Merge pull request #2387 from boutproject/v4.3.3-rc

Release V4.3.3

CHANGELOG.md

@@ -17,6 +17,31 @@
 
   See [\#2154](https://github.com/boutproject/BOUT-dev/pull/2154).
 
+## [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)
+
+**Merged pull requests:**
+
+- Fix documentation for examples/wave-slab [\#2369](https://github.com/boutproject/BOUT-dev/pull/2369) ([ZedThree](https://github.com/users/ZedThree))
+- Make include optional [\#2360](https://github.com/boutproject/BOUT-dev/pull/2360) ([dschwoerer](https://github.com/users/dschwoerer))
+- Fix ReadTheDocs (master) [\#2319](https://github.com/boutproject/BOUT-dev/pull/2319) ([ZedThree](https://github.com/users/ZedThree))
+- Fix for FindPETSc not being reentrant if pkg-config used [\#2317](https://github.com/boutproject/BOUT-dev/pull/2317) ([ZedThree](https://github.com/users/ZedThree))
+- Add missing snb.cxx to CMakeLists.txt [\#2315](https://github.com/boutproject/BOUT-dev/pull/2315) ([bendudson](https://github.com/users/bendudson))
+- Add notes on installing SUNDIALS [\#2311](https://github.com/boutproject/BOUT-dev/pull/2311) ([bendudson](https://github.com/users/bendudson))
+- Make blob2d example self contained [\#2288](https://github.com/boutproject/BOUT-dev/pull/2288) ([dschwoerer](https://github.com/users/dschwoerer))
+- Fix some Solvers not always using user preconditioner/Jacobian [\#2283](https://github.com/boutproject/BOUT-dev/pull/2283) ([ZedThree](https://github.com/users/ZedThree))
+- Bump jinja2 from 2.10.1 to 2.11.3 [\#2266](https://github.com/boutproject/BOUT-dev/pull/2266) ([dependabot[bot]](https://github.com/users/dependabot%5Bbot%5D))
+- Fix use of uninitialised value in Delp2 [\#2262](https://github.com/boutproject/BOUT-dev/pull/2262) ([johnomotani](https://github.com/users/johnomotani))
+- Add requirements to boutcore/print test [\#2175](https://github.com/boutproject/BOUT-dev/pull/2175) ([ZedThree](https://github.com/users/ZedThree))
+- Update docs on supported PETSc versions [\#2171](https://github.com/boutproject/BOUT-dev/pull/2171) ([johnomotani](https://github.com/users/johnomotani))
+- Convert Travis to Github Actions (master) [\#2170](https://github.com/boutproject/BOUT-dev/pull/2170) ([ZedThree](https://github.com/users/ZedThree))
+- Boutcore improvements [\#2166](https://github.com/boutproject/BOUT-dev/pull/2166) ([dschwoerer](https://github.com/users/dschwoerer))
+- Fix shiftOutput (master) [\#2158](https://github.com/boutproject/BOUT-dev/pull/2158) ([johnomotani](https://github.com/users/johnomotani))
+- Fix test-restart-io and FieldPerp writes [\#2154](https://github.com/boutproject/BOUT-dev/pull/2154) ([johnomotani](https://github.com/users/johnomotani))
+- Ignore more test data [\#2125](https://github.com/boutproject/BOUT-dev/pull/2125) ([dschwoerer](https://github.com/users/dschwoerer))
+- Fix links to open-mpi.org and lam-mpi.org [\#2122](https://github.com/boutproject/BOUT-dev/pull/2122) ([tobyjamez](https://github.com/users/tobyjamez))
+
 ## [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)

CITATION.cff

@@ -37,15 +37,18 @@ authors:
 
   - family-names: Shanahan
     given-names: Brendan
+    affiliation: Max Planck Institute for Plasma Physics, Greifswald
 
   - family-names: Friedman
     given-names: Brett
 
   - family-names: Ma
     given-names: Chenhao
 
-  - family-names: Schwörer
+  - family-names: Bold
     given-names: David
+    affiliation: Max Planck Institute for Plasma Physics, Greifswald
+    orcid: https://orcid.org/0000-0003-0911-8606
 
   - family-names: Meyerson
     given-names: Dmitry
@@ -154,11 +157,15 @@ authors:
 
   - family-names: Wang
     given-names: Zhanhui
-version: 4.3.2
-date-released: 2020-10-19
+
+  - family-names: James
+    given-names: Toby
+
+version: 4.3.3
+date-released: 2021-07-29
 repository-code: https://github.com/boutproject/BOUT-dev
 url: http://boutproject.github.io/
-doi: 10.5281/zenodo.4046792
+doi: 10.5281/zenodo.5142504
 license: 'LGPL-3.0-or-later'
 references:
   - type: article

change_summary.md

@@ -3,6 +3,16 @@
 This is a slightly more readable, and therefore incomplete, summary of
 the changes from the full [changelog](CHANGELOG.md)
 
+4.3.3 is a bugfix release:
+- Better documentation and tests
+- Fix `shiftOutput` for aligned fields
+- Some improvements to the Python API, including support for Python's
+  exponentiation operator `**`, and MPI-aware logging
+- Fix an uninitialised variable in `Delp2`
+- Bump the version of jinja2 from 2.10 to 2.11
+- Fix for some Solvers not always using user preconditioner/Jacobian
+- Some minor fixes to the build systems
+
 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`

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for BOUT++ 4.3.2.
+# Generated by GNU Autoconf 2.69 for BOUT++ 4.3.3.
 #
 # Report bugs to <[email protected]>.
 #
@@ -580,8 +580,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='BOUT++'
 PACKAGE_TARNAME='bout--'
-PACKAGE_VERSION='4.3.2'
-PACKAGE_STRING='BOUT++ 4.3.2'
+PACKAGE_VERSION='4.3.3'
+PACKAGE_STRING='BOUT++ 4.3.3'
 PACKAGE_BUGREPORT='[email protected]'
 PACKAGE_URL=''
 
@@ -1395,7 +1395,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures BOUT++ 4.3.2 to adapt to many kinds of systems.
+\`configure' configures BOUT++ 4.3.3 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1460,7 +1460,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of BOUT++ 4.3.2:";;
+     short | recursive ) echo "Configuration of BOUT++ 4.3.3:";;
    esac
   cat <<\_ACEOF
 
@@ -1606,7 +1606,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-BOUT++ configure 4.3.2
+BOUT++ configure 4.3.3
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2187,7 +2187,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by BOUT++ $as_me 4.3.2, which was
+It was created by BOUT++ $as_me 4.3.3, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -15924,7 +15924,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by BOUT++ $as_me 4.3.2, which was
+This file was extended by BOUT++ $as_me 4.3.3, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -15981,7 +15981,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-BOUT++ config.status 4.3.2
+BOUT++ config.status 4.3.3
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 
@@ -17290,7 +17290,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by BOUT++ $as_me 4.3.2, which was
+This file was extended by BOUT++ $as_me 4.3.3, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -17347,7 +17347,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-BOUT++ config.status 4.3.2
+BOUT++ config.status 4.3.3
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 

configure.ac

@@ -32,7 +32,7 @@
 #
 
 AC_PREREQ([2.69])
-AC_INIT([BOUT++],[4.3.2],[[email protected]])
+AC_INIT([BOUT++],[4.3.3],[[email protected]])
 AC_CONFIG_AUX_DIR([build-aux])
 AC_CONFIG_MACRO_DIR([m4])
 

makefile

@@ -16,7 +16,7 @@ shared: libfast
 	@$(CXX) -shared -Wl,-soname,libpvpre.so.1.0.0 -o $(BOUT_TOP)/lib/libpvpre_.so -L $(BOUT_TOP)/lib -Wl,--whole-archive -lpvpre -Wl,--no-whole-archive
 	@mv $(BOUT_TOP)/lib/libpvode_.so $(BOUT_TOP)/lib/libpvode.so.1.0.0
 	@mv $(BOUT_TOP)/lib/libpvpre_.so $(BOUT_TOP)/lib/libpvpre.so.1.0.0
-	@ln -s libbout++.so.4.3.1 $(LIB_SO)
+	@ln -s libbout++.so.4.3.3 $(LIB_SO)
 	@ln -s libpvode.so.1.0.0 lib/libpvode.so
 	@ln -s libpvpre.so.1.0.0 lib/libpvpre.so
 

manual/doxygen/Doxyfile

@@ -38,7 +38,7 @@ PROJECT_NAME           = BOUT++
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 4.3.2
+PROJECT_NUMBER         = 4.3.3
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

manual/doxygen/Doxyfile_readthedocs

@@ -38,7 +38,7 @@ PROJECT_NAME           = BOUT++
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 4.3.2
+PROJECT_NUMBER         = 4.3.3
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

manual/sphinx/conf.py

@@ -134,7 +134,7 @@ def __getattr__(cls, name):
 # The short X.Y version.
 version = '4.3'
 # The full version, including alpha/beta/rc tags.
-release = '4.3.2'
+release = '4.3.3'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

manual/sphinx/requirements.txt

@@ -1,2 +1,2 @@
 breathe~=4.12
-future~=0.16
+sphinx==4.0.1