Sign upLogin

KarrLab/wc_lang

View on GitHub
Star
wc_lang/__main__.py

Summary

Maintainability
F
3 days
Test Coverage
A
100%

File __main__.py has 325 lines of code (exceeds 250 allowed). Consider refactoring.
Open

""" Command line programs for manipulating model definitions

:Author: Jonathan Karr <karr@mssm.edu>
:Author: Arthur Goldberg <Arthur.Goldberg@mssm.edu>
:Date: 2016-12-07
Severity: Minor
Found in wc_lang/__main__.py - About 3 hrs to fix

    Function remove_metadata has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
    Open

        def remove_metadata(model):
        """ Remove metadata from model

        Args:
            model (:obj:`wc_utils.workbook.Workbook`): model
    Severity: Minor
    Found in wc_lang/__main__.py - About 45 mins to fix

    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 _default has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
    Open

        def _default(self):
        args = self.app.pargs

        if args.compare_files:
            model1 = read_workbook(args.path_1)
    Severity: Minor
    Found in wc_lang/__main__.py - About 25 mins to fix

    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 Meta:
        label = 'update-version-metadata'
        description = 'Update the version metadata (repository URL, branch, revision; wc_lang version) of a model'
        help = 'Update the version metadata (repository URL, branch, revision; wc_lang version) of a model'
        stacked_on = 'base'
    Severity: Major
    Found in wc_lang/__main__.py and 1 other location - About 5 hrs to fix
    wc_lang/__main__.py on lines 287..298

    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 87.

    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

    Further Reading

    Similar blocks of code found in 2 locations. Consider refactoring.
    Open

        class Meta:
        label = 'create-template'
        description = 'Create file with model template: blank file(s) with row and column labels'
        help = 'Create file with model template: blank file(s) with row and column labels'
        stacked_on = 'base'
    Severity: Major
    Found in wc_lang/__main__.py and 1 other location - About 5 hrs to fix
    wc_lang/__main__.py on lines 311..322

    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 87.

    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

    Further Reading

    Similar blocks of code found in 3 locations. Consider refactoring.
    Open

        class Meta:
        label = 'cut-submodels'
        description = 'Cut submodels into separate models'
        help = 'Cut submodels into separate models'
        stacked_on = 'base'
    Severity: Major
    Found in wc_lang/__main__.py and 2 other locations - About 4 hrs to fix
    wc_lang/__main__.py on lines 265..274
    wc_lang/__main__.py on lines 359..368

    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 81.

    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

    Further Reading

    Similar blocks of code found in 3 locations. Consider refactoring.
    Open

        class Meta:
        label = 'convert'
        description = 'Convert model among .csv, .json, .tsv, .xlsx, .yaml, and .yml formats'
        help = 'Convert model among .csv, .json, .tsv, .xlsx, .yaml, and .yml formats'
        stacked_on = 'base'
    Severity: Major
    Found in wc_lang/__main__.py and 2 other locations - About 4 hrs to fix
    wc_lang/__main__.py on lines 42..51
    wc_lang/__main__.py on lines 359..368

    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 81.

    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

    Further Reading

    Similar blocks of code found in 3 locations. Consider refactoring.
    Open

        class Meta:
        label = 'import'
        description = 'Import a model from SBML'
        help = 'Import a model from SBML'
        stacked_on = 'base'
    Severity: Major
    Found in wc_lang/__main__.py and 2 other locations - About 4 hrs to fix
    wc_lang/__main__.py on lines 42..51
    wc_lang/__main__.py on lines 265..274

    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 81.

    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

    Further Reading

    There are no issues that match your filters.

    Category
    Status