Initial files for the package

setup.py

@@ -0,0 +1,68 @@
+import os
+from setuptools import setup, Extension
+
+from Cython.Build import cythonize
+import numpy
+
+
+include_dirs = [numpy.get_include(), 'gromacs/src','gromacs/src/external/tng_io/include',]
+library_dirs = []
+if 'LD_LIBRARY_PATH' in os.environ:
+    lib = os.environ['LD_LIBRARY_PATH'].split(':')[0]
+    library_dirs.insert(0, lib)
+    include = lib.replace('/lib', '/include')
+    if os.path.exists(include):
+        include_dirs.insert(0, include)
+elif os.path.exists('gromacs/build/lib'):
+    library_dirs.insert(0, 'gromacs/build/lib')
+
+if not library_dirs:
+    raise OSError("""
+        Gromacs library not found.
+        Activate a gromacs module or specify environment variable LD_LIBRARY_PATH.
+        """)
+
+library_dirs.append('gromacs/src/external/tng_io/build/lib')
+
+library_dirs = [os.path.abspath(p) for p in library_dirs]
+
+
+extensions = [
+    # Extension('mdevaluate.gromacs.coordinates', [
+    #           'mdevaluate/gromacs/coordinates.pyx'], include_dirs=include_dirs),
+    # Extension('mdevaluate.gromacs.logarithmic', [
+    #           'mdevaluate/gromacs/logarithmic.pyx'], include_dirs=include_dirs),
+    Extension('pygmx.tpxio',
+              sources=['pygmx/tpxio.pyx'],
+              include_dirs=include_dirs,
+              libraries=['gromacs'],
+              library_dirs=library_dirs,
+              runtime_library_dirs=library_dirs,
+              language='c++'),
+    Extension('pygmx.xtcio',
+              sources=['pygmx/xtcio.pyx'],
+              include_dirs=include_dirs,
+              libraries=['gromacs'],
+              library_dirs=library_dirs,
+              runtime_library_dirs=library_dirs,
+              language='c++'),
+    Extension('pygmx.tngio',
+              sources=['pygmx/tngio.pyx'],
+              include_dirs=include_dirs,
+              libraries=['gromacs'],
+              library_dirs=library_dirs,
+              runtime_library_dirs=library_dirs,
+              #language='c++'
+              ),
+
+]
+
+setup(
+    name='pygmx',
+    description='Python wrapper for gromacs library.',
+    author_email='niels.mueller@physik.tu-darmstadt.de',
+    packages=['pygmx', ],
+    version='0.0.2',
+    requires=['numpy', 'Cython'],
+    ext_modules=cythonize(extensions),
+)