[REVIEW]: udpPacketManager: An International LOFAR Station Data (Pre-)Processor

[editorialbot]

Submitting author: @David-McKenna (David McKenna)
Repository: https://github.com/David-McKenna/udpPacketManager/
Branch with paper.md (empty if default branch):
Version: 0.9.2
Editor: @dfm
Reviewers: @pritchardn, @plaplant
Archive: 10.5281/zenodo.11019139

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/727594ee41e844048c4edb7031f68a6e"><img src="https://joss.theoj.org/papers/727594ee41e844048c4edb7031f68a6e/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/727594ee41e844048c4edb7031f68a6e/status.svg)](https://joss.theoj.org/papers/727594ee41e844048c4edb7031f68a6e)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@shmookey & @pritchardn, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @plaplant know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @pritchardn

📝 Checklist for @plaplant

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.08 s (830.3 files/s, 296771.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C                               19           1933           2726           7530
C++                              7            874            443           3827
C/C++ Header                    16            475            502           1858
Markdown                         7            242              0            892
CMake                            3             64             43            265
TeX                              1             18              0            231
YAML                             4             10              0            145
Python                           1             38             46            137
Bourne Shell                     3             37             15             95
Dockerfile                       1             10             20             26
JSON                             1              1              0             16
-------------------------------------------------------------------------------
SUM:                            63           3702           3795          15022
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 864

[editorialbot]

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

OK DOIs

- 10.1017/S1743921312024623 is OK
- 10.1071/AS10021 is OK
- 10.1109/JPROC.2004.840301 is OK
- 10.1088/1538-3873/ab3e82 is OK
- 10.5281/ZENODO.7871665 is OK
- 10.1093/rasti/rzac005 is OK
- 10.48550/ARXIV.2302.12661 is OK
- 10.1051/0004-6361/202140415 is OK
- 10.1051/0004-6361/201220873 is OK
- 10.17487/RFC8878 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[pritchardn]

Review checklist for @pritchardn

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/David-McKenna/udpPacketManager/?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@David-McKenna) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[pritchardn]

Hello all

I plan on finishing my review by the end of June and will add comments as I see them.

[plaplant]

@shmookey when you get a chance, please reply to this comment with:

@editorialbot generate my checklist

This will create your reviewer checklist that you can then begin going through. Please let me know if you have any questions!

[pritchardn]

A few minor comments on the Software Paper (mainly typos) which is otherwise excellent:

• [29] - pecular -> peculiar
• [43] - 2 times -> two times
• [61-66] - I suggest mentioning the names of the CLIs directly to make it completely clear which you refer to

[pritchardn]

I've tried to install the library today, but a problem installing psrdada is preventing me.
This looks like it's on their end, however, so I'll try again in a few days

[David-McKenna]

Hey @pritchardn,

Thanks! I've made changes to the paper and the general documentation comments you made in the docsPass branch (PR David-McKenna/udpPacketManager#13 ).

As for the PSRDADA issue, are sourceforge's certs out of date again? That's been a chronic issue over the past few years. I'll see if there's another way for me to download their source in my CMake script.

Cheers,
David

[plaplant]

@shmookey when you get a chance, please begin your review of this package. You can get your reviewer checklist by responding to this thread with:

@editorialbot generate my checklist

If you feel that you are no longer able to review, please let me know, and I can work on finding another reviewer. Thanks!

[arfon]

@plaplant – I think it might be time to find a different reviewer here?

[plaplant]

@arfon yes, I agree. I've actually been working behind the scenes to reach out to other potential reviewers, but have been coming up empty. I will reach out to additional folks and see if I can get someone to volunteer. Thanks for keeping up with this!

[plaplant]

Given that this submission has languished a bit, I'm going to go ahead and step in as a reviewer here to make sure the submission keeps moving forward. To keep things conflict-of-interest-free, @dfm has graciously agreed to take over as editor. I will review this as soon as I can, and hopefully we can get this fully reviewed soon.

@David-McKenna thanks so much for your patience thus far! Please let me (or @dfm) know if you have any questions.

[plaplant]

@editorialbot assign @plaplant as reviewer

[editorialbot]

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[plaplant]

@editorialbot add @plaplant as reviewer

[editorialbot]

@plaplant added to the reviewers list!

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[editorialbot]

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

OK DOIs

- 10.1017/S1743921312024623 is OK
- 10.1071/AS10021 is OK
- 10.1109/JPROC.2004.840301 is OK
- 10.1088/1538-3873/ab3e82 is OK
- 10.5281/ZENODO.7871665 is OK
- 10.1093/rasti/rzac005 is OK
- 10.48550/ARXIV.2302.12661 is OK
- 10.1051/0004-6361/202140415 is OK
- 10.1051/0004-6361/201220873 is OK
- 10.17487/RFC8878 is OK

MISSING DOIs

- No DOI given, and none found for title: LOFAR Und MPIfR Pulsare
- No DOI given, and none found for title: Station Data Cookbook
- No DOI given, and none found for title: dreamBeam
- No DOI given, and none found for title: LOFAR Data Format ICD Beam-Formed Data
- No DOI given, and none found for title: Simultaneous Dual-Site SETI with LOFAR Internation...
- No DOI given, and none found for title: Making Observations with Mode-357
- No DOI given, and none found for title: Pelican/Pelican-Lofar
- No DOI given, and none found for title: PSRDADA: Distributed Acquisition and Data Analysis...
- No DOI given, and none found for title: SIGPROC: Pulsar Signal Processing Programs

INVALID DOIs

- None

[dfm]

@pritchardn, @plaplant — Thanks for your thorough and constructive reviews!!

@David-McKenna — I've opened a small PR with some minor edits to the manuscript, please take a look and merge or let me know what you think.

Once you've done that:

1. Take one last read through the manuscript to make sure that you're happy with it (it's harder to make changes later!), especially the author names and affiliations. I've taken a pass and it looks good to me!
2. Increment the version number of the software and report that version number back here.
3. Create an archived release of that version of the software (using Zenodo or something similar). Please make sure that the metadata (title and author list) exactly match the paper. Then report the DOI of the release back to this thread.

[dfm]

@David-McKenna — Checking in here. We're so close to publication, could up update me on the status of these steps that I asked for above?

[David-McKenna]

Hey @dfm, Apologies, I apparently forgot to swap my GitHub account to my new work email so I never saw the prior comments. I'll get this handled by the end of today.

[David-McKenna]

Tagged and released 0.9.2 with your proposed changes, the Zenodo DOI is 10.5281/zenodo.11019139.

Cheers,
David

[dfm]

@David-McKenna — Thanks! Can you update the metadata for the Zenodo deposit (there should be an "edit" button on the top right corner of that page) so that the title and author list match the paper?

[David-McKenna]

Whoops, should be fixed up now.

[dfm]

@editorialbot set 10.5281/zenodo.11019139 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.11019139

[dfm]

@editorialbot set 0.9.2 as version

[editorialbot]

Done! version is now 0.9.2

[dfm]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[dfm]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

👋 @openjournals/aass-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5259, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[editorialbot]

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

OK DOIs

- 10.1017/S1743921312024623 is OK
- 10.1071/AS10021 is OK
- 10.1109/JPROC.2004.840301 is OK
- 10.1088/1538-3873/ab3e82 is OK
- 10.5281/ZENODO.7871665 is OK
- 10.1093/rasti/rzac005 is OK
- 10.48550/ARXIV.2302.12661 is OK
- 10.1051/0004-6361/202140415 is OK
- 10.1051/0004-6361/201220873 is OK
- 10.17487/RFC8878 is OK

MISSING DOIs

- No DOI given, and none found for title: LOFAR Und MPIfR Pulsare
- No DOI given, and none found for title: Station Data Cookbook
- No DOI given, and none found for title: dreamBeam
- No DOI given, and none found for title: LOFAR Data Format ICD Beam-Formed Data
- No DOI given, and none found for title: Simultaneous Dual-Site SETI with LOFAR Internation...
- No DOI given, and none found for title: Making Observations with Mode-357
- No DOI given, and none found for title: Pelican/Pelican-Lofar
- No DOI given, and none found for title: PSRDADA: Distributed Acquisition and Data Analysis...
- No DOI given, and none found for title: SIGPROC: Pulsar Signal Processing Programs

INVALID DOIs

- None

[dfm]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: McKenna
  given-names: David J.
  orcid: "https://orcid.org/0000-0001-7185-1310"
- family-names: Keane
  given-names: Evan F.
  orcid: "https://orcid.org/0000-0002-4553-655X"
- family-names: Gallagher
  given-names: Peter T.
  orcid: "https://orcid.org/0000-0001-9745-0400"
- family-names: McCauley
  given-names: Joe
  orcid: "https://orcid.org/0000-0003-4399-2233"
contact:
- family-names: McKenna
  given-names: David J.
  orcid: "https://orcid.org/0000-0001-7185-1310"
doi: 10.5281/zenodo.11019139
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: McKenna
    given-names: David J.
    orcid: "https://orcid.org/0000-0001-7185-1310"
  - family-names: Keane
    given-names: Evan F.
    orcid: "https://orcid.org/0000-0002-4553-655X"
  - family-names: Gallagher
    given-names: Peter T.
    orcid: "https://orcid.org/0000-0001-9745-0400"
  - family-names: McCauley
    given-names: Joe
    orcid: "https://orcid.org/0000-0003-4399-2233"
  date-published: 2024-04-22
  doi: 10.21105/joss.05517
  issn: 2475-9066
  issue: 96
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5517
  title: "udpPacketManager: An International LOFAR Station Data
    (Pre-)Processor"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05517"
  volume: 9
title: "udpPacketManager: An International LOFAR Station Data
  (Pre-)Processor"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.05517 joss-papers#5260
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05517
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[dfm]

@pritchardn, @plaplant — Many thanks for your reviews here! And also thanks to @plaplant for getting the review started as editor. JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you!!

@David-McKenna — Your paper is now accepted and published in JOSS! ⚡🚀💥

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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</a>

reStructuredText:
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