[REVIEW]: 21cmFAST v3: A Python-integrated C code for generating 3D realizations of the cosmic 21cm signal.

whedon commented 4 years ago

Submitting author: @steven-murray (Steven Murray) Repository: https://github.com/21cmFAST/21cmFAST Version: v3.0.3 Editor: @dfm Reviewer: @sambit-giri, @sultan-hassan Archive: 10.5281/zenodo.4107189

: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/56b5f5228d04377a9d612b30ce82b447"><img src="https://joss.theoj.org/papers/56b5f5228d04377a9d612b30ce82b447/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/56b5f5228d04377a9d612b30ce82b447/status.svg)](https://joss.theoj.org/papers/56b5f5228d04377a9d612b30ce82b447)

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

@sambit-giri & @sultanier, 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 @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 @sambit-giri

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 (@steven-murray) 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: Do the authors clearly state 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 @sultan-hassan

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 (@steven-murray) 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: Do the authors clearly state 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

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

OK DOIs

- 10.1086/521806 is OK
- 10.1111/j.1365-2966.2010.17731.x is OK
- 10.1086/423025 is OK
- 10.1046/j.1365-8711.2002.04999.x is OK
- 10.1103/PhysRevLett.123.131301 is OK
- 10.1103/PhysRevD.100.063538 is OK
- 10.1093/mnras/staa1131 is OK
- 10.1103/PhysRevLett.121.121301 is OK
- 10.1093/mnras/staa2797 is OK
- 10.1093/mnras/stv571 is OK

MISSING DOIs

- None

INVALID DOIs

- None

dfm commented 3 years ago

@whedon generate pdf

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:

dfm commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

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

OK DOIs

- 10.1086/521806 is OK
- 10.1111/j.1365-2966.2010.17731.x is OK
- 10.1086/423025 is OK
- 10.1046/j.1365-8711.2002.04999.x is OK
- 10.1103/PhysRevLett.123.131301 is OK
- 10.1103/PhysRevD.100.063538 is OK
- 10.1093/mnras/staa1131 is OK
- 10.1103/PhysRevLett.121.121301 is OK
- 10.1093/mnras/staa2797 is OK
- 10.1093/mnras/stv571 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 3 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/1834

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1834, 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 3 years ago

Hi @steven-murray, I am the EIC on duty this week, doing some final checks before publishing.

I noticed that in the paper, journal names are not appearing for your references. Can you replace all the macros in your .bib file (e.g., \apj) with the spelled-out journal names?

steven-murray commented 3 years ago

Thanks @kyleniemeyer . This is done now and in master.

kyleniemeyer commented 3 years ago

@whedon generate pdf

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:

kyleniemeyer commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

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

OK DOIs

- 10.1086/521806 is OK
- 10.1111/j.1365-2966.2010.17731.x is OK
- 10.1086/423025 is OK
- 10.1046/j.1365-8711.2002.04999.x is OK
- 10.1103/PhysRevLett.123.131301 is OK
- 10.1103/PhysRevD.100.063538 is OK
- 10.1093/mnras/staa1131 is OK
- 10.1103/PhysRevLett.121.121301 is OK
- 10.1093/mnras/staa2797 is OK
- 10.1093/mnras/stv571 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 3 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/1840

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1840, 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 3 years ago

@whedon accept deposit=true

whedon commented 3 years ago

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

whedon commented 3 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 3 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/1841
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02582
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 3 years ago

Congrats @steven-murray on your article's publication in JOSS!

Many thanks to @sambit-giri and @sultan-hassan for reviewing this, and @dfm for editing.

whedon commented 3 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.02582/status.svg)](https://doi.org/10.21105/joss.02582)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02582">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02582/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02582/status.svg
   :target: https://doi.org/10.21105/joss.02582

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

steven-murray commented 3 years ago

Thanks @dfm , @sultan-hassan, @sambit-giri and @kyleniemeyer!

openjournals / joss-reviews