Merge pull request #242 from DavidT3/paper/writeJOSSPaper

Paper/write joss paper
DavidT3 · Mar 12, 2024 · ebc992b · ebc992b
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diff --git a/.github/workflows/joss_paper_draft.yml b/.github/workflows/joss_paper_draft.yml
@@ -0,0 +1,58 @@
+# This modification is heavily based on GitHub user zonca's version linked
+#  in https://github.com/openjournals/joss/issues/132#issuecomment-890440692
+
+# The overall name of this action
+name: Compile draft DAXA JOSS Paper
+
+# Triggers on a push to the master branch - as I've decided that the paper can live in master
+on:
+  push:
+    branches:
+      - master
+      - paper/writeJOSSPaper
+    paths:
+      - paper/**
+
+# This action only really does one job, using the JOSS paper action to compile the MarkDown into something
+#  slightly more pretty
+jobs:
+  paper:
+    # Sets up the run on the latest version of Ubuntu they have 'in stock'
+    runs-on: ubuntu-latest
+    # Names the job
+    name: Paper Draft
+    # Sets up the steps of the job, firstly we check out the master branch
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Build TeX and PDF
+        uses: docker://openjournals/paperdraft:latest
+        with:
+          args: '-k paper/paper.md'
+        # Sets the specific journal to be built for, and where the Markdown file lives
+        env:
+          GIT_SHA: $GITHUB_SHA
+          JOURNAL: joss
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          path: paper/
+
+#    # Sets up the steps of the job, firstly we check out the master branch
+#    steps:
+#      - name: Checkout
+#        uses: actions/checkout@v2
+#        # Then use the JOSS action to build the paper
+#      - name: Build draft PDF
+#        uses: openjournals/openjournals-draft-action@master
+#        # Sets the specific journal to be built for, and where the Markdown file lives
+#        with:
+#          journal: joss
+#          paper-path: paper/paper.md
+#      - name: Upload
+#        uses: actions/upload-artifact@v1
+#        with:
+#          name: paper
+#          # This is the output path where Pandoc will write the compiled PDF
+#          path: paper/paper.pdf
diff --git a/paper/paper.bib b/paper/paper.bib
@@ -0,0 +1,125 @@
+@ARTICLE{xcsmethod,
+       author = {{Lloyd-Davies}, E.~J. and {Romer}, A. Kathy and {Mehrtens}, Nicola and
+         {Hosmer}, Mark and {Davidson}, Michael and {Sabirli}, Kivanc and
+         {Mann}, Robert G. and {Hilton}, Matt and {Liddle}, Andrew R. and
+         {Viana}, Pedro T.~P. and {Campbell}, Heather C. and
+         {Collins}, Chris A. and {Dubois}, E. Naomi and {Freeman}, Peter and
+         {Harrison}, Craig D. and {Hoyle}, Ben and {Kay}, Scott T. and
+         {Kuwertz}, Emma and {Miller}, Christopher J. and {Nichol}, Robert C. and
+         {Sahl{\'e}n}, Martin and {Stanford}, S.~A. and {Stott}, John P.},
+        title = "{The XMM Cluster Survey: X-ray analysis methodology}",
+      journal = {\mnras},
+     keywords = {surveys, galaxies: clusters: intracluster medium, cosmology: observations, X-rays: galaxies: clusters, Astrophysics - Cosmology and Nongalactic Astrophysics},
+         year = 2011,
+        month = nov,
+       volume = {418},
+       number = {1},
+        pages = {14-53},
+          doi = {10.1111/j.1365-2966.2011.19117.x},
+archivePrefix = {arXiv},
+       eprint = {1010.0677},
+ primaryClass = {astro-ph.CO},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2011MNRAS.418...14L},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+
+@ARTICLE{xcsfoundation,
+       author = {{Romer}, A. Kathy and {Viana}, Pedro T.~P. and {Liddle}, Andrew R. and {Mann}, Robert G.},
+        title = "{A Serendipitous Galaxy Cluster Survey with XMM: Expected Catalog Properties and Scientific Applications}",
+      journal = {\apj},
+     keywords = {Cosmology: Miscellaneous, Galaxies: Clusters: General, X-Rays: Galaxies},
+         year = 2001,
+        month = feb,
+       volume = {547},
+       number = {2},
+        pages = {594-608},
+          doi = {10.1086/318382},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2001ApJ...547..594R},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{matcha,
+       author = {{Hollowood}, Devon L. and {Jeltema}, Tesla and {Chen}, Xinyi and {Farahi}, Arya and {Evrard}, August and {Everett}, Spencer and {Rozo}, Eduardo and {Rykoff}, Eli and {Bernstein}, Rebecca and {Bermeo-Hernandez}, Alberto and {Eiger}, Lena and {Giles}, Paul and {Israel}, Holger and {Michel}, Renee and {Noorali}, Raziq and {Romer}, A. Kathy and {Rooney}, Philip and {Splettstoesser}, Megan},
+        title = "{Chandra Follow-up of the SDSS DR8 Redmapper Catalog Using the MATCha Pipeline}",
+      journal = {\apjs},
+     keywords = {cosmology: observations, dark energy, galaxies: clusters: general, X-rays: galaxies: clusters, Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - High Energy Astrophysical Phenomena},
+         year = 2019,
+        month = oct,
+       volume = {244},
+       number = {2},
+          eid = {22},
+        pages = {22},
+          doi = {10.3847/1538-4365/ab3d27},
+archivePrefix = {arXiv},
+       eprint = {1808.06637},
+ primaryClass = {astro-ph.CO},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2019ApJS..244...22H},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{xrism,
+       author = {{XRISM Science Team}},
+        title = "{Science with the X-ray Imaging and Spectroscopy Mission (XRISM)}",
+      journal = {arXiv e-prints},
+     keywords = {Astrophysics - High Energy Astrophysical Phenomena},
+         year = 2020,
+        month = mar,
+          eid = {arXiv:2003.04962},
+        pages = {arXiv:2003.04962},
+archivePrefix = {arXiv},
+       eprint = {2003.04962},
+ primaryClass = {astro-ph.HE},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2020arXiv200304962X},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{athena,
+       author = {{Nandra}, Kirpal and {Barret}, Didier and {Barcons}, Xavier and {Fabian}, Andy and {den Herder}, Jan-Willem and {Piro}, Luigi and {Watson}, Mike and {Adami}, Christophe and {Aird}, James and {Afonso}, Jose Manuel and {Alexander}, Dave and {Argiroffi}, Costanza and {Amati}, Lorenzo and {Arnaud}, Monique and {Atteia}, Jean-Luc and {Audard}, Marc and {Badenes}, Carles and {Ballet}, Jean and {Ballo}, Lucia and {Bamba}, Aya and {Bhardwaj}, Anil and {Stefano Battistelli}, Elia and {Becker}, Werner and {De Becker}, Micha{\"e}l and {Behar}, Ehud and {Bianchi}, Stefano and {Biffi}, Veronica and {B{\^\i}rzan}, Laura and {Bocchino}, Fabrizio and {Bogdanov}, Slavko and {Boirin}, Laurence and {Boller}, Thomas and {Borgani}, Stefano and {Borm}, Katharina and {Bouch{\'e}}, Nicolas and {Bourdin}, Herv{\'e} and {Bower}, Richard and {Braito}, Valentina and {Branchini}, Enzo and {Branduardi-Raymont}, Graziella and {Bregman}, Joel and {Brenneman}, Laura and {Brightman}, Murray and {Br{\"u}ggen}, Marcus and {Buchner}, Johannes and {Bulbul}, Esra and {Brusa}, Marcella and {Bursa}, Michal and {Caccianiga}, Alessandro and {Cackett}, Ed and {Campana}, Sergio and {Cappelluti}, Nico and {Cappi}, Massimo and {Carrera}, Francisco and {Ceballos}, Maite and {Christensen}, Finn and {Chu}, You-Hua and {Churazov}, Eugene and {Clerc}, Nicolas and {Corbel}, Stephane and {Corral}, Amalia and {Comastri}, Andrea and {Costantini}, Elisa and {Croston}, Judith and {Dadina}, Mauro and {D'Ai}, Antonino and {Decourchelle}, Anne and {Della Ceca}, Roberto and {Dennerl}, Konrad and {Dolag}, Klaus and {Done}, Chris and {Dovciak}, Michal and {Drake}, Jeremy and {Eckert}, Dominique and {Edge}, Alastair and {Ettori}, Stefano and {Ezoe}, Yuichiro and {Feigelson}, Eric and {Fender}, Rob and {Feruglio}, Chiara and {Finoguenov}, Alexis and {Fiore}, Fabrizio and {Galeazzi}, Massimiliano and {Gallagher}, Sarah and {Gandhi}, Poshak and {Gaspari}, Massimo and {Gastaldello}, Fabio and {Georgakakis}, Antonis and {Georgantopoulos}, Ioannis and {Gilfanov}, Marat and {Gitti}, Myriam and {Gladstone}, Randy and {Goosmann}, Rene and {Gosset}, Eric and {Grosso}, Nicolas and {Guedel}, Manuel and {Guerrero}, Martin and {Haberl}, Frank and {Hardcastle}, Martin and {Heinz}, Sebastian and {Alonso Herrero}, Almudena and {Herv{\'e}}, Anthony and {Holmstrom}, Mats and {Iwasawa}, Kazushi and {Jonker}, Peter and {Kaastra}, Jelle and {Kara}, Erin and {Karas}, Vladimir and {Kastner}, Joel and {King}, Andrew and {Kosenko}, Daria and {Koutroumpa}, Dimita and {Kraft}, Ralph and {Kreykenbohm}, Ingo and {Lallement}, Rosine and {Lanzuisi}, Giorgio and {Lee}, J. and {Lemoine-Goumard}, Marianne and {Lobban}, Andrew and {Lodato}, Giuseppe and {Lovisari}, Lorenzo and {Lotti}, Simone and {McCharthy}, Ian and {McNamara}, Brian and {Maggio}, Antonio and {Maiolino}, Roberto and {De Marco}, Barbara and {de Martino}, Domitilla and {Mateos}, Silvia and {Matt}, Giorgio and {Maughan}, Ben and {Mazzotta}, Pasquale and {Mendez}, Mariano and {Merloni}, Andrea and {Micela}, Giuseppina and {Miceli}, Marco and {Mignani}, Robert and {Miller}, Jon and {Miniutti}, Giovanni and {Molendi}, Silvano and {Montez}, Rodolfo and {Moretti}, Alberto and {Motch}, Christian and {Naz{\'e}}, Ya{\"e}l and {Nevalainen}, Jukka and {Nicastro}, Fabrizio and {Nulsen}, Paul and {Ohashi}, Takaya and {O'Brien}, Paul and {Osborne}, Julian and {Oskinova}, Lida and {Pacaud}, Florian and {Paerels}, Frederik and {Page}, Mat and {Papadakis}, Iossif and {Pareschi}, Giovanni and {Petre}, Robert and {Petrucci}, Pierre-Olivier and {Piconcelli}, Enrico and {Pillitteri}, Ignazio and {Pinto}, C. and {de Plaa}, Jelle and {Pointecouteau}, Etienne and {Ponman}, Trevor and {Ponti}, Gabriele and {Porquet}, Delphine and {Pounds}, Ken and {Pratt}, Gabriel and {Predehl}, Peter and {Proga}, Daniel and {Psaltis}, Dimitrios and {Rafferty}, David and {Ramos-Ceja}, Miriam and {Ranalli}, Piero and {Rasia}, Elena and {Rau}, Arne and {Rauw}, Gregor and {Rea}, Nanda and {Read}, Andy and {Reeves}, James and {Reiprich}, Thomas and {Renaud}, Matthieu and {Reynolds}, Chris and {Risaliti}, Guido and {Rodriguez}, Jerome and {Rodriguez Hidalgo}, Paola and {Roncarelli}, Mauro and {Rosario}, David and {Rossetti}, Mariachiara and {Rozanska}, Agata and {Rovilos}, Emmanouil and {Salvaterra}, Ruben and {Salvato}, Mara and {Di Salvo}, Tiziana and {Sanders}, Jeremy and {Sanz-Forcada}, Jorge and {Schawinski}, Kevin and {Schaye}, Joop and {Schwope}, Axel and {Sciortino}, Salvatore and {Severgnini}, Paola and {Shankar}, Francesco and {Sijacki}, Debora and {Sim}, Stuart and {Schmid}, Christian and {Smith}, Randall and {Steiner}, Andrew and {Stelzer}, Beate and {Stewart}, Gordon and {Strohmayer}, Tod and {Str{\"u}der}, Lothar and {Sun}, Ming and {Takei}, Yoh and {Tatischeff}, V. and {Tiengo}, Andreas and {Tombesi}, Francesco and {Trinchieri}, Ginevra and {Tsuru}, T.~G. and {Ud-Doula}, Asif and {Ursino}, Eugenio and {Valencic}, Lynne and {Vanzella}, Eros and {Vaughan}, Simon and {Vignali}, Cristian and {Vink}, Jacco and {Vito}, Fabio and {Volonteri}, Marta and {Wang}, Daniel and {Webb}, Natalie and {Willingale}, Richard and {Wilms}, Joern and {Wise}, Michael and {Worrall}, Diana and {Young}, Andrew and {Zampieri}, Luca and {In't Zand}, Jean and {Zane}, Silvia and {Zezas}, Andreas and {Zhang}, Yuying and {Zhuravleva}, Irina},
+        title = "{The Hot and Energetic Universe: A White Paper presenting the science theme motivating the Athena+ mission}",
+      journal = {arXiv e-prints},
+     keywords = {Astrophysics - High Energy Astrophysical Phenomena, Astrophysics - Cosmology and Extragalactic Astrophysics, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Solar and Stellar Astrophysics},
+         year = 2013,
+        month = jun,
+          eid = {arXiv:1306.2307},
+        pages = {arXiv:1306.2307},
+archivePrefix = {arXiv},
+       eprint = {1306.2307},
+ primaryClass = {astro-ph.HE},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2013arXiv1306.2307N},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{lynx,
+       author = {{Gaskin}, Jessica A. and {Swartz}, Douglas A. and {Vikhlinin}, Alexey and {{\"O}zel}, Feryal and {Gelmis}, Karen E. and {Arenberg}, Jonathan W. and {Bandler}, Simon R. and {Bautz}, Mark W. and {Civitani}, Marta M. and {Dominguez}, Alexandra and {Eckart}, Megan E. and {Falcone}, Abraham D. and {Figueroa-Feliciano}, Enectali and {Freeman}, Mark D. and {G{\"u}nther}, Hans M. and {Havey}, Keith A. and {Heilmann}, Ralf K. and {Kilaru}, Kiranmayee and {Kraft}, Ralph P. and {McCarley}, Kevin S. and {McEntaffer}, Randall L. and {Pareschi}, Giovanni and {Purcell}, William and {Reid}, Paul B. and {Schattenburg}, Mark L. and {Schwartz}, Daniel A. and {Schwartz}, Eric D. and {Tananbaum}, Harvey D. and {Tremblay}, Grant R. and {Zhang}, William W. and {Zuhone}, John A.},
+        title = "{Lynx X-Ray Observatory: an overview}",
+      journal = {Journal of Astronomical Telescopes, Instruments, and Systems},
+         year = 2019,
+        month = apr,
+       volume = {5},
+          eid = {021001},
+        pages = {021001},
+          doi = {10.1117/1.JATIS.5.2.021001},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2019JATIS...5b1001G},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{erosita,
+       author = {{Predehl}, P. and {Andritschke}, R. and {Arefiev}, V. and {Babyshkin}, V. and {Batanov}, O. and {Becker}, W. and {B{\"o}hringer}, H. and {Bogomolov}, A. and {Boller}, T. and {Borm}, K. and {Bornemann}, W. and {Br{\"a}uninger}, H. and {Br{\"u}ggen}, M. and {Brunner}, H. and {Brusa}, M. and {Bulbul}, E. and {Buntov}, M. and {Burwitz}, V. and {Burkert}, W. and {Clerc}, N. and {Churazov}, E. and {Coutinho}, D. and {Dauser}, T. and {Dennerl}, K. and {Doroshenko}, V. and {Eder}, J. and {Emberger}, V. and {Eraerds}, T. and {Finoguenov}, A. and {Freyberg}, M. and {Friedrich}, P. and {Friedrich}, S. and {F{\"u}rmetz}, M. and {Georgakakis}, A. and {Gilfanov}, M. and {Granato}, S. and {Grossberger}, C. and {Gueguen}, A. and {Gureev}, P. and {Haberl}, F. and {H{\"a}lker}, O. and {Hartner}, G. and {Hasinger}, G. and {Huber}, H. and {Ji}, L. and {Kienlin}, A. v. and {Kink}, W. and {Korotkov}, F. and {Kreykenbohm}, I. and {Lamer}, G. and {Lomakin}, I. and {Lapshov}, I. and {Liu}, T. and {Maitra}, C. and {Meidinger}, N. and {Menz}, B. and {Merloni}, A. and {Mernik}, T. and {Mican}, B. and {Mohr}, J. and {M{\"u}ller}, S. and {Nandra}, K. and {Nazarov}, V. and {Pacaud}, F. and {Pavlinsky}, M. and {Perinati}, E. and {Pfeffermann}, E. and {Pietschner}, D. and {Ramos-Ceja}, M.~E. and {Rau}, A. and {Reiffers}, J. and {Reiprich}, T.~H. and {Robrade}, J. and {Salvato}, M. and {Sanders}, J. and {Santangelo}, A. and {Sasaki}, M. and {Scheuerle}, H. and {Schmid}, C. and {Schmitt}, J. and {Schwope}, A. and {Shirshakov}, A. and {Steinmetz}, M. and {Stewart}, I. and {Str{\"u}der}, L. and {Sunyaev}, R. and {Tenzer}, C. and {Tiedemann}, L. and {Tr{\"u}mper}, J. and {Voron}, V. and {Weber}, P. and {Wilms}, J. and {Yaroshenko}, V.},
+        title = "{The eROSITA X-ray telescope on SRG}",
+      journal = {\aap},
+     keywords = {space vehicles: instruments, X-rays: general, surveys, dark energy, Astrophysics - High Energy Astrophysical Phenomena, Astrophysics - Instrumentation and Methods for Astrophysics},
+         year = 2021,
+        month = mar,
+       volume = {647},
+          eid = {A1},
+        pages = {A1},
+          doi = {10.1051/0004-6361/202039313},
+archivePrefix = {arXiv},
+       eprint = {2010.03477},
+ primaryClass = {astro-ph.HE},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2021A&A...647A...1P},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+
diff --git a/paper/paper.md b/paper/paper.md
@@ -0,0 +1,74 @@
+---
+title: 'DAXA: Democratising archival X-ray astronomy through the easy creation of multi-mission datasets'
+tags:
+  - Python
+  - Astronomy
+  - Astrophysics
+  - X-ray astronomy
+  - Galaxy clusters
+  - AGN
+  - Instrumentation
+  - XMM
+  - eROSITA
+  - Chandra
+authors:
+  - name: David J. Turner[^*]
+    orcid: 0000-0001-9658-1396
+    affiliation: 1,2
+  - name: Jessica E. Pilling
+    orcid: 0000-0002-3211-928X
+    affiliation: 2
+  - name: Megan Donahue
+    orcid: 0000-0002-2808-0853
+    affiliation: 1
+  - name: Paul A. Giles
+    orcid: 0000-0003-4937-8453
+    affiliation: 2
+  - name: Kathy Romer
+    orcid: 0000-0002-9328-879X
+    affiliation: 2
+  - name: Agrim Gupta
+    affiliation: 1
+  - name: Toby Wallage
+    affiliation: 2
+affiliations:
+  - name: Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan, 48824, USA
+    index: 1
+  - name: Department of Physics and Astronomy, University of Sussex, Brighton, BN1 9QH, UK
+    index: 2
+date: 31 July 2023
+bibliography: paper.bib
+---
+
+# Summary
+We introduce a new, open-source, Python module for the acquisition and processing of archival data from multiple X-ray telescopes, Democratising Archival X-ray Astronomy (hereafter referred to as \texttt{DAXA}). The aim of \texttt{DAXA} is to provide a consistent, easy-to-use, interface with the disparate interfaces to different X-ray telescope data archives, and their processing packges, thus enabling much greater access to X-ray data for non-specialists. This in addition to providing low-level control of processing for X-ray experts.
+
+
+# Statement of need
+
+
+[^*]: [email protected]
+
+# Features
+
+
+# Existing software packages
+Th
+
+# Research projects using DAXA
+
+
+# Future Work
+
+
+# Acknowledgements
+David J Turner and Megan Donague acknowledge support from NASA ADAP...
+
+Kathy Romer (KR), and Paul A. Giles (PG)
+acknowledge support from the UK Science and Technology Facilities
+Council via grants ST/P006760/1 (DT), ST/P000525/1 and ST/T000473/1 (PG,
+KR). ADD JESS' STFC CODE
+
+DO I INCLUDE THIS?? We acknowledge contributions to the _XMM_ Cluster Survey from A. Bermeo, M. Hilton, P. J. Rooney, S. Bhargava, L. Ebrahimpour, R. G. Mann, M. Manolopoulou, J. Mayers, E. W. Upsdell, C. Vergara, P. T. P. Viana, R. Wilkinson, C. A. Collins, R. C. Nichol, J. P. Stott, and others.
+
+# References