File analyze.py has 934 lines of code (exceeds 250 allowed). Consider refactoring. Open
#!/usr/local/bin/env python
# ==============================================================================
# MODULE DOCSTRING
# ==============================================================================Function extract_trajectory has a Cognitive Complexity of 47 (exceeds 5 allowed). Consider refactoring. Open
def extract_trajectory(nc_path, nc_checkpoint_file=None, state_index=None, replica_index=None,
start_frame=0, end_frame=-1, skip_frame=1, keep_solvent=True,
discard_equilibration=False, image_molecules=False):
"""Extract phase trajectory from the NetCDF4 file.
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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 run_all_analysis has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring. Open
def run_all_analysis(self, serialize_data=True, serial_data_path=None, **analyzer_kwargs):
"""
Run all the automatic analysis through the :func:`ExperimentAnalyzer.auto_analyze`
Parameters- 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 extract_trajectory has 10 arguments (exceeds 4 allowed). Consider refactoring. Open
def extract_trajectory(nc_path, nc_checkpoint_file=None, state_index=None, replica_index=None,Function get_experiment_free_energy_data has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring. Open
def get_experiment_free_energy_data(self):
"""
Get the free Yank Experiment free energy, broken down by phase and total experiment
Output is of the form:- 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 get_equilibration_data has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring. Open
def get_equilibration_data(self, discard_from_start=1):
"""
Create the equilibration scatter plots showing the trend lines, correlation time,
and number of effective samples
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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 print_analysis_data has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring. Open
def print_analysis_data(analysis_data, header=None):
"""
Helper function of printing the analysis data payload from a :func:`ExperimentAnalyzer.auto_analyze` call
Parameters- 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 __init__ has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def __init__(self, store_directory, **analyzer_kwargs):
# Convert analyzer string quantities into variables.
for key, value in analyzer_kwargs.items():
try:
quantity = utils.quantity_from_string(value)- 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 get_general_simulation_data has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def get_general_simulation_data(self):
"""
General purpose simulation data on number of iterations, number of states, and number of atoms.
This just prints out this data in a regular, formatted pattern.
- 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"