Remove variable-function name conflict and cleanups

Author: tritemio

pybromo/diffusion.py

@@ -38,7 +38,7 @@ def get_seed(seed, ID=0, EID=0):
     return seed + EID + 100 * ID
 
 
-def hash_(x):
+def hashfunc(x):
     return hashlib.sha1(repr(x).encode()).hexdigest()
 
 
@@ -166,7 +166,7 @@ def __init__(self, num_particles, D, box, rs=None, seed=1, particles=None):
             self._plist = self._generate(num_particles, D, box, rs)
         else:
             self._plist = list(particles)
-        self.rs_hash = hash_(self.init_random_state)[:3]
+        self.rs_hash = hashfunc(self.init_random_state)[:3]
 
     def add(self, num_particles, D):
         """Add particles with diffusion coefficient `D` at random positions.
@@ -505,8 +505,8 @@ def _open_store(self, store, prefix='', path='./', chunksize=2**19,
         attr_params = dict(particles=self.particles.to_json(), box=self.box)
         kwargs = dict(path=path, nparams=nparams, attr_params=attr_params,
                       mode=mode)
-        store = store(store_fname, **kwargs)
-        return store
+        store_obj = store(store_fname, **kwargs)
+        return store_obj
 
     def open_store_traj(self, path='./', chunksize=2**19, chunkslice='bytes',
                         mode='w', radial=False):
@@ -711,7 +711,7 @@ def _get_ts_name_mix_core(self, max_rates, populations, bg_rate,
     def _get_ts_name_mix(self, max_rates, populations, bg_rate, rs,
                          hashsize=6):
         s = self._get_ts_name_mix_core(max_rates, populations, bg_rate)
-        return '%s_rs_%s' % (s, hash_(rs.get_state())[:hashsize])
+        return '%s_rs_%s' % (s, hashfunc(rs.get_state())[:hashsize])
 
     def timestamps_match_pattern(self, pattern):
         return [t for t in self.timestamp_names if pattern in t]

pybromo/psflib.py

@@ -23,6 +23,8 @@
 
 
 def psf_from_pytables(psf_pytables):
+    """Load a PSF object (either numeric or gauss) from a pytables array.
+    """
     if 'kind' not in psf_pytables.attrs:
         # old files may not have the `kind` attribute, assume NumericPSF
         psf_type = 'numeric'
@@ -48,7 +50,7 @@ def __init__(self, xc=0, yc=0, zc=0, sx=0.2e-6, sy=0.2e-6, sz=0.8e-6, psf_pytabl
         arguments.
         """
         self.kind = 'gauss'
-        self.fname = 'gaussian_psf' 
+        self.fname = 'gaussian_psf'
         if psf_pytables is not None:
             assert psf_pytables.attrs['kind'] == 'gauss'
             self.rc, self.s = psf_pytables.read().astype(np.float64)
@@ -89,15 +91,15 @@ def eval_xz(self, x, z):
         xc, yc, zc = self.rc
         sx, sy, sz = self.s
         return exp(-(((x-xc)**2)/(2*sx**2) + ((z-zc)**2)/(2*sz**2)))
-       
+
     def hash(self):
         """Return an hash string computed on the PSF data."""
         return hashlib.md5(repr(self).encode()).hexdigest()
 
     def to_hdf5(self, file_handle, parent_node='/'):
         """Store the PSF data in `file_handle` (pytables) in `parent_node`.
 
-        The PSF data is stored in an array named `gauss_psf_params` with 
+        The PSF data is stored in an array named `gauss_psf_params` with
         shape 2 x 3. Columns are x, y, z coordinates, rows are mean and
         standard deviation.
         """