Showing 120 of 121 total issues
File experiment.py has 2390 lines of code (exceeds 250 allowed). Consider refactoring. Open
#!/usr/bin/env python
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# MODULE DOCSTRING
# =============================================================================File restraints.py has 1924 lines of code (exceeds 250 allowed). Consider refactoring. Open
#!/usr/local/bin/env python
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# ==============================================================================File pipeline.py has 1832 lines of code (exceeds 250 allowed). Consider refactoring. Open
#!/usr/bin/env python
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# =============================================================================================File utils.py has 1331 lines of code (exceeds 250 allowed). Consider refactoring. Open
#!/usr/local/bin/env python
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# MODULE DOCSTRING
# ==============================================================================File yank.py has 1051 lines of code (exceeds 250 allowed). Consider refactoring. Open
#!/usr/local/bin/env python
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# MODULE DOCSTRING
# ==============================================================================File analyze.py has 934 lines of code (exceeds 250 allowed). Consider refactoring. Open
#!/usr/local/bin/env python
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# MODULE DOCSTRING
# ==============================================================================Function _setup_molecules has a Cognitive Complexity of 100 (exceeds 5 allowed). Consider refactoring. Open
def _setup_molecules(self, *args):
"""Set up the files needed to generate the system for all the molecules.
If OpenEye tools are installed, this generate the molecules when the source is
not a file. If two (or more) molecules generated by OpenEye have overlapping- 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
File notebook.py has 541 lines of code (exceeds 250 allowed). Consider refactoring. Open
"""
YANK Health Report Notebook formatter
This module handles all the figure formatting and processing to minimize the code shown in the Health Report Jupyter
Notebook. All data processing and analysis is handled by the main multistate.analyzers package,Function _setup_system has a Cognitive Complexity of 53 (exceeds 5 allowed). Consider refactoring. Open
def _setup_system(self, system_file_path, pack, alchemical_charge,
system_parameters, solvent_id, *molecule_ids, **kwargs):
"""Setup a system and create its prmtop/inpcrd files.
IMPORTANT: This function does not check if it's about to overwrite- 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 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 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.
- 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 dispatch has a Cognitive Complexity of 44 (exceeds 5 allowed). Consider refactoring. Open
def dispatch(args):
import re
import doctest
import pkgutil- 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 _pick_restrained_atoms has a Cognitive Complexity of 44 (exceeds 5 allowed). Consider refactoring. Open
def _pick_restrained_atoms(self, sampler_state, topography):
"""Select atoms to be used in restraint.
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
File validator.py has 440 lines of code (exceeds 250 allowed). Consider refactoring. Open
import os
import collections
import copy
import inspect
import loggingFunction dispatch has a Cognitive Complexity of 40 (exceeds 5 allowed). Consider refactoring. Open
def dispatch(args):
"""
Set up and run YANK calculation from a script.
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
ExperimentBuilder has 41 functions (exceeds 20 allowed). Consider refactoring. Open
class ExperimentBuilder(object):
"""Parse YAML configuration file and build the experiment.
The relative paths indicated in the script are assumed to be relative to
the script directory. However, if ExperimentBuilder is initiated with a stringFunction _configure_platform has a Cognitive Complexity of 32 (exceeds 5 allowed). Consider refactoring. Open
def _configure_platform(cls, platform_name, platform_precision):
"""
Configure the platform to be used for simulation for the given precision.
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 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 _check_resume has a Cognitive Complexity of 30 (exceeds 5 allowed). Consider refactoring. Open
def _check_resume(self, check_setup=True, check_experiments=True):
"""Perform dry run to check if we are going to overwrite files.
If we find folders that ExperimentBuilder should create we raise an exception
unless resume_setup or resume_simulation are found, in which case we- 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 run has a Cognitive Complexity of 30 (exceeds 5 allowed). Consider refactoring. Open
def run(self, n_iterations=None):
"""
Run the experiment.
Runs until either the maximum number of iterations have been reached or the sampler- 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"