Text Format Organizer

Source: https://github.com/aipoch/medical-research-skills

Validation Shortcut

Run this minimal command first to verify the supported execution path:

python scripts/init_run.py --help

When to Use

• Cleaning biomedical manuscripts where extra blank lines, trailing spaces, or mixed line endings break journal templates.
• Normalizing Markdown notes (lists/tables/code blocks) before converting to PDF/Word.
• Formatting clinical research reports or protocol records exported from multiple editors (Windows/macOS/Linux).
• Pre-processing .docx drafts before running downstream proofreading/QA tools (e.g., academic-proofreader).
• Preparing theses/dissertations to enforce consistent indentation and whitespace rules across chapters.

Key Features

• Intelligent cleaning
  • Removes redundant empty lines while keeping paragraph boundaries.
  • Strips trailing whitespace while preserving leading indentation.
  • Unifies line endings (unix, windows, mac).
  • Converts tabs to spaces (configurable indentation size).
• Structure protection
  • Preserves Markdown list structures (-, *, 1.).
  • Keeps fenced code blocks (...) unchanged.
  • Preserves Markdown table formatting.
• Multi-format I/O
  • Supports .txt, .md, and .docx input/output.

Dependencies

• python >= 3.8
• python-docx >= 1.0.0

Example Usage

1) Format a Markdown or text file

python scripts/init_run.py --input input.md --output output.md

2) Format a Word document

python scripts/init_run.py -i paper.docx -o paper_clean.docx

3) Preview changes without writing output

python scripts/init_run.py -i input.md --preview

4) Programmatic usage (core module)

from scripts.text_formatter import TextFormatter, FormatOptions

text = "Line with trailing spaces   \n\n\n- item 1\n\t- item 2\n"
options = FormatOptions(
    line_ending="unix",
    indent="spaces",
    indent_size=4,
)

formatter = TextFormatter(options=options)
formatted = formatter.format(text)
print(formatted)

5) Workflow with an academic proofreading tool

# Step 1: Format organization
python scripts/init_run.py -i paper.docx -o paper_clean.docx

# Step 2: Content/format checking (separate project)
cd ../academic-proofreader
python scripts/init_run.py -i paper_clean.docx

Implementation Details

CLI parameters

Formatting rules (high level)

• Whitespace normalization
  • Collapses excessive blank lines while preserving paragraph separation.
  • Removes trailing spaces at line ends; does not remove leading indentation.
• Line ending normalization
  • Converts all line endings to the selected target (unix/windows/mac).
• Indentation normalization
  • Converts tab characters to spaces when indent=spaces, using indent_size.
• Markdown-safe processing
  • Skips transformations inside fenced code blocks.
  • Preserves list markers and table pipes/alignment to avoid structural breakage.
• DOCX handling
  • Reads .docx, applies the same normalization at the text/paragraph level, then writes a new .docx using the configured font and size.

When Not to Use

• Do not use this skill when the required source data, identifiers, files, or credentials are missing.
• Do not use this skill when the user asks for fabricated results, unsupported claims, or out-of-scope conclusions.
• Do not use this skill when a simpler direct answer is more appropriate than the documented workflow.

Required Inputs

• A clearly specified task goal aligned with the documented scope.
• All required files, identifiers, parameters, or environment variables before execution.
• Any domain constraints, formatting requirements, and expected output destination if applicable.

Recommended Workflow

1. Validate the request against the skill boundary and confirm all required inputs are present.
2. Select the documented execution path and prefer the simplest supported command or procedure.
3. Produce the expected output using the documented file format, schema, or narrative structure.
4. Run a final validation pass for completeness, consistency, and safety before returning the result.