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LucaCappelletti94/epigenomic_dataset

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Showing 35 of 35 total issues

Function inactive_enhancers_vs_inactive_promoters has 9 arguments (exceeds 4 allowed). Consider refactoring.
Open

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

    Function active_enhancers_vs_active_promoters has 9 arguments (exceeds 4 allowed). Consider refactoring.
    Open

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

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

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

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

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

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

          def extract(
          Severity: Major
          Found in epigenomic_dataset/extract.py - About 50 mins to fix

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

            def extract(
            Severity: Major
            Found in build/lib/epigenomic_dataset/extract.py - About 50 mins to fix

              Function run_pipeline has 6 arguments (exceeds 4 allowed). Consider refactoring.
              Open

              def run_pipeline(
              Severity: Minor
              Found in run_crr_build.py - About 45 mins to fix

                Function build_extraction_tasks has 6 arguments (exceeds 4 allowed). Consider refactoring.
                Open

                def build_extraction_tasks(
                Severity: Minor
                Found in build/lib/epigenomic_dataset/extract.py - About 45 mins to fix

                  Function build_extraction_tasks has 6 arguments (exceeds 4 allowed). Consider refactoring.
                  Open

                  def build_extraction_tasks(
                  Severity: Minor
                  Found in epigenomic_dataset/extract.py - About 45 mins to fix

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

                    Severity: Minor
                    Found in epigenomic_dataset/__init__.py and 1 other location - About 40 mins to fix
                    build/lib/epigenomic_dataset/__init__.py on lines 0..19

                    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 34.

                    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: Minor
                    Found in build/lib/epigenomic_dataset/__init__.py and 1 other location - About 40 mins to fix
                    epigenomic_dataset/__init__.py on lines 0..19

                    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 34.

                    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 extraction_job has 5 arguments (exceeds 4 allowed). Consider refactoring.
                    Open

                    def extraction_job(
                    Severity: Minor
                    Found in build/lib/epigenomic_dataset/extract.py - About 35 mins to fix

                      Function get_target_path has 5 arguments (exceeds 4 allowed). Consider refactoring.
                      Open

                      def get_target_path(root: str, cell_line: str, assembly: str, assay_term_name: str, target: str) -> str:
                      Severity: Minor
                      Found in epigenomic_dataset/mine.py - About 35 mins to fix

                        Function extraction_job has 5 arguments (exceeds 4 allowed). Consider refactoring.
                        Open

                        def extraction_job(
                        Severity: Minor
                        Found in epigenomic_dataset/extract.py - About 35 mins to fix

                          Function get_target_path has 5 arguments (exceeds 4 allowed). Consider refactoring.
                          Open

                          def get_target_path(root: str, cell_line: str, assembly: str, assay_term_name: str, target: str) -> str:
                          Severity: Minor
                          Found in build/lib/epigenomic_dataset/mine.py - About 35 mins to fix
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