API & DSL Reference
===================

Complete reference documentation for py3plex APIs, algorithms, DSL syntax, and configuration.

**This section includes:**

Python API Reference
--------------------

* :doc:`api_index` — Full API documentation for all modules and classes
* :doc:`algorithm_reference` — Complete algorithm reference with parameters and examples

DSL & Query Reference
---------------------

* :doc:`dsl_reference` — Complete DSL syntax and operator reference
* :doc:`layer_set_algebra` — Layer set algebra for composable layer selection
* :doc:`configuration` — Configuration options and environment variables

**Reading Paths:**

* **Need DSL syntax?** → :doc:`dsl_reference` for complete grammar
* **Looking for an algorithm?** → :doc:`algorithm_reference` for all available algorithms
* **Need API details?** → :doc:`api_index` for function signatures and parameters
* **Configuration options?** → :doc:`configuration` for setup and tuning

**Relation to other sections:**

* **How-to Guides** show you *how* to accomplish tasks. This Reference section documents *what* each function does.
* **Concepts** explain *why* algorithms work. This section provides precise API details.
* **Examples** show complete workflows. This section provides isolated reference information.