Ran black....was this a mistake?

docs/source/conf.py

@@ -10,7 +10,7 @@
 import os
 import sys
 
-sys.path.insert(0, os.path.abspath('../..'))
+sys.path.insert(0, os.path.abspath("../.."))
 import qcengine
 
 # -- Path setup --------------------------------------------------------------
@@ -26,9 +26,9 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'QCEngine'
-copyright = f'2018-{datetime.datetime.today().year}, The Molecular Sciences Software Institute'
-author = 'The QCArchive Development Team'
+project = "QCEngine"
+copyright = f"2018-{datetime.datetime.today().year}, The Molecular Sciences Software Institute"
+author = "The QCArchive Development Team"
 
 # The short X.Y version
 version = qcengine.__version__
@@ -46,26 +46,26 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.doctest',
-    'sphinx.ext.todo',
-    'sphinx.ext.coverage',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.extlinks',
-    'sphinx.ext.graphviz',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.napoleon',
-    'sphinx_automodapi.automodapi',
-    'sphinx_automodapi.automodsumm',
-    'sphinx_automodapi.smart_resolver',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.doctest",
+    "sphinx.ext.todo",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.extlinks",
+    "sphinx.ext.graphviz",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.napoleon",
+    "sphinx_automodapi.automodapi",
+    "sphinx_automodapi.automodsumm",
+    "sphinx_automodapi.smart_resolver",
     "sphinx_autodoc_typehints",
     "sphinxcontrib.autodoc_pydantic",
 ]
 
 autosummary_generate = True
-automodapi_toctreedirnm = 'api'
+automodapi_toctreedirnm = "api"
 autodoc_typehints = "description"
 napoleon_use_param = True
 napoleon_use_rtype = True
@@ -74,16 +74,16 @@
 autodoc_pydantic_field_swap_name_and_alias = True
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -98,15 +98,15 @@
 exclude_patterns = []
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'default'
+pygments_style = "default"
 
 
 # -- 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"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -117,7 +117,7 @@
 # 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"]
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
@@ -133,7 +133,7 @@
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'QCEnginedoc'
+htmlhelp_basename = "QCEnginedoc"
 
 
 # -- Options for LaTeX output ------------------------------------------------
@@ -142,15 +142,12 @@
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -160,19 +157,15 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'QCEngine.tex', 'QCEngine Documentation',
-     'The QCArchive Development Team', 'manual'),
+    (master_doc, "QCEngine.tex", "QCEngine Documentation", "The QCArchive Development Team", "manual"),
 ]
 
 
 # -- Options for manual page output ------------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'qcengine', 'QCEngine Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "qcengine", "QCEngine Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------------
@@ -181,30 +174,37 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'QCEngine', 'QCEngine Documentation',
-     author, 'QCEngine', 'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "QCEngine",
+        "QCEngine Documentation",
+        author,
+        "QCEngine",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]
 
 
 # -- Extension configuration -------------------------------------------------
 
 extlinks = {
-    'issue': ('https://github.com/MolSSI/QCEngine/issues/%s', 'GH#%s'),
-    'pr': ('https://github.com/MolSSI/QCEngine/pull/%s', 'GH#%s')
+    "issue": ("https://github.com/MolSSI/QCEngine/issues/%s", "GH#%s"),
+    "pr": ("https://github.com/MolSSI/QCEngine/pull/%s", "GH#%s"),
 }
 
 # -- Options for intersphinx extension ---------------------------------------
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'python': ('https://docs.python.org/3.10', None),
-                       "numpy": ("https://numpy.org/doc/stable/", None),
-                       'scipy': ('https://docs.scipy.org/doc/scipy/', None),
-                       'matplotlib': ('https://matplotlib.org/stable/', None),
-                       "qcelemental": ("http://docs.qcarchive.molssi.org/projects/QCElemental/en/latest/", None),
-                       "qcportal": ("http://docs.qcarchive.molssi.org/projects/QCPortal/en/latest/", None),
-                       "qcfractal": ("http://docs.qcarchive.molssi.org/projects/QCFractal/en/latest/", None),
-                      }
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3.10", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/", None),
+    "matplotlib": ("https://matplotlib.org/stable/", None),
+    "qcelemental": ("http://docs.qcarchive.molssi.org/projects/QCElemental/en/latest/", None),
+    "qcportal": ("http://docs.qcarchive.molssi.org/projects/QCPortal/en/latest/", None),
+    "qcfractal": ("http://docs.qcarchive.molssi.org/projects/QCFractal/en/latest/", None),
+}
 
 # -- Options for todo extension ----------------------------------------------
 

qcengine/compute.py

@@ -1,6 +1,7 @@
 """
 Integrates the computes together
 """
+
 import warnings
 from typing import TYPE_CHECKING, Any, Dict, Optional, Union
 

qcengine/config.py

@@ -37,7 +37,7 @@ def get_global(key: Optional[str] = None) -> Union[str, Dict[str, Any]]:
     if _global_values is None:
         _global_values = {}
         _global_values["hostname"] = socket.gethostname()
-        _global_values["memory"] = round(psutil.virtual_memory().available / (1024 ** 3), 3)
+        _global_values["memory"] = round(psutil.virtual_memory().available / (1024**3), 3)
         _global_values["username"] = getpass.getuser()
 
         # Work through VMs and logical cores.

qcengine/mdi_server.py

@@ -2,6 +2,7 @@
 For details regarding MDI, see https://molssi.github.io/MDI_Library/html/index.html.
 
 """
+
 from typing import Any, Dict, List, Optional
 
 import numpy as np

qcengine/programs/adcc.py

@@ -1,6 +1,7 @@
 """
 Calls adcc
 """
+
 from typing import TYPE_CHECKING, Dict
 
 from qcelemental.models import AtomicResult, BasisSet, Provenance

qcengine/programs/empirical_dispersion_resources.py

@@ -1159,9 +1159,9 @@ def from_arrays(
                 "d3mbj2b",
             ]
             for d in ["d3zero", "d3bj", "d3mzero", "d3mbj"]:
-                psi4.procrouting.empirical_dispersion._capable_engines_for_disp[
-                    d + "2b"
-                ] = psi4.procrouting.empirical_dispersion._capable_engines_for_disp.pop(d)
+                psi4.procrouting.empirical_dispersion._capable_engines_for_disp[d + "2b"] = (
+                    psi4.procrouting.empirical_dispersion._capable_engines_for_disp.pop(d)
+                )
     except ImportError:
         pass
 

qcengine/programs/gamess/runner.py

@@ -119,7 +119,7 @@ def build_input(
         # * docs on mwords: "This is given in units of 1,000,000 words (as opposed to 1024*1024 words)"
         # * docs: "the memory required on each processor core for a run using p cores is therefore MEMDDI/p + MWORDS."
         # * int() rounds down
-        mwords_total = int(config.memory * (1024 ** 3) / 8e6)
+        mwords_total = int(config.memory * (1024**3) / 8e6)
 
         for mem_frac_replicated in (1, 0.5, 0.1, 0.75):
             mwords, memddi = self._partition(mwords_total, mem_frac_replicated, config.ncores)

qcengine/programs/molpro.py

@@ -184,7 +184,7 @@ def build_input(
                 unrestricted = True
 
             # Memory is in megawords per core for Molpro
-            memory_mw_core = int(config.memory * (1024 ** 3) / 8e6 / config.ncores)
+            memory_mw_core = int(config.memory * (1024**3) / 8e6 / config.ncores)
             input_file.append("memory,{},M".format(memory_mw_core))
             input_file.append("")
 
@@ -338,7 +338,7 @@ def parse_output(self, outfiles: Dict[str, str], input_model: "AtomicInput") ->
         molpro_variable_map = {
             "_ENUC": "nuclear_repulsion_energy",
             "_DFTFUN": "scf_xc_energy",
-            "_NELEC": ["calcinfo_nalpha", "calcinfo_nbeta"]
+            "_NELEC": ["calcinfo_nalpha", "calcinfo_nbeta"],
             # "_EMP2_SCS": "scs_mp2_total_energy"
         }
 

qcengine/programs/mopac.py

@@ -1,6 +1,7 @@
 """
 Calls the Psi4 executable.
 """
+
 import os
 from typing import Any, Dict, List, Optional, Tuple
 

qcengine/programs/mrchem.py

@@ -1,6 +1,7 @@
 """
 Calls the MRChem executable.
 """
+
 import copy
 import json
 import logging

qcengine/programs/nwchem/errors.py

@@ -1,4 +1,5 @@
 """Known errors for NWChem"""
+
 import logging
 from typing import Any, Dict
 

qcengine/programs/nwchem/harvester.py

@@ -583,9 +583,9 @@ def harvest_outfile_pass(outtext):
                     if ext_energy_list[nroot] in e_val:
                         symm = k
                         # in hartree
-                        psivar[
-                            f"EOM-{cc_name} ROOT 0 -> ROOT {nroot + 1} EXCITATION ENERGY - {symm} SYMMETRY"
-                        ] = ext_energy_list[nroot]
+                        psivar[f"EOM-{cc_name} ROOT 0 -> ROOT {nroot + 1} EXCITATION ENERGY - {symm} SYMMETRY"] = (
+                            ext_energy_list[nroot]
+                        )
                         psivar[f"EOM-{cc_name} ROOT 0 -> ROOT {nroot + 1} TOTAL ENERGY - {symm} SYMMETRY"] = psivar[
                             f"{cc_name} TOTAL ENERGY"
                         ] + Decimal(ext_energy_list[nroot])

qcengine/programs/nwchem/runner.py

@@ -1,6 +1,7 @@
 """
 Calls the NWChem executable.
 """
+
 import copy
 import hashlib
 import logging
@@ -168,7 +169,7 @@ def build_input(
         # * int() rounds down
         # * was [GiB] --> [B] c. v6.6 but fails in v7.0 probably b/c https://github.com/nwchemgit/nwchem/commit/fca382eab477c3e85548457bfceb1fc9be31b47c#diff-7baaf4807cc9b853af14d9127f63db47d706e12f697a98560bc98bb647ef8326
         #   * memory_size = int(config.memory * (1024 ** 3))
-        memory_size = int(config.memory * (1024 ** 3) / 8)
+        memory_size = int(config.memory * (1024**3) / 8)
         if config.use_mpiexec:  # It is the memory per MPI rank
             memory_size //= config.nnodes * config.ncores // config.cores_per_rank
         opts["memory"] = memory_size

qcengine/programs/openmm.py

@@ -3,6 +3,7 @@
 
 Requires RDKit
 """
+
 import datetime
 import hashlib
 import os

qcengine/programs/psi4.py

@@ -1,6 +1,7 @@
 """
 Calls the Psi4 executable.
 """
+
 import json
 import os
 import sys

qcengine/programs/terachem_frontend.py

@@ -1,4 +1,5 @@
 """Harness for TeraChem Frontend"""
+
 import logging
 from os import getenv
 from typing import Any, Dict

qcengine/programs/terachem_pbs.py

@@ -1,6 +1,7 @@
 """
 Calls TeraChem in its "server mode" via a protobuf interface.
 """
+
 import logging
 from importlib import import_module
 from os import getenv

qcengine/programs/tests/test_adcc.py

@@ -1,4 +1,5 @@
 """Tests for adcc functionality"""
+
 import numpy as np
 import pytest
 import qcelemental as qcel

qcengine/programs/tests/test_canonical_config.py

@@ -1,6 +1,7 @@
 """
 Tests the DQM compute dispatch module
 """
+
 import pprint
 import re
 import sys

qcengine/programs/tests/test_mrchem.py

@@ -1,4 +1,5 @@
 """Tests for MRChem functionality"""
+
 import numpy as np
 import pytest
 import qcelemental as qcel