From 804a6570e39ef7a2f37a68a19bb95a42d372fb4d Mon Sep 17 00:00:00 2001
From: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Date: Fri, 16 Feb 2024 01:44:51 -0700
Subject: [PATCH] linted!

---
 openfe/analysis/plotting.py                          |  2 +-
 openfe/due.py                                        |  2 +-
 .../openmm_rfe/_rfe_utils/lambdaprotocol.py          |  2 +-
 openfe/protocols/openmm_rfe/_rfe_utils/multistate.py | 10 +++++-----
 .../openmm_rfe/_rfe_utils/topologyhelpers.py         | 12 +++++-------
 openfe/protocols/openmm_utils/system_validation.py   |  2 +-
 .../abstract_alchemical_network_planner.py           |  2 +-
 .../relative_alchemical_network_planner.py           |  5 +++--
 openfe/setup/atom_mapping/ligandatommapper.py        |  2 +-
 .../abstract_chemicalsystem_generator.py             |  2 +-
 .../easy_chemicalsystem_generator.py                 |  3 ++-
 openfe/setup/ligand_network_planning.py              |  9 +++++----
 openfe/storage/metadatastore.py                      |  2 +-
 .../protocols/test_openmm_equil_rfe_protocols.py     |  4 ++--
 openfe/tests/setup/atom_mapping/conftest.py          |  8 ++++----
 openfe/tests/storage/test_metadatastore.py           |  4 ++--
 openfe/tests/storage/test_resultclient.py            |  2 +-
 openfe/tests/storage/test_resultserver.py            |  6 +++---
 openfe/tests/utils/conftest.py                       |  3 ++-
 .../tests/utils/test_atommapping_network_plotting.py |  2 +-
 openfe/tests/utils/test_network_plotting.py          |  2 +-
 openfe/utils/atommapping_network_plotting.py         |  6 +++---
 openfe/utils/network_plotting.py                     |  8 ++++----
 openfe/utils/system_probe.py                         |  3 ++-
 openfe/utils/visualization_3D.py                     | 11 ++++++-----
 openfecli/commands/gather.py                         |  4 ++--
 openfecli/commands/plan_rbfe_network.py              |  2 +-
 openfecli/commands/plan_rhfe_network.py              |  2 +-
 openfecli/parameters/plan_network_options.py         |  2 +-
 openfecli/tests/commands/test_quickrun.py            |  2 +-
 30 files changed, 65 insertions(+), 61 deletions(-)

diff --git a/openfe/analysis/plotting.py b/openfe/analysis/plotting.py
index de907749d..fffb225f6 100644
--- a/openfe/analysis/plotting.py
+++ b/openfe/analysis/plotting.py
@@ -33,7 +33,7 @@ def plot_lambda_transition_matrix(matrix: npt.NDArray) -> Axes:
             ax.axhline(y=i, ls="-", lw=0.5, color="k", alpha=0.25)
         for j in range(num_states):
             val = matrix[i, j]
-            val_str = "{:.2f}".format(val)[1:]
+            val_str = f"{val:.2f}"[1:]
             rel_prob = val / matrix.max()
 
             # shade box
diff --git a/openfe/due.py b/openfe/due.py
index 4a4179488..cdc7d8a7f 100644
--- a/openfe/due.py
+++ b/openfe/due.py
@@ -27,7 +27,7 @@
 __version__ = "0.0.9"
 
 
-class InactiveDueCreditCollector(object):
+class InactiveDueCreditCollector:
     """Just a stub at the Collector which would not do anything"""
 
     def _donothing(self, *args, **kwargs):
diff --git a/openfe/protocols/openmm_rfe/_rfe_utils/lambdaprotocol.py b/openfe/protocols/openmm_rfe/_rfe_utils/lambdaprotocol.py
index 38b494c93..66869775d 100644
--- a/openfe/protocols/openmm_rfe/_rfe_utils/lambdaprotocol.py
+++ b/openfe/protocols/openmm_rfe/_rfe_utils/lambdaprotocol.py
@@ -9,7 +9,7 @@
 from openmmtools.alchemy import AlchemicalState
 
 
-class LambdaProtocol(object):
+class LambdaProtocol:
     """Protocols for perturbing each of the component energy terms in alchemical
     free energy simulations.
 
diff --git a/openfe/protocols/openmm_rfe/_rfe_utils/multistate.py b/openfe/protocols/openmm_rfe/_rfe_utils/multistate.py
index 7c7fd8c1e..6545b0707 100644
--- a/openfe/protocols/openmm_rfe/_rfe_utils/multistate.py
+++ b/openfe/protocols/openmm_rfe/_rfe_utils/multistate.py
@@ -24,7 +24,7 @@
 logger = logging.getLogger(__name__)
 
 
-class HybridCompatibilityMixin(object):
+class HybridCompatibilityMixin:
     """
     Mixin that allows the MultistateSampler to accommodate the situation where
     unsampled endpoints have a different number of degrees of freedom.
@@ -32,7 +32,7 @@ class HybridCompatibilityMixin(object):
 
     def __init__(self, *args, hybrid_factory=None, **kwargs):
         self._hybrid_factory = hybrid_factory
-        super(HybridCompatibilityMixin, self).__init__(*args, **kwargs)
+        super().__init__(*args, **kwargs)
 
     def setup(
         self,
@@ -167,7 +167,7 @@ class HybridRepexSampler(HybridCompatibilityMixin, replicaexchange.ReplicaExchan
     """
 
     def __init__(self, *args, hybrid_factory=None, **kwargs):
-        super(HybridRepexSampler, self).__init__(*args, hybrid_factory=hybrid_factory, **kwargs)
+        super().__init__(*args, hybrid_factory=hybrid_factory, **kwargs)
         self._factory = hybrid_factory
 
 
@@ -178,7 +178,7 @@ class HybridSAMSSampler(HybridCompatibilityMixin, sams.SAMSSampler):
     """
 
     def __init__(self, *args, hybrid_factory=None, **kwargs):
-        super(HybridSAMSSampler, self).__init__(*args, hybrid_factory=hybrid_factory, **kwargs)
+        super().__init__(*args, hybrid_factory=hybrid_factory, **kwargs)
         self._factory = hybrid_factory
 
 
@@ -189,7 +189,7 @@ class HybridMultiStateSampler(HybridCompatibilityMixin, multistatesampler.MultiS
     """
 
     def __init__(self, *args, hybrid_factory=None, **kwargs):
-        super(HybridMultiStateSampler, self).__init__(*args, hybrid_factory=hybrid_factory, **kwargs)
+        super().__init__(*args, hybrid_factory=hybrid_factory, **kwargs)
         self._factory = hybrid_factory
 
 
diff --git a/openfe/protocols/openmm_rfe/_rfe_utils/topologyhelpers.py b/openfe/protocols/openmm_rfe/_rfe_utils/topologyhelpers.py
index c816ba6fd..181e7345b 100644
--- a/openfe/protocols/openmm_rfe/_rfe_utils/topologyhelpers.py
+++ b/openfe/protocols/openmm_rfe/_rfe_utils/topologyhelpers.py
@@ -277,13 +277,11 @@ def get_alchemical_waters(
         periodic=True,
     )[0]
 
-    solvent_indices = set(
-        [
-            atom.residue.index
-            for atom in traj.topology.atoms
-            if (atom.index in water_atoms) and (atom.index not in excluded_waters)
-        ],
-    )
+    solvent_indices = {
+        atom.residue.index
+        for atom in traj.topology.atoms
+        if (atom.index in water_atoms) and (atom.index not in excluded_waters)
+    }
 
     if len(solvent_indices) < 1:
         errmsg = (
diff --git a/openfe/protocols/openmm_utils/system_validation.py b/openfe/protocols/openmm_utils/system_validation.py
index 8f99b4d2e..65eb4e866 100644
--- a/openfe/protocols/openmm_utils/system_validation.py
+++ b/openfe/protocols/openmm_utils/system_validation.py
@@ -126,7 +126,7 @@ def validate_protein(state: ChemicalSystem):
         raise ValueError(errmsg)
 
 
-ParseCompRet = Tuple[
+ParseCompRet = tuple[
     Optional[SolventComponent],
     Optional[ProteinComponent],
     list[SmallMoleculeComponent],
diff --git a/openfe/setup/alchemical_network_planner/abstract_alchemical_network_planner.py b/openfe/setup/alchemical_network_planner/abstract_alchemical_network_planner.py
index 70b5f79d9..2d1b7fce5 100644
--- a/openfe/setup/alchemical_network_planner/abstract_alchemical_network_planner.py
+++ b/openfe/setup/alchemical_network_planner/abstract_alchemical_network_planner.py
@@ -2,7 +2,7 @@
 # For details, see https://github.com/OpenFreeEnergy/openfe
 
 import abc
-from typing import Iterable
+from collections.abc import Iterable
 
 from gufe import AlchemicalNetwork
 
diff --git a/openfe/setup/alchemical_network_planner/relative_alchemical_network_planner.py b/openfe/setup/alchemical_network_planner/relative_alchemical_network_planner.py
index 1046bf645..9b4b0eb08 100644
--- a/openfe/setup/alchemical_network_planner/relative_alchemical_network_planner.py
+++ b/openfe/setup/alchemical_network_planner/relative_alchemical_network_planner.py
@@ -2,7 +2,8 @@
 # For details, see https://github.com/OpenFreeEnergy/openfe
 import abc
 import copy
-from typing import Callable, Iterable, Optional, Type
+from collections.abc import Iterable
+from typing import Callable, Optional, Type
 
 from gufe import (
     AlchemicalNetwork,
@@ -93,7 +94,7 @@ def transformation_protocol(self) -> Protocol:
     @property
     def chemical_system_generator_type(
         self,
-    ) -> Type[AbstractChemicalSystemGenerator]:
+    ) -> type[AbstractChemicalSystemGenerator]:
         return self._chemical_system_generator_type
 
     def _construct_ligand_network(self, ligands: Iterable[SmallMoleculeComponent]) -> LigandNetwork:
diff --git a/openfe/setup/atom_mapping/ligandatommapper.py b/openfe/setup/atom_mapping/ligandatommapper.py
index c68e6a7b0..17a493b90 100644
--- a/openfe/setup/atom_mapping/ligandatommapper.py
+++ b/openfe/setup/atom_mapping/ligandatommapper.py
@@ -1,7 +1,7 @@
 # This code is part of OpenFE and is licensed under the MIT license.
 # For details, see https://github.com/OpenFreeEnergy/openfe
 import abc
-from typing import Iterable
+from collections.abc import Iterable
 
 import gufe
 from gufe import SmallMoleculeComponent
diff --git a/openfe/setup/chemicalsystem_generator/abstract_chemicalsystem_generator.py b/openfe/setup/chemicalsystem_generator/abstract_chemicalsystem_generator.py
index af515555f..cd96d0c23 100644
--- a/openfe/setup/chemicalsystem_generator/abstract_chemicalsystem_generator.py
+++ b/openfe/setup/chemicalsystem_generator/abstract_chemicalsystem_generator.py
@@ -1,8 +1,8 @@
 # This code is part of OpenFE and is licensed under the MIT license.
 # For details, see https://github.com/OpenFreeEnergy/openfe
 import abc
+from collections.abc import Iterable
 from enum import Enum
-from typing import Iterable
 
 from gufe import ChemicalSystem
 
diff --git a/openfe/setup/chemicalsystem_generator/easy_chemicalsystem_generator.py b/openfe/setup/chemicalsystem_generator/easy_chemicalsystem_generator.py
index 344b0f16d..be138b682 100644
--- a/openfe/setup/chemicalsystem_generator/easy_chemicalsystem_generator.py
+++ b/openfe/setup/chemicalsystem_generator/easy_chemicalsystem_generator.py
@@ -1,7 +1,8 @@
 # This code is part of OpenFE and is licensed under the MIT license.
 # For details, see https://github.com/OpenFreeEnergy/openfe
 
-from typing import Iterable, Optional
+from collections.abc import Iterable
+from typing import Optional
 
 from gufe import ChemicalSystem, Component, ProteinComponent, SmallMoleculeComponent, SolventComponent
 
diff --git a/openfe/setup/ligand_network_planning.py b/openfe/setup/ligand_network_planning.py
index ec5977950..c5e9de184 100644
--- a/openfe/setup/ligand_network_planning.py
+++ b/openfe/setup/ligand_network_planning.py
@@ -5,8 +5,9 @@
 import math
 import warnings
 from collections import Counter
+from collections.abc import Iterable
 from pathlib import Path
-from typing import Callable, Iterable, Optional, Union
+from typing import Callable, Optional, Union
 
 import networkx as nx
 from gufe import AtomMapper, SmallMoleculeComponent
@@ -330,7 +331,7 @@ def generate_network_from_names(
     nm2idx = {l.name: i for i, l in enumerate(ligands)}
 
     if len(nm2idx) < len(ligands):
-        dupes = Counter((l.name for l in ligands))
+        dupes = Counter(l.name for l in ligands)
         dupe_names = [k for k, v in dupes.items() if v > 1]
         raise ValueError(f"Duplicate names: {dupe_names}")
 
@@ -418,7 +419,7 @@ def load_orion_network(
       If an unexpected line format is encountered.
     """
 
-    with open(network_file, "r") as f:
+    with open(network_file) as f:
         network_lines = [l.strip().split(" ") for l in f if not l.startswith("#")]
 
     names = []
@@ -458,7 +459,7 @@ def load_fepplus_network(
       If an unexpected line format is encountered.
     """
 
-    with open(network_file, "r") as f:
+    with open(network_file) as f:
         network_lines = [l.split() for l in f.readlines()]
 
     names = []
diff --git a/openfe/storage/metadatastore.py b/openfe/storage/metadatastore.py
index ff702ee60..5916777dd 100644
--- a/openfe/storage/metadatastore.py
+++ b/openfe/storage/metadatastore.py
@@ -19,7 +19,7 @@ def store_metadata(self, location: str, metadata: Metadata):
         raise NotImplementedError()
 
     @abc.abstractmethod
-    def load_all_metadata(self) -> Dict[str, Metadata]:
+    def load_all_metadata(self) -> dict[str, Metadata]:
         raise NotImplementedError()
 
     @abc.abstractmethod
diff --git a/openfe/tests/protocols/test_openmm_equil_rfe_protocols.py b/openfe/tests/protocols/test_openmm_equil_rfe_protocols.py
index 22efeacd1..0a916148e 100644
--- a/openfe/tests/protocols/test_openmm_equil_rfe_protocols.py
+++ b/openfe/tests/protocols/test_openmm_equil_rfe_protocols.py
@@ -1477,7 +1477,7 @@ def tyk2_xml(tmp_path_factory):
 def tyk2_reference_xml():
     with resources.files("openfe.tests.data.openmm_rfe") as d:
         f = d / "reference.xml"
-        with open(f, "r") as i:
+        with open(f) as i:
             xmldata = i.read()
     return ET.fromstring(xmldata)
 
@@ -1620,7 +1620,7 @@ def test_filenotfound_replica_states(self, protocolresult):
 def test_get_charge_difference(mapping_name, result, request):
     mapping = request.getfixturevalue(mapping_name)
     if result != 0:
-        ion = "Na\+" if result == -1 else "Cl\-"
+        ion = r"Na\+" if result == -1 else r"Cl\-"
         wmsg = (
             f"A charge difference of {result} is observed "
             "between the end states. This will be addressed by "
diff --git a/openfe/tests/setup/atom_mapping/conftest.py b/openfe/tests/setup/atom_mapping/conftest.py
index 0890a277b..e21b9215d 100644
--- a/openfe/tests/setup/atom_mapping/conftest.py
+++ b/openfe/tests/setup/atom_mapping/conftest.py
@@ -13,12 +13,12 @@
 from ...conftest import mol_from_smiles
 
 
-def _translate_lomap_mapping(atom_mapping_str: str) -> Dict[int, int]:
+def _translate_lomap_mapping(atom_mapping_str: str) -> dict[int, int]:
     mapped_atom_tuples = map(lambda x: tuple(map(int, x.split(":"))), atom_mapping_str.split(","))
     return {i: j for i, j in mapped_atom_tuples}
 
 
-def _get_atom_mapping_dict(lomap_atom_mappings) -> Dict[Tuple[int, int], Dict[int, int]]:
+def _get_atom_mapping_dict(lomap_atom_mappings) -> dict[tuple[int, int], dict[int, int]]:
     return {
         mol_pair: _translate_lomap_mapping(atom_mapping_str)
         for mol_pair, atom_mapping_str in lomap_atom_mappings.mcs_map_store.items()
@@ -29,7 +29,7 @@ def _get_atom_mapping_dict(lomap_atom_mappings) -> Dict[Tuple[int, int], Dict[in
 def gufe_atom_mapping_matrix(
     lomap_basic_test_files_dir,
     atom_mapping_basic_test_files,
-) -> Dict[Tuple[int, int], LigandAtomMapping]:
+) -> dict[tuple[int, int], LigandAtomMapping]:
     dbmols = lomap.DBMolecules(lomap_basic_test_files_dir, verbose="off")
     _, _ = dbmols.build_matrices()
     molecule_pair_atom_mappings = _get_atom_mapping_dict(dbmols)
@@ -48,7 +48,7 @@ def gufe_atom_mapping_matrix(
 
 
 @pytest.fixture()
-def mol_pair_to_shock_perses_mapper() -> Tuple[SmallMoleculeComponent, SmallMoleculeComponent]:
+def mol_pair_to_shock_perses_mapper() -> tuple[SmallMoleculeComponent, SmallMoleculeComponent]:
     """
     This pair of Molecules leads to an empty Atom mapping in
     Perses Mapper with certain settings.
diff --git a/openfe/tests/storage/test_metadatastore.py b/openfe/tests/storage/test_metadatastore.py
index 40dd34dcc..4ca116d68 100644
--- a/openfe/tests/storage/test_metadatastore.py
+++ b/openfe/tests/storage/test_metadatastore.py
@@ -75,7 +75,7 @@ def test_store_metadata(self, json_metadata):
         base_path = json_metadata.external_store.root_dir
         metadata_json = base_path / "metadata.json"
         assert metadata_json.exists()
-        with open(metadata_json, mode="r") as f:
+        with open(metadata_json) as f:
             metadata_dict = json.load(f)
 
         metadata = {key: Metadata(**val) for key, val in metadata_dict.items()}
@@ -117,7 +117,7 @@ def test_store_metadata(self, per_file_metadata):
         per_file_metadata.store_metadata("path/to/other.txt", meta)
         assert expected_path.exists()
         expected = {"path": "path/to/other.txt", "metadata": {"md5": "other"}}
-        with open(expected_path, mode="r") as f:
+        with open(expected_path) as f:
             assert json.load(f) == expected
 
     def test_load_all_metadata(self, per_file_metadata):
diff --git a/openfe/tests/storage/test_resultclient.py b/openfe/tests/storage/test_resultclient.py
index 68a72c646..470a3844a 100644
--- a/openfe/tests/storage/test_resultclient.py
+++ b/openfe/tests/storage/test_resultclient.py
@@ -14,7 +14,7 @@ def result_client(tmpdir):
     result_client = ResultClient(external)
 
     # store one file with contents "foo"
-    result_client.result_server.store_bytes("transformations/MAIN_TRANS/0/0/file.txt", "foo".encode("utf-8"))
+    result_client.result_server.store_bytes("transformations/MAIN_TRANS/0/0/file.txt", b"foo")
 
     # create some empty files as well
     empty_files = [
diff --git a/openfe/tests/storage/test_resultserver.py b/openfe/tests/storage/test_resultserver.py
index 35729fd9b..b3a2ef075 100644
--- a/openfe/tests/storage/test_resultserver.py
+++ b/openfe/tests/storage/test_resultserver.py
@@ -15,7 +15,7 @@ def result_server(tmpdir):
     external = FileStorage(tmpdir)
     metadata = JSONMetadataStore(external)
     result_server = ResultServer(external, metadata)
-    result_server.store_bytes("path/to/foo.txt", "foo".encode("utf-8"))
+    result_server.store_bytes("path/to/foo.txt", b"foo")
     return result_server
 
 
@@ -32,7 +32,7 @@ def test_store_bytes(self, result_server):
         mock_hash = mock.Mock(return_value=mock.Mock(hexdigest=mock.Mock(return_value="deadbeef")))
         bar_loc = "path/to/bar.txt"
         with mock.patch("hashlib.md5", mock_hash):
-            result_server.store_bytes(bar_loc, "bar".encode("utf-8"))
+            result_server.store_bytes(bar_loc, b"bar")
 
         assert len(metadata_store) == 2
         assert bar_loc in metadata_store
@@ -46,7 +46,7 @@ def test_store_path(self, result_server, tmp_path):
         orig_file = tmp_path / ".hidden" / "bar.txt"
         orig_file.parent.mkdir(parents=True, exist_ok=True)
         with open(orig_file, mode="wb") as f:
-            f.write("bar".encode("utf-8"))
+            f.write(b"bar")
 
         mock_hash = mock.Mock(return_value=mock.Mock(hexdigest=mock.Mock(return_value="deadc0de")))
         bar_loc = "path/to/bar.txt"
diff --git a/openfe/tests/utils/conftest.py b/openfe/tests/utils/conftest.py
index 3799f5837..90be909d3 100644
--- a/openfe/tests/utils/conftest.py
+++ b/openfe/tests/utils/conftest.py
@@ -1,7 +1,8 @@
 # This code is part of OpenFE and is licensed under the MIT license.
 # For details, see https://github.com/OpenFreeEnergy/openfe
+from collections.abc import Iterable
 from importlib import resources
-from typing import Iterable, NamedTuple
+from typing import NamedTuple
 
 import pytest
 from rdkit import Chem
diff --git a/openfe/tests/utils/test_atommapping_network_plotting.py b/openfe/tests/utils/test_atommapping_network_plotting.py
index bf421465a..1ce12d91d 100644
--- a/openfe/tests/utils/test_atommapping_network_plotting.py
+++ b/openfe/tests/utils/test_atommapping_network_plotting.py
@@ -101,7 +101,7 @@ def test_select_mock_drawing(self, edge_str, left_right, molA_to_molB, network_d
         node_dict = {node.smiles: node for node in network_drawing.graph.nodes}
         edge_tuple = tuple(node_dict[node] for node in edge_str)
         edge = network_drawing.edges[edge_tuple]
-        left, right = [network_drawing.nodes[node_dict[node]] for node in left_right]
+        left, right = (network_drawing.nodes[node_dict[node]] for node in left_right)
         # ensure that we have them labelled correctly
         assert left.xy[0] < right.xy[0]
         func = edge._draw_mapped_molecule  # save for bound_args
diff --git a/openfe/tests/utils/test_network_plotting.py b/openfe/tests/utils/test_network_plotting.py
index d65c78179..18bef583b 100644
--- a/openfe/tests/utils/test_network_plotting.py
+++ b/openfe/tests/utils/test_network_plotting.py
@@ -158,7 +158,7 @@ def test_on_drag(self):
         event = mock_event("drag", 0.7, 0.7, self.fig)
         # this test some integration, so we need more than a mock
         drawing_graph = GraphDrawing(
-            nx.MultiDiGraph(([("A", "B"), ("B", "C"), ("B", "D")])),
+            nx.MultiDiGraph([("A", "B"), ("B", "C"), ("B", "D")]),
             positions={"A": (0.0, 0.0), "B": (0.5, 0.0), "C": (0.5, 0.5), "D": (0.0, 0.5)},
         )
         # set up things that should happen on mousedown
diff --git a/openfe/utils/atommapping_network_plotting.py b/openfe/utils/atommapping_network_plotting.py
index 7f6b1cd6b..cd26299b4 100644
--- a/openfe/utils/atommapping_network_plotting.py
+++ b/openfe/utils/atommapping_network_plotting.py
@@ -27,17 +27,17 @@ class AtomMappingEdge(Edge):
         to an :class:`.AtomMapping`.
     """
 
-    def __init__(self, node_artist1: Node, node_artist2: Node, data: Dict):
+    def __init__(self, node_artist1: Node, node_artist2: Node, data: dict):
         super().__init__(node_artist1, node_artist2, data)
         self.left_image = None
         self.right_image = None
 
     def _draw_mapped_molecule(
         self,
-        extent: Tuple[float, float, float, float],
+        extent: tuple[float, float, float, float],
         molA: SmallMoleculeComponent,
         molB: SmallMoleculeComponent,
-        molA_to_molB: Dict[int, int],
+        molA_to_molB: dict[int, int],
     ):
         # create the image in a format matplotlib can handle
         d2d = Chem.Draw.rdMolDraw2D.MolDraw2DCairo(300, 300, 300, 300)
diff --git a/openfe/utils/network_plotting.py b/openfe/utils/network_plotting.py
index 6a6c9da62..11a4f38f1 100644
--- a/openfe/utils/network_plotting.py
+++ b/openfe/utils/network_plotting.py
@@ -44,7 +44,7 @@ def __init__(self, node, x: float, y: float, dx=0.1, dy=0.1):
         self.dy = dx
         self.artist = self._make_artist(x, y, dx, dy)
         self.picked = False
-        self.press: Optional[ClickLocation] = None
+        self.press: ClickLocation | None = None
 
     def _make_artist(self, x, y, dx, dy):
         return Rectangle((x, y), dx, dy, color="blue")
@@ -245,9 +245,9 @@ class EventHandler:
 
     def __init__(self, graph: GraphDrawing):
         self.graph = graph
-        self.active: Optional[Union[Node, Edge]] = None
-        self.selected: Optional[Union[Node, Edge]] = None
-        self.click_location: Optional[tuple[Optional[float], Optional[float]]] = None
+        self.active: Node | Edge | None = None
+        self.selected: Node | Edge | None = None
+        self.click_location: tuple[float | None, float | None] | None = None
         self.connections: list[int] = []
 
     def connect(self, canvas: MPL_FigureCanvasBase):
diff --git a/openfe/utils/system_probe.py b/openfe/utils/system_probe.py
index e752be258..dee600e59 100644
--- a/openfe/utils/system_probe.py
+++ b/openfe/utils/system_probe.py
@@ -4,7 +4,8 @@
 import socket
 import subprocess
 import sys
-from typing import Iterable, Optional
+from collections.abc import Iterable
+from typing import Optional
 
 import psutil
 from psutil._common import bytes2human
diff --git a/openfe/utils/visualization_3D.py b/openfe/utils/visualization_3D.py
index 9905c15a4..0b86003bf 100644
--- a/openfe/utils/visualization_3D.py
+++ b/openfe/utils/visualization_3D.py
@@ -1,4 +1,5 @@
-from typing import Dict, Iterable, Optional, Tuple, Union
+from collections.abc import Iterable
+from typing import Dict, Optional, Tuple, Union
 
 import numpy as np
 from matplotlib import pyplot as plt
@@ -43,7 +44,7 @@ def _get_max_dist_in_x(atom_mapping: AtomMapping) -> float:
     return estm if (estm > 5) else 5
 
 
-def _translate(mol, shift: Union[Tuple[float, float, float], NDArray[np.float64]]):
+def _translate(mol, shift: Union[tuple[float, float, float], NDArray[np.float64]]):
     """
         shifts the molecule by the shift vector
 
@@ -68,7 +69,7 @@ def _translate(mol, shift: Union[Tuple[float, float, float], NDArray[np.float64]
     return mol
 
 
-def _add_spheres(view: py3Dmol.view, mol1: Chem.Mol, mol2: Chem.Mol, mapping: Dict[int, int]):
+def _add_spheres(view: py3Dmol.view, mol1: Chem.Mol, mol2: Chem.Mol, mapping: dict[int, int]):
     """
         will add spheres according to mapping to the view. (inplace!)
 
@@ -111,7 +112,7 @@ def _add_spheres(view: py3Dmol.view, mol1: Chem.Mol, mol2: Chem.Mol, mapping: Di
 def view_components_3d(
     mols: Iterable[ExplicitMoleculeComponent],
     style: Optional[str] = "stick",
-    shift: Optional[Tuple[float, float, float]] = None,
+    shift: Optional[tuple[float, float, float]] = None,
     view: py3Dmol.view = None,
 ) -> py3Dmol.view:
     """visualize multiple component coordinates in one interactive view.
@@ -160,7 +161,7 @@ def view_mapping_3d(
     spheres: Optional[bool] = True,
     show_atomIDs: Optional[bool] = False,
     style: Optional[str] = "stick",
-    shift: Optional[Union[Tuple[float, float, float], NDArray[np.float64]]] = None,
+    shift: Optional[Union[tuple[float, float, float], NDArray[np.float64]]] = None,
 ) -> py3Dmol.view:
     """
     Render relative transformation edge in 3D using py3Dmol.
diff --git a/openfecli/commands/gather.py b/openfecli/commands/gather.py
index d9c71b62c..a8a33dd0a 100644
--- a/openfecli/commands/gather.py
+++ b/openfecli/commands/gather.py
@@ -47,7 +47,7 @@ def format_estimate_uncertainty(
 
 def is_results_json(f):
     # sanity check on files before we try and deserialize
-    return "estimate" in open(f, "r").read(20)
+    return "estimate" in open(f).read(20)
 
 
 def load_results(f):
@@ -56,7 +56,7 @@ def load_results(f):
 
     from gufe.tokenization import JSON_HANDLER
 
-    return json.load(open(f, "r"), cls=JSON_HANDLER.decoder)
+    return json.load(open(f), cls=JSON_HANDLER.decoder)
 
 
 def get_names(result) -> tuple[str, str]:
diff --git a/openfecli/commands/plan_rbfe_network.py b/openfecli/commands/plan_rbfe_network.py
index 7819d0416..d712053f4 100644
--- a/openfecli/commands/plan_rbfe_network.py
+++ b/openfecli/commands/plan_rbfe_network.py
@@ -81,7 +81,7 @@ def plan_rbfe_network_main(
 )
 @print_duration
 def plan_rbfe_network(
-    molecules: List[str],
+    molecules: list[str],
     protein: str,
     cofactors: tuple[str],
     yaml_settings: str,
diff --git a/openfecli/commands/plan_rhfe_network.py b/openfecli/commands/plan_rhfe_network.py
index 39d05136e..539114338 100644
--- a/openfecli/commands/plan_rhfe_network.py
+++ b/openfecli/commands/plan_rhfe_network.py
@@ -68,7 +68,7 @@ def plan_rhfe_network_main(
     default="alchemicalNetwork",
 )
 @print_duration
-def plan_rhfe_network(molecules: List[str], yaml_settings: str, output_dir: str):
+def plan_rhfe_network(molecules: list[str], yaml_settings: str, output_dir: str):
     """
     Plan a relative hydration free energy network, saved as JSON files for
     the quickrun command.
diff --git a/openfecli/parameters/plan_network_options.py b/openfecli/parameters/plan_network_options.py
index 96bff0049..e17371e6e 100644
--- a/openfecli/parameters/plan_network_options.py
+++ b/openfecli/parameters/plan_network_options.py
@@ -113,7 +113,7 @@ def load_yaml_planner_options(path: Optional[str], context) -> PlanNetworkOption
     )
 
     if path is not None:
-        with open(path, "r") as f:
+        with open(path) as f:
             raw = f.read()
 
         # convert raw yaml to normalised pydantic model
diff --git a/openfecli/tests/commands/test_quickrun.py b/openfecli/tests/commands/test_quickrun.py
index e2ea1b4d6..71ffdd158 100644
--- a/openfecli/tests/commands/test_quickrun.py
+++ b/openfecli/tests/commands/test_quickrun.py
@@ -31,7 +31,7 @@ def test_quickrun(extra_args, json_file):
 
         if outfile := extra_args.get("-o"):
             assert pathlib.Path(outfile).exists()
-            with open(outfile, mode="r") as outf:
+            with open(outfile) as outf:
                 dct = json.load(outf, cls=JSON_HANDLER.decoder)
 
             assert set(dct) == {"estimate", "uncertainty", "protocol_result", "unit_results"}