Disclaimer

The views and opinions expressed in this presentation are those of the individual presenters and do not represent those of their affiliated organizations or institutions.

Acknowledgements

• R/Pharma organizers

  • It is a fun and productive annual gathering
  • Please consider sharing stories and use cases to expand the community

• Team members from Meta Platforms and Merck & Co., Inc., Rahway, NJ, USA

• Contributors of pycsr and r4csr training materials

  • Please consider submitting issues or PR in the repos

Key components

rtflite provides Python classes RTFDocument that map to table elements. The goal is to help you translate data frame to tables in RTF file.

rtflite

Example

import polars as pl
import rtflite as rtf

# Load and prepare data
df = pl.read_parquet("data/adsl.parquet")

# Create RTF document
doc = rtf.RTFDocument(
    df=df.head(6),
    rtf_body=rtf.RTFBody(),
)

doc.write_rtf("output.rtf")

What is an analysis package?

A Python package designed specifically to organize analysis scripts and code for a clinical trial project.

Purpose:

Our primary focus is creating a standard folder structure to organize the project, with 3 goals in mind:

• Project folder structure for clinical trial deliverables
• Reproducible environments for analyses
• Submission-ready structures for regulatory review

Combines:

• Python package structure (code organization)
• Quarto project (report generation)
• Regulatory requirements (eCTD submission)

Package structure

Posit Cloud workspace

demo-py-esub/
├── pyproject.toml          # Project metadata
├── .python-version         # Python version
├── uv.lock                 # Locked dependencies
├── src/demo001/            # Study-specific code
│   ├── __init__.py
│   └── utils.py
├── analysis/               # Quarto analysis docs
│   └── tlf-*.qmd
├── data/                   # ADaM datasets
├── output/                 # Generated TLFs
└── tests/                  # Validation tests

See: https://pycsr.org/pkg-structure.html

Benefits

Git-centric workflow

Core principle: All project assets in version control.

Plain text workflow:

• .qmd files for analysis (not .ipynb for final deliverables)
• .md files for documentation
• .toml files for configuration
• Avoid .xlsx files for tracking

Project tracking:

• Issues for requirements
• Pull requests for review
• Project boards (Kanban)

See: https://pycsr.org/pkg-management.html

Development lifecycle

FDA requirements

FDA Study Data Technical Conformance Guide Section 4.1.2.10:

Submit programs for primary and secondary efficacy analyses. Specify software in ADRG. Use ASCII text format. No executable extensions.

Goal: Enable reviewers to understand and confirm analysis algorithms.

See: https://pycsr.org/submission-overview.html

Demo repositories

Analysis package: https://github.com/elong0527/demo-py-esub

Submission package: https://github.com/elong0527/demo-py-ectd

Clone and explore to see complete examples.

eCTD Module 5 structure

m5/datasets/<study-id>/analysis/adam/
├── datasets/
│   ├── *.xpt               # ADaM datasets
│   ├── define.xml
│   ├── adrg.pdf            # Instructions
│   └── analysis-results-metadata.pdf
└── programs/
    ├── py0pkgs.txt         # Packed Python package
    ├── tlf-01-*.txt        # Analysis programs
    └── tlf-02-*.txt

Key: All files in programs/ must be ASCII text.

The solution: pkglite for Python

Packs Python projects into portable text files.

Why needed:

• Python packages have directory structure
• May contain binary files
• FDA requires ASCII text format

pkglite capabilities:

• Pack entire project into single .txt file
• Preserve file paths and metadata
• Unpack to restore original structure
• Support multiple packages in one file

Documentation: https://pharmaverse.github.io/py-pkglite/

Packing workflow

1. Create .pkgliteignore

uvx pkglite use demo-py-esub/

2. Pack the package

uvx pkglite pack demo-py-esub/ \
  -o programs/py0pkgs.txt

3. Convert Quarto to Python scripts

• Render .qmd -> verify it works
• Convert .qmd -> .ipynb -> .py
• Clean and format with ruff
• Save as .txt (no .py extension)

See: https://pycsr.org/submission-package.html

Packed file format

Human-readable Debian Control File (DCF) format:

# Generated by py-pkglite
# Use `pkglite unpack` to restore

Package: demo-py-esub
File: pyproject.toml
Format: text
Content:
  [project]
  name = "demo001"
  version = "0.1.0"
  ...

Reviewers can read without special tools.

Updating ADRG

Document the Python environment:

Python environment:

Packages:

Appendix: Step-by-step reproduction instructions.

Resources

• Workshop Page pos.it/pycsr-rpharma-2026
• Book: pycsr.org

Regulatory:

• FDA Study Data Technical Conformance Guide
• eCTD specifications

Technical:

• rtflite
• pkglite for Python
• uv documentation