Merge branch 'master' into merge-441

* master: (27 commits)
  Fix contributor's name
  Update release date
  Update changelog
  Revert SONAME/SOVERSION to 4.4.0
  Fix test-bout-override-default-option for cmake
  Update DOI and release date for 4.4.1
  Update changelog for 4.4.1
  Update translation files for 4.4.1
  Bump version to 4.4.1
  Enable setting SNES solver PETSc options from input file
  Try to consolidate some loops/branches in SNESSolver
  Use `BOUT_ENUM_CLASS` for `SNESSolver::equation_form`
  Use `std::vector/array` instead of C style arrays
  Remove `__FUNCT__` macros for PETSc callbacks
  Update backport of beuler/snes solver
  Fix typo in docs
  Remove IDL section and recommend xBOUT for analysis
  Recommend using xBOUT for manipulating restart files
  Update log output in "running BOUT++" manual section
  Move "Initialising solver" message to top of `Solver::solve`
  ...

CHANGELOG.md

@@ -91,6 +91,26 @@
 
   See [\#2154](https://github.com/boutproject/BOUT-dev/pull/2154).
 
+## [v4.4.1](https://github.com/boutproject/BOUT-dev/tree/v4.4.1) (2021-12-15)
+
+[Full Changelog](https://github.com/boutproject/BOUT-dev/compare/v4.4.0...v4.4.1)
+
+**Merged pull requests:**
+
+- Back-port beuler/snes improvements to master [\#2459](https://github.com/boutproject/BOUT-dev/pull/2459) ([bendudson](https://github.com/users/bendudson))
+- Update "Running BOUT++" documentation [\#2475](https://github.com/boutproject/BOUT-dev/pull/2475) ([ZedThree](https://github.com/users/ZedThree))
+- Raise more descriptive error if converting Option fails [\#2474](https://github.com/boutproject/BOUT-dev/pull/2474) ([ZedThree](https://github.com/users/ZedThree))
+- Print correct CMake build directory in configure message [\#2473](https://github.com/boutproject/BOUT-dev/pull/2473) ([ZedThree](https://github.com/users/ZedThree))
+- CMake: Fix using the build directory directly [\#2464](https://github.com/boutproject/BOUT-dev/pull/2464) ([ZedThree](https://github.com/users/ZedThree))
+- Add `bout::utils::` prefix to `visit` [\#2463](https://github.com/boutproject/BOUT-dev/pull/2463) ([ZedThree](https://github.com/users/ZedThree))
+- Fix SUNDIALS download git tag [\#2462](https://github.com/boutproject/BOUT-dev/pull/2462) ([ZedThree](https://github.com/users/ZedThree))
+- Fix permission of shared objects [\#2433](https://github.com/boutproject/BOUT-dev/pull/2433) ([dschwoerer](https://github.com/users/dschwoerer))
+- Fix BOUT_OVERRIDE_DEFAULT_OPTION() [\#2417](https://github.com/boutproject/BOUT-dev/pull/2417) ([johnomotani](https://github.com/users/johnomotani))
+- Ensure MPI is initialised before writing [\#2409](https://github.com/boutproject/BOUT-dev/pull/2409) ([dschwoerer](https://github.com/users/dschwoerer))
+- Remove `<optional>` include from uuid (v4.4.1) [\#2407](https://github.com/boutproject/BOUT-dev/pull/2407) ([ZedThree](https://github.com/users/ZedThree))
+- Fix make install [\#2401](https://github.com/boutproject/BOUT-dev/pull/2401) ([dschwoerer](https://github.com/users/dschwoerer))
+- Fix soname [\#2400](https://github.com/boutproject/BOUT-dev/pull/2400) ([dschwoerer](https://github.com/users/dschwoerer))
+
 ## [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)

CITATION.cff

@@ -56,7 +56,7 @@ authors:
   - family-names: Grinaker
     given-names: Eric
 
-  - family-names: Breyiannia
+  - family-names: Breyiannis
     given-names: George
 
   - family-names: Muhammed
@@ -164,11 +164,11 @@ authors:
   - family-names: James
     given-names: Toby
 
-version: 4.4.0
-date-released: 2020-08-06
+version: 4.4.1
+date-released: 2022-01-13
 repository-code: https://github.com/boutproject/BOUT-dev
 url: http://boutproject.github.io/
-doi: 10.5281/zenodo.5167527
+doi: 10.5281/zenodo.5776785
 license: 'LGPL-3.0-or-later'
 references:
   - type: article

CMakeLists.txt

@@ -660,7 +660,7 @@ if (BOUT_USE_SUNDIALS)
     FetchContent_Declare(
       sundials
       GIT_REPOSITORY https://github.com/ZedThree/sundials
-      GIT_TAG        "4f3bb8281c7b27343bcb95386ebbb665fb6196a5"
+      GIT_TAG        cmake-export-fixes
       )
     set(EXAMPLES_ENABLE_C OFF CACHE BOOL "" FORCE)
     set(EXAMPLES_INSTALL OFF CACHE BOOL "" FORCE)

bout++Config.cmake.in

@@ -52,6 +52,8 @@ if(EXISTS "@SLEPC_DIR@")
 endif()
 if(EXISTS "@SUNDIALS_ROOT@")
   set(SUNDIALS_ROOT "@SUNDIALS_ROOT@")
+elseif(EXISTS "@SUNDIALS_BINARY_DIR@")
+  list(APPEND CMAKE_PREFIX_PATH "@SUNDIALS_BINARY_DIR@")
 endif()
 if(EXISTS "@FFTW_ROOT@")
   set(FFTW_ROOT "@FFTW_ROOT@")
@@ -64,6 +66,8 @@ if(EXISTS "@ScoreP_ROOT@")
 endif()
 if(EXISTS "@netCDFCxx_ROOT@")
   set(netCDFCxx_ROOT "@netCDFCxx_ROOT@")
+elseif(EXISTS "@NCXX_BINARY_DIR@")
+  list(APPEND CMAKE_PREFIX_PATH "@NCXX_BINARY_DIR@")
 endif()
 if(EXISTS "@PVODE_ROOT@")
   set(PVODE_ROOT "@PVODE_ROOT@")

change_summary.md

@@ -3,6 +3,13 @@
 This is a slightly more readable, and therefore incomplete, summary of
 the changes from the full [changelog](CHANGELOG.md)
 
+4.4.1 is a bugfix release:
+- Fixed some issues building BOUT++ on MacOS
+- Fixed some issues when installing
+- Fixed some issues when downloading SUNDIALS and netCDF C++
+- Fixed some out of date documentation
+- Some improvements/fixes to the `beuler/snes` solver
+
 4.4.0 is a feature release. The main new features are:
 - The CMake support has been expanded, and will replace the autotools build
   system in the next major release. See [the CMake installation

include/bout/petsclib.hxx

@@ -86,6 +86,12 @@ public:
   /// was passed to the constructor.
   void setOptionsFromInputFile(KSP& ksp);
 
+  /// Set options for a SNES linear solver that uses the options specific to this PetscLib,
+  /// by setting an options prefix for the SNES, and adding that prefix to all the options
+  /// set in the [petsc] section, or [petsc] subsection of the options, if non-null 'opt'
+  /// was passed to the constructor.
+  void setOptionsFromInputFile(SNES& snes);
+
   /*!
    * Force cleanup. This will call PetscFinalize, printing a warning
    * if any instances of PetscLib still exist
@@ -125,6 +131,7 @@ private:
 // PETSc not available, so KSP not already defined. KSP should never be called, so forward
 // declaration OK here.
 class KSP;
+class SNES;
 
 class PetscLib {
 public:
@@ -134,6 +141,7 @@ public:
   static void setArgs(int &UNUSED(c), char** &UNUSED(v)) {}
 
   void setOptionsFromInputFile(KSP& UNUSED(ksp)) {}
+  void setOptionsFromInputFile(SNES& UNUSED(snes)) {}
 
   static void cleanup() {}
 };

include/bout/sys/variant.hxx

@@ -137,7 +137,7 @@ struct StaticCastOrThrow {
 /// in which case std::bad_cast will be thrown at runtime
 template <typename Variant, typename T>
 T variantStaticCastOrThrow(const Variant &v) {
-  return visit( details::StaticCastOrThrow<T>(), v );
+  return bout::utils::visit( details::StaticCastOrThrow<T>(), v );
 }
 
 namespace details {
@@ -152,7 +152,7 @@ struct ToString {
 } // namespace details
 
 template <typename Variant>
-std::string variantToString(const Variant& v) { return visit(details::ToString(), v); }
+std::string variantToString(const Variant& v) { return bout::utils::visit(details::ToString(), v); }
 
 } // namespace utils
 } // namespace bout

make.config.in

@@ -181,6 +181,15 @@ endif
 	$(INSTALL_DATA) lib/libbout++.a $(DESTDIR)@libdir@
 	$(INSTALL_DATA) lib/libpvode.a $(DESTDIR)@libdir@
 	$(INSTALL_DATA) lib/libpvpre.a $(DESTDIR)@libdir@
+ifneq ("@SHARED_EXTRA@x", "x")
+	$(INSTALL_PROGRAM) lib/libbout++.so.$(SONAME) $(DESTDIR)@libdir@
+	$(INSTALL_PROGRAM) lib/libpvode.so.* $(DESTDIR)@libdir@
+	$(INSTALL_PROGRAM) lib/libpvpre.so.* $(DESTDIR)@libdir@
+	rm -f $(DESTDIR)@libdir@/lib{bout++,pvode,pvpre}.so
+	ln -s libbout++.so.$(SONAME) $(DESTDIR)@libdir@/libbout++.so
+	ln -s libpvode.so.1.0.0 $(DESTDIR)@libdir@/libpvode.so
+	ln -s libpvpre.so.1.0.0 $(DESTDIR)@libdir@/libpvpre.so
+endif
 	$(INSTALL_PROGRAM)  bin/bout-config $(DESTDIR)@bindir@
 	$(INSTALL_PROGRAM)  bin/bout-log-color $(DESTDIR)@bindir@
 	$(INSTALL_DATA)  tools/idllib/*.pro $(DESTDIR)@datadir@/bout++/idllib/