Showing 542 of 542 total issues
File core.py
has 7031 lines of code (exceeds 250 allowed). Consider refactoring. Open
""" Toolkit for modeling complex datasets with collections of user-friendly tables
Many classes contain the methods ``serialize()`` and `deserialize()``, which invert each other.
``serialize()`` converts a python object instance into a string representation, whereas
``deserialize()`` parses an object's string representation -- as would be stored in a file or spreadsheet
File migrate.py
has 2830 lines of code (exceeds 250 allowed). Consider refactoring. Open
""" Support schema migration
:Author: Arthur Goldberg <Arthur.Goldberg@mssm.edu>
:Date: 2018-11-18
:Copyright: 2018, Karr Lab
File io.py
has 2243 lines of code (exceeds 250 allowed). Consider refactoring. Open
""" Reading/writing schema objects to/from files
* Comma separated values (.csv)
* XLSX (.xlsx)
* JavaScript Object Notation (.json)
File expression.py
has 1493 lines of code (exceeds 250 allowed). Consider refactoring. Open
""" Utilities for processing mathematical expressions used by obj_tables models
:Author: Arthur Goldberg <Arthur.Goldberg@mssm.edu>
:Author: Jonathan Karr <karr@mssm.edu>
:Date: 2018-12-19
Function init_schema
has a Cognitive Complexity of 154 (exceeds 5 allowed). Consider refactoring. Open
def init_schema(filename, out_filename=None):
""" Initialize an `ObjTables` schema from a tabular declarative specification in
:obj:`filename`. :obj:`filename` can be a XLSX, CSV, or TSV file.
Schemas (classes and attributes) should be defined using the following tabular 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 run
has a Cognitive Complexity of 147 (exceeds 5 allowed). Consider refactoring. Open
def run(self, path, schema_name=None, models=None,
allow_multiple_sheets_per_model=False,
ignore_missing_models=False, ignore_extra_models=False,
ignore_sheet_order=False,
include_all_attributes=True, ignore_missing_attributes=False, ignore_extra_attributes=False,
- 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
Similar blocks of code found in 2 locations. Consider refactoring. Open
class QuantityInfo(obj_tables.Model):
quantity_type = obj_tables.StringAttribute(verbose_name='QuantityType')
symbol = obj_tables.StringAttribute(verbose_name='Symbol')
unit = obj_tables.StringAttribute(verbose_name='Unit')
constant = obj_tables.StringAttribute(verbose_name='Constant')
- Read upRead up
Duplicated Code
Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:
Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.
When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).
Tuning
This issue has a mass of 305.
We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.
The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.
If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.
See codeclimate-duplication
's documentation for more information about tuning the mass threshold in your .codeclimate.yml
.
Refactorings
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Similar blocks of code found in 2 locations. Consider refactoring. Open
class Enzyme(obj_tables.Model):
comment = obj_tables.StringAttribute(verbose_name='Comment')
reference_name = obj_tables.StringAttribute(verbose_name='ReferenceName')
reference_pub_med = obj_tables.StringAttribute(verbose_name='ReferencePubMed')
reference_d_o_i = obj_tables.StringAttribute(verbose_name='ReferenceDOI')
- Read upRead up
Duplicated Code
Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:
Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.
When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).
Tuning
This issue has a mass of 305.
We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.
The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.
If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.
See codeclimate-duplication
's documentation for more information about tuning the mass threshold in your .codeclimate.yml
.
Refactorings
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
File SBtab.py
has 1031 lines of code (exceeds 250 allowed). Consider refactoring. Open
# Schema automatically generated at 2020-05-29 00:27:56
import obj_tables
Function import_module_for_migration
has a Cognitive Complexity of 116 (exceeds 5 allowed). Consider refactoring. Open
def import_module_for_migration(self, validate=True, required_attrs=None, debug=False,
mod_patterns=None, print_code=False):
""" Import a schema from a Python module in a file, which may be in a package
Args:
- 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 read_model
has a Cognitive Complexity of 109 (exceeds 5 allowed). Consider refactoring. Open
def read_model(self, reader, sheet_name, schema_name, model, include_all_attributes=True,
ignore_missing_attributes=False, ignore_extra_attributes=False,
ignore_attribute_order=False, ignore_empty_rows=True,
validate=True):
""" Instantiate a list of objects from data in a table in a 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
File utils.py
has 881 lines of code (exceeds 250 allowed). Consider refactoring. Open
""" Utilities
:Author: Jonathan Karr <karr@mssm.edu>
:Author: Arthur Goldberg <Arthur.Goldberg@mssm.edu>
:Date: 2016-11-23
File core.py
has 865 lines of code (exceeds 250 allowed). Consider refactoring. Open
""" Chemistry attributes
:Author: Jonathan Karr <karr@mssm.edu>
:Date: 2017-05-10
:Copyright: 2017, Karr Lab
Function write_model
has a Cognitive Complexity of 94 (exceeds 5 allowed). Consider refactoring. Open
def write_model(self, writer, model, objects, schema_name, date, doc_metadata, doc_metadata_model, model_metadata, sheet_models,
include_all_attributes=True, encoded=None, write_empty_models=True, write_empty_cols=True,
extra_entries=0, protected=True):
""" Write a list of model objects to a 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 from_dict
has a Cognitive Complexity of 89 (exceeds 5 allowed). Consider refactoring. Open
def from_dict(json, models, decode_primary_objects=True, primary_objects=None, decoded=None, ignore_extra_models=False,
validate=False, output_format=None):
""" Decode a simple Python representation (dict, list, str, float, bool, None) of an object that
is compatible with JSON and YAML, including references to objects through :obj:`__id` keys.
- 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
Similar blocks of code found in 2 locations. Consider refactoring. Open
def get_xlsx_validation(self, sheet_models=None, doc_metadata_model=None):
""" Get XLSX validation
Args:
sheet_models (:obj:`list` of :obj:`Model`, optional): models encoded as separate sheets
- Read upRead up
Duplicated Code
Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:
Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.
When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).
Tuning
This issue has a mass of 193.
We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.
The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.
If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.
See codeclimate-duplication
's documentation for more information about tuning the mass threshold in your .codeclimate.yml
.
Refactorings
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Similar blocks of code found in 2 locations. Consider refactoring. Open
def get_xlsx_validation(self, sheet_models=None, doc_metadata_model=None):
""" Get XLSX validation
Args:
sheet_models (:obj:`list` of :obj:`Model`, optional): models encoded as separate sheets
- Read upRead up
Duplicated Code
Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:
Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.
When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).
Tuning
This issue has a mass of 193.
We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.
The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.
If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.
See codeclimate-duplication
's documentation for more information about tuning the mass threshold in your .codeclimate.yml
.
Refactorings
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Function viz_schema
has a Cognitive Complexity of 79 (exceeds 5 allowed). Consider refactoring. Open
def viz_schema(module, filename, attributes=True, tail_labels=True, hidden_classes=None, extra_edges=None,
model_names=None,
rank_sep=None,
node_sep=None,
node_width=None,
- 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
Similar blocks of code found in 2 locations. Consider refactoring. Open
if objects and self.species_cls:
if not isinstance(self.species_cls, type):
for cls in objects.keys():
if '.' in self.species_cls:
if cls.__module__ + '.' + cls.__name__ == self.species_cls:
- Read upRead up
Duplicated Code
Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:
Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.
When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).
Tuning
This issue has a mass of 167.
We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.
The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.
If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.
See codeclimate-duplication
's documentation for more information about tuning the mass threshold in your .codeclimate.yml
.
Refactorings
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Similar blocks of code found in 2 locations. Consider refactoring. Open
if objects and self.compartment_cls:
if not isinstance(self.compartment_cls, type):
for cls in objects.keys():
if '.' in self.compartment_cls:
if cls.__module__ + '.' + cls.__name__ == self.compartment_cls:
- Read upRead up
Duplicated Code
Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:
Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.
When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).
Tuning
This issue has a mass of 167.
We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.
The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.
If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.
See codeclimate-duplication
's documentation for more information about tuning the mass threshold in your .codeclimate.yml
.
Refactorings
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76