format with black 20

MolSSI · Aug 31, 2020 · ba6b49b · ba6b49b
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commit ba6b49b
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Showing 13 changed files with 520 additions and 102 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,3 +1,3 @@
 [tool.black]
 line-length = 120
-target-version = ['py37']
+target-version = ['py37', 'py38']
diff --git a/qcengine/extras.py b/qcengine/extras.py
@@ -26,11 +26,11 @@ def get_information(key):
 
 def provenance_stamp(routine):
     """Return dictionary satisfying QCSchema,
-   https://github.com/MolSSI/QCSchema/blob/master/qcschema/dev/definitions.py#L23-L41
-   with QCEngine's credentials for creator and version. The
-   generating routine's name is passed in through `routine`.
+    https://github.com/MolSSI/QCSchema/blob/master/qcschema/dev/definitions.py#L23-L41
+    with QCEngine's credentials for creator and version. The
+    generating routine's name is passed in through `routine`.
 
-   """
+    """
     return {"creator": "QCEngine", "version": get_information("version"), "routine": routine}
 
 

diff --git a/qcengine/mdi_server.py b/qcengine/mdi_server.py
@@ -50,7 +50,7 @@ def __init__(
         raise_error: bool = False,
         local_options: Optional[Dict[str, Any]] = None,
     ):
-        """ Initialize an MDIServer object for communication with MDI
+        """Initialize an MDIServer object for communication with MDI
 
         Parameters
         ----------
@@ -157,7 +157,7 @@ def __init__(
         self.comm = MDI_Accept_Communicator()
 
     def update_molecule(self, key: str, value):
-        """ Update the molecule
+        """Update the molecule
 
         Parameters
         ----------
@@ -195,7 +195,7 @@ def update_molecule(self, key: str, value):
 
     # Respond to the <@ command
     def send_node(self) -> str:
-        """ Send the name of the current node through MDI
+        """Send the name of the current node through MDI
 
         Returns
         -------
@@ -208,7 +208,7 @@ def send_node(self) -> str:
 
     # Respond to the <NATOMS command
     def send_natoms(self) -> int:
-        """ Send the number of atoms through MDI
+        """Send the number of atoms through MDI
 
         Returns
         -------
@@ -221,7 +221,7 @@ def send_natoms(self) -> int:
 
     # Respond to the <COORDS command
     def send_coords(self) -> np.ndarray:
-        """ Send the nuclear coordinates through MDI
+        """Send the nuclear coordinates through MDI
 
         Returns
         -------
@@ -237,7 +237,7 @@ def send_coords(self) -> np.ndarray:
 
     # Respond to the >COORDS command
     def recv_coords(self, coords: Optional[np.ndarray] = None) -> None:
-        """ Receive a set of nuclear coordinates through MDI and assign them to the atoms in the current molecule
+        """Receive a set of nuclear coordinates through MDI and assign them to the atoms in the current molecule
 
         Parameters
         ----------
@@ -253,7 +253,7 @@ def recv_coords(self, coords: Optional[np.ndarray] = None) -> None:
 
     # Respond to the <ENERGY command
     def send_energy(self) -> float:
-        """ Send the total energy through MDI
+        """Send the total energy through MDI
 
         Returns
         -------
@@ -270,7 +270,7 @@ def send_energy(self) -> float:
 
     # Respond to the <FORCES command
     def send_forces(self) -> np.ndarray:
-        """ Send the nuclear forces through MDI
+        """Send the nuclear forces through MDI
 
         Returns
         -------
@@ -294,8 +294,7 @@ def send_forces(self) -> np.ndarray:
 
     # Respond to the SCF command
     def run_energy(self) -> None:
-        """ Run an energy calculation
-        """
+        """Run an energy calculation"""
         input = qcel.models.AtomicInput(
             molecule=self.molecule, driver="energy", model=self.model, keywords=self.keywords
         )
@@ -305,7 +304,7 @@ def run_energy(self) -> None:
 
     # Respond to the <ELEMENTS command
     def send_elements(self):
-        """ Send the atomic number of each nucleus through MDI
+        """Send the atomic number of each nucleus through MDI
 
         Returns
         -------
@@ -319,7 +318,7 @@ def send_elements(self):
 
     # Respond to the >ELEMENTS command
     def recv_elements(self, elements: Optional[List[int]] = None):
-        """ Receive a set of atomic numbers through MDI and assign them to the atoms in the current molecule
+        """Receive a set of atomic numbers through MDI and assign them to the atoms in the current molecule
 
         Parameters
         ----------
@@ -337,7 +336,7 @@ def recv_elements(self, elements: Optional[List[int]] = None):
 
     # Respond to the <MASSES command
     def send_masses(self) -> np.ndarray:
-        """ Send the nuclear masses through MDI
+        """Send the nuclear masses through MDI
 
         Returns
         -------
@@ -351,7 +350,7 @@ def send_masses(self) -> np.ndarray:
 
     # Respond to the >MASSES command
     def recv_masses(self, masses: Optional[List[float]] = None) -> None:
-        """ Receive a set of nuclear masses through MDI and assign them to the atoms in the current molecule
+        """Receive a set of nuclear masses through MDI and assign them to the atoms in the current molecule
 
         Parameters
         ----------
@@ -365,7 +364,7 @@ def recv_masses(self, masses: Optional[List[float]] = None) -> None:
 
     # Respond to the <TOTCHARGE command
     def send_total_charge(self) -> float:
-        """ Send the total system charge through MDI
+        """Send the total system charge through MDI
 
         Returns
         -------
@@ -378,7 +377,7 @@ def send_total_charge(self) -> float:
 
     # Respond to the >TOTCHARGE command
     def recv_total_charge(self, charge: Optional[float] = None) -> None:
-        """ Receive the total system charge through MDI
+        """Receive the total system charge through MDI
 
         Parameters
         ----------
@@ -397,7 +396,7 @@ def recv_total_charge(self, charge: Optional[float] = None) -> None:
 
     # Respond to the <ELEC_MULT command
     def send_multiplicity(self) -> int:
-        """ Send the electronic multiplicity through MDI
+        """Send the electronic multiplicity through MDI
 
         Returns
         -------
@@ -410,7 +409,7 @@ def send_multiplicity(self) -> int:
 
     # Respond to the >ELEC_MULT command
     def recv_multiplicity(self, multiplicity: Optional[int] = None) -> None:
-        """ Receive the electronic multiplicity through MDI
+        """Receive the electronic multiplicity through MDI
 
         Parameters
         ----------
@@ -429,14 +428,12 @@ def recv_multiplicity(self, multiplicity: Optional[int] = None) -> None:
 
     # Respond to the EXIT command
     def stop(self) -> None:
-        """ Stop listening for MDI commands
-        """
+        """Stop listening for MDI commands"""
         self.stop_listening = True
 
     # Enter server mode, listening for commands from the driver
     def start(self) -> None:
-        """ Receive commands through MDI and respond to them as defined by the MDI Standard
-        """
+        """Receive commands through MDI and respond to them as defined by the MDI Standard"""
 
         while not self.stop_listening:
             if self.world_rank == 0:

diff --git a/qcengine/procedures/berny.py b/qcengine/procedures/berny.py
@@ -19,7 +19,10 @@ class BernyProcedure(ProcedureHarness):
 
     def found(self, raise_error: bool = False) -> bool:
         return which_import(
-            "berny", return_bool=True, raise_error=raise_error, raise_msg="Please install via `pip install pyberny`.",
+            "berny",
+            return_bool=True,
+            raise_error=raise_error,
+            raise_msg="Please install via `pip install pyberny`.",
         )
 
     def build_input_model(self, data: Union[Dict[str, Any], "OptimizationInput"]) -> "OptimizationInput":

diff --git a/qcengine/programs/cfour/harvester.py b/qcengine/programs/cfour/harvester.py
@@ -920,9 +920,7 @@ def harvest_GRD(grd):
 
 
 def harvest_DIPOL(dipol):
-    """Parses the contents *dipol* of the Cfour DIPOL file into a dipol vector.
-
-    """
+    """Parses the contents *dipol* of the Cfour DIPOL file into a dipol vector."""
     dipol = dipol.splitlines()
     lline = dipol[0].split()
     dip = [float(lline[0]), float(lline[1]), float(lline[2])]

diff --git a/qcengine/programs/gamess/harvester.py b/qcengine/programs/gamess/harvester.py
@@ -44,8 +44,8 @@ def harvest(p4Mol, gamessout: str, **largs) -> Tuple[PreservingDict, Molecule, l
 
 def harvest_output(outtext):
     """Function to separate portions of a gamess output file *outtext*,
-        divided by "Step".
-        """
+    divided by "Step".
+    """
     pass_qcvar = []
     pass_coord = []
     pass_grad = []

diff --git a/qcengine/programs/openmm.py b/qcengine/programs/openmm.py
@@ -67,9 +67,7 @@ def _get_cache(self, key):
         return self._CACHE[key]["value"]
 
     def _cache_it(self, key, value):
-        """Add to our LRU cache, possibly popping off least used key.
-
-        """
+        """Add to our LRU cache, possibly popping off least used key."""
         self._CACHE[key] = {"value": value, "last_used": datetime.datetime.utcnow()}
 
         # if cache is beyond max size, whittle it down by dropping entry least

diff --git a/qcengine/programs/tests/standard_suite_contracts.py b/qcengine/programs/tests/standard_suite_contracts.py
@@ -188,7 +188,12 @@ def contractual_mp2(
             )
             or (
                 ((qc_module == "psi4-occ" and reference == "rohf" and method in ["olccd"]))
-                and pv in ["MP2 CORRELATION ENERGY", "MP2 TOTAL ENERGY", "MP2 SINGLES ENERGY",]
+                and pv
+                in [
+                    "MP2 CORRELATION ENERGY",
+                    "MP2 TOTAL ENERGY",
+                    "MP2 SINGLES ENERGY",
+                ]
             )
             or (
                 (
@@ -481,11 +486,21 @@ def contractual_ccsd(
             )
             or (
                 (qc_module == "cfour-vcc" and reference in ["rohf"] and method in ["ccsd", "ccsd(t)"])
-                and pv in ["CCSD SAME-SPIN CORRELATION ENERGY", "CCSD SINGLES ENERGY", "CCSD DOUBLES ENERGY",]
+                and pv
+                in [
+                    "CCSD SAME-SPIN CORRELATION ENERGY",
+                    "CCSD SINGLES ENERGY",
+                    "CCSD DOUBLES ENERGY",
+                ]
             )
             or (
                 (qc_module == "cfour-ecc" and reference in ["rohf"] and method in ["ccsd", "ccsd(t)"])
-                and pv in ["CCSD OPPOSITE-SPIN CORRELATION ENERGY", "CCSD SINGLES ENERGY", "CCSD DOUBLES ENERGY",]
+                and pv
+                in [
+                    "CCSD OPPOSITE-SPIN CORRELATION ENERGY",
+                    "CCSD SINGLES ENERGY",
+                    "CCSD DOUBLES ENERGY",
+                ]
             )
             or (
                 (