Merge pull request #2104 from boutproject/v4.3.2-rc

Bugfix release: v4.3.2

.travis.yml

@@ -57,6 +57,7 @@ jobs:
       - SCRIPT_FLAGS='-uim'
       - PIP_PACKAGES='cython~=0.29 netcdf4~=1.5 sympy~=1.5'
       - LD_LIBRARY_PATH=$HOME/local/lib:$LD_LIBRARY_PATH
+      - BOUT_TEST_TIMEOUT="5m"
       - *petsc_vars
   - name: "GCC 7"
     addons:
@@ -75,7 +76,7 @@ jobs:
     env:
       - *default_env
       - CONFIGURE_OPTIONS="--enable-shared --with-petsc --with-slepc --with-sundials=$HOME/local"
-      - SCRIPT_FLAGS="-uim -t python -t shared"
+      - SCRIPT_FLAGS="-uim -t shared -t python"
   - name: "4to5 test"
     env:
       - *default_env
@@ -97,7 +98,7 @@ jobs:
       - mkdir build && cd build
       - cmake .. -DUSE_PETSC=ON -DUSE_SLEPC=ON -DUSE_SUNDIALS=ON -DSUNDIALS_ROOT="$HOME/local" -DENABLE_OPENMP=ON
       - cmake --build .
-      - ctest --output-on-failure
+      - ctest --output-on-failure --timeout 300
 #CLANG
   - name: "Clang"
     env:
@@ -162,6 +163,15 @@ script:
   # Configure, compile and run test_suite
   - "./.travis_script.sh ${SCRIPT_FLAGS}"
 
+# sleep a little bit after the build finishes to try and make sure stdout gets flushed
+after_failure:
+  - echo "Build failed!"
+  - sleep 5
+
+after_success:
+  - echo "Build passed!"
+  - sleep 1
+
 notifications:
   # Send a notification to the BOUT++ Slack team
   slack:

.travis_script.sh

@@ -38,7 +38,7 @@ do
 	    TESTS=1
 	    ;;
         t) ### Set target to build
-            MAIN_TARGET="$OPTARG"
+            MAIN_TARGET="$MAIN_TARGET $OPTARG"
             ;;
         5) ### Run the update to version 5 script
             UPDATE_SCRIPT=1
@@ -98,6 +98,7 @@ export PYTHONPATH=$(pwd)/tools/pylib/:$PYTHONPATH
 for target in ${MAIN_TARGET[@]}
 do
     make_exit=0
+    echo "make $target"
     time make $target || make_exit=$?
     if [[ $make_exit -gt 0 ]]; then
 	make clean > /dev/null

CHANGELOG.md

@@ -1,4 +1,31 @@
-# Change Log
+# Changelog
+
+## [v4.3.2](https://github.com/boutproject/BOUT-dev/tree/v4.3.2) (2020-10-19)
+
+[Full Changelog](https://github.com/boutproject/BOUT-dev/compare/v4.3.1...v4.3.2)
+
+**Merged pull requests:**
+
+- Make output nicer + add info about timeout'ed tests [\#2120](https://github.com/boutproject/BOUT-dev/pull/2120) ([dschwoerer](https://github.com/dschwoerer))
+- Add timeout to tests [\#2118](https://github.com/boutproject/BOUT-dev/pull/2118) ([ZedThree](https://github.com/ZedThree))
+- Fix reading/writing `std::string` attributes when using HDF5 [\#2116](https://github.com/boutproject/BOUT-dev/pull/2116) ([ZedThree](https://github.com/ZedThree))
+- Rename death tests according to gtest recommendations [\#2115](https://github.com/boutproject/BOUT-dev/pull/2115) ([ZedThree](https://github.com/ZedThree))
+- Update breathe for readthedocs [\#2114](https://github.com/boutproject/BOUT-dev/pull/2114) ([ZedThree](https://github.com/ZedThree))
+- Fix `Div_par` when using more than one y guard cell [\#2113](https://github.com/boutproject/BOUT-dev/pull/2113) ([ZedThree](https://github.com/ZedThree))
+- Update documentation on processor splitting and advanced installation [\#2109](https://github.com/boutproject/BOUT-dev/pull/2109) ([ZedThree](https://github.com/ZedThree))
+- Soname v4.3.2 [\#2108](https://github.com/boutproject/BOUT-dev/pull/2108) ([dschwoerer](https://github.com/dschwoerer))
+- Add configure option to use system mpark.variant [\#2107](https://github.com/boutproject/BOUT-dev/pull/2107) ([dschwoerer](https://github.com/dschwoerer))
+- CI: Turn off patch coverage check [\#2103](https://github.com/boutproject/BOUT-dev/pull/2103) ([ZedThree](https://github.com/ZedThree))
+- Make examples relocatable [\#2100](https://github.com/boutproject/BOUT-dev/pull/2100) ([dschwoerer](https://github.com/dschwoerer))
+- Handle FieldPerps in `Datafile::varAdded()` and `Datafile::varPtr()` [\#2093](https://github.com/boutproject/BOUT-dev/pull/2093) ([johnomotani](https://github.com/johnomotani))
+- Correct `Grad2_par2` implementation in `InvertParCR` [\#2076](https://github.com/boutproject/BOUT-dev/pull/2076) ([johnomotani](https://github.com/johnomotani))
+- Enable staggered versions of `SplitFluxDerivativeType` [\#2058](https://github.com/boutproject/BOUT-dev/pull/2058) ([johnomotani](https://github.com/johnomotani))
+- Fixes for `tokamak-2fluid` example [\#2043](https://github.com/boutproject/BOUT-dev/pull/2043) ([johnomotani](https://github.com/johnomotani))
+- Add location checks to `Div_par_K_Grad_par` [\#2039](https://github.com/boutproject/BOUT-dev/pull/2039) ([bshanahan](https://github.com/bshanahan))
+- Add clang-format bot command for pull requests [\#2032](https://github.com/boutproject/BOUT-dev/pull/2032) ([ZedThree](https://github.com/ZedThree))
+- Update the staggered grids section of the manual [\#2029](https://github.com/boutproject/BOUT-dev/pull/2029) ([johnomotani](https://github.com/johnomotani))
+- Make dz in boutcore a property [\#2024](https://github.com/boutproject/BOUT-dev/pull/2024) ([dschwoerer](https://github.com/dschwoerer))
+- Prevent deadlock in downloading mpark [\#2017](https://github.com/boutproject/BOUT-dev/pull/2017) ([dschwoerer](https://github.com/dschwoerer))
 
 ## [v4.3.1](https://github.com/boutproject/BOUT-dev/tree/v4.3.1) (2020-03-27)
 
@@ -1417,6 +1444,3 @@
 
 
 \* *This Changelog was automatically generated by [github_changelog_generator](https://github.com/github-changelog-generator/github-changelog-generator)*
-
-
-\* *This Change Log was automatically generated by [github_changelog_generator](https://github.com/skywinder/Github-Changelog-Generator)*

CITATION.bib

@@ -1,4 +1,4 @@
-@misc{BOUTv4-3-1,
+@misc{BOUTv4-3-2,
   author = {
             Benjamin Daniel Dudson and
             Peter Alec Hill and
@@ -48,8 +48,8 @@ @misc{BOUTv4-3-1
          },
 title  = {{BOUT++}},
 month  = {10},
-year   = {2019},
-doi    = {10.5281/zenodo.3727089},
+year   = {2020},
+doi    = {10.5281/zenodo.4046792},
 url    = {https://github.com/boutproject/BOUT-dev}
 }
 

CITATION.cff

@@ -154,11 +154,11 @@ authors:
 
   - family-names: Wang
     given-names: Zhanhui
-version: 4.3.1
-date-released: 2020-03-27
+version: 4.3.2
+date-released: 2020-10-19
 repository-code: https://github.com/boutproject/BOUT-dev
 url: http://boutproject.github.io/
-doi: 10.5281/zenodo.3727089
+doi: 10.5281/zenodo.4046792
 license: 'LGPL-3.0-or-later'
 references:
   - type: article

CMakeLists.txt

@@ -8,7 +8,7 @@ endif()
 
 project(BOUT++
   DESCRIPTION "Fluid PDE solver framework"
-  VERSION 4.2.2
+  VERSION 4.3.2
   LANGUAGES CXX)
 
 # This might not be entirely sensible, but helps CMake to find the

change_summary.md

@@ -3,6 +3,19 @@
 This is a slightly more readable, and therefore incomplete, summary of
 the changes from the full [changelog](CHANGELOG.md)
 
+4.3.2 is a bugfix release:
+- Make downloading the submodules a bit nicer, including an option for
+  using non-bundled versions when using `configure`
+- Make `dz` in the Python API a property
+- Make `Div_par_K_Grad_par` check the staggered location of its inputs
+- Enable split-flux derivatives on staggered fields
+- Fix `Grad2_par2` implementation in `InvertParCR`
+- Fix an issue writing `FieldPerp`s
+- Make it easier to compile the examples with different versions of
+  BOUT++, plus fixes for the `tokamak-2fluid` example
+- Fix `Div_par` when using more than one y-guard cell
+- Fix an issue with text attributes in HDF5 files
+
 4.3.1 is a bugfix release, with a few minor fixes to library code,
 notably:
 - Fix the creation of the `RGN_OUTER_X` region