refactor: all files are refactored

[cmeesters]

applied

• black or
• snakefmt

Summary by CodeRabbit

• Style

  • Improved code formatting and style consistency across workflow and script files, including standardized use of double quotes, spacing, indentation, and trailing commas.
  • Enhanced readability of multi-line statements and declarations in workflow rules and Python scripts.

• Chores

  • Performed code cleanup and minor stylistic adjustments without affecting any logic, control flow, or functionality. No user-facing features or behaviors have changed.

[coderabbitai]

Caution

Review failed

The pull request is closed.

Walkthrough

This update applies consistent formatting and style improvements across the workflow and script files of the project. Changes include standardized spacing, string quoting, indentation, and the addition of trailing commas for readability. No logic, control flow, or error handling has been altered; all modifications are purely syntactic and stylistic.

Changes

Cohort / File(s)	Change Summary
Snakemake Workflow Formatting workflow/Snakefile, workflow/rules/analyse.smk, workflow/rules/docking.smk, workflow/rules/preparation.smk	Consistent formatting: spacing around operators, multi-line argument lists, trailing commas in rule declarations, and string quoting. No logic or control flow changes.
Script Formatting: General workflow/scripts/ResultTxt.py, workflow/scripts/makeHistogram.py, workflow/scripts/mergeOutput.py, workflow/scripts/prepareReceptor.py, workflow/scripts/sortResult.py, workflow/scripts/splitFile.py, workflow/scripts/union_venn.py, workflow/scripts/venn.py	Purely stylistic changes: standardizing string delimiters, adding spaces around operators and after commas, and minor whitespace adjustments. No logic or error handling changes.
Script Formatting: Minor/Single-Line workflow/scripts/ZINCdownload.py, workflow/scripts/concatPDBQT.py	Added a single blank line after module-level docstrings for style consistency. No functional changes.
Script Formatting: Multi-line String Construction workflow/scripts/downloadZINCsubsets.py, workflow/scripts/prepareDocking.py	Reformatted long string constructions and file open statements to multi-line style for readability. No logic changes.
Script Formatting: Minor Assignment/Keyword Cleanup workflow/scripts/generateIRODS.py	Removed extra spaces around assignment operators and keyword arguments. No functional changes.

Sequence Diagram(s)

No sequence diagrams are generated, as the changes are exclusively stylistic and do not affect control flow or introduce new features.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~8 minutes

Poem

In the warren where code bunnies dwell,
We tidied up spaces, made quotes look swell.
No logic was changed, just a style parade—
Trailing commas and spacing carefully laid.
Now our workflow reads clear,
With each script in good cheer,
🐇✨ A formatting hop, perfectly made!

Note

⚡️ Unit Test Generation is now available in beta!

Learn more here, or try it out under "Finishing Touches" below.

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📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 966cedf and 8834537.

📒 Files selected for processing (17)

• workflow/Snakefile (1 hunks)
• workflow/rules/analyse.smk (3 hunks)
• workflow/rules/docking.smk (3 hunks)
• workflow/rules/preparation.smk (1 hunks)
• workflow/scripts/ResultTxt.py (2 hunks)
• workflow/scripts/ZINCdownload.py (1 hunks)
• workflow/scripts/concatPDBQT.py (1 hunks)
• workflow/scripts/downloadZINCsubsets.py (1 hunks)
• workflow/scripts/generateIRODS.py (2 hunks)
• workflow/scripts/makeHistogram.py (3 hunks)
• workflow/scripts/mergeOutput.py (1 hunks)
• workflow/scripts/prepareDocking.py (2 hunks)
• workflow/scripts/prepareReceptor.py (4 hunks)
• workflow/scripts/sortResult.py (1 hunks)
• workflow/scripts/splitFile.py (1 hunks)
• workflow/scripts/union_venn.py (2 hunks)
• workflow/scripts/venn.py (11 hunks)

✨ Finishing Touches

• 📝 Generate Docstrings

🧪 Generate unit tests

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch refactor/all

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