|a| is the main component of the Bayesian Large Scale Structure inference
pipeline. The present version of the ARES framework is 2.1. Please consult
:ref:`CHANGES overview` for an overview of the different improvements over the
different versions.

|a| is written in C++14 and has been parallelized with OpenMP and MPI. It currently compiles with major compilers (gcc, intel, clang).

Table of contents
-----------------

.. toctree::
   :maxdepth: 1
   :caption: Theory
   
   theory/ARES
   theory/BORG
   theory/ARES&BORG_FFT_normalization
   
.. toctree::
   :maxdepth: 1
   :caption: User documentation
   
   changes
   user/building
   user/inputs
   user/outputs
   user/running
   user/postprocessing
   user/extras
   user/clusters

.. toctree::
   :maxdepth: 1
   :caption: Developer documentation

   developer/development_with_git
   developer/code_architecture
   developer/life_cycles_of_objects
   developer/ares_modules
   developer/code_tutorials
   developer/contributing_to_this_documentation
   developer/copyright_and_authorship

Citing
------

If you are using |a| for your project, please cite the following articles for ARES2 and ARES3:

* Jasche, Kitaura, Wandelt, 2010, MNRAS, 406, 1 (arxiv 0911.2493)
* Jasche & Lavaux, 2015, MNRAS, 447, 2 (arxiv 1402.1763)
* Lavaux & Jasche, 2016, MNRAS, 455, 3 (arxiv 1509.05040)
* Jasche & Lavaux, 2019, A&A, 625, A64 (arxiv 1806.11117)

However, bear in mind that depending on the features that you are using you may want to cite other papers as well.
Here is a non-exhaustive list of those articles:

* Model development:

  * HADES epoch:

    * HMC, exponential transform, linear bias: Jasche, Kitaura, Wandelt, 2010, 406, 1 (arXiv 0911.2493)
    * HMC, exponential transform, power law bias:

      * Jasche, Leclercq, Wandelt, 2015
      * Jasche, Wandelt, 2012, MNRAS, 425, 1042 (arXiv 1106.2757)

  * Foreground/Robustification:

    * Jasche, Lavaux, 2017, A&A (arXiv:1706.08971)
    * Porqueres, Kodi Ramanah, Jasche, Lavaux, 2019, A&A (arXiv: 1812.05113)

  * Cosmic expansion model:

    * Kodi Ramanah, Lavaux, Jasche, Wandelt, 2019, A&A (arXiv: 1808.07496)

  * Photometric redshifts

    * HADES with Photo-Z: Jasche & Wandelt, 2012, MNRAS, 425, 1042 (arXiv: 1106.2757)

  * Galaxy shear:

    * Porqueres, Heavens, Mortlock & Lavaux, 2021, MNRAS, 502, 3035 (arXiv 2011.07722)
    * Porqueres, Heavens, Mortlock & Lavaux, 2022, MNRAS, 509, 3194 (arXiv 2108.04825)

  * Cosmic velocity field:

    * Prideaux-Ghee, Leclercq, Lavaux, Heavens, Jasche, 2022, MNRAS (arXiv: 2204.00023)
    * Boruah, Lavaux, Hudson, 2022, MNRAS (arXiv 2111.15535)

  * BORG-PM

    * Jasche & Lavaux, 2019, A&A, 625, A64 (arXiv 1806.11117)

  * EFT bias model and likelihood

    * Schmidt, Elsner, Jasche, Nguyen, Lavaux, JCAP 01, 042 (2019) (arXiv:1808.02002)
    * Schmidt, Cabass, Jasche, Lavaux, JCAP 11, 008 (2020) (arXiv:2004.06707)

* Data applications

  * SDSS Main Galaxy sample:
  * SDSS3 LRG sample:

    * Lavaux, Jasche & Leclercq, 2019, arXiv:1909.06396

  * 2M++ sample:

    * Lavaux & Jasche, 2016, MNRAS, 455, 3 (arXiv 1509.05040)
    * Jasche & Lavaux, 2019, A&A, 625, A64 (arXiv 1806.11117)


*HADES* and *BORG* papers have a different listing.

For a full listing of publications from the Aquila consortium, please check the 
`Aquila website <https://aquila-consortium.org/publications/>`_.

Acknowledgements
----------------


This work has been funded by the following grants and institutions over the
years:

* The DFG cluster of excellence "Origin and Structure of the Universe"
  (http://www.universe-cluster.de).
* Institut Lagrange de Paris (grant ANR-10-LABX-63, http://ilp.upmc.fr) within 
  the context of the Idex SUPER subsidized by the French government through
  the Agence Nationale de la Recherche (ANR-11-IDEX-0004-02).
* BIG4 (ANR-16-CE23-0002) (https://big4.iap.fr)
* The "Programme National de Cosmologie et Galaxies" (PNCG, CNRS/INSU)
* Through the grant code ORIGIN, it has received support from
  the "Domaine d'Interet Majeur (DIM) Astrophysique et Conditions d'Apparitions
  de la Vie (ACAV)" from Ile-de-France region.
* The Starting Grant (ERC-2015-STG 678652) "GrInflaGal" of the European Research Council.



.. Indices and tables
.. ==================
.. 
.. * :ref:`genindex`
.. * :ref:`modindex`
.. * :ref:`search`

..  Order of headings used throughout the documentation:
    
    ######### part
    ********* chapter
    ========= sections
    --------- subsections
    ~~~~~~~~~ subsubsections
    ^^^^^^^^^
    '''''''''

.. toctree-filt::
   :maxdepth: 1
   :caption: Python reference documentation

   :aquila:pythonref.rst