Merge pull request #82 from avmarchenko/master

Minor fixes removing debug prints and respecting all input args

Author: avmarchenko

exatomic/__init__.py

@@ -18,7 +18,7 @@
 
 .. _atomic: https://en.wikipedia.org/wiki/Atomic_units
 """
-__exatomic_version__ = (0, 3, 3)
+__exatomic_version__ = (0, 3, 4)
 __version__ = '.'.join((str(v) for v in __exatomic_version__))
 
 

exatomic/algorithms/diffusion.py

@@ -33,4 +33,6 @@ def einstein_relation(universe, length='cm', time='s'):
     '''
     msd = absolute_squared_displacement(universe).mean(axis=1)
     t = universe.frame['time'].values
+    msd *= Length['au', length]**2
+    t /= Time['ps', time]
     return msd / (6 * t)

exatomic/algorithms/neighbors.py

@@ -48,12 +48,7 @@ def nearest_molecules(universe, n, sources, restrictions=None, how='atom',
         unis (dict): Dictionary of number of neighbors keys, universe values
     """
     source_atoms, other_atoms, source_molecules, other_molecules, n = _slice_atoms_molecules(universe, sources, restrictions, n)
-    print(source_atoms.shape)
-    print(other_atoms.shape)
-    print(source_molecules.shape)
-    print(other_molecules.shape)
     ordered_molecules, ordered_twos = _compute_neighbors_by_atom(universe, source_atoms, other_atoms, source_molecules)
-    print(ordered_molecules.shape)
     unis = {}
     if free_boundary == True:
         for nn in n:
@@ -82,21 +77,17 @@ def _slice_atoms_molecules(universe, sources, restrictions, n):
     symbols = universe.atom['symbol'].unique()
     classification = universe.molecule['classification'].unique()
     if all(source in labels for source in sources):
-        print("all  labels")
         source_atoms = universe.atom[universe.atom['label'].isin(sources)]
         mdx = source_atoms['molecule'].astype(np.int64)
         source_molecules = universe.molecule[universe.molecule.index.isin(mdx)]
     elif all(source in symbols for source in sources):
-        print("all symbols")
         source_atoms = universe.atom[universe.atom['symbol'].isin(sources)]
         mdx = source_atoms['molecule'].astype(np.int64)
         source_molecules = universe.molecule[universe.molecule.index.isin(mdx)]
     elif all(source in classification for source in sources):
-        print("all mols")
         source_molecules = universe.molecule[universe.molecule['classification'].isin(sources)]
         source_atoms = universe.atom[universe.atom['molecule'].isin(source_molecules.index)]
     else:
-        print("all other")
         classif = [source for source in sources if source in classification]
         syms = [source for source in sources if source in symbols]
         lbls = [source for source in sources if source in labels]

exatomic/algorithms/pcf.py

@@ -88,5 +88,7 @@ def radial_pair_correlation(universe, a, b, dr=0.05, start=1.0, stop=13.0,
     glabel = r"$g_\mathrm{" + a + b + r"}(r)$"
     nlabel = r"$n_\mathrm{" + a + b + r"}(r)$"
     df = pd.DataFrame.from_dict({rlabel: r, glabel: g, nlabel: n})
+    if window > 1:
+        df = df.rolling(window=window).mean()
     df.set_index(rlabel, inplace=True)
     return df

meta.yaml

@@ -1,9 +1,9 @@
 package:
     name: exatomic
-    version: "0.3.3"
+    version: "0.3.4"
 
 source:
-    git_rev: v0.3.3
+    git_rev: v0.3.4
     git_url: https://github.com/exa-analytics/exatomic.git
 
 requirements:

publish.py

@@ -22,7 +22,6 @@ def get_args():
     parser = argparse.ArgumentParser(description="Deployment script for Exa Analytics")
     parser.add_argument("pkg", nargs="?")
     parser.add_argument("version", nargs="?")
-    parser.add_argument("which_pypi", nargs="?", default="pypi")
     return parser.parse_args()
 
 
@@ -119,11 +118,11 @@ def conda_build(pys):
                 raise Exception("Upload failed with command {}".format(string))
 
 
-def pypi_build(pypi):
+def pypi_build():
     """
     Deploy to pypi/pypitest.
     """
-    string = "python setup.py sdist upload {}".format(pypi)
+    string = "python setup.py sdist upload"
     ret = subprocess.run([string], shell=True, check=True,
                          stdout=subprocess.PIPE, stdin=subprocess.PIPE)
 
@@ -147,5 +146,5 @@ def cleanup():
     chk = check(args.pkg, args.version, pys)
     if chk:
         conda_build(pys)
-        pypi_build(args.which_pypi)
+        pypi_build()
     cleanup()