Merge pull request #1996 from boutproject/v4.3.1-rc

Release V4.3.1

Author: ZedThree

CHANGELOG.md

@@ -1,5 +1,52 @@
 # Change Log
 
+## [v4.3.1](https://github.com/boutproject/BOUT-dev/tree/v4.3.1) (2020-03-27)
+
+[Full Changelog](https://github.com/boutproject/BOUT-dev/compare/v4.3.0...v4.3.1)
+
+**Merged pull requests:**
+
+- Fix examples/make-script [\#1995](https://github.com/boutproject/BOUT-dev/pull/1995) ([ZedThree](https://github.com/ZedThree))
+- Travis: Update pinned pip packages [\#1994](https://github.com/boutproject/BOUT-dev/pull/1994) ([ZedThree](https://github.com/ZedThree))
+- Remove unused VERSIONS file [\#1993](https://github.com/boutproject/BOUT-dev/pull/1993) ([ZedThree](https://github.com/ZedThree))
+- Minor Travis fixes and job names (master) [\#1990](https://github.com/boutproject/BOUT-dev/pull/1990) ([ZedThree](https://github.com/ZedThree))
+- conditionally add -Og for non-gcc [\#1987](https://github.com/boutproject/BOUT-dev/pull/1987) ([dschwoerer](https://github.com/dschwoerer))
+- fix test-laplace-petsc3d [\#1985](https://github.com/boutproject/BOUT-dev/pull/1985) ([dschwoerer](https://github.com/dschwoerer))
+- Use '==' to compare to literals in Python [\#1980](https://github.com/boutproject/BOUT-dev/pull/1980) ([ZedThree](https://github.com/ZedThree))
+- Read staggered J and Bxy from grid if present (master) [\#1975](https://github.com/boutproject/BOUT-dev/pull/1975) ([johnomotani](https://github.com/johnomotani))
+- Remove reference to deleted test in documentation [\#1973](https://github.com/boutproject/BOUT-dev/pull/1973) ([ZedThree](https://github.com/ZedThree))
+- Remove -Og from debug flags [\#1972](https://github.com/boutproject/BOUT-dev/pull/1972) ([ZedThree](https://github.com/ZedThree))
+- Fix documented requirements [\#1971](https://github.com/boutproject/BOUT-dev/pull/1971) ([ZedThree](https://github.com/ZedThree))
+- Compat make.config for make 4.3 [\#1970](https://github.com/boutproject/BOUT-dev/pull/1970) ([dschwoerer](https://github.com/dschwoerer))
+- Install make.config with header files [\#1969](https://github.com/boutproject/BOUT-dev/pull/1969) ([dschwoerer](https://github.com/dschwoerer))
+- Translations 4.3.1 [\#1968](https://github.com/boutproject/BOUT-dev/pull/1968) ([dschwoerer](https://github.com/dschwoerer))
+- Fix collect when given similar name [\#1966](https://github.com/boutproject/BOUT-dev/pull/1966) ([bendudson](https://github.com/bendudson))
+- Fix deprecated initialisation and boundary options [\#1956](https://github.com/boutproject/BOUT-dev/pull/1956) ([ZedThree](https://github.com/ZedThree))
+- make README.md readabile [\#1953](https://github.com/boutproject/BOUT-dev/pull/1953) ([dschwoerer](https://github.com/dschwoerer))
+- Fix lapd\_drift input files [\#1950](https://github.com/boutproject/BOUT-dev/pull/1950) ([bendudson](https://github.com/bendudson))
+- Remove FieldData::setBoundary [\#1949](https://github.com/boutproject/BOUT-dev/pull/1949) ([bendudson](https://github.com/bendudson))
+- Fixes for staggering in lapd-drift example (master) [\#1928](https://github.com/boutproject/BOUT-dev/pull/1928) ([johnomotani](https://github.com/johnomotani))
+- Fix segfaults from PvodeSolver (master) [\#1927](https://github.com/boutproject/BOUT-dev/pull/1927) ([johnomotani](https://github.com/johnomotani))
+- pkg-config petsc (master) [\#1913](https://github.com/boutproject/BOUT-dev/pull/1913) ([dschwoerer](https://github.com/dschwoerer))
+- Fix hypnotoad [\#1911](https://github.com/boutproject/BOUT-dev/pull/1911) ([johnomotani](https://github.com/johnomotani))
+- complete instructions for archlinux [\#1892](https://github.com/boutproject/BOUT-dev/pull/1892) ([dschwoerer](https://github.com/dschwoerer))
+- Petsc interface generalisation [\#1889](https://github.com/boutproject/BOUT-dev/pull/1889) ([cmacmackin](https://github.com/cmacmackin))
+- fix citation [\#1888](https://github.com/boutproject/BOUT-dev/pull/1888) ([dschwoerer](https://github.com/dschwoerer))
+- If variable is added to Datafile twice, do not write twice [\#1876](https://github.com/boutproject/BOUT-dev/pull/1876) ([johnomotani](https://github.com/johnomotani))
+- Fix loss of restart files caused by crash during initialisation [\#1875](https://github.com/boutproject/BOUT-dev/pull/1875) ([johnomotani](https://github.com/johnomotani))
+- Do not include if is released [\#1871](https://github.com/boutproject/BOUT-dev/pull/1871) ([dschwoerer](https://github.com/dschwoerer))
+- Easier instructions for Fedora [\#1870](https://github.com/boutproject/BOUT-dev/pull/1870) ([dschwoerer](https://github.com/dschwoerer))
+- Basic lock for mpark.variant [\#1869](https://github.com/boutproject/BOUT-dev/pull/1869) ([dschwoerer](https://github.com/dschwoerer))
+- Add BOUT\_REVISION (git hash of compiled version) to dump files [\#1867](https://github.com/boutproject/BOUT-dev/pull/1867) ([johnomotani](https://github.com/johnomotani))
+- Mesh requires Option to stay around. [\#1860](https://github.com/boutproject/BOUT-dev/pull/1860) ([dschwoerer](https://github.com/dschwoerer))
+- Try to prevent race condition while building. [\#1856](https://github.com/boutproject/BOUT-dev/pull/1856) ([dschwoerer](https://github.com/dschwoerer))
+- Address needs to be aligned [\#1855](https://github.com/boutproject/BOUT-dev/pull/1855) ([dschwoerer](https://github.com/dschwoerer))
+- set OMPI\_MCA\_rmaps\_base\_oversubscribe=yes for tests [\#1854](https://github.com/boutproject/BOUT-dev/pull/1854) ([dschwoerer](https://github.com/dschwoerer))
+- Loosen tolerance for other arches [\#1853](https://github.com/boutproject/BOUT-dev/pull/1853) ([dschwoerer](https://github.com/dschwoerer))
+- Bugfix: $MPIRUN should include -np [\#1851](https://github.com/boutproject/BOUT-dev/pull/1851) ([dschwoerer](https://github.com/dschwoerer))
+- Add some documentation on setting locales [\#1845](https://github.com/boutproject/BOUT-dev/pull/1845) ([bendudson](https://github.com/bendudson))
+- Fix typo in initialisation of rgn\_outer\_x [\#1838](https://github.com/boutproject/BOUT-dev/pull/1838) ([ZedThree](https://github.com/ZedThree))
+
 ## [v4.3.0](https://github.com/boutproject/BOUT-dev/tree/v4.3.0) (2019-10-24)
 [Full Changelog](https://github.com/boutproject/BOUT-dev/compare/v4.2.3...v4.3.0)
 

CITATION.bib

@@ -1,4 +1,4 @@
-@misc{BOUTv4-3-0,
+@misc{BOUTv4-3-1,
   author = {
             Benjamin Daniel Dudson and
             Peter Alec Hill and
@@ -36,6 +36,7 @@ @misc{BOUTv4-3-0
             Olivier Izacard and
             Pengwei Xi and
             Peter Naylor and
+            Fabio Riva and
             Sanat Tiwari and
             Sean Farley and
             Simon Myers and
@@ -48,7 +49,7 @@ @misc{BOUTv4-3-0
 title  = {{BOUT++}},
 month  = {10},
 year   = {2019},
-doi    = {10.5281/zenodo.3518905},
+doi    = {10.5281/zenodo.3727089},
 url    = {https://github.com/boutproject/BOUT-dev}
 }
 

CITATION.cff

@@ -126,6 +126,11 @@ authors:
   - family-names: Naylor
     given-names: Peter
 
+  - family-names: Riva
+    given-names: Fabio
+    orcid: https://orcid.org/0000-0002-0264-442X
+    affiliation: Culham Centre for Fusion Energy
+
   - family-names: Tiwari
     given-names: Sanat
 
@@ -149,11 +154,11 @@ authors:
 
   - family-names: Wang
     given-names: Zhanhui
-version: 4.3.0
-date-released: 2019-10-25
+version: 4.3.1
+date-released: 2020-03-27
 repository-code: https://github.com/boutproject/BOUT-dev
 url: http://boutproject.github.io/
-doi: 10.5281/zenodo.3518905
+doi: 10.5281/zenodo.3727089
 license: 'LGPL-3.0-or-later'
 references:
   - type: article

change_summary.md

@@ -3,6 +3,18 @@
 This is a slightly more readable, and therefore incomplete, summary of
 the changes from the full [changelog](CHANGELOG.md)
 
+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
+- Several small bugs in the Python API
+- Preserve restart files if there's a crash during initialisation
+- Fix some segfaults in the PvodeSolver
+- Fix some issues with Hypnotoad (see
+  [\#1783](https://github.com/boutproject/BOUT-dev/pull/1783)
+  ([friva000](https://github.com/friva000)))
+
+Other changes are mostly housekeeping changes for the BOUT++ project.
+
 4.3.0 is a big feature release:
 - `Field`s are now "tagged" with their "y-direction": that is, whether
   they are in field-aligned space or not. This allows us to perform

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for BOUT++ 4.3.0.
+# Generated by GNU Autoconf 2.69 for BOUT++ 4.3.1.
 #
 # Report bugs to <bd512@york.ac.uk>.
 #
@@ -580,8 +580,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='BOUT++'
 PACKAGE_TARNAME='bout--'
-PACKAGE_VERSION='4.3.0'
-PACKAGE_STRING='BOUT++ 4.3.0'
+PACKAGE_VERSION='4.3.1'
+PACKAGE_STRING='BOUT++ 4.3.1'
 PACKAGE_BUGREPORT='bd512@york.ac.uk'
 PACKAGE_URL=''
 
@@ -1392,7 +1392,7 @@ 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++ 4.3.0 to adapt to many kinds of systems.
+\`configure' configures BOUT++ 4.3.1 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1457,7 +1457,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of BOUT++ 4.3.0:";;
+     short | recursive ) echo "Configuration of BOUT++ 4.3.1:";;
    esac
   cat <<\_ACEOF
 
@@ -1601,7 +1601,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-BOUT++ configure 4.3.0
+BOUT++ configure 4.3.1
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2182,7 +2182,7 @@ 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 4.3.0, which was
+It was created by BOUT++ $as_me 4.3.1, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -15365,7 +15365,7 @@ cat >>$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 4.3.0, which was
+This file was extended by BOUT++ $as_me 4.3.1, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -15422,7 +15422,7 @@ _ACEOF
 cat >>$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 4.3.0
+BOUT++ config.status 4.3.1
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 
@@ -16734,7 +16734,7 @@ 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 4.3.0, which was
+This file was extended by BOUT++ $as_me 4.3.1, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -16791,7 +16791,7 @@ _ACEOF
 cat >>$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 4.3.0
+BOUT++ config.status 4.3.1
 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++],[4.3.0],[bd512@york.ac.uk])
+AC_INIT([BOUT++],[4.3.1],[bd512@york.ac.uk])
 AC_CONFIG_AUX_DIR([build-aux])
 AC_CONFIG_MACRO_DIR([m4])
 

locale/makefile

@@ -12,7 +12,7 @@ locale: $(MO_FILES)
 
 # Create the template file, combining all source files
 libbout.pot: FORCE
-	xgettext --keyword=_ --language=c++ --add-comments --sort-output -o $@ `find ../ -name "[^.#]*.[ch]xx"`
+	xgettext --keyword=_ --language=c++ --add-comments --sort-output -o $@ `find ../src ../include ../tests ../examples -name "[^.#]*.[ch]xx"`
 
 # Update a .po file
 # If it doesn't exist then create; if it exists then update

manual/RELEASE_HOWTO.md

@@ -23,6 +23,10 @@ releases
 
 Before merging PR:
 
+- [ ] Update locale translation files
+    - `make -C locale update-all`
+    - Be aware that this *will* update the timestamps and *possibly*
+      reorder file paths in the .po and .pot files
 - [ ] Update [`CHANGELOG.md`][changelog]:
     - Install [`github_changelog_generator`][gcg]
         - Make sure it is at least v1.15!

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         = 4.3.0
+PROJECT_NUMBER         = 4.3.1
 
 # 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         = 4.3.0
+PROJECT_NUMBER         = 4.3.1
 
 # 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