File yank.py has 1051 lines of code (exceeds 250 allowed). Consider refactoring. Open
#!/usr/local/bin/env python
# ==============================================================================
# MODULE DOCSTRING
# ==============================================================================Function select has a Cognitive Complexity of 52 (exceeds 5 allowed). Consider refactoring. Open
def select(self, selection, as_set=False, sort_by='auto', subset=None) -> Union[List[int], Set[int]]:
"""
Select atoms based on selection format which can be a number of formats:
* Single integer (a bit redundant)- Read upRead up
Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
Function create has a Cognitive Complexity of 31 (exceeds 5 allowed). Consider refactoring. Open
def create(self, thermodynamic_state, sampler_states, topography, protocol,
storage, restraint=None, anisotropic_dispersion_cutoff=None,
alchemical_regions=None, alchemical_factory=None, metadata=None):
"""Create a new AlchemicalPhase calculation for a specified protocol.
- Read upRead up
Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
Function _expand_state_cutoff has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring. Open
def _expand_state_cutoff(thermodynamic_state, expanded_cutoff_distance,
replace_reaction_field=False, switch_width=None):
"""Expand the thermodynamic state cutoff to the given one.
If replace_reaction_field is True, the system will be modified- Read upRead up
Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
Function create has 10 arguments (exceeds 4 allowed). Consider refactoring. Open
def create(self, thermodynamic_state, sampler_states, topography, protocol,Function create has 29 lines of code (exceeds 25 allowed). Consider refactoring. Open
def create(self, thermodynamic_state, sampler_states, topography, protocol,
storage, restraint=None, anisotropic_dispersion_cutoff=None,
alchemical_regions=None, alchemical_factory=None, metadata=None):
"""Create a new AlchemicalPhase calculation for a specified protocol.
Function _find_similar_sampler_states has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring. Open
def _find_similar_sampler_states(sampler_states):
"""Groups SamplerStates that have the same positions.
Returns
-------- Read upRead up
Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
Function create has 6 arguments (exceeds 4 allowed). Consider refactoring. Open
def create(self, thermodynamic_state, sampler_states, storage,Function _minimize_sampler_state has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring. Open
def _minimize_sampler_state(sampler_state_id, sampler_states, thermodynamic_state,
tolerance, max_iterations):
"""Minimize the specified sampler state at the given thermodynamic state.
"""
sampler_state = sampler_states[sampler_state_id]- Read upRead up
Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
Function _build_default_alchemical_region has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def _build_default_alchemical_region(system, topography, protocol):
"""Create a default AlchemicalRegion if the user hasn't provided one."""
# TODO: we should probably have a second region that annihilate sterics of counterions.
alchemical_region_kwargs = {}
- Read upRead up
Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"