Fix lints

.github/workflows/tests.yml

@@ -15,7 +15,7 @@ jobs:
           python-version: "3.11"
           cache: "pip"
       - run: "pip install '.[dev]'"
-      - run: ruff .
+      - run: ruff check .
   mypy:
     runs-on: ubuntu-22.04
     steps:

pyproject.toml

@@ -10,7 +10,8 @@ maintainers = [
   { name = "Lukas Turcani", email = "[email protected]" },
 ]
 dependencies = [
-  "rdkit",
+  "numpy==1.26.4",  # remove pin when ecosystem updates to 2.0
+  "rdkit==2023.9.5",  # remove pin when type issues are resolved
   "stk",
   "networkx",
 ]

src/stko/_internal/calculators/extractors/utilities.py

@@ -17,7 +17,4 @@ def check_line(line: str, option: str, options_dict: dict[str, str]) -> bool:
         Returns ``True`` if the desired string is present.
 
     """
-    if options_dict[option] in line:
-        return True
-
-    return False
+    return options_dict[option] in line

src/stko/_internal/calculators/orca_calculators.py

@@ -248,13 +248,13 @@ def _run_orca(  # noqa: PLR0913
                 with out_file.open("w") as f:
                     # Note that sp.call will hold the program until
                     # completion of the calculation.
-                    sp.call(
+                    sp.call(  # noqa: S602
                         cmd,
                         stdin=sp.PIPE,
                         stdout=f,
                         stderr=sp.PIPE,
                         # Shell is required to run complex arguments.
-                        shell=True,  # noqa: S602
+                        shell=True,
                     )
                 self._check_outcome(out_file)
                 if self._discard_output:

src/stko/_internal/calculators/xtb_calculators.py

@@ -323,13 +323,13 @@ def _run_xtb(
             with out_file.open("w") as f:
                 # Note that sp.call will hold the program until
                 # completion of the calculation.
-                sp.call(
+                sp.call(  # noqa: S602
                     cmd,
                     stdin=sp.PIPE,
                     stdout=f,
                     stderr=sp.PIPE,
                     # Shell is required to run complex arguments.
-                    shell=True,  # noqa: S602
+                    shell=True,
                 )
         finally:
             os.chdir(init_dir)

src/stko/_internal/optimizers/collapser.py

@@ -661,10 +661,10 @@ def _output_top_lines(self) -> str:
 
     def _plot_progess(  # noqa: PLR0913
         self,
-        steps: abc.Iterable,
-        maxds: abc.Iterable,
-        spots: abc.Iterable,
-        npots: abc.Iterable,
+        steps: list,
+        maxds: list,
+        spots: list,
+        npots: list,
         output_dir: Path,
     ) -> None:
         fig, ax = plt.subplots(figsize=(8, 5))

src/stko/_internal/optimizers/gulp.py

@@ -5,6 +5,7 @@
 import shutil
 import subprocess as sp
 import uuid
+import warnings
 from pathlib import Path
 
 import stk
@@ -547,12 +548,15 @@ def assign_FF(self, mol: stk.Molecule) -> None:  # noqa: N802
                 The molecule to be optimized.
 
         """
-        FutureWarning(
-            "We have found some minor discrepancies in this "
-            "assignment algorithm, which is based off rdkit code. "
-            "Changes should come soon. This UFF optimisation should "
-            " not be your final step! Due to this, some tests in "
-            "test_uff_assign_ff.py have been muted."
+        warnings.warn(
+            FutureWarning(
+                "We have found some minor discrepancies in this "
+                "assignment algorithm, which is based off rdkit code. "
+                "Changes should come soon. This UFF optimisation should "
+                " not be your final step! Due to this, some tests in "
+                "test_uff_assign_ff.py have been muted."
+            ),
+            stacklevel=2,
         )
 
         metal_atoms = get_metal_atoms(mol)
@@ -595,13 +599,13 @@ def _run_gulp(self, in_file: Path, out_file: Path) -> None:
         with out_file.open("w") as f:
             # Note that sp.call will hold the program until completion
             # of the calculation.
-            sp.call(
+            sp.call(  # noqa: S602
                 cmd,
                 stdin=sp.PIPE,
                 stdout=f,
                 stderr=sp.PIPE,
                 # Shell is required to run complex arguments.
-                shell=True,  # noqa: S602
+                shell=True,
             )
 
     def extract_final_energy(self, out_file: Path) -> float:

src/stko/_internal/optimizers/macromodel.py

@@ -137,8 +137,8 @@ def _run_bmin(self, mol: stk.Molecule, run_name: str) -> None:
 
         incomplete = True
         while incomplete:
-            process = sp.Popen(
-                opt_cmd,  # noqa: S603
+            process = sp.Popen(  # noqa: S603
+                opt_cmd,
                 stdout=sp.PIPE,
                 stderr=sp.STDOUT,
                 universal_newlines=True,
@@ -227,8 +227,8 @@ def _kill_bmin(self, run_name: str) -> None:
 
         incomplete = True
         while incomplete:
-            out = sp.run(
-                cmd,  # noqa: S603
+            out = sp.run(  # noqa: S603
+                cmd,
                 stdout=sp.PIPE,
                 stderr=sp.STDOUT,
                 text=True,
@@ -248,8 +248,8 @@ def _kill_bmin(self, run_name: str) -> None:
         output = name
         start = time.time()
         while name in output:
-            output = sp.run(
-                cmd,  # noqa: S603
+            output = sp.run(  # noqa: S603
+                cmd,
                 stdout=sp.PIPE,
                 stderr=sp.STDOUT,
                 text=True,
@@ -303,10 +303,7 @@ def _license_found(
         with Path(f"{run_name}.log").open() as f:
             log_file = f.read()
 
-        if "Could not check out a license for mmlibs" in log_file:
-            return False
-
-        return True
+        return "Could not check out a license for mmlibs" not in log_file
 
     @staticmethod
     def _get_com_line(  # noqa: PLR0913
@@ -344,8 +341,8 @@ def _run_structconvert(self, input_path: Path, output_path: Path) -> None:
         while incomplete:
             # Execute the file conversion.
             try:
-                convrt_return = sp.run(
-                    convrt_cmd,  # noqa: S603
+                convrt_return = sp.run(  # noqa: S603
+                    convrt_cmd,
                     stdout=sp.PIPE,
                     stderr=sp.STDOUT,
                     text=True,

src/stko/_internal/optimizers/utilities.py

@@ -306,10 +306,7 @@ def has_h_atom(bond: stk.Bond) -> bool:
     """
     if bond.get_atom1().get_atomic_number() == 1:
         return True
-    if bond.get_atom2().get_atomic_number() == 1:
-        return True
-
-    return False
+    return bond.get_atom2().get_atomic_number() == 1
 
 
 def has_metal_atom(bond: stk.Bond, metal_atoms: list[stk.Atom]) -> bool:
@@ -328,10 +325,7 @@ def has_metal_atom(bond: stk.Bond, metal_atoms: list[stk.Atom]) -> bool:
     """
     if bond.get_atom1() in metal_atoms:
         return True
-    if bond.get_atom2() in metal_atoms:
-        return True
-
-    return False
+    return bond.get_atom2() in metal_atoms
 
 
 def metal_atomic_numbers() -> abc.Iterable:

src/stko/_internal/optimizers/xtb.py

@@ -376,13 +376,13 @@ def _run_xtb(self, xyz: str, out_file: Path | str) -> None:
         with out_file.open("w") as f:
             # Note that sp.call will hold the program until completion
             # of the calculation.
-            sp.call(
+            sp.call(  # noqa: S602
                 cmd,
                 stdin=sp.PIPE,
                 stdout=f,
                 stderr=sp.PIPE,
                 # Shell is required to run complex arguments.
-                shell=True,  # noqa: S602
+                shell=True,
             )
 
     def _write_detailed_control(self) -> None:
@@ -804,13 +804,13 @@ def _run_crest(self, xyz: str, out_file: Path | str) -> None:
         with out_file.open("w") as f:
             # Note that sp.call will hold the program until completion
             # of the calculation.
-            sp.call(
+            sp.call(  # noqa: S602
                 cmd,
                 stdin=sp.PIPE,
                 stdout=f,
                 stderr=sp.PIPE,
                 # Shell is required to run complex arguments.
-                shell=True,  # noqa: S602
+                shell=True,
             )
 
     def _run_optimization(
@@ -1050,13 +1050,13 @@ def _run_xtb(self, xyz: str, out_file: Path | str) -> None:
         with out_file.open("w") as f:
             # Note that sp.call will hold the program until completion
             # of the calculation.
-            sp.call(
+            sp.call(  # noqa: S602
                 cmd,
                 stdin=sp.PIPE,
                 stdout=f,
                 stderr=sp.PIPE,
                 # Shell is required to run complex arguments.
-                shell=True,  # noqa: S602
+                shell=True,
             )
 
     def _run_optimization(
@@ -1392,13 +1392,13 @@ def _run_crest(self, xyz: Path, out_file: Path) -> None:
         with out_file.open("w") as f:
             # Note that sp.call will hold the program until completion
             # of the calculation.
-            sp.call(
+            sp.call(  # noqa: S602
                 cmd,
                 stdin=sp.PIPE,
                 stdout=f,
                 stderr=sp.PIPE,
                 # Shell is required to run complex arguments.
-                shell=True,  # noqa: S602
+                shell=True,
             )
 
     def _run_optimization(