Showing 527 of 527 total issues
Similar blocks of code found in 2 locations. Consider refactoring. Open
return v[0] + v[1] + v[2]
- 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 33.
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 create_hierarchy
has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def create_hierarchy(radius):
root = f.add_node(str(radius), RMF.REPRESENTATION)
for i in frange(0., 8, radius):
for j in frange(0., 8, radius):
for k in frange(0., 8, radius):
- 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 __init__
has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def __init__(self, name, attribute_type, function_name=None,
default=None):
if attribute_type in ('String', 'Strings'):
self._check_string_name(name)
if not function_name:
- 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 clean_gcdas
has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def clean_gcdas():
for dirpath, dirnames, filenames in os.walk('.'):
for f in filenames:
if f.endswith('.gcda'):
os.unlink(os.path.join(dirpath, f))
- 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
Can't follow non-constant source. Use a directive to specify location. Open
source "${SCRIPT_DIR}/../dev_tools/git/subtree-utils.sh"
- Read upRead up
- Exclude checks
Can't follow non-constant source. Use a directive to specify location.
Problematic code:
. "$(find_install_dir)/lib.sh"
Correct code:
# shellcheck source=src/lib.sh
. "$(find_install_dir)/lib.sh"
Rationale:
ShellCheck is not able to include sourced files from paths that are determined at runtime. The file will not be read, potentially resulting in warnings about unassigned variables and similar.
Use a [[Directive]] to point shellcheck to a fixed location it can read instead.
Exceptions:
If you don't care that ShellCheck is unable to account for the file, specify # shellcheck source=/dev/null
.
Notice
Original content from the ShellCheck https://github.com/koalaman/shellcheck/wiki.
Use $(..) instead of legacy ..
. Open
CODENAME=`lsb_release -c -s`
- Read upRead up
- Exclude checks
Use $(STATEMENT) instead of legacy `STATEMENT`
Problematic code
echo "Current time: `date`"
Correct code
echo "Current time: $(date)"
Rationale
Backtick command substitution `STATEMENT`
is legacy syntax with several issues.
- It has a series of undefined behaviors related to quoting in POSIX.
- It imposes a custom escaping mode with surprising results.
- It's exceptionally hard to nest.
$(STATEMENT)
command substitution has none of these problems, and is therefore strongly encouraged.
Exceptions
None.
See also
Notice
Original content from the ShellCheck https://github.com/koalaman/shellcheck/wiki.
Use $(..) instead of legacy ..
. Open
TOOL_DIR=`dirname "$0"`
- Read upRead up
- Exclude checks
Use $(STATEMENT) instead of legacy `STATEMENT`
Problematic code
echo "Current time: `date`"
Correct code
echo "Current time: $(date)"
Rationale
Backtick command substitution `STATEMENT`
is legacy syntax with several issues.
- It has a series of undefined behaviors related to quoting in POSIX.
- It imposes a custom escaping mode with surprising results.
- It's exceptionally hard to nest.
$(STATEMENT)
command substitution has none of these problems, and is therefore strongly encouraged.
Exceptions
None.
See also
Notice
Original content from the ShellCheck https://github.com/koalaman/shellcheck/wiki.
Headers should be surrounded by blank lines Open
# Building and installing #
- Read upRead up
- Exclude checks
MD022 - Headers should be surrounded by blank lines
Tags: headers, blank_lines
Aliases: blanks-around-headers
This rule is triggered when headers (any style) are either not preceded or not followed by a blank line:
# Header 1
Some text
Some more text
## Header 2
To fix this, ensure that all headers have a blank line both before and after (except where the header is at the beginning or end of the document):
# Header 1
Some text
Some more text
## Header 2
Rationale: Aside from aesthetic reasons, some parsers, including kramdown, will not parse headers that don't have a blank line before, and will parse them as regular text.
Line length Open
RMF uses a [fork of AvroCpp](https://github.com/salilab/avrocpp) to encode data. See that repository for more information. The fork is mostly necessary in order to add seek support to the DataFileReader and to support writing to memory buffers with the DataFileWriter. The other big patch has made it into Avro 1.7.6.
- Read upRead up
- Exclude checks
MD013 - Line length
Tags: line_length
Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)
This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.
This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.
You also have the option to exclude this rule for code blocks and tables. To
do this, set the code_blocks
and/or tables
parameters to false.
Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.
Code block style Open
https://www.apache.org/licenses/LICENSE-2.0
- Exclude checks
Header style Open
# Sequence # {#sequence}
- Read upRead up
- Exclude checks
MD003 - Header style
Tags: headers
Aliases: header-style
Parameters: style ("consistent", "atx", "atxclosed", "setext", "setextwith_atx"; default "consistent")
This rule is triggered when different header styles (atx, setext, and 'closed' atx) are used in the same document:
# ATX style H1
## Closed ATX style H2 ##
Setext style H1
===============
Be consistent with the style of header used in a document:
# ATX style H1
## ATX style H2
The setextwithatx doc style allows atx-style headers of level 3 or more in documents with setext style headers:
Setext style H1
===============
Setext style H2
---------------
### ATX style H3
Note: the configured header style can be a specific style to use (atx, atxclosed, setext, setextwith_atx), or simply require that the usage be consistent within the document.
Line length Open
| `representation` | RMF::Ints | The NodeIDs of the nodes involved in this score |
- Read upRead up
- Exclude checks
MD013 - Line length
Tags: line_length
Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)
This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.
This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.
You also have the option to exclude this rule for code blocks and tables. To
do this, set the code_blocks
and/or tables
parameters to false.
Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.
Line length Open
| Name | Node Type | Attributes |
- Read upRead up
- Exclude checks
MD013 - Line length
Tags: line_length
Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)
This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.
This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.
You also have the option to exclude this rule for code blocks and tables. To
do this, set the code_blocks
and/or tables
parameters to false.
Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.
Line length Open
| `sampling method` | string | Sampling method utilized |
- Read upRead up
- Exclude checks
MD013 - Line length
Tags: line_length
Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)
This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.
This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.
You also have the option to exclude this rule for code blocks and tables. To
do this, set the code_blocks
and/or tables
parameters to false.
Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.
Line length Open
| `cluster members` | int | Number of members in a cluster |
- Read upRead up
- Exclude checks
MD013 - Line length
Tags: line_length
Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)
This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.
This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.
You also have the option to exclude this rule for code blocks and tables. To
do this, set the code_blocks
and/or tables
parameters to false.
Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.
Multiple headers with the same content Open
## Attributes ## {#aliasattributes}
- Read upRead up
- Exclude checks
MD024 - Multiple headers with the same content
Tags: headers
Aliases: no-duplicate-header
Parameters: allowdifferentnesting (boolean; default false)
This rule is triggered if there are multiple headers in the document that have the same text:
# Some text
## Some text
To fix this, ensure that the content of each header is different:
# Some text
## Some more text
Rationale: Some markdown parses generate anchors for headers based on the header name, and having headers with the same content can cause problems with this.
If the parameter allow_different_nesting
is set to true
, header duplication
under different nesting is allowed, like it usually happens in change logs:
# Change log
## 2.0.0
### Bug fixes
### Features
## 1.0.0
### Bug fixes
Line length Open
RMF::decorator::Colored, RMF::decorator::Ball etc. See [Decorators](\ref decoratorsattributes) for
- Read upRead up
- Exclude checks
MD013 - Line length
Tags: line_length
Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)
This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.
This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.
You also have the option to exclude this rule for code blocks and tables. To
do this, set the code_blocks
and/or tables
parameters to false.
Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.
Lists should be surrounded by blank lines Open
- most biological molecules have a natural hierarchical structure
- Read upRead up
- Exclude checks
MD032 - Lists should be surrounded by blank lines
Tags: bullet, ul, ol, blank_lines
Aliases: blanks-around-lists
This rule is triggered when lists (of any kind) are either not preceded or not followed by a blank line:
Some text
* Some
* List
1. Some
2. List
Some text
To fix this, ensure that all lists have a blank line both before and after (except where the block is at the beginning or end of the document):
Some text
* Some
* List
1. Some
2. List
Some text
Rationale: Aside from aesthetic reasons, some parsers, including kramdown, will not parse lists that don't have blank lines before and after them.
Note: List items without hanging indents are a violation of this rule; list items with hanging indents are okay:
* This is
not okay
* This is
okay
Lists should be surrounded by blank lines Open
- low resolution and multiresolution structures are then more natural
- Read upRead up
- Exclude checks
MD032 - Lists should be surrounded by blank lines
Tags: bullet, ul, ol, blank_lines
Aliases: blanks-around-lists
This rule is triggered when lists (of any kind) are either not preceded or not followed by a blank line:
Some text
* Some
* List
1. Some
2. List
Some text
To fix this, ensure that all lists have a blank line both before and after (except where the block is at the beginning or end of the document):
Some text
* Some
* List
1. Some
2. List
Some text
Rationale: Aside from aesthetic reasons, some parsers, including kramdown, will not parse lists that don't have blank lines before and after them.
Note: List items without hanging indents are a violation of this rule; list items with hanging indents are okay:
* This is
not okay
* This is
okay
Header style Open
## Download {#installation_download}
- Read upRead up
- Exclude checks
MD003 - Header style
Tags: headers
Aliases: header-style
Parameters: style ("consistent", "atx", "atxclosed", "setext", "setextwith_atx"; default "consistent")
This rule is triggered when different header styles (atx, setext, and 'closed' atx) are used in the same document:
# ATX style H1
## Closed ATX style H2 ##
Setext style H1
===============
Be consistent with the style of header used in a document:
# ATX style H1
## ATX style H2
The setextwithatx doc style allows atx-style headers of level 3 or more in documents with setext style headers:
Setext style H1
===============
Setext style H2
---------------
### ATX style H3
Note: the configured header style can be a specific style to use (atx, atxclosed, setext, setextwith_atx), or simply require that the usage be consistent within the document.