Tutorials
=========

Basics of Reflected Light
-------------------------

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   :maxdepth: 1

   Getting Started  </notebooks/1_GetStarted.ipynb>
   Adding Clouds  </notebooks/2_AddingClouds.ipynb>
   Adding Surface Reflectivity </notebooks/3_AddingSurfaceReflectivity.ipynb>
   Plot Diagnostics </notebooks/4_PlotDiagnostics.ipynb>

Basics of Transmisison
----------------------

.. toctree::
   :maxdepth: 2
   
   Transmission Spectroscopy Exoplanets </notebooks/5_AddingTransitSpectrum.ipynb>

Basics of Thermal Emission
--------------------------

.. toctree::
   :maxdepth: 2

   Thermal Emission Exoplanets </notebooks/5_AddingThermalFlux.ipynb>
   Brown Dwarfs </notebooks/6_BrownDwarfs.ipynb>



Cloud Modeling with `Virga`
---------------------------

.. toctree::
   :maxdepth: 2

   Moving Away From Box Models </notebooks/7_PairingPICASOToVIRGA.ipynb>

Moving to 3 Dimensions
----------------------
Relevant Citatons: `Adams et al. 2022 <https://ui.adsabs.harvard.edu/abs/2022ApJ...926..157A/abstract>`_ for 3D spectra and `Robbins-Blanch et al. 2022 <http://arxiv.org/abs/2204.03545>`_ for Phase Curves. 

.. toctree::
   :maxdepth: 1

   Non-Zero Phase and Spherical Integration </notebooks/8_SphericalIntegration.ipynb>
   Basics of a 3D Calculation </notebooks/9a_3DInputsWithPICASOandXarray.ipynb>
   Post-Processing Chemistry for 3D runs </notebooks/9b_PostProcess3Dinput-Chemistry.ipynb>
   Post-Processing Clouds for 3D runs </notebooks/9c_PostProcess3Dinput-Clouds.ipynb>
   Modeling a 3D Spectrum (Adams et al. 2022)</notebooks/9d_3DSpectra.ipynb>
   Modeling a Phase Curve pt 1 (Robbins-Blanch et al. 2022)</notebooks/9e_PhaseCurves.ipynb>
   Modeling a Phase Curve pt 2 (Robbins-Blanch et al. 2022)</notebooks/9f_PhaseCurves-wChemEq.ipynb>

1D Climate Modeling
-------------------
Relevant Citatons: `Mukherjee et al. 2022 <https://ui.adsabs.harvard.edu/abs/2022arXiv220807836M/abstract>`_

.. toctree::
   :maxdepth: 1

   Brown Dwarfs </notebooks/climate/12a_BrownDwarf.ipynb>
   Planet </notebooks/climate/12b_Exoplanet.ipynb>
   Brown Dwarfs w/ Disequilibrium Chemistry </notebooks/climate/12c_BrownDwarf_DEQ.ipynb>

Fitting models to data
----------------------
Relevant Citatons: `JWST Transiting Exoplanet Community Early Release Science Team (2022) <https://www.nature.com/articles/s41586-022-05269-w>`_

.. toctree::
   :maxdepth: 1

   Grid Search Analysis </notebooks/fitdata/GridSearch.ipynb>


Model Storage & Reuse
---------------------

.. toctree::
   :maxdepth: 1

   How to store and reuse models </notebooks/ModelStorage.ipynb>

Opacities
---------

.. toctree::
   :maxdepth: 1

   Query Opacites </notebooks/10_QueryOpacities.ipynb>
   Opacity Factory: Creating Custom Databases </notebooks/10_CreatingOpacityDb.ipynb>
   What Resampling do I Need? </notebooks/10_ResamplingOpacities.ipynb>
   Using Correlated-K Tables </notebooks/10_CorrelatedKTables.ipynb>

Radiative Transfer Techniques 
-----------------------------

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   :maxdepth: 1

   Toon Radiative Transfer in Reflected Light </notebooks/10a_AnalyzingApproximationsReflectedLightToon.ipynb>
   Spherical Harmonics Radiative Transfer in Reflected Light </notebooks/10b_AnalyzingApproximationsReflectedLightSH.ipynb>
   Spherical Harmonics Radiative Transfer in Thermal Emission </notebooks/10c_AnalyzingApproximationsThermal.ipynb>

FAQs
----

.. toctree::
   :maxdepth: 1

   Misc FAQs </notebooks/FAQs.ipynb>
   Contribution Functions </notebooks/11_ContributionFunctions.ipynb>


Code Help
---------

.. toctree::
   :maxdepth: 1
   
   Data Storage Uniformity </notebooks/codehelp/data_uniformity_tutorial.ipynb>
   SQLITE Tutorial </notebooks/codehelp/Sqlite3Tutorial.ipynb>

References
----------

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   :maxdepth: 2

   Citation Tools </notebooks/References.ipynb>