Lint and format with ruff 0.3.0

matterhorn103 · Mar 1, 2024 · e66fec4 · e66fec4
1 parent fc9efc6
commit e66fec4
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Showing 8 changed files with 113 additions and 59 deletions.
diff --git a/config.py b/config.py
@@ -41,7 +41,7 @@
     "energy_units": "kJ/mol",
     "method": 2,
     "opt_lvl": "normal",
-    }.items():
+}.items():
     if option not in config:
         config[option] = default
 
@@ -177,7 +177,6 @@ def find_obabel():
 methods = ["GFN0-xTB", "GFN1-xTB", "GFN2-xTB"]
 
 
-
 if __name__ == "__main__":
     parser = argparse.ArgumentParser()
     parser.add_argument("--debug", action="store_true")
@@ -207,14 +206,14 @@ def find_obabel():
                     "type": "string",
                     "label": "Run calculations (in subfolder) in",
                     "default": str(calc_dir.parent),
-                    "order": 3.0
+                    "order": 3.0,
                 },
                 "energy_units": {
                     "type": "stringList",
                     "label": "Preferred energy units",
                     "values": ["kJ/mol", "kcal/mol"],
                     "default": 0,
-                    "order": 4.0
+                    "order": 4.0,
                 },
                 "solvent": {
                     "type": "stringList",
@@ -254,7 +253,7 @@ def find_obabel():
                     "label": "Method (xtb only)",
                     "values": methods,
                     "default": methods[-1],
-                    "order": 6.0
+                    "order": 6.0,
                 },
                 "opt_lvl": {
                     "type": "stringList",
@@ -267,17 +266,17 @@ def find_obabel():
                         "normal",
                         "tight",
                         "vtight",
-                        "extreme"
-                        ],
+                        "extreme",
+                    ],
                     "default": 4,
-                    "order": 7.0
+                    "order": 7.0,
                 },
                 "warning": {
                     "type": "text",
                     "label": "Note",
                     "default": "Some changes here will only affect other\nmenus after restarting Avogadro!",
-                    "order": 10.0
-                }
+                    "order": 10.0,
+                },
             }
         }
         # Set other options' defaults to match that found in user config
@@ -316,7 +315,7 @@ def find_obabel():
         if avo_input["obabel_bin"] != str(obabel_bin):
             obabel_bin = Path(avo_input["obabel_bin"])
             config["obabel_bin"] = str(obabel_bin)
-        
+
         # Update energy units
         config["energy_units"] = avo_input["energy_units"]
 
@@ -327,9 +326,9 @@ def find_obabel():
             solvent_selected = avo_input["solvent"]
         # Update solvent
         config["solvent"] = solvent_selected
-        
+
         # Update method
         config["method"] = methods.index(avo_input["method"])
-        
+
         with open(config_file, "w", encoding="utf-8") as config_path:
             json.dump(config, config_path, indent=2)
diff --git a/conformers.py b/conformers.py
@@ -251,7 +251,10 @@ def conformers(
             json.dump(result["cjson"], save_file, indent=2)
 
         # If user specified a save location, copy calculation directory to there
-        if not (avo_input["save_dir"] in ["", None] or Path(avo_input["save_dir"]) == calc_dir):
+        if not (
+            avo_input["save_dir"] in ["", None]
+            or Path(avo_input["save_dir"]) == calc_dir
+        ):
             copytree(calc_dir, Path(avo_input["save_dir"]), dirs_exist_ok=True)
 
         # Pass back to Avogadro

diff --git a/energy.py b/energy.py
@@ -22,7 +22,16 @@ def energy(
 ) -> float:
     """Calculate energy in hartree for given geometry."""
     unpaired_e = multiplicity - 1
-    command = ["xtb", geom_file, "--chrg", str(charge), "--uhf", str(unpaired_e), "--gfn", str(method)]
+    command = [
+        "xtb",
+        geom_file,
+        "--chrg",
+        str(charge),
+        "--uhf",
+        str(unpaired_e),
+        "--gfn",
+        str(method),
+    ]
     # Add solvation if requested
     if solvation is not None:
         command.extend(["--alpb", solvation])
@@ -80,12 +89,13 @@ def energy(
         # Start by passing back the original cjson, then add changes
         result = {"moleculeFormat": "cjson", "cjson": avo_input["cjson"]}
         # Currently Avogadro ignores the energy result
-        result["message"] = (f"Energy from GFN{config["method"]}-xTB:\n"
-                             + f"{str(round(energy_hartree, 7))} hartree\n"
-                             + f"{str(round(energies['eV'], 7))} eV\n"
-                             + f"{str(round(energies['kJ'], 7))} kJ/mol\n"
-                             + f"{str(round(energies['kcal'], 7))} kcal/mol\n"
-                             )
+        result["message"] = (
+            f"Energy from GFN{config["method"]}-xTB:\n"
+            + f"{str(round(energy_hartree, 7))} hartree\n"
+            + f"{str(round(energies['eV'], 7))} eV\n"
+            + f"{str(round(energies['kJ'], 7))} kJ/mol\n"
+            + f"{str(round(energies['kcal'], 7))} kcal/mol\n"
+        )
         result["cjson"]["properties"]["totalEnergy"] = str(round(energies["eV"], 7))
         # Pass back to Avogadro
         print(json.dumps(result))
diff --git a/freq.py b/freq.py
@@ -14,16 +14,25 @@
 
 
 def frequencies(
-
-        geom_file: Path,
-        charge: int = 0,
-        multiplicity: int = 1,
-        solvation: str | None = None,
-        method: int = 2,
-        ) -> Path:
+    geom_file: Path,
+    charge: int = 0,
+    multiplicity: int = 1,
+    solvation: str | None = None,
+    method: int = 2,
+) -> Path:
     """Calculate vibrational frequencies and return Gaussian 98 format output file."""
     unpaired_e = multiplicity - 1
-    command = ["xtb", geom_file, "--hess", "--chrg", str(charge), "--uhf", str(unpaired_e), "--gfn", str(method)]
+    command = [
+        "xtb",
+        geom_file,
+        "--hess",
+        "--chrg",
+        str(charge),
+        "--uhf",
+        str(unpaired_e),
+        "--gfn",
+        str(method),
+    ]
 
     # Add solvation if requested
     if solvation is not None:
@@ -77,7 +86,7 @@ def frequencies(
             multiplicity=avo_input["spin"],
             solvation=config["solvent"],
             method=config["method"],
-            )
+        )
 
         # Currently Avogadro fails to convert the g98 file to cjson itself
         # So we have to convert output in g98 format to cjson ourselves

diff --git a/ohess.py b/ohess.py
@@ -15,16 +15,27 @@
 
 
 def opt_freq(
-        geom_file: Path,
-        charge: int = 0,
-        multiplicity: int = 1,
-        solvation: str | None = None,
-        method: int = 2,
-        level: str = "normal",
-        ) -> tuple[Path, Path, float]:
+    geom_file: Path,
+    charge: int = 0,
+    multiplicity: int = 1,
+    solvation: str | None = None,
+    method: int = 2,
+    level: str = "normal",
+) -> tuple[Path, Path, float]:
     """Optimize geometry then calculate vibrational frequencies. Distort and reoptimize if negative frequency detected."""
     spin = multiplicity - 1
-    command = ["xtb", geom_file, "--ohess", level, "--chrg", str(charge), "--uhf", str(spin), "--gfn", str(method)]
+    command = [
+        "xtb",
+        geom_file,
+        "--ohess",
+        level,
+        "--chrg",
+        str(charge),
+        "--uhf",
+        str(spin),
+        "--gfn",
+        str(method),
+    ]
     # Add solvation if requested
     if solvation is not None:
         command.extend(["--alpb", solvation])
@@ -88,8 +99,8 @@ def opt_freq(
             solvation=config["solvent"],
             method=config["method"],
             level=config["level"],
-            )
-        
+        )
+
         # Convert frequencies
         # Currently Avogadro fails to convert the g98 file to cjson itself
         # So we have to convert output in g98 format to cjson ourselves

diff --git a/opt.py b/opt.py
@@ -14,16 +14,27 @@
 
 
 def optimize(
-        geom_file: Path,
-        charge: int = 0,
-        multiplicity: int = 1,
-        solvation: str | None = None,
-        method: int = 2,
-        level: str = "normal",
-        ) -> tuple[Path, float]:
+    geom_file: Path,
+    charge: int = 0,
+    multiplicity: int = 1,
+    solvation: str | None = None,
+    method: int = 2,
+    level: str = "normal",
+) -> tuple[Path, float]:
     """Return optimized geometry as file in same format as the input, along with the energy."""
     unpaired_e = multiplicity - 1
-    command = ["xtb", geom_file, "--opt", level, "--chrg", str(charge), "--uhf", str(unpaired_e), "--gfn", str(method)]
+    command = [
+        "xtb",
+        geom_file,
+        "--opt",
+        level,
+        "--chrg",
+        str(charge),
+        "--uhf",
+        str(unpaired_e),
+        "--gfn",
+        str(method),
+    ]
 
     # Add solvation if requested
     if solvation is not None:
@@ -77,7 +88,7 @@ def optimize(
             solvation=config["solvent"],
             method=config["method"],
             level=config["level"],
-            )
+        )
 
         # Read the xyz file
         with open(result_path.with_name("xtbopt.xyz"), encoding="utf-8") as result_xyz:

diff --git a/orbitals.py b/orbitals.py
@@ -13,17 +13,26 @@
 
 
 def orbitals(
-        geom_file: Path,
-        charge: int = 0,
-        multiplicity: int = 1,
-        solvation: str | None = None,
-        method: int = 2,
-        ) -> Path:
-
+    geom_file: Path,
+    charge: int = 0,
+    multiplicity: int = 1,
+    solvation: str | None = None,
+    method: int = 2,
+) -> Path:
     """Calculate molecular orbitals for given geometry, return file in Molden format."""
     spin = multiplicity - 1
     # Just do a single point calculation but pass molden option to get orbital printout
-    command = ["xtb", geom_file, "--molden", "--chrg", str(charge), "--uhf", str(spin), "--gfn", str(method)]
+    command = [
+        "xtb",
+        geom_file,
+        "--molden",
+        "--chrg",
+        str(charge),
+        "--uhf",
+        str(spin),
+        "--gfn",
+        str(method),
+    ]
     # Add solvation if requested
     if solvation is not None:
         command.extend(["--alpb", solvation])
@@ -76,7 +85,7 @@ def orbitals(
             multiplicity=avo_input["spin"],
             solvation=config["solvent"],
             method=config["method"],
-            )
+        )
 
         # Get molden file as string
         with open(result_path, encoding="utf-8") as molden_file:

diff --git a/run_calc.py b/run_calc.py
@@ -74,7 +74,9 @@
         }
         # Add solvation to default command if found in user config
         if config["solvent"] is not None:
-            options["userOptions"]["command"]["default"] += f" --alpb {config['solvent']}"
+            options["userOptions"]["command"]["default"] += (
+                f" --alpb {config['solvent']}"
+            )
         # Add method to default command but only if not the default (currently GFN2-xTB)
         if config["method"] != 2:
             options["userOptions"]["command"]["default"] += f" --gfn {config['method']}"