🚀 Ultimate Developer Onboarding Guide

Welcome to the BioPro SDK Developer Ecosystem! Whether you are a computational biologist, software engineer, or a lab automation specialist, this guide is designed to take you from a fresh installation to publishing your first cryptographically signed BioPro plugin.

This master guide covers everything you need to know, combining elements from our core documentation into one seamless onboarding journey.

🗺️ The Onboarding Journey

Phase 1: Environment Setup
Phase 2: Cryptographic Identity
Phase 3: Bootstrapping Your First Plugin
Phase 4: Developing the User Interface
Phase 5: Code Signing & Security
Phase 6: CI/CD & Publishing

🛠️ Phase 1: Environment Setup

BioPro relies heavily on modern Python standards and ultra-fast dependency management using uv.

1. Create a Virtual Environment

You should always isolate your development environment to prevent version conflicts.

# Create the virtual environment using uv
uv venv

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

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

2. Install the BioPro SDK

Install the SDK into your activated virtual environment. This will expose the biopro-sdk CLI globally within your environment.

uv pip install -e .

For more details on the environment setup, read the Quickstart Guide.

🔑 Phase 2: Cryptographic Identity

Before you can write code, you must establish a developer identity. The BioPro host application requires all loaded plugins to be signed by a trusted developer to prevent malicious code execution.

Run the identity initialization command:

biopro-sdk init-identity

What this does: - Generates an asymmetric Ed25519 private key (~/.biopro/dev_keys/private.key). NEVER SHARE THIS FILE. - Generates a public key certificate (~/.biopro/dev_keys/public.pub). - Registers you as an authenticated developer on your local machine.

For a deep dive into our Trust Engine, read the Security & CI/CD Guide.

🏗️ Phase 3: Bootstrapping Your First Plugin

Instead of manually creating boilerplate files, the BioPro SDK provides a scaffolding tool.

biopro-sdk bootstrap my_first_plugin

This generates a robust plugin structure:

my_first_plugin/
├── pyproject.toml           # The plugin manifest (metadata & configuration)
├── src/
│   ├── __init__.py          # The entry point
│   └── ui.py                # The User Interface (PyQt6/PySide6)
└── .github/workflows/       # Pre-configured CI/CD pipelines

Understanding the Manifest (`pyproject.toml`)

The pyproject.toml file contains standard Python packaging data alongside BioPro-specific metadata:

[tool.biopro.plugin]
id = "my_first_plugin"
min_core_version = "1.4.9"
entry_point = "my_first_plugin:get_panel_class"

🖥️ Phase 4: Developing the User Interface

BioPro plugins are natively built using PyQt6 / PySide6. To ensure a cohesive visual aesthetic across the entire platform, the SDK provides pre-built, styled UI components.

Open src/ui.py and import the BioPro SDK components:

from biopro_sdk.plugin import PluginBase, PrimaryButton, SecondaryButton, SectionHeader

class MyPluginUI(PluginBase):
    def __init__(self, parent=None):
        super().__init__(parent)

        # Add a stylized header
        header = SectionHeader("Gel Analysis Pipeline", self)
        self.layout.addWidget(header)

        # Add a primary call-to-action button
        btn = PrimaryButton("Run Analysis", self)
        btn.clicked.connect(self._run_analysis)
        self.layout.addWidget(btn)

    def _run_analysis(self):
        print("Analysis started...")

For advanced UI state binding, threading, and local storage, read the Developer Handbook.

🔐 Phase 5: Code Signing & Security

Once your code is ready, you must sign it before distributing it to the community or running it in a production BioPro instance.

Run the signing tool from the root of your plugin directory:

biopro-sdk sign my_first_plugin

What this does: 1. Computes a SHA-256 integrity hash for every file in your src/ folder. 2. Generates a security.json ledger. 3. Cryptographically signs the ledger using your private key, outputting signature.bin. 4. Attaches a trust_chain.json file to establish your identity.

🚀 Phase 6: CI/CD & Publishing

When you bootstrap a plugin, the SDK automatically generates GitHub Actions workflows in .github/workflows/. These are designed to automate your supply chain:

ci.yml: Runs your tests and linters on every pull request.
deploy-docs.yml: Automatically generates and deploys MkDocs documentation to GitHub Pages.
release.yml: Automatically packages your plugin into a .zip artifact when you publish a new GitHub Release. It runs the signing command dynamically using a GitHub Secret (BIOPRO_PRIVATE_KEY).

🔄 Migration Guide for V1 Developers

If you are an existing developer upgrading your plugins from BioPro V1 to the new V2 ecosystem, you need to make a few critical changes:

Adopt the Split-Manifest Architecture:
V1 relied on a custom manifest.json. In V2, all configuration must be moved to standard Python pyproject.toml.
Your entry point must now be declared under [tool.biopro.plugin] in your pyproject.toml.
Move Source Code to src/:
V1 allowed flat directory structures. V2 enforces a strict src/ layout. Move all your Python logic into src/ and ensure your entry point is resolvable.
Generate Developer Keys:
V1 had no cryptographic signing. You must run biopro-sdk init-identity to generate an Ed25519 keypair.
Sign Your Old Plugins:
Before a V2 host can load your old plugin, you must run biopro-sdk sign <path_to_plugin> to generate a security.json, signature.bin, and trust_chain.json.
Use SDK UI Components:
V2 introduces biopro_sdk.plugin.PluginBase. You should subclass this instead of a raw QWidget for out-of-the-box styling and standardized event routing.

Next Steps

Now that you understand the full lifecycle, you are ready to start building powerful bioinformatics plugins! - Want to build complex UI layouts? Check out the Developer Handbook. - Need to understand the Cryptographic pipeline? Read the Security Guide. - Looking for API specifics? Browse the API Reference.

Happy hacking! 🎉