scons_support.py

#!/usr/bin/env python
#  This file is part of LOOS.
#
#  LOOS (Lightweight Object-Oriented Structure library)
#  Copyright (c) 2013, Tod D. Romo
#  Department of Biochemistry and Biophysics
#  School of Medicine & Dentistry, University of Rochester
#
#  This package (LOOS) 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 under version 3 of the License.
#
#  This package 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/>.


# This file contains support code for SCons for building LOOS

import sys
import os
import glob
import platform
import re
from subprocess import *
from time import strftime
import shutil
import distutils.sysconfig
import distutils.spawn
import string
from distutils.version import LooseVersion
from sysconfig import get_paths, get_config_var

import SCons

import loos_build_config


default_lib_path = None
conda_path = None

# Attempt to canonicalize system name, type and other related info...
# Note: this exports to globals rather than being contained within the check
# framework.
def CheckSystemType(conf):
    conf.Message("Determining platform ...")
    loos_build_config.host_type = platform.system()

    # Detect CYGWIN & canonicalize linux type, setting defaults...
    if re.search("(?i)cygwin", loos_build_config.host_type):
        loos_build_config.host_type = "Cygwin"
        loos_build_config.suffix = "dll.a"
    elif loos_build_config.host_type == "Linux":
        # Determine linux variant...
        linux_type = platform.platform()

        if re.search("(?i)ubuntu", linux_type):
            linux_type = "ubuntu"
        elif re.search("(?i)suse", linux_type):
            linux_type = "suse"
        elif re.search("(?i)debian", linux_type):
            linux_type = "debian"
        elif re.search("(?i)centos", linux_type):
            linux_type = "centos"
        elif re.search("(?i)fedora", linux_type):
            linux_type = "fedora"

        loos_build_config.linux_type = linux_type

    # MacOS is special (of course...)
    elif loos_build_config.host_type == "Darwin":
        loos_build_config.suffix = "dylib"

    typemsg = loos_build_config.host_type
    if typemsg == "Linux":
        typemsg = typemsg + " [" + loos_build_config.linux_type + "]"

    conf.Result(typemsg)


# Create a revision file for linking against.
def setupRevision(env):

    # Divine the current revision...
    revision = loos_build_config.loos_version + " " + strftime("%y%m%d")

    # Now, write this out to a cpp file that can be linked in. This avoids
    # having to recompile everything when building on a new date.  We also
    # rely on SCons using the MD5 checksum to detect changes in the file
    # (even though it's always rewritten)
    revfile = open("src/revision.cpp", "w")
    revfile.write("#include <string>\n")
    revfile.write('std::string revision_label = "')
    revfile.write(revision)
    revfile.write('";\n')
    revfile.close()


# Let environment variables override or modify some build paramaters...
def environOverride(conf):
    # Allow overrides from environment...
    if "CXX" in os.environ:
        conf.env.Replace(CXX=os.environ["CXX"])
        print(("*** Using compiler " + os.environ["CXX"]))

    if "CCFLAGS" in os.environ:
        conf.env.Append(CCFLAGS=os.environ["CCFLAGS"])
        print(("*** Appending custom build flags: " + os.environ["CCFLAGS"]))

    if "LDFLAGS" in os.environ:
        conf.env.Append(LINKFLAGS=os.environ["LDFLAGS"])
        print(("*** Appending custom link flag: " + os.environ["LDFLAGS"]))


# Builder for setup scripts


def expand_scons_paths(path, topdir):
    newpath = []
    for item in path:
        item = item.replace("#", topdir + "/")
        newpath.append(item)
    return newpath


# This copies the environment setup script while changing the directory
# that's used for setting up PATH and [DY]LD_LIBRARY_PATH.  If LOOS
# is being built in a directory, the env script will be setup to use
# the built-in-place distribution.  If LOOS is being installed, then
# it will use the installation directory instead.


def script_builder_python(target, source, env):

    libpaths = env["LIBPATH"]
    libpaths.pop(0)

    cpppaths = env["CPPPATH"]
    cpppaths.pop(0)

    ldlibrary = list(loos_build_config.user_libdirs.values())

    if "install" not in SCons.Script.COMMAND_LINE_TARGETS:
        toolpath = "$LOOS/Tools:" + ":".join(
            [
                "$LOOS/Packages/" + s
                for s in [
                    loos_build_config.package_list[i]
                    for i in loos_build_config.package_list
                ]
            ]
        )
        loos_dir = env.Dir(".").abspath
        libpaths.insert(0, loos_dir)
        cpppaths.insert(0, loos_dir)
        ldlibrary.insert(0, loos_dir)

        libpaths = expand_scons_paths(libpaths, loos_dir)
        cpppaths = expand_scons_paths(cpppaths, loos_dir)
        ldlibrary = expand_scons_paths(ldlibrary, loos_dir)

        loos_pythonpath = loos_dir

    else:
        loos_dir = env["PREFIX"]
        toolpath = loos_dir + "/bin"
        libpaths.insert(0, loos_dir + "/lib")
        cpppaths.insert(0, loos_dir + "/include")
        ldlibrary.insert(0, loos_dir + "/lib")
        loos_pythonpath = loos_dir + "/lib"

    file = open(str(source[0]), "r")
    script = file.read()
    script_template = string.Template(script)
    script = script_template.substitute(
        loos_path=loos_dir,
        tool_path=toolpath,
        libpath=":".join(libpaths),
        cpppath=":".join(cpppaths),
        linkflags=env["LINKFLAGS"],
        libs=":".join(env["LIBS"]),
        ccflags=env["CCFLAGS"],
        loos_cxx=env["CXX"],
        loos_pythonpath=loos_pythonpath,
        ldlibrary=":".join(ldlibrary),
    )

    outfile = open(str(target[0]), "w")
    outfile.write(script)

    return None


# Verify that we have swig and it's v2.0+
# Returns the path to swig
def CheckForSwig(conf, min_version):
    conf.Message("Checking for Swig...")
    # Need to use has_key() for older distros...
    if "SWIGVERSION" in conf.env:
        if LooseVersion(conf.env["SWIGVERSION"]) >= LooseVersion(min_version):
            conf.Result("yes [%s]" % (conf.env["SWIGVERSION"]))
            return 1
        else:
            conf.Result(
                "too old [%s, requires at least %s; pyloos disabled]"
                % (conf.env["SWIGVERSION"], min_version)
            )
            return 0

    conf.Result("no [pyloos disabled]")
    return 0


# See if a library requires another to link...
def CheckAtlasRequires(conf, name, lib, required):

    conf.Message("Checking if %s requires %s ... " % (name, required))
    lastLIBS = list(conf.env["LIBS"])
    conf.env.Append(LIBS=lib)

    #test_code = """
    # extern "C"{void dgesvd_(char*, char*, int*, int*, double*, int*, double*,
    # double*, int*, double*, int*#, double*, int*, int*);}
    # int main(int argc, char *argv[]) { char C[1]; double D[1];int
    # I[1];dgesvd_(C, C, I, I, D, I, D, D, I, #D, I, D, I, I); }
    # """
    test_code = "int main(){return(0);}"

    result = conf.TryLink(test_code, ".cpp")
    if not result:
        conf.env.Append(LIBS=required)
        result = conf.TryLink(test_code, ".cpp")
        conf.env.Replace(LIBS=lastLIBS)
        if not result:
            conf.Result("fail")
            return ()
        conf.Result("yes")
        return (lib, required)

    conf.env.Replace(LIBS=lastLIBS)
    conf.Result("no")
    return lib


# Check for IEC-559 compliance
def CheckForIEC559(conf):

    conf.Message("Checking for IEC-559/IEE-754 support... ")

    test_code = """
#include <iostream>
#include <limits>

int main(int argc, char *argv[]) {
  if (std::numeric_limits<double>::is_iec559 && std::numeric_limits<float>::is_iec559)
     std::cout << "yes";
  else
     std::cout << "no";
}
"""

    result = conf.TryRun(test_code, ".cpp")
    if not result[0]:
        conf.Result("unable to check")
        return 0

    if result[1] != "yes":
        conf.Result("no")
        return 0

    conf.Result("yes")

    return 1


# Check for existince of boost library with various naming variants
# Will return a tuple containing the correct name and a flag indicating
# whether this is the threaded or non-threaded version.
# This will only search specified paths, not the built-in paths for g++,
# so some libraries may be missed...
def CheckForBoostLibrary(conf, name, path, suffix):
    conf.Message("Checking for Boost library %s..." % name)
    name = "boost_" + name

    def sortByLength(w):
        return len(w)

    # Now check for names lib libboost_regex-gcc43-mt.so ...
    files = glob.glob(os.path.join(path, "lib%s*-mt.%s" % (name, suffix)))
    files.sort(key=sortByLength)
    if files:
        conf.Result(name + "-mt")
        name = os.path.basename(files[0])[3 : -(len(suffix) + 1)]
        return (name, 1)

    files = glob.glob(os.path.join(path, "lib%s*.%s" % (name, suffix)))
    files.sort(key=sortByLength)
    if files:
        conf.Result(name)
        name = os.path.basename(files[0])[3 : -(len(suffix) + 1)]
        return (name, 0)

    conf.Result("missing")
    return ("", -1)


# Check for Boost include files...
def CheckBoostHeaders(conf):
    test_code = """
#include <boost/version.hpp>
int main(int argc, char *argv[]) { return(0); }
"""

    conf.Message("Checking for Boost... ")
    result = conf.TryLink(test_code, ".cpp")
    if not result:
        conf.Result("no")
        return 0

    conf.Result("yes")
    return 1


# Check for version of Boost includes
def CheckBoostHeaderVersion(conf, min_boost_version):
    source_code = """
#include <iostream>
#include <boost/version.hpp>
int main(int argc, char *argv[]) { std::cout << BOOST_LIB_VERSION; return(0); }
"""

    conf.Message("Checking Boost version... ")
    result = conf.TryRun(source_code, ".cpp")
    if not result[0]:
        conf.Result("boost missing or incomplete?")
        return 0
    boost_version = result[1]
    loos_build_config.versions["boost"] = boost_version

    if LooseVersion(boost_version) < LooseVersion(min_boost_version):
        conf.Result(
            "%s [too old, LOOS requires at least %s]"
            % (boost_version, min_boost_version)
        )
        return 0

    conf.Result("%s [ok]" % boost_version)
    return 1


# Check for presence of a directory
def CheckDirectory(conf, dirname):

    conf.Message("Checking for directory %s... " % dirname)
    if os.path.isdir(dirname):
        conf.Result("yes")
        return 1
    conf.Result("no")
    return 0


def CheckNumpy(conf, pythonpath):
    global default_lib_path
    conf.Message("Checking for numpy... ")

    if conf.env.USING_CONDA:
        python_lib_dir = get_config_var("MACHDESTLIB")
        # some older compilers require this directory explicitly in the
        # include path
        numpy_inc_path = python_lib_dir + "/site-packages/numpy/core/include"
        if CheckDirectory(conf, numpy_inc_path):
            conf.env.Append(CPPPATH=numpy_inc_path)
            conf.Result("yes")
            return 1
        else:
            print("Numpy not found inside conda, looking elsewhere...")

    env = conf.env["ENV"]

    ok = checkForPythonHeader(conf, "numpy/arrayobject.h")
    if ok:
        conf.Result("yes")
        return 1
    newpaths = []

    if "PYTHON_PATH" in conf.env:
        envpath = conf.env["PYTHON_PATH"]
        # Catch cases where PYTHON_PATH is present but null...
        if len(envpath) > 1:
            newpaths.extend(envpath.split(":"))

    newpaths.append(default_lib_path)
    for dir in newpaths:
        for p, d, f in os.walk(dir):
            for file in f:
                if file == "arrayobject.h":
                    (prefix, numpydir) = os.path.split(p)
                    ok = checkForPythonHeaderInPath(
                        conf, "numpy/arrayobject.h", [prefix]
                    )
                    if ok:
                        conf.Result("yes")
                        return 1

    # Special handling for MacOS
    if loos_build_config.host_type == "Darwin":
        ok = checkForPythonHeaderInPath(
            conf,
            "numpy/arrayobject.h",
            [
"/System/Library/Frameworks/Python.framework/Versions/Current/Extras/lib/python/numpy/core/include"
            ],
        )
        if ok:
            conf.Result("yes")
            return 1

    conf.Result("no")
    return 0


def SetupBoostPaths(env):

    BOOST = env["BOOST"]
    BOOST_INCLUDE = env["BOOST_INCLUDE"]
    BOOST_LIBPATH = env["BOOST_LIBPATH"]
    BOOST_LIBS = env["BOOST_LIBS"]

    # If boost is not set but we're inside a conda environment,
    # automatically redirect boost into here...
    if not BOOST and env.USING_CONDA:
        BOOST = env["CONDA_PREFIX"]

    boost_libpath = ""
    boost_include = ""

    if BOOST:
        boost = BOOST
        boost_include = boost + "/include"
        boost_libpath = boost + "/lib"
        loos_build_config.user_libdirs["BOOST"] = boost_libpath
        loos_build_config.user_boost_flag = 1

    if BOOST_INCLUDE:
        boost_include = BOOST_INCLUDE
    if BOOST_LIBPATH:
        boost_libpath = BOOST_LIBPATH
        loos_build_config.user_libdirs["BOOST"] = boost_libpath
        loos_build_config.user_boost_flag = 1

    if boost_libpath:
        env.Prepend(LIBPATH=[boost_libpath])
        env["BOOST_LIBPATH"] = boost_libpath
    if boost_include:
        env.Prepend(CPPPATH=[boost_include])
        env["BOOST_INCLUDE"] = boost_include


def SetupNetCDFPaths(env):
    NETCDF = env["NETCDF"]
    NETCDF_INCLUDE = env["NETCDF_INCLUDE"]
    NETCDF_LIBPATH = env["NETCDF_LIBPATH"]
    NETCDF_LIBS = env["NETCDF_LIBS"]

    # If netcdf is not set but we're inside a conda environment,
    # automatically redirect netcdf into here...
    if not NETCDF and env.USING_CONDA:
        NETCDF=env['CONDA_PREFIX']

    netcdf_libpath = ""
    netcdf_include = ""

    if NETCDF:
        netcdf = NETCDF
        netcdf_include = netcdf + "/include"
        netcdf_libpath = netcdf + "/lib"
        loos_build_config.user_libdirs["NETCDF"] = netcdf_libpath

    if NETCDF_INCLUDE:
        netcdf_include = NETCDF_INCLUDE
    if NETCDF_LIBPATH:
        netcdf_libpath = NETCDF_LIBPATH
        loos_build_config.user_libdirs["NETCDF"] = netcdf_libpath

    if netcdf_libpath:
        env.Prepend(LIBPATH=[netcdf_libpath])
    if netcdf_include:
        env.Prepend(CPPPATH=[netcdf_include])

def SetupEigen(conf):
    EIGEN = conf.env["EIGEN"]
    if EIGEN:
        eigen_include_path = EIGEN
    elif conf.env.USING_CONDA:
        eigen_include_path = conf.env['CONDA_PREFIX'] + "/include/eigen3"
    else:
        eigen_include_path = "/usr/include/eigen3"

    # TODO: add check for existence of the chosen directory
    if conf.CheckDirectory(eigen_include_path):
        conf.env.Prepend(CPPPATH=[eigen_include_path])
    else:
        print("Warning: Eigen not found at include path " + eigen_include_path)
        print("Some tools may not build correctly. You can override this path")
        print("by setting the EIGEN environment variable.")

def AutoConfigSystemBoost(conf):
    boost_libs = []
    first = 1
    thread_suffix = 0

    for libname in loos_build_config.required_boost_libraries:
        if first:
            first = 0
            full_libname = "boost_" + libname + "-mt"
            result = conf.CheckLib(full_libname, autoadd=0)
            if result:
                boost_libs.append(full_libname)
                thread_suffix = 1
            else:
                full_libname = "boost_" + libname
                result = conf.CheckLib(full_libname, autoadd=0)
                if result:
                    boost_libs.append(full_libname)
        else:
            full_libname = "boost_" + libname
            if thread_suffix:
                full_libname += "-mt"
            result = conf.CheckLib(full_libname, autoadd=0)
            if result:
                boost_libs.append(full_libname)
            else:
                print(("Error- missing Boost library %s" % libname))
                conf.env.Exit(1)

    return boost_libs


def AutoConfigUserBoost(conf):
    boost_libs = []
    first = 1
    thread_suffix = 0

    for libname in loos_build_config.required_boost_libraries:
        result = conf.CheckForBoostLibrary(
            libname, conf.env["BOOST_LIBPATH"], loos_build_config.suffix
        )
        if not result[0]:
            print(("Error- missing Boost library %s" % libname))
            conf.env.Exit(1)
        if first:
            thread_suffix = result[1]
        else:
            if thread_suffix and not result[1]:
                print(("Error- expected %s-mt but found %s" % (libname, libname)))
                conf.env.Exit(1)
            elif not thread_suffix and result[1]:
                print(("Error- expected %s but found %s-mt" % (libname, libname)))
                conf.env.Exit(1)
        boost_libs.append(result[0])

    return boost_libs


# Check to see if a function exists with current libs
# If gfortran is present and function is not found, then
# try appending gfortran to lib list...


def checkForFunction(context, funcname, libs, has_gfortran):
    old_libs = list(context.env["LIBS"])
    context.env.Append(LIBS=libs)
    requires_gf = 0

    ok = context.CheckFunc(funcname)
    if not ok and has_gfortran:
        print("Trying again with gfortran...")
        context.env.Append(LIBS=["gfortran"])
        ok = context.CheckFunc(funcname)
        if ok:
            requires_gf = 1

    context.env["LIBS"] = old_libs
    return (ok, requires_gf)


# Tries adding each library from list to the build lib list
# and sees if funcname is present.  Any lib in the excludelist
# is ignored.  No special handling for gfortran...


def checkLibsForFunction(context, funcname, liblist, excludelist):
    for lib in liblist:
        if lib in excludelist:
            continue
        old_libs = list(context.env["LIBS"])
        context.env.Append(LIBS=lib)
        print(("> Checking in %s ..." % lib))
        ok = context.CheckFunc(funcname)
        context.env["LIBS"] = old_libs
        if ok:
            return lib
    return ""


def checkForPythonHeader(context, header):
    test_code = (
        """
#include <Python.h>
#include <%s>
"""
        % header
    )

    oldcpp = None
    if "CPPFLAGS" in context.env:
        oldcpp = context.env["CPPFLAGS"]
    if "CPPPATH" in context.env and not ("CONDA_PREFIX" in context.env):
        for dir in context.env["CPPPATH"]:
            context.env.Append(CPPFLAGS="-I%s " % dir)
            print("CPPFLAGS", context.env["CPPFLAGS"])

    ok = context.TryCompile(test_code, ".cpp")

    if oldcpp:
        context.env["CPPFLAGS"] = oldcpp

    return ok


def checkForPythonHeaderInPath(context, header, pathlist):

    for path in pathlist:
        oldcpp = None
        if "CPPPATH" in context.env:
            oldcpp = context.env["CPPPATH"]
        context.env.Append(CPPPATH=[path])
        ok = checkForPythonHeader(context, header)
        if ok:
            return True
        if oldcpp:
            context.env["CPPPATH"] = oldcpp
    return False


def AutoConfiguration(env):
    global default_lib_path
    global conda_path

    conf = env.Configure(
        custom_tests={
            "CheckForSwig": CheckForSwig,
            "CheckBoostHeaders": CheckBoostHeaders,
            "CheckForBoostLibrary": CheckForBoostLibrary,
            "CheckBoostHeaderVersion": CheckBoostHeaderVersion,
            "CheckDirectory": CheckDirectory,
            "CheckAtlasRequires": CheckAtlasRequires,
            "CheckForIEC559": CheckForIEC559,
            "CheckSystemType": CheckSystemType,
            "CheckNumpy": CheckNumpy,
        }
    )

    use_threads = int(env["threads"])

    # Get system information
    conf.CheckSystemType()

    conf.env["host_type"] = loos_build_config.host_type
    conf.env["linux_type"] = loos_build_config.linux_type

    if env.GetOption("clean") or env.GetOption("help"):
        env["HAS_NETCDF"] = 1
    else:
        has_netcdf = 0

        if env.USING_CONDA:
            conda_path = env["CONDA_PREFIX"]
            default_lib_path = conda_path + "/lib"
            if loos_build_config.host_type != "Darwin":
                conf.env.Append(RPATH=default_lib_path)
        else:
            default_lib_path = "/usr/lib"

            # if we're not in conda, add system library directory
            if not conf.CheckDirectory("/usr/lib64"):
                if not conf.CheckDirectory("/usr/lib"):
                    print("Fatal error- cannot find your system library directory")
                    conf.env.Exit(1)
            else:
                # /usr/lib64 is found, so make sure we link against this
                # (and not against any 32-bit libs)
                default_lib_path = "/usr/lib64"
        conf.env.Append(LIBPATH=default_lib_path)

        # Only setup ATLAS if we're not on a Mac and we're not using conda
        if loos_build_config.host_type != "Darwin" and not env.USING_CONDA:
            atlas_libpath = ""
            ATLAS_LIBPATH = env["ATLAS_LIBPATH"]
            ATLAS_LIBS = env["ATLAS_LIBS"]
            if not ATLAS_LIBPATH:
                # Some distros have atlas in /atlas-base, so must check that...
                if conf.CheckDirectory(default_lib_path + "/atlas-base"):
                    atlas_libpath = default_lib_path + "/atlas-base"
                elif conf.CheckDirectory(default_lib_path + "/atlas"):
                    atlas_libpath = default_lib_path + "/atlas"
                else:
                    print("Warning: Could not find an atlas directory! ")
            else:
                atlas_libpath = ATLAS_LIBPATH
                loos_build_config.user_libdirs["ATLAS"] = atlas_libpath

            if atlas_libpath:
                conf.env.Prepend(LIBPATH=[atlas_libpath])

        if not conf.CheckLib("pthread"):
            print("Error- LOOS requires a pthread library installed")

        # Now that we know the default library path, setup Boost, NetCDF, and
        # ATLAS based on the environment or custom.py file
        SetupBoostPaths(conf.env)
        SetupNetCDFPaths(conf.env)

        # Check for standard typedefs...
        if not conf.CheckType("ulong", "#include <sys/types.h>\n"):
            conf.env.Append(CCFLAGS="-DREQUIRES_ULONG")
        if not conf.CheckType("uint", "#include <sys/types.h>\n"):
            conf.env.Append(CCFLAGS="-DREQUIRES_UINT")

        # Check for floating point format...
        if not conf.CheckForIEC559():
            print("Error- your system must use the IEC559/IEEE754 floating point")
            print("       format for Gromacs support in LOOS.  Check your compiler")
            print("       options or contact the LOOS developers at")
            print("       loos.maintainer@gmail.com")
            conf.env.Exit(1)

        # --- NetCDF Autoconf
        has_netcdf = 0
        if conf.env["NETCDF_LIBS"]:
            netcdf_libs = env["NETCDF_LIBS"]
            conf.env.Append(CCFLAGS=["-DHAS_NETCDF"])
            has_netcdf = 1
        else:
            if conf.CheckLibWithHeader(
                "netcdf", "netcdf.h", "c"
            ):  # Should we check C or C++?
                netcdf_libs = "netcdf"
                conf.env.Append(CCFLAGS=["-DHAS_NETCDF"])
                has_netcdf = 1

        conf.env["HAS_NETCDF"] = has_netcdf

        # --- Swig Autoconf (unless user requested NO PyLOOS)
        if int(env["pyloos"]):
            if conf.CheckForSwig(loos_build_config.min_swig_version):
                conf.env["pyloos"] = 1
                pythonpath = get_paths()['include']
                if "PYTHON_INC" in conf.env:
                    if conf.env["PYTHON_INC"] != "":
                        pythonpath = conf.env["PYTHON_INC"]

                conf.env.Append(CPPPATH=[pythonpath])
                if not conf.CheckNumpy(pythonpath):
                    print("ERROR- PyLOOS build requires NumPy")
                    conf.env.Exit(1)
            else:
                conf.env["pyloos"] = 0

        # --- Boost Autoconf
        if not conf.CheckBoostHeaders():
            conf.env.Exit(1)

        if not conf.CheckBoostHeaderVersion(loos_build_config.min_boost_version):
            conf.env.Exit(1)

        if conf.env["BOOST_LIBS"]:
            boost_libs = env.Split(env["BOOST_LIBS"])
        if env.USING_CONDA:
            boost_libs = AutoConfigUserBoost(conf)
        elif not loos_build_config.user_boost_flag:
            boost_libs = AutoConfigSystemBoost(conf)
        else:
            boost_libs = AutoConfigUserBoost(conf)

        env.Append(LIBS=boost_libs)

        SetupEigen(conf)

        # --- Check for ATLAS/LAPACK and how to build

        if loos_build_config.host_type != "Darwin" and not env.USING_CONDA:
            atlas_libs = ""  # List of numerics libs required for LOOS

            if env["ATLAS_LIBS"]:
                atlas_libs = env.Split(env["ATLAS_LIBS"])
            else:

                numerics = {
                    "openblas": 0,
                    "satlas": 0,
                    "atlas": 0,
                    "lapack": 0,
                    "f77blas": 0,
                    "cblas": 0,
                    "blas": 0,
                }

                if use_threads:
                    numerics["tatlas"] = 0
                    numerics["ptcblas"] = 0
                    numerics["ptf77blas"] = 0

                for libname in numerics:
                    if conf.CheckLib(libname, autoadd=0):
                        numerics[libname] = 1

                atlas_libs = []
                atlas_name = ""

                has_gfortran = 0
                if conf.CheckLib("gfortran", autoadd=0):
                    has_gfortran = 1

                if use_threads and numerics["tatlas"]:
                    atlas_libs.append("tatlas")
                    atlas_name = "tatlas"
                elif numerics["satlas"]:
                    atlas_libs.append("satlas")
                    atlas_name = "satlas"
                else:

                    if numerics["lapack"]:
                        atlas_libs.append("lapack")

                    if use_threads and (numerics["ptf77blas"] and numerics["ptcblas"]):
                        atlas_libs.extend(["ptf77blas", "ptcblas"])
                    elif numerics["f77blas"] and numerics["cblas"]:
                        atlas_libs.extend(["f77blas", "cblas"])
                    elif numerics["blas"]:
                        atlas_libs.append("blas")
                    else:
                        print("Error- you must have some kind of blas installed")
                        conf.env.Exit(1)

                    if numerics["atlas"]:
                        atlas_libs.append("atlas")
                        atlas_name = "atlas"

                # Try to figure out how to build with ATLAS...
                # We need these functions, so find a combination of libs and
                # libpaths will work...
                for funcname in ("dgesvd_", "dgemm_", "dtrmm_", "dsyev_"):
                    (ok, requires_gfortran) = checkForFunction(
                        conf, funcname, atlas_libs, has_gfortran
                    )
                    if requires_gfortran:
                        print("Build Requires gfortran")
                        atlas_libs.append("gfortran")

                    if not ok:
                        lib = checkLibsForFunction(
                            conf, funcname, list(numerics.keys()), atlas_libs
                        )
                        if lib:
                            atlas_libs.insert(0, lib)
                        else:
                            # Try putting scanning default_lib_path
                            # first...SUSE requires
                            # the lapack in /usr/lib first...
                            print(
                                (
                                    "Searching %s first for libraries..."
                                    % default_lib_path
                                )
                            )
                            # Remove the default_lib_path from the list and
                            # prepend...
                            libpaths = list(conf.env["LIBPATH"])
                            libpaths.remove(default_lib_path)
                            libpaths.insert(0, default_lib_path)
                            conf.env["LIBPATH"] = libpaths
                            (ok, requires_gfortran) = checkForFunction(
                                conf, funcname, atlas_libs, has_gfortran
                            )
                            if requires_gfortran:
                                print("Build requires gfortran")
                                atlas_libs.append("gfortran")

                            if not ok:
                                lib = checkLibsForFunction(
                                    conf, funcname, list(numerics.keys()), atlas_libs
                                )
                                if lib:
                                    atlas_libs.insert(0, lib)
                                else:
                                    print(
                                        "Error- could not figure out where ", funcname, " is located.",
                                    )
                                    print(
                                        "Try manually specifying ATLAS_LIBS and ATLAS_LIBPATH"
                                    )
                                    conf.env.Exit(1)

            # Hack to extend list rather than append a list into a list
            for lib in atlas_libs:
                conf.env.Append(LIBS=lib)
        elif env.USING_CONDA:
            conf.env.Append(LIBS="openblas")

        # Suppress those annoying maybe used unitialized warnings that -Wall
        # gives us...
        ccflags = conf.env["CCFLAGS"]
        conf.env.Append(
            CCFLAGS=["-Wno-maybe-uninitialized", "-Werror"]
        )  # Try suppressing, make bad flags an error
        ok = conf.TryCompile("", ".c")
        conf.env["CCFLAGS"] = ccflags
        if ok:
            conf.env.Append(CCFLAGS=["-Wno-maybe-uninitialized"])

        environOverride(conf)
        if "LIBS" in conf.env:
            print(
                "Autoconfigure will use these libraries to build LOOS:\n\t",
                conf.env["LIBS"],
            )
        if "LIBPATH" in conf.env:
            print(
                "Autoconfigure will add the following directories to find libs:\n\t",
                conf.env["LIBPATH"],
            )
        env = conf.Finish()


#########################################################################################3


def addDeprecatedOptions(opt):
    from SCons.Variables import PathVariable

    opt.Add(PathVariable("LAPACK", "Path to LAPACK", "",
PathVariable.PathAccept))
    opt.Add(PathVariable("ATLAS", "Path to ATLAS", "", PathVariable.PathAccept))
    opt.Add(
        PathVariable("ATLASINC", "Path to ATLAS includes", "",
PathVariable.PathAccept)
    )
    opt.Add(
        PathVariable("BOOSTLIB", "Path to BOOST libraries", "",
PathVariable.PathAccept)
    )
    opt.Add(
        PathVariable("BOOSTINC", "Path to BOOST includes", "",
PathVariable.PathAccept)
    )
    opt.Add("BOOSTREGEX", "Boost regex library name", "")
    opt.Add("BOOSTPO", "Boost program options library name", "")
    opt.Add(
        PathVariable(
            "LIBXTRA", "Path to additional libraries", "",
PathVariable.PathAccept
        )
    )
    opt.Add(
        PathVariable(
            "NETCDFINC", "Path to netcdf include files", "",
PathVariable.PathAccept
        )
    )
    opt.Add(
        PathVariable(
            "NETCDFLIB", "Path to netcdf library files", "",
PathVariable.PathAccept
        )
    )
    opt.Add(
        PathVariable(
            "ALTPATH", "Additional path to commands", "",
PathVariable.PathAccept
        )
    )
    opt.Add(
        PathVariable(
            "LIBS_OVERRIDE", "Override linked libs", "", PathVariable.PathAccept
        )
    )
    opt.Add(
        PathVariable(
            "LIBS_PATHS_OVERRIDE", "Override paths to libs", "",
PathVariable.PathAccept
        )
    )


def makeDeprecatedVariableWarning():
    state = {"warned": 0}

    def warning(what, mapto):
        if not state["warned"]:
            state["warned"] = 1
            print(
                """
***WARNING***
You are using old-style (deprecated) variables either
on the command line or in your custom.py file.  These
will be ignored.  The following deprecated variables
are set,
"""
            )
        print("\t%s: %s" % (what, mapto))

    return warning


def checkForDeprecatedOptions(env):
    mapping = {
        "LAPACK": "use ATLAS_LIBPATH",
        "ATLAS": "use ATLAS_LIBPATH",
        "ATLASINC": "no replacement",
        "BOOSTLIB": "use BOOST_LIBPATH or BOOST",
        "BOOSTINC": "use BOOST_INCLUDE or BOOST",
        "BOOSTREGEX": "use BOOST_LIBS",
        "BOOSTPO": "use BOOST_LIBS",
        "LIBXTRA": "use ATLAS_LIBS, BOOST_LIBS, or NETCDF_LIBS",
        "NETCDFINC": "use NETCDF_INCLUDE or NETCDF",
        "NETCDFLIB": "use NETCDF_LIBPATH or NETCDF",
        "ALTPATH": "Set your shell PATH instead",
        "LIBS_OVERRIDE": "use ATLAS_LIBS, BOOST_LIBS, or NETCDF_LIBS",
        "LIBS_PATHS_OVERRIDE": "use ATLAS_LIBPATH, BOOST_LIBPATH, or NETCDF_LIBPATH",
    }

    warner = makeDeprecatedVariableWarning()
    for name in mapping:
        if name in env:
            if env[name]:
                warner(name, mapping[name])