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[REVIEW]: ORION2: A magnetohydrodynamics code for star formation #3771

Closed whedon closed 2 years ago

whedon commented 2 years ago

Submitting author: @soffner (Stella Offner) Repository: https://bitbucket.org/orionmhdteam/orion2_release1/src/master/ Version: 1.0 Editor: @dfm Reviewer: @zingale, @changgoo Archive: 10.5281/zenodo.5791188

: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

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/c8c824a316e16f6929ad490ee93d9f5d"><img src="https://joss.theoj.org/papers/c8c824a316e16f6929ad490ee93d9f5d/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/c8c824a316e16f6929ad490ee93d9f5d/status.svg)](https://joss.theoj.org/papers/c8c824a316e16f6929ad490ee93d9f5d)

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

@zingale & @changgoo, 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 @dfm 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 @zingale

✨ 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

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @changgoo

✨ 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

Code of Conduct

General checks

Functionality

Documentation

Software paper

dfm commented 2 years ago

Great!

@zingale, @changgoo: Thanks for your reviews!! I really appreciate the time that you have volunteered to this project.

@soffner: Thanks for all your work responding to this feedback! Give me a couple of days for some final editorial tasks, and then I'll have a few last steps for you before publication.

Thanks again for participating in this process everyone!

soffner commented 2 years ago

Yes, thank you very much @zingale, @changgoo for your careful reviews and very helpful feedback!!

On Wed, Dec 8, 2021 at 2:32 PM Dan Foreman-Mackey @.***> wrote:

Great!

@zingale https://github.com/zingale, @changgoo https://github.com/changgoo: Thanks for your reviews!! I really appreciate the time that you have volunteered to this project.

@soffner https://github.com/soffner: Thanks for all your work responding to this feedback! Give me a couple of days for some final editorial tasks, and then I'll have a few last steps for you before publication.

Thanks again for participating in this process everyone!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3771#issuecomment-989173521, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAFACU5HYVROT7X6OLHSXJTUP66HTANCNFSM5E3I6I3A . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

dfm commented 2 years ago

@soffner: I've just opened a small PR over on your repo. Once that's merged here are a few last steps for you, then we'll be ready to go!

  1. Comment @whedon generate pdf, then take one last read through the manuscript to make sure that you're happy with it (it's harder to make changes later!), especially the author names and affiliations. I've taken a pass and it looks good to me!
  2. Increment the version number of the software and report that version number back here.
  3. Create an archived release of that version of the software (using Zenodo or something similar). Please make sure that the metadata (title and author list) exactly match the paper. Then report the DOI of the release back to this thread.
soffner commented 2 years ago

@whedon generate pdf

On Mon, Dec 13, 2021 at 7:38 PM Dan Foreman-Mackey @.***> wrote:

@soffner https://github.com/soffner: I've just opened a small PR https://bitbucket.org/orionmhdteam/orion2_release1/pull-requests/3/edits-for-joss-publication over on your repo. Once that's merged here are a few last steps for you, then we'll be ready to go!

  1. Comment @whedon generate pdf, then take one last read through the manuscript to make sure that you're happy with it (it's harder to make changes later!), especially the author names and affiliations. I've taken a pass and it looks good to me!
  2. Increment the version number of the software and report that version number back here.
  3. Create an archived release of that version of the software (using Zenodo or something similar). Please make sure that the metadata (title and author list) exactly match the paper. Then report the DOI of the release back to this thread.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3771#issuecomment-993074405, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAFACU3EGQFHWTMPEDGIVNDUQ2NY7ANCNFSM5E3I6I3A . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

soffner commented 2 years ago

@whedon generate pdf

On Mon, Sep 27, 2021 at 2:22 PM whedon @.***> wrote:

Submitting author: @soffner https://github.com/soffner (Stella Offner http://orcid.org/0000-0003-1252-9916) Repository: https://bitbucket.org/orionmhdteam/orion2_release1/src/master/ https://bitbucket.org/orionmhdteam/orion2_release1/src/master/ Version: v1.0.0 Editor: @dfm https://github.com/dfm Reviewer: @zingale https://github.com/zingale, @changgoo https://github.com/changgoo Archive: Pending

⚠️ 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 https://blog.joss.theoj.org/2020/05/reopening-joss. Status

[image: status] https://joss.theoj.org/papers/c8c824a316e16f6929ad490ee93d9f5d

Status badge code:

HTML:

Markdown: status

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository https://bitbucket.org/orionmhdteam/orion2_release1/src/master/ 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

@zingale https://github.com/zingale & @changgoo https://github.com/changgoo, 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 @dfm https://github.com/dfm 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 @zingale https://github.com/zingale

✨ 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 https://bitbucket.org/orionmhdteam/orion2_release1/src/master/. ✨ Conflict of interest

Code of Conduct

General checks

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 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 https://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html#citation_syntax ?

Review checklist for @changgoo https://github.com/changgoo

✨ 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 https://bitbucket.org/orionmhdteam/orion2_release1/src/master/. ✨ Conflict of interest

Code of Conduct

General checks

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 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 https://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html#citation_syntax ?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3771, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAFACU3UFUMNO7RDVBWTM23UEC757ANCNFSM5E3I6I3A . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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:

soffner commented 2 years ago

@whedon generate pdf

On Fri, Dec 17, 2021 at 6:31 PM whedon @.***> wrote:

👉📄 Download article proof https://raw.githubusercontent.com/openjournals/joss-papers/joss.03771/joss.03771/10.21105.joss.03771.pdf 📄 View article proof on GitHub https://github.com/openjournals/joss-papers/blob/joss.03771/joss.03771/10.21105.joss.03771.pdf 📄 👈

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3771#issuecomment-997106743, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAFACU57C7T4JEQ4ZZP56BLURPI5ZANCNFSM5E3I6I3A . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you were mentioned.Message ID: @.***>

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:

soffner commented 2 years ago

Hi @dfm.

We have updated the affiliations and acknowledgements of the submission, so it's all set to go.

I have defined a version tag of 1.0 with the latest repository check-in on bitbucket.

I created an archived release on Zenodo: https://doi.org/10.5281/zenodo.5791188

Thanks, Stella

On Mon, Dec 13, 2021 at 7:38 PM Dan Foreman-Mackey @.***> wrote:

@soffner https://github.com/soffner: I've just opened a small PR https://bitbucket.org/orionmhdteam/orion2_release1/pull-requests/3/edits-for-joss-publication over on your repo. Once that's merged here are a few last steps for you, then we'll be ready to go!

  1. Comment @whedon generate pdf, then take one last read through the manuscript to make sure that you're happy with it (it's harder to make changes later!), especially the author names and affiliations. I've taken a pass and it looks good to me!
  2. Increment the version number of the software and report that version number back here.
  3. Create an archived release of that version of the software (using Zenodo or something similar). Please make sure that the metadata (title and author list) exactly match the paper. Then report the DOI of the release back to this thread.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3771#issuecomment-993074405, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAFACU3EGQFHWTMPEDGIVNDUQ2NY7ANCNFSM5E3I6I3A . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

dfm 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

- 10.1093/mnras/stz653 is OK
- 10.1093/mnras/stx2611 is OK
- 10.1093/mnras/stv1437 is OK
- 10.1088/0004-637X/747/1/22 is OK
- 10.1016/j.jcp.2007.07.035 is OK
- 10.1016/j.jcp.2007.09.032 is OK
- 10.1086/421935 is OK
- 10.1088/0004-637X/745/2/139 is OK
- 10.1086/305329 is OK
- 10.1016/s0377-0427(99)00156-9 is OK
- 10.1086/310975 is OK
- 10.1088/0004-637X/740/2/107 is OK
- 10.1088/0004-637X/811/2/146 is OK
- 10.1086/426051 is OK
- 10.1086/590238 is OK
- 10.1088/0004-6256/136/1/404 is OK
- 10.1088/0004-637X/703/1/131 is OK
- 10.1088/0004-637X/693/1/914 is OK
- 10.1088/0004-637X/704/2/L124 is OK
- 10.1093/mnras/stu052 is OK
- 10.1038/nature13662 is OK
- 10.1088/0004-637X/783/1/50 is OK
- 10.1038/s41550-018-0566-1 is OK
- 10.3847/1538-4357/ab584b is OK
- 10.1086/513316 is OK
- 10.1088/0067-0049/198/1/7 is OK

MISSING DOIs

- None

INVALID DOIs

- None
dfm commented 2 years ago

@whedon set 10.5281/zenodo.5791188 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.5791188 is the archive.

dfm commented 2 years ago

@whedon set 1.0 as version

whedon commented 2 years ago

OK. 1.0 is the version.

dfm 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

- 10.1093/mnras/stz653 is OK
- 10.1093/mnras/stx2611 is OK
- 10.1093/mnras/stv1437 is OK
- 10.1088/0004-637X/747/1/22 is OK
- 10.1016/j.jcp.2007.07.035 is OK
- 10.1016/j.jcp.2007.09.032 is OK
- 10.1086/421935 is OK
- 10.1088/0004-637X/745/2/139 is OK
- 10.1086/305329 is OK
- 10.1016/s0377-0427(99)00156-9 is OK
- 10.1086/310975 is OK
- 10.1088/0004-637X/740/2/107 is OK
- 10.1088/0004-637X/811/2/146 is OK
- 10.1086/426051 is OK
- 10.1086/590238 is OK
- 10.1088/0004-6256/136/1/404 is OK
- 10.1088/0004-637X/703/1/131 is OK
- 10.1088/0004-637X/693/1/914 is OK
- 10.1088/0004-637X/704/2/L124 is OK
- 10.1093/mnras/stu052 is OK
- 10.1038/nature13662 is OK
- 10.1088/0004-637X/783/1/50 is OK
- 10.1038/s41550-018-0566-1 is OK
- 10.3847/1538-4357/ab584b is OK
- 10.1086/513316 is OK
- 10.1088/0067-0049/198/1/7 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/2849

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2849, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
dfm commented 2 years ago

@soffner Looks great - thanks for your patience! I've handed this off to the EiC team to handle the final processing. They may have some last small edits before publication, but then we'll be all set. Thanks again for your submission and your participation in this process.

soffner commented 2 years ago

Great, thanks @dfm!

On Mon, Dec 27, 2021 at 9:56 AM Dan Foreman-Mackey @.***> wrote:

@soffner https://github.com/soffner Looks great - thanks for your patience! I've handed this off to the EiC team to handle the final processing. They may have some last small edits before publication, but then we'll be all set. Thanks again for your submission and your participation in this process.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3771#issuecomment-1001631497, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAFACU5MEMNHNJQBTRI6YWDUTCEDBANCNFSM5E3I6I3A . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you were mentioned.Message ID: @.***>

arfon 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:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/2850
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03771
  3. If everything looks good, then close this review issue.

  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

    Any issues? Notify your editorial technical team...

arfon commented 2 years ago

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

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

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.03771/status.svg)](https://doi.org/10.21105/joss.03771)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03771">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03771/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03771/status.svg
   :target: https://doi.org/10.21105/joss.03771

This is how it will look in your documentation:

DOI

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