[REVIEW]: SwiftVISA: Controlling Instrumentation with a Swift-based Implementation of the VISA Communication Protocol

[editorialbot]

Submitting author: @OHildreth (Owen Hildreth)
Repository: https://github.com/SwiftVISA/SwiftVISASwift.git
Branch with paper.md (empty if default branch):
Version: 0.2.0
Editor: @dhhagan
Reviewers: @MatthieuDartiailh, @jarrah42
Archive: 10.5281/zenodo.7767610

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/2c7d5cc7cbf2d71652aecba6f34ee790"><img src="https://joss.theoj.org/papers/2c7d5cc7cbf2d71652aecba6f34ee790/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/2c7d5cc7cbf2d71652aecba6f34ee790/status.svg)](https://joss.theoj.org/papers/2c7d5cc7cbf2d71652aecba6f34ee790)

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

@MatthieuDartiailh, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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

📝 Checklist for @jarrah42

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (694.1 files/s, 114661.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                       5             19             16           1807
HTML                             6             81              0           1224
CSS                              2             50             59            514
Swift                            7             71            107            365
Markdown                         2             85              0            264
TeX                              1             16              4            126
JSON                             2              0              0             62
XML                              3              0              0             35
SVG                              1              0              0             28
YAML                             1              1              4             18
-------------------------------------------------------------------------------
SUM:                            30            323            190           4443
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1972

[editorialbot]

Failed to discover a valid open source license

[editorialbot]

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

[arfon]

Noting from the pre-review issue there are multiple repositories associated with this submission: https://github.com/orgs/SwiftVISA/repositories

- SwiftVISASwift
- CoreSwiftVISA
- SwiftVISAMessenger
- NISwiftVISA
- NISwiftVISAMessenger
- CVISATypes
- SwiftVISA
- NISwiftVISAService

[editorialbot]

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

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- None

[arfon]

@MatthieuDartiailh – This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above. Please create your checklist typing:

@editorialbot generate my checklist

As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/4752 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

[MatthieuDartiailh]

Review checklist for @MatthieuDartiailh

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/SwiftVISA/SwiftVISASwift.git?
  I believe all the repository of the organization https://github.com/SwiftVISA are actually relevant to this work
• 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 (@OHildreth) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  From what I could find in the repos the first and last authors have made visible contributions but the implication of the others is less clear.
• 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

I do not have access to a MacOS system and may be not have the time to run test on a Linux box since I have no Swift experience.

• 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?
  The tests exists but require some external hardware and do not appear to have been written in a way allowing to easily use a different one.
• 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
  1 is covered the other 2 not really (I only checked SwiftVisaSwift)

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?

[dhhagan]

@editorialbot add @jarrah42 as reviewer

[editorialbot]

@jarrah42 added to the reviewers list!

[dhhagan]

Hi @jarrah42 - please comment with "@editorialbot generate my checklist" as seen a few comments above to generate your review checklist. Feel free to reach out to me with any questions. Thanks!

[OHildreth]

Hi @dhhagan,

I noticed that some of the repositories within the SwiftVISA organization were missing the MIT license. I've fixed that and all of the repositories now have a dedicated LICENSE file containing a plain-text MIT license.

[dhhagan]

HI @jarrah42 - did you have issues creating your checklist? Happy to help if needed. Feel free to ping me here or email at david.hagan@quant-aq.com

[OHildreth]

@dhhagan
Thanks, it took me some time to fix everything in the manuscript, have some students in my group members review the manuscript for clarity and typos, and get the paper to compile cleanly.

I've responded to all of the comments and closed the simplest ones. Should I close the rest of the issues or leave them open until the Reviewers and Editors have verified that I've sufficiently addressed the comments/issues?

[jarrah42]

Review checklist for @jarrah42

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/SwiftVISA/SwiftVISASwift.git?
• 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 (@OHildreth) 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?

[dhhagan]

@OHildreth Thanks for doing all of that!

@MatthieuDartiailh and @jarrah42 - please let me know if you have any questions about the review process, otherwise, I will check in a week from now to see how things are proceeding.

[editorialbot]

Done! Archive is now 10.5281/zenodo.7767610

[dhhagan]

@editorialbot recommend-accept

[editorialbot]

Done! version is now 0.2.0

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

👋 @openjournals/pe-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#4083, 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

- None

MISSING DOIs

- None

INVALID DOIs

- None

[kyleniemeyer]

Hi @OHildreth, before we publish the article, can you please clean up the citations in the text? I noticed that many/most need a space separating them from the preceding text, and in other cases they should occur prior to any punctuation (meaning, before a period or comma).

[OHildreth]

@kyleniemeyer
I fixed the spacing and location of the citations. I couldn't edit the release build (0.2.0) so I made another release (0.2.1) and all the changes are also on main. Please let me know if that does or doesn't work.

[kyleniemeyer]

@editorialbot generate pdf

[kyleniemeyer]

@OHildreth thanks - no worries about the version, the paper changes do not need to be captured in the archive or anything associated with the software, since we archive the paper itself.

[editorialbot]

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

[kyleniemeyer]

@editorialbot accept

[editorialbot]

Paper is not ready for acceptance yet, the archive is missing

[kyleniemeyer]

@editorialbot set 10.5281/zenodo.7767610 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7767610

[kyleniemeyer]

@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: Barnes
  given-names: Connor
- family-names: Henke
  given-names: Luke
- family-names: Henke
  given-names: Lorena
- family-names: Krukov
  given-names: Ivan
- family-names: Hildreth
  given-names: Owen
  orcid: "https://orcid.org/0000-0001-5358-9080"
contact:
- family-names: Hildreth
  given-names: Owen
  orcid: "https://orcid.org/0000-0001-5358-9080"
doi: 10.5281/zenodo.7767610
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Barnes
    given-names: Connor
  - family-names: Henke
    given-names: Luke
  - family-names: Henke
    given-names: Lorena
  - family-names: Krukov
    given-names: Ivan
  - family-names: Hildreth
    given-names: Owen
    orcid: "https://orcid.org/0000-0001-5358-9080"
  date-published: 2023-03-29
  doi: 10.21105/joss.04752
  issn: 2475-9066
  issue: 83
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 4752
  title: "SwiftVISA: Controlling Instrumentation with a Swift-based
    Implementation of the VISA Communication Protocol"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.04752"
  volume: 8
title: "SwiftVISA: Controlling Instrumentation with a Swift-based
  Implementation of the VISA Communication Protocol"

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]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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🐘🐘🐘 👉 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.04752 joss-papers#4090
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04752
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...

[kyleniemeyer]

Congratulations @OHildreth on your article's publication in JOSS!

Many thanks to @MatthieuDartiailh and @jarrah42 for reviewing this, and @dhhagan for editing.

[editorialbot]

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

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

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.04752/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04752/status.svg
   :target: https://doi.org/10.21105/joss.04752

This is how it will look in your documentation:

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[MatthieuDartiailh]

Congrats @OHildreth !

[OHildreth]

@MatthieuDartiailh @kyleniemeyer @dhhagan @jarrah42

Thanks again for all of your help! This is super exciting for me and the students that worked on the project. I know that this one was a lot of work for the editors and reviewers given how niche Swift, Instrumentation, and macOS is.