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LucaCappelletti94/epigenomic_dataset

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

Severity: Major
Found in build/lib/epigenomic_dataset/logging.py and 1 other location - About 1 day to fix
epigenomic_dataset/logging.py on lines 0..20

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 130.

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

Severity: Major
Found in epigenomic_dataset/logging.py and 1 other location - About 1 day to fix
build/lib/epigenomic_dataset/logging.py on lines 0..20

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 130.

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 load_tasks.py has 456 lines of code (exceeds 250 allowed). Consider refactoring.
Open

"""Module providing straightforward methods to load the tasks."""
from typing import Tuple, Dict
import pandas as pd
from tqdm.auto import tqdm
from .load_epigenomes import load_epigenomes
Severity: Minor
Found in epigenomic_dataset/load_tasks.py - About 6 hrs to fix

    File load_tasks.py has 434 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    """Module providing straightforward methods to load the tasks."""
from typing import Tuple, Dict
import pandas as pd
from tqdm.auto import tqdm
from .load_epigenomes import load_epigenomes
    Severity: Minor
    Found in build/lib/epigenomic_dataset/load_tasks.py - About 6 hrs to fix

      Function load_task has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
      Open

      def load_task(
    cell_line: str = "K562",
    assembly: str = "hg38",
    dataset: str = "fantom",
    metric: str = "mean",
      Severity: Minor
      Found in build/lib/epigenomic_dataset/load_tasks.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

      Function load_task has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
      Open

      def load_task(
    cell_line: str = "K562",
    assembly: str = "hg38",
    dataset: str = "fantom",
    metric: str = "mean",
      Severity: Minor
      Found in epigenomic_dataset/load_tasks.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

      Function load_task has 14 arguments (exceeds 4 allowed). Consider refactoring.
      Open

      def load_task(
      Severity: Major
      Found in epigenomic_dataset/load_tasks.py - About 1 hr to fix

        Function load_task has 14 arguments (exceeds 4 allowed). Consider refactoring.
        Open

        def load_task(
        Severity: Major
        Found in build/lib/epigenomic_dataset/load_tasks.py - About 1 hr to fix

          Function build has 13 arguments (exceeds 4 allowed). Consider refactoring.
          Open

          def build(
          Severity: Major
          Found in build/lib/epigenomic_dataset/build.py - About 1 hr to fix

            Function build has 13 arguments (exceeds 4 allowed). Consider refactoring.
            Open

            def build(
            Severity: Major
            Found in epigenomic_dataset/build.py - About 1 hr to fix

              Function parse_extracted_epigenome has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
              Open

              def parse_extracted_epigenome(sources: List[str], target: str, statistics: Dict[str, bool]):
    """Parse the given source bed-like file.

    Parameters
    ----------------------------
              Severity: Minor
              Found in build/lib/epigenomic_dataset/mine.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 parse_extracted_epigenome has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
              Open

              def parse_extracted_epigenome(sources: List[str], target: str, statistics: Dict[str, bool]):
    """Parse the given source bed-like file.

    Parameters
    ----------------------------
              Severity: Minor
              Found in epigenomic_dataset/mine.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 load_epigenomes has 11 arguments (exceeds 4 allowed). Consider refactoring.
              Open

              def load_epigenomes(
              Severity: Major
              Found in epigenomic_dataset/load_epigenomes.py - About 1 hr to fix

                Function load_all_tasks has 11 arguments (exceeds 4 allowed). Consider refactoring.
                Open

                def load_all_tasks(
                Severity: Major
                Found in epigenomic_dataset/load_tasks.py - About 1 hr to fix

                  Function load_all_tasks has 11 arguments (exceeds 4 allowed). Consider refactoring.
                  Open

                  def load_all_tasks(
                  Severity: Major
                  Found in build/lib/epigenomic_dataset/load_tasks.py - About 1 hr to fix

                    Function load_epigenomes has 11 arguments (exceeds 4 allowed). Consider refactoring.
                    Open

                    def load_epigenomes(
                    Severity: Major
                    Found in build/lib/epigenomic_dataset/load_epigenomes.py - About 1 hr to fix

                      Function active_promoters_vs_inactive_promoters has 10 arguments (exceeds 4 allowed). Consider refactoring.
                      Open

                      def active_promoters_vs_inactive_promoters(
                      Severity: Major
                      Found in build/lib/epigenomic_dataset/load_tasks.py - About 1 hr to fix

                        Function active_promoters_vs_inactive_promoters has 10 arguments (exceeds 4 allowed). Consider refactoring.
                        Open

                        def active_promoters_vs_inactive_promoters(
                        Severity: Major
                        Found in epigenomic_dataset/load_tasks.py - About 1 hr to fix

                          Function active_enhancers_vs_inactive_enhancers has 10 arguments (exceeds 4 allowed). Consider refactoring.
                          Open

                          def active_enhancers_vs_inactive_enhancers(
                          Severity: Major
                          Found in epigenomic_dataset/load_tasks.py - About 1 hr to fix

                            Function active_enhancers_vs_inactive_enhancers has 10 arguments (exceeds 4 allowed). Consider refactoring.
                            Open

                            def active_enhancers_vs_inactive_enhancers(
                            Severity: Major
                            Found in build/lib/epigenomic_dataset/load_tasks.py - About 1 hr to fix
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