gal_goku Package
================

This is the main package containing the emulator framework and galaxy clustering models.

Main Modules
------------

gal Module
~~~~~~~~~~

.. automodule:: gal_goku.gal
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GalBase Class
^^^^^^^^^^^^^

.. autoclass:: gal_goku.gal.GalBase
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   :special-members: __init__

   The base class for galaxy clustering computations.

   **Key Methods:**

   .. automethod:: get_init_linear_power
   .. automethod:: configure_logging

LargeScaleGal Class
^^^^^^^^^^^^^^^^^^^

.. autoclass:: gal_goku.gal.LargeScaleGal
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   Computes galaxy correlation functions at large scales (r > 40 Mpc/h).

emus Module
~~~~~~~~~~~

.. automodule:: gal_goku.emus
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BaseStatEmu Class
^^^^^^^^^^^^^^^^^

.. autoclass:: gal_goku.emus.BaseStatEmu
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   :special-members: __init__

   Base emulator class for summary statistics.

   **Key Methods:**

   .. automethod:: predict
   .. automethod:: loo_train_pred
   .. automethod:: train_pred_all_sims
   .. automethod:: leave_bunch_out

Hmf Class
^^^^^^^^^

.. autoclass:: gal_goku.emus.Hmf
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   :special-members: __init__

   Halo Mass Function emulator.

   **Parameters:**
   
   - **data_dir** (str): Directory containing the training data
   - **y_log** (bool): Whether to use log-space for predictions
   - **fid** (str): Fiducial cosmology identifier
   - **multi_bin** (bool): Use multi-bin mode
   - **logging_level** (str): Logging verbosity level
   - **narrow** (bool): Use narrow parameter range
   - **no_merge** (bool): Don't merge data from multiple sources

emu_cosmo Module
~~~~~~~~~~~~~~~~

.. automodule:: gal_goku.emu_cosmo
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Cosmological emulator utilities.

halo_tools Module
~~~~~~~~~~~~~~~~~

.. automodule:: gal_goku.halo_tools
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Tools for halo manipulations, mass conversions, and halo model calculations.

init_power Module
~~~~~~~~~~~~~~~~~

.. automodule:: gal_goku.init_power
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Initial conditions and linear power spectrum calculations using ClassyLSS.

summary_stats Module
~~~~~~~~~~~~~~~~~~~~

.. automodule:: gal_goku.summary_stats
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Summary statistics computations from simulation data.

single_fid Module
~~~~~~~~~~~~~~~~~

.. automodule:: gal_goku.single_fid
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Single-fidelity Gaussian Process emulator implementations.

multi_fid Module
~~~~~~~~~~~~~~~~

.. automodule:: gal_goku.multi_fid
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Multi-fidelity Gaussian Process emulator implementations.

utils Module
~~~~~~~~~~~~

.. automodule:: gal_goku.utils
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Utility functions for data processing and manipulation.

plot Module
~~~~~~~~~~~

.. automodule:: gal_goku.plot
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Plotting utilities for visualization of results.

plot_gal Module
~~~~~~~~~~~~~~~

.. automodule:: gal_goku.plot_gal
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Specialized plotting functions for galaxy clustering visualizations.