trying to include pysi in docs

docs/sphinx/source/index.rst

@@ -19,7 +19,7 @@ stands for Simulating Ionization and Radiation in Outflows Created by Compact Ob
 
 The program is written in C and can be compiled on systems runining various flavors of linux, including macOS and the
 Windows Subsystem for Linux (WSL). The code is is available on `GitHub <https://github.com/sirocco-rt/sirocco>`_. Issues
-regarding the code and suggestions for improvement should be reported there.  We actively encourage other to make use of
+regarding the code and suggestions for improvement should be reported there.  We actively encourage others to make use of
 the code for their own science.  If anyone has questions about whether the code might be useful for a project, we
 encourage you to contact one of the authors of the code.
 
@@ -30,52 +30,18 @@ Documentation \& Publications
 Various documentation exists:
 
 * A :doc:`Quick Guide <quick>` describing how to install and run SIROCCO (in a fairly mechanistic fashion).
-* More detailed documentation on this site
+* More detailed documentation on this site and in the docs/sphinx/ folder of the repository. 
 * A code release paper, submitted in October 2024
-* Various PhD theses that describe 
+* Various PhD theses that describe the code in more detail: 
+    * Higginbottom, N (2014): `Modelling accretion disk winds in quasars <https://eprints.soton.ac.uk/368584/>`_, 
+    * Matthews, J. (2016): `Disc Winds Matter: Modelling Accretion And Outflow On All Scales <https://ui.adsabs.harvard.edu/abs/2016PhDT.......348M/abstract>`_, 
+    * Mangham, S. (2019): `The reverberation signatures of accretion disk winds in active galactic nuclei <https://eprints.soton.ac.uk/437717/>`_, 
+    * Parkinson, E. (2022): `Shining lights, even in death: modelling the optical and ultraviolet emission from tidal disruption events <https://eprints.soton.ac.uk/457482/>`_ . 
 
 For more information on how this page was generated and how to create documentation for SIROCCO,
 look at the page for :doc:`documentation on the documentation <meta>`.
 
-The following papers have used SIROCCO: 
-
-- Parkinson, E. J., Knigge, C., Dai, L., Thomsen, L. L., Matthews, J. H., & Long, K. S. (2024). *arXiv*, arXiv:2408.16371. DOI: [10.48550/arXiv.2408.16371](https://doi.org/10.48550/arXiv.2408.16371), ADS: [Link](https://ui.adsabs.harvard.edu/abs/2024arXiv240816371P)
-
-- Tampo, Y., Knigge, C., Long, K. S., Matthews, J. H., & Segura, N. C. (2024). *MNRAS*, 532, 1199. DOI: [10.1093/mnras/stae1557](https://doi.org/10.1093/mnras/stae1557), ADS: [Link](https://ui.adsabs.harvard.edu/abs/2024MNRAS.532.1199T)
-
-- Higginbottom, N., Scepi, N., Knigge, C., Long, K. S., Matthews, J. H., & Sim, S. A. (2024). *MNRAS*, 527, 9236. DOI: [10.1093/mnras/stad3830](https://doi.org/10.1093/mnras/stad3830), ADS: [Link](https://ui.adsabs.harvard.edu/abs/2024MNRAS.527.9236H)
-
-- Matthews, J. H., Strong-Wright, J., Knigge, C., Hewett, P., Temple, M. J., Long, K. S., Rankine, A. L., et al. (2023). *MNRAS*, 526, 3967. DOI: [10.1093/mnras/stad2895](https://doi.org/10.1093/mnras/stad2895), ADS: [Link](https://ui.adsabs.harvard.edu/abs/2023MNRAS.526.3967M)
-
-- Koljonen, K. I. I., Long, K. S., Matthews, J. H., & Knigge, C. (2023). *MNRAS*, 521, 4190. DOI: [10.1093/mnras/stad809](https://doi.org/10.1093/mnras/stad809), ADS: [Link](https://ui.adsabs.harvard.edu/abs/2023MNRAS.521.4190K)
-
-- Parkinson, E. J., Knigge, C., Matthews, J. H., Long, K. S., Higginbottom, N., & Sim, S. A. (2022). *MNRAS*, 510, 5426. DOI: [10.1093/mnras/stac027](https://doi.org/10.1093/mnras/stac027), ADS: [Link](https://ui.adsabs.harvard.edu/abs/2022MNRAS.510.5426P)
-
-- Middleton, M. J., Higginbottom, N., Knigge, C., Khan, N., & Wiktorowicz, G. (2022). *MNRAS*, 509, 1119. DOI: [10.1093/mnras/stab2991](https://doi.org/10.1093/mnras/stab2991), ADS: [Link](https://ui.adsabs.harvard.edu/abs/2022MNRAS.509.1119M)
-
-- Parkinson, E. J., Knigge, C., Long, K. S., Matthews, J. H., Higginbottom, N., Sim, S. A., & Hewitt, H. A. (2020). *MNRAS*, 494, 4914. DOI: [10.1093/mnras/staa1060](https://doi.org/10.1093/mnras/staa1060), ADS: [Link](https://ui.adsabs.harvard.edu/abs/2020MNRAS.494.4914P)
-
-- Matthews, J. H., Knigge, C., Higginbottom, N., Long, K. S., Sim, S. A., Mangham, S. W., Parkinson, E. J., et al. (2020). *MNRAS*, 492, 5540. DOI: [10.1093/mnras/staa136](https://doi.org/10.1093/mnras/staa136), ADS: [Link](https://ui.adsabs.harvard.edu/abs/2020MNRAS.492.5540M)
-
-- Higginbottom, N., Knigge, C., Sim, S. A., Long, K. S., Matthews, J. H., & Hewitt, H. A. (2020). *MNRAS*, 492, 5271. DOI: [10.1093/mnras/staa209](https://doi.org/10.1093/mnras/staa209), ADS: [Link](https://ui.adsabs.harvard.edu/abs/2020MNRAS.492.5271H)
-
-- Charles, P., Matthews, J. H., Buckley, D. A. H., Gandhi, P., Kotze, E., & Paice, J. (2019). *MNRAS*, 489, L47. DOI: [10.1093/mnrasl/slz120](https://doi.org/10.1093/mnrasl/slz120), ADS: [Link](https://ui.adsabs.harvard.edu/abs/2019MNRAS.489L..47C)
-
-- Mangham, S. W., Knigge, C., Williams, P., Horne, K., Pancoast, A., Matthews, J. H., Long, K. S., et al. (2019). *MNRAS*, 488, 2780. DOI: [10.1093/mnras/stz1713](https://doi.org/10.1093/mnras/stz1713), ADS: [Link](https://ui.adsabs.harvard.edu/abs/2019MNRAS.488.2780M)
-
-- Higginbottom, N., Knigge, C., Long, K. S., Matthews, J. H., & Parkinson, E. J. (2019). *MNRAS*, 484, 4635. DOI: [10.1093/mnras/stz310](https://doi.org/10.1093/mnras/stz310), ADS: [Link](https://ui.adsabs.harvard.edu/abs/2019MNRAS.484.4635H)
-
-- Milliner, K., Matthews, J. H., Long, K. S., & Hartmann, L. (2019). *MNRAS*, 483, 1663. DOI: [10.1093/mnras/sty3197](https://doi.org/10.1093/mnras/sty3197), ADS: [Link](https://ui.adsabs.harvard.edu/abs/2019MNRAS.483.1663M)
-
-- Higginbottom, N., Knigge, C., Long, K. S., Matthews, J. H., Sim, S. A., & Hewitt, H. A. (2018). *MNRAS*, 479, 3651. DOI: [10.1093/mnras/sty1599](https://doi.org/10.1093/mnras/sty1599), ADS: [Link](https://ui.adsabs.harvard.edu/abs/2018MNRAS.479.3651H)
-
-- Mangham, S. W., Knigge, C., Matthews, J. H., Long, K. S., Sim, S. A., & Higginbottom, N. (2017). *MNRAS*, 471, 4788. DOI: [10.1093/mnras/stx1863](https://doi.org/10.1093/mnras/stx1863), ADS: [Link](https://ui.adsabs.harvard.edu/abs/2017MNRAS.471.4788M)
-
-- Higginbottom, N., Proga, D., Knigge, C., & Long, K. S. (2017). *ApJ*, 836, 42. DOI: [10.3847/1538-4357/836/1/42](https://doi.org/10.3847/1538-4357/836/1/42), ADS: [Link](https://ui.adsabs.harvard.edu/abs/2017ApJ...836...42H)
-
-- Matthews, J. H. (2016). *PhDT*. DOI: [10.5281/zenodo.1256805](https://doi.org/10.5281/zenodo.1256805), ADS: [Link](https://ui.adsabs.harvard.edu/abs/2016PhDT.......348M)
-
-- Matthews, J. H., Knigge, C., Long, K. S., Sim, S. A., Higginbottom, N., & Mangham, S
+`This ADS library <https://ui.adsabs.harvard.edu/public-libraries/dRea2kBFSCmzAji_7yTK9Q>`_ contains a list of publications using SIROCCO to date. 
 
 
 -------

docs/sphinx/source/plotting.rst

@@ -3,6 +3,19 @@ Plotting \& Processing Outputs
 
 SIROCCO produces a large number of files in both binary and ascii format. Tools exist to examine the binary files.
 
+PySi 
+==============
+PySi, short for PySIROCCO, is a python package designed to interface with the SIROCCO code.
+It can be installed from its `own Github repository <https://github.com/sirocco-rt/pysi>`_ 
+under the sirocco-rt organisation. We recommend installing this package for reading code outputs.:
+isntructions to do so can be found in the README of that repository.
+
+.. admonition :: Warning to users
+
+These tutorials are not complete, and our approach to interfacing 
+with the code has not been uniform across the collaboration. Nevertheless, these 
+tutorials should give you the basic tools needed to look at spectra and wind properties, 
+with more detail on python scripts and packages provided in :ref:`the API documentation <py_progs>`. 
 
 .. toctree::
    :glob:

docs/sphinx/source/quick.rst

@@ -12,3 +12,4 @@ the inputs correspond to a plausible model of an astrophysical system.
 * :ref:`Creating the input file for SIROCCO <Inputs>`  -- Simple instructions how to set up a model interactively
 * :ref:`The files produced by SIROCCO <Outputs>`  -- A quick look at the output files
 * :ref:`Evaluation of the results <Evaluation>` -- A discussion of whether a model has run as required, or not
+* :ref:`Plotting \& Processing Outputs <plotting>` -- Some tutorials for plotting and processing outputs with PySi and other tools.