[REVIEW]: Virgo: A Versatile Spectrometer for Radio Astronomy

[whedon]

Submitting author: @0xCoto (Apostolos Spanakis-Misirlis)
Repository: https://github.com/0xCoto/Virgo
Version: v3.7.0
Editor: @xuanxu
Reviewer: @astrom-tom, @ygrange
Archive: 10.5281/zenodo.4778382

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/612c2634c1dd83749e95a93449740861"><img src="https://joss.theoj.org/papers/612c2634c1dd83749e95a93449740861/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/612c2634c1dd83749e95a93449740861/status.svg)](https://joss.theoj.org/papers/612c2634c1dd83749e95a93449740861)

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

@astrom-tom & @ygrange, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

Review checklist for @astrom-tom

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 repository url?
• 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 (@0xCoto) 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

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: Does the paper have a section titled 'Statement of Need' that clearly states 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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• 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?

Review checklist for @ygrange

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 repository url?
• 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 (@0xCoto) 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

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: Does the paper have a section titled 'Statement of Need' that clearly states 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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @astrom-tom , @ygrange it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.38 s (32.0 files/s, 20474.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                              2              0              0           5511
Python                           6            279            173           1058
Markdown                         2             93              0            347
TeX                              1              8              0            189
YAML                             1              5              2             24
-------------------------------------------------------------------------------
SUM:                            12            385            175           7129
-------------------------------------------------------------------------------


Statistical information for the repository 'c140d87333016fe88b823a86' was
gathered on 2021/02/26.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
0xCoto                          99          2263            753          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
0xCoto                     1510           66.7          3.6               10.73

[whedon]

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

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1142/9446 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.1051/0004-6361:20041864 is OK
- 10.1051/0004-6361/201015362 is OK

MISSING DOIs

- 10.1016/b978-0-12-804547-3.00007-3 may be a valid DOI for title: Multirate Digital Signal Processing

INVALID DOIs

- None

[whedon]

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

[xuanxu]

@whedon remind @astrom-tom in 2 weeks

[whedon]

Reminder set for @astrom-tom in 2 weeks

[whedon]

👋 @astrom-tom , please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @ygrange, please update us on how your review is going (this is an automated reminder).

[ygrange]

I created a directory and cloned the repo... Sorry, things are nog going as fast as I'd like :). I will try to push doing something the coming period

[xuanxu]

👋 @astrom-tom, @ygrange please update us on how your reviews are going

[ygrange]

I finally started. Thanks for the reminder. Those are crazy times and things tend to fall of plates. Many apologies. I have some time explicitly booked in my calendar for this this week now.

[astrom-tom]

Hi @xuanxu
For me it is the same, I already have some points for the authors but I cannot check the box in the review. Can you send me again the invitation for the review? Thanks!

[xuanxu]

@whedon invite @astrom-tom

[whedon]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

[astrom-tom]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

[xuanxu]

@whedon re-invite @astrom-tom as reviewer

[whedon]

OK, the reviewer has been re-invited.

@astrom-tom please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[ygrange]

First reading of the paper I have some minor comments

Minor comments:

• I noticed that there are four authors on the paper, while only one did contribute to the repo. This is not against the JOSS policy. They are also explicitly thanked for their contributions in the README. Just wanted to make sure you are aware of the relevant policy on co-athorship.
• You cite the FITS 3.0 standard in the paper. I think you basically import from astropy.io.fits and I couldn't really find what version that is. Since version 4.0 seems to have recently appeared I was wondering whether you have a reason to cite this specific version, or that this is more of a "generic FITS" citation.
• Seems like the DOI proposed by Whedon for the book is wrong btw.

[ygrange]

The goal of the tool is to make radio telescopes accessible to a larger community, mainly targeting amateurs, students and educators. I'm struggling a bit with the target audience. This is because I personally think this is a very great group to focus on, because the field of radio astronomy tends to have a bit of an image to be hard to start working in, and those are important groups in general. On the other hand I can imagine the JOSS target audience to be more scientists than educators or amateurs. Would it be possible to add a sentence about use by professional astronomers, even though they may not necessarily be the original target audience?

[astrom-tom]

Dear @xuanxu,
I created the three following issues for the paper.
JOSS review: Documentation general comment #10
JOSS review: Installation and Usage #11
JOSS review: functionality documentation & testing #12

There is a fair amount of work to be done to have the paper accepted. I am happy to give a hand where I can! I will continue the review when these points will be addressed as they are all about the documentation.

[ygrange]

I have to admit that the issues mentioned by @astrom-tom are sort of blocking continuation for me too. I will follow those threads and try to lend a hand myself wherever I can too.

[xuanxu]

@astrom-tom / @ygrange: Thanks!

@0xCoto Please keep us updated here about your progress addressing the mentioned comments and issues.

[ygrange]

I didn't have access to my laptop before, so I hoped replying to the email would do, but I totally agree with that wording!

[astrom-tom]

Hi @xuanxu
The review on my side is done. I am happy with what has been implemented and I closed the few tickets I opened in the repo. All good for me. Thanks @0xCoto for the work!

[xuanxu]

Thanks, @astrom-tom!

[xuanxu]

@whedon generate pdf

[whedon]

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

[xuanxu]

@whedon check references

[whedon]

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

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1142/9446 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.1051/0004-6361:20041864 is OK
- 10.1051/0004-6361/201015362 is OK

MISSING DOIs

- 10.1016/b978-0-12-804547-3.00007-3 may be a valid DOI for title: Multirate Digital Signal Processing

INVALID DOIs

- None

[xuanxu]

OK @0xCoto, everything looks good, here are the next steps:

• Please release a new tagged version from the current master branch so it includes all the changes made during the review process
• Then archive that latest release in Zenodo or a similar service
• Check the Zenodo deposit has the correct metadata: title and authors names should match the paper; you may also add authors' ORCIDs.

Once you do that please report here the version number and archive DOI

[0xCoto]

@xuanxu - Version number: v3.7.0

Zenodo DOI: 10.5281/zenodo.4778382

[xuanxu]

@whedon set v3.7.0 as version

[whedon]

OK. v3.7.0 is the version.

[xuanxu]

@whedon set 10.5281/zenodo.4778382 as archive

[whedon]

OK. 10.5281/zenodo.4778382 is the archive.

[xuanxu]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1142/9446 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.1051/0004-6361:20041864 is OK
- 10.1051/0004-6361/201015362 is OK

MISSING DOIs

- 10.1016/b978-0-12-804547-3.00007-3 may be a valid DOI for title: Multirate Digital Signal Processing

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2353

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2353, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[Kevin-Mattheus-Moerman]

@0xCoto I've proofread your paper and it looks good so I'll now proceed to accept this work in JOSS. Congratulations. Thanks @astrom-tom and @ygrange for reviewing this work!

[Kevin-Mattheus-Moerman]

@whedon accept deposit=true

[whedon]

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

[Kevin-Mattheus-Moerman]

Thanks for editing this @xuanxu!

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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.03067 joss-papers#2362
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03067
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...

[whedon]

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03067/status.svg)](https://doi.org/10.21105/joss.03067)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03067">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03067/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03067/status.svg
   :target: https://doi.org/10.21105/joss.03067

This is how it will look in your documentation:

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[0xCoto]

Thank you @Kevin-Mattheus-Moerman ! I'd once again like to thank the editor @xuanxu and the reviewers @ygrange @astrom-tom for providing valuable comments and significantly improving the quality of the software! Very much appreciate the amount of time you volunteer.