End2EndPaper

A Python-based workflow engine designed to write scientific papers with absolute "end-to-end reproducibility." By leveraging Python f-strings, every statistical value, p-value, and numeric result in your manuscript can be directly linked to your underlying data structures. The compiled output is a completely formatted, native Microsoft Word document.

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Key Features

• Data-Driven Manuscripts: Eliminate manual copy-paste errors by injecting analysis variables straight into your text.
• Dynamic Updating: If your data pipeline or sample size changes, re-running the script updates every number throughout the entire document instantly.
• Word Integration: Outputs clean, standard styled .docx files ready for journal submission.
• Math Support: Author equations using familiar LaTeX syntax directly inside your text strings.

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Requirements

This tool requires the python-docx-template library. Install it via pip:

pip install docx-tpl

For more details on the template engine, visit the python-docx-template GitHub repository.

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Getting Started

1. Clone the Repository: Place this repository inside your active data analysis or research project directory.
2. Configure Directories: Open example_paper.py and update the root directory paths to align with your project's local folder structure.
3. Draft Your Manuscript: Modify the text variables for each section of your paper (e.g., abstract, introduction, methods, results).
4. Compile: Run the master script to build your paper:

python example_paper.py

A freshly formatted docx document will automatically save directly into your project folder.

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LaTeX and Equation Support

You can author inline math formulas natively by surrounding them with single dollar signs, like $a^2 + b^2 = c^2$. Because Word does not parse LaTeX natively on import, a custom VBA macro is provided to automatically transform these text strings into native Microsoft Word Equation blocks.

Setting Up the Word Macro

1. Open your generated .docx document in Microsoft Word.
2. Press Alt + F11 to open the VBA Editor.
3. Click Insert > Module and paste the following macro script into the editor:

Sub ConvertSingleDollarLaTeX()
    Dim rng As Range
    Dim rawText As String
    Dim objMath As Object
    
    Set rng = ActiveDocument.Content
    
    ' Enable Wildcard search for single dollar signs $(everything inside)$
    With rng.Find
        .ClearFormatting
        .Text = "\$(?*)\$"
        .MatchWildcards = True
        .Forward = True
        .Wrap = wdFindStop
        
        Do While .Execute
            ' 1. Grab the raw text including the dollar signs
            rawText = rng.Text
            
            ' 2. Strip the starting and ending dollar signs from the string
            rawText = Mid(rawText, 2, Len(rawText) - 2)
            
            ' 3. Fix the Python f-string issue by converting tabs back to \t
            rawText = Replace(rawText, vbTab, "\t")
            
            ' 4. Clear the text inside the range (removes the dollar signs entirely)
            rng.Text = ""
            
            ' 5. Add a clean native math block container at the empty range
            Dim mathRange As Range
            Set mathRange = rng.OMaths.Add(Range:=rng)
            
            ' 6. Extract the actual equation object from the range, inject text, and build up
            Set objMath = mathRange.OMaths(1)
            objMath.Range.Text = rawText
            objMath.BuildUp
            
            ' 7. Cleanly advance past this newly made equation block
            rng.Collapse wdCollapseEnd
        Loop
    End With
    
    MsgBox "All single-dollar LaTeX equations have been successfully converted without dollar signs!", vbInformation
End Sub

4. Close the VBA Editor and return to your Word document.
5. Press Alt + F8, select ConvertSingleDollarLaTeX, and click Run. All inline LaTeX markup will convert instantly into native, publication-ready Word equations.