fix formatting

MolSSI · May 5, 2024 · 4bfade3 · 4bfade3
1 parent 0b88aaa
commit 4bfade3
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Showing 3 changed files with 47 additions and 33 deletions.
diff --git a/qcengine/procedures/optking.py b/qcengine/procedures/optking.py
@@ -86,12 +86,16 @@ def found(self, raise_error: bool = False) -> bool:
 
         return qc and dep
 
-    def build_input_model(self, data: Union[Dict[str, Any], "GeneralizedOptimizationInput"]) -> "GeneralizedOptimizationInput":
+    def build_input_model(
+        self, data: Union[Dict[str, Any], "GeneralizedOptimizationInput"]
+    ) -> "GeneralizedOptimizationInput":
         from qcmanybody.models.generalized_optimization import GeneralizedOptimizationInput
 
         return self._build_model(data, GeneralizedOptimizationInput)
 
-    def compute(self, input_model: "GeneralizedOptimizationInput", config: "TaskConfig") -> "GeneralizedOptimizationResult":
+    def compute(
+        self, input_model: "GeneralizedOptimizationInput", config: "TaskConfig"
+    ) -> "GeneralizedOptimizationResult":
         self.found(raise_error=True)
 
         import optking
@@ -102,13 +106,13 @@ def compute(self, input_model: "GeneralizedOptimizationInput", config: "TaskConf
         # Set retries to two if zero while respecting local_config
         local_config = config.dict()
         local_config["retries"] = local_config.get("retries", 2) or 2
-        #TODO input_data["input_specification"]["extras"]["_qcengine_local_config"] = local_config
+        # TODO input_data["input_specification"]["extras"]["_qcengine_local_config"] = local_config
 
         # Run the program
         output_data = optking.optwrapper.optimize_qcengine(input_data)
 
         output_data["schema_name"] = "qcschema_generalizedoptimizationresult"
-        #TODO output_data["input_specification"]["extras"].pop("_qcengine_local_config", None)
+        # TODO output_data["input_specification"]["extras"].pop("_qcengine_local_config", None)
         if output_data["success"]:
             output_data = GeneralizedOptimizationResult(**output_data)
 

diff --git a/qcengine/procedures/qcmanybody.py b/qcengine/procedures/qcmanybody.py
@@ -31,6 +31,7 @@ def found(self, raise_error: bool = False) -> bool:
 
     def build_input_model(self, data: Union[Dict[str, Any], "ManyBodyInput"]) -> "ManyBodyInput":
         from qcmanybody.models import ManyBodyInput
+
         return self._build_model(data, ManyBodyInput)
 
     def get_version(self) -> str:

diff --git a/qcengine/tests/test_mbe_ne2.py b/qcengine/tests/test_mbe_ne2.py
@@ -11,12 +11,15 @@
 
 
 @using("qcmanybody")
-@pytest.mark.parametrize("qcprog", [
-    pytest.param("cfour", marks=using("cfour")),
-    pytest.param("gamess", marks=using("gamess")),
-    pytest.param("nwchem", marks=using("nwchem")),
-    pytest.param("psi4", marks=using("psi4")),
-])
+@pytest.mark.parametrize(
+    "qcprog",
+    [
+        pytest.param("cfour", marks=using("cfour")),
+        pytest.param("gamess", marks=using("gamess")),
+        pytest.param("nwchem", marks=using("nwchem")),
+        pytest.param("psi4", marks=using("psi4")),
+    ],
+)
 def test_tu6_cp_ne2(qcprog):
     """
     from https://github.com/psi4/psi4/blob/master/tests/tu6-cp-ne2/input.dat
@@ -44,7 +47,7 @@ def test_tu6_cp_ne2(qcprog):
             "specification": {
                 "model": {
                     "method": "ccsd(t)",
-                    #TODO error handling cfour "basis": "aug-cc-pvdz",
+                    # TODO error handling cfour "basis": "aug-cc-pvdz",
                     "basis": basis[qcprog],
                 },
                 "driver": "energy",
@@ -61,7 +64,9 @@ def test_tu6_cp_ne2(qcprog):
 
     for R in tu6_ie_scan:
         # TODO fix_symmetry='c1' propagate
-        nene = Molecule(symbols=["Ne", "Ne"], fragments=[[0], [1]], geometry=[0, 0, 0, 0, 0, R / constants.bohr2angstroms])
+        nene = Molecule(
+            symbols=["Ne", "Ne"], fragments=[[0], [1]], geometry=[0, 0, 0, 0, 0, R / constants.bohr2angstroms]
+        )
         mbe_data["molecule"] = nene
 
         mbe_model = ManyBodyInput(**mbe_data)
@@ -113,14 +118,15 @@ def test_mbe_error():
                 "driver": "energy",
                 "program": "cms",
             },
-            "keywords": {
-            },
+            "keywords": {},
             "driver": "energy",
         },
         "molecule": None,
     }
 
-    nene = Molecule(symbols=["Ne", "Ne"], fragments=[[0], [1]], geometry=[0, 0, 0, 0, 0, 3.0 / constants.bohr2angstroms])
+    nene = Molecule(
+        symbols=["Ne", "Ne"], fragments=[[0], [1]], geometry=[0, 0, 0, 0, 0, 3.0 / constants.bohr2angstroms]
+    )
     mbe_data["molecule"] = nene
 
     mbe_model = ManyBodyInput(**mbe_data)
@@ -151,7 +157,8 @@ def test_mbe_error():
 def test_optimization_qcmanybody(optimizer, bsse_type):
     from qcmanybody.models.generalized_optimization import GeneralizedOptimizationInput
 
-    initial_molecule = Molecule.from_data("""
+    initial_molecule = Molecule.from_data(
+        """
 F         -0.04288        2.78905        0.00000
 H          0.59079        2.03435        0.00000
 --
@@ -161,7 +168,8 @@ def test_optimization_qcmanybody(optimizer, bsse_type):
 F          2.03569       -0.60531       -0.00000
 H          1.06527       -0.77673        0.00000
 units ang
-""")
+"""
+    )
 
     at_spec = {
         "model": {
@@ -174,20 +182,20 @@ def test_optimization_qcmanybody(optimizer, bsse_type):
     }
 
     mbe_spec = {
-         "specification": {
-             "model": {
-                 "method": "hf",
-                 "basis": "6-31g",
-             },
-             "driver": "energy",
-             "program": "psi4",
-             "keywords": {},
-         },
-         "keywords": {
-             "bsse_type": bsse_type,
-         },
-         "driver": "energy",
-     }
+        "specification": {
+            "model": {
+                "method": "hf",
+                "basis": "6-31g",
+            },
+            "driver": "energy",
+            "program": "psi4",
+            "keywords": {},
+        },
+        "keywords": {
+            "bsse_type": bsse_type,
+        },
+        "driver": "energy",
+    }
 
     opt_data = {
         "initial_molecule": initial_molecule,
@@ -204,11 +212,12 @@ def test_optimization_qcmanybody(optimizer, bsse_type):
 
     ret = qcng.compute_procedure(opt_data, optimizer, raise_error=True)
     import pprint
+
     pprint.pprint(ret.dict())
 
     r_fh_hb = {
-        "none": 2.18 /constants.bohr2angstroms,
-        "nocp": 2.18 /constants.bohr2angstroms,
+        "none": 2.18 / constants.bohr2angstroms,
+        "nocp": 2.18 / constants.bohr2angstroms,
         "cp": 2.27 / constants.bohr2angstroms,
     }
     r_fh_computed = ret.final_molecule.measure([1, 3])