[REVIEW]: SIMIO-continuum: Connecting simulations to interferometric observations

[editorialbot]

Submitting author: @nicokurtovic (Nicolas Kurtovic)
Repository: https://github.com/nicokurtovic/SIMIO
Branch with paper.md (empty if default branch): main
Version: 1.2
Editor: @ivastar
Reviewers: @adeleplunkett, @jeffjennings
Archive: 10.5281/zenodo.10879411

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/99967c47b9d7e13c7066fffa61e88575"><img src="https://joss.theoj.org/papers/99967c47b9d7e13c7066fffa61e88575/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/99967c47b9d7e13c7066fffa61e88575/status.svg)](https://joss.theoj.org/papers/99967c47b9d7e13c7066fffa61e88575)

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

@adeleplunkett & @jeffjennnings, 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 @ivastar 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 @jeffjennings

📝 Checklist for @adeleplunkett

[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:

@editorialbot commands

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

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=1.34 s (37.4 files/s, 101900.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          29           7979          24827         101392
TeX                              1              5              0             83
Markdown                         2             27              0             56
reStructuredText                 3             98            229             36
YAML                             2              5             11             27
make                             1              4              7              9
Jupyter Notebook                12              0           1596              0
-------------------------------------------------------------------------------
SUM:                            50           8118          26670         101603
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 610

[editorialbot]

Failed to discover a Statement of need section in paper

[editorialbot]

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

OK DOIs

- 10.3847/1538-4357/aaa1e7 is OK
- 10.1051/0004-6361/202140535 is OK
- 10.3847/1538-4365/ac1430 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[ivastar]

@editorialbot add @jeffjennings as reviewer

[editorialbot]

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

@editorialbot commands

[ivastar]

@editorialbot add @jeffjennings as reviewer

[editorialbot]

@jeffjennings added to the reviewers list!

[ivastar]

@editorialbot remove @jeffjennnings as reviewer

[editorialbot]

@jeffjennnings removed from the reviewers list!

[jeffjennings]

Review checklist for @jeffjennings

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/nicokurtovic/SIMIO?
• 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 (@nicokurtovic) 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?

[adeleplunkett]

Review checklist for @adeleplunkett

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/nicokurtovic/SIMIO?
• 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 (@nicokurtovic) 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?

[adeleplunkett]

@ivastar , I have completed my review. It's not clear where I should leave comments. A new comment here, or inline with the checklist?

[ivastar]

@adeleplunkett please open issues in the SIMIO repository for any item that you did not check. Summary of the review, comments on the text of the paper or anything else can be captured comments in this thread.

[ivastar]

@jeffjennings a gentle nudge to complete the review by early next week if possible.

[editorialbot]

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

OK DOIs

- 10.1088/1538-3873/ac9642 is OK
- 10.3847/1538-4357/aaa1e7 is OK
- 10.1051/0004-6361/202140535 is OK
- 10.3847/1538-4365/ac1430 is OK
- 10.1093/mnras/sty409 is OK

MISSING DOIs

- No DOI given, and none found for title: The CASA Software for Radio Astronomy: Status Upda...
- No DOI given, and none found for title: CASA Architecture and Applications
- No DOI given, and none found for title: fakeobs

INVALID DOIs

- None

[ivastar]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1088/1538-3873/ac9642 is OK
- 10.3847/1538-4357/aaa1e7 is OK
- 10.1051/0004-6361/202140535 is OK
- 10.3847/1538-4365/ac1430 is OK
- 10.1093/mnras/sty409 is OK

MISSING DOIs

- No DOI given, and none found for title: The CASA Software for Radio Astronomy: Status Upda...
- No DOI given, and none found for title: CASA Architecture and Applications
- No DOI given, and none found for title: fakeobs

INVALID DOIs

- None

[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#5284, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[ivastar]

@nicokurtovic, @adeleplunkett, @jeffjennings thank you all for the work on this paper! I am happy to see it finally published!

[jeffjennings]

That's great news, congrats @nicokurtovic!

[dfm]

@nicokurtovic — just in case you didn't see it, please check out and merge (or otherwise address) my PR linked above that makes some final editorial fixes. Then I can proceed with the final steps. Thanks!

[dfm]

@nicokurtovic — Please take a look at that PR ASAP so that we can get this published! Thanks.

[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]

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

OK DOIs

- 10.1088/1538-3873/ac9642 is OK
- 10.3847/1538-4357/aaa1e7 is OK
- 10.1051/0004-6361/202140535 is OK
- 10.3847/1538-4365/ac1430 is OK
- 10.1093/mnras/sty409 is OK

MISSING DOIs

- No DOI given, and none found for title: The CASA Software for Radio Astronomy: Status Upda...
- No DOI given, and none found for title: CASA Architecture and Applications
- No DOI given, and none found for title: fakeobs

INVALID DOIs

- None

[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#5326, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[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: Kurtovic
  given-names: Nicolas T.
  orcid: "https://orcid.org/0000-0002-2358-4796"
doi: 10.5281/zenodo.10879411
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Kurtovic
    given-names: Nicolas T.
    orcid: "https://orcid.org/0000-0002-2358-4796"
  date-published: 2024-05-08
  doi: 10.21105/joss.04942
  issn: 2475-9066
  issue: 97
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 4942
  title: "SIMIO-continuum: Connecting simulations to ALMA observations"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.04942"
  volume: 9
title: "SIMIO-continuum: Connecting simulations to ALMA observations"

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.04942 joss-papers#5327
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04942
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]

Many thanks to @adeleplunkett and @jeffjennings for reviewing and to @ivastar for editing! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you!!

@nicokurtovic — Your paper is now accepted and published in JOSS! ⚡🚀💥

[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:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.04942/status.svg)](https://doi.org/10.21105/joss.04942)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04942">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04942/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04942/status.svg
   :target: https://doi.org/10.21105/joss.04942

This is how it will look in your documentation:

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