diff --git a/src/stko/_internal/calculators/orca_calculators.py b/src/stko/_internal/calculators/orca_calculators.py
index ef26d04..8155420 100644
--- a/src/stko/_internal/calculators/orca_calculators.py
+++ b/src/stko/_internal/calculators/orca_calculators.py
@@ -254,7 +254,7 @@ def _run_orca(  # noqa: PLR0913
                         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:
diff --git a/src/stko/_internal/calculators/xtb_calculators.py b/src/stko/_internal/calculators/xtb_calculators.py
index 0aa90d6..afbabe9 100644
--- a/src/stko/_internal/calculators/xtb_calculators.py
+++ b/src/stko/_internal/calculators/xtb_calculators.py
@@ -329,7 +329,7 @@ def _run_xtb(
                     stdout=f,
                     stderr=sp.PIPE,
                     # Shell is required to run complex arguments.
-                    shell=True,  # noqa: S602
+                    shell=True,
                 )
         finally:
             os.chdir(init_dir)
diff --git a/src/stko/_internal/optimizers/gulp.py b/src/stko/_internal/optimizers/gulp.py
index 4347ed0..d40497e 100644
--- a/src/stko/_internal/optimizers/gulp.py
+++ b/src/stko/_internal/optimizers/gulp.py
@@ -601,7 +601,7 @@ def _run_gulp(self, in_file: Path, out_file: Path) -> None:
                 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:
diff --git a/src/stko/_internal/optimizers/macromodel.py b/src/stko/_internal/optimizers/macromodel.py
index a313024..7d9fdc1 100644
--- a/src/stko/_internal/optimizers/macromodel.py
+++ b/src/stko/_internal/optimizers/macromodel.py
@@ -138,7 +138,7 @@ def _run_bmin(self, mol: stk.Molecule, run_name: str) -> None:
         incomplete = True
         while incomplete:
             process = sp.Popen(
-                opt_cmd,  # noqa: S603
+                opt_cmd,
                 stdout=sp.PIPE,
                 stderr=sp.STDOUT,
                 universal_newlines=True,
@@ -228,7 +228,7 @@ def _kill_bmin(self, run_name: str) -> None:
         incomplete = True
         while incomplete:
             out = sp.run(
-                cmd,  # noqa: S603
+                cmd,
                 stdout=sp.PIPE,
                 stderr=sp.STDOUT,
                 text=True,
@@ -249,7 +249,7 @@ def _kill_bmin(self, run_name: str) -> None:
         start = time.time()
         while name in output:
             output = sp.run(
-                cmd,  # noqa: S603
+                cmd,
                 stdout=sp.PIPE,
                 stderr=sp.STDOUT,
                 text=True,
@@ -345,7 +345,7 @@ def _run_structconvert(self, input_path: Path, output_path: Path) -> None:
             # Execute the file conversion.
             try:
                 convrt_return = sp.run(
-                    convrt_cmd,  # noqa: S603
+                    convrt_cmd,
                     stdout=sp.PIPE,
                     stderr=sp.STDOUT,
                     text=True,
diff --git a/src/stko/_internal/optimizers/xtb.py b/src/stko/_internal/optimizers/xtb.py
index 40ccd91..15e2653 100644
--- a/src/stko/_internal/optimizers/xtb.py
+++ b/src/stko/_internal/optimizers/xtb.py
@@ -382,7 +382,7 @@ def _run_xtb(self, xyz: str, out_file: Path | str) -> None:
                 stdout=f,
                 stderr=sp.PIPE,
                 # Shell is required to run complex arguments.
-                shell=True,  # noqa: S602
+                shell=True,
             )
 
     def _write_detailed_control(self) -> None:
@@ -810,7 +810,7 @@ def _run_crest(self, xyz: str, out_file: Path | str) -> None:
                 stdout=f,
                 stderr=sp.PIPE,
                 # Shell is required to run complex arguments.
-                shell=True,  # noqa: S602
+                shell=True,
             )
 
     def _run_optimization(
@@ -1056,7 +1056,7 @@ def _run_xtb(self, xyz: str, out_file: Path | str) -> None:
                 stdout=f,
                 stderr=sp.PIPE,
                 # Shell is required to run complex arguments.
-                shell=True,  # noqa: S602
+                shell=True,
             )
 
     def _run_optimization(
@@ -1398,7 +1398,7 @@ def _run_crest(self, xyz: Path, out_file: Path) -> None:
                 stdout=f,
                 stderr=sp.PIPE,
                 # Shell is required to run complex arguments.
-                shell=True,  # noqa: S602
+                shell=True,
             )
 
     def _run_optimization(