Ignore Cython c files.

.gitignore

@@ -5,3 +5,7 @@ dist/
 .cache/
 *.cpp
 /gromacs
+logarithmic.*.so
+logarithmic.c
+coordinates.*.so
+coordinates.c

pygmx/gromacs/coordinates.pyx

@@ -1,4 +1,4 @@
-# distutils: sources = mdevaluate/gromacs/compression.c
+# distutils: sources = pygmx/gromacs/compression.c
 
 from cython cimport view
 from array import array
@@ -19,28 +19,28 @@ cdef extern from "compression.h":
 
 
 def decompress(int size, float precision, minint, maxint, int smallidx, bytes blob):
-     
+
     assert len(minint) == 3
     assert len(maxint) == 3
-    
+
     cdef int minints[3]
     cdef int maxints[3]
-    
+
     for i in range(3):
         minints[i] = minint[i]
         maxints[i] = maxint[i]
-    
+
-    
+
     cdef np.ndarray[float, ndim=2] coordinates = np.empty((size,3), dtype=np.float32)
     cdef size_t readed
-    
+
     xdrfile_decompress_coord_float(
-        <float *>coordinates.data, 
+        <float *>coordinates.data,
-        size, 
+        size,
         precision,
         maxints,
-        minints, 
+        minints,
-        smallidx, 
+        smallidx,
         blob,
         len(blob),
         &readed)

pygmx/gromacs/reader.py

@@ -2,9 +2,9 @@ import xdrlib
 import io
 import os
 from .coordinates import decompress
-from ..utils import hash_anything, merge_hashes
 from functools import partial
 import numpy as np
+import hashlib
 
 TRR_MAGIC = 1993
 XTC_MAGIC = 1995
@@ -352,7 +352,11 @@ class XTCReader(BaseReader):
         return [self[i].time for i in indices]
 
     def __hash__(self):
-        return merge_hashes(hash_anything(self.filename), hash_anything(self._cache))
+        m = hashlib.md5()
+        m.update(self.filename.encode())
+        m.update(str(self._cache).encode())
+        return int.from_bytes(m.digest(), 'big')
+        # return merge_hashes(hash_anything(self.filename), hash_anything(self._cache))
 
 
 class TRRHeader:

setup.py

@@ -35,10 +35,10 @@ library_dirs = [os.path.abspath(p) for p in library_dirs]
 
 
 extensions = [
-    # Extension('mdevaluate.gromacs.coordinates', [
+     Extension('pygmx.gromacs.coordinates', [
-    #           'mdevaluate/gromacs/coordinates.pyx'], include_dirs=include_dirs),
+               'pygmx/gromacs/coordinates.pyx'], include_dirs=include_dirs),
-    # Extension('mdevaluate.gromacs.logarithmic', [
+     Extension('pygmx.gromacs.logarithmic', [
-    #           'mdevaluate/gromacs/logarithmic.pyx'], include_dirs=include_dirs),
+               'pygmx/gromacs/logarithmic.pyx'], include_dirs=include_dirs),
     Extension('pygmx.tpxio',
               sources=['pygmx/tpxio.pyx'],
               include_dirs=include_dirs,
@@ -76,8 +76,8 @@ setup(
     name='pygmx',
     description='Python wrapper for gromacs library.',
     author_email='niels.mueller@physik.tu-darmstadt.de',
-    packages=['pygmx', ],
+    packages=['pygmx', 'pygmx.gromacs'],
-    version='0.0.2',
+    version='0.1',
     requires=['numpy', 'Cython'],
     ext_modules=cythonize(extensions),
 )