From b3a144cf8ab0a6f52a6b5f53bbc861145e46acc8 Mon Sep 17 00:00:00 2001
From: Tom Close <tclose@oist.jp>
Date: Tue, 18 Oct 2016 11:30:34 +1100
Subject: [PATCH] touching up setup.py to install libninemlnrn

---
 AUTHORS  |  4 +--
 setup.py | 79 +++++++++++++-------------------------------------------
 2 files changed, 20 insertions(+), 63 deletions(-)

diff --git a/AUTHORS b/AUTHORS
index b42e9eea..d8750ac6 100644
--- a/AUTHORS
+++ b/AUTHORS
@@ -1,7 +1,7 @@
 The following people have contributed to PyPe9. Their affiliations at the time of the contributions are shown below.
 
-* Thomas Close [1,2]
-* Andrew Davison [3]
+* Thomas G. Close [1,2]
+* Andrew P. Davison [3]
 
 1. Computational Neuroscience Unit, Okinawa Institute of Science and Technology (OIST), Onna-son, Okinawa, Japan
 2. Monash Biomedical Imaging, Monash University, Clayton, Victoria, Australia
diff --git a/setup.py b/setup.py
index 9cfac5a3..9fef291b 100644
--- a/setup.py
+++ b/setup.py
@@ -20,61 +20,23 @@
 
 packages = [p for p in find_packages() if p != 'test']
 
-# Attempt to find the prefix of the gsl and gslcblas libraries used by NEST
-
-
 # Check /usr and /usr/local to see if there is a version of libgsl and
 # libgslcblas there
-system_gsl = set()
-for system_path in ('/usr', join('/usr', 'local')):
-    system_libs = os.listdir(system_path)
-    if any(l.startswith('libgsl.') or l.startswith('libgslcblas.')
-           for l in system_libs):
-        system_gsl.add(system_path)
-
-# Check for the version of gsl linked to the pynestkernel
-try:
-    # Import NEST with suppressed NEST splash
-    import nest
-    cwd = os.getcwd()
-    os.chdir(dirname(nest.__file__))
-    if platform.platform().startswith('Darwin'):
-        ldd_cmd = 'otool -L'
-    else:
-        ldd_cmd = 'ldd'
-    ldd_out = sp.check_output('{} pynestkernel.so'.format(ldd_cmd),
-                              shell=True)
-    nest_gsl = set(dirname(dirname(abspath(l.split()[0]))) + sep
-                       for l in ldd_out.split('\n\t') if 'libgsl' in l)
-    assert nest_gsl, "NEST not linked to GSL? ldd output:\n{}".format(ldd_out)
-except ImportError:
-    nest_gsl = set()  # Assume they are already on system path
-    print ("WARNING, Could not import NEST to determine which gsl libraries it"
-           " uses")
-
-if system_gsl:
-    if nest_gsl and nest_gsl != system_gsl:
-        raise Exception(
-            "System GSL version found at '{}' is different from that linked "
-            "to NEST at '{}'. Please specify which version you would like to "
-            "use in setup.cfg in the include-dirs and link-dirs options under "
-            "[build_ext]".format("', '".join(nest_gsl),
-                                 "', '".join(system_gsl)))
-    else:
-        print ("Using system gsl version at '{}'"
-               .format("', '".join(system_gsl)))
-        gsl_prefixes = system_gsl
-elif nest_gsl:
-    print ("Using gsl version linked to NEST at '{}'"
-           .format("', '".join(nest_gsl)))
-    gsl_prefixes = nest_gsl
-else:
-    raise Exception(
-        "No version of GSL found in system paths or by inspecting libs linked"
-        "to NEST. Please install GNU Scientific Library if necessary and/or "
-        "specify its location in setup.cfg in both include-dirs and link-dirs "
-        "options of [build_ext]")
+found_libgsl = False
+found_libgslcblas = False
+for pth in ('/usr', join('/usr', 'local')):
+    libs = os.listdir(pth)
+    if any(l.startswith('libgsl.') for l in libs):
+        found_libgsl = True
+    if any(l.startswith('libgslcblas.') for l in libs):
+        found_libgslcblas = True
 
+#if not found_libgsl or not found_libgslcblas:
+#    raise Exception(
+#        "Could not find GNU Scientific Library on system paths or those "
+#        "defined in setup.cfg. Please ensure a recent version is installed "
+#        "and the path is appened to include-dirs and library-dirs in "
+#        "setup.cfg.")
 
 # Set up the required extension to handle random number generation using GSL
 # RNG in NEURON components
@@ -82,24 +44,19 @@
                          sources=[os.path.join('neuron', 'cells', 'code_gen',
                                                'libninemlnrn', 'nineml.cpp')],
                          libraries=['m', 'gslcblas', 'gsl', 'c'],
-                         language="c++",
-                         extra_compile_args=[join('-I', p, 'include')
-                                             for p in gsl_prefixes],
-                         extra_link_args=[join('-L', p, 'lib')
-                                          for p in gsl_prefixes])
+                         language="c++")
 
 setup(
     name="pype9",
     version="0.1a",
     package_data={package_name: package_data},
     packages=packages,
-    author="Thomas G. Close and Andrew P. Davison",
-    # add your name here if you contribute to the code
+    author="The PyPe9 Team (see AUTHORS)",
     author_email="tom.g.close@gmail.com",
     description=("\"Python PipelinEs for 9ML (PyPe9)\" to simulate neuron and "
-                 "neuron network models described in 9ML in the NEURON and "
+                 "neuron network models described in 9ML with the NEURON and "
                  "NEST simulators."),
-    long_description=open("README.rst").read(),
+    long_description=open(join(dirname(__file__), "README.rst")).read(),
     license="The MIT License (MIT)",
     keywords=("NineML pipeline computational neuroscience modeling "
               "interoperability XML 9ML neuron nest"),