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liger_iris_pipeline Documentation
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The Liger-IRIS Data Reduction System is based on the suite of packages from Space Telescope Science Institute
used to process data from JWST and NGRST.

With ``stpipe`` and ``stdatamodels`` we can configure each step of a pipeline through one or more text based .INI style files,
then we provide one input FITS file or a set of multiple inputs defined in JSON (named `Associations <https://jwst-pipeline.readthedocs.io/en/latest/jwst/associations/overview.html>`_).
Custom analysis steps and pipelines for IRIS are defined as classes in the current repository ``liger_iris_pipeline``

Then execute the pipeline from the command line using the ``tmtrun`` executable or using
directly the Python library.

The pipeline also dynamically interfaces to the ``CRDS`` the Calibration References Data System,
to retrieve the best calibration datasets given the metadata in the headers of the input FITS files.
The ``CRDS`` client can also load data from a local cache, so for now we do not have a actual
``CRDS`` server and we only rely on a local cache.

The ``CRDS`` is not under our control, the Thirty Meter Telescope will deliver a database system
to replace the ``CRDS`` and we can adapt our code to that in the future.

Getting Started
===============

.. toctree::
   :maxdepth: 2

   getting-started

Example run
===========

.. toctree::
   :maxdepth: 2

   example-run

Design
======

.. toctree::
   :maxdepth: 2

   design

Calibration and CRDS
====================

.. toctree::
   :maxdepth: 2

   calibration-database

Algorithms
==========

.. toctree::
   :maxdepth: 1

   available-steps
   algorithms

Subarrays
=========

.. toctree::
   :maxdepth: 1

   subarrays

Reference/API
=============

.. automodapi:: liger_iris_pipeline