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🏁 Quickstart Guide

This step-by-step tutorial walks you through setting up your local environment, creating a new BioPro module from scratch, understanding the repository structure, and securing it with cryptographic signing.

🛠️ Step 1: Environment Setup

BioPro SDK utilizes uv for lightning-fast and highly secure dependency management. Follow these instructions to initialize your workspace:

1. Initialize Python Environment

Create a local Python virtual environment and activate it: 

# Create virtual environment
uv venv

# Activate on macOS/Linux
source .venv/bin/activate

# Activate on Windows Powershell
.venv\Scripts\Activate.ps1

2. Install BioPro SDK

Install the SDK into your virtual environment: 

uv pip install -e .
This registers the global CLI shim biopro-sdk directly into your path!

🔑 Step 2: Initialize Your Developer Identity

To load plugins into a production instance of the host application, they must be signed by an approved private key. BioPro provides a standard command-line utility to bootstrap your development environment.

Run the onboarding command: 

biopro-sdk init-identity

What happens behind the scenes?

  1. Generates an Ed25519 Private Key: Writes a PKCS#8 pem file to ~/.biopro/dev_keys/private.key.
  2. Generates Public Key: Writes a public certificate stub to ~/.biopro/dev_keys/public.pub.
  3. Local Registration: The CLI establishes this key pair as your local developer identity for subsequent signing operations.

🏗️ Step 3: Bootstrap a New BioPro Module

Instead of creating files manually, you can use the SDK CLI to automatically scaffold a new plugin repository that conforms to the latest V2 architecture.

Run the bootstrap command: 

biopro-sdk bootstrap my_first_plugin

How to Organize a Repo

The bootstrap command creates the standard directory structure required by BioPro. Let's look at how your repo is organized:

my_first_plugin/
├── pyproject.toml           # The plugin manifest and Python configuration
├── src/
│   └── __init__.py          # The core plugin logic and entry point
├── docs/
│   └── 01_getting_started.md # Local documentation for your plugin
└── .github/
    └── workflows/           # CI/CD pipelines (ci, deploy-docs, release)
  • pyproject.toml: The split-manifest architecture uses this standard Python file to define your plugin ID, required SDK version, permissions, dependencies, and the entry_point for the BioPro host application.
  • src/: All your Python source code lives here. The __init__.py file contains a class inheriting from AnalysisBase (or PluginBase) which serves as the entry point.
  • docs/: Markdown documentation files that will be compiled into the BioPro Help Center.

🔐 Step 4: Security Signing

Before your plugin can be loaded by the BioPro host application, it must be cryptographically signed. The Trust Engine verifies that the code hasn't been tampered with.

Run the signing utility on your plugin directory: 

biopro-sdk sign my_first_plugin

What happens during signing?

  1. File Hashing: The CLI crawls your src/ and other critical directories, computing a SHA-256 integrity hash for every file.
  2. Ledger Generation: A security.json ledger is generated, binding the hashes of your files to the hash of your pyproject.toml.
  3. Cryptographic Signature: The ledger is signed with your developer private key, generating signature.bin.
  4. Trust Chain: A trust_chain.json file is created to link your public key to the signature.

Your plugin directory will now have the necessary security assets: 

my_first_plugin/
├── pyproject.toml
├── security.json        # NEW: Integrity hashes
├── signature.bin        # NEW: Cryptographic signature
├── trust_chain.json     # NEW: Developer public key chain
├── src/
├── docs/
└── .github/

Note: You must re-run biopro-sdk sign my_first_plugin every time you modify your code before testing it in the host application!

🚀 Step 5: Validate Your Plugin

To ensure your newly created and signed plugin meets all BioPro SDK standards before distribution, you can run the built-in evaluator:

biopro-sdk evaluate my_first_plugin

This will run a 3-part audit: 1. Manifest Audit: Verifies the pyproject.toml configuration. 2. Structure & SDK Compliance: Checks that you are properly subclassing BioPro base classes like AnalysisBase. 3. Security Audit: Validates that the cryptographic signatures are present and correct.

If you get a green status, your plugin is ready to be loaded into the BioPro host application!