Cleaned up setup.py & Readme

README.md

@@ -21,16 +21,18 @@ If gromacs is installed as a module in your system, run
 
 and skip to the section *Installing pygmx*.
 
-#### Manual setup
+#### Through package manager
 
-The shared library of GROMACS 5.1and the corresponding c++ header files need to be present on the system.
+Pygmx requires the shared library and header files of Gromacs 5.1 or higher to be installed.
-If the shared library is installed globally, the environment variable `LD_LIBRARY_PATH` must be set.
+On many Unix distributions Gromacs may be installed through the package manager.
-The installation process will look for the header files by replacing any `lib` folder
+The required packages, which provide the headers, are usually named `gromacs-devel` or `gromcas-dev`.
-in `LD_LIBRARY_PATH` with `include`.
 
-If no header files are present, simply pull the submodule `gromacs` in this repository.
+#### Manual build
-To build the shared library, follow the [official installation instructions](http://manual.gromacs.org/documentation/5.1.2/install-guide/index.html),
+
-starting with step 4 (creating a build directory).
+To build the shared library manually, follow the [official installation instructions](http://manual.gromacs.org/documentation/5.1.2/install-guide/index.html).
+Make sure to source the `GMXRC` script, which sets the environment variable `LD_LIBRARY_PATH` to the correct location or set this variable manually.
+Don't bother with advanced features like GPU support if the Gromacs installation will only be used for pygmx,
+since the file io functions do not use these features.
 
 ### Installing pygmx
 
@@ -40,13 +42,3 @@ Navigate to the top folder of the repository and run the command
     python setup.py install
 
 This builds the cython modules and installs them into the local python distribution.
-
-
-### Deploy on intranet
-
-For any installed version of mdevaluate modules do:
-
-    version=dev # or maybe: version=$(python ../mdevaluate/setup.py --version)
-    module load gromacs/5.1
-    module load mdevaluate/$version
-    python setup.py install --prefix=/autohome/niels/modules/mdevaluate-$version

setup.py

@@ -5,54 +5,53 @@ from Cython.Build import cythonize
 import numpy
 
 
-def locate_lib(directory, lib):
+def check_header_version(include_path):
-    flib = 'lib{}.so'.format(lib)
+    with open(os.path.join(include_path, 'version.h')) as f:
-    for root, dirs, files in os.walk(directory):
+        for l in f.readlines():
-        if flib in files:
+            if '#define GMX_API_VERSION' in l:
-            return root
+                print(l)
+                version = int(l.split()[-1])
+                assert version >= 50100, 'Installed gromacs version is too low!'
+                return
+    print('Gromacs version could not be checked.')
 
+include_dirs = [numpy.get_include()]
 
-include_dirs = [numpy.get_include(), 'gromacs/src', 'gromacs/src/external/tng_io/include']
+if 'gromacs' in os.environ.get('LD_LIBRARY_PATH', ''):
-library_dirs = []
+    for p in os.environ['LD_LIBRARY_PATH'].split(':'):
-if 'LD_LIBRARY_PATH' in os.environ:
+        if 'gromacs' in p:
-    lib = os.environ['LD_LIBRARY_PATH'].split(':')[0]
+            lib = p
-    library_dirs.insert(0, locate_lib(lib, 'gromacs'))
+    gmx_root = lib.split('lib')[0]
-    include = lib.replace('/lib', '/include')
+    include = os.path.join(gmx_root, 'include')
     if os.path.exists(include):
-        include_dirs.insert(0, include)
+        include_dirs.append(include)
-elif os.path.exists('gromacs/build/lib'):
+        check_header_version(include)
-    library_dirs.insert(0, 'gromacs/build/lib')
-
-if not library_dirs:
-    raise OSError("""
-        Gromacs library not found.
-        Activate a gromacs module or set 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('pygmx.gromacs.coordinates', [
+    Extension(
-               'pygmx/gromacs/coordinates.pyx'], include_dirs=include_dirs),
+        'pygmx.gromacs.coordinates',
-     Extension('pygmx.gromacs.logarithmic', [
+        ['pygmx/gromacs/coordinates.pyx'],
-               'pygmx/gromacs/logarithmic.pyx'], include_dirs=include_dirs),
+        include_dirs=include_dirs
-    Extension('pygmx.tpxio',
+    ),
-              sources=['pygmx/tpxio.pyx'],
+    Extension(
-              include_dirs=include_dirs,
+        'pygmx.gromacs.logarithmic',
-              libraries=['gromacs'],
+        ['pygmx/gromacs/logarithmic.pyx'],
-              library_dirs=library_dirs,
+        include_dirs=include_dirs
-              runtime_library_dirs=library_dirs,
+    ),
-              language='c++'),
+    Extension(
-    Extension('pygmx.xtcio',
+        'pygmx.tpxio',
-              sources=['pygmx/xtcio.pyx'],
+        sources=['pygmx/tpxio.pyx'],
-              include_dirs=include_dirs,
+        include_dirs=include_dirs,
-              libraries=['gromacs'],
+        libraries=['gromacs'],
-              library_dirs=library_dirs,
+        language='c++'
-              runtime_library_dirs=library_dirs,
+    ),
-              language='c++'),
+    Extension(
+        'pygmx.xtcio',
+        sources=['pygmx/xtcio.pyx'],
+        include_dirs=include_dirs,
+        libraries=['gromacs'],
+        language='c++'
+    ),
 #    Extension('pygmx.enxio',
 #              sources=['pygmx/enxio.pyx'],
 #              include_dirs=include_dirs,
@@ -69,12 +68,11 @@ extensions = [
 #              runtime_library_dirs=library_dirs,
               #language='c++'
 #              ),
-
 ]
 
 setup(
     name='pygmx',
-    description='Python wrapper for gromacs library.',
+    description='Python wrapper around the gromacs library for file io.',
     author_email='niels.mueller@physik.tu-darmstadt.de',
     packages=['pygmx', 'pygmx.gromacs'],
     version='0.1',