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+# Sphinx build info version 1
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 5b5a45ef54eeffa5f91a1a24e317bc7c
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/.doctrees/api_ref/arena.doctree b/.doctrees/api_ref/arena.doctree
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diff --git a/.doctrees/api_ref/examples/index.doctree b/.doctrees/api_ref/examples/index.doctree
diff --git a/.doctrees/api_ref/examples/locomotion.doctree b/.doctrees/api_ref/examples/locomotion.doctree
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diff --git a/.doctrees/tutorials/turning.doctree b/.doctrees/tutorials/turning.doctree
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diff --git a/.nojekyll b/.nojekyll
diff --git a/CNAME b/CNAME
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+neuromechfly.org
diff --git a/_images/fly_anatomy.jpg b/_images/fly_anatomy.jpg
diff --git a/_images/neuromechfly.png b/_images/neuromechfly.png
diff --git a/_sources/api_ref/arena.rst.txt b/_sources/api_ref/arena.rst.txt
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+Arena
+=====
+
+An arena is a physical environment in which the simulated fly is placed. Arenas can have rugged surfaces, visual features, odor features, or any combination thereof. The user can implement their own arenas by inheriting from the ``flygym.arena.BaseArena`` class.
+
+This page provides the API reference for the ``BaseArena`` abstract class as well as the preprogrammed arenas.
+
+Base arena
+----------
+.. autoclass:: flygym.arena.BaseArena
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
+
+.. autoclass:: flygym.arena.FlatTerrain
+
+Preprogrammed complex terrain arenas
+------------------------------------
+
+.. autoclass:: flygym.arena.GappedTerrain
+
+.. autoclass:: flygym.arena.BlocksTerrain
+
+.. autoclass:: flygym.arena.MixedTerrain
+
+Preprogrammed arenas with sensory features
+------------------------------------------
+
+.. autoclass:: flygym.arena.OdorArena
diff --git a/_sources/api_ref/camera.rst.txt b/_sources/api_ref/camera.rst.txt
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+Camera
+======
+
+The ``Camera`` class defines how images should be rendered from a camera in the world model. Note that the ``Camera`` class does not by itself add a camera to the MuJoCo model — the camera must have already existed and can be referenced by its name. The camera can be added in two ways:
+
+1. By adding a camera to the MuJoCo model file. Refer to the `section on camera <https://mujoco.readthedocs.io/en/stable/XMLreference.html#body-camera>`_ in the MuJoCo XML reference for more information. As an example, the following XML code adds a tracking camera to the MuJoCo model:
+
+.. code-block:: xml
+
+    <worldbody>
+        <!-- ... other things ... -->
+        <camera name="camera_top" class="nmf" mode="track" ipd="0.068" pos="0 0 8" euler="0 0 0"/>
+    </worldbody>
+
+2. By calling ``.worldbody.add()`` on the root element of the MuJoCo model programmatically in Python. Practically, this can be done by extending an existing FlyGym Arena class and adding the camera in the ``__init__`` method. For example, the following code adds a stationary bird's eye camera to the MuJoCo model:
+
+.. code-block:: python3
+
+    from flygym.arena import BaseArena
+
+    class MyArena(BaseArena):
+        def __init__(self):
+            super().__init__()
+            self.birdeye_cam = self.root_element.worldbody.add(
+                "camera",
+                name="birdseye_cam",
+                mode="fixed",
+                pos=(20, 0, 20),
+                euler=(0, 0, 0),
+                fovy=60,
+            )
+            # ... other things ...
+
+Once the camera is added to the MuJoCo model, it can be referenced by its name to initialize the ``Camera`` object with additional parameters assigned to it. These can include: rendering rate in frames-per-second (FPS), window size, play speed, etc. Furthermore, the ``Camera`` class has useful methods such as ``.save_video``, ``.reset``, etc. Logics such as rotating the camera in tilted terrain are also implemented in the ``Camera`` class. The ``.render`` method is the main point of entry for fetching images from the camera.
+
+The full API reference of the ``Camera`` class is as follows:
+
+.. autoclass:: flygym.camera.Camera
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/_sources/api_ref/examples/head_stabilization.rst.txt b/_sources/api_ref/examples/head_stabilization.rst.txt
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+Head Stabilization
+==================
+
+Model
+-----
+.. autoclass:: flygym.examples.head_stabilization.JointAngleScaler
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
+
+.. autoclass:: flygym.examples.head_stabilization.WalkingDataset
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. autoclass:: flygym.examples.head_stabilization.ThreeLayerMLP
+    :members:
+    :show-inheritance:
+
+.. autoclass:: flygym.examples.head_stabilization.HeadStabilizationInferenceWrapper
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
+
+
+Utilities
+---------
+.. autofunction:: flygym.examples.head_stabilization.util.get_head_stabilization_model_paths
+
diff --git a/_sources/api_ref/examples/index.rst.txt b/_sources/api_ref/examples/index.rst.txt
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+FlyGym Examples
+===============
+
+This section of the documentation provides the complete API reference for the examples accompanying the FlyGym package.
+
+
+.. toctree::
+   :maxdepth: 2
+
+   locomotion
+   vision
+   olfaction
+   path_integration
+   head_stabilization
diff --git a/_sources/api_ref/examples/locomotion.rst.txt b/_sources/api_ref/examples/locomotion.rst.txt
@@ -0,0 +1,58 @@
+Locomotion
+==========
+
+Preprogrammed steps
+-------------------
+
+.. autoclass:: flygym.examples.locomotion.PreprogrammedSteps
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
+
+CPG controller
+--------------
+
+.. autoclass:: flygym.examples.locomotion.CPGNetwork
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
+
+Rule-based controller
+---------------------
+
+.. autoclass:: flygym.examples.locomotion.RuleBasedController
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
+
+Hybrid turning controller
+-------------------------
+
+.. autoclass:: flygym.examples.locomotion.HybridTurningController
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
+
+Hybrid turning fly
+------------------
+
+.. autoclass:: flygym.examples.locomotion.HybridTurningFly
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
+
+Utility class for coloring body segments of the fly
+---------------------------------------------------
+
+The following utility class is a wrapper around the ``Fly`` class that facilitates the recoloring of specific segments. This is useful for, as an example, recoloring parts of the leg depending on the activation of specific correction rules.
+
+.. autoclass:: flygym.examples.locomotion.ColorableFly
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
diff --git a/_sources/api_ref/examples/olfaction.rst.txt b/_sources/api_ref/examples/olfaction.rst.txt
@@ -0,0 +1,40 @@
+Advanced Olfaction
+==================
+
+Arenas
+------
+
+.. autoclass:: flygym.examples.vision.arena.ObstacleOdorArena
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
+    :noindex:
+
+.. autoclass:: flygym.examples.olfaction.OdorPlumeArena
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
+
+
+Tracking complex plumes
+-----------------------
+
+.. autoclass:: flygym.examples.olfaction.PlumeNavigationTask
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
+
+.. autoclass:: flygym.examples.olfaction.WalkingState
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
+
+.. autoclass:: flygym.examples.olfaction.PlumeNavigationController
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
diff --git a/_sources/api_ref/examples/path_integration.rst.txt b/_sources/api_ref/examples/path_integration.rst.txt
@@ -0,0 +1,52 @@
+Path Integration
+================
+
+Arena
+-----
+
+.. autoclass:: flygym.examples.path_integration.PathIntegrationArenaBase
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
+
+.. autoclass:: flygym.examples.path_integration.PathIntegrationArenaFlat
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. autoclass:: flygym.examples.path_integration.PathIntegrationArenaBlocks
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Controller
+----------
+.. autoclass:: flygym.examples.path_integration.RandomExplorationController
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
+
+.. autoclass:: flygym.examples.path_integration.PathIntegrationController
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
+
+Model
+-----
+.. autoclass:: flygym.examples.path_integration.LinearModel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
+
+.. autofunction:: flygym.examples.path_integration.path_integrate
+
+Utilities
+---------
+.. autofunction:: flygym.examples.path_integration.util.get_leg_mask
+
+.. autofunction:: flygym.examples.path_integration.util.extract_variables
+
diff --git a/_sources/api_ref/examples/vision.rst.txt b/_sources/api_ref/examples/vision.rst.txt
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+Advanced Vision
+===============
+
+Arenas
+------
+.. autoclass:: flygym.examples.vision.arena.MovingObjArena
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
+
+.. autoclass:: flygym.examples.vision.arena.MovingFlyArena
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
+
+.. autoclass:: flygym.examples.vision.arena.MovingBarArena
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
+
+.. autoclass:: flygym.examples.vision.arena.ObstacleOdorArena
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
+
+Simple visual taxis
+-------------------
+
+.. autoclass:: flygym.examples.vision.simple_visual_taxis.VisualTaxis
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Connectome-constrained vision model
+-----------------------------------
+
+.. autoclass:: flygym.examples.vision.RealTimeVisionNetwork
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. autoclass:: flygym.examples.vision.RealTimeVisionNetworkView
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. autoclass:: flygym.examples.vision.RetinaMapper
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
+
+.. autoclass:: flygym.examples.vision.RealisticVisionFly
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/_sources/api_ref/fly.rst.txt b/_sources/api_ref/fly.rst.txt
@@ -0,0 +1,7 @@
+Fly
+===
+
+An object of the ``Fly`` class is an instance of a simulated fly. There can be multiple flies in a `Simulation <simulation.html>`_. The ``Fly`` object contains parameters related to the fly but not the whole simulation: for example, the set of actuated joints, spawn position, joint actuator parameters (stiffness, damping, etc.), and initial pose.
+
+.. autoclass:: flygym.Fly
+    :members:
diff --git a/_sources/api_ref/index.rst.txt b/_sources/api_ref/index.rst.txt
@@ -0,0 +1,21 @@
+API Reference
+=============
+
+This section of the documentation provides the complete API reference for the FlyGym package.
+
+
+.. toctree::
+   :maxdepth: 2
+
+   mdp_specs
+   fly
+   arena
+   camera
+   simulation
+   state
+   vision
+   olfaction
+   utils
+   preprogrammed
+   examples/index
+   legacy
diff --git a/_sources/api_ref/legacy.rst.txt b/_sources/api_ref/legacy.rst.txt
@@ -0,0 +1,11 @@
+Legacy API
+==========
+
+.. warning::
+
+    This API, inherited from the 0.x.x versions, is deprecated and will be removed in a future release. Please use the new API (the rest of the documentation) instead.
+
+.. automodule:: flygym.core
+    :members:
+    :undoc-members:
+    :show-inheritance: