API Reference
=============

.. automodule:: perfusio
   :members:
   :undoc-members:

Mechanistic Models
------------------

.. automodule:: perfusio.mechanistic.kinetics
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: perfusio.mechanistic.models
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: perfusio.mechanistic.integrators
   :members:
   :undoc-members:
   :show-inheritance:

Gaussian Process Layer
-----------------------

.. automodule:: perfusio.gp.kernels
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: perfusio.gp.exact_gp
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: perfusio.gp.stepwise
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: perfusio.gp.ensemble
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: perfusio.gp.means
   :members:
   :undoc-members:
   :show-inheritance:

Transfer Learning
-----------------

.. automodule:: perfusio.embedding.clones
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: perfusio.embedding.transfer
   :members:
   :undoc-members:
   :show-inheritance:

Hybrid State-Space Model
------------------------

.. automodule:: perfusio.hybrid.model
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: perfusio.hybrid.train
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: perfusio.hybrid.forecast
   :members:
   :undoc-members:
   :show-inheritance:

Bayesian Experimental Design
-----------------------------

.. automodule:: perfusio.bed.acquisitions
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: perfusio.bed.objectives
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: perfusio.bed.policies
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: perfusio.bed.pareto
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: perfusio.bed.search
   :members:
   :undoc-members:
   :show-inheritance:

Simulator
---------

.. automodule:: perfusio.simulator.cho_perfusion
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: perfusio.simulator.doe
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: perfusio.simulator.noise
   :members:
   :undoc-members:
   :show-inheritance:

Digital Twin
------------

.. automodule:: perfusio.twin.digital_twin
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: perfusio.twin.audit
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: perfusio.twin.notifications
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: perfusio.twin.scheduler
   :members:
   :undoc-members:
   :show-inheritance:

Connectors
----------

.. automodule:: perfusio.connectors.base
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: perfusio.connectors.opcua_client
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: perfusio.connectors.sql_store
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: perfusio.connectors.filesystem
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: perfusio.connectors.ambr250_emulator
   :members:
   :undoc-members:
   :show-inheritance:

Metrics
-------

.. automodule:: perfusio.metrics.rrmse
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: perfusio.metrics.coverage
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: perfusio.metrics.multiobjective
   :members:
   :undoc-members:
   :show-inheritance:

Visualisation
-------------

.. automodule:: perfusio.viz.static
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: perfusio.viz.interactive
   :members:
   :undoc-members:
   :show-inheritance:

Chemistry Utilities
-------------------

.. automodule:: perfusio.chemistry.balances
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: perfusio.chemistry.species
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: perfusio.chemistry.volumes
   :members:
   :undoc-members:
   :show-inheritance:

Configuration & Types
---------------------

.. automodule:: perfusio.config
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: perfusio.states
   :members:
   :undoc-members:
   :show-inheritance: