[PRE REVIEW]: pyuvdata v3: an interface for astronomical interferometeric datasets in python

[editorialbot]

Submitting author: !--author-handle-->@kartographer<!--end-author-handle-- (Garrett Keating) Repository: https://github.com/RadioAstronomySoftwareGroup/pyuvdata/ Branch with paper.md (empty if default branch): joss_update Version: v3.0 Editor: !--editor-->@JBorrow<!--end-editor-- Reviewers: @David-McKenna, @ptiede Managing EiC: Dan Foreman-Mackey

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.81 s (246.1 files/s, 178182.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         127          16373          25130          78423
C                                7           1116           2586           5152
TeX                              8            431            268           3308
Markdown                         7            305              0           1654
Cython                           6            314            191           1126
reStructuredText                 9            745           2173           1062
JSON                             1              0              0            866
YAML                            17             68             43            737
CSV                              2              0              0            614
C/C++ Header                     7            114            147            513
make                             1             31              6            193
TOML                             1             14              6            125
IDL                              1             13              4            109
Prolog                           1             22              0             47
Bourne Shell                     3              9              5             18
HTML                             1              1              0              3
-------------------------------------------------------------------------------
SUM:                           199          19556          30559          93950
-------------------------------------------------------------------------------

Commit count by author:

  2544  Bryna Hazelton
   580  Matthew Kolopanis
   461  Garrett 'Karto' Keating
   395  Paul La Plante
   274  Adam Beardsley
   209  Steven Murray
   173  Garrett Keating
   159  Garrett "Karto" Keating
   159  Nicholas Kern
   139  pyxieloustar
   117  Aaron Ewall-Wice
    91  Adam Lanman
    75  Jonathan Pober
    75  Mike Wilensky
    69  aelanman
    65  Zaki Ali
    57  Danny Jacobs
    53  pre-commit-ci[bot]
    52  Danny Price
    41  Josh Dillon
    39  Dara Storer
    35  e-koch
    34  Peter Williams
    26  WSK
    25  PyxieLouStar
    23  Christopher Moriarty
    22  Jacob Burba
    20  Theodora Kunicki
    14  Ruby Byrne
    13  Alex Foster
    13  Chuneeta
    11  Will S
     7  PStar
     6  Aaron Parsons
     6  James Aguirre
     6  Zachary Martinot
     6  radonnachie
     5  Adrian Liu
     5  Benjamin
     5  jburba
     4  Theo Kunicki
     2  Duncan
     2  Ross Donnachie
     2  Will Sutherland
     2  Willow Smith
     2  anguta
     1  Jonnie Pober
     1  Josh Kerrigan
     1  TrellixVulnTeam
     1  Unknown
     1  elillesk
     1  jaycedowell
     1  kartographer

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1088/0004-637X/759/1/17 is OK
- 10.1088/1538-3873/ac9642 is OK
- 10.21105/joss.00140 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Astronomical Interferometry in PYthon
- No DOI given, and none found for title: AIPS FITS File Format
- No DOI given, and none found for title: A Retrospective View of MIRIAD
- No DOI given, and none found for title: MeasurementSet definition version 2.0
- No DOI given, and none found for title: The MIR Cookbook
- No DOI given, and none found for title: Memo: UVCal FITS Format
- No DOI given, and none found for title: Memo: UVBeam FITS Format
- No DOI given, and none found for title: Memo: UVH5 file format
- No DOI given, and none found for title: Memo: CalH5 file format

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 739

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: BSD 2-Clause "Simplified" License (Valid open source OSI approved license)

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[editorialbot]

Five most similar historical JOSS papers:

pyuvsim: A comprehensive simulation package for radio interferometers in python. Submitting author: @aelanman Handling editor: @arfon (Active) Reviewers: @ygrange Similarity score: 0.8136

pyradiosky: A Python package for Radio Sky Models Submitting author: @bhazelton Handling editor: @xuanxu (Active) Reviewers: @pritchardn, @0xCoto Similarity score: 0.8037

EISPAC - The EIS Python Analysis Code Submitting author: @MJWeberg Handling editor: @mbobra (Active) Reviewers: @nabobalis, @PaulJWright Similarity score: 0.7360

DBSP_DRP: A Python package for automated spectroscopic data reduction of DBSP data Submitting author: @finagle29 Handling editor: @arfon (Active) Reviewers: @crhea93, @arjunsavel Similarity score: 0.7351

udpPacketManager: An International LOFAR Station Data (Pre-)Processor Submitting author: @David-McKenna Handling editor: @dfm (Active) Reviewers: @pritchardn, @plaplant Similarity score: 0.7334

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[dfm]

@kartographer — Thanks for your submission! All the suitable JOSS editors are currently working at capacity so I'm going to "waitlist" this review until an editor with the relevant expertise is available to take it on. Thanks for your patience!

In the meantime, since this submission is specifically about the updates to this project, could you add a comment here with more details about exactly what should be considered part of this review? It would also be useful to include a link to the commit history for this version so that we can also see what changed explicitly in the code. Thanks!

[kartographer]

Hi @dfm!

In the meantime, since this submission is specifically about the updates to this project, could you add a comment here with more details about exactly what should be considered part of this review?

There's actually a section on this in the submitted paper, but in brief, since our original JOSS paper the package has undergone a pretty substantial expansion in capabilities, as three of the four main modules (UVBeam, UVCal, and UVFlag) are new to the package, and the last one (UVData) has been fairly extensively re-written to expand the capabilities of the package. As such, I don't think there's anything that I would consider "out of scope". Hopefully that addresses your question here, but let me know if there's some more detail you're looking for here.

It would also be useful to include a link to the commit history for this version so that we can also see what changed explicitly in the code.

Commit history is here, tag for the relevant release is here, and tag for the previously published release is here.

[JBorrow]

La Planete is mis-spelled in the references as far as I can see.

[JBorrow]

@editorialbot assign me as editor

[editorialbot]

Assigned! @JBorrow is now the editor

[JBorrow]

Hello! I'll be the handling editor for your submission. The next step is to find reviewers; please let me know if there's anyone that you have in mind who would be appropriate.

[JBorrow]

Hi @David-McKenna, I noticed you were an author of a similar package submitted to JOSS and I think you'd be a great reviewer for this paper. Would that be something you'd be interested in? Our reviewer's guide is available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

[David-McKenna]

Sure @JBorrow, though my availability over the next 3 weeks is admittedly spotty, but I'd aim to be finished within a month or so, if that's an acceptable timeline.

[JBorrow]

That's perfectly fine, thank you!

[JBorrow]

@editorialbot add @David-McKenna as reviewer

[editorialbot]

@David-McKenna added to the reviewers list!

[JBorrow]

Hi @ptiede and @pritchardn, I found your names in the JOSS reviewer's database and think you'd be a great reviewer for this package. Would that be something you'd be interested in? Our reviewer's guide is available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

[JBorrow]

Hi @ptiede and @pritchardn, just checking in to see if either of you have any availability to review as I think you'd be excellent for this paper.

[ptiede]

Hi @JBorrow I can review this. Just one thing to note: I am at the same institute as @kartographer, but I haven't worked with him on pyuvfits.

[warrickball]

Hi @ptiede, I'm taking over some of the assistant editor-in-chief duties and just want to ask for a bit more detail about your collaboration with the authors. In principle your co-authorships and employment at the same institution represent conflicts of interest by the JOSS policy but the co-authored papers have long authors lists and the institution you're both employed at happens to be a particularly large one.

Are you confident that you can make an impartial assessment of pyuvdata?

[JBorrow]

Hi @ptiede just checking in to see if you're ok with the JOSS COI policy and can provide an impartial review of pyuvdata?

[ptiede]

Hi I believe I can give an impartial review. I've never worked directly with any of the authors.

[JBorrow]

@editorialbot add @ptiede as reviewer

[editorialbot]

@ptiede added to the reviewers list!

[JBorrow]

Amazing! Thank you, we will get started with the checklist based review in the review thread (posted below). Please do let me know if you have any questions!

[JBorrow]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/7482.