Fixing various typos (#1882)

* Playing around with codespell

* revert some things

---------

Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

Code_of_Conduct.md

@@ -39,4 +39,4 @@ Enforcement of this Code of Conduct will be respectful and not include any haras
 
 You deserve sincere thanks for helping to make this a welcoming, friendly community for all.
 
-This Code of Conduct was adpated from the [cmelab](https://github.com/cmelab/getting-started/blob/master/wiki/pages/Code_of_Conduct.md).
+This Code of Conduct was adapted from the [cmelab](https://github.com/cmelab/getting-started/blob/master/wiki/pages/Code_of_Conduct.md).

docs/CHANGELOG.rst

@@ -103,7 +103,7 @@ The openfe lock file and docker and apptainer images use Python 3.12, and so cha
 
 **Changed:**
 
-* The default atom mapper used in the CLI has been changed from ``LomapAtomMapper`` to ``KartografAtomMapper`` in line with the recommended defaults from the industry benchmarking paper. Users who whish to continue to use ``LomapAtomMapper`` can do so via the YAML configuration file. See the `documentation <https://docs.openfree.energy/en/latest/tutorials/rbfe_cli_tutorial.html#customize-your-campaign-setup>`_ for details (`PR #1530 <https://github.com/OpenFreeEnergy/openfe/pull/1530>`_).
+* The default atom mapper used in the CLI has been changed from ``LomapAtomMapper`` to ``KartografAtomMapper`` in line with the recommended defaults from the industry benchmarking paper. Users who wish to continue to use ``LomapAtomMapper`` can do so via the YAML configuration file. See the `documentation <https://docs.openfree.energy/en/latest/tutorials/rbfe_cli_tutorial.html#customize-your-campaign-setup>`_ for details (`PR #1530 <https://github.com/OpenFreeEnergy/openfe/pull/1530>`_).
 * An improved error message is now shown when a mapping involving a changing constraint length cannot be fixed (`PR #1529 <https://github.com/OpenFreeEnergy/openfe/pull/1529>`_).
 * The default platform for OpenMM-based Protocols is now CUDA and will fail by default on a non-Nvidia GPU enabled system (`PR #1576 <https://github.com/OpenFreeEnergy/openfe/pull/1576>`_).
 * Remove unnecessary limit on residues ids (``resids``) when getting mappings from topology in ``topology_helpers.py`` utility module (`PR #1539 <https://github.com/OpenFreeEnergy/openfe/pull/1539>`_).

docs/guide/execution/execution_theory.rst

@@ -31,7 +31,7 @@ the :class:`.Protocol` may create one or more ``ProtocolDAG``\ s, the
 :class:`.ProtocolResult` will be made from one or more
 :class:`.ProtocolDAGResult`\ s.  Finally, each :class:`.ProtocolDAGResult`
 may carry information about multiple :class:`.ProtocolUnitResult`\ s, just a
-single ``ProtocolDAG`` may involve mutliple ``ProtocolUnit``\ s.
+single ``ProtocolDAG`` may involve multiple ``ProtocolUnit``\ s.
 
 .. TODO FUTURE: figure showing the relations of protocol objects and result
    objects

docs/guide/protocols/absolutebinding.rst

@@ -29,7 +29,7 @@ Scientific Details
 Orientational restraints
 ~~~~~~~~~~~~~~~~~~~~~~~~
 
-Orientational, or Boresch-style, restraints are automaticallly (unless manually specified) applied between three
+Orientational, or Boresch-style, restraints are automatically (unless manually specified) applied between three
 protein and three ligand atoms using one bond, two angle, and three dihedral restraints.
 Reference atoms are picked based on different criteria, such as the root mean squared
 fluctuation of the atoms in a short MD simulation, the secondary structure of the protein,

docs/guide/protocols/plainmd.rst

@@ -43,7 +43,7 @@ If there is a ``SolventComponent`` in the :class:`.ChemicalSystem`, the each :cl
 A MonteCarloBarostat is used in the NPT ensemble to maintain constant pressure.
 Relevant settings under solvent conditions include the solvation settings that control the ``solvent_model`` and ``solvent_padding``.
 
-If the :class:`.ChemicalSystem` does not contain a ``SolventComponent``, the protocol runs an MD simulation in vacuum. After a minimization, the protocol performs an equilibration, followed by a production run with no periodic boundary conditions and infinite cutoffs. Settings that control the barostat or the solvation are ignored for vaccum MD simulations.
+If the :class:`.ChemicalSystem` does not contain a ``SolventComponent``, the protocol runs an MD simulation in vacuum. After a minimization, the protocol performs an equilibration, followed by a production run with no periodic boundary conditions and infinite cutoffs. Settings that control the barostat or the solvation are ignored for vacuum MD simulations.
 
 Performance consideration for gas phase MD simulations
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

docs/guide/protocols/relativehybridtopology.rst

@@ -152,7 +152,7 @@ difference produced.
       this analysis calculates the free energy difference, both in forward and backward directions.
       In this analysis, forward and backward estimates that agree within error using only a fraction of the total data
       suggest convergence [5]_. Note: the error bars reported in this plot are
-      MBAR analytical errors instead of boostrap errors.
+      MBAR analytical errors instead of bootstrap errors.
     - .. image:: img/forward_reverse_convergence.png
   * - **Timeseries of replica states.**
 

docs/guide/protocols/septop.rst

@@ -32,7 +32,7 @@ Scientific Details
 Orientational restraints
 ~~~~~~~~~~~~~~~~~~~~~~~~
 
-Orientational, or Boresch-style, restraints are automaticallly (unless manually specified) applied between three protein and three ligand atoms using one bond,
+Orientational, or Boresch-style, restraints are automatically (unless manually specified) applied between three protein and three ligand atoms using one bond,
 two angle, and three dihedral restraints. Reference atoms are picked based on different criteria, such as the root mean squared
 fluctuation of the atoms in a short MD simulation, the secondary structure of the protein, and the distance between atoms,
 based on heuristics from Baumann et al. [2]_ and Alibay et al. [3]_.

docs/reference/api/openmm_protocol_settings.rst

@@ -17,7 +17,7 @@ can be found on the individual Protocol API reference documentation pages:
 Shared OpenMM Protocol Settings
 -------------------------------
 
-The following are Settings clases which are shared between multiple
+The following are Settings classes which are shared between multiple
 OpenMM-based Protocols. Please note that not all Protocols use these
 Settings classes.
 

src/openfe/analysis/plotting.py

@@ -88,7 +88,7 @@ def plot_lambda_transition_matrix(matrix: npt.NDArray) -> Axes:
                 color=("k" if rel_prob < 0.5 else "w"),
             )
 
-        # anotate axes
+        # annotate axes
         base_settings: dict[str, Union[str, int]] = {
             "size": 10,
             "va": "center",

src/openfe/protocols/openmm_afe/afe_protocol_results.py

@@ -55,7 +55,7 @@ class AbsoluteProtocolResultMixin:
         -------
         forward_reverse : dict[str, list[Optional[dict[str, Union[npt.NDArray, openff.units.Quantity]]]]]
             A dictionary, keyed for each leg of the thermodynamic cycle,
-            either ``solvent`` and ``vaccuum` for a solvation free energy or
+            either ``solvent`` and ``vacuum` for a solvation free energy or
           ``solvent`` and ``complex`` for a binding free energy,
             with each containing a list of dictionaries containing the forward
             and reverse analysis of each repeat of that simulation type.
@@ -109,7 +109,7 @@ class AbsoluteProtocolResultMixin:
         -------
         overlap_stats : dict[str, list[dict[str, npt.NDArray]]]
           A dictionary keyed for each leg of the thermodynamic cycle, either
-          ``solvent`` and ``vaccuum` for a solvation free energy or
+          ``solvent`` and ``vacuum` for a solvation free energy or
           ``solvent`` and ``complex`` for a binding free energy,
           with each containing a list of dictionaries with the MBAR overlap
           estimates of each repeat of that simulation type.
@@ -146,7 +146,7 @@ class AbsoluteProtocolResultMixin:
         -------
         repex_stats : dict[str, list[dict[str, npt.NDArray]]]
           A dictionary with keys for each leg of the thermodynamic cycle, either
-          ``solvent`` and ``vaccuum` for a solvation free energy or
+          ``solvent`` and ``vacuum` for a solvation free energy or
           ``solvent`` and ``complex`` for a binding free energy,
           with each containing a list of dictionaries containing the replica
           transition statistics for each repeat of that simulation type.

src/openfe/protocols/openmm_afe/base_afe_units.py

@@ -5,8 +5,8 @@
 
 Base classes for the OpenMM absolute free energy ProtocolUnits.
 
-Thist mostly implements BaseAbsoluteUnit whose methods can be
+This mostly implements BaseAbsoluteUnit whose methods can be
-overriden to define different types of alchemical transformations.
+overridden to define different types of alchemical transformations.
 
 TODO
 ----

src/openfe/protocols/openmm_afe/equil_afe_settings.py

@@ -56,7 +56,7 @@ class AlchemicalSettings(SettingsBaseModel):
     """
     annihilate_sterics: bool = False
     """
-    If True, sterics (Lennard-Jones) will be annhilated instead
+    If True, sterics (Lennard-Jones) will be annihilated instead
     of decoupled. Default is False.
     """
     softcore_alpha: float = 0.5

src/openfe/protocols/openmm_afe/equil_binding_afe_method.py

@@ -14,7 +14,7 @@ alchemical sampling methods:
 Current limitations
 -------------------
 * Alchemical species with a net charge are not currently supported.
-* Disapearing molecules are only allowed in state A.
+* Disappearing molecules are only allowed in state A.
 * Only small molecules are allowed to act as alchemical molecules.
 
 Acknowledgements
@@ -254,7 +254,7 @@ class AbsoluteBindingProtocol(gufe.Protocol):
 
         if not isinstance(diff[0][0], SmallMoleculeComponent):
             errmsg = (
-                "Only dissapearing small molecule components "
+                "Only disappearing small molecule components "
                 "are supported by this protocol. "
                 f"Found a {type(diff[0][0])}"
             )
@@ -366,7 +366,7 @@ class AbsoluteBindingProtocol(gufe.Protocol):
         )
 
         # If the complex restraints schedule is all zero, it might be bad
-        # but we don't dissallow it.
+        # but we don't disallow it.
         if all([i == 0.0 for i in self.settings.complex_lambda_settings.lambda_restraints]):
             wmsg = (
                 "No restraints are being applied in the complex phase, "

src/openfe/protocols/openmm_afe/equil_solvation_afe_method.py

@@ -14,7 +14,7 @@ alchemical sampling methods:
 Current limitations
 -------------------
 * Alchemical species with a net charge are not currently supported.
-* Disapearing molecules are only allowed in state A. Support for
+* Disappearing molecules are only allowed in state A. Support for
   appearing molecules will be added in due course.
 * Only small molecules are allowed to act as alchemical molecules.
   Alchemically changing protein or solvent components would induce
@@ -266,7 +266,7 @@ class AbsoluteSolvationProtocol(gufe.Protocol):
         # Make sure that the state A unique is an SMC
         if not isinstance(diff[0][0], SmallMoleculeComponent):
             errmsg = (
-                "Only dissapearing SmallMoleculeComponents "
+                "Only disappearing SmallMoleculeComponents "
                 "are supported by this protocol. "
                 f"Found a {type(diff[0][0])}"
             )

src/openfe/protocols/openmm_md/plain_md_methods.py

@@ -585,7 +585,7 @@ class PlainMDProtocolUnit(gufe.ProtocolUnit):
         solvent_comp, protein_comp, small_mols = system_validation.get_components(stateA)
 
         # 1. Create stateA system
-        # Create a dictionary of OFFMol for each SMC for bookeeping
+        # Create a dictionary of OFFMol for each SMC for bookkeeping
         smc_components: dict[SmallMoleculeComponent, OFFMolecule]
 
         smc_components = {i: i.to_openff() for i in small_mols}
@@ -692,7 +692,7 @@ class PlainMDProtocolUnit(gufe.ProtocolUnit):
             if not output["last_checkpoint"].exists():
                 output["last_checkpoint"] = None
 
-            # The NVT PDB can be ommitted if we don't run the simulation
+            # The NVT PDB can be omitted if we don't run the simulation
             # Note: we could also just check the file exist
             if (
                 output_settings.equil_nvt_structure

src/openfe/protocols/openmm_rfe/_rfe_utils/lambdaprotocol.py

@@ -216,7 +216,7 @@ class LambdaProtocol(object):
             if self.functions[function](0) != 0:
                 raise ValueError("lambda functions must start at 0")
             if self.functions[function](1) != 1:
-                raise ValueError("lambda fucntions must end at 1")
+                raise ValueError("lambda functions must end at 1")
 
             # now validatate that it's monotonic
             global_lambda = np.linspace(0., 1., n)
@@ -268,7 +268,7 @@ class LambdaProtocol(object):
 
         Parameters
         ----------
-        shedule : np.ndarray
+        schedule : np.ndarray
             The lambda schedule to plot the function along. If ``None`` plot
             the one stored within this class. Default ``None``.
         """

src/openfe/protocols/openmm_rfe/_rfe_utils/relative.py

@@ -408,7 +408,7 @@ class HybridTopologyFactory:
         """
         Convenience method to invert a dictionary (since we do it so often).
 
-        Paramters:
+        Parameters:
         ----------
         dictionary : dict
             Dictionary you want to invert
@@ -657,7 +657,7 @@ class HybridTopologyFactory:
                 ):
                     errmsg = (f"new index exceptions {new_indices} include "
                               "unique new and environment atoms, which is "
-                              "dissallowed")
+                              "disallowed")
                     raise AssertionError
 
     def _handle_constraints(self):
@@ -710,7 +710,7 @@ class HybridTopologyFactory:
         Parameters
         ----------
         atm_map : dict[int, int]
-          The atom map correspondance between the two Systems.
+          The atom map correspondence between the two Systems.
         env_atoms: set[int]
           A list of environment atoms for the target System. This
           checks that no alchemical atoms are being tied to.
@@ -1940,7 +1940,7 @@ class HybridTopologyFactory:
                     atom_pair[0], atom_pair[1])
 
             # TODO: work out why there's a bunch of commented out code here
-            # Exerpt:
+            # Excerpt:
             # If it's not handled by an exception in the original system, we
             # just add the regular parameters as an exception
             # TODO: this implies that the old-old nonbonded interactions (those
@@ -2142,7 +2142,7 @@ class HybridTopologyFactory:
             # If it's a subset of unique_new_atoms, then this is an
             # intra-unique interaction and should have its exceptions
             # specified in the regular nonbonded force. However, this is
-            # handled elsewhere as above due to pecularities with exception
+            # handled elsewhere as above due to peculiarities with exception
             # handling
             if index_set.issubset(self._atom_classes['unique_new_atoms']):
                 continue
@@ -2210,7 +2210,7 @@ class HybridTopologyFactory:
     def _handle_old_new_exceptions(self):
         """
         Find the exceptions associated with old-old and old-core interactions,
-        as well as new-new and new-core interactions.  Theses exceptions will
+        as well as new-new and new-core interactions.  These exceptions will
         be placed in CustomBondedForce that will interpolate electrostatics and
         a softcore potential.
 

src/openfe/protocols/openmm_rfe/hybridtop_protocols.py

@@ -258,7 +258,7 @@ class RelativeHybridTopologyProtocol(gufe.Protocol):
         mapping : Optional[Union[ComponentMapping, list[ComponentMapping]]]
           all mappings between transforming components.
         alchemical_components : dict[str, list[Component]]
-          Dictionary contatining the alchemical components for
+          Dictionary containing the alchemical components for
           states A and B.
 
         Raises

src/openfe/protocols/openmm_rfe/hybridtop_units.py

@@ -348,7 +348,7 @@ class HybridTopologySetupUnit(gufe.ProtocolUnit, HybridTopologyUnitMixin):
           Dictionary of OpenFF Molecules keyed by SmallMoleculeComponent
           to be present in system B.
         mapping : LigandAtomMapping
-          LigandAtomMapping defining the correspondance betwee state A
+          LigandAtomMapping defining the correspondence between state A
           and B's alchemical ligand.
         stateA_topology : openmm.app.Topology
           The OpenMM topology for state A.
@@ -479,7 +479,7 @@ class HybridTopologySetupUnit(gufe.ProtocolUnit, HybridTopologyUnitMixin):
         stateB_positions : openmm.unit.Quantity
           Positions of partials for state B System.
         system_mapping : dict[str, dict[int, int]]
-          Dictionary of mappings defining the correspondance between
+          Dictionary of mappings defining the correspondence between
           the two state Systems.
         """
         if self.verbose:
@@ -1058,7 +1058,7 @@ class HybridTopologyMultiStateSimulationUnit(gufe.ProtocolUnit, HybridTopologyUn
         }
 
         # note we if/else around sampler method because in the future
-        # we will try to re-use this method and just have _SAMPLERs be
+        # we will try to reuse this method and just have _SAMPLERs be
         # defined elsewhere
         sampler_method = simulation_settings.sampler_method.lower()
         try:

src/openfe/protocols/openmm_septop/base.py

@@ -5,8 +5,8 @@
 
 Base classes for the equilibrium OpenMM SepTop free energy ProtocolUnits.
 
-Thist mostly implements BaseSepTopUnit whose methods can be
+This mostly implements BaseSepTopUnit whose methods can be
-overriden to define different types of alchemical transformations.
+overridden to define different types of alchemical transformations.
 
 TODO
 ----

src/openfe/protocols/openmm_utils/multistate_analysis.py

@@ -167,7 +167,7 @@ class MultistateEquilFEAnalysis:
         Parameters
         ----------
         forward_reverse_samples : int
-          Number of samples to take in the foward and reverse analysis of
+          Number of samples to take in the forward and reverse analysis of
           the free energies.
         """
         # Do things that get badly cached later

src/openfe/protocols/openmm_utils/settings_validation.py

@@ -246,7 +246,7 @@ def convert_real_time_analysis_iterations(
 ) -> tuple[Optional[int], Optional[int]]:
     """Convert time units in Settings to various other units
 
-    Interally openmmtools uses various quantities with units of time,
+    Internally openmmtools uses various quantities with units of time,
     steps, and iterations.
 
     Our Settings objects instead have things defined in time (fs or ps).

src/openfe/protocols/openmm_utils/system_creation.py

@@ -34,7 +34,7 @@ def get_system_generator(
     """
     Create a SystemGenerator based on Protocol settings.
 
-    Paramters
+    Parameters
     ---------
     forcefield_settings : OpenMMSystemGeneratorFFSettings
       Force field settings, including necessary information
@@ -204,7 +204,7 @@ def get_omm_modeller(
     for comp, mol in small_mols.items():
         _add_small_mol(comp, mol, system_modeller, component_resids)
 
-    # Add solvent if neeeded
+    # Add solvent if needed
     if solvent_comp is not None:
         # Do unit conversions if necessary
         solvent_padding = None

src/openfe/protocols/restraint_utils/geometry/boresch/host.py

@@ -208,7 +208,7 @@ class EvaluateBoreschAtoms(AnalysisBase):
       in that order.
     angle_force_constant : openff.units.Quantity
       The force constant for the angle.
-    temperature : openff.units.Quanity
+    temperature : openff.units.Quantity
       The system temperature in units compatible with Kelvin.
     """
 
@@ -567,7 +567,7 @@ def _get_lowest_variance_restraint_hostanchor(
       restraint atoms, in that order.
     angle_force_constant : openff.units.Quantity
       The force constant for the angle.
-    temperature : openff.units.Quanity
+    temperature : openff.units.Quantity
       The system temperature in units compatible with Kelvin.
 
     Returns

src/openfe/storage/resultclient.py

@@ -20,7 +20,7 @@ GUFEKEY_JSON_REGEX = re.compile('":gufe-key:": "(?P<token>[A-Za-z0-9_]+-[0-9a-f]
 
 class _ResultContainer(abc.ABC):
     """
-    Abstract class, represents all data under some level of the heirarchy.
+    Abstract class, represents all data under some level of the hierarchy.
     """
 
     def __init__(self, parent, path_component):
@@ -143,7 +143,7 @@ class ResultClient(_ResultContainer):
     def store_transformation(self, transformation):
         """Store a :class:`.Transformation`.
 
-        Parmeters
+        Parameters
         ---------
         transformation: :class:`.Transformation`
             the transformation to store
@@ -153,7 +153,7 @@ class ResultClient(_ResultContainer):
     def store_network(self, network):
         """Store a :class:`.AlchemicalNetwork`.
 
-        Parmeters
+        Parameters
         ---------
         network: :class:`.AlchemicalNetwork`
             the network to store
@@ -165,7 +165,7 @@ class ResultClient(_ResultContainer):
         registry = {}
 
         def recursive_build_object_cache(gufe_key):
-            """DFS to rebuild object heirarchy"""
+            """DFS to rebuild object hierarchy"""
             # This implementation is a bit fragile, because ensuring that we
             # don't duplicate objects in memory depends on the fact that
             # `key_decode_dependencies` gets keyencoded objects from a cache
@@ -237,7 +237,7 @@ class ResultClient(_ResultContainer):
     def _load_next_level(self, transformation):
         return TransformationResult(self, transformation)
 
-    # override these two inherited properies since this is always the end of
+    # override these two inherited properties since this is always the end of
     # the recursive chain
     @property
     def path(self):

src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol.py

@@ -502,7 +502,7 @@ class TestT4LysozymeTIP4PExtraSettingsDryRun(TestT4LysozymeDryRun):
         s.forcefield_settings.nonbonded_cutoff = 0.8 * offunit.nanometer
         s.forcefield_settings.forcefields = [
             "amber/ff14SB.xml",  # ff14SB protein force field
-            "amber/tip4pew_standard.xml",  # FF we are testsing with the fun VS
+            "amber/tip4pew_standard.xml",  # FF we are testing with the fun VS
             "amber/phosaa10.xml",  # Handles THE TPO
         ]
         s.integrator_settings.reassign_velocities = True

src/openfe/tests/protocols/openmm_abfe/test_abfe_validation.py

@@ -212,7 +212,7 @@ def test_validate_solvent_endstates_solvent_dissapearing(
         }
     )
 
-    errmsg = "Only dissapearing small molecule components"
+    errmsg = "Only disappearing small molecule components"
     with pytest.raises(ValueError, match=errmsg):
         AbsoluteBindingProtocol._validate_endstates(stateA, stateB)
 

src/openfe/tests/protocols/openmm_ahfe/test_ahfe_protocol.py

@@ -406,12 +406,12 @@ def test_setup_solv_benzene(benzene_system, protocol_dry_settings, tmpdir):
 def test_dry_run_vsite_fail(benzene_system, tmpdir, protocol_dry_settings):
     protocol_dry_settings.vacuum_forcefield_settings.forcefields = [
         "amber/ff14SB.xml",  # ff14SB protein force field
-        "amber/tip4pew_standard.xml",  # FF we are testsing with the fun VS
+        "amber/tip4pew_standard.xml",  # FF we are testing with the fun VS
         "amber/phosaa10.xml",  # Handles THE TPO
     ]
     protocol_dry_settings.solvent_forcefield_settings.forcefields = [
         "amber/ff14SB.xml",  # ff14SB protein force field
-        "amber/tip4pew_standard.xml",  # FF we are testsing with the fun VS
+        "amber/tip4pew_standard.xml",  # FF we are testing with the fun VS
         "amber/phosaa10.xml",  # Handles THE TPO
     ]
     protocol_dry_settings.solvation_settings.solvent_model = "tip4pew"
@@ -451,12 +451,12 @@ def test_dry_run_vsite_fail(benzene_system, tmpdir, protocol_dry_settings):
 def test_setup_dry_sim_solv_benzene_tip4p(benzene_system, protocol_dry_settings, tmpdir):
     protocol_dry_settings.vacuum_forcefield_settings.forcefields = [
         "amber/ff14SB.xml",  # ff14SB protein force field
-        "amber/tip4pew_standard.xml",  # FF we are testsing with the fun VS
+        "amber/tip4pew_standard.xml",  # FF we are testing with the fun VS
         "amber/phosaa10.xml",  # Handles THE TPO
     ]
     protocol_dry_settings.solvent_forcefield_settings.forcefields = [
         "amber/ff14SB.xml",  # ff14SB protein force field
-        "amber/tip4pew_standard.xml",  # FF we are testsing with the fun VS
+        "amber/tip4pew_standard.xml",  # FF we are testing with the fun VS
         "amber/phosaa10.xml",  # Handles THE TPO
     ]
     protocol_dry_settings.solvation_settings.solvent_model = "tip4pew"

src/openfe/tests/protocols/openmm_ahfe/test_ahfe_validation.py

@@ -238,7 +238,7 @@ def test_validate_alchem_nonsmc(benzene_modifications):
         }
     )
 
-    errmsg = "Only dissapearing SmallMoleculeComponents"
+    errmsg = "Only disappearing SmallMoleculeComponents"
     with pytest.raises(ValueError, match=errmsg):
         AbsoluteSolvationProtocol._validate_endstates(stateA, stateB)
 

src/openfe/tests/protocols/openmm_md/test_plain_md_protocol.py

@@ -380,7 +380,7 @@ def test_dry_run_ligand_tip4p(benzene_system, tmpdir):
     settings.engine_settings.compute_platform = None
     settings.forcefield_settings.forcefields = [
         "amber/ff14SB.xml",  # ff14SB protein force field
-        "amber/tip4pew_standard.xml",  # FF we are testsing with the fun VS
+        "amber/tip4pew_standard.xml",  # FF we are testing with the fun VS
         "amber/phosaa10.xml",  # Handles THE TPO
     ]
     # we need a larger padding distance when using the dodecahedron box

src/openfe/tests/protocols/openmm_rfe/test_hybrid_top_protocol.py

@@ -568,7 +568,7 @@ def tip4p_hybrid_factory(
     settings.engine_settings.compute_platform = None
     settings.forcefield_settings.forcefields = [
         "amber/ff14SB.xml",  # ff14SB protein force field
-        "amber/tip4pew_standard.xml",  # FF we are testsing with the fun VS
+        "amber/tip4pew_standard.xml",  # FF we are testing with the fun VS
         "amber/phosaa10.xml",  # Handles THE TPO
     ]
     settings.solvation_settings.solvent_padding = 1.5 * unit.nanometer
@@ -900,7 +900,7 @@ def test_setup_user_charges(benzene_modifications, vac_settings, tmpdir):
         prop_chgs = np.array(prop_chgs.split(), dtype=float)
         np.testing.assert_allclose(prop_chgs, charge_array.m)
 
-    # Create new smc with overriden charges
+    # Create new smc with overridden charges
     benzene_offmol = benzene_modifications["benzene"].to_openff()
     toluene_offmol = benzene_modifications["toluene"].to_openff()
     benzene_rand_chg = assign_fictitious_charges(benzene_offmol)
@@ -910,7 +910,7 @@ def test_setup_user_charges(benzene_modifications, vac_settings, tmpdir):
     benzene_smc = openfe.SmallMoleculeComponent.from_openff(benzene_offmol)
     toluene_smc = openfe.SmallMoleculeComponent.from_openff(toluene_offmol)
 
-    # Check that the new smcs have the new overriden charges
+    # Check that the new smcs have the new overridden charges
     check_propchgs(benzene_smc, benzene_rand_chg)
     check_propchgs(toluene_smc, toluene_rand_chg)
 
@@ -1001,7 +1001,7 @@ def test_virtual_sites_no_reassign(
     """
     solv_settings.forcefield_settings.forcefields = [
         "amber/ff14SB.xml",  # ff14SB protein force field
-        "amber/tip4pew_standard.xml",  # FF we are testsing with the fun VS
+        "amber/tip4pew_standard.xml",  # FF we are testing with the fun VS
         "amber/phosaa10.xml",  # Handles THE TPO
     ]
     solv_settings.solvation_settings.solvent_padding = 1.0 * unit.nanometer

src/openfe/tests/protocols/openmm_septop/test_septop_protocol.py

@@ -952,7 +952,7 @@ def test_dry_run_benzene_toluene_tip4p(
 ):
     protocol_dry_settings.forcefield_settings.forcefields = [
         "amber/ff14SB.xml",  # ff14SB protein force field
-        "amber/tip4pew_standard.xml",  # FF we are testsing with the fun VS
+        "amber/tip4pew_standard.xml",  # FF we are testing with the fun VS
         "amber/phosaa10.xml",  # Handles THE TPO
     ]
     protocol_dry_settings.solvent_solvation_settings.solvent_model = "tip4pew"

src/openfe/tests/protocols/restraints/test_geometry_utils.py

@@ -524,7 +524,7 @@ class TestStableSelection:
 
     def test_small_chain(self, t4_lysozyme_trajectory_universe):
         """
-        Artifically set min_structure_size so large that no chains are recognised.
+        Artificially set min_structure_size so large that no chains are recognised.
         """
         stable_protein = stable_secondary_structure_selection(
             atomgroup=t4_lysozyme_trajectory_universe.atoms,

src/openfe/tests/setup/atom_mapping/test_lomap_atommapper.py

@@ -74,7 +74,7 @@ def test_bad_mapping(atom_mapping_basic_test_files, lomap_old_mapper):
         next(mapping_gen)
 
 
-# TODO: Remvoe these test when element changes are allowed - START
+# TODO: Remove these test when element changes are allowed - START
 def test_simple_no_element_changes(atom_mapping_basic_test_files, lomap_old_mapper):
     # basic sanity check on the LigandAtomMapper
     mol1 = atom_mapping_basic_test_files["methylcyclohexane"]
@@ -101,4 +101,4 @@ def test_bas_mapping_no_element_changes(atom_mapping_basic_test_files, lomap_old
         next(mapping_gen)
 
 
-# TODO: Remvoe these test when element changes are allowed - END
+# TODO: Remove these test when element changes are allowed - END

src/openfe/utils/optional_imports.py

@@ -11,7 +11,7 @@ from typing import Callable
 
 def requires_package(package_name: str) -> Callable:
     """
-    Helper function to denote that a funciton requires some optional
+    Helper function to denote that a function requires some optional
     dependency. A function decorated with this decorator will raise
     `MissingDependencyError` if the package is not found by
     `importlib.import_module()`.