JOSS paper on v3

.github/workflows/draft-pdf.yml

@@ -0,0 +1,24 @@
+name: Draft PDF
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v3
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper.pdf

paper.bib

@@ -33,15 +33,15 @@ @INPROCEEDINGS{miriad
               for taking raw data through to the image analysis stage. The
               Miriad project, begun in 1988, is now middle-aged. With the wisdom
               of hindsight, we review design decisions and some of Miriad's
-              characteristics.}
+              characteristics.},
   year = 1995,
   series = {Astronomical Society of the Pacific Conference Series},
   volume = 77,
   eprint = {astro-ph/0612759},
   editor = {{Shaw}, R.~A. and {Payne}, H.~E. and {Hayes}, J.~J.~E.},
   pages = {433},
   adsurl = {http://adsabs.harvard.edu/abs/1995ASPC...77..433S},
-  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System},
   url = {http://www.atnf.csiro.au/computing/software/miriad/}
 }
 
@@ -75,6 +75,90 @@ @ARTICLE{fhd
   pages = {17},
   doi = {10.1088/0004-637X/759/1/17},
   adsurl = {http://adsabs.harvard.edu/abs/2012ApJ...759...17S},
-  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System},
   url = {https://github.com/EoRImaging/FHD}
 }
+
+@TECHREPORT{ms,
+  author = {{Kemball}, A.~J. and {Wieringa}, M.~H.},
+  title = "{MeasurementSet definition version 2.0}",
+  year = 2000,
+  month = jan,
+  file = {https://casa.nrao.edu/Memos/229.ps.gz},
+  url = {https://casper.berkeley.edu/astrobaki/index.php/AIPY}}
+}
+
+@TECHREPORT{mir,
+  author = {{Qi}, C.},
+  title = "{The MIR Cookbook}",
+  year = 2022,
+  month = mar,
+  file = {https://lweb.cfa.harvard.edu/~cqi/mircook.pdf},
+  url = {https://lweb.cfa.harvard.edu/~cqi/mircook.html}}
+}
+
+@TECHREPORT{calfits,
+  author = {{Ali}, Z. and  {Hazelton}, B. and {Beardsley}, A. and {La Plante}, P. and {Kunicki}, T. and {the pyuvdata team}},
+  title = "{Memo: UVCal FITS Format}",
+  year = 2017,
+  month = jul,
+  file = {https://github.com/RadioAstronomySoftwareGroup/pyuvdata/blob/main/docs/references/calfits_memo.pdf},
+}
+
+@TECHREPORT{beamfits,
+  author = {{Hazelton}, B. and {the pyuvdata team}},
+  title = "{Memo: UVBeam FITS Format}",
+  year = 2018,
+  month = jan,
+  file = {https://github.com/RadioAstronomySoftwareGroup/pyuvdata/blob/main/docs/references/beamfits_memo.pdf},
+}
+
+@TECHREPORT{uvh5,
+  author = {{La Plante}, P. and {the pyuvdata team}},
+  title = "{Memo: UVH5 file format}",
+  year = 2024,
+  month = apr,
+  file = {https://github.com/RadioAstronomySoftwareGroup/pyuvdata/blob/main/docs/references/uvh5_memo.pdf},
+}
+
+@TECHREPORT{calh5,
+  author = {{Hazelton}, B. and {the pyuvdata team}},
+  title = "{Memo: CalH5 file format}",
+  year = 2024,
+  month = aug,
+  file = {https://github.com/RadioAstronomySoftwareGroup/pyuvdata/blob/main/docs/references/calh5_memo.pdf},
+}
+
+@ARTICLE{casa,
+       author = {{CASA Team} and {Bean}, Ben and {Bhatnagar}, Sanjay and {Castro}, Sandra and {Donovan Meyer}, Jennifer and {Emonts}, Bjorn and {Garcia}, Enrique and {Garwood}, Robert and {Golap}, Kumar and {Gonzalez Villalba}, Justo and {Harris}, Pamela and {Hayashi}, Yohei and {Hoskins}, Josh and {Hsieh}, Mingyu and {Jagannathan}, Preshanth and {Kawasaki}, Wataru and {Keimpema}, Aard and {Kettenis}, Mark and {Lopez}, Jorge and {Marvil}, Joshua and {Masters}, Joseph and {McNichols}, Andrew and {Mehringer}, David and {Miel}, Renaud and {Moellenbrock}, George and {Montesino}, Federico and {Nakazato}, Takeshi and {Ott}, Juergen and {Petry}, Dirk and {Pokorny}, Martin and {Raba}, Ryan and {Rau}, Urvashi and {Schiebel}, Darrell and {Schweighart}, Neal and {Sekhar}, Srikrishna and {Shimada}, Kazuhiko and {Small}, Des and {Steeb}, Jan-Willem and {Sugimoto}, Kanako and {Suoranta}, Ville and {Tsutsumi}, Takahiro and {van Bemmel}, Ilse M. and {Verkouter}, Marjolein and {Wells}, Akeem and {Xiong}, Wei and {Szomoru}, Arpad and {Griffith}, Morgan and {Glendenning}, Brian and {Kern}, Jeff},
+        title = "{CASA, the Common Astronomy Software Applications for Radio Astronomy}",
+      journal = {\pasp},
+     keywords = {Single-dish antennas, Aperture synthesis, Radio astronomy, Radio interferometry, Long baseline interferometry, Astronomy software, Open source software, Software documentation, Astronomy data reduction, Astronomy data analysis, 1460, 53, 1338, 1346, 932, 1855, 1866, 1869, 1861, 1858, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Astrophysics of Galaxies, Astrophysics - High Energy Astrophysical Phenomena, Astrophysics - Solar and Stellar Astrophysics},
+         year = 2022,
+        month = nov,
+       volume = {134},
+       number = {1041},
+          eid = {114501},
+        pages = {114501},
+          doi = {10.1088/1538-3873/ac9642},
+archivePrefix = {arXiv},
+       eprint = {2210.02276},
+ primaryClass = {astro-ph.IM},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2022PASP..134k4501C},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{pyuvdata_v1,
+       author = {{Hazelton}, Bryna J. and {Jacobs}, Daniel C. and {Pober}, Jonathan C. and {Beardsley}, Adam P.},
+        title = "{pyuvdata: an interface for astronomical interferometeric datasets in python}",
+      journal = {The Journal of Open Source Software},
+         year = 2017,
+        month = feb,
+       volume = {2},
+       number = {10},
+          eid = {140},
+        pages = {140},
+          doi = {10.21105/joss.00140},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2017JOSS....2..140H},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}

paper.md

@@ -1,53 +1,118 @@
 ---
-title: 'pyuvdata: an interface for astronomical interferometeric datasets in python'
+title: 'pyuvdata v3: an interface for astronomical interferometeric datasets in python'
 tags:
  - radio astronomy
  - uvfits
  - miriad
 authors:
+ - name: Garrett K. Keating
+   orcid: 0000-0002-3490-146X
+   affiliation: 1
  - name: Bryna J. Hazelton
    orcid: 0000-0001-7532-645X
-   affiliation: 1, 2
+   affiliation: 2, 3
+ - name: Matthew Kolopanis
+   orcid: 0000-0002-2950-2974
+   affiliation: 4
+ - name: Steven Murray
+   orcid: 0000-0003-3059-3823
+   affiliation: 4
+ - name: Adam P. Beardsley
+   orcid: 0000-0001-9428-8233
+   affiliation: 5
  - name: Daniel C. Jacobs
    orcid: 0000-0002-0917-2269
    affiliation: 3
+ - name: Nicholas Kern
+   affiliation: 6
+   orcid: 0000-0002-8211-1892
+ - name: Adam Lanman
+   affiliation: 7
+   orcid: 0000-0003-2116-3573
+ - name: Paul La Plante
+   affiliation: 8
+   orcid: 0000-0002-4693-0102
  - name: Jonathan C. Pober
    orcid: 0000-0002-3492-0433
-   affiliation: 4
- - name: Adam P. Beardsley
-   orcid: 0000-0001-9428-8233
+   affiliation: 9
+ - name: Pyxie Star
    affiliation: 3
 affiliations:
- - name: University of Washington, eScience Institute
+ - name: Center for Astrophysics | Harvard & Smithsonian
    index: 1
- - name: University of Washington, Physics Department
+ - name: University of Washington, eScience Institute
    index: 2
- - name: Arizona State University, School of Earth and Space Exploration
+ - name: University of Washington, Physics Department
    index: 3
- - name: Brown University, Physics Department
+ - name: Scuola Normale Superiore, Italy
    index: 4
-date: 22 November 2016
+ - name: Winona State University, Physics Department
+   index: 5
+ - name: Massachusetts Institute of Technology, Physics Department
+   index: 6
+ - name: Kavli Institute of Astrophysics and Space Research
+   index: 7
+ - name: University of Nevada, Las Vegas, Department of Computer Science
+   index: 8
+ - name: Brown University, Physics Department
+   index: 9
+date: 2 July 2024
 bibliography: paper.bib
 ---
 
 # Summary
+pyuvdata is an open-source software package that seeks to provide a well-documented,
+feature-rich interface for many of the different data formats that exist within radio
+interferometry, including support for reading and writing UVH5 [@uvh5], UVFITS
+[@uvfits], MIRIAD [@miriad], and measurement set [@ms] visibility files; and reading of
+FHD [@fhd] and MIR [@mir] visibility save files. Additionally, pyuvdata supports reading
+and writing measurement set, CalFITS [@calfits], and CalH5 [@calh5] calibration
+solutions; and reading of FHD calibration solutions. pyuvdata also provides interfaces
+for and handling of models of antenna primary beams, including reading and writing of
+BeamFITS [@beamfits], and reading CST and MWA beam formats, as well as for flags.
 
+# Statement of Need
 There are several standard formats for astronomical interferometric data, but
-converting between them in a stable and repeatable way has historically been
-very challenging. This is partly because of subtle assumptions in the
-implementations of the formats and the complexity of the mathematical
-relationships between the different formats (e.g. drift mode vs phased data)
-and partly because data analysis for individual telescopes
-typically used just one of the standards along with the associated analysis
-code. New low frequency instruments (e.g. MWA (http://www.mwatelescope.org/),
-PAPER (http://eor.berkeley.edu/), HERA (http://reionization.org/)),
-have required custom analysis and simulation software that rely on a range of
-different file formats. pyuvdata was designed to facilitate interoperability
-between these instruments and codes by providing high quality, well documented
-conversion routines as well as an interface to interact with interferometric
-data and simulations directly in python.
+converting between them in a stable, repeatable way has historically been
+challenging.  This is partially due to conflicting assumptions and standards, giving
+rise to significant (though sometimes subtle) differences between formats.
+Interfacing with different data formats -- like one does when they convert from one
+format to another -- thus requires careful accounting for the complex mathematical
+relationships between both data and metadata to ensure proper data fidelity. This is
+required both for leveraging existing community-favored tools that typically built
+to interface with a specific data format, as well as analyses requiring bespoke tools
+for specialized types of analyses and simulations leveraging data in a variety of
+formats.
+
+pyuvdata has been designed to facilitate interoperability between different instruments
+and codes by providing high quality, well documented conversion routines as well as an
+interface to interact with interferometric data and simulations directly in Python.
+Originally motivated to support new low frequency instruments (e.g. MWA
+(http://www.mwatelescope.org/), PAPER (http://eor.berkeley.edu/), HERA
+(http://reionization.org/)), the capabilities of pyuvdata have been steadily expanded
+to support handling of data from several telescopes, ranging from meter to submillimeter
+wavelengths, including SMA, ALMA, SMA, VLA, ATCA, CARMA, LWA, among others.
+
+# Major updates in this version
+In the time since it was initially published [@pyuvdata_v1], pyuvdata has undergone a
+significant expansion in capabilities. In addition to general performance improvements
+and restructuring, the newest version of pyuvdata includes several new major features,
+including:
 
-pyuvdata currently supports reading and writing uvfits [@uvfits] and
-miriad [@miriad] files and reading FHD [@fhd] visibility save files.
+- The addition of the `UVCal` class, which provides a container for handling calibration
+solutions (bandpass, delays, and gains) for interferometric data. Supported data formats
+include MS, FHD, CalFITS, and CalH5.
+- The addition of the `UVBeam` class, which provides a container for handling models
+of the primary beam for antennas within an interferometric array. Supported data formats
+include BeamFITS, MWA, and CST.
+- The addition of the `UVFlag` class, which provides a container for handling flags/masking
+of bad data for visibility data.
+- Drastically improved handling of astrometry and increased speed and accuracy of algorithms
+used to ``phase-up'' data (i.e., change the sky position where the interferometer is centered
+up on).
+- Support for several new visibility data formats, including MIR, MS, and MWA/MWAX.
+- Support for data sets containing multiple spectral windows.
+- Support for data sets containing observations of multiple sources/phase centers.
+-Many new convenience methods for working with interferometric data, including splitting and combining data sets, averaging in time and frequency and applying calibration solutions and flags.
 
 # References