Paper ready for submission! (#27)

* first draft paper

* update

* dunno

* paper

* updated paper and docs

* updated the toml file - copied main over

* updated data access section to be shorter

* fixed refs i think

* bla

* updated README

* Specify packages to install in setuptools

* updated paper text

* fixed typos

* typo and middle names

---------

Co-authored-by: Heloise Stevance <hfstevance@gmail.com>
Co-authored-by: Jack Leland <jack.leland@dtc.ox.ac.uk>

Author: 3 people

paper/paper.bib

@@ -1,3 +1,56 @@
+
+@ARTICLE{soxs,
+       author = {{Radhakrishnan Santhakumari}, Kalyan Kumar and {Battaini}, Federico and {Di Filippo}, Simone and {Di Rosa}, Silvio and {Cabona}, Lorenzo and {Claudi}, Riccardo and {Lessio}, Luigi and {Dima}, Marco and {Young}, David and {Landoni}, Marco and {Colapietro}, Mirko and {D'Orsi}, Sergio and {Aliverti}, Matteo and {Genoni}, Matteo and {Munari}, Matteo and {Zanmar Sanchez}, Ricardo and {Vitali}, Fabrizio and {Ricci}, Davide and {Schipani}, Pietro and {Campana}, Sergio and {Achren}, Jani and {Araiza-Duran}, Jose and {Arcavi}, Iair and {Baruffolo}, Andrea and {Ben-Ami}, Sagi and {Bitchkovsky}, Alex and {Brucalassi}, Anna and {Bruch}, Rachel and {Capasso}, Giulio and {Cappellaro}, Enrico and {Cosentino}, Rosario and {D'Alessio}, Francesco and {D'Avanzo}, Paolo and {Della Valle}, Massimo and {Di Benedetto}, Rosario and {Gal-Yam}, Avishay and {Hernandez Diaz}, Marcos and {Hershko}, Ofir and {Kotilainen}, Jari and {Kuncarayakti}, Hanindyo and {Li Causi}, Gianluca and {Marafatto}, Luca and {Martinetti}, Eugenio and {Marty}, Laurent and {Mattila}, Seppo and {Micciche}, Antonio and {Nicotra}, Gaetano and {Oggioni}, Luca and {Perez Ventura}, Hector and {Pariani}, Giorgio and {Pignata}, Giuliano and {Rappaport}, Michael and {Riva}, Marco and {Rubin}, Adam and {Salasnich}, Bernardo and {Savarese}, Salvatore and {Scuderi}, Salvatore and {Smartt}, Steven and {Stritzinger}, Maximilian},
+        title = "{What is your favorite transient event? SOXS is almost ready to observe!}",
+      journal = {arXiv e-prints},
+     keywords = {Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Earth and Planetary Astrophysics},
+         year = 2024,
+        month = jul,
+          eid = {arXiv:2407.17288},
+        pages = {arXiv:2407.17288},
+          doi = {10.48550/arXiv.2407.17288},
+archivePrefix = {arXiv},
+       eprint = {2407.17288},
+ primaryClass = {astro-ph.IM},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2024arXiv240717288R},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@INPROCEEDINGS{erasmus2024spie,
+       author = {{Erasmus}, Nicolas and {Potter}, Stephen B. and {van Gend}, Carel H.~D.~R. and {Loubser}, Egan and {Rosie}, Kathryn and {Titus}, Keegan and {Chandra}, Sunil and {Worters}, Hannah L. and {Gajjar}, Hitesh and {Hlakola}, Moloko and {Julie}, Roufurd},
+        title = "{Instrumentation at the SAAO for autonomous rapid-response observing}",
+    booktitle = {Ground-based and Airborne Instrumentation for Astronomy X},
+         year = 2024,
+       editor = {{Bryant}, Julia J. and {Motohara}, Kentaro and {Vernet}, Jo{\"e}l. R.~D.},
+       series = {Society of Photo-Optical Instrumentation Engineers (SPIE) Conference Series},
+       volume = {13096},
+        month = jul,
+          eid = {130968K},
+        pages = {130968K},
+          doi = {10.1117/12.3015250},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2024SPIE13096E..8KE},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@software{heloise_2025vra,
+  author       = {Heloise and
+                  genghisken},
+  title        = {HeloiseS/atlasvras: VRA 1.1},
+  month        = mar,
+  year         = 2025,
+  publisher    = {Zenodo},
+  version      = {v1.1},
+  doi          = {10.5281/zenodo.14983116},
+  url          = {https://doi.org/10.5281/zenodo.14983116},
+  swhid        = {swh:1:dir:d58f7330359b6c76e796cc182ac71d0d1524d84f
+                   ;origin=https://doi.org/10.5281/zenodo.14363396;vi
+                   sit=swh:1:snp:46746f947d79fd3b95b63ea09ee85fd2e8b3
+                   a397;anchor=swh:1:rel:5af41e199f18b3e1baafe237eb35
+                   1b4dc7d05a62;path=HeloiseS-atlasvras-f64733f
+                  },
+}
+
+
 @ARTICLE{class2025arc,
        author = {{Erasmus}, N. and {Cunnama}, D. and {Potter}, S. and {Stevance}, H.},
         title = "{SAAO IO Transient Classification Report for 2025-02-04}",
@@ -28,7 +81,6 @@ @ARTICLE{class2025cy
 }
 
 
-
 @ARTICLE{smith2020,
        author = {{Smith}, K.~W. and {Smartt}, S.~J. and {Young}, D.~R. and {Tonry}, J.~L. and {Denneau}, L. and {Flewelling}, H. and {Heinze}, A.~N. and {Weiland}, H.~J. and {Stalder}, B. and {Rest}, A. and {Stubbs}, C.~W. and {Anderson}, J.~P. and {Chen}, T. -W. and {Clark}, P. and {Do}, A. and {F{\"o}rster}, F. and {Fulton}, M. and {Gillanders}, J. and {McBrien}, O.~R. and {O'Neill}, D. and {Srivastav}, S. and {Wright}, D.~E.},
         title = "{Design and Operation of the ATLAS Transient Science Server}",

paper/paper.md

@@ -9,62 +9,77 @@ authors:
     orcid: 0000-0002-0504-4323
     equal-contrib: true
     affiliation: "1,2" # (Multiple affiliations must be quoted)
-  - name: Ken Smith 
-    orcid: 0000-0001-9535-3199
-    corresponding: true # (This is how to denote the corresponding author)
-    affiliation: "1,2"
   - name: Jack Leland 
     orcid: 0000-0001-9262-3587
     equal-contrib: true # (This is how you can denote equal contributions between multiple authors)
     affiliation: 3
+  - name: Ken W. Smith 
+    orcid: 0000-0001-9535-3199
+    corresponding: true # (This is how to denote the corresponding author)
+    affiliation: "1,2"
 affiliations:
  - name: Astrophysics sub-Department, Department of Physics, University of Oxford, Keble Road, Oxford, OX1 3RH, UK
    index: 1
  - name: Astrophysics Research Center, Queen's University Belfast, Belfast, BT7 1NN, UK
    index: 2
- - name: Oxford Research Software Engineering, Doctoral Training Centre, University of Oxford, Keble Road, Oxford, OX1 3RH, UK
+ - name: Oxford Research Software Engineering Group, Doctoral Training Centre, University of Oxford, Keble Road, Oxford, OX1 3RH, UK
    index: 3
-date: 17 December 2024
+date: 15 May 2025
 bibliography: paper.bib
 
 ---
 
 # Summary
 
 The Asteroid Terrestrial-impact Last Alert System (ATLAS) is an all-sky optical
-sky survey with a cadence of 24 to 48 hours [@tonry2018].
-The ATLAS Transient Server [@smith2020] processes the alert stream to enable the discovery
-and follow-up of extra-galactic transients. 
-As part of routine operations, many other types of objects are detected, which are available on the ATLAS transient server. 
-Accessing these data is done through the ATLAS API. 
-Here we make available a python client to facilitate the use of tha ATLAS API
-and ensure that production codes that make calls to the server can remain 
-unaffected by internal changes to the API.
+sky survey with a cadence of 24 to 48 hours [@tonry2018], and
+the ATLAS Transient Server [@smith2020] processes the alert stream to enable the discovery
+and follow-up of extra-galactic transients.
+The data from the ATLAS server can be accessed through a REST API,
+which has allowed the development of bots that need direct access to the data
+to help rank alerts  and
+trigger follow-up observations of promising targets.
+Here we present the python client we have developed for the ATLAS API 
+to help connect bots and scientists to our data. 
+
 
 
 # Statement of need
 
-`atlasapiclient` is a python client that facilitates the use of the ATLAS API.
+
+`atlasapiclient` is a python client that facilitates the use of the ATLAS REST API.
 It provides a class-based interface to all the read-write utilities of the API and
 abstracts away the endpoint URLs and the token management.
 The `atlasapiclient` was initially designed to be used in our transient 
-stream processing pipeline, but it can now also be used to connect 
+stream processing pipeline, particularly for the ATLAS Virtual Research Assistant [@heloise_2025vra],
+but it can now also be used to connect 
 other astronomy projects to the ATLAS data and its stream. 
 It is currently allowing the follow-up of ATLAS alerts by the Mookodi telescope
-in the South African Astronomical Observatory, which has allowed automated triggering
+in the South African Astronomical Observatory [@erasmus2024spie], which has allowed automated triggering
 and classification of transients within 100 Mpc (e.g. [@class2025arc], [@class2025cy]), since early 2025.
+In the future this will allow us to connect our stream to other surveys and 
+follow-up facilities (e.g. [@soxs])
 
 We expect the API to evolve over time which could break the production codes 
-that connect to the ATLAS servers. 
+that connect to the ATLAS servers.
 By having a dedicated client package that includes a full set of unit and
-integration tests we can mitigate these issues by releasing updates to the client 
+integration tests we can release updates to the client 
 that are compatible with the new API but do not require users to change their
 existing code. 
+Decoupling the user's code form the implementation of the API therefore
+increases robustness from the users side. 
 
+# Data Access 
+In order to gain access to the servers, prospective users will need to fill a 
+[Data Request Form](https://forms.gle/Jvy18eejkvxmcN2f6) including 
+a short (no longer than 1 page) science case justifying their access needs
+(length of time; Read-only or Read-Write access).
+We have also included data policies compliant with the General Data Protection Regulation (GDPR).
 
-# Acknowledgements
 
+# Acknowledgements
 HFS and JL are supported by the Schmidt Sciences foundation.
-KS is supported by **[TBD]**.
+KS is supported by the Royal Society.
+
 
 # References