clean up setup.py, add dep openbabel for qchem functionality, test.yml install [complete] deps

Author: janosh

atomate/vasp/workflows/base/adsorption.py

@@ -3,17 +3,15 @@
 """
 
 import numpy as np
-
 from fireworks import Workflow
-
-from atomate.vasp.fireworks.core import OptimizeFW, TransmuterFW
-from atomate.utils.utils import get_meta_from_structure
-
 from pymatgen.analysis.adsorption import AdsorbateSiteFinder
-from pymatgen.core.surface import generate_all_slabs, Slab
+from pymatgen.core.surface import Slab, generate_all_slabs
+from pymatgen.io.vasp.sets import MVLSlabSet
 from pymatgen.transformations.advanced_transformations import SlabTransformation
 from pymatgen.transformations.standard_transformations import SupercellTransformation
-from pymatgen.io.vasp.sets import MVLSlabSet
+
+from atomate.utils.utils import get_meta_from_structure
+from atomate.vasp.fireworks.core import OptimizeFW, TransmuterFW
 
 __author__ = "Joseph Montoya, Richard Tran"
 __email__ = "[email protected]"
@@ -176,12 +174,6 @@ def get_slab_trans_params(slab):
 
     min_slab_size = slab_cell_height * slab_layers / total_layers - 0.001
     min_vac_size = slab_cell_height * vac_layers / total_layers - 0.001
-    # params = {"miller_index": [0, 0, 1], "shift": slab.shift,
-    #           "min_slab_size": min_slab_size, "min_vacuum_size": min_vac_size}
-    # trans = SlabTransformation(**params)
-    # new_slab = trans.apply_transformation(slab.oriented_unit_cell)
-    # if slab.composition.reduced_formula == "Si":
-    #     import nose; nose.tools.set_trace()
 
     return {
         "miller_index": [0, 0, 1],

setup.py

@@ -1,18 +1,16 @@
-#!/usr/bin/env python
-
 import os
+from os.path import abspath, dirname, join
 
-from setuptools import setup, find_packages
+from setuptools import find_packages, setup
 
-module_dir = os.path.dirname(os.path.abspath(__file__))
+module_dir = dirname(abspath(__file__))
 
 if __name__ == "__main__":
     setup(
         name="atomate",
         version="1.0.1",
-        description="atomate has implementations of FireWorks workflows for "
-        "Materials Science",
-        long_description=open(os.path.join(module_dir, "README.md")).read(),
+        description="atomate has implementations of FireWorks workflows for Materials Science",
+        long_description=open(join(module_dir, "README.md")).read(),
         url="https://github.com/hackingmaterials/atomate",
         author="Anubhav Jain, Kiran Mathew",
         author_email="[email protected], [email protected]",
@@ -40,10 +38,15 @@
             "maggma>=0.26.0",
         ],
         extras_require={
-            "rtransfer": ["paramiko>=2.4.2"],
             "plotting": ["matplotlib>=1.5.2"],
             "phonons": ["phonopy>=1.10.8"],
-            "complete": ["paramiko>=2.4.2", "matplotlib>=1.5.2", "phonopy>=1.10.8"],
+            "qchem": ["openbabel"],
+            "complete": [
+                "paramiko>=2.4.2",
+                "matplotlib>=1.5.2",
+                "phonopy>=1.10.8",
+                "openbabel",
+            ],
         },
         classifiers=[
             "Programming Language :: Python :: 3",
@@ -57,10 +60,5 @@
             "Topic :: Other/Nonlisted Topic",
             "Topic :: Scientific/Engineering",
         ],
-        test_suite="nose.collector",
-        tests_require=["nose"],
-        scripts=[
-            os.path.join("scripts", f)
-            for f in os.listdir(os.path.join(module_dir, "scripts"))
-        ],
+        scripts=[join("scripts", f) for f in os.listdir(join(module_dir, "scripts"))],
     )