Sign upLogin

salilab/rmf

View on GitHub
Star

Showing 523 of 523 total issues

File _decorators.py has 521 lines of code (exceeds 250 allowed). Consider refactoring.
Open

#!/usr/bin/env python

import os.path
import sys
import subprocess
Severity: Major
Found in tools/build/_decorators.py - About 1 day to fix

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

        return (
        ((v0[0] - v1[0]) ** 2 + (v0[1] - v1[1])
         ** 2 + (v0[1] - v1[1]) ** 2) ** .5 - r0 - r1
    Severity: Major
    Found in examples/motion.py and 1 other location - About 6 hrs to fix
    examples/motion.py on lines 33..36

    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 105.

    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

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

    def get_distance(v0, r0, v1, r1):
    return (
        ((v0[0] - v1[0]) ** 2 + (v0[1] - v1[1])
         ** 2 + (v0[1] - v1[1]) ** 2) ** .5 - r0 - r1
    Severity: Major
    Found in examples/motion.py and 1 other location - About 6 hrs to fix
    examples/motion.py on lines 126..128

    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 105.

    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 PathAttribute(Attribute):
    """Similar to a string Attribute, but designed for storing paths.
       Paths are stored internally relative to the directory containing
       the RMF file (in-memory RMFs are considered to be in the current
       working directory) but the API always returns absolute paths."""
    Severity: Major
    Found in tools/build/_decorators.py and 1 other location - About 5 hrs to fix
    tools/build/_decorators.py on lines 201..236

    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 93.

    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 OptionalPathAttribute(Attribute):
    """Like a PathAttribute, but it can be empty."""

    def _check_string_name(self, name):
        if not self._is_path(name):
    Severity: Major
    Found in tools/build/_decorators.py and 1 other location - About 5 hrs to fix
    tools/build/_decorators.py on lines 168..198

    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 93.

    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 copy_to_residues has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.
    Open

    def copy_to_residues(pin, pout, rcf, rf, pcf, pf, acf, af, ccf, cf, bf, prev):
    if rcf.get_is(pin):
        rpin = rcf.get(pin)
        rpout = rf.get(pout)
        rpout.set_residue_type(rpin.get_residue_type())
    Severity: Minor
    Found in examples/add_bonds.py - About 2 hrs 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

    Cyclomatic complexity is too high in function copy_to_residues. (9)
    Open

    def copy_to_residues(pin, pout, rcf, rf, pcf, pf, acf, af, ccf, cf, bf, prev):
    if rcf.get_is(pin):
        rpin = rcf.get(pin)
        rpout = rf.get(pout)
        rpout.set_residue_type(rpin.get_residue_type())
    Severity: Minor
    Found in examples/add_bonds.py by radon

    Cyclomatic Complexity

    Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

    Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

    Construct Effect on CC Reasoning
    if +1 An if statement is a single decision.
    elif +1 The elif statement adds another decision.
    else +0 The else statement does not cause a new decision. The decision is at the if.
    for +1 There is a decision at the start of the loop.
    while +1 There is a decision at the while statement.
    except +1 Each except branch adds a new conditional path of execution.
    finally +0 The finally block is unconditionally executed.
    with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
    assert +1 The assert statement internally roughly equals a conditional statement.
    Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
    Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

    Source: http://radon.readthedocs.org/en/latest/intro.html

    Cyclomatic complexity is too high in function visit. (7)
    Open

    def visit(node, reference_frame, reference_frame_factory, particle_factory,
          segment_factory, ball_factory):
    if reference_frame_factory.get_is(node):
        reference_frame = RMF.CoordinateTransformer(
            reference_frame, reference_frame_factory.get(node))
    Severity: Minor
    Found in examples/reference_frames.py by radon

    Cyclomatic Complexity

    Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

    Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

    Construct Effect on CC Reasoning
    if +1 An if statement is a single decision.
    elif +1 The elif statement adds another decision.
    else +0 The else statement does not cause a new decision. The decision is at the if.
    for +1 There is a decision at the start of the loop.
    while +1 There is a decision at the while statement.
    except +1 Each except branch adds a new conditional path of execution.
    finally +0 The finally block is unconditionally executed.
    with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
    assert +1 The assert statement internally roughly equals a conditional statement.
    Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
    Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

    Source: http://radon.readthedocs.org/en/latest/intro.html

    Cyclomatic complexity is too high in function mkdir. (7)
    Open

    def mkdir(path, clean=True):
    if os.path.isdir(path):
        if clean:
            # remove any old links
            for f in glob.glob(os.path.join(path, "*")):
    Severity: Minor
    Found in tools/build/make-embed.py by radon

    Cyclomatic Complexity

    Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

    Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

    Construct Effect on CC Reasoning
    if +1 An if statement is a single decision.
    elif +1 The elif statement adds another decision.
    else +0 The else statement does not cause a new decision. The decision is at the if.
    for +1 There is a decision at the start of the loop.
    while +1 There is a decision at the while statement.
    except +1 Each except branch adds a new conditional path of execution.
    finally +0 The finally block is unconditionally executed.
    with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
    assert +1 The assert statement internally roughly equals a conditional statement.
    Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
    Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

    Source: http://radon.readthedocs.org/en/latest/intro.html

    Cyclomatic complexity is too high in method _get_checks. (6)
    Open

        def _get_checks(self, use_all=False):
        ret = [self._get_type_check()]
        if self.check_all_attributes or use_all:
            for a in self.attributes:
                ret.append(a.get_check())
    Severity: Minor
    Found in tools/build/_decorators.py by radon

    Cyclomatic Complexity

    Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

    Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

    Construct Effect on CC Reasoning
    if +1 An if statement is a single decision.
    elif +1 The elif statement adds another decision.
    else +0 The else statement does not cause a new decision. The decision is at the if.
    for +1 There is a decision at the start of the loop.
    while +1 There is a decision at the while statement.
    except +1 Each except branch adds a new conditional path of execution.
    finally +0 The finally block is unconditionally executed.
    with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
    assert +1 The assert statement internally roughly equals a conditional statement.
    Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
    Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

    Source: http://radon.readthedocs.org/en/latest/intro.html

    Function mkdir has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
    Open

    def mkdir(path, clean=True):
    if os.path.isdir(path):
        if clean:
            # remove any old links
            for f in glob.glob(os.path.join(path, "*")):
    Severity: Minor
    Found in tools/build/make-embed.py - About 1 hr 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 _create_atoms has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
    Open

    def _create_atoms(helper, mydata, model, cgol, created):
    child = False
    for ch in helper.get_children():
        if _create_atoms(ch, mydata, model, cgol, created):
            child = True
    Severity: Minor
    Found in plugins/pymol/plugin.py - About 1 hr 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

    Error: Missing parentheses in call to 'print'. Did you mean print(print "color", name, c, ck # noqa: E999)? (<unknown>, line 40)</unknown>
    Open

    Severity: Minor
    Found in plugins/pymol/plugin.py by radon

    We encountered an error attempting to analyze this line.

    Error: invalid syntax (<unknown>, line 4)</unknown>
    Open

    sys.path.append(os.path.join( % CMAKE_BINARY_DIR%, "lib"))
    Severity: Minor
    Found in plugins/pymol/loader-template.py by radon

    We encountered an error attempting to analyze this line.

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

    software = Decorator(["PROVENANCE"], "provenance",
                     "SoftwareProvenance",
                     [Attribute("software name", "String",
                                function_name='name'),
                      Attribute("software version", "String",
    Severity: Major
    Found in tools/build/make_decorators.py and 1 other location - About 1 hr to fix
    tools/build/make_decorators.py on lines 135..141

    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 45.

    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

    filterp = Decorator(["PROVENANCE"], "provenance",
                    "FilterProvenance",
                    [Attribute("filter method", "String",
                               function_name='method'),
                     Attribute("filter threshold", "Float",
    Severity: Major
    Found in tools/build/make_decorators.py and 1 other location - About 1 hr to fix
    tools/build/make_decorators.py on lines 158..164

    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 45.

    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

        def _get_methods(self, const):
        ret = []
        for a in self.attributes:
            ret.append(a.get_get_set_methods(const))
        return "\n".join(ret)
    Severity: Major
    Found in tools/build/_decorators.py and 2 other locations - About 1 hr to fix
    tools/build/_decorators.py on lines 468..472
    tools/build/_decorators.py on lines 486..490

    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 44.

    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 copy_to_residues has 12 arguments (exceeds 4 allowed). Consider refactoring.
    Open

    def copy_to_residues(pin, pout, rcf, rf, pcf, pf, acf, af, ccf, cf, bf, prev):
    Severity: Major
    Found in examples/add_bonds.py - About 1 hr to fix

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

          def _get_bulk_methods(self, const):
        ret = []
        for a in self.attributes:
            ret.append(a.get_bulk_methods(const))
        return "\n".join(ret)
      Severity: Major
      Found in tools/build/_decorators.py and 2 other locations - About 1 hr to fix
      tools/build/_decorators.py on lines 462..466
      tools/build/_decorators.py on lines 486..490

      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 44.

      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

          def _get_data_pass(self, member):
        ret = []
        for a in self.attributes:
            ret.append(a.get_data_pass(member))
        return ",\n".join(ret)
      Severity: Major
      Found in tools/build/_decorators.py and 2 other locations - About 1 hr to fix
      tools/build/_decorators.py on lines 462..466
      tools/build/_decorators.py on lines 468..472

      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 44.

      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

      Severity
      Category
      Status
      Source
      Language