ADD: made package ready for PyPI

MANIFEST.in

@@ -0,0 +1,6 @@
+global-include *.c
+global-include *.h
+include MDAnalysis/coordinates/xdrfile/src/*
+include LICENSE
+include setup.py
+global-exclude *.pyc

README.md

@@ -1,23 +1,31 @@
 
-
 Lightweight coordinate-only trajectory reader based on code from [GROMACS](http://www.gromacs.org/), [MDAnalysis](http://www.mdanalysis.org/) and [VMD](http://www.ks.uiuc.edu/Research/vmd/).
 
 Used for coordinate retrieval in [MDSrv](https://github.com/arose/mdsrv) and [nglview](https://github.com/arose/nglview).
 
+Should work with Python 2 and 3. If you experience problems, please file an [issue](https://github.com/arose/simpletraj/issues).
+
 
 Installation
 ============
 
+From PyPI:
+
+    pip install simpletraj
+
+
+netCDF4
+-------
 
-Some libraries need to be installed. First, make sure you have the Python development files installed, e.g.
+If you use `conda` as your Python package manager:
 
-    sudo apt-get install python-dev python-numpy
+    conda install netcdf4
 
 
-Then install the NetCDF libraries and its Python package
+To install the NetCDF libraries and its Python package on debian/ubuntu:
 
     sudo apt-get install libhdf5-serial-dev libnetcdf-dev
-    sudo pip install netCDF4
+    pip install netCDF4
 
 
 In case you get "ValueError: did not find HDF5 headers" try:
@@ -29,18 +37,13 @@ In case you get "ValueError: did not find HDF5 headers" try:
     pip install netCDF4
 
 
-Finally install simpletraj itself:
-
-    sudo python setup.py install
-
-
 Changelog
 =========
 
 Version 0.2dev
 --------------
 
-* WIP: preparing packaging
+* ADD: package ready for PyPI
 * CODE: Python 3 compatibility
 * CODE: handle errors during offsets file reading/writing
 

setup.cfg

@@ -0,0 +1,2 @@
+[metadata]
+description-file = README.md

setup.py

@@ -1,28 +1,84 @@
 #!/usr/bin/env python
 
-"""
-Setup script for trajectory file reading modules.
+import sys
+from setuptools import setup, Extension, find_packages
 
-A working installation of NumPy <http://numpy.scipy.org> is required.
 
-For a basic installation just type the command::
+VERSION = "0.2.dev4"
+CLASSIFIERS = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)",
+    "Programming Language :: C",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 2",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Chemistry",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX",
+    "Operating System :: Unix",
+    "Operating System :: MacOS",
+]
 
-    python setup.py build_ext --inplace
 
-Based on setup.py from MDAnalysis:
+# from MDAnalysis setup.py (http://www.mdanalysis.org/)
+class NumpyExtension(Extension, object):
+    """Derived class to cleanly handle setup-time (numpy) dependencies.
+    """
+    # The only setup-time numpy dependency comes when setting up its
+    #  include dir.
+    # The actual numpy import and call can be delayed until after pip
+    #  has figured it must install numpy.
+    # This is accomplished by passing the get_numpy_include function
+    #  as one of the include_dirs. This derived Extension class takes
+    #  care of calling it when needed.
+    def __init__(self, *args, **kwargs):
+        self._np_include_dirs = []
+        super(NumpyExtension, self).__init__(*args, **kwargs)
 
-    http://www.mdanalysis.org/
-"""
+    @property
+    def include_dirs(self):
+        if not self._np_include_dirs:
+            for item in self._np_include_dir_args:
+                try:
+                    self._np_include_dirs.append(item())  # The numpy callable
+                except TypeError:
+                    self._np_include_dirs.append(item)
+        return self._np_include_dirs
 
+    @include_dirs.setter
+    def include_dirs(self, val):
+        self._np_include_dir_args = val
 
-from setuptools import setup, Extension
 
-import numpy
-try:
-    numpy_include = numpy.get_include()
-except AttributeError:
-    numpy_include = numpy.get_numpy_include()
-include_dirs = [ numpy_include ]
+# from MDAnalysis setup.py (http://www.mdanalysis.org/)
+def get_numpy_include():
+    try:
+        # Obtain the numpy include directory. This logic works across numpy
+        # versions.
+        # setuptools forgets to unset numpy's setup flag and we get a crippled
+        # version of it unless we do it ourselves.
+        try:
+            import __builtin__  # py2
+            __builtin__.__NUMPY_SETUP__ = False
+        except:
+            import builtins  # py3
+            builtins.__NUMPY_SETUP__ = False
+        import numpy as np
+    except ImportError as e:
+        print(e)
+        print('*** package "numpy" not found ***')
+        print('Simpletraj requires a version of NumPy, even for setup.')
+        print('Please get it from http://numpy.scipy.org/ or install it through '
+              'your package manager.')
+        sys.exit(-1)
+    try:
+        numpy_include = np.get_include()
+    except AttributeError:
+        numpy_include = np.get_numpy_include()
+    return numpy_include
 
 
 # Needed for large-file seeking under 32bit systems (for xtc/trr indexing and access).
@@ -36,29 +92,32 @@
     setup(
         name = "simpletraj",
         author = "Alexander S. Rose",
-        description = "Simple coordinate-only trajectory reader based on code from GROMACS, MDAnalysis, VMD.",
-        version = "0.2dev",
+        author_email = "[email protected]",
+        description = "Lightweight coordinate-only trajectory reader based on code from GROMACS, MDAnalysis, VMD.",
+        version = VERSION,
+        classifiers = CLASSIFIERS,
         license = "GPL2",
         url = "https://github.com/arose/simpletraj",
-        packages = [ "simpletraj", "simpletraj.xdrfile", "simpletraj.dcd" ],
+        zip_safe = False,
+        packages = find_packages(),
         ext_modules = [
-            Extension(
+            NumpyExtension(
                 "simpletraj/xdrfile._libxdrfile2",
                 sources = [
                     "simpletraj/xdrfile/libxdrfile2_wrap.c",
                     "simpletraj/xdrfile/xdrfile.c",
                     "simpletraj/xdrfile/xdrfile_trr.c",
                     "simpletraj/xdrfile/xdrfile_xtc.c"
                 ],
-                include_dirs = include_dirs,
+                include_dirs = [ get_numpy_include ],
                 define_macros = largefile_macros
             ),
-            Extension(
+            NumpyExtension(
                 "simpletraj/dcd._dcdmodule",
                 sources = [
                     "simpletraj/dcd/dcd.c"
                 ],
-                include_dirs = include_dirs + [ "simpletraj/dcd/include" ],
+                include_dirs = [ get_numpy_include, "simpletraj/dcd/include" ],
             ),
         ],
         setup_requires = [ "numpy" ],