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docs: add Getting Started section to README for Python/Poetry setup and quick run commands#2

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docs: add Getting Started section to README for Python/Poetry setup and quick run commands#2
kaddujames501-ship-it wants to merge 2 commits into
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kaddujames501-ship-it:Documentation

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@kaddujames501-ship-it kaddujames501-ship-it commented Mar 22, 2026

Added a "Getting Started" section to the README.md to guide new users through initial setup and a basic workflow.
This includes verifying Python 3.9+ and Poetry installation, running poetry install, and executing sample commands like flan global fit and flan global predict.
The update reduces onboarding friction by providing clear, actionable steps before the detailed Usage section.

Summary by Sourcery

Add an introductory Getting Started section to the README to guide new users through basic Python/Poetry setup and a simple local workflow.

Documentation:

  • Document prerequisite checks for Python 3.9+ and Poetry, and outline initial install and shell commands for running the tool.
  • Add quick-start examples for fitting and predicting globally using the CLI to streamline onboarding.

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sourcery-ai Bot commented Mar 22, 2026

Reviewer's guide (collapsed on small PRs)

Reviewer's Guide

Adds a concise 'Getting Started' section to README.md outlining Python/Poetry prerequisites, environment setup, and example flan commands to streamline new user onboarding before the detailed Usage section.

File-Level Changes

Change Details Files
Document a minimal end-to-end setup and run workflow for new users.
  • Introduce a 'Getting Started' section immediately after installation instructions in the README.
  • Document verification steps for Python 3.9+ and Poetry installation using command-line checks.
  • Describe environment setup using 'poetry install' and interactive shell or 'poetry run'.
  • Provide example commands for running a quick local workflow with 'flan global fit' and 'flan global predict' using a sample VCF file.
README.md

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Hey - I've left some high level feedback:

  • Consider making it explicit that the flan commands in step 3 should be run either inside poetry shell or prefixed with poetry run (e.g., poetry run flan ...) to avoid confusion for users unfamiliar with Poetry-managed environments.
  • It might help to mention where the user should expect path/to/your_sample.vcf.gz to come from (e.g., sample data in the repo or their own VCF) so newcomers know how to obtain or prepare this file for the quick workflow.
Prompt for AI Agents
Please address the comments from this code review:

## Overall Comments
- Consider making it explicit that the `flan` commands in step 3 should be run either inside `poetry shell` or prefixed with `poetry run` (e.g., `poetry run flan ...`) to avoid confusion for users unfamiliar with Poetry-managed environments.
- It might help to mention where the user should expect `path/to/your_sample.vcf.gz` to come from (e.g., sample data in the repo or their own VCF) so newcomers know how to obtain or prepare this file for the quick workflow.

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