Merge pull request #82 from avmarchenko/master

Minor fixes removing debug prints and respecting all input args

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()