mostly black v20 formatting

Author: loriab

.github/workflows/QCSchema.yml

@@ -64,7 +64,8 @@ jobs:
         make qcschema
         ls -l qcschema
         #cp -p qcschema/* ../qcsk/qcschema_json/
-        cp -p qcschema/* ../qcsk/qcschema/
+        cp -p qcschema/* ../qcsk/qcschema/data/vdev/
+        mv ../qcsk/qcschema/data/vdev/QCSchema.schema ../qcsk/qcschema/dev/
         # Note: `qcschema_json` is a folder in the py2json branch containing plain JSON files of the schema,
         #       rather than the python module of the current repo
 

Makefile

@@ -46,7 +46,7 @@ cpu_data:
 .PHONY: qcschema
 qcschema:
 	mkdir -p qcschema
-	python -c "exec(\"import pathlib, qcelemental\nfor md in qcelemental.models.qcschema_models():\n\tmfile = (pathlib.Path('qcschema') / md.__name__).with_suffix('.schema')\n\twith open(mfile, 'w') as fp:\n\t\tfp.write(md.schema_json(indent=4))\")"
+	python -c "exec(\"import pathlib, qcelemental\nfor md in qcelemental.models.qcschema_models():\n\tmfile = (pathlib.Path('qcschema') / md.__name__).with_suffix('.schema')\n\twith open(mfile, 'w') as fp:\n\t\tfp.write(md.schema_json(indent=None))\")"
 	python -c "exec(\"import json, pathlib, pydantic, qcelemental\nwith open((pathlib.Path('qcschema') / 'QCSchema').with_suffix('.schema'), 'w') as fp:\n\tjson.dump(pydantic.schema.schema(qcelemental.models.qcschema_models(), title='QCSchema'), fp, indent=4)\")"
 
 .PHONY: clean

qcelemental/info/cpu_info.py

@@ -14,8 +14,7 @@
 
 
 class VendorEnum(str, Enum):
-    """Allowed processor vendors, used for validation.
-    """
+    """Allowed processor vendors, used for validation."""
 
     amd = "amd"
     intel = "intel"
@@ -24,8 +23,7 @@ class VendorEnum(str, Enum):
 
 
 class InstructionSetEnum(int, Enum):
-    """Allowed instruction sets for CPUs in an ordinal enum.
-    """
+    """Allowed instruction sets for CPUs in an ordinal enum."""
 
     none = 0
     sse = 1

qcelemental/models/align.py

@@ -21,15 +21,9 @@ class AlignmentMill(ProtoModel):
 
     """
 
-    shift: Optional[Array[float]] = Field(  # type: ignore
-        None, description="Translation array (3,) for coordinates."
-    )
-    rotation: Optional[Array[float]] = Field(  # type: ignore
-        None, description="Rotation array (3, 3) for coordinates."
-    )
-    atommap: Optional[Array[int]] = Field(  # type: ignore
-        None, description="Atom exchange map (nat,) for coordinates."
-    )
+    shift: Optional[Array[float]] = Field(None, description="Translation array (3,) for coordinates.")  # type: ignore
+    rotation: Optional[Array[float]] = Field(None, description="Rotation array (3, 3) for coordinates.")  # type: ignore
+    atommap: Optional[Array[int]] = Field(None, description="Atom exchange map (nat,) for coordinates.")  # type: ignore
     mirror: bool = Field(False, description="Do mirror invert coordinates?")
 
     class Config:

qcelemental/models/common_models.py

@@ -63,8 +63,7 @@ class Config(ProtoModel.Config):
 
 
 class DriverEnum(str, Enum):
-    """Allowed computation driver values.
-    """
+    """Allowed computation driver values."""
 
     energy = "energy"
     gradient = "gradient"

qcelemental/models/results.py

@@ -391,7 +391,7 @@ class WavefunctionProtocolEnum(str, Enum):
 
 class ErrorCorrectionProtocol(ProtoModel):
     """Configuration for how QCEngine handles error correction
-    
+
     WARNING: These protocols are currently experimental and only supported by NWChem tasks
     """
 
@@ -452,7 +452,8 @@ class AtomicInput(ProtoModel):
     )
 
     extras: Dict[str, Any] = Field(
-        {}, description="Extra fields not part of the schema. Used for schema development and scratch space.",
+        {},
+        description="Extra fields not part of the schema. Used for schema development and scratch space.",
     )
 
     provenance: Provenance = Field(

qcelemental/physical_constants/context.py

@@ -269,8 +269,7 @@ def get(self, physical_constant: str, return_tuple: bool = False) -> Union[float
     #       me                        'electron mass'                             = 9.10938215E-31       # Electron rest mass (in kg)
 
     def Quantity(self, data: str) -> "quantity._Quantity":
-        """Returns a Pint Quantity.
-        """
+        """Returns a Pint Quantity."""
 
         return self.ureg.Quantity(data)
 

qcelemental/physical_constants/ureg.py

@@ -129,8 +129,7 @@ def build_units_registry(context):
     # Add contexts
 
     def _find_nist_unit(unit):
-        """Converts pint datatypes to NIST datatypes
-        """
+        """Converts pint datatypes to NIST datatypes"""
         for value in unit.to_tuple()[1]:
             if value[1] < 1:
                 continue

qcelemental/testing.py

@@ -11,8 +11,7 @@
 
 
 def _handle_return(passfail: bool, label: str, message: str, return_message: bool, quiet: bool = False):
-    """Function to print a '*label*...PASSED' line to log.
-    """
+    """Function to print a '*label*...PASSED' line to log."""
 
     if not quiet:
         if passfail:
@@ -28,8 +27,7 @@ def _handle_return(passfail: bool, label: str, message: str, return_message: boo
 
 
 def tnm() -> str:
-    """Returns the name of the calling function, usually name of test case.
-    """
+    """Returns the name of the calling function, usually name of test case."""
 
     return sys._getframe().f_back.f_code.co_name
 
@@ -480,11 +478,7 @@ def compare_molrecs(
     return_message: bool = False,
     return_handler: Callable = None,
 ) -> bool:
-    """Function to compare Molecule dictionaries. Prints
-#    :py:func:`util.success` when elements of `computed` match elements of
-#    `expected` to `tol` number of digits (for float arrays).
-
-    """
+    """Function to compare Molecule dictionaries."""
     # Need to manipulate the dictionaries a bit, so hold values
     xptd = copy.deepcopy(expected)
     cptd = copy.deepcopy(computed)

qcelemental/util/gph_uno_bipartite.py

@@ -45,10 +45,10 @@ def _formDirected(g, match):
     Returns
     -------
     networkx.DiGraph
-	    Directed graph, with edges in `match` pointing from set-0
-	    (bipartite attribute==0) to set-1 (bipartite attrbiute==1), and
-	    the other edges in `g` but not in `match` pointing from set-1 to
-	    set-0.
+        Directed graph, with edges in `match` pointing from set-0
+        (bipartite attribute==0) to set-1 (bipartite attrbiute==1), and
+        the other edges in `g` but not in `match` pointing from set-1 to
+        set-0.
 
     """
     import networkx as nx
@@ -127,8 +127,8 @@ def _enumMaximumMatchingIter(g, match, all_matches, add_e=None):
     match :
         List of edges forming one maximum matching of `g`.
     all_matches :
-	    List, each is a list of edges forming a maximum matching of `g`.
-	    Newly found matchings will be appended into this list.
+        List, each is a list of edges forming a maximum matching of `g`.
+        Newly found matchings will be appended into this list.
     add_e : tuple, optional
         Edge used to form subproblems. If not `None`, will be added to each
         newly found matchings.
@@ -335,32 +335,32 @@ def _enumMaximumMatching2(g):
 
 def _enumMaximumMatchingIter2(adj, matchadj, all_matches, n1, add_e=None, check_cycle=True):
     """Recurively search maximum matchings.
-    Similar to _enumMaximumMatching but implemented using adjacency matrix
-    of graph for a slight speed boost.
-
-    Parameters
-    ----------
-#    g :
-#        Undirected bipartite graph. Nodes are separated by their
-#        'bipartite' attribute.
-#    match :
-#        List of edges forming one maximum matching of `g`.
-#    all_matches :
-#	    List, each is a list of edges forming a maximum matching of `g`.
-#	    Newly found matchings will be appended into this list.
-    add_e : tuple, optional
-        Edge used to form subproblems. If not `None`, will be added to each
-        newly found matchings.
-
-    Returns
-    -------
-    list
-        Updated list of all maximum matchings.
-
-    Author
-    ------
-    guangzhi XU (xugzhi1987@gmail.com; guangzhi.xu@outlook.com)
-    Update time: 2017-05-21 20:09:06.
+        Similar to _enumMaximumMatching but implemented using adjacency matrix
+        of graph for a slight speed boost.
+
+        Parameters
+        ----------
+    #    g :
+    #        Undirected bipartite graph. Nodes are separated by their
+    #        'bipartite' attribute.
+    #    match :
+    #        List of edges forming one maximum matching of `g`.
+    #    all_matches :
+    #        List, each is a list of edges forming a maximum matching of `g`.
+    #        Newly found matchings will be appended into this list.
+        add_e : tuple, optional
+            Edge used to form subproblems. If not `None`, will be added to each
+            newly found matchings.
+
+        Returns
+        -------
+        list
+            Updated list of all maximum matchings.
+
+        Author
+        ------
+        guangzhi XU (xugzhi1987@gmail.com; guangzhi.xu@outlook.com)
+        Update time: 2017-05-21 20:09:06.
 
     """
     import networkx as nx