.gitignore

+Makefile.in
+aclocal.m4
+autom4te.cache/
+configure
+example/Makefile.in
+example/basiccmdline/Makefile.in
+example/compressor/Makefile.in
+example/gapcode/Makefile.in
+example/nclsimplest/Makefile.in
+example/ncltest/Makefile.in
+example/normalizer/Makefile.in
+example/patristic/Makefile.in
+example/phylobaseinterface/Makefile.in
+example/splitsinfile/Makefile.in
+example/subsetter/Makefile.in
+example/translate/Makefile.in
+ncl/Makefile.in
+test/Makefile.in
+config/compile

.travis.yml

+sudo: false
+language: C++
+compiler:
+    - clang++
+install:
+    - sh travis-build-and-test.sh
+script:
+    - echo 'Success. The tests are in the travis-build-and-test.sh script'

AUTHORS

@@ -19,13 +19,13 @@ Other contributors to these versions include:
   Derrick Zwickl
   Brian O'Meara
   Brandon Chisham
-  Franois Michonneau
+  Franois Michonneau
   Jeet Sukumaran
 
 The code in examples/phylobase... was written by Brian O'Meara and Derrick Zwickl
 for phylobase.
 
-David Surez Pascal contributed SWIG bindings which heavily influenced those
+David Surez Pascal contributed SWIG bindings which heavily influenced those
    found in branches/v2.2 
 
 Michael Elliot contributed some code to the branches/xml branch.

CMakeLists.txt

+cmake_minimum_required (VERSION 3.1)
+
+if(MSVC)
+  # Force to always compile with W4
+  if(CMAKE_CXX_FLAGS MATCHES "/W[0-4]")
+    string(REGEX REPLACE "/W[0-4]" "/W4" CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
+  else()
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /W4")
+  endif()
+  add_definitions(/D_CRT_SECURE_NO_WARNINGS)
+else()
+  # Update if necessary
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -fPIC")
+  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wall -fPIC")
+  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -DDEBUG")
+  set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} -DDEBUG")
+endif()
+add_subdirectory (ncl)

README

-NCL README -- the NEXUS Class Library (NCL) README file
-
-Most documentation for this C++ class library is in the form of HTML
-files in the html directory. Please begin by viewing the html/index.html
-file in your web browser.
-
-See the INSTALL file for important information about building and installing
-the NCL and example programs, and incorporating the NCL into your own
-applications.
-
-As of March 09, 2012, NCL is available under a Simplified BSD license (see
-BSDLicense.txt) in addition to the GPL license.
-
-ACKNOWLEDGEMENTS
-	Many of the files used for testing were provided by Arlin Stoltzfus (see
-http://www.molevol.org/camel/projects/nexus/ for more information), the Mesquite
-package, and from TreeBase (thanks, to Bill Piel!).
-
-	The SWIG bindings for version 2.1 were inspired by the work of David Suarez
-Pascal in the 2007 Google Summer of Code.  They were simplified using new
-features of NCL 2.1.  Thanks to David for blazing the way on the old version,
-Google for funding, and NESCent (in particular Hilmar Lapp) for getting the
-NESCent GSoC program going.
-
-    The 2010 GSoC effort also led to enhancements in terms of annotation storage
-and xml parsing which are currently on 
-    https://ncl.svn.sourceforge.net/svnroot/ncl/branches/xml
-    Thanks to NESCent, Google, and Michael Elliot for that support.

README.md

+# NCL - the NEXUS Class Library
+[![Build Status](https://secure.travis-ci.org/OpenTreeOfLife/ncl.png)](http://travis-ci.org/OpenTreeOfLife/ncl)
+
+This is version 2.1.21-dev of NCL by Paul O. Lewis (and others see below)
+
+This git repo was forked from https://github.com/mtholder/ncl
+so that all of the open tree of life developers would have write
+permissions.
+Mark is adding several example programs for dealing with trees from
+the Open Tree project.
+They are being added to this repo just because it is easier to distribute
+NCL-dependent code as a part of the library than it is to document the 
+procedure of installing C++ libraries and linking to them.
+If we keep using these tools, we can fairly easily pull out these examples
+as free standing client repo(s).
+
+If we find any changes need to be made to the existing files in the `ncl`
+subdir, we should try to remember to pull those back into the mtholder
+fork of the repo so that other users of NCL can benefit.
+
+
+Most documentation for this C++ class library is in the form of HTML
+files in the html directory. Please begin by viewing the html/index.html
+file in your web browser.
+
+See the INSTALL file for important information about building and installing
+the NCL and example programs, and incorporating the NCL into your own
+applications.
+
+As of March 09, 2012, NCL is available under a Simplified BSD license (see
+BSDLicense.txt) in addition to the GPL license.
+
+# ACKNOWLEDGEMENTS
+NCL AUTHORS -- the author of the NEXUS Class Library (NCL) version 2.0 is
+
+  Paul O. Lewis, Ph.D.
+  Department of Ecology and Evolutionary Biology
+  The University of Connecticut
+  75 North Eagleville Road, Unit 3043
+  Storrs, CT 06269-3043
+  U.S.A.
+
+  WWW: http://lewis.eeb.uconn.edu/lewishome
+  Email: paul.lewis@uconn.edu
+
+
+Versions after 2.0 contain changes primarily made by:
+  Mark T. Holder  mholder@users.sourceforge.net
+
+Other contributors to these versions include:
+  Derrick Zwickl
+  Brian O'Meara
+  Brandon Chisham
+  François Michonneau
+  Jeet Sukumaran
+
+Chris Desjardins (https://github.com/cdesjardins) provided the cmake files.
+
+The code in examples/phylobase... was written by Brian O'Meara and Derrick Zwickl
+for phylobase.
+
+David Suárez Pascal contributed SWIG bindings which heavily influenced those
+   found in branches/v2.2. Thanks to David for blazing the way on the swig binding,
+    Google for funding, and NESCent (in particular Hilmar Lapp) for getting the
+    NESCent GSoC program going.
+
+The 2010 GSoC effort also led to enhancements in terms of annotation storage and
+xml parsing which are currently on. Michael Elliot contributed some code to the branches/xml branch.
+Thanks to NESCent and  Google for supporting that work.
+
+Many of the files used for testing were provided by Arlin Stoltzfus (see
+http://www.molevol.org/camel/projects/nexus/ for more information), the Mesquite
+package, and from TreeBase (thanks, Bill Piel!).
+

bootstrap.sh

+#!/bin/sh
+# This script should be run  whenever the inputs to autoconf/automake change
+#	(namely the configure.ac file or the m4 macros in config/m4)
+# It appears that the autogenerated Makefiles enough contain dependency
+#		information to know that it needs to run automake and config.status
+#		whenever an Makefile.am changes.
+set -x
+aclocal -I config || exit
+#libtoolize --copy --force || exit;
+autoheader || exit
+automake --add-missing || exit
+autoconf

config/ac_cxx_rtti.m4

+##### http://autoconf-archive.cryp.to/ac_cxx_rtti.html
+#
+# SYNOPSIS
+#
+#   AC_CXX_RTTI
+#
+# DESCRIPTION
+#
+#   If the compiler supports Run-Time Type Identification (typeinfo
+#   header and typeid keyword), define HAVE_RTTI.
+#
+# LAST MODIFICATION
+#
+#   2004-02-04
+#
+# COPYLEFT
+#
+#   Copyright (c) 2004 Todd Veldhuizen
+#   Copyright (c) 2004 Luc Maisonobe <luc@spaceroots.org>
+#
+#   Copying and distribution of this file, with or without
+#   modification, are permitted in any medium without royalty provided
+#   the copyright notice and this notice are preserved.
+
+AC_DEFUN([AC_CXX_RTTI],
+[AC_CACHE_CHECK(whether the compiler supports Run-Time Type Identification,
+ac_cv_cxx_rtti,
+[AC_LANG_SAVE
+ AC_LANG_CPLUSPLUS
+ AC_TRY_COMPILE([#include <typeinfo>
+class Base { public :
+             Base () {}
+             virtual int f () { return 0; }
+           };
+class Derived : public Base { public :
+                              Derived () {}
+                              virtual int f () { return 1; }
+                            };
+],[Derived d;
+Base *ptr = &d;
+return typeid (*ptr) == typeid (Derived);
+],
+ ac_cv_cxx_rtti=yes, ac_cv_cxx_rtti=no)
+ AC_LANG_RESTORE
+])
+if test "$ac_cv_cxx_rtti" = yes; then
+  AC_DEFINE(HAVE_RTTI,,
+            [define if the compiler supports Run-Time Type Identification])
+fi
+])

config/ac_pkg_swig.m4

+# ===========================================================================
+#              http://autoconf-archive.cryp.to/ac_pkg_swig.html
+# ===========================================================================
+#
+# SYNOPSIS
+#
+#   AC_PROG_SWIG([major.minor.micro])
+#
+# DESCRIPTION
+#
+#   This macro searches for a SWIG installation on your system. If found you
+#   should call SWIG via $(SWIG). You can use the optional first argument to
+#   check if the version of the available SWIG is greater than or equal to
+#   the value of the argument. It should have the format: N[.N[.N]] (N is a
+#   number between 0 and 999. Only the first N is mandatory.)
+#
+#   If the version argument is given (e.g. 1.3.17), AC_PROG_SWIG checks that
+#   the swig package is this version number or higher.
+#
+#   In configure.in, use as:
+#
+#     AC_PROG_SWIG(1.3.17)
+#     SWIG_ENABLE_CXX
+#     SWIG_MULTI_MODULE_SUPPORT
+#     SWIG_PYTHON
+#
+# LAST MODIFICATION
+#
+#   2008-04-12
+#
+# COPYLEFT
+#
+#   Copyright (c) 2008 Sebastian Huber <sebastian-huber@web.de>
+#   Copyright (c) 2008 Alan W. Irwin <irwin@beluga.phys.uvic.ca>
+#   Copyright (c) 2008 Rafael Laboissiere <rafael@laboissiere.net>
+#   Copyright (c) 2008 Andrew Collier <colliera@ukzn.ac.za>
+#
+#   This program is free software; you can redistribute it and/or modify it
+#   under the terms of the GNU General Public License as published by the
+#   Free Software Foundation; either version 2 of the License, or (at your
+#   option) any later version.
+#
+#   This program is distributed in the hope that it will be useful, but
+#   WITHOUT ANY WARRANTY; without even the implied warranty of
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
+#   Public License for more details.
+#
+#   You should have received a copy of the GNU General Public License along
+#   with this program. If not, see <http://www.gnu.org/licenses/>.
+#
+#   As a special exception, the respective Autoconf Macro's copyright owner
+#   gives unlimited permission to copy, distribute and modify the configure
+#   scripts that are the output of Autoconf when processing the Macro. You
+#   need not follow the terms of the GNU General Public License when using
+#   or distributing such scripts, even though portions of the text of the
+#   Macro appear in them. The GNU General Public License (GPL) does govern
+#   all other use of the material that constitutes the Autoconf Macro.
+#
+#   This special exception to the GPL applies to versions of the Autoconf
+#   Macro released by the Autoconf Macro Archive. When you make and
+#   distribute a modified version of the Autoconf Macro, you may extend this
+#   special exception to the GPL to apply to your modified version as well.
+
+AC_DEFUN([AC_PROG_SWIG],[
+        AC_PATH_PROG([SWIG],[swig])
+        if test -z "$SWIG" ; then
+                AC_MSG_WARN([cannot find 'swig' program. You should look at http://www.swig.org])
+                SWIG='echo "Error: SWIG is not installed. You should look at http://www.swig.org" ; false'
+        elif test -n "$1" ; then
+                AC_MSG_CHECKING([for SWIG version])
+                [swig_version=`$SWIG -version 2>&1 | grep 'SWIG Version' | sed 's/.*\([0-9][0-9]*\.[0-9][0-9]*\.[0-9][0-9]*\).*/\1/g'`]
+                AC_MSG_RESULT([$swig_version])
+                if test -n "$swig_version" ; then
+                        # Calculate the required version number components
+                        [required=$1]
+                        [required_major=`echo $required | sed 's/[^0-9].*//'`]
+                        if test -z "$required_major" ; then
+                                [required_major=0]
+                        fi
+                        [required=`echo $required | sed 's/[0-9]*[^0-9]//'`]
+                        [required_minor=`echo $required | sed 's/[^0-9].*//'`]
+                        if test -z "$required_minor" ; then
+                                [required_minor=0]
+                        fi
+                        [required=`echo $required | sed 's/[0-9]*[^0-9]//'`]
+                        [required_patch=`echo $required | sed 's/[^0-9].*//'`]
+                        if test -z "$required_patch" ; then
+                                [required_patch=0]
+                        fi
+                        # Calculate the available version number components
+                        [available=$swig_version]
+                        [available_major=`echo $available | sed 's/[^0-9].*//'`]
+                        if test -z "$available_major" ; then
+                                [available_major=0]
+                        fi
+                        [available=`echo $available | sed 's/[0-9]*[^0-9]//'`]
+                        [available_minor=`echo $available | sed 's/[^0-9].*//'`]
+                        if test -z "$available_minor" ; then
+                                [available_minor=0]
+                        fi
+                        [available=`echo $available | sed 's/[0-9]*[^0-9]//'`]
+                        [available_patch=`echo $available | sed 's/[^0-9].*//'`]
+                        if test -z "$available_patch" ; then
+                                [available_patch=0]
+                        fi
+                        if test $available_major -ne $required_major \
+                                -o $available_minor -ne $required_minor \
+                                -o $available_patch -lt $required_patch ; then
+                                AC_MSG_WARN([SWIG version >= $1 is required.  You have $swig_version.  You should look at http://www.swig.org])
+                                SWIG='echo "Error: SWIG version >= $1 is required.  You have '"$swig_version"'.  You should look at http://www.swig.org" ; false'
+                        else
+                                AC_MSG_NOTICE([SWIG executable is '$SWIG'])
+                                SWIG_LIB=`$SWIG -swiglib`
+                                AC_MSG_NOTICE([SWIG library directory is '$SWIG_LIB'])
+                        fi
+                else
+                        AC_MSG_WARN([cannot determine SWIG version])
+                        SWIG='echo "Error: Cannot determine SWIG version.  You should look at http://www.swig.org" ; false'
+                fi
+        fi
+        AC_SUBST([SWIG_LIB])
+])

config/ac_python_devel.m4

+# ===========================================================================
+#            http://autoconf-archive.cryp.to/ac_python_devel.html
+# ===========================================================================
+#
+# SYNOPSIS
+#
+#   AC_PYTHON_DEVEL([version])
+#
+# DESCRIPTION
+#
+#   Note: Defines as a precious variable "PYTHON_VERSION". Don't override it
+#   in your configure.ac.
+#
+#   This macro checks for Python and tries to get the include path to
+#   'Python.h'. It provides the $(PYTHON_CPPFLAGS) and $(PYTHON_LDFLAGS)
+#   output variables. It also exports $(PYTHON_EXTRA_LIBS) and
+#   $(PYTHON_EXTRA_LDFLAGS) for embedding Python in your code.
+#
+#   You can search for some particular version of Python by passing a
+#   parameter to this macro, for example ">= '2.3.1'", or "== '2.4'". Please
+#   note that you *have* to pass also an operator along with the version to
+#   match, and pay special attention to the single quotes surrounding the
+#   version number. Don't use "PYTHON_VERSION" for this: that environment
+#   variable is declared as precious and thus reserved for the end-user.
+#
+#   This macro should work for all versions of Python >= 2.1.0. As an end
+#   user, you can disable the check for the python version by setting the
+#   PYTHON_NOVERSIONCHECK environment variable to something else than the
+#   empty string.
+#
+#   If you need to use this macro for an older Python version, please
+#   contact the authors. We're always open for feedback.
+#
+# LAST MODIFICATION
+#
+#   2008-04-12
+#
+# COPYLEFT
+#
+#   Copyright (c) 2008 Sebastian Huber <sebastian-huber@web.de>
+#   Copyright (c) 2008 Alan W. Irwin <irwin@beluga.phys.uvic.ca>
+#   Copyright (c) 2008 Rafael Laboissiere <rafael@laboissiere.net>
+#   Copyright (c) 2008 Andrew Collier <colliera@ukzn.ac.za>
+#   Copyright (c) 2008 Matteo Settenvini <matteo@member.fsf.org>
+#   Copyright (c) 2008 Horst Knorr <hk_classes@knoda.org>
+#
+#   This program is free software: you can redistribute it and/or modify it
+#   under the terms of the GNU General Public License as published by the
+#   Free Software Foundation, either version 3 of the License, or (at your
+#   option) any later version.
+#
+#   This program is distributed in the hope that it will be useful, but
+#   WITHOUT ANY WARRANTY; without even the implied warranty of
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
+#   Public License for more details.
+#
+#   You should have received a copy of the GNU General Public License along
+#   with this program. If not, see <http://www.gnu.org/licenses/>.
+#
+#   As a special exception, the respective Autoconf Macro's copyright owner
+#   gives unlimited permission to copy, distribute and modify the configure
+#   scripts that are the output of Autoconf when processing the Macro. You
+#   need not follow the terms of the GNU General Public License when using
+#   or distributing such scripts, even though portions of the text of the
+#   Macro appear in them. The GNU General Public License (GPL) does govern
+#   all other use of the material that constitutes the Autoconf Macro.
+#
+#   This special exception to the GPL applies to versions of the Autoconf
+#   Macro released by the Autoconf Macro Archive. When you make and
+#   distribute a modified version of the Autoconf Macro, you may extend this
+#   special exception to the GPL to apply to your modified version as well.
+
+AC_DEFUN([AC_PYTHON_DEVEL],[
+	#
+	# Allow the use of a (user set) custom python version
+	#
+	AC_ARG_VAR([PYTHON_VERSION],[The installed Python
+		version to use, for example '2.3'. This string
+		will be appended to the Python interpreter
+		canonical name.])
+
+	AC_PATH_PROG([PYTHON],[python[$PYTHON_VERSION]])
+	if test -z "$PYTHON"; then
+	   AC_MSG_ERROR([Cannot find python$PYTHON_VERSION in your system path])
+	   PYTHON_VERSION=""
+	fi
+
+	#
+	# Check for a version of Python >= 2.1.0
+	#
+	AC_MSG_CHECKING([for a version of Python >= '2.1.0'])
+	ac_supports_python_ver=`$PYTHON -c "import sys, string; \
+		ver = string.split(sys.version)[[0]]; \
+		print ver >= '2.1.0'"`
+	if test "$ac_supports_python_ver" != "True"; then
+		if test -z "$PYTHON_NOVERSIONCHECK"; then
+			AC_MSG_RESULT([no])
+			AC_MSG_FAILURE([
+This version of the AC@&t@_PYTHON_DEVEL macro
+doesn't work properly with versions of Python before
+2.1.0. You may need to re-run configure, setting the
+variables PYTHON_CPPFLAGS, PYTHON_LDFLAGS, PYTHON_SITE_PKG,
+PYTHON_EXTRA_LIBS and PYTHON_EXTRA_LDFLAGS by hand.
+Moreover, to disable this check, set PYTHON_NOVERSIONCHECK
+to something else than an empty string.
+])
+		else
+			AC_MSG_RESULT([skip at user request])
+		fi
+	else
+		AC_MSG_RESULT([yes])
+	fi
+
+	#
+	# if the macro parameter ``version'' is set, honour it
+	#
+	if test -n "$1"; then
+		AC_MSG_CHECKING([for a version of Python $1])
+		ac_supports_python_ver=`$PYTHON -c "import sys, string; \
+			ver = string.split(sys.version)[[0]]; \
+			print ver $1"`
+		if test "$ac_supports_python_ver" = "True"; then
+	   	   AC_MSG_RESULT([yes])
+		else
+			AC_MSG_RESULT([no])
+			AC_MSG_ERROR([this package requires Python $1.
+If you have it installed, but it isn't the default Python
+interpreter in your system path, please pass the PYTHON_VERSION
+variable to configure. See ``configure --help'' for reference.
+])
+			PYTHON_VERSION=""
+		fi
+	fi
+
+	#
+	# Check if you have distutils, else fail
+	#
+	AC_MSG_CHECKING([for the distutils Python package])
+	ac_distutils_result=`$PYTHON -c "import distutils" 2>&1`
+	if test -z "$ac_distutils_result"; then
+		AC_MSG_RESULT([yes])
+	else
+		AC_MSG_RESULT([no])
+		AC_MSG_ERROR([cannot import Python module "distutils".
+Please check your Python installation. The error was:
+$ac_distutils_result])
+		PYTHON_VERSION=""
+	fi
+
+	#
+	# Check for Python include path
+	#
+	AC_MSG_CHECKING([for Python include path])
+	if test -z "$PYTHON_CPPFLAGS"; then
+		python_path=`$PYTHON -c "import distutils.sysconfig; \
+           		print distutils.sysconfig.get_python_inc();"`
+		if test -n "${python_path}"; then
+		   	python_path="-I$python_path"
+		fi
+		PYTHON_CPPFLAGS=$python_path
+	fi
+	AC_MSG_RESULT([$PYTHON_CPPFLAGS])
+	AC_SUBST([PYTHON_CPPFLAGS])
+
+	#
+	# Check for Python library path
+	#
+	AC_MSG_CHECKING([for Python library path])
+	if test -z "$PYTHON_LDFLAGS"; then
+		# (makes two attempts to ensure we've got a version number
+		# from the interpreter)
+		py_version=`$PYTHON -c "from distutils.sysconfig import *; \
+			from string import join; \
+			print join(get_config_vars('VERSION'))"`
+		if test "$py_version" == "[None]"; then
+			if test -n "$PYTHON_VERSION"; then
+				py_version=$PYTHON_VERSION
+			else
+				py_version=`$PYTHON -c "import sys; \
+					print sys.version[[:3]]"`
+			fi
+		fi
+
+		PYTHON_LDFLAGS=`$PYTHON -c "from distutils.sysconfig import *; \
+			from string import join; \
+			print '-L' + get_python_lib(0,1), \
+		      	'-lpython';"`$py_version
+	fi
+	AC_MSG_RESULT([$PYTHON_LDFLAGS])
+	AC_SUBST([PYTHON_LDFLAGS])
+
+	#
+	# Check for site packages
+	#
+	AC_MSG_CHECKING([for Python site-packages path])
+	if test -z "$PYTHON_SITE_PKG"; then
+		PYTHON_SITE_PKG=`$PYTHON -c "import distutils.sysconfig; \
+		        print distutils.sysconfig.get_python_lib(0,0);"`
+	fi
+	AC_MSG_RESULT([$PYTHON_SITE_PKG])
+	AC_SUBST([PYTHON_SITE_PKG])
+
+	#
+	# libraries which must be linked in when embedding
+	#
+	AC_MSG_CHECKING(python extra libraries)
+	if test -z "$PYTHON_EXTRA_LIBS"; then
+	   PYTHON_EXTRA_LIBS=`$PYTHON -c "import distutils.sysconfig; \
+                conf = distutils.sysconfig.get_config_var; \
+                print conf('LOCALMODLIBS'), conf('LIBS')"`
+	fi
+	AC_MSG_RESULT([$PYTHON_EXTRA_LIBS])
+	AC_SUBST(PYTHON_EXTRA_LIBS)
+
+	#
+	# linking flags needed when embedding
+	#
+	AC_MSG_CHECKING(python extra linking flags)
+	if test -z "$PYTHON_EXTRA_LDFLAGS"; then
+		PYTHON_EXTRA_LDFLAGS=`$PYTHON -c "import distutils.sysconfig; \
+			conf = distutils.sysconfig.get_config_var; \
+			print conf('LINKFORSHARED')"`
+	fi
+	AC_MSG_RESULT([$PYTHON_EXTRA_LDFLAGS])
+	AC_SUBST(PYTHON_EXTRA_LDFLAGS)
+
+	#
+	# final check to see if everything compiles alright
+	#
+	AC_MSG_CHECKING([consistency of all components of python development environment])
+	AC_LANG_PUSH([C])
+	# save current global flags
+	LIBS="$ac_save_LIBS $PYTHON_LDFLAGS"
+	CPPFLAGS="$ac_save_CPPFLAGS $PYTHON_CPPFLAGS"
+	AC_TRY_LINK([
+		#include <Python.h>
+	],[
+		Py_Initialize();
+	],[pythonexists=yes],[pythonexists=no])
+
+	AC_MSG_RESULT([$pythonexists])
+
+        if test ! "$pythonexists" = "yes"; then
+	   AC_MSG_ERROR([
+  Could not link test program to Python. Maybe the main Python library has been
+  installed in some non-standard library path. If so, pass it to configure,
+  via the LDFLAGS environment variable.
+  Example: ./configure LDFLAGS="-L/usr/non-standard-path/python/lib"
+  ============================================================================
+   ERROR!
+   You probably have to install the development version of the Python package
+   for your distribution.  The exact name of this package varies among them.
+  ============================================================================
+	   ])
+	  PYTHON_VERSION=""
+	fi
+	AC_LANG_POP
+	# turn back to default flags
+	CPPFLAGS="$ac_save_CPPFLAGS"
+	LIBS="$ac_save_LIBS"
+
+	#
+	# all done!
+	#
+])

config/swig_enable_cxx.m4

+##### http://autoconf-archive.cryp.to/swig_enable_cxx.html
+#
+# SYNOPSIS
+#
+#   SWIG_ENABLE_CXX
+#
+# DESCRIPTION
+#
+#   Enable SWIG C++ support. This affects all invocations of $(SWIG).
+#
+# LAST MODIFICATION
+#
+#   2006-10-22
+#
+# COPYLEFT
+#
+#   Copyright (c) 2006 Sebastian Huber <sebastian-huber@web.de>
+#   Copyright (c) 2006 Alan W. Irwin <irwin@beluga.phys.uvic.ca>
+#   Copyright (c) 2006 Rafael Laboissiere <rafael@laboissiere.net>
+#   Copyright (c) 2006 Andrew Collier <colliera@ukzn.ac.za>
+#
+#   This program is free software; you can redistribute it and/or
+#   modify it under the terms of the GNU General Public License as
+#   published by the Free Software Foundation; either version 2 of the
+#   License, or (at your option) any later version.
+#
+#   This program is distributed in the hope that it will be useful, but
+#   WITHOUT ANY WARRANTY; without even the implied warranty of
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+#   General Public License for more details.
+#
+#   You should have received a copy of the GNU General Public License
+#   along with this program; if not, write to the Free Software
+#   Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
+#   02111-1307, USA.
+#
+#   As a special exception, the respective Autoconf Macro's copyright
+#   owner gives unlimited permission to copy, distribute and modify the
+#   configure scripts that are the output of Autoconf when processing
+#   the Macro. You need not follow the terms of the GNU General Public
+#   License when using or distributing such scripts, even though
+#   portions of the text of the Macro appear in them. The GNU General
+#   Public License (GPL) does govern all other use of the material that
+#   constitutes the Autoconf Macro.
+#
+#   This special exception to the GPL applies to versions of the
+#   Autoconf Macro released by the Autoconf Macro Archive. When you
+#   make and distribute a modified version of the Autoconf Macro, you
+#   may extend this special exception to the GPL to apply to your
+#   modified version as well.
+
+AC_DEFUN([SWIG_ENABLE_CXX],[
+        AC_REQUIRE([AC_PROG_SWIG])
+        AC_REQUIRE([AC_PROG_CXX])
+        SWIG="$SWIG -c++"
+])

config/swig_python.m4

+##### http://autoconf-archive.cryp.to/swig_python.html
+#
+# SYNOPSIS
+#
+#   SWIG_PYTHON([use-shadow-classes = {no, yes}])
+#
+# DESCRIPTION
+#
+#   Checks for Python and provides the $(SWIG_PYTHON_CPPFLAGS), and
+#   $(SWIG_PYTHON_OPT) output variables.
+#
+#   $(SWIG_PYTHON_OPT) contains all necessary SWIG options to generate
+#   code for Python. Shadow classes are enabled unless the value of the
+#   optional first argument is exactly 'no'. If you need multi module
+#   support (provided by the SWIG_MULTI_MODULE_SUPPORT macro) use
+#   $(SWIG_PYTHON_LIBS) to link against the appropriate library. It
+#   contains the SWIG Python runtime library that is needed by the type
+#   check system for example.
+#
+# LAST MODIFICATION
+#
+#   2006-10-22
+#
+# COPYLEFT
+#
+#   Copyright (c) 2006 Sebastian Huber <sebastian-huber@web.de>
+#   Copyright (c) 2006 Alan W. Irwin <irwin@beluga.phys.uvic.ca>
+#   Copyright (c) 2006 Rafael Laboissiere <rafael@laboissiere.net>
+#   Copyright (c) 2006 Andrew Collier <colliera@ukzn.ac.za>
+#
+#   This program is free software; you can redistribute it and/or
+#   modify it under the terms of the GNU General Public License as
+#   published by the Free Software Foundation; either version 2 of the
+#   License, or (at your option) any later version.
+#
+#   This program is distributed in the hope that it will be useful, but
+#   WITHOUT ANY WARRANTY; without even the implied warranty of
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+#   General Public License for more details.
+#
+#   You should have received a copy of the GNU General Public License
+#   along with this program; if not, write to the Free Software
+#   Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
+#   02111-1307, USA.
+#
+#   As a special exception, the respective Autoconf Macro's copyright
+#   owner gives unlimited permission to copy, distribute and modify the
+#   configure scripts that are the output of Autoconf when processing
+#   the Macro. You need not follow the terms of the GNU General Public
+#   License when using or distributing such scripts, even though
+#   portions of the text of the Macro appear in them. The GNU General
+#   Public License (GPL) does govern all other use of the material that
+#   constitutes the Autoconf Macro.
+#
+#   This special exception to the GPL applies to versions of the
+#   Autoconf Macro released by the Autoconf Macro Archive. When you
+#   make and distribute a modified version of the Autoconf Macro, you
+#   may extend this special exception to the GPL to apply to your
+#   modified version as well.
+
+AC_DEFUN([SWIG_PYTHON],[
+        AC_REQUIRE([AC_PROG_SWIG])
+        AC_REQUIRE([AC_PYTHON_DEVEL])
+        test "x$1" != "xno" || swig_shadow=" -noproxy"
+        AC_SUBST([SWIG_PYTHON_OPT],[-python$swig_shadow])
+        AC_SUBST([SWIG_PYTHON_CPPFLAGS],[$PYTHON_CPPFLAGS])
+])

configure.ac

 #                                               -*- Autoconf -*-
 # Process this file with autoconf to produce a configure script.
-
-AC_INIT(NCL, 2.1.18, mtholder@gmail.com)
+AC_INIT(NCL, 2.1.21-dev, mtholder@gmail.com)
 AC_CONFIG_HEADERS([config.h])
 
 AC_PREREQ(2.57)
@@ -30,8 +29,8 @@ AC_PROG_LIBTOOL
 # So we cache the argument to configure
 #	here in ARG_CXX_FLAGS (so that our macro does not override them)
 ARG_CXX_FLAGS="$CXXFLAGS"
+ARG_CPP_FLAGS="$CPPFLAGS"
 ################################################################################
-ARG_CXX_FLAGS="$CXXFLAGS"
 AC_PROG_CXX
 
 #Ranlib handled by check for libtool
@@ -39,10 +38,11 @@ CXXFLAGS="$ARG_CXX_FLAGS"
 AX_CXXFLAGS
 
 AC_MSG_CHECKING([whether C++ compiler works])
+AC_LANG(C++)
 AC_LANG_PUSH(C++)
-AC_COMPILE_IFELSE(AC_LANG_PROGRAM([[
+AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
 #include <vector>
-]], [[]]), [compiler_works='yes'], [compiler_works='no'])
+]], [[]])], [compiler_works='yes'], [compiler_works='no'])
 AC_MSG_RESULT([$compiler_works])
 AC_LANG_POP()
 if test x$compiler_works = xno
@@ -113,7 +113,7 @@ fi
 AC_SUBST(CXXFLAGS)
 #AC_CXX_RTTI
 
-CPPFLAGS="-I\$(top_srcdir) $CPPFLAGS"
+CPPFLAGS="-I\$(top_srcdir) $CPPFLAGS $ARG_CPP_FLAGS"
 # Checks for libraries.
 
 # Checks for header files.
@@ -184,13 +184,19 @@ AC_CONFIG_FILES([					\
 	Makefile 						\
 	example/Makefile				\
 	example/basiccmdline/Makefile	\
+	example/check-taxo-nodes/Makefile	\
 	example/compressor/Makefile	\
+	example/find-unsupported-edges/Makefile	\
 	example/gapcode/Makefile		\
+	example/ot-subtree/Makefile \
+	example/ot-tree-inspect/Makefile \
 	example/nclsimplest/Makefile	\
 	example/ncltest/Makefile		\
 	example/normalizer/Makefile		\
 	example/patristic/Makefile		\
 	example/phylobaseinterface/Makefile		\
+	example/polytomy-count/Makefile		\
+	example/outdeg1count/Makefile	\
 	example/splitsinfile/Makefile	\
 	example/subsetter/Makefile	\
 	example/translate/Makefile   	\

debian/changelog

-libncl (2.1.21+dfsg-1) UNRELEASED; urgency=medium
+libncl (2.1.21+git20171002.4becff7-1) unstable; urgency=medium
 
-  * New upstream version(now on Github)
-  TODO: Wait for release tags (https://github.com/mtholder/ncl/issues/15)
+  * New upstream version
+  * d/watch: use git mode since upstream does not provide release tags
   * Add missing citation
-
- -- Andreas Tille <tille@debian.org>  Tue, 07 Feb 2017 17:15:45 +0100
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.1.4
+  * Drop now unneeded get-orig-source target
+  * hardening=+all
+  * Fix spelling
+  * Add symbols file
+  * Bump soname since interface has changed
+
+ -- Andreas Tille <tille@debian.org>  Thu, 05 Jul 2018 15:02:26 +0200
 
 libncl (2.1.18+dfsg-2) unstable; urgency=medium
 

debian/compat

-9
+11

debian/control

@@ -3,13 +3,12 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9),
-               dh-autoreconf,
+Build-Depends: debhelper (>= 11~),
                d-shlibs,
                python
-Standards-Version: 3.9.6
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libncl.git
-Vcs-Git: https://anonscm.debian.org/debian-med/libncl.git
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/libncl
+Vcs-Git: https://salsa.debian.org/med-team/libncl.git
 Homepage: https://github.com/mtholder/ncl
 
 Package: ncl-tools
@@ -23,7 +22,7 @@ Description: tools to deal with NEXUS files
  phylogenetic programs such as Paup, MrBayes, Mesquite, and MacClade use
  this format.
 
-Package: libncl1
+Package: libncl2
 Architecture: any
 Section: libs
 Depends: ${shlibs:Depends},
@@ -42,7 +41,7 @@ Architecture: any
 Section: libdevel
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         libncl1 (= ${binary:Version})
+         libncl2 (= ${binary:Version})
 Description: NEXUS Class Library (static lib and header files)
  The NEXUS Class Library is a C++ library for parsing NEXUS files.
  .