https://github.com/sanger-pathogens/gubbins
Revision ea26d93b0398d089a0d711a92a430adffde855e7 authored by andrewjpage on 27 August 2014, 12:25:42 UTC, committed by andrewjpage on 27 August 2014, 12:25:42 UTC
1 parent 7e6bd0d
Tip revision: ea26d93b0398d089a0d711a92a430adffde855e7 authored by andrewjpage on 27 August 2014, 12:25:42 UTC
if you have less than 4 sequences you cant build a tree with raxml
if you have less than 4 sequences you cant build a tree with raxml
Tip revision: ea26d93
ax_python_devel.m4
# ===========================================================================
# http://www.gnu.org/software/autoconf-archive/ax_python_devel.html
# ===========================================================================
#
# SYNOPSIS
#
# AX_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.
#
# LICENSE
#
# Copyright (c) 2009 Sebastian Huber <sebastian-huber@web.de>
# Copyright (c) 2009 Alan W. Irwin <irwin@beluga.phys.uvic.ca>
# Copyright (c) 2009 Rafael Laboissiere <rafael@laboissiere.net>
# Copyright (c) 2009 Andrew Collier <colliera@ukzn.ac.za>
# Copyright (c) 2009 Matteo Settenvini <matteo@member.fsf.org>
# Copyright (c) 2009 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 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.
#serial 8
AU_ALIAS([AC_PYTHON_DEVEL], [AX_PYTHON_DEVEL])
AC_DEFUN([AX_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=`$PYTHON -c "import sys; \
ver = sys.version.split ()[[0]]; \
print (ver >= '2.1.0')"`
if test "$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; \
ver = sys.version.split ()[[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)
ac_python_version=`cat<<EOD | $PYTHON -
# join all versioning strings, on some systems
# major/minor numbers could be in different list elements
from distutils.sysconfig import *
ret = ''
for e in get_config_vars ('VERSION'):
if (e != None):
ret += e
print (ret)
EOD`
if test -z "$ac_python_version"; then
if test -n "$PYTHON_VERSION"; then
ac_python_version=$PYTHON_VERSION
else
ac_python_version=`$PYTHON -c "import sys; \
print (sys.version[[:3]])"`
fi
fi
# Make the versioning information available to the compiler
AC_DEFINE_UNQUOTED([HAVE_PYTHON], ["$ac_python_version"],
[If available, contains the Python version number currently in use.])
# First, the library directory:
ac_python_libdir=`cat<<EOD | $PYTHON -
# There should be only one
import distutils.sysconfig
for e in distutils.sysconfig.get_config_vars ('LIBDIR'):
if e != None:
print (e)
break
EOD`
# Before checking for libpythonX.Y, we need to know
# the extension the OS we're on uses for libraries
# (we take the first one, if there's more than one fix me!):
ac_python_soext=`$PYTHON -c \
"import distutils.sysconfig; \
print (distutils.sysconfig.get_config_vars('SO')[[0]])"`
# Now, for the library:
ac_python_soname=`$PYTHON -c \
"import distutils.sysconfig; \
print (distutils.sysconfig.get_config_vars('LDLIBRARY')[[0]])"`
# Strip away extension from the end to canonicalize its name:
ac_python_library=`echo "$ac_python_soname" | sed "s/${ac_python_soext}$//"`
# This small piece shamelessly adapted from PostgreSQL python macro;
# credits goes to momjian, I think. I'd like to put the right name
# in the credits, if someone can point me in the right direction... ?
#
if test -n "$ac_python_libdir" -a -n "$ac_python_library" \
-a x"$ac_python_library" != x"$ac_python_soname"
then
# use the official shared library
ac_python_library=`echo "$ac_python_library" | sed "s/^lib//"`
PYTHON_LDFLAGS="-L$ac_python_libdir -l$ac_python_library"
else
# old way: use libpython from python_configdir
ac_python_libdir=`$PYTHON -c \
"from distutils.sysconfig import get_python_lib as f; \
import os; \
print (os.path.join(f(plat_specific=1, standard_lib=1), 'config'));"`
PYTHON_LDFLAGS="-L$ac_python_libdir -lpython$ac_python_version"
fi
if test -z "PYTHON_LDFLAGS"; then
AC_MSG_ERROR([
Cannot determine location of your Python DSO. Please check it was installed with
dynamic libraries enabled, or try setting PYTHON_LDFLAGS by hand.
])
fi
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])
# save current global flags
ac_save_LIBS="$LIBS"
ac_save_CPPFLAGS="$CPPFLAGS"
LIBS="$ac_save_LIBS $PYTHON_LDFLAGS $PYTHON_EXTRA_LDFLAGS $PYTHON_EXTRA_LIBS"
CPPFLAGS="$ac_save_CPPFLAGS $PYTHON_CPPFLAGS"
AC_LANG_PUSH([C])
AC_LINK_IFELSE([
AC_LANG_PROGRAM([[#include <Python.h>]],
[[Py_Initialize();]])
],[pythonexists=yes],[pythonexists=no])
AC_LANG_POP([C])
# turn back to default flags
CPPFLAGS="$ac_save_CPPFLAGS"
LIBS="$ac_save_LIBS"
AC_MSG_RESULT([$pythonexists])
if test ! "x$pythonexists" = "xyes"; then
AC_MSG_FAILURE([
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
#
# all done!
#
])
![swh spinner](/static/img/swh-spinner.gif)
Computing file changes ...