Showing 288 of 347 total issues
Function _perform_ncmc_protocol
has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring. Open
def _perform_ncmc_protocol(
self,
titration_group_indices: List[int],
initial_titration_states: List[int],
final_titration_states: List[int],
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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 _parse_fortran_namelist
has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring. Open
def _parse_fortran_namelist(filename, namelist_name):
"""
Parse a fortran namelist generated by AMBER 11 constant-pH python scripts.
Parameters
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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 get_versions
has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring. Open
def get_versions(verbose=False):
"""Get the project version from whatever source is available.
Returns dict with two keys: 'version' and 'full'.
"""
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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 bar_all_states
has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring. Open
def bar_all_states(
dataset: Union[netCDF4.Dataset, List[netCDF4.Dataset]],
bootstrap: bool = False,
num_bootstrap_samples: int = 1000,
to_first_state_only: bool = True,
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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 gather_trajectories
has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring. Open
def gather_trajectories(
datasets: List[netCDF4.Dataset],
from_state: int,
to_state: int,
cumulative: bool = True,
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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 get_populations
has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring. Open
def get_populations(self, pH, temperature=None, ionic_strength=None, strict=True):
"""Return the state populations for a given pH.
Parameters
----------
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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_command
has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring. Open
def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=None):
"""Call the given command(s)."""
assert isinstance(commands, list)
p = None
for c in commands:
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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 from_system
has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring. Open
def from_system(cls, system: openmm.System, indices: Dict[str, int]):
"""Instantiate a COOHDummyMover for a single C-COOH moiety in your system.
Parameters
----------
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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_command
has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring. Open
def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
env=None):
"""Call the given command(s)."""
assert isinstance(commands, list)
p = None
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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
File schrodinger.py
has 264 lines of code (exceeds 250 allowed). Consider refactoring. Open
#!/usr/bin/env python
"""Miscellaneous wrapper functions to Schrodinger's computational chemistry tools.
Adapted from openmoltools: https://github.com/choderalab/openmoltools.
_TitratableResidue
has 22 functions (exceeds 20 allowed). Consider refactoring. Open
class _TitratableResidue:
"""Representation of a single residue with multiple titration states."""
def __init__(self):
"""
Function import_gk_values
has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring. Open
def import_gk_values(self, gk_dict: Dict[str, np.ndarray], strict=False):
"""Import precalibrated gk values. Only use this if your simulation settings are exactly the same.
If you changed any details, rerun calibrate instead!
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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 _find_all_potential_bond_types_to_atom
has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring. Open
def _find_all_potential_bond_types_to_atom(
self, atomname, final_types, potential_types
):
""" Find all the atoms it is bonded to, and collect their types
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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 git_get_keywords
has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring. Open
def git_get_keywords(versionfile_abs):
"""Extract version information from the given file."""
# the code embedded in _version.py can just fetch the value of these
# keywords. When used from setup.py, we don't want to import _version.py,
# so we do it with a regexp instead. This function is not used from
- 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 adapt
has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring. Open
def adapt(self):
"""
Adapt the weights for the residue that is being calibrated.
"""
if self.drive.calibration_state is None:
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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 plot_heatmap
has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring. Open
def plot_heatmap(
dataset: netCDF4.Dataset,
ax: plt.Axes = None,
color: str = "charge",
residues: list = None,
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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 git_get_keywords
has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring. Open
def git_get_keywords(versionfile_abs):
"""Extract version information from the given file."""
# the code embedded in _version.py can just fetch the value of these
# keywords. When used from setup.py, we don't want to import _version.py,
# so we do it with a regexp instead. This function is not used from
- 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 _get14exceptions
has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring. Open
def _get14exceptions(self, system, particle_indices):
"""
Return a list of all 1,4 exceptions involving the specified particles that are not exclusions.
Parameters
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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 from_xml
has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring. Open
def from_xml(cls, root: etree.Element):
"""Instantiate this object from xml."""
if not root.tag == "SAMSState":
raise ValueError(
"Wrong XML element provided. Expected 'SAMSState', got '{}'".format(
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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 git_versions_from_keywords
has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring. Open
def git_versions_from_keywords(keywords, tag_prefix, verbose):
"""Get version information from git keywords."""
if not keywords:
raise NotThisMethod("no keywords at all, weird")
date = keywords.get("date")
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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"