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

.. _base_ref:

:mod:`bids.layout`: Querying BIDS datasets
------------------------------------------

.. autosummary:: bids.layout
   :toctree: generated/

   bids.layout.BIDSLayout
   bids.layout.BIDSValidator
   bids.layout.BIDSFile
   bids.layout.BIDSDataFile
   bids.layout.BIDSJSONFile
   bids.layout.Config
   bids.layout.Entity
   bids.layout.Tag
   bids.layout.parse_file_entities
   bids.layout.add_config_paths
   bids.layout.index.BIDSLayoutIndexer
   bids.layout.writing

.. currentmodule:: bids

.. _calibration_ref:


:mod:`bids.modeling`: Model specification for BIDS datasets
------------------------------------------------------------

.. autosummary:: bids.modeling
   :toctree: generated/

   bids.modeling.statsmodels
   bids.modeling.auto_model
   bids.modeling.statsmodels.BIDSStatsModelsGraph
   bids.modeling.statsmodels.BIDSStatsModelsNode

.. currentmodule:: bids

.. _calibration_ref:


:mod:`bids.reports`: Data acquisition report generation
--------------------------------------------------------

.. autosummary:: bids.reports
   :toctree: generated/

   bids.reports.BIDSReport
   bids.reports.parsing
   bids.reports.parameters
   bids.reports.utils

.. currentmodule:: bids

.. _calibration_ref:


:mod:`bids.variables`: Variables
--------------------------------------------------

.. autosummary:: bids.variables
   :toctree: generated/

   bids.variables.SimpleVariable
   bids.variables.SparseRunVariable
   bids.variables.DenseRunVariable
   bids.variables.BIDSVariableCollection
   bids.variables.BIDSRunVariableCollection
   bids.variables.merge_collections
   bids.variables.load_variables
   bids.variables.merge_variables
   bids.variables.io
   bids.variables.entities
   bids.variables.collections
   bids.variables.variables

.. currentmodule:: bids

.. _calibration_ref:


:mod:`bids.config`: PyBIDS Configuration utilities
--------------------------------------------------

.. autosummary:: bids.config
   :toctree: generated/

   bids.config.set_option
   bids.config.set_options
   bids.config.get_option
   bids.config.from_file
   bids.config.reset_options

.. currentmodule:: bids

.. _calibration_ref:


:mod:`bids.utils`: Utility functions
--------------------------------------------------

.. autosummary:: bids.utils
   :toctree: generated/

   bids.utils.listify
   bids.utils.matches_entities
   bids.utils.convert_JSON
   bids.utils.make_bidsfile


.. currentmodule:: bids

.. _calibration_ref: