[REVIEW]: disksurf: Extracting the 3D Structure of Protoplanetary Disks

whedon commented 3 years ago

Submitting author: @richteague (Richard Teague) Repository: https://github.com/richteague/disksurf Version: v0.1.7 Editor: @christinahedges Reviewer: @emptymalei, @cpinte Archive: 10.5281/zenodo.5670586

:warning: JOSS reduced service mode :warning:

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/436317ccf31e271043309092032ccf08"><img src="https://joss.theoj.org/papers/436317ccf31e271043309092032ccf08/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/436317ccf31e271043309092032ccf08/status.svg)](https://joss.theoj.org/papers/436317ccf31e271043309092032ccf08)

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

@emptymalei & @cpinte, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
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 @christinahedges 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 @emptymalei

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
[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 (@richteague) 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 and who the target audience is?
[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?

Review checklist for @cpinte

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
[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 (@richteague) 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 and who the target audience is?
[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?

whedon commented 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @emptymalei, @cpinte it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

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.

:star: Important :star:

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:

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

watching

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

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 commented 3 years ago

Wordcount for paper.md is 709

whedon commented 3 years ago

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

OK DOIs

- 10.1051/0004-6361/201629098 is OK
- 10.21105/joss.01632 is OK
- 10.1086/670067 is OK
- 10.1038/s41586-019-1642-0 is OK
- 10.3847/1538-4357/abf92e is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.5281/zenodo.4599319 is OK
- 10.1051/0004-6361/201731377 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 3 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.07 s (202.0 files/s, 43357.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           6            318            822           1143
TeX                              1             11              0            177
Markdown                         3             22              0             65
Jupyter Notebook                 1              0            485             55
reStructuredText                 2             19             15             33
DOS Batch                        1              8              1             26
make                             1              4              6              9
-------------------------------------------------------------------------------
SUM:                            15            382           1329           1508
-------------------------------------------------------------------------------

Statistical information for the repository '19f2eaae75f8267d394caeb7' was
gathered on 2021/10/14.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Jane Huang                       1             4              2            0.05
Richard Teague                  54          6994           4983           97.65
richteague                       3           276              6            2.30

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
Richard Teague             2283           32.6          1.5                9.77

whedon commented 3 years ago

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

christinahedges commented 3 years ago

@richteague, @emptymalei , @cpinte – This is the review thread for the paper. Please don't hesitate to message me here if you have questions.

Please read the "Reviewer instructions & questions" in the first comment above to get started. If you get lost, you can also see the reviewer guidelines.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. If you are concerned about a requirement, please discuss it here on this thread 🧵 . Feel free to post about questions/concerns as they come up as you go through your review.

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 #3827 so that a link is created to this thread (and I can keep an eye on what is happening).

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. When you're finished with your checklist, leave a comment and @ me to let everyone know your review is complete.

christinahedges commented 2 years ago

Hi @emptymalei and @cpinte, just wanted to add a gentle prompt here as we're now at the two week mark. Please let me know if you are struggling with any aspect of the review!

whedon commented 2 years ago

:wave: @emptymalei, please update us on how your review is going (this is an automated reminder).

whedon commented 2 years ago

:wave: @cpinte, please update us on how your review is going (this is an automated reminder).

cpinte commented 2 years ago

Hi @richteague, I have tried disksurf, it appears to work as expected. Very nice package !

The paper describes clearly the aims and functions. Maybe it is worth mentioning my own implementation https://github.com/cpinte/CO_layers (it is not as polished nor documented as disksurf, but it basically does the same thing).

I have run the tutorial, it is also clear and I can reproduce the results.

@christinahedges : I don't seem to be able to edit the checklist, it says the invitation expired

kthyng commented 2 years ago

@whedon re-invite @cpinte as reviewer

whedon commented 2 years ago

OK, the reviewer has been re-invited.

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

kthyng commented 2 years ago

@cpinte ☝️

cpinte commented 2 years ago

Thanks !

whedon 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:

emptymalei commented 2 years ago

Hmm, I found a strange thing about the markdown to pdf generator.

CleanShot 2021-11-01 at 20 11 44@2x

The order of ' and , is different from the original markdown file:

https://github.com/richteague/disksurf/blob/8b1fdf1c1780eefa6c6d008ca4a6739a5a1f45df/paper/paper.md?plain=1#L40

~Is this some special use case that I am not aware of?~

richteague commented 2 years ago

Apologies for missing that code, @cpinte! Do you have a Zenodo reference that I could use to reference it, or would a link to the GitHub repository be OK?

@kthyng - Do you have a preference from an editorial point of view?

danielskatz commented 2 years ago

It is odd that it's being generated differently than specified, though in this case, correct grammar would be

'scattering surface,' the emission surface equivalent for small, submicron grains, was described

both the first comma inside the quote, and the second comma added.

kthyng commented 2 years ago

I didn't know that would happen in the pdf compilation! My understanding for the order of quotes vs. commas in a sentence is geographically dependent with different accepted rules in the U.S. vs the U.K. for example.

cpinte commented 2 years ago

@richteague thanks, a link to github would be great.

christinahedges commented 2 years ago

@cpinte and @emptymalei it seems like both of your review checklists are complete. Thank you for your speedy work! If you have any further comments for the authors please do post them, otherwise let me know on the thread if you're happy with the submission and would like to complete your review and recommend acceptance.

emptymalei commented 2 years ago

Hi @christinahedges , from my side, I'm happy with the submission and would like to recommend accepting the current manuscript.

cpinte commented 2 years ago

Hi @christinahedges, I am also happy to recommend the paper for publication.

whedon 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:

christinahedges commented 2 years ago

@whedon check references

whedon commented 2 years ago

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

OK DOIs

- 10.1051/0004-6361/201629098 is OK
- 10.21105/joss.01632 is OK
- 10.1086/670067 is OK
- 10.1038/s41586-019-1642-0 is OK
- 10.3847/1538-4357/abf92e is OK
- 10.3847/1538-4365/ac1434 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.3847/1538-4365/ac143b is OK
- 10.3847/1538-4365/ac143d is OK
- 10.5281/zenodo.4599319 is OK
- 10.1051/0004-6361/201731377 is OK

MISSING DOIs

- None

INVALID DOIs

- None

christinahedges commented 2 years ago

Thank you very much reviewers! @richteague your paper submission looks good to me. If you are happy and would like to make no further changes based on the review, please make a tagged release 🏷️ of the code and archive it, and then please report the version number and archive DOI here in this thread. Please make sure this archived version has all the correct meta data (author names, title etc)!

I can then recommend to our EIC that we accept this submission.

Thank you again to @emptymalei and @cpinte for your hard work and thorough review!

richteague commented 2 years ago

Thanks @christinahedges! I've made a version of the code and archived version here: 10.5281/zenodo.5670586.

Thanks also to @cpinte and @emptymalei for reviewing this submission!

kyleniemeyer commented 2 years ago

Hi @richteague, can you edit the metadata of the Zenodo archive so that the title and author list match the JOSS paper?

richteague commented 2 years ago

Hi @kyleniemeyer, I should have changed that now.

kyleniemeyer commented 2 years ago

@whedon set 10.5281/zenodo.5670586 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.5670586 is the archive.

kyleniemeyer commented 2 years ago

@whedon recommend-accept

whedon commented 2 years ago

Attempting dry run of processing paper acceptance...

whedon commented 2 years ago

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

OK DOIs

- 10.1051/0004-6361/201629098 is OK
- 10.21105/joss.01632 is OK
- 10.1086/670067 is OK
- 10.1038/s41586-019-1642-0 is OK
- 10.3847/1538-4357/abf92e is OK
- 10.3847/1538-4365/ac1434 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.3847/1538-4365/ac143b is OK
- 10.3847/1538-4365/ac143d is OK
- 10.5281/zenodo.4599319 is OK
- 10.1051/0004-6361/201731377 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 2 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2747

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2747, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

kyleniemeyer commented 2 years ago

@whedon accept deposit=true

whedon commented 2 years ago

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

whedon commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon 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/2748
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03827
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer commented 2 years ago

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

Many thanks to @emptymalei and @cpinte for reviewing this, and @christinahedges for editing.

whedon commented 2 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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.03827/status.svg)](https://doi.org/10.21105/joss.03827)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03827">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03827/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03827/status.svg
   :target: https://doi.org/10.21105/joss.03827

This is how it will look in your documentation:

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

openjournals / joss-reviews