04"
             os: ubuntu-20.04
             cmake_options: "-DBUILD_SHARED_LIBS=ON
-                            -DENABLE_OPENMP=ON
-                            -DUSE_PETSC=ON
-                            -DUSE_SLEPC=ON
-                            -DUSE_HDF5=ON
-                            -DUSE_SUNDIALS=ON
+                            -DBOUT_ENABLE_OPENMP=ON
+                            -DBOUT_USE_PETSC=ON
+                            -DBOUT_USE_SLEPC=ON
+                            -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_BUILD_DOCS=OFF
                             -DSUNDIALS_ROOT=/home/runner/local"
             omp_num_threads: 2
 
@@ -157,12 +157,7 @@ jobs:
 
       - name: Build (CMake)
         if: ${{ contains(matrix.config.name, 'CMake') }}
-        run: |
-          cmake --version
-          cmake . -B build ${{ matrix.config.cmake_options }}
-          cmake --build build -j 2
-          cd build
-          ctest --output-on-failure --timeout 300
+        run: ./.ci_with_cmake.sh ${{ matrix.config.cmake_options }}
 
       - name: Capture coverage
         if: ${{ matrix.config.name == 'Coverage' }}

.gitignore

@@ -25,6 +25,7 @@
 autom4te.cache/
 aclocal.m4
 /bin/bout-config
+/src/makefile
 /include/pvode
 /lib/
 /manual/*.pdf
@@ -41,3 +42,6 @@ src/.libfast
 .BOUT.pid.*
 build/
 build*/
+/.vs
+/CMakeSettings.json
+/CppProperties.json

.gitmodules

@@ -7,3 +7,9 @@
 [submodule "mpark.variant"]
 	path = externalpackages/mpark.variant
 	url = https://github.com/mpark/variant.git
+[submodule "externalpackages/boututils"]
+	path = externalpackages/boututils
+	url = https://github.com/boutproject/boututils.git
+[submodule "externalpackages/boutdata"]
+	path = externalpackages/boutdata
+	url = https://github.com/boutproject/boutdata.git

.travis_script.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-set -e
+set -ex
 
 #Default flags
 COVERAGE=0
@@ -126,7 +126,6 @@ fi
 if [[ ${INTEGRATED} == 1 ]]
 then
     time make check-integrated-tests
-    time py.test-3 tools/pylib/
 fi
 
 if [[ ${MMS} == 1 ]]

CHANGELOG.md

@@ -17,6 +17,76 @@
 
   See [\#2154](https://github.com/boutproject/BOUT-dev/pull/2154).
 
+## [v4.4.0](https://github.com/boutproject/BOUT-dev/tree/v4.4.0) (2021-07-30)
+
+[Full Changelog](https://github.com/boutproject/BOUT-dev/compare/v4.3.3...v4.4.4)
+
+**Merged pull requests:**
+
+- Add ability to use FieldPerp in Options (v.4.4) [\#2395](https://github.com/boutproject/BOUT-dev/pull/2395) ([ZedThree](https://github.com/users/ZedThree))
+- Fix some HDF5 related issues and add Mesh::getLocal{X,Y,Z}Index (v4.4) [\#2394](https://github.com/boutproject/BOUT-dev/pull/2394) ([ZedThree](https://github.com/users/ZedThree))
+- Add Mesh::getRegion<T> for use in generic code (v4.4) [\#2393](https://github.com/boutproject/BOUT-dev/pull/2393) ([ZedThree](https://github.com/users/ZedThree))
+- Adding an adaptive, arbitrary order, Adams-Bashforth solver (v4.4) [\#2392](https://github.com/boutproject/BOUT-dev/pull/2392) ([ZedThree](https://github.com/users/ZedThree))
+- Allow PETSc options to be passed from BOUT.inp (v4.4) [\#2391](https://github.com/boutproject/BOUT-dev/pull/2391) ([ZedThree](https://github.com/users/ZedThree))
+- Add new contributors [\#2386](https://github.com/boutproject/BOUT-dev/pull/2386) ([dschwoerer](https://github.com/users/dschwoerer))
+- Update locale [\#2385](https://github.com/boutproject/BOUT-dev/pull/2385) ([dschwoerer](https://github.com/users/dschwoerer))
+- Fix RTD [\#2384](https://github.com/boutproject/BOUT-dev/pull/2384) ([dschwoerer](https://github.com/users/dschwoerer))
+- Rename `max_nonlinear_it` to `max_nonlinear_iterations` [\#2339](https://github.com/boutproject/BOUT-dev/pull/2339) ([johnomotani](https://github.com/users/johnomotani))
+- CVODE constraints and max_noinlinear_iterations options (4.4) [\#2304](https://github.com/boutproject/BOUT-dev/pull/2304) ([johnomotani](https://github.com/users/johnomotani))
+- Fix some Solvers not always using user preconditioner/Jacobian (v4.4) [\#2284](https://github.com/boutproject/BOUT-dev/pull/2284) ([ZedThree](https://github.com/users/ZedThree))
+- Fix formatting strings for pre-fmt in beuler solver [\#2278](https://github.com/boutproject/BOUT-dev/pull/2278) ([bendudson](https://github.com/users/bendudson))
+- Backport of Backward Euler solver to v4.4 [\#2265](https://github.com/boutproject/BOUT-dev/pull/2265) ([bendudson](https://github.com/users/bendudson))
+- Fix use of uninitialised value in Delp2 (4.4) [\#2263](https://github.com/boutproject/BOUT-dev/pull/2263) ([johnomotani](https://github.com/users/johnomotani))
+- Save provenance tracking info from grid file (4.4) [\#2231](https://github.com/boutproject/BOUT-dev/pull/2231) ([johnomotani](https://github.com/users/johnomotani))
+- Generate random run ID, track restarts (4.4) [\#2224](https://github.com/boutproject/BOUT-dev/pull/2224) ([johnomotani](https://github.com/users/johnomotani))
+- Generate report for Timers (4.4) [\#2216](https://github.com/boutproject/BOUT-dev/pull/2216) ([johnomotani](https://github.com/users/johnomotani))
+- Replace boutdata and boututils directories with submodules (v4.4) [\#2198](https://github.com/boutproject/BOUT-dev/pull/2198) ([johnomotani](https://github.com/users/johnomotani))
+- Use bout_type="string" for strings in H5Format (4.4) [\#2194](https://github.com/boutproject/BOUT-dev/pull/2194) ([johnomotani](https://github.com/users/johnomotani))
+- Write descriptions for std::vector<int> and std::string variables [\#2191](https://github.com/boutproject/BOUT-dev/pull/2191) ([johnomotani](https://github.com/users/johnomotani))
+- Fix reading of char* in Ncxx4 (4.4) [\#2189](https://github.com/boutproject/BOUT-dev/pull/2189) ([johnomotani](https://github.com/users/johnomotani))
+- Merge master into v4.4.0-alpha [\#2174](https://github.com/boutproject/BOUT-dev/pull/2174) ([ZedThree](https://github.com/users/ZedThree))
+- I/O for std::vector<int> and std::string (4.4) [\#2155](https://github.com/boutproject/BOUT-dev/pull/2155) ([johnomotani](https://github.com/users/johnomotani))
+- Check DataFile grid sizes match those in existing mesh (v4.4) [\#2148](https://github.com/boutproject/BOUT-dev/pull/2148) ([johnomotani](https://github.com/users/johnomotani))
+- Call checkData() before returning result in Laplace inversions (v4.4) [\#2134](https://github.com/boutproject/BOUT-dev/pull/2134) ([johnomotani](https://github.com/users/johnomotani))
+- Allow setting FFTW_EXHAUSTIVE (v4.4) [\#2132](https://github.com/boutproject/BOUT-dev/pull/2132) ([johnomotani](https://github.com/users/johnomotani))
+- Make example relocatable [\#2127](https://github.com/boutproject/BOUT-dev/pull/2127) ([dschwoerer](https://github.com/users/dschwoerer))
+- Merge master into v4.4.0-alpha [\#2121](https://github.com/boutproject/BOUT-dev/pull/2121) ([ZedThree](https://github.com/users/ZedThree))
+- Handle FieldPerps in Datafile::varAdded() and Datafile::varPtr() (v4.4.0) [\#2094](https://github.com/boutproject/BOUT-dev/pull/2094) ([johnomotani](https://github.com/users/johnomotani))
+- Staggered grids in InvertPar (v4.4.0) [\#2088](https://github.com/boutproject/BOUT-dev/pull/2088) ([johnomotani](https://github.com/users/johnomotani))
+- Allow descriptions of output variables; save some diagnostics for solvers (v4.4) [\#2086](https://github.com/boutproject/BOUT-dev/pull/2086) ([johnomotani](https://github.com/users/johnomotani))
+- Correct Grad2_par2 implementation in InvertParCR (v4.4.0) [\#2077](https://github.com/boutproject/BOUT-dev/pull/2077) ([johnomotani](https://github.com/users/johnomotani))
+- Enable staggered versions of SplitFluxDerivativeType (4.4) [\#2059](https://github.com/boutproject/BOUT-dev/pull/2059) ([johnomotani](https://github.com/users/johnomotani))
+- Merge master into v4.4.0-alpha [\#1998](https://github.com/boutproject/BOUT-dev/pull/1998) ([ZedThree](https://github.com/users/ZedThree))
+- LaplaceXY: finite difference option (v4.4) [\#1924](https://github.com/boutproject/BOUT-dev/pull/1924) ([johnomotani](https://github.com/users/johnomotani))
+- Backport of Laplace performance test [\#1910](https://github.com/boutproject/BOUT-dev/pull/1910) ([JosephThomasParker](https://github.com/users/JosephThomasParker))
+- Macro for creating enum classes (v4.4) [\#1895](https://github.com/boutproject/BOUT-dev/pull/1895) ([johnomotani](https://github.com/users/johnomotani))
+- Implement toFieldAligned and fromFieldAligned for Vector3D (v4.4) [\#1878](https://github.com/boutproject/BOUT-dev/pull/1878) ([johnomotani](https://github.com/users/johnomotani))
+- Remove 3-element list indexers for collect() [\#1862](https://github.com/boutproject/BOUT-dev/pull/1862) ([johnomotani](https://github.com/users/johnomotani))
+- Allow user to override library option defaults (v4.4) [\#1849](https://github.com/boutproject/BOUT-dev/pull/1849) ([johnomotani](https://github.com/users/johnomotani))
+
+The following were backported from v5.0.0 in [\#2389](https://github.com/boutproject/BOUT-dev/pull/2389):
+
+- Add remaining integrated tests to CMake build [\#1833](https://github.com/boutproject/BOUT-dev/pull/1833) ([ZedThree](https://github.com/users/ZedThree))
+- Fixes for Windows [\#1874](https://github.com/boutproject/BOUT-dev/pull/1874) ([ZedThree](https://github.com/users/ZedThree))
+- CMake: fix FindSlepc for non-make generators [\#1881](https://github.com/boutproject/BOUT-dev/pull/1881) ([ZedThree](https://github.com/users/ZedThree))
+- CMake: enable using external mpark.variant [\#1900](https://github.com/boutproject/BOUT-dev/pull/1900) ([ZedThree](https://github.com/users/ZedThree))
+- Cmake fixes [\#1909](https://github.com/boutproject/BOUT-dev/pull/1909) ([dschwoerer](https://github.com/users/dschwoerer))
+- CMake: find package fixes [\#1912](https://github.com/boutproject/BOUT-dev/pull/1912) ([ZedThree](https://github.com/users/ZedThree))
+- Fix runtest for non-make generators [\#1952](https://github.com/boutproject/BOUT-dev/pull/1952) ([ZedThree](https://github.com/users/ZedThree))
+- CMake: Generate Field arithmetic operators [\#2119](https://github.com/boutproject/BOUT-dev/pull/2119) ([dschwoerer](https://github.com/users/dschwoerer))
+- CMake: Add option to download and build netCDF C++ API [\#2138](https://github.com/boutproject/BOUT-dev/pull/2138) ([ZedThree](https://github.com/users/ZedThree))
+- Fix CMake config file following change to netCDF cmake module [\#2162](https://github.com/boutproject/BOUT-dev/pull/2162) ([ZedThree](https://github.com/users/ZedThree))
+- Make input Options case sensitive and error on unused Options [\#2210](https://github.com/boutproject/BOUT-dev/pull/2210) ([ZedThree](https://github.com/users/ZedThree))
+- Next CMake fixes [\#2275](https://github.com/boutproject/BOUT-dev/pull/2275) ([bendudson](https://github.com/users/bendudson))
+- Add MMS tests to CMake build [\#2286](https://github.com/boutproject/BOUT-dev/pull/2286) ([ZedThree](https://github.com/users/ZedThree))
+- CMake: Build documentation [\#2300](https://github.com/boutproject/BOUT-dev/pull/2300) ([ZedThree](https://github.com/users/ZedThree))
+- Fix for FindPETSc not being reentrant if pkg-config used (next) [\#2318](https://github.com/boutproject/BOUT-dev/pull/2318) ([ZedThree](https://github.com/users/ZedThree))
+- CMake: Fix a few minor issues, generate `bout-config` [\#2328](https://github.com/boutproject/BOUT-dev/pull/2328) ([ZedThree](https://github.com/users/ZedThree))
+- CMake: Add option to download SUNDIALS at configure time [\#2331](https://github.com/boutproject/BOUT-dev/pull/2331) ([ZedThree](https://github.com/users/ZedThree))
+- CMake rename PACKAGE_TESTS to BOUT_TESTS [\#2347](https://github.com/boutproject/BOUT-dev/pull/2347) ([bendudson](https://github.com/users/bendudson))
+- CMake: Add SOVERSION; fix FindSUNDIALS [\#2358](https://github.com/boutproject/BOUT-dev/pull/2358) ([dschwoerer](https://github.com/users/dschwoerer))
+- Faster recompile [\#2294](https://github.com/boutproject/BOUT-dev/pull/2294) ([dschwoerer](https://github.com/users/dschwoerer))
+
 ## [v4.3.3](https://github.com/boutproject/BOUT-dev/tree/v4.3.2) (2021-07-28)
 
 [Full Changelog](https://github.com/boutproject/BOUT-dev/compare/v4.3.2...master)

CITATION.cff

@@ -158,14 +158,17 @@ authors:
   - family-names: Wang
     given-names: Zhanhui
 
+  - family-names: Ahmed
+    given-names: Sajidah
+
   - family-names: James
     given-names: Toby
 
-version: 4.3.3
-date-released: 2021-07-29
+version: 4.4.0
+date-released: 2020-08-06
 repository-code: https://github.com/boutproject/BOUT-dev
 url: http://boutproject.github.io/
-doi: 10.5281/zenodo.5142504
+doi: 10.5281/zenodo.5167527
 license: 'LGPL-3.0-or-later'
 references:
   - type: article