Sign upLogin

LiberTEM/LiberTEM

View on GitHub
Star

Showing 902 of 903 total issues

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

    test('handles inputs without brackets', () => {
        const inputErrors: ErrorObject[] = [
            {
                "keyword": "minimum",
                "instancePath": ".nav_shape",
Severity: Major
Found in client/src/dataset/__tests__/validate.test.ts and 1 other location - About 3 hrs to fix
client/src/dataset/__tests__/validate.test.ts on lines 9..21

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 104.

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

File cached.py has 459 lines of code (exceeds 400 allowed). Consider refactoring.
Open

import os
import json
import hashlib
import sqlite3
import time
Severity: Minor
Found in src/libertem/io/dataset/cached.py - About 3 hrs to fix

    Cyclomatic complexity is too high in method __init__. (15)
    Open

        def __init__(self, tileshape=None, num_partitions=None, data=None, sig_dims=None,
                 check_cast=True, tiledelay=None, datashape=None, base_shape=None,
                 force_need_decode=False, io_backend=None,
                 nav_shape=None, sig_shape=None, sync_offset=0, array_backends=None):
        super().__init__(io_backend=io_backend)
    Severity: Minor
    Found in src/libertem/io/dataset/memory.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 initialize. (15)
    Open

        def initialize(self, executor: JobExecutor):
        self._filesize = executor.run_function(self._get_filesize)
        files = executor.run_function(get_filenames, self._path)

        # The series header is contained in the first file:
    Severity: Minor
    Found in src/libertem/io/dataset/tvips.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 __init__. (15)
    Open

        def __init__(self, masks: MaskContainer, meta: UDFMeta, use_torch: bool):
        self.masks = masks
        self.meta = meta

        try:
    Severity: Minor
    Found in src/libertem/udf/masks.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 block_get_min_fill_factor has a Cognitive Complexity of 23 (exceeds 5 allowed). Consider refactoring.
    Open

    def block_get_min_fill_factor(rrs):
    """
    Try to find out how sparse the given read ranges are, per file.

    Returns the smallest fill factor and maximum required buffer size.
    Severity: Minor
    Found in src/libertem/io/dataset/base/backend_buffered.py - About 3 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 _build_sparse. (14)
    Open

    def _build_sparse(m, dtype: npt.DTypeLike, sparse_backend: SparseSupportedT, backend: ArrayBackend):
    if sparse_backend == 'sparse.pydata' and backend == NUMPY:
        # sparse.pydata.org is fastest for masks with few layers
        # and few entries
        return m.astype(dtype)
    Severity: Minor
    Found in src/libertem/common/container.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_scheme. (14)
    Open

        def get_scheme(
            self,
            udfs: Sequence[UDFProtocol],
            dataset,
            read_dtype: "nt.DTypeLike",
    Severity: Minor
    Found in src/libertem/io/dataset/base/tiling_scheme.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 jobReducer has 79 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

    export const jobReducer = (state = initialJobState, action: AllActions): JobReducerState => {
    switch (action.type) {
        case jobActions.ActionTypes.CREATE: {
            const createResult = insertById(
                state,
    Severity: Major
    Found in client/src/job/reducers.ts - About 3 hrs to fix

      File tvips.py has 448 lines of code (exceeds 400 allowed). Consider refactoring.
      Open

      from io import SEEK_SET
import math
import os
import re
from typing import IO, TYPE_CHECKING, NamedTuple, Optional
      Severity: Minor
      Found in src/libertem/io/dataset/tvips.py - About 3 hrs to fix

        Function _apply_part_result has a Cognitive Complexity of 22 (exceeds 5 allowed). Consider refactoring.
        Open

            def _apply_part_result(self, udfs: Iterable[UDF], damage, part_results, task):
        for part_results_udf, udf in zip(part_results, udfs):
            # Allow user to define an alternative merge strategy
            # using dask-compatible functions. In the Delayed case we
            # won't be getting partial results with damage anyway.
        Severity: Minor
        Found in src/libertem/executor/delayed.py - About 3 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

        Function getFormInitial has a Cognitive Complexity of 22 (exceeds 5 allowed). Consider refactoring.
        Open

        const getFormInitial = (didReset: boolean, openState: OpenDatasetState) => {
    const { formCachedParams, formDetectedParams } = openState;
    if (didReset) {
        if (formDetectedParams) {
            return {
        Severity: Minor
        Found in client/src/dataset/components/DatasetOpen.tsx - About 3 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

        UDFData has 26 functions (exceeds 20 allowed). Consider refactoring.
        Open

        class UDFData:
    '''
    Container for result buffers, return value from running UDFs
    '''
        Severity: Minor
        Found in src/libertem/udf/base.py - About 3 hrs to fix

          UDFBase has 26 functions (exceeds 20 allowed). Consider refactoring.
          Open

          class UDFBase(UDFProtocol):
    '''
    Base class for UDFs with helper functions.
    '''
    def __init__(self, *args, **kwargs) -> None:
          Severity: Minor
          Found in src/libertem/udf/base.py - About 3 hrs to fix

            Cyclomatic complexity is too high in method _apply_part_result. (13)
            Open

                def _apply_part_result(self, udfs: Iterable[UDF], damage, part_results, task):
        for part_results_udf, udf in zip(part_results, udfs):
            # Allow user to define an alternative merge strategy
            # using dask-compatible functions. In the Delayed case we
            # won't be getting partial results with damage anyway.
            Severity: Minor
            Found in src/libertem/executor/delayed.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 detect_shape. (13)
            Open

            def detect_shape(path: str) -> tuple[int, tuple[int, ...]]:
    series_header = read_series_header(path)

    if series_header.version != 2:
        raise DetectionError(
            Severity: Minor
            Found in src/libertem/io/dataset/tvips.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 _prepare_run_for_dataset. (13)
            Open

                def _prepare_run_for_dataset(
        self,
        dataset: DataSet,
        executor: JobExecutor,
        roi: Optional[np.ndarray],
            Severity: Minor
            Found in src/libertem/udf/base.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 actionsFromChannel has 74 lines of code (exceeds 25 allowed). Consider refactoring.
            Open

            export function* actionsFromChannel(socketChannel: SocketChannel) {
    try {
        while (true) {
            const msg = (yield take(socketChannel)) as channelMessages.Messages;
            const timestamp = Date.now();
            Severity: Major
            Found in client/src/channel/sagas.ts - About 2 hrs to fix

              Function __init__ has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.
              Open

                  def __init__(self, tileshape=None, num_partitions=None, data=None, sig_dims=None,
                 check_cast=True, tiledelay=None, datashape=None, base_shape=None,
                 force_need_decode=False, io_backend=None,
                 nav_shape=None, sig_shape=None, sync_offset=0, array_backends=None):
        super().__init__(io_backend=io_backend)
              Severity: Minor
              Found in src/libertem/io/dataset/memory.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 cluster_spec. (12)
              Open

              def cluster_spec(
    cpus: Union[int, Iterable[int]],
    cudas: Union[int, Iterable[int]],
    has_cupy: bool,
    name: str = 'default',
              Severity: Minor
              Found in src/libertem/executor/dask.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

              Severity
              Category
              Status
              Source
              Language