Merge pull request #769 from DavidT3/docs/readyForRelease

Docs/ready for release

Author: DavidT3

README.md

@@ -5,7 +5,7 @@
 [![Documentation Status](https://readthedocs.org/projects/xga/badge/?version=latest)](https://xga.readthedocs.io/en/latest/?badge=latest)
 [![Coverage Percentage](https://raw.githubusercontent.com/DavidT3/XGA/master/tests/coverage_badge.svg)](https://raw.githubusercontent.com/DavidT3/XGA/master/tests/coverage_badge.svg)
 
-# What is XMM: Generate and Analyse (XGA)?
+# What is X-ray: Generate and Analyse (XGA)?
 
 XGA is a Python module designed to make it easy to analyse X-ray sources that have been observed by the XMM-Newton Space telescope. It is based around declaring different types of source and sample objects which correspond to real X-ray sources, finding all available data, and then insulating the user from the tedious generation and basic analysis of X-ray data products.
 
@@ -17,6 +17,16 @@ This module also supports more complex analyses for specific object types; the e
 This is a slightly more complex installation than many Python modules, but shouldn't be too difficult. If you're
 having issues feel free to contact me.
 
+## Data Required to use XGA
+### Cleaned Event Lists
+**This is very important** - Currently, to make use of this module, you **must** have access to cleaned XMM-Newton
+event lists, as XGA is not yet capable of producing them itself.
+
+### Region Files
+It will be beneficial if you have region files available, as it will allow XGA to remove interloper sources. If you
+wish to use existing region files, then they must be in a DS9 compatible format, **point sources** must be **red** and
+**extended sources** must be **green**.
+
 ## The Module
 XGA has been uploaded to PyPi, so you can simply run:
 ```shell script
@@ -34,8 +44,7 @@ python setup.py install
 XGA depends on two non-Python pieces of software:
 * XMM's Science Analysis System (SAS) - Version 17.0.0, but other versions should be largely compatible with the
     software. SAS version 14.0.0 however, does not support features that PSF correction of images depends on.
-* HEASoft's XSPEC - Version 12.10.1, **I can't guarantee later versions will work.**
-* HEASoft's XSPEC - Version 12.10.1, **I can't guarantee later versions will work.**
+* HEASoft's XSPEC - Version 12.10.1, but other versions should be largely compatible even if I have not tested them.
 
 All required Python modules can be found in requirements.txt, and should be added to your system during the 
 installation of XGA.

docs/source/conf.py

@@ -1,3 +1,6 @@
+#  This code is a part of X-ray: Generate and Analyse (XGA), a module designed for the XMM Cluster Survey (XCS).
+#  Last modified by David J Turner (david.turner@sussex.ac.uk) 02/02/2022, 11:37. Copyright (c) The Contributors
+
 # Configuration file for the Sphinx documentation builder.
 #
 # This file only contains a selection of the most common options. For a full
@@ -58,8 +61,8 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'XMM: Generate and Analyse (XGA)'
-copyright = '2021, David J Turner'
+project = 'X-ray: Generate and Analyse (XGA)'
+copyright = '2022, David J Turner'
 author = 'David J Turner'
 
 # The full version, including alpha/beta/rc tags

docs/source/future.rst

@@ -11,7 +11,7 @@ Planned XGA Features
 
 * **Ability to save ScalingRelation objects** - The ability to save ScalingRelation objects to disk in some way, so that code to generate them doesn't need to be run multiple times.
 
-* **Support for other X-ray telescopes** - Support for generation and analysis of data products from other telescopes (I guess than XGA will come to mean 'X-ray: Generate and Analyse', rather than 'XMM: Generate and Analyse').
+* **Support for other X-ray telescopes** - Support for generation and analysis of data products from other telescopes.
 
 * **Creating a Docker image for users to download** - Creating a Docker environment with SAS and HEASoft already installed, for ease of use.
 

docs/source/index.rst

@@ -1,9 +1,9 @@
-.. XMM: Generate and Analyse (XGA) documentation master file, created by
+.. X-ray: Generate and Analyse (XGA) documentation master file, created by
    sphinx-quickstart on Thu Dec 17 12:18:33 2020.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to XMM: Generate and Analyse (XGA)'s documentation!
+Welcome to X-ray: Generate and Analyse (XGA)'s documentation!
 ===========================================================
 .. toctree::
    :maxdepth: 2

docs/source/intro.rst

@@ -1,7 +1,7 @@
 Introduction to XGA
 ===================
 
-XMM: Generate and Analyse (XGA) is a Python module designed to make it easy to analyse X-ray sources that have been
+X-ray: Generate and Analyse (XGA) is a Python module designed to make it easy to analyse X-ray sources that have been
 observed by the XMM-Newton Space telescope. It is based around declaring different types of source and sample
 objects which correspond to real X-ray sources, finding all available data, and then insulating the user from the
 tedious generation and basic analysis of X-ray data products (though with the option to get stuck into the data
@@ -21,9 +21,7 @@ to investigate how properties change radially with distance from the centre, and
 masses of clusters.
 
 While XGA is a piece of open source software, I would appreciate it if any work that makes use of it would cite the
-Journal of Open Source Software paper that will accompany this package. It is in preparation, but has not yet been
-submitted, so if you are going to use this module in a piece of work please get in touch with me so we can work
-something out.
+paper accompanying this package, which can be found in the :doc:`publications` section.
 
 If wish to contribute to XGA, have feature suggestions, or any comments at all, then please go to the
 "Getting Support" section and submit an issue on GitHub/send me an email, I'll be happy to hear from you!

docs/source/notebooks/advanced_tutorials/annular_spectra.ipynb

@@ -810,4 +810,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}

docs/source/publications.rst

@@ -6,26 +6,31 @@ using XGA please cite the XGA software paper, which is the first entry in this t
 your work to this page.
 
 .. list-table::
-   :widths: 20 15 20 15 30
+   :widths: 20 15 10 15 40
    :header-rows: 1
 
    * - Lead Author
      - Year
-     - DOI
-     - NASA/ADS
+     - ADS
+     - Code
      - Notes
    * - `D. J. Turner <https://orcid.org/0000-0001-9658-1396>`_
-     - In Prep
-     -
+     - 2022
      -
+     - `Repo <https://github.com/DavidT3/XGA>`_
      - XGA Software Paper
    * - `D. J. Turner <https://orcid.org/0000-0001-9658-1396>`_
      - 2021
-     -
      - `ADS <https://ui.adsabs.harvard.edu/abs/2021arXiv210911807T/abstract>`_
-     - eFEDS-XCS Cluster Comparison
+     - `Repo <https://github.com/DavidT3/eFEDS-XCS-Paper>`_
+     - eFEDS-XCS Cluster Analysis
    * - `D. S. Pillay <https://orcid.org/0000-0002-1602-4168>`_
      - 2021
-     - `MDPI Galaxies <https://doi.org/10.3390/galaxies9040097>`_
      - `ADS <https://ui.adsabs.harvard.edu/abs/2021arXiv211104340P/abstract>`_
-     - ACTCL J0019.6+0336 Follow-up
+     -
+     - ACTCLJ0019.6+0336 Analysis
+   * - `C. J. Burke <https://orcid.org/0000-0001-9947-6911>`_
+     - 2021
+     - `ADS <https://ui.adsabs.harvard.edu/abs/2021arXiv211103079B/abstract>`_
+     - `Repo <https://github.com/DavidT3/XCS-DES-AGN-Prelim>`_
+     - DES AGN Confirmation

setup.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
-#  This code is a part of XMM: Generate and Analyse (XGA), a module designed for the XMM Cluster Survey (XCS).
-#  Last modified by David J Turner (david.turner@sussex.ac.uk) 10/03/2021, 16:22. Copyright (c) David J Turner
+#  This code is a part of X-ray: Generate and Analyse (XGA), a module designed for the XMM Cluster Survey (XCS).
+#  Last modified by David J Turner (david.turner@sussex.ac.uk) 02/02/2022, 11:37. Copyright (c) The Contributors
 
 from os import path
 

tests/__init__.py

@@ -1,8 +1,8 @@
-#  This code is a part of XMM: Generate and Analyse (XGA), a module designed for the XMM Cluster Survey (XCS).
-#  Last modified by David J Turner (david.turner@sussex.ac.uk) 12/10/2021, 10:53. Copyright (c) David J Turner
+#  This code is a part of X-ray: Generate and Analyse (XGA), a module designed for the XMM Cluster Survey (XCS).
+#  Last modified by David J Turner (david.turner@sussex.ac.uk) 02/02/2022, 11:37. Copyright (c) The Contributors
 
-import sys
 import os
+import sys
 
 from astropy.units import Quantity
 

tests/all_test_and_badge.sh

@@ -1,2 +1,7 @@
+#
+# This code is a part of X-ray: Generate and Analyse (XGA), a module designed for the XMM Cluster Survey (XCS).
+# Last modified by David J Turner (david.turner@sussex.ac.uk) 02/02/2022, 11:37. Copyright (c) The Contributors
+#
+
 pytest --cov
 coverage-badge -o coverage_badge.svg