diff --git a/README.md b/README.md
index 57d6ad57..3b555bcb 100644
--- a/README.md
+++ b/README.md
@@ -33,9 +33,9 @@ Once you have `micromamba` installed and have already cloned this repo, you can
 
 ### Linux
 ```bash
-micromamba create -n qligfep_new python=3.11
+micromamba create -n qligfep_new python=3.14
 micromamba activate qligfep_new
-micromamba install gfortran=11.3.0 openff-toolkit=0.17.1 "openff-utilities>=0.1.12" openff-forcefields=2026.01.0 openmm=8.1.1 openff-nagl=0.5.4 openff-nagl-models=2025.9.0 lomap2 kartograf=1.0.1 michellab::fkcombu konnektor -c conda-forge --yes
+micromamba install gfortran=11.3.0 openff-toolkit=0.18.1 "openff-utilities>=0.1.12" openff-forcefields=2026.01.0 openmm=8.4.0 openff-nagl=0.5.5 openff-nagl-models=2025.9.0 lomap2 kartograf=1.0.1 michellab::fkcombu konnektor -c conda-forge --yes
 ```
 
 Now that you have the environment ready and activated, [clone the repository](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository), enter the `Q` directory with `cd Q/`, and install qligfep:
@@ -49,7 +49,7 @@ The `qprep` Fortran binary will be automatically compiled during installation.
 <summary>To install everything in one line...</summary>
 
 ```bash
-micromamba create -n qligfep_new python=3.11 gfortran=11.3.0 openff-toolkit=0.17.1 "openff-utilities>=0.1.12" openff-forcefields=2026.01.0 openmm=8.1.1 openff-nagl=0.5.4 openff-nagl-models=2025.9.0 lomap2 kartograf=1.0.1 michellab::fkcombu konnektor -c conda-forge --yes && micromamba activate qligfep_new && python -m pip install -e .
+micromamba create -n qligfep_new python=3.14 gfortran=11.3.0 openff-toolkit=0.18.1 "openff-utilities>=0.1.12" openff-forcefields=2026.01.0 openmm=8.4.0 openff-nagl=0.5.5 openff-nagl-models=2025.9.0 lomap2 kartograf=1.0.1 michellab::fkcombu konnektor -c conda-forge --yes && micromamba activate qligfep_new && python -m pip install -e .
 ```
 </details>
 
@@ -58,7 +58,7 @@ micromamba create -n qligfep_new python=3.11 gfortran=11.3.0 openff-toolkit=0.17
 Similar to Linux, [clone the repository](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository), enter the `Q` directory with `cd Q/`, create the environment and install:
 
 ``` bash
-micromamba create -n qligfep_new python=3.11 gfortran=11.3.0 openff-toolkit=0.17.1 "openff-utilities>=0.1.12" openff-forcefields=2026.01.0 openmm=8.1.1 openff-nagl=0.5.4 openff-nagl-models=2025.9.0 lomap2 kartograf=1.0.1 davidararipe::kcombu_bss konnektor -c conda-forge --yes
+micromamba create -n qligfep_new python=3.14 gfortran=11.3.0 openff-toolkit=0.18.1 "openff-utilities>=0.1.12" openff-forcefields=2026.01.0 openmm=8.4.0 openff-nagl=0.5.5 openff-nagl-models=2025.9.0 lomap2 kartograf=1.0.1 davidararipe::kcombu_bss konnektor -c conda-forge --yes
 micromamba activate qligfep_new
 python -m pip install joblib scipy tqdm
 python -m pip install -e .
@@ -70,7 +70,7 @@ The `qprep` Fortran binary will be automatically compiled during installation.
 <summary>To install everything in one line...</summary>
 
 ```bash
-micromamba create -n qligfep_new python=3.11 gfortran=11.3.0 openff-toolkit=0.17.1 "openff-utilities>=0.1.12" openff-forcefields=2026.01.0 openmm=8.1.1 openff-nagl=0.5.4 openff-nagl-models=2025.9.0 lomap2 kartograf=1.0.1 davidararipe::kcombu_bss konnektor -c conda-forge --yes && micromamba activate qligfep_new && python -m pip install joblib scipy tqdm && python -m pip install -e .
+micromamba create -n qligfep_new python=3.14 gfortran=11.3.0 openff-toolkit=0.18.1 "openff-utilities>=0.1.12" openff-forcefields=2026.01.0 openmm=8.4.0 openff-nagl=0.5.5 openff-nagl-models=2025.9.0 lomap2 kartograf=1.0.1 davidararipe::kcombu_bss konnektor -c conda-forge --yes && micromamba activate qligfep_new && python -m pip install joblib scipy tqdm && python -m pip install -e .
 ```
 </details>
 
diff --git a/pyproject.toml b/pyproject.toml
index 9f6df315..126abc9d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,7 +7,7 @@ name = "QligFEP"
 dynamic = ["version"]
 description = "Python CLI designed to facilitate a robust and fast setup of free energy perturbation (FEP)."
 readme = { file = "README.md", content-type = "text/markdown" }
-requires-python = ">=3.10"
+requires-python = ">=3.14"
 license = { file = "LICENSE" }
 # keywords = [""]
 authors = [{ name = "Willem Jespers", email = "w.jespers@rug.nl" },
@@ -24,7 +24,7 @@ classifiers = [
     "Intended Audience :: Science/Research",
     "Topic :: Scientific/Engineering :: Chemistry",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.10" # todo: might have other versions
+    "Programming Language :: Python :: 3.14" # todo: might have other versions
 ]
 dependencies = [
     "joblib",
@@ -69,15 +69,16 @@ repository = "https://github.com/qusers/qligfep"
 
 [tool.black]
 line-length =  110
-target-version = ['py310']
+target-version = ['py314']
 
 [tool.isort]
 profile = "black"
+line_length = 110
 
 [tool.ruff]
 line-length = 110
 indent-width = 4
-target-version = 'py39'
+target-version = 'py314'
 
 [tool.ruff.lint]
 select = [
diff --git a/src/QligFEP/CLI/cog_cli.py b/src/QligFEP/CLI/cog_cli.py
index 89d61d9b..7eb7a734 100644
--- a/src/QligFEP/CLI/cog_cli.py
+++ b/src/QligFEP/CLI/cog_cli.py
@@ -65,7 +65,7 @@ def _cog_sdf(self):
             for i, center in enumerate(centers):
                 logger.debug(f"Ligand {i+1} center: {center}")
 
-        overall_center = [sum(x) / len(centers) for x in zip(*centers)]
+        overall_center = [sum(x) / len(centers) for x in zip(*centers, strict=False)]
         return f"[{round(overall_center[0], 3):.3f} {round(overall_center[1], 3):.3f} {round(overall_center[2], 3):.3f}]"
 
     def _calculate_center(self, coordinates):
diff --git a/src/QligFEP/CLI/konnektor_cli.py b/src/QligFEP/CLI/konnektor_cli.py
index 7468ee68..92f8ed97 100644
--- a/src/QligFEP/CLI/konnektor_cli.py
+++ b/src/QligFEP/CLI/konnektor_cli.py
@@ -3,7 +3,6 @@
 import argparse
 import json
 from pathlib import Path
-from typing import Optional
 
 import numpy as np
 from kartograf import KartografAtomMapper, SmallMoleculeComponent
@@ -34,18 +33,18 @@ class KonnektorWrap:
     def __init__(
         self,
         inp: str,
-        out: Optional[str] = None,
+        out: str | None = None,
         network: str = "mst",
         scorer: str = "combined",
         restraint_method: str = "heavyatom_p",
         processes: int = 1,
         log_level: str = "info",
-        central_ligand: Optional[str] = None,
+        central_ligand: str | None = None,
         n_redundancy: int = 2,
         connectivity: int = 3,
         separate_charges: bool = False,
         charge_changes_score: float = 0.0,
-        exp_key: Optional[str] = None,
+        exp_key: str | None = None,
         self_solve: bool = False,
     ):
         self.inp = inp
@@ -66,7 +65,7 @@ def __init__(
         self.out = self._parse_output(out)
         self._sdf_dir = self._prepare_input()
 
-    def _parse_output(self, output: Optional[str]) -> str:
+    def _parse_output(self, output: str | None) -> str:
         inpath = Path(self.inp)
         if output is None:
             if inpath.is_dir():
@@ -310,7 +309,7 @@ def run(self) -> dict:
 
         return result
 
-    def _resolve_sdf_path(self) -> Optional[Path]:
+    def _resolve_sdf_path(self) -> Path | None:
         """Find the SDF file used as input."""
         inp = Path(self.inp)
         if inp.is_file() and inp.suffix == ".sdf":
@@ -354,7 +353,7 @@ def _mcs_rmsd(mol_a, mol_b, timeout=5):
     conf_a = ha.GetConformer()
     conf_b = hb.GetConformer()
     sq_dists = []
-    for ia, ib in zip(match_a, match_b):
+    for ia, ib in zip(match_a, match_b, strict=False):
         pa = conf_a.GetAtomPosition(ia)
         pb = conf_b.GetAtomPosition(ib)
         sq_dists.append((pa.x - pb.x) ** 2 + (pa.y - pb.y) ** 2 + (pa.z - pb.z) ** 2)
@@ -423,7 +422,7 @@ def _realign_to_neighbors(outlier_mol, neighbor_mols):
             continue
         conf_n = hn.GetConformer()
         o_to_core = {oa: i for i, oa in enumerate(match_o)}
-        for oa, na in zip(match_o_nb, match_n_nb):
+        for oa, na in zip(match_o_nb, match_n_nb, strict=False):
             if oa in o_to_core:
                 p = conf_n.GetAtomPosition(na)
                 core_positions.setdefault(o_to_core[oa], []).append(
diff --git a/src/QligFEP/CLI/lomap_wrap_cli.py b/src/QligFEP/CLI/lomap_wrap_cli.py
index 5fac38ff..a61a6e19 100644
--- a/src/QligFEP/CLI/lomap_wrap_cli.py
+++ b/src/QligFEP/CLI/lomap_wrap_cli.py
@@ -5,7 +5,6 @@
 import re
 from multiprocessing import cpu_count
 from pathlib import Path
-from typing import Optional
 
 import lomap
 import numpy as np
@@ -22,10 +21,10 @@ class LomapWrap:
     def __init__(
         self,
         inp: str,
-        out: Optional[str] = None,
+        out: str | None = None,
         time=30,
         verbose="info",
-        exp_key: Optional[str] = None,
+        exp_key: str | None = None,
         **kwargs,
     ):
         self.nodes = {}
diff --git a/src/QligFEP/CLI/qligfep_cli.py b/src/QligFEP/CLI/qligfep_cli.py
index 9d67edd8..03408dc3 100644
--- a/src/QligFEP/CLI/qligfep_cli.py
+++ b/src/QligFEP/CLI/qligfep_cli.py
@@ -4,7 +4,6 @@
 import datetime
 import json
 from pathlib import Path
-from typing import Optional
 
 from QligFEP import __version__
 
@@ -15,7 +14,7 @@
 from .parser_base import parse_arguments
 
 
-def main(args: Optional[argparse.Namespace] = None, **kwargs) -> None:
+def main(args: argparse.Namespace | None = None, **kwargs) -> None:
     """Main function for qligfep_cli.py. Takes arguments from argparse and passes them
     to QligFEP class. If no arguments are given, the function will use the keyword arguments
     that are passed to it.
diff --git a/src/QligFEP/CLI/setupFEP.py b/src/QligFEP/CLI/setupFEP.py
index f634b76b..3f422326 100644
--- a/src/QligFEP/CLI/setupFEP.py
+++ b/src/QligFEP/CLI/setupFEP.py
@@ -7,7 +7,6 @@
 import shutil
 import subprocess
 from pathlib import Path
-from typing import Optional
 
 from ..IO import parse_qprep_total_charge
 from ..logger import logger, setup_logger
@@ -76,7 +75,7 @@ def submit_command(command: str) -> None:
         raise
 
 
-def main(args: Optional[argparse.Namespace] = None, **kwargs) -> None:
+def main(args: argparse.Namespace | None = None, **kwargs) -> None:
     # setup the logger with the desired log level
     setup_logger(level=args.log)
 
@@ -113,7 +112,7 @@ def main(args: Optional[argparse.Namespace] = None, **kwargs) -> None:
 
     lig_pairs = ligpairs_from_json(args.json_map)
     protein_dir = cwd / "2.protein"
-    for system, sys_dir in zip(systems, sys_directories):
+    for system, sys_dir in zip(systems, sys_directories, strict=False):
         for lig1, lig2, same_charge in lig_pairs:
 
             # For cross-charge water edges, look up the protein leg's total charge
diff --git a/src/QligFEP/IO.py b/src/QligFEP/IO.py
index 6f409e4e..1e11a3fd 100644
--- a/src/QligFEP/IO.py
+++ b/src/QligFEP/IO.py
@@ -4,7 +4,7 @@
 import stat
 import subprocess
 from pathlib import Path
-from typing import NamedTuple, Optional
+from typing import NamedTuple
 
 import numpy as np
 import pandas as pd
@@ -34,8 +34,8 @@ class SlurmRunInfo(NamedTuple):
     """Per-replicate run metadata parsed from one ``slurm*.out`` footer."""
 
     runtime: str
-    seed: Optional[str]
-    replicate: Optional[str]
+    seed: str | None
+    replicate: str | None
     status: str
 
 
diff --git a/src/QligFEP/README.md b/src/QligFEP/README.md
deleted file mode 100644
index 620419c3..00000000
--- a/src/QligFEP/README.md
+++ /dev/null
@@ -1,66 +0,0 @@
-# QligFEP v2.0 and QresFEP v1.0
-
-This collection of python command line functions is designed with the
-aim to facilitate a robust and fast setup of FEP calculations for the
-software package **Q**. These modules use python 3, python 2 is no 
-longer supported, and an old version of the code using python 2
-is now only available in the python2 branch.
-
-This package includes at the moment two main modules:  
-- QligFEP.py: module to generate ligand FEP calculations using a
-dual topology approach, 
-see Jespers et al. (https://doi.org/10.1186/s13321-019-0348-5).  
-
-- QresFEP.py: module to generate protein FEP calculations using a
-single topology approach, 
-see Jespers et al. (https://doi.org/10.1021/acs.jctc.9b00538). 
-
-Future versions will include QLIE, dual topology QresFEP and several
-translation tools for new forcefields (at the moment we support opls,
-charmm,amber and openFF).
-
-A few toplevel scripts are included in the scripts folder to facilitate
-high throughput setup. Additionally, a tutorials folder is included
-with a detailed description of the setup procedure as published in
-Jespers et al. (QresFEP/QligFEP). This tutorial includes the generation
-of ligand parameters using OPLS, how to prepare a protein system, and
-how to run ligand and protein FEP calculations. These examples are 
-based on ligand binding of CDk2 inhibitors.
-
-# Installing QligFEP and QresFEP  
-
-- Install a working version of Q, e.g.:  
-
-    <https://github.com/esguerra/Q6>  
-
-  
-- Clone this repository:  
-
-    git clone https://github.com/qusers/qligfep.git
-
-- Create the shipped conda environment
-
-    conda env create -f environment.yml
-
-In settings.py:  
-
-- Change SCHROD_DIR to the Schrodinger location, if you want to be
-able to generate OPLS ligand parameters using ffld_server.  
-
-- Change Q_DIR to the location of the q executables. This can be
-particularly useful if you use setupFEP from a local machine on
-a mounted directory. (In which case, the executables of the preparation
-part and running part of Q are at several places).  
-
-- You can add slurm specific parameters in the CLUSTER INPUTS section,
-according to the given example.   
-
-## Requirements  
-- ffld_server  
-- cgenff  
-- Protein Preparation Wizard  
-- Python3.10  
-- Q  
-
-contact: [Willem Jespers (PhD)](mailto:w.jespers@lacdr.leidenuniv.nl?subject=[QLigFEP]%20[QResFEP])
-
diff --git a/src/QligFEP/analysis_plotting.py b/src/QligFEP/analysis_plotting.py
index 6a651972..c3f39965 100644
--- a/src/QligFEP/analysis_plotting.py
+++ b/src/QligFEP/analysis_plotting.py
@@ -238,7 +238,7 @@ def result_to_latex(res, latexify_each=False):  # TODO: move this out of this me
         (1.04, hori_height - spacing),
         (1.04, hori_height - spacing * 2),
     )
-    for txt_position, body in zip(txt_positions, text_body):
+    for txt_position, body in zip(txt_positions, text_body, strict=False):
         plt.text(
             *txt_position,
             body,
diff --git a/src/QligFEP/analyze_FEP.py b/src/QligFEP/analyze_FEP.py
index 1deda388..fbca5175 100644
--- a/src/QligFEP/analyze_FEP.py
+++ b/src/QligFEP/analyze_FEP.py
@@ -4,7 +4,6 @@
 import json
 import os
 from pathlib import Path
-from typing import Optional
 
 import numpy as np
 import pandas as pd
@@ -31,7 +30,7 @@ def __init__(
         system: str,
         target_name: str,
         mapping_json: str,
-        n_lambdas: Optional[int] = None,
+        n_lambdas: int | None = None,
         allow_missing_edges: bool = False,
     ) -> None:
         """Initialize the FEP reader class. This class will store the FEP information inside
diff --git a/src/QligFEP/analyze_neq.py b/src/QligFEP/analyze_neq.py
index f95575aa..8e584103 100644
--- a/src/QligFEP/analyze_neq.py
+++ b/src/QligFEP/analyze_neq.py
@@ -26,7 +26,6 @@
 import os
 from collections import defaultdict
 from pathlib import Path
-from typing import Optional
 
 import numpy as np
 import pandas as pd
@@ -75,7 +74,7 @@ def dF_to_kcal(dF: float, work_units: str, temperature: float) -> float:
 WORK_TAIL_BYTES = 256 * 1024
 
 
-def read_final_work(log_path: str) -> Optional[float]:
+def read_final_work(log_path: str) -> float | None:
     """Read the final accumulated switching work from a qdyn NEQ-mode log.
 
     Each switch prints ``At step N, work accumulated was <W> ...`` every output interval;
@@ -101,7 +100,7 @@ def read_final_work(log_path: str) -> Optional[float]:
         if "work accumulated" in line:
             try:
                 return float(line.split()[6])
-            except (IndexError, ValueError):
+            except IndexError, ValueError:
                 logger.warning(f"Could not parse the work value in {log_path}")
                 return None
     return None
@@ -264,7 +263,7 @@ def _dF_by_rep_from_works(by_rep: dict, beta: float, work_units: str, temperatur
             continue
         try:
             result[rep] = dF_to_kcal(bar_delta_f(forward, reverse, beta), work_units, temperature)
-        except (ValueError, RuntimeError):
+        except ValueError, RuntimeError:
             result[rep] = None
     return result
 
@@ -573,7 +572,7 @@ def populate_mapping_json(df: pd.DataFrame, mapping_json: str, output_file: str)
     logger.info(f"Injected NEQ ddG into {matched} edge(s); wrote {output_file}")
 
 
-def _nan_to_none(value) -> Optional[float]:
+def _nan_to_none(value) -> float | None:
     """Return ``None`` for a missing/NaN value (so it serializes to JSON null), else a float."""
     return None if pd.isna(value) else float(value)
 
diff --git a/src/QligFEP/chemIO.py b/src/QligFEP/chemIO.py
index 8b0c4e7d..81ae388b 100644
--- a/src/QligFEP/chemIO.py
+++ b/src/QligFEP/chemIO.py
@@ -1,7 +1,7 @@
 from io import StringIO
 from itertools import product
 from pathlib import Path
-from typing import Generator, Optional, Union  # noqa: UP035
+from typing import Generator  # noqa: UP035
 
 import pandas as pd
 import py3Dmol
@@ -55,7 +55,7 @@ def __init__(self, lig, pattern: str = "*.sdf", reindex_hydrogens: bool = True):
         self.setup_mols_and_names(self.lig, pattern)
         self.parse_sdf_contents()  # add the sdf content to the dictionary
 
-    def __getitem__(self, name: str) -> Optional[Molecule]:
+    def __getitem__(self, name: str) -> Molecule | None:
         """Retrieve a molecule by its name.
 
         Args:
@@ -71,12 +71,12 @@ def __getitem__(self, name: str) -> Optional[Molecule]:
             logger.warning(f"Molecule with name {name} not found.")
             return None
 
-    def __iter__(self) -> Generator[tuple[str, Molecule], None, None]:
+    def __iter__(self) -> Generator[tuple[str, Molecule]]:
         """Iterate over the names and the Molecule objects"""
-        yield from zip(self.lig_names, self.molecules)
+        yield from zip(self.lig_names, self.molecules, strict=False)
 
     def display_overlay(
-        self, *ligands: Union[str, Chem.Mol, Molecule], size=(800, 600), render=False
+        self, *ligands: str | Chem.Mol | Molecule, size=(800, 600), render=False
     ) -> py3Dmol.view:
         """Display the overlay of the ligands using py3Dmol.
 
@@ -138,7 +138,7 @@ def _rdkit_to_openff(self, rdkit_mol: Chem.Mol, hydrogens_are_explicit: bool) ->
                 rdkit_mol, hydrogens_are_explicit=hydrogens_are_explicit, allow_undefined_stereo=True
             )
 
-    def _parse_mol(self, ligpath: Union[Path, str]) -> tuple[list[Molecule], list[str]]:
+    def _parse_mol(self, ligpath: Path | str) -> tuple[list[Molecule], list[str]]:
         """Parse a .sdf file into a list of Molecule objects and their names.
 
         Loads via RDKit first to inspect the original hydrogen state, then converts
@@ -193,7 +193,7 @@ def _parse_mol(self, ligpath: Union[Path, str]) -> tuple[list[Molecule], list[st
 
         if self._reindex_hydrogens:
             mols = [self._force_H_reindexing(mol) for mol in mols]
-        for mol, name in zip(mols, lig_names):
+        for mol, name in zip(mols, lig_names, strict=False):
             mol.name = name
         return mols, lig_names
 
@@ -246,7 +246,7 @@ def parse_sdf_contents(self):
             mol.to_file(string_buffer, file_format="sdf")
             self.sdf_contents.update({name: string_buffer.getvalue().splitlines()})
 
-    def write_sdf_separate(self, output_dir, molecules: Optional[list[Molecule]] = None) -> None:
+    def write_sdf_separate(self, output_dir, molecules: list[Molecule] | None = None) -> None:
         """Function to write the separate multiple molecules within a sdf file into their own
         .sdf, placed under `output_dir`.
 
@@ -273,7 +273,7 @@ def write_sdf_separate(self, output_dir, molecules: Optional[list[Molecule]] = N
             for mol in molecules:
                 mol.to_file(file_path=f"{mol.name}.sdf", file_format="sdf")
 
-    def write_to_single_sdf(self, output_name: str, molecules: Optional[list[Molecule]] = None) -> None:
+    def write_to_single_sdf(self, output_name: str, molecules: list[Molecule] | None = None) -> None:
         """Writes all `self.molecules` to a single `.sdf` file.
 
         Args:
@@ -304,7 +304,7 @@ def write_to_single_pdb(self, output_name: str, init_offset: int = 0) -> pd.Data
         lig_resn = ["LI", "LG", "LH"]
         last_lig_resn = [d for d in "ABCDEFGHIJKLMNOPQRSTUVWXYZ"]
         lig_resnames = ["".join(i) for i in product(lig_resn, last_lig_resn)]
-        for mol, resn in zip(self.molecules, lig_resnames):
+        for mol, resn in zip(self.molecules, lig_resnames, strict=False):
             # write the molecule pdb lines in memory and convert them to pd.DataFrame
             output = StringIO()
             mol.to_file(output, file_format="pdb")
diff --git a/src/QligFEP/conformer_generator.py b/src/QligFEP/conformer_generator.py
index 7bc50eda..7c8781ae 100644
--- a/src/QligFEP/conformer_generator.py
+++ b/src/QligFEP/conformer_generator.py
@@ -8,7 +8,6 @@
 """
 
 from pathlib import Path
-from typing import Union
 
 from rdkit import Chem
 from rdkit.Chem import AllChem, rdFMCS
@@ -38,7 +37,7 @@ class BiasedConformerGenerator(MoleculeIO):
 
     def __init__(
         self,
-        references: Union[str, Path, MoleculeIO],
+        references: str | Path | MoleculeIO,
         reindex_hydrogens: bool = True,
         mcs_atom_compare: str = "any",
         mcs_bond_compare: str = "any",
diff --git a/src/QligFEP/lig_aligner.py b/src/QligFEP/lig_aligner.py
index b2e1821b..0c66a9a9 100644
--- a/src/QligFEP/lig_aligner.py
+++ b/src/QligFEP/lig_aligner.py
@@ -5,7 +5,7 @@
 from concurrent.futures import ThreadPoolExecutor, as_completed
 from functools import partial
 from pathlib import Path
-from typing import Any, Optional, Union
+from typing import Any
 
 from openff.toolkit import Molecule
 from rdkit import Chem
@@ -45,12 +45,12 @@ def __init__(
         pattern: str = f"*{SDF_EXTENSION}",
         reindex_hydrogens: bool = True,
         n_threads: int = 1,
-        protein: Optional[str] = None,
+        protein: str | None = None,
         energy: str = "a",
         search: str = "f",
         steep_descend: bool = True,
         connectivity: str = "t",
-        top_constraint_tol: Optional[int] = None,
+        top_constraint_tol: int | None = None,
         atom_type: str = "X",
         bond_type: str = "X",
         scaffold_lock: bool = False,
@@ -114,10 +114,10 @@ def __init__(
         super().__init__(lig, pattern=pattern, reindex_hydrogens=reindex_hydrogens)
         self.kcombu_exe = self._set_fkcombu_exe()
         self.n_threads = n_threads
-        self.reference_mol: Optional[Molecule] = None
+        self.reference_mol: Molecule | None = None
         self.aligned_molecules: dict[str, Molecule] = {}
         self.alignment_scores: dict[str, dict[str, float]] = {}
-        self.temp_dir: Optional[tempfile.TemporaryDirectory] = None
+        self.temp_dir: tempfile.TemporaryDirectory | None = None
         self.fkparams = self._process_fkparams(
             {
                 "P": protein,
@@ -373,10 +373,10 @@ def _transfer_charges_metadata(molA, molB):
         matchB = molB.GetSubstructMatch(mcs_mol)
 
         logger.trace("Mapping of atoms:")
-        for a, b in zip(matchA, matchB):  # trace the mapping; used for debugging
+        for a, b in zip(matchA, matchB, strict=False):  # trace the mapping; used for debugging
             logger.trace(f"MolA atom {a} maps to MolB atom {b}")
 
-        for a, b in zip(matchA, matchB):  # iterate atoms and transfer charges
+        for a, b in zip(matchA, matchB, strict=False):  # iterate atoms and transfer charges
             atomA = molA.GetAtomWithIdx(a)
             atomB = molB.GetAtomWithIdx(b)
             formal_charge = atomA.GetFormalCharge()
@@ -403,7 +403,7 @@ def _transfer_sdf_metadata(self, original_file: Path, aligned_file: Path):
         aligned_supplier = Chem.SDMolSupplier(str(aligned_file), removeHs=True, sanitize=False)
 
         aligned_mols = []
-        for original_mol, aligned_mol in zip(original_supplier, aligned_supplier):
+        for original_mol, aligned_mol in zip(original_supplier, aligned_supplier, strict=False):
             if original_mol is not None and aligned_mol is not None:
                 Chem.SanitizeMol(aligned_mol, sanitizeOps=Chem.SanitizeFlags.SANITIZE_SETAROMATICITY)
 
@@ -423,7 +423,7 @@ def _transfer_sdf_metadata(self, original_file: Path, aligned_file: Path):
         aligned_writer.close()
 
     def align_single_molecule(
-        self, molecule: Union[str, Molecule], reference: Union[str, Molecule]
+        self, molecule: str | Molecule, reference: str | Molecule
     ) -> tuple[Molecule, dict[str, float]]:
         """
         Align a single molecule to a reference molecule.
@@ -464,7 +464,7 @@ def align_single_molecule(
         return aligned_molecule, scores
 
     def kcombu_align(
-        self, reference: Union[str, Molecule], molecules_to_align: Optional[list[Union[str, Molecule]]] = None
+        self, reference: str | Molecule, molecules_to_align: list[str | Molecule] | None = None
     ) -> list[Molecule]:
         """
         Aligns the specified molecules to a reference molecule using kcombu. The aligned molecules returned
@@ -531,9 +531,7 @@ def kcombu_align(
         self.cleanup()
         return aligned_ligands
 
-    def output_aligned_ligands(
-        self, output_name: str, ref_names: Optional[Union[str, list[str]]] = None
-    ) -> None:
+    def output_aligned_ligands(self, output_name: str, ref_names: str | list[str] | None = None) -> None:
         """
         Write the aligned molecules to a single .sdf file, optionally including the original reference ligand(s).
 
@@ -575,7 +573,7 @@ def output_aligned_ligands(
             self.temp_dir.cleanup()
             logger.info("Temporary directory cleaned up")
 
-    def get_molecule(self, name: str, aligned: bool = True) -> Optional[Molecule]:
+    def get_molecule(self, name: str, aligned: bool = True) -> Molecule | None:
         """
         Retrieve a molecule by name, either aligned or original.
 
@@ -642,11 +640,11 @@ def __init__(
         self.opt_param = opt_param
         self.max_preiters = max_preiters
         self.max_postiters = max_postiters
-        self.reference_mol: Optional[Molecule] = None
+        self.reference_mol: Molecule | None = None
         self.aligned_molecules: dict[str, Molecule] = {}
         self.alignment_scores: dict[str, tuple[float, float]] = {}
 
-    def _resolve_molecule(self, mol_or_name: Union[str, Molecule]) -> Molecule:
+    def _resolve_molecule(self, mol_or_name: str | Molecule) -> Molecule:
         """Resolve a molecule from a name string or return the Molecule directly.
 
         Args:
@@ -687,7 +685,7 @@ def _align_rdkit_mol(self, ref_rdkit: Chem.Mol, probe_rdkit: Chem.Mol) -> tuple[
         return shape_tani, color_tani
 
     def align_single_molecule(
-        self, molecule: Union[str, Molecule], reference: Union[str, Molecule]
+        self, molecule: str | Molecule, reference: str | Molecule
     ) -> tuple[Molecule, float, float]:
         """Align a single molecule to a reference molecule.
 
@@ -712,7 +710,7 @@ def align_single_molecule(
         return aligned_mol, shape_tani, color_tani
 
     def align(
-        self, reference: Union[str, Molecule], molecules_to_align: Optional[list[Union[str, Molecule]]] = None
+        self, reference: str | Molecule, molecules_to_align: list[str | Molecule] | None = None
     ) -> dict[str, Molecule]:
         """Align molecules to a reference using shape+color overlap.
 
@@ -766,9 +764,7 @@ def align(
 
         return self.aligned_molecules
 
-    def output_aligned_ligands(
-        self, output_name: str, ref_names: Optional[Union[str, list[str]]] = None
-    ) -> None:
+    def output_aligned_ligands(self, output_name: str, ref_names: str | list[str] | None = None) -> None:
         """Write aligned molecules to a single SDF file, including alignment scores as SD properties.
 
         Args:
@@ -803,7 +799,7 @@ def output_aligned_ligands(
         writer.close()
         logger.info(f"Aligned molecules written to {output_name}")
 
-    def get_molecule(self, name: str, aligned: bool = True) -> Optional[Molecule]:
+    def get_molecule(self, name: str, aligned: bool = True) -> Molecule | None:
         """Retrieve a molecule by name, either aligned or original.
 
         Args:
diff --git a/src/QligFEP/openff2Q.py b/src/QligFEP/openff2Q.py
index b7d8f453..8779b7d5 100644
--- a/src/QligFEP/openff2Q.py
+++ b/src/QligFEP/openff2Q.py
@@ -2,7 +2,7 @@
 
 from io import StringIO
 from pathlib import Path
-from typing import Optional, TextIO
+from typing import TextIO
 
 import numpy as np
 from joblib import Parallel, delayed, parallel_config
@@ -104,7 +104,7 @@ def __init__(
         self.total_charges = {}  # store the total charges
         self._set_nagl(nagl=nagl, nagl_model=nagl_model)
 
-    def _set_forcefield(self, ffstring: Optional[str]) -> ForceField:
+    def _set_forcefield(self, ffstring: str | None) -> ForceField:
         if ffstring is None:
             # why not the constrained: https://docs.openforcefield.org/projects/toolkit/en/stable/faq.html
             ffstring = "openff-2.3.0.offxml"
@@ -148,7 +148,7 @@ def _assign_charge(self, molecule: Molecule) -> np.ndarray:
     def set_topologies_and_parameters(self):
         topologies = {}
         parameters = {}
-        for lname, mol in zip(self.lig_names, self.molecules):
+        for lname, mol in zip(self.lig_names, self.molecules, strict=False):
             topology = Topology.from_molecules(mol)
             topologies.update({lname: topology})
             parameters.update({lname: self.forcefield.label_molecules(topology)[0]})
@@ -163,7 +163,7 @@ def process_ligands(self) -> None:
             charges_magnitudes = Parallel()(delayed(self._assign_charge)(molecule) for molecule in molecules)
         logger.info("Done! Writing .lib, .prm and .pdb files for each ligand")
         logger.debug(f"Output path: {self.out_dir}")
-        for lname, charges in zip(self.lig_names, charges_magnitudes):
+        for lname, charges in zip(self.lig_names, charges_magnitudes, strict=False):
             charges = round_charges_preserving_sum(charges)
             self.charges_list_magnitude.update({lname: charges})
             formatted_sum = f"{charges.sum():.3f}"
@@ -243,8 +243,8 @@ def create_atom_prm_mapping(self, lname):
     def write_lib_Q(
         self,
         lname: str,
-        outfile: Optional[TextIO] = None,
-        prefix: Optional[str] = None,
+        outfile: TextIO | None = None,
+        prefix: str | None = None,
         residue_name: str = "LIG",
     ):
         """Writes Q's .lib file for a given ligand.
@@ -302,7 +302,7 @@ def write_lib_Q(
             if should_close:
                 outfile.close()
 
-    def write_prm_Q(self, lname: str, outfile: Optional[TextIO] = None, prefix: Optional[str] = None):
+    def write_prm_Q(self, lname: str, outfile: TextIO | None = None, prefix: str | None = None):
         """Writes Q's .prm file for a given ligand.
 
         Args:
@@ -316,7 +316,7 @@ def write_prm_Q(self, lname: str, outfile: Optional[TextIO] = None, prefix: Opti
                 Defaults to "LIG".
         """
 
-        def insert_prefix(at_name, prefix: Optional[str]):
+        def insert_prefix(at_name, prefix: str | None):
             if prefix is not None:
                 return prefix + at_name
             return at_name
@@ -442,7 +442,7 @@ def insert_prefix(at_name, prefix: Optional[str]):
             if should_close:
                 outfile.close()
 
-    def write_PDB(self, lname: str, outfile: Optional[TextIO] = None, residue_name: str = "LIG"):
+    def write_PDB(self, lname: str, outfile: TextIO | None = None, residue_name: str = "LIG"):
         """Writes pdb file for a given ligand.
 
         Args:
@@ -514,7 +514,7 @@ def write_cofactor_plus_ff_files(self, ff: str):
             )
 
         lig_prm_contents = {}
-        for name, prefix, res in zip(self.lig_names, prefixes, residues):
+        for name, prefix, res in zip(self.lig_names, prefixes, residues, strict=False):
             lib_out = StringIO()
             self.write_lib_Q(name, outfile=lib_out, prefix=prefix, residue_name=res)
             lib_lines = lib_out.getvalue().split("\n")
diff --git a/src/QligFEP/pdb_utils.py b/src/QligFEP/pdb_utils.py
index 7cb227fe..3c50a981 100644
--- a/src/QligFEP/pdb_utils.py
+++ b/src/QligFEP/pdb_utils.py
@@ -5,7 +5,6 @@
 import warnings
 from pathlib import Path
 from string import ascii_uppercase
-from typing import Optional, Union
 
 import MDAnalysis as mda
 import numpy as np
@@ -21,10 +20,10 @@ def rm_HOH_clash_NN(
     pdb_df_query: pd.DataFrame,
     pdb_df_target: pd.DataFrame,
     th: float = 2.5,
-    output_file: Union[str, Path] = None,
+    output_file: str | Path = None,
     heavy_only: bool = True,
     ligand_only: bool = False,
-    header: Optional[str] = None,
+    header: str | None = None,
     save_removed: bool = False,
 ):
     """Use a NearestNeighbors approach to find water molecules within a distance threshold
@@ -189,11 +188,11 @@ def next_chain_id(existing_ids):
 
 
 def append_pdb_to_another(
-    main_pdb: Union[pd.DataFrame, str, list[str]],
-    to_append_pdb: Union[pd.DataFrame, str, list[str]],
-    save_pdb: Optional[str] = None,
+    main_pdb: pd.DataFrame | str | list[str],
+    to_append_pdb: pd.DataFrame | str | list[str],
+    save_pdb: str | None = None,
     assign_new_chain: bool = False,
-    new_ligname: Optional[str] = None,
+    new_ligname: str | None = None,
     ignore_waters: bool = False,
 ) -> pd.DataFrame:
     """Reads the two pdbs as DataFrames, appends the second to the end of the protein
@@ -370,7 +369,9 @@ def disulfide_search(npdb, min_dist=1.8, max_dist_cyx=4.0, max_dist_cys=2.5):
     # Find disulfide pairs with appropriate distance cutoffs
     for ii, res_i in enumerate(cys_residues):
         for res_j in cys_residues[ii + 1 :]:
-            distance = math.sqrt(sum((a - b) ** 2 for a, b in zip(res_i["coords"], res_j["coords"])))
+            distance = math.sqrt(
+                sum((a - b) ** 2 for a, b in zip(res_i["coords"], res_j["coords"], strict=False))
+            )
 
             # Use wide range only when both residues are CYX/CYD (confirmed disulfide
             # partners). Mixed CYX+CYS pairs use the strict cutoff to avoid false
@@ -407,7 +408,7 @@ def get_coords(atomname, residue):
 
 
 def calculate_distance(atom_coords, center_coords) -> float:
-    return math.sqrt(sum((a - b) ** 2 for a, b in zip(atom_coords, center_coords)))
+    return math.sqrt(sum((a - b) ** 2 for a, b in zip(atom_coords, center_coords, strict=False)))
 
 
 def _convert_to(value, dtype):
@@ -477,7 +478,7 @@ def read_pdb_to_dataframe(pdb_file):
     return df
 
 
-def residue_atom_serial_range(pdb_df, residue_names: Union[str, list[str]]) -> Optional[tuple[int, int]]:
+def residue_atom_serial_range(pdb_df, residue_names: str | list[str]) -> tuple[int, int] | None:
     """Return the (first, last) atom serial numbers for the given residue name(s).
 
     Returns None when no atoms match, so callers can skip building restraints
@@ -497,7 +498,7 @@ def residue_atom_serial_range(pdb_df, residue_names: Union[str, list[str]]) -> O
 
 
 def write_dataframe_to_pdb(
-    df, output_file, header: Optional[str] = None, ter_after_indices: Optional[set[int]] = None
+    df, output_file, header: str | None = None, ter_after_indices: set[int] | None = None
 ):
     """Save a DataFrame object created from read_pdb_to_dataframe function to a PDB file.
 
diff --git a/src/QligFEP/qligfep.py b/src/QligFEP/qligfep.py
index 2d6c678a..fa63f080 100644
--- a/src/QligFEP/qligfep.py
+++ b/src/QligFEP/qligfep.py
@@ -5,7 +5,7 @@
 import shutil
 import stat
 from pathlib import Path
-from typing import Literal, Optional, Union
+from typing import Literal
 
 import numpy as np
 import pandas as pd
@@ -64,7 +64,7 @@
 COUNTER_WATER_RESNAME = "CWT"
 
 
-def lrf_required_for_edge(same_charge: "bool | None") -> bool:
+def lrf_required_for_edge(same_charge: bool | None) -> bool:
     """Whether this edge must run with LRF on.
 
     A charge-changing edge (``same_charge`` is False) changes the in-sphere net charge, whose
@@ -96,10 +96,10 @@ def __init__(
         replicates: str = "10",
         sampling: Literal["sigmoidal", "linear", "exponential", "reverse_exponential"] = "sigmoidal",
         timestep: Literal["1fs", "2fs"] = "2fs",
-        to_clean: Optional[list[str]] = None,
-        water_thresh: Union[float, int] = 1.4,
+        to_clean: list[str] | None = None,
+        water_thresh: float | int = 1.4,
         dr_force: float = 0.5,
-        random_state: Optional[int] = 42,
+        random_state: int | None = 42,
         wath_ligand_only: bool = False,
         neq: bool = False,
         neq_reps: int = 5,
@@ -108,7 +108,7 @@ def __init__(
         neq_relax_steps: int = 5000,
         neq_L: float = 8.0,
         neq_schedule: Literal["sigmoidal", "linear"] = "sigmoidal",
-        protein_charge: Optional[int] = None,
+        protein_charge: int | None = None,
         charge_method: str = "ion_match",
     ):
         self.timestep = timestep
@@ -159,7 +159,7 @@ def __init__(
             raise ValueError(f"charge_method={charge_method!r} not in {valid_charge_methods}")
         self.charge_method = charge_method
         # Populated by read_files() once formal charges are known.
-        self.same_charge: Optional[bool] = None
+        self.same_charge: bool | None = None
         # Co-alchemical water state, populated by place_counter_water() when
         # charge_method == "coalchemical_water". Each entry is a dict with
         # keys "topology_indices" (3 ints) and "qatoms" (3 Q-atom descriptors).
@@ -175,7 +175,7 @@ def __init__(
                     try:
                         resnr = int(line[22:26])
                         atnr = int(line[6:11])
-                    except (IndexError, ValueError):
+                    except IndexError, ValueError:
                         continue
                     break
             self.residueoffset = resnr
@@ -594,7 +594,7 @@ def place_counter_ions(self, writedir: str) -> int:
                 try:
                     last_atnr = max(last_atnr, int(line[6:11]))
                     last_resnr = max(last_resnr, int(line[22:26]))
-                except (ValueError, IndexError):
+                except ValueError, IndexError:
                     continue
 
         # Append ion ATOM lines to the combined PDB
@@ -1605,7 +1605,7 @@ def write_runfile(self, writedir, file_list):
 
                     elif self.start == "0.5":
                         outfile.write(f"{mpirun} md_0500_0500.inp > md_0500_0500.log\n\n")
-                        for md1, md2 in zip(md_1, md_2):
+                        for md1, md2 in zip(md_1, md_2, strict=False):
                             outfile.write(f"{mpirun} {md1[:-4]}.inp > {md1[:-4]}.log\n")
                             outfile.write(f"{mpirun} {md2[:-4]}.inp > {md2[:-4]}.log\n")
                             outfile.write("\n")
@@ -1629,7 +1629,7 @@ def write_qfep(self, windows, lambdas):
         with open(qfep_out, "w") as outfile:
             outfile.write(content)
 
-    def avoid_water_protein_clashes(self, writedir, header: Optional[str] = None, save_removed: bool = False):
+    def avoid_water_protein_clashes(self, writedir, header: str | None = None, save_removed: bool = False):
         """Function to remove water molecules too close to protein & ligands | ligands (water leg).
         Thresholds are the distances in Ångström from the protein & ligands | ligands atoms
         to the nearest heavy atom in the water molecule (HOH).
diff --git a/src/QligFEP/qmapfep.py b/src/QligFEP/qmapfep.py
index 0b84699a..3b14765e 100644
--- a/src/QligFEP/qmapfep.py
+++ b/src/QligFEP/qmapfep.py
@@ -8,7 +8,7 @@
 from collections import namedtuple
 from functools import cached_property, lru_cache
 from pathlib import Path
-from typing import Literal, Optional
+from typing import Literal
 
 import networkx as nx
 from networkx.readwrite import json_graph
@@ -345,7 +345,9 @@ def png(self):
             self._remove_hs()  # Does this three belongs here ??
             self._reorient_molecule()  #
             # Loop over R groups.
-            for color, (label, group) in zip(self.palette, self.pool.groups[self.pool_idx].items()):
+            for color, (label, group) in zip(
+                self.palette, self.pool.groups[self.pool_idx].items(), strict=False
+            ):
                 if label == "Core":
                     continue
                 self._highlight_residue(group, color, highlights)
@@ -1020,11 +1022,11 @@ def makeplot_dG(self):
 class Init:
     def __init__(
         self,
-        input_sdf: Optional[str] = None,
-        input_json: Optional[str] = None,
+        input_sdf: str | None = None,
+        input_json: str | None = None,
         metric: Literal["MFP", "Tanimoto", "MCS", "SMILES"] = "Tanimoto",
-        output: Optional[str] = None,
-        wrkdir: Optional[str] = None,
+        output: str | None = None,
+        wrkdir: str | None = None,
     ):
         metric = metric
         o = output
diff --git a/src/QligFEP/restraints/restraint_setter.py b/src/QligFEP/restraints/restraint_setter.py
index 2178ddbd..9226b029 100644
--- a/src/QligFEP/restraints/restraint_setter.py
+++ b/src/QligFEP/restraints/restraint_setter.py
@@ -3,7 +3,6 @@
 from copy import deepcopy
 from itertools import zip_longest
 from pathlib import Path
-from typing import Union
 
 import numpy as np
 from kartograf import KartografAtomMapper, SmallMoleculeComponent
@@ -53,7 +52,7 @@ def __init__(self, molA: str, molB: str, kartograf_max_atom_distance: float | in
 
     @staticmethod
     def input_to_small_molecule_component(
-        input_molecule: Union[Molecule, Chem.Mol, str, Path],
+        input_molecule: Molecule | Chem.Mol | str | Path,
     ) -> SmallMoleculeComponent:
         if isinstance(input_molecule, SmallMoleculeComponent):
             mol = input_molecule
@@ -257,7 +256,7 @@ def is_ring_equivalent(
             return False
 
         # Further check the atomic number and connectivity
-        for a, b in zip(ring_atoms_a_indices, ring_atoms_b_indices):
+        for a, b in zip(ring_atoms_a_indices, ring_atoms_b_indices, strict=False):
             logger.trace(f"Comparison method: {compare_method}")
             atom_a = mol_a.GetAtomWithIdx(a)
             atom_b = mol_b.GetAtomWithIdx(b)
diff --git a/src/QligFEP/visualization.py b/src/QligFEP/visualization.py
index 3341590e..d32b9590 100644
--- a/src/QligFEP/visualization.py
+++ b/src/QligFEP/visualization.py
@@ -1,7 +1,6 @@
 """Module to hold utility visualization functions for QligFEP."""
 
 from pathlib import Path
-from typing import Optional, Union
 
 import matplotlib.pyplot as plt
 import py3Dmol
@@ -15,15 +14,15 @@
 from .restraints.restraint_setter import RestraintSetter
 
 
-def mol_to_molblock(mol: Union[Molecule, Chem.Mol]) -> str:
+def mol_to_molblock(mol: Molecule | Chem.Mol) -> str:
     if isinstance(mol, Molecule):
         mol = mol.to_rdkit()
     return Chem.MolToMolBlock(mol)
 
 
 def render_system(
-    molecules: list[Union[Molecule, Chem.Mol]],
-    protein_path: Optional[Union[Path, str]] = None,
+    molecules: list[Molecule | Chem.Mol],
+    protein_path: Path | str | None = None,
     protein_style: str = "stick",
     size: tuple[int, int] = (600, 500),
 ) -> None:
@@ -83,8 +82,8 @@ def render_system(
 # Credit to: https://github.com/OpenFreeEnergy/openfe/blob/main/openfe/utils/visualization_3D.py
 # And to: https://github.com/OpenFreeEnergy/kartograf/blob/main/src/kartograf/utils/mapping_visualization_widget.py
 def render_ligand_restraints(
-    ligand1: Union[Chem.Mol, Molecule, SmallMoleculeComponent],
-    ligand2: Union[Chem.Mol, Molecule, SmallMoleculeComponent],
+    ligand1: Chem.Mol | Molecule | SmallMoleculeComponent,
+    ligand2: Chem.Mol | Molecule | SmallMoleculeComponent,
     restraint_mapping: dict[int, int],
     show_atom_idxs: bool = True,
     size: tuple[int, int] = (900, 500),
@@ -177,8 +176,8 @@ def add_spheres(view, mol, mapping, is_ligand1=True, viewer=(0, 0)):
 
 
 def apply_and_render_restraint(
-    ligand1: Union[Molecule, Chem.Mol, str, Path],
-    ligand2: Union[Molecule, Chem.Mol, str, Path],
+    ligand1: Molecule | Chem.Mol | str | Path,
+    ligand2: Molecule | Chem.Mol | str | Path,
     restraint_method: str = "hybridization_p",
     show_atom_idxs: bool = True,
     size: tuple[int, int] = (900, 500),
diff --git a/test/conftest.py b/test/conftest.py
index 73f3d4c1..f4b76d0e 100644
--- a/test/conftest.py
+++ b/test/conftest.py
@@ -300,7 +300,7 @@ def tyk2_tutorial_path(tutorials_path: Path) -> Path:
 
 
 @pytest.fixture
-def temp_work_dir() -> Generator[Path, None, None]:
+def temp_work_dir() -> Generator[Path]:
     """Create a temporary working directory that is cleaned up after the test."""
     temp_dir = Path(tempfile.mkdtemp())
     try:
@@ -611,7 +611,7 @@ def compare_inp_files(self, actual: dict, expected: dict, ignore_keys: list[str]
                         f"[{section}] length mismatch: expected {len(expected_section)}, got {len(actual_section)}"
                     )
                 else:
-                    for i, (exp_line, act_line) in enumerate(zip(expected_section, actual_section)):
+                    for i, (exp_line, act_line) in enumerate(zip(expected_section, actual_section, strict=False)):
                         if exp_line != act_line:
                             differences.append(f"[{section}][{i}]: expected '{exp_line}', got '{act_line}'")
 
diff --git a/test/neq/test_analysis_plotting.py b/test/neq/test_analysis_plotting.py
index 4029e0fa..b42c4d24 100644
--- a/test/neq/test_analysis_plotting.py
+++ b/test/neq/test_analysis_plotting.py
@@ -66,7 +66,7 @@ def test_create_ddG_plot_axis_bounds_include_all_points():
     fig, ax = create_ddG_plot(df, target_name="test")
     xlo, xhi = ax.get_xlim()
     ylo, yhi = ax.get_ylim()
-    for exp, calc in zip(df["ddg_value"], df["Q_ddG_avg"]):
+    for exp, calc in zip(df["ddg_value"], df["Q_ddG_avg"], strict=False):
         assert xlo <= exp <= xhi, f"exp {exp} outside x-range [{xlo}, {xhi}]"
         assert ylo <= calc <= yhi, f"calc {calc} outside y-range [{ylo}, {yhi}]"
 
diff --git a/test/qligfep/test_fep_input_files.py b/test/qligfep/test_fep_input_files.py
index 4e216875..180f23c9 100644
--- a/test/qligfep/test_fep_input_files.py
+++ b/test/qligfep/test_fep_input_files.py
@@ -155,7 +155,9 @@ def test_distance_restraints_match_golden(self, generated_fep_dir: Path):
         ), f"Distance restraints count mismatch: expected {len(golden_restraints)}, got {len(actual_restraints)}"
 
         # Compare each restraint line
-        for i, (golden_line, actual_line) in enumerate(zip(golden_restraints, actual_restraints)):
+        for i, (golden_line, actual_line) in enumerate(
+            zip(golden_restraints, actual_restraints, strict=False)
+        ):
             assert (
                 actual_line == golden_line
             ), f"Distance restraint {i} mismatch:\n  expected: {golden_line}\n  actual: {actual_line}"
diff --git a/test/qligfep/test_qprep_cli.py b/test/qligfep/test_qprep_cli.py
index 8858672a..5fffa770 100644
--- a/test/qligfep/test_qprep_cli.py
+++ b/test/qligfep/test_qprep_cli.py
@@ -350,6 +350,7 @@ def test_dna_with_c1_inside_sphere_unchanged(self):
         for (aname, elem), (px, py, pz) in zip(
             [("P", "P"), ("OP1", "O"), ("OP2", "O"), ("O5'", "O"), ("C1'", "C")],
             positions,
+            strict=False,
         ):
             rows.append(_make_atom("ATOM", serial, aname, "DA", "E", 1, px, py, pz, elem))
             serial += 1