adds black linting

Pipfile

@@ -11,6 +11,7 @@ graphviz = "*"
 sphinx = "*"
 pytest = "*"
 sphinx-rtd-theme = "*"
+black = "*"
 
 [requires]
 python_version = "3.10"

docs/conf.py

@@ -12,56 +12,59 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../'))
+
+sys.path.insert(0, os.path.abspath("../"))
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'Runner'
-author = 'Yashasvi S. Ranawat'
+project = "Runner"
+author = "Yashasvi S. Ranawat"
 
 # The full version, including alpha/beta/rc tags
-release = '0.1'
+release = "0.1"
 
 
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinx.ext.napoleon',
-              'sphinx.ext.autodoc',
-              'sphinx.ext.doctest',
-              'sphinx.ext.intersphinx',
-              'sphinx.ext.todo',
-              'sphinx.ext.viewcode',
-              'sphinx.ext.coverage',
-              'sphinx.ext.mathjax',
-              'sphinx.ext.ifconfig',
-              'sphinx.ext.githubpages',
-              'sphinx.ext.autosectionlabel']
-
-modindex_common_prefix = ['runner.']
+extensions = [
+    "sphinx.ext.napoleon",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.githubpages",
+    "sphinx.ext.autosectionlabel",
+]
+
+modindex_common_prefix = ["runner."]
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 doctest_global_setup = """
 import runner

docs/examples/BFGS.py

@@ -2,15 +2,16 @@
 
 from ase.optimize import BFGS
 
+
 def main(atoms_list, fmax=0.05):
     """Does BFGS relaxations of atoms
-    
+
     Args:
         atoms_list (list): list of atoms, as given by runner
     Returns:
         atoms object: relaxed atoms object"""
     atoms = atoms_list[0]
     opt = BFGS(atoms)
     opt.run(fmax=fmax)
-    
+
     return atoms

docs/examples/interaction_energy.py

@@ -1,25 +1,26 @@
 # interaction_energy.py
 
+
 def main(atoms_list, d=1):
     """Combines atoms with a distance d
-    
+
     Args:
         atoms_list (list): list of atoms, as given by runner
-    
+
     Returns:
         atoms object: combined atoms with calculated energies"""
-    
+
     atoms0 = atoms_list[1]
-    
+
     atoms0.positions[:, 2] += d + 1
-    
+
     atoms0 += atoms_list[2]
-    
+
     # making sure new energies are used in the system with updated atoms
     atoms0.get_potential_energy()
-    
+
     # adding key_value_pairs for column search in database
     # these are updated to the old key_value_pairs already in database
-    atoms0.info['key_value_pairs'] = {'d': d}
-    
+    atoms0.info["key_value_pairs"] = {"d": d}
+
     return atoms0

docs/examples/min_energy.py

@@ -1,17 +1,18 @@
 # min_energy.py
 
+
 def main(atoms_list):
     """Returns atoms with the lowest energy
-    
+
     Args:
         atoms_list (list): list of atoms, as given by runner
-    
+
     Returns:
         atoms object: atoms with lowest calculated energies"""
     import numpy as np
-    
+
     en_list = [atoms.get_potential_energy() for atoms in atoms_list[1:]]
-    
+
     indx = np.argmin(en_list)
-    
+
     return atoms_list[indx + 1]

runner/__init__.py

@@ -6,5 +6,5 @@
 from runner.utils.runnerdata import RunnerData
 
 
-__all__ = ['SlurmRunner', 'TerminalRunner', 'RunnerData', 'utils', 'Relay']
-__version__ = '0.1'
+__all__ = ["SlurmRunner", "TerminalRunner", "RunnerData", "utils", "Relay"]
+__version__ = "0.1"

runner/__main__.py

@@ -1,2 +1,3 @@
 from runner.cli import main
+
 main()