[REVIEW]: Comrade: Composable Modeling of Radio Emission

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@ptiede@arfon<!--end-editor-- Reviewers: @mileslucas, @cescalara Archive: 10.5281/zenodo.6977819

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/ad2af695e3987cfa61091d7c9d077ac4"><img src="https://joss.theoj.org/papers/ad2af695e3987cfa61091d7c9d077ac4/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/ad2af695e3987cfa61091d7c9d077ac4/status.svg)](https://joss.theoj.org/papers/ad2af695e3987cfa61091d7c9d077ac4)

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

@mileslucas & @cescalara, 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 @arfon 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 @mileslucas

📝 Checklist for @cescalara

editorialbot commented 2 years ago

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

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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 commented 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (1006.1 files/s, 162914.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TOML                             6            754              2           3593
Julia                           39            812            455           3377
Markdown                         7             86              0            279
TeX                              2             36              2            278
YAML                             4              7              4            135
JSON                             2              0              0             32
HTML                             1              0              0             26
-------------------------------------------------------------------------------
SUM:                            61           1695            463           7720
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

Wordcount for paper.md is 1132

editorialbot commented 2 years ago

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

OK DOIs

- 10.1137/141000671 is OK
- 10.1145/3276490 is OK
- 10.3847/1538-4357/ab9c1f is OK
- 10.5281/zenodo.5520061 is OK
- 10.3847/1538-3881/abe3f8 is OK
- 10.3847/1538-4357/aab6a8 is OK
- 10.1051/aas:1996146 is OK
- 10.3847/2041-8213/ab0ec7 is OK
- 10.5281/zenodo.5808196 is OK
- 10.3847/2041-8213/ab0e85 is OK
- 10.3847/2041-8213/ab1141 is OK
- 10.3847/1538-4357/ab91a4 is OK

MISSING DOIs

- None

INVALID DOIs

- None

arfon commented 2 years ago

@mileslucas, @cescalara – 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/4457 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.

editorialbot commented 2 years ago

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

mileslucas commented 2 years ago

Review checklist for @mileslucas

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/ptiede/Comrade.jl?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@ptiede) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

cescalara commented 2 years ago

Review checklist for @cescalara

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/ptiede/Comrade.jl?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@ptiede) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

mileslucas commented 2 years ago

@arfon I'm satisfied with my review of Comrade, let me know if there's anything I need to do!

arfon commented 2 years ago

Thanks for confirming @mileslucas!

@cescalara - how are you getting along with your review?

cescalara commented 2 years ago

I plan to send my review this week or early next week!

arfon commented 2 years ago

Excellent! Thanks for the update.

cescalara commented 2 years ago

Hi @arfon, I've also completed my review and can recommend Comrade.jl for publication!

ptiede commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

arfon commented 2 years ago

Hi @arfon, I've also completed my review and can recommend Comrade.jl for publication!

Awesome news, thanks so much @cescalara!

@ptiede – At this point could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

The title of the archive is the same as the JOSS paper title
That the authors of the archive are the same as the JOSS paper authors

I can then move forward with accepting the submission.

ptiede commented 2 years ago

First, @cescalara and @mileslucas thanks for all your hard work the package is much better now!

The most recent version of Comrade has all the requested updates during the referee process. I have gone ahead and created a zenodo release for the most recent version the doi is:

https://doi.org/10.5281/zenodo.6977819

Let me know if you need anything else!

arfon commented 2 years ago

@editorialbot set 10.5281/zenodo.6977819 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.6977819

arfon commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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

OK DOIs

- 10.1137/141000671 is OK
- 10.1051/0004-6361/201321236 is OK
- 10.1145/3276490 is OK
- 10.3847/1538-4357/ab9c1f is OK
- 10.5281/zenodo.5520061 is OK
- 10.3847/1538-3881/abe3f8 is OK
- 10.3847/1538-4357/aab6a8 is OK
- 10.1051/aas:1996146 is OK
- 10.3847/2041-8213/ab0ec7 is OK
- 10.5281/zenodo.5808196 is OK
- 10.1038/s41550-021-01548-0 is OK
- 10.3847/2041-8213/ab0e85 is OK
- 10.3847/2041-8213/ab1141 is OK
- 10.3847/1538-4357/ab91a4 is OK
- 10.3847/2041-8213/ab0e85 is OK
- 10.3847/2041-8213/ab1141 is OK
- 10.3847/1538-4357/ab91a4 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

:warning: Error prepararing paper acceptance. The generated XML metadata file is invalid.

ID ref-EHTCIV already defined
ID ref-EHTCVI already defined
ID ref-themis already defined

arfon commented 2 years ago

@ptiede - it looks like EHTCIV, EHTCVI, and themis are all listed twice in your bibtex file. Could you please delete the duplicates? This messes up our production pipeline (as you can see above).

ptiede commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

ptiede commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

ptiede commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

ptiede commented 2 years ago

@arfon should be fixed now! sorry about that

arfon commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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

OK DOIs

- 10.1137/141000671 is OK
- 10.1051/0004-6361/201321236 is OK
- 10.1145/3276490 is OK
- 10.3847/1538-4357/ab9c1f is OK
- 10.5281/zenodo.5520061 is OK
- 10.3847/1538-3881/abe3f8 is OK
- 10.3847/1538-4357/aab6a8 is OK
- 10.1051/aas:1996146 is OK
- 10.3847/2041-8213/ab0ec7 is OK
- 10.5281/zenodo.5808196 is OK
- 10.1038/s41550-021-01548-0 is OK
- 10.3847/2041-8213/ab0e85 is OK
- 10.3847/2041-8213/ab1141 is OK
- 10.3847/1538-4357/ab91a4 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3430, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

arfon commented 2 years ago

@ptiede – found a couple of typos in the paper: https://github.com/ptiede/Comrade.jl/pull/170

arfon commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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

OK DOIs

- 10.1137/141000671 is OK
- 10.1051/0004-6361/201321236 is OK
- 10.1145/3276490 is OK
- 10.3847/1538-4357/ab9c1f is OK
- 10.5281/zenodo.5520061 is OK
- 10.3847/1538-3881/abe3f8 is OK
- 10.3847/1538-4357/aab6a8 is OK
- 10.1051/aas:1996146 is OK
- 10.3847/2041-8213/ab0ec7 is OK
- 10.5281/zenodo.5808196 is OK
- 10.1038/s41550-021-01548-0 is OK
- 10.3847/2041-8213/ab0e85 is OK
- 10.3847/2041-8213/ab1141 is OK
- 10.3847/1538-4357/ab91a4 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3431, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

arfon commented 2 years ago

@editorialbot accept

editorialbot commented 2 years ago

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

editorialbot commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 2 years ago

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/3432
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04457
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon commented 2 years ago

@mileslucas, @cescalara – many thanks for your reviews here! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@ptiede – your paper is now accepted and published in JOSS :zap::rocket::boom:

editorialbot commented 2 years ago

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