Merge pull request #12 from andrewjpage/master

midpoint rerooting and pairwise comparison

.gitignore

@@ -1,7 +1,13 @@
 *.o
 gubbins
 tests/run_all_tests
+src/run_all_tests
 .DS_Store
 Makefile
 src/.deps
 autom4te.cache/*
+*.lo
+*~
+src/.libs/*
+src/libPyGubbins_la-PyGubbins.loT
+src/libgubbins.la

Makefile.in

@@ -29,13 +29,16 @@ POST_INSTALL = :
 NORMAL_UNINSTALL = :
 PRE_UNINSTALL = :
 POST_UNINSTALL = :
+build_triplet = @build@
+host_triplet = @host@
 subdir = .
 DIST_COMMON = README $(am__configure_deps) $(srcdir)/Makefile.am \
 	$(srcdir)/Makefile.in $(srcdir)/config.h.in \
-	$(top_srcdir)/configure AUTHORS ChangeLog depcomp install-sh \
-	missing
+	$(top_srcdir)/configure AUTHORS ChangeLog INSTALL config.guess \
+	config.sub depcomp install-sh ltmain.sh missing
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.ac
+am__aclocal_m4_deps = $(top_srcdir)/m4/ax_python_devel.m4 \
+	$(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \
@@ -70,6 +73,7 @@ distuninstallcheck_listfiles = find . -type f -print
 distcleancheck_listfiles = find . -type f -print
 ACLOCAL = @ACLOCAL@
 AMTAR = @AMTAR@
+AR = @AR@
 AUTOCONF = @AUTOCONF@
 AUTOHEADER = @AUTOHEADER@
 AUTOMAKE = @AUTOMAKE@
@@ -79,14 +83,21 @@ CCDEPMODE = @CCDEPMODE@
 CFLAGS = @CFLAGS@
 CPP = @CPP@
 CPPFLAGS = @CPPFLAGS@
+CXX = @CXX@
+CXXCPP = @CXXCPP@
+CXXDEPMODE = @CXXDEPMODE@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEFS = @DEFS@
 DEPDIR = @DEPDIR@
+ECHO = @ECHO@
 ECHO_C = @ECHO_C@
 ECHO_N = @ECHO_N@
 ECHO_T = @ECHO_T@
 EGREP = @EGREP@
 EXEEXT = @EXEEXT@
+F77 = @F77@
+FFLAGS = @FFLAGS@
 GREP = @GREP@
 INSTALL = @INSTALL@
 INSTALL_DATA = @INSTALL_DATA@
@@ -96,6 +107,8 @@ INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
 LDFLAGS = @LDFLAGS@
 LIBOBJS = @LIBOBJS@
 LIBS = @LIBS@
+LIBTOOL = @LIBTOOL@
+LN_S = @LN_S@
 LTLIBOBJS = @LTLIBOBJS@
 MAKEINFO = @MAKEINFO@
 MKDIR_P = @MKDIR_P@
@@ -107,6 +120,14 @@ PACKAGE_STRING = @PACKAGE_STRING@
 PACKAGE_TARNAME = @PACKAGE_TARNAME@
 PACKAGE_VERSION = @PACKAGE_VERSION@
 PATH_SEPARATOR = @PATH_SEPARATOR@
+PYTHON = @PYTHON@
+PYTHON_CPPFLAGS = @PYTHON_CPPFLAGS@
+PYTHON_EXTRA_LDFLAGS = @PYTHON_EXTRA_LDFLAGS@
+PYTHON_EXTRA_LIBS = @PYTHON_EXTRA_LIBS@
+PYTHON_LDFLAGS = @PYTHON_LDFLAGS@
+PYTHON_SITE_PKG = @PYTHON_SITE_PKG@
+PYTHON_VERSION = @PYTHON_VERSION@
+RANLIB = @RANLIB@
 SET_MAKE = @SET_MAKE@
 SHELL = @SHELL@
 STRIP = @STRIP@
@@ -116,20 +137,30 @@ abs_srcdir = @abs_srcdir@
 abs_top_builddir = @abs_top_builddir@
 abs_top_srcdir = @abs_top_srcdir@
 ac_ct_CC = @ac_ct_CC@
+ac_ct_CXX = @ac_ct_CXX@
+ac_ct_F77 = @ac_ct_F77@
 am__include = @am__include@
 am__leading_dot = @am__leading_dot@
 am__quote = @am__quote@
 am__tar = @am__tar@
 am__untar = @am__untar@
 bindir = @bindir@
+build = @build@
 build_alias = @build_alias@
+build_cpu = @build_cpu@
+build_os = @build_os@
+build_vendor = @build_vendor@
 builddir = @builddir@
 datadir = @datadir@
 datarootdir = @datarootdir@
 docdir = @docdir@
 dvidir = @dvidir@
 exec_prefix = @exec_prefix@
+host = @host@
 host_alias = @host_alias@
+host_cpu = @host_cpu@
+host_os = @host_os@
+host_vendor = @host_vendor@
 htmldir = @htmldir@
 includedir = @includedir@
 infodir = @infodir@
@@ -208,6 +239,15 @@ $(srcdir)/config.h.in:  $(am__configure_deps)
 distclean-hdr:
 	-rm -f config.h stamp-h1
 
+mostlyclean-libtool:
+	-rm -f *.lo
+
+clean-libtool:
+	-rm -rf .libs _libs
+
+distclean-libtool:
+	-rm -f libtool
+
 # This directory's subdirectories are mostly independent; you can cd
 # into them and run `make' without going through this Makefile.
 # To change the values of `make' variables: instead of editing Makefiles,
@@ -512,12 +552,13 @@ maintainer-clean-generic:
 	@echo "it deletes files that may require special tools to rebuild."
 clean: clean-recursive
 
-clean-am: clean-generic mostlyclean-am
+clean-am: clean-generic clean-libtool mostlyclean-am
 
 distclean: distclean-recursive
 	-rm -f $(am__CONFIG_DISTCLEAN_FILES)
 	-rm -f Makefile
-distclean-am: clean-am distclean-generic distclean-hdr distclean-tags
+distclean-am: clean-am distclean-generic distclean-hdr \
+	distclean-libtool distclean-tags
 
 dvi: dvi-recursive
 
@@ -555,7 +596,7 @@ maintainer-clean-am: distclean-am maintainer-clean-generic
 
 mostlyclean: mostlyclean-recursive
 
-mostlyclean-am: mostlyclean-generic
+mostlyclean-am: mostlyclean-generic mostlyclean-libtool
 
 pdf: pdf-recursive
 
@@ -572,18 +613,19 @@ uninstall-am:
 
 .PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
 	all all-am am--refresh check check-am clean clean-generic \
-	ctags ctags-recursive dist dist-all dist-bzip2 dist-gzip \
-	dist-shar dist-tarZ dist-zip distcheck distclean \
-	distclean-generic distclean-hdr distclean-tags distcleancheck \
-	distdir distuninstallcheck dvi dvi-am html html-am info \
-	info-am install install-am install-data install-data-am \
-	install-dvi install-dvi-am install-exec install-exec-am \
-	install-html install-html-am install-info install-info-am \
-	install-man install-pdf install-pdf-am install-ps \
-	install-ps-am install-strip installcheck installcheck-am \
-	installdirs installdirs-am maintainer-clean \
-	maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
-	pdf-am ps ps-am tags tags-recursive uninstall uninstall-am
+	clean-libtool ctags ctags-recursive dist dist-all dist-bzip2 \
+	dist-gzip dist-shar dist-tarZ dist-zip distcheck distclean \
+	distclean-generic distclean-hdr distclean-libtool \
+	distclean-tags distcleancheck distdir distuninstallcheck dvi \
+	dvi-am html html-am info info-am install install-am \
+	install-data install-data-am install-dvi install-dvi-am \
+	install-exec install-exec-am install-html install-html-am \
+	install-info install-info-am install-man install-pdf \
+	install-pdf-am install-ps install-ps-am install-strip \
+	installcheck installcheck-am installdirs installdirs-am \
+	maintainer-clean maintainer-clean-generic mostlyclean \
+	mostlyclean-generic mostlyclean-libtool pdf pdf-am ps ps-am \
+	tags tags-recursive uninstall uninstall-am
 
 # Tell versions [3.59,3.63) of GNU make to not export all variables.
 # Otherwise a system limit (for SysV at least) may be exceeded.