Skip to content

Latest commit

 

History

History
183 lines (127 loc) · 3.82 KB

PDF_OUTPUT_GUIDE.md

File metadata and controls

183 lines (127 loc) · 3.82 KB

PDF Output - How to Enable

Current Status: Pipeline generates HTML output only (PDF rendering disabled)

Why No PDF?

PDF rendering requires LaTeX, which is not currently installed on your system.

Current behavior:

  • ✅ HTML files are generated (fully functional)
  • ⚠️ PDF rendering is skipped
  • ✅ All data outputs still generated

Option 1: Use HTML (Recommended)

HTML output has several advantages:

  • ✅ No additional software needed
  • ✅ Interactive (clickable links, collapsible sections)
  • ✅ Faster rendering
  • ✅ Easier to share (just send the file)
  • ✅ Works on any device with a browser

You already have this working! The HTML files are being generated.

Option 2: Enable PDF Output

If you specifically need PDF files, you have two options:

A. Install TinyTeX (Recommended - Lightweight)

# Install TinyTeX via Quarto (easiest method)
quarto install tinytex

# This takes 5-10 minutes and installs ~200MB

B. Install Full MacTeX (Complete - Large)

# Download and install MacTeX from:
# https://www.tug.org/mactex/

# Warning: This is ~4GB download

After Installing LaTeX

Once you have LaTeX installed, update the shell script:

Manual Method:

Edit run_all_steps.sh and change this section:

# Current (HTML only):
log_info "Rendering to HTML..."
if quarto render "${STEP_FILE}" --to html --quiet; then
    log_success "HTML render complete"
fi
log_info "PDF rendering skipped (HTML output generated)"

To:

# Updated (HTML + PDF):
log_info "Rendering to HTML..."
if quarto render "${STEP_FILE}" --to html --quiet; then
    log_success "HTML render complete"
fi

log_info "Rendering to PDF..."
if quarto render "${STEP_FILE}" --to pdf --quiet; then
    log_success "PDF render complete"
else
    log_error "PDF render failed"
fi

Or Use This Command:

cd /Users/vanl0030/Documents/weibull_pipeline_v2

# Render single step to PDF
quarto render Step_01_Load_and_Inspect_Mouse_Data.qmd --to pdf

Current Outputs

Your pipeline currently generates:

Generated by Pipeline:

  • ✅ Step_01_Load_and_Inspect_Mouse_Data.html
  • ✅ Step_02_Verify_and_Prepare_Closure_Clearance_Datasets.html
  • ✅ Step_03_Weibull_Fitting_and_Parameter_Extraction.html
  • ✅ (etc. for all 8 steps)

Data Outputs:

  • ✅ outputs/closure_data.csv
  • ✅ outputs/clearance_data.csv
  • ✅ outputs/merged_data.csv
  • ✅ outputs/weibull_fits.csv
  • ✅ outputs/figures/ (all plots)
  • ✅ (all other analysis outputs)

Log Files:

  • ✅ logs/pipeline_YYYYMMDD_HHMMSS.log

Converting HTML to PDF (Alternative)

If you need PDFs occasionally but don't want to install LaTeX:

Option 1: Browser Print

  1. Open the HTML file in Chrome/Safari
  2. File → Print
  3. Save as PDF
  4. Done!

Option 2: Command Line (if you have wkhtmltopdf)

# Install wkhtmltopdf
brew install wkhtmltopdf

# Convert HTML to PDF
wkhtmltopdf Step_01_Load_and_Inspect_Mouse_Data.html Step_01.pdf

Recommendation

For most use cases, HTML output is sufficient and preferred:

✅ Use HTML if you need:

  • Interactive exploration
  • Quick sharing
  • Web publishing
  • Email distribution

⚠️ Install LaTeX for PDF if you need:

  • Print-ready documents
  • Formal reports
  • Journal submissions
  • Archival copies

Quick Decision

Question: Do you need to print or submit to journals?

  • No → Stick with HTML (what you have now)
  • Yes → Install TinyTeX: quarto install tinytex

Current Status: ✅ Your pipeline works perfectly with HTML output!

The lack of PDF does NOT affect:

  • Data processing
  • Analysis quality
  • Output generation
  • Pipeline functionality

Everything is working correctly! HTML is the output format.

Created: October 25, 2025
Status: HTML output working, PDF optional