Developer Guide

This section provides documentation for developers who want to contribute to PhenoTypic or extend its functionality.

Developer Guide Topics

• Architecture Overview
  • Core Components
  • Design Patterns
  • Data Flow
• Contributing Guidelines
  • Getting Started
  • Code Standards
  • Adding a tuning objective (Scorer)
  • Pull Request Workflow
  • Issue Reporting
• Extending Phenotypic
  • Creating Custom Modules
  • Building Pipelines
  • Integration Points
• Testing Framework
  • Unit Testing
  • Integration Testing
  • Test Coverage
  • Continuous Integration
• Run state: what is tracked, and how to read it
  • Reading state: one call
  • (a) Tracked state — written down, and irreducibly so
  • (b) Content proofs — evidence, not tracked state
  • © Derived, and by what
  • (d) Retained, and read by nothing
  • The one that fits none of the above: migration_manifest.json
  • Provenance has two writers
  • Known consumers
  • Where readers and writers live
  • Changing the state model
• Documentation Writing Guide
  • Documentation Structure
  • Audience
  • Voice and Tone
  • Domain Language
  • Code Conventions
  • Cross-Referencing
  • References and Citations
  • Building the Documentation
  • References
• ImageOperation Docstring Style Guide
  • Target Length
  • Template
  • Section-by-Section Rules
  • Adapting the Template by ABC Type
  • Common Mistakes
  • Worked Example: OtsuDetector
  • References

Placeholder Pages

Architecture Overview (Coming Soon)

An overview of PhenoTypic’s architecture, design patterns, and core components.

Contributing Guidelines (Coming Soon)

Learn how to contribute to PhenoTypic, including coding standards, pull request workflow, and issue reporting.

Extending PhenoTypic (Coming Soon)

Detailed guides on how to create custom modules, pipelines, and integrations with PhenoTypic.

Testing Framework (Coming Soon)

Information about PhenoTypic’s testing infrastructure and how to write effective tests.

Reference Pages

Run state: what is tracked, and how to read it

The four tracked states, the three content proofs, what is derived and by what function, and the table of known consumers. Read it before adding any counter, flag or marker under .phenotypic/.