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Function draw_polymer has 8 arguments (exceeds 4 allowed). Consider refactoring.
Open

def draw_polymer(Form, polymer, dirname, filename, show_atom_nums=False,
Severity: Major
Found in docs/build_examples.py - About 1 hr to fix

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

        try:
        alphabet_obj = bpforms.util.get_alphabet(alphabet)
    except ValueError as error:
        flask_restplus.abort(400, 'Invalid alphabet "{}"'.format(alphabet))
    Severity: Major
    Found in bpforms/rest.py and 1 other location - About 1 hr to fix
    bpforms/rest.py on lines 237..240

    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 38.

    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

        try:
        alphabet_obj = bpforms.util.get_alphabet(id)
    except ValueError as error:
        flask_restplus.abort(400, 'Invalid alphabet "{}"'.format(id))
    Severity: Major
    Found in bpforms/rest.py and 1 other location - About 1 hr to fix
    bpforms/rest.py on lines 281..284

    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 38.

    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

    Function check_atom has 8 arguments (exceeds 4 allowed). Consider refactoring.
    Open

            def check_atom(molecule, atom_type, i_monomer, i_atom, structure, atom_md, bonding_hydrogens, el_table, errors):
    Severity: Major
    Found in bpforms/core.py - About 1 hr to fix

      Function plot_codes has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
      Open

      def plot_codes(code_freq, monomer_codes, axis, ignore_canonical=False, use_rel=True,
               title=None, x_axis_label=None, y_axis_label='Frequency (%)',
               axis_font_size=10, tick_font_size=6, font_family='Raleway',
               x_label_pad=None):
    monomer_ids = {}
      Severity: Minor
      Found in examples/modomics.py - About 55 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 load_onto has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
      Open

      def load_onto(filename=onto_filename):
    """ Load an ontology of crosslinks from a YAML file

    Args:
        filename (:obj:`str`): path to ontology
      Severity: Minor
      Found in bpforms/xlink/core.py - About 55 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 __setitem__ has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
      Open

          def __setitem__(self, slice, monomer):
        """ Set monomeric form(s) at slice

        Args:
            slice (:obj:`int` or :obj:`slice`): position(s) to set monomeric form
      Severity: Minor
      Found in bpforms/core.py - About 55 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 __setitem__ has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
      Open

          def __setitem__(self, slice, atom):
        """ Set atom(s) at slice

        Args:
            slice (:obj:`int` or :obj:`slice`): position(s) to set atom
      Severity: Minor
      Found in bpforms/core.py - About 55 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 from_dict has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
      Open

          def from_dict(self, dict, alphabet=None):
        """ Get a dictionary representation of the monomeric form

        Args:
            dict (:obj:`dict`): dictionary representation of the monomeric form
      Severity: Minor
      Found in bpforms/core.py - About 55 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 4 locations. Consider refactoring.
      Open

          results_dict['Number of modified U'] = canonical_seq.count('U') - rna_form.seq.count(bpforms.rna_alphabet.monomers.U)
      Severity: Major
      Found in examples/modomics.py and 3 other locations - About 55 mins to fix
      examples/modomics.py on lines 256..256
      examples/modomics.py on lines 257..257
      examples/modomics.py on lines 258..258

      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 37.

      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 4 locations. Consider refactoring.
      Open

          results_dict['Number of modified C'] = canonical_seq.count('C') - rna_form.seq.count(bpforms.rna_alphabet.monomers.C)
      Severity: Major
      Found in examples/modomics.py and 3 other locations - About 55 mins to fix
      examples/modomics.py on lines 256..256
      examples/modomics.py on lines 258..258
      examples/modomics.py on lines 259..259

      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 37.

      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 4 locations. Consider refactoring.
      Open

          results_dict['Number of modified G'] = canonical_seq.count('G') - rna_form.seq.count(bpforms.rna_alphabet.monomers.G)
      Severity: Major
      Found in examples/modomics.py and 3 other locations - About 55 mins to fix
      examples/modomics.py on lines 256..256
      examples/modomics.py on lines 257..257
      examples/modomics.py on lines 259..259

      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 37.

      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

      Function is_equal has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
      Open

          def is_equal(self, other):
        """ Determine two alphabets are semantically equal

        Args:
            other (:obj:`type`): other alphabet
      Severity: Minor
      Found in bpforms/core.py - About 55 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 4 locations. Consider refactoring.
      Open

          results_dict['Number of modified A'] = canonical_seq.count('A') - rna_form.seq.count(bpforms.rna_alphabet.monomers.A)
      Severity: Major
      Found in examples/modomics.py and 3 other locations - About 55 mins to fix
      examples/modomics.py on lines 257..257
      examples/modomics.py on lines 258..258
      examples/modomics.py on lines 259..259

      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 37.

      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

      Function __init__ has 7 arguments (exceeds 4 allowed). Consider refactoring.
      Open

          def __init__(self, seq=None, alphabet=None, backbone=None, bond=None, circular=False,
      Severity: Major
      Found in bpforms/core.py - About 50 mins to fix

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

                    if i_protein % 100 == 0:
                print('Generating BpForms {} of {}'.format(i_protein + 1, len(parsed_proteins)))
        Severity: Minor
        Found in examples/pro.py and 1 other location - About 50 mins to fix
        examples/pro.py on lines 106..107

        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 36.

        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 CovMod(DeclarativeBase):
        """"""
        __tablename__ = 'covmod'
        __table_args__ = {'autoload': True, 'extend_existing': True}
        cmodid = sqlalchemy.Column(primary_key=True)
        Severity: Major
        Found in bpforms/alphabet/dna.py and 2 other locations - About 50 mins to fix
        bpforms/alphabet/dna.py on lines 78..82
        bpforms/alphabet/dna.py on lines 84..88

        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 36.

        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

                    if i_protein % 100 == 0:
                print('Parsing protein {} of {}'.format(i_protein + 1, len(proteins)))
        Severity: Minor
        Found in examples/pro.py and 1 other location - About 50 mins to fix
        examples/pro.py on lines 177..178

        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 36.

        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 ModBaseParents(DeclarativeBase):
        """"""
        __tablename__ = 'modbase_parents'
        __table_args__ = {'autoload': True, 'extend_existing': True}
        nameid = sqlalchemy.Column(primary_key=True)
        Severity: Major
        Found in bpforms/alphabet/dna.py and 2 other locations - About 50 mins to fix
        bpforms/alphabet/dna.py on lines 78..82
        bpforms/alphabet/dna.py on lines 90..94

        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 36.

        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 ModBase(DeclarativeBase):
        """"""
        __tablename__ = 'modbase'
        __table_args__ = {'autoload': True, 'extend_existing': True}
        nameid = sqlalchemy.Column(primary_key=True)
        Severity: Major
        Found in bpforms/alphabet/dna.py and 2 other locations - About 50 mins to fix
        bpforms/alphabet/dna.py on lines 84..88
        bpforms/alphabet/dna.py on lines 90..94

        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 36.

        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

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