Update changelog; bump version; run autogen

Bump version to 0.3.1.

CHANGELOG.md

@@ -2,6 +2,33 @@
 
 ---
 
+## 0.3.1
+
+---
+
+JOSS revision.
+
+### Added
+
+* Add section in README and documentation on how to use the API.
+* Add simple Navier-Stokes solver using the PetIBM API in the folder `examples/api_examples`.
+
+### Changed
+
+* Rename application code `tairacolonius` into `ibpm` (Immersed Boundary Projection Method); binary program now named `petibm-ibpm`.
+* Make YAML converters and operator< private.
+* Move example of oscillating cylinder to folder `examples/api_examples`.
+* Update optional dependency `AmgXWrapper` with latest version (1.4).
+
+### Fixed
+
+* Remove MPI barrier in routine that creates a directory.
+* Fixed memory leaks in solver programs and utility programs.
+
+### Removed
+
+---
+
 ## 0.3.0
 
 ---

Makefile.in

@@ -1,7 +1,7 @@
-# Makefile.in generated by automake 1.15.1 from Makefile.am.
+# Makefile.in generated by automake 1.15 from Makefile.am.
 # @configure_input@
 
-# Copyright (C) 1994-2017 Free Software Foundation, Inc.
+# Copyright (C) 1994-2014 Free Software Foundation, Inc.
 
 # This Makefile.in is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -173,8 +173,8 @@ am__DIST_COMMON = $(srcdir)/Makefile.in $(top_srcdir)/config/compile \
 	$(top_srcdir)/config/config.sub \
 	$(top_srcdir)/config/install-sh $(top_srcdir)/config/ltmain.sh \
 	$(top_srcdir)/config/missing config/ar-lib config/compile \
-	config/config.guess config/config.sub config/install-sh \
-	config/ltmain.sh config/missing
+	config/config.guess config/config.sub config/depcomp \
+	config/install-sh config/ltmain.sh config/missing
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 distdir = $(PACKAGE)-$(VERSION)
 top_distdir = $(distdir)
@@ -273,7 +273,6 @@ LIBTOOL = @LIBTOOL@
 LIPO = @LIPO@
 LN_S = @LN_S@
 LTLIBOBJS = @LTLIBOBJS@
-LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
 MAINT = @MAINT@
 MAKEINFO = @MAKEINFO@
 MANIFEST_TOOL = @MANIFEST_TOOL@
@@ -349,6 +348,7 @@ pdfdir = @pdfdir@
 prefix = @prefix@
 program_transform_name = @program_transform_name@
 psdir = @psdir@
+runstatedir = @runstatedir@
 sbindir = @sbindir@
 sharedstatedir = @sharedstatedir@
 srcdir = @srcdir@
@@ -599,7 +599,7 @@ distdir: $(DISTFILES)
 	  ! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \
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 dist-gzip: distdir
-	tardir=$(distdir) && $(am__tar) | eval GZIP= gzip $(GZIP_ENV) -c >$(distdir).tar.gz
+	tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
 	$(am__post_remove_distdir)
 
 dist-bzip2: distdir
@@ -625,7 +625,7 @@ dist-shar: distdir
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 	@echo WARNING: "It will be removed altogether in Automake 2.0" >&2
-	shar $(distdir) | eval GZIP= gzip $(GZIP_ENV) -c >$(distdir).shar.gz
+	shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz
 	$(am__post_remove_distdir)
 
 dist-zip: distdir
@@ -643,7 +643,7 @@ dist dist-all:
 distcheck: dist
 	case '$(DIST_ARCHIVES)' in \
 	*.tar.gz*) \
-	  eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).tar.gz | $(am__untar) ;;\
+	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\
 	*.tar.bz2*) \
 	  bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\
 	*.tar.lz*) \
@@ -653,7 +653,7 @@ distcheck: dist
 	*.tar.Z*) \
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 	*.shar.gz*) \
-	  eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).shar.gz | unshar ;;\
+	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).shar.gz | unshar ;;\
 	*.zip*) \
 	  unzip $(distdir).zip ;;\
 	esac

aclocal.m4

@@ -1,6 +1,6 @@
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+# Copyright (C) 1996-2014 Free Software Foundation, Inc.
 
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 If you have problems, you may need to regenerate the build system entirely.
 To do so, use the procedure documented by the package, typically 'autoreconf'.])])
 
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+# Copyright (C) 2002-2014 Free Software Foundation, Inc.
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 dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to
 dnl require some minimum version.  Point them to the right macro.
-m4_if([$1], [1.15.1], [],
+m4_if([$1], [1.15], [],
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@@ -51,14 +51,14 @@ m4_define([_AM_AUTOCONF_VERSION], [])
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 AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],
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-# Copyright (C) 1999-2017 Free Software Foundation, Inc.
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@@ -332,7 +332,7 @@ _AM_SUBST_NOTMAKE([am__nodep])dnl
 
 # Generate code to set up dependency tracking.              -*- Autoconf -*-
 
-# Copyright (C) 1999-2017 Free Software Foundation, Inc.
+# Copyright (C) 1999-2014 Free Software Foundation, Inc.
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 # Do all the work for Automake.                             -*- Autoconf -*-
 
-# Copyright (C) 1996-2017 Free Software Foundation, Inc.
+# Copyright (C) 1996-2014 Free Software Foundation, Inc.
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@@ -605,7 +605,7 @@ for _am_header in $config_headers :; do
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 echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_count])
 
-# Copyright (C) 2001-2017 Free Software Foundation, Inc.
+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
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@@ -626,7 +626,7 @@ if test x"${install_sh+set}" != xset; then
 fi
 AC_SUBST([install_sh])])
 
-# Copyright (C) 2003-2017 Free Software Foundation, Inc.
+# Copyright (C) 2003-2014 Free Software Foundation, Inc.
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@@ -648,7 +648,7 @@ AC_SUBST([am__leading_dot])])
 # Add --enable-maintainer-mode option to configure.         -*- Autoconf -*-
 # From Jim Meyering
 
-# Copyright (C) 1996-2017 Free Software Foundation, Inc.
+# Copyright (C) 1996-2014 Free Software Foundation, Inc.
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@@ -683,7 +683,7 @@ AC_MSG_CHECKING([whether to enable maintainer-specific portions of Makefiles])
 
 # Check to see how 'make' treats includes.	            -*- Autoconf -*-
 
-# Copyright (C) 2001-2017 Free Software Foundation, Inc.
+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
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@@ -733,7 +733,7 @@ rm -f confinc confmf
 
 # Fake the existence of programs that GNU maintainers use.  -*- Autoconf -*-
 
-# Copyright (C) 1997-2017 Free Software Foundation, Inc.
+# Copyright (C) 1997-2014 Free Software Foundation, Inc.
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 # gives unlimited permission to copy and/or distribute it,
@@ -772,7 +772,7 @@ fi
 
 # Helper functions for option handling.                     -*- Autoconf -*-
 
-# Copyright (C) 2001-2017 Free Software Foundation, Inc.
+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
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 AC_DEFUN([_AM_IF_OPTION],
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-# Copyright (C) 1999-2017 Free Software Foundation, Inc.
+# Copyright (C) 1999-2014 Free Software Foundation, Inc.
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 # For backward compatibility.
 AC_DEFUN_ONCE([AM_PROG_CC_C_O], [AC_REQUIRE([AC_PROG_CC])])
 
-# Copyright (C) 2001-2017 Free Software Foundation, Inc.
+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
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 # Check to make sure that the build environment is sane.    -*- Autoconf -*-
 
-# Copyright (C) 1996-2017 Free Software Foundation, Inc.
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@@ -948,7 +948,7 @@ AC_CONFIG_COMMANDS_PRE(
 rm -f conftest.file
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-# Copyright (C) 2009-2017 Free Software Foundation, Inc.
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 _AM_SUBST_NOTMAKE([AM_BACKSLASH])dnl
 ])
 
-# Copyright (C) 2001-2017 Free Software Foundation, Inc.
+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
 #
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@@ -1036,7 +1036,7 @@ fi
 INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
 AC_SUBST([INSTALL_STRIP_PROGRAM])])
 
-# Copyright (C) 2006-2017 Free Software Foundation, Inc.
+# Copyright (C) 2006-2014 Free Software Foundation, Inc.
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 # Check how to create a tarball.                            -*- Autoconf -*-
 
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applications/Makefile.in

@@ -1,7 +1,7 @@
-# Makefile.in generated by automake 1.15.1 from Makefile.am.
+# Makefile.in generated by automake 1.15 from Makefile.am.
 # @configure_input@
 
-# Copyright (C) 1994-2017 Free Software Foundation, Inc.
+# Copyright (C) 1994-2014 Free Software Foundation, Inc.
 
 # This Makefile.in is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -246,7 +246,6 @@ LIBTOOL = @LIBTOOL@
 LIPO = @LIPO@
 LN_S = @LN_S@
 LTLIBOBJS = @LTLIBOBJS@
-LT_SYS_LIBRARY_PATH = @LT_SYS_LIBRARY_PATH@
 MAINT = @MAINT@
 MAKEINFO = @MAKEINFO@
 MANIFEST_TOOL = @MANIFEST_TOOL@
@@ -322,6 +321,7 @@ pdfdir = @pdfdir@
 prefix = @prefix@
 program_transform_name = @program_transform_name@
 psdir = @psdir@
+runstatedir = @runstatedir@
 sbindir = @sbindir@
 sharedstatedir = @sharedstatedir@
 srcdir = @srcdir@

applications/createxdmf/Makefile.in

@@ -1,7 +1,7 @@
-# Makefile.in generated by automake 1.15.1 from Makefile.am.
+# Makefile.in generated by automake 1.15 from Makefile.am.
 # @configure_input@
 
-# Copyright (C) 1994-2017 Free Software Foundation, Inc.
+# Copyright (C) 1994-2014 Free Software Foundation, Inc.
 
 # This Makefile.in is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -240,7 +240,6 @@ LIBTOOL = @LIBTOOL@
 LIPO = @LIPO@
 LN_S = @LN_S@
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 MAKEINFO = @MAKEINFO@
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@@ -316,6 +315,7 @@ pdfdir = @pdfdir@
 prefix = @prefix@
 program_transform_name = @program_transform_name@
 psdir = @psdir@
+runstatedir = @runstatedir@
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 srcdir = @srcdir@

applications/decoupledibpm/Makefile.in

@@ -1,7 +1,7 @@
-# Makefile.in generated by automake 1.15.1 from Makefile.am.
+# Makefile.in generated by automake 1.15 from Makefile.am.
 # @configure_input@
 
-# Copyright (C) 1994-2017 Free Software Foundation, Inc.
+# Copyright (C) 1994-2014 Free Software Foundation, Inc.
 
 # This Makefile.in is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -241,7 +241,6 @@ LIBTOOL = @LIBTOOL@
 LIPO = @LIPO@
 LN_S = @LN_S@
 LTLIBOBJS = @LTLIBOBJS@
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 MAKEINFO = @MAKEINFO@
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@@ -317,6 +316,7 @@ pdfdir = @pdfdir@
 prefix = @prefix@
 program_transform_name = @program_transform_name@
 psdir = @psdir@
+runstatedir = @runstatedir@
 sbindir = @sbindir@
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 srcdir = @srcdir@