Fixed code formatting

cvpack/cvpack.py

@@ -227,7 +227,7 @@ def getPeriod(self) -> t.Optional[mmunit.SerializableQuantity]:
         return mmunit.SerializableQuantity(self._period, self.getUnit())
 
     def addToSystem(
-        self, system: openmm.System, set_unused_force_group: bool = True
+        self, system: openmm.System, setUnusedForceGroup: bool = True
     ) -> None:
         """
         Add this collective variable to an :OpenMM:`System`.
@@ -236,11 +236,11 @@ def addToSystem(
         ----------
         system
             The system to which this collective variable should be added
-        set_unused_force_group
+        setUnusedForceGroup
             If True, the force group of this collective variable will be set to the
             first available force group in the system
         """
-        if set_unused_force_group:
+        if setUnusedForceGroup:
             self._setUnusedForceGroup(system)
         system.addForce(self)
 

cvpack/tests/test_cvpack.py

@@ -59,7 +59,7 @@ def __init__(self, first: int, second: float, third: str = "3"):
 
     # pylint: enable=missing-class-docstring, unused-argument
 
-    args, defaults = Test._getArguments()
+    args, defaults = Test._getArguments()  # pylint: disable=protected-access
     assert args["first"] is int
     assert args["second"] is float
     assert args["third"] is str
@@ -82,7 +82,7 @@ def perform_common_tests(
     assert unity.value_in_unit_system(unit.md_unit_system) == 1
 
     # Class must have full type annotation (except for argument `self`)
-    args, _ = collectiveVariable._getArguments()
+    args, _ = collectiveVariable._getArguments()  # pylint: disable=protected-access
     for _, annotation in args.items():
         assert annotation is not inspect.Parameter.empty
 

cvpack/utils.py

@@ -19,6 +19,8 @@
 
 from .serializer import Serializable
 
+# pylint: disable=protected-access,c-extension-no-member
+
 
 class NonbondedForceSurrogate(
     Serializable
@@ -210,7 +212,6 @@ def get_single_force_state(
         return context.getState(
             getEnergy=getEnergy, getForces=getForces, groups=1 << self_group
         )
-    # old_group = force.getForceGroup()
     new_group = force._setUnusedForceGroup(context.getSystem())
     context.reinitialize(preserveState=True)
     state = context.getState(
@@ -237,7 +238,6 @@ def compute_effective_mass(force: openmm.Force, context: openmm.Context) -> floa
     float
         The effective mass of the force at the given context
     """
-    # pylint: disable=protected-access,c-extension-no-member
     state = get_single_force_state(force, context, getForces=True)
     get_mass = functools.partial(
         openmm._openmm.System_getParticleMass, context.getSystem()
@@ -249,4 +249,3 @@ def compute_effective_mass(force: openmm.Force, context: openmm.Context) -> floa
         return mmunit.Quantity(np.inf, force._mass_unit)
     mass_values = np.fromiter(map(get_mass, nonzeros), dtype=np.float64)
     return 1.0 / np.sum(squared_forces[nonzeros] / mass_values)
-    # pylint: enable=protected-access,c-extension-no-member