Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[REVIEW]: Sarracen: a Python package for analysis and visualization of smoothed particle hydrodynamics data #5263

Closed
editorialbot opened this issue Mar 16, 2023 · 54 comments
Assignees
Labels
accepted published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review Track: 1 (AASS) Astronomy, Astrophysics, and Space Sciences

Comments

@editorialbot
Copy link
Collaborator

editorialbot commented Mar 16, 2023

Submitting author: @ttricco (Terrence Tricco)
Repository: https://github.com/ttricco/sarracen
Branch with paper.md (empty if default branch):
Version: v1.2.1
Editor: @warrickball
Reviewers: @hlim88, @JBorrow
Archive: 10.5281/zenodo.8034448

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/2263841d0c1591faff829b736d36a7dd"><img src="https://joss.theoj.org/papers/2263841d0c1591faff829b736d36a7dd/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/2263841d0c1591faff829b736d36a7dd/status.svg)](https://joss.theoj.org/papers/2263841d0c1591faff829b736d36a7dd)

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

@hlim88 & @JBorrow, 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 @warrickball 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 @hlim88

📝 Checklist for @JBorrow

@editorialbot editorialbot added Python review Track: 1 (AASS) Astronomy, Astrophysics, and Space Sciences labels Mar 16, 2023
@editorialbot
Copy link
Collaborator Author

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
Copy link
Collaborator Author

Software report:

github.com/AlDanial/cloc v 1.88  T=0.09 s (435.9 files/s, 86469.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          24           1282           1725           3784
TeX                              1             27              0            264
reStructuredText                 7            160             77            161
Markdown                         2             30              0            116
DOS Batch                        1              8              1             26
YAML                             2              3              4             26
TOML                             1              2              0             20
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            39           1516           1814           4406
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

@editorialbot
Copy link
Collaborator Author

Wordcount for paper.md is 859

@editorialbot
Copy link
Collaborator Author

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

OK DOIs

- 10.1086/112164 is OK
- 10.1093/mnras/181.3.375 is OK
- 10.1088/0034-4885/68/8/R01 is OK
- 10.1016/j.jcp.2010.12.011 is OK
- 10.1017/pasa.2018.25 is OK
- 10.1093/mnras/stx1643 is OK
- 10.1071/AS07022 is OK
- 10.1088/0067-0049/192/1/9 is OK
- 10.21105/joss.02430 is OK
- 10.21105/joss.01884 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1016/j.jcp.2017.10.024 is OK
- 10.21105/joss.03021 is OK
- 10.1145/2833157.2833162 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@editorialbot
Copy link
Collaborator Author

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

@warrickball
Copy link

warrickball commented Mar 16, 2023

@hlim88 & @JBorrow, thanks again for agreeing to review. This is the review thread for the paper. All of our correspondence will now happen here.

Please read the "Reviewer instructions & questions" in the first comment above, and generate your checklists by commenting @editorialbot generate my checklist on this issue. 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. We aim to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. We also encourage reviewers to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#4992 so that the issue/PR is linked to this thread. Please also feel free to comment and ask questions on this thread. JOSS editors have found it 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 start whenever you can. JOSS reviews are iterative and the authors can start responding while you continue to review other parts of the submission.

@JBorrow
Copy link

JBorrow commented Mar 16, 2023

Thanks, looking forward to it! I will review formally shortly, but for now I would strongly suggest the authors check out this relevant paper:

https://ui.adsabs.harvard.edu/abs/2021arXiv210605281B/abstract

@hlim88
Copy link

hlim88 commented Mar 16, 2023

Review checklist for @hlim88

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/ttricco/sarracen?
  • 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 (@ttricco) 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?

@JBorrow
Copy link

JBorrow commented Mar 17, 2023

Review checklist for @JBorrow

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/ttricco/sarracen?
  • 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 (@ttricco) 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?

@warrickball
Copy link

Thanks @hlim88 and @JBorrow, it looks like the reviews are progressing steadily and there are issues for @ttricco to work on. Let me know if there's anything you feel you need guidance on, otherwise I'll check in again after the Easter break.

@JBorrow
Copy link

JBorrow commented Apr 17, 2023

@ttricco the only thing missing for me now is a clear set of contribution/community guidelines within the software repository.

@warrickball
Copy link

Thanks @JBorrow! @hlim88, how is your review progressing? Let me know if there's anything I can possibly help with.

@JBorrow
Copy link

JBorrow commented Apr 28, 2023

@warrickball as I noted above just waiting on a contributing guide/community guidelines then we're good to go.

@hlim88
Copy link

hlim88 commented Apr 28, 2023

Thanks @JBorrow! @hlim88, how is your review progressing? Let me know if there's anything I can possibly help with.

@warrickball Sorry I was busy on recent weeks for travels and others. Finalizing the review and also has same comment as @JBorrow about contributing guide/community guide line

@ttricco
Copy link

ttricco commented May 2, 2023

Sorry for the delay on this last piece about contributing / community guide lines -- have been on vacation. We will address this once I'm back in the office next week.

@ttricco
Copy link

ttricco commented May 10, 2023

@JBorrow @hlim88 We have updated our contributions guide and community code of conduct. You will find this on the GitHub front page and also on the read the docs (under "Contributing").

@JBorrow
Copy link

JBorrow commented May 10, 2023

Excellent, congrats! I am now happy with the package. Thanks Terrence & Andrew!

@warrickball
Copy link

Hi @hlim88, it looks we're now only waiting for your review. I can see you've already worked through some items, so if there's anything you'd like the authors to work on, you can mention it right away so they can work on it while you finish your review.

@hlim88
Copy link

hlim88 commented May 24, 2023

Sorry I will finalize today only thing I need to check is the software paper which will be short to review

@hlim88
Copy link

hlim88 commented May 24, 2023

@warrickball Finish to review the software paper.

@ttricco only one minor comment is you may want to mention/compare general visualization software such as Paraview and Visit (of course these are not targeting to visualize SPH data but it is well-known and widely used, also used for SPH data too).

Other than that, I think this is ready to be out! Thanks @ttricco I am also looking forward to using Sarracen too!

@ttricco
Copy link

ttricco commented May 30, 2023

@hlim88 @warrickball Done. References have been added for Paraview and Visit in the paper. Thanks.

@warrickball
Copy link

@editorialbot generate pdf

@warrickball
Copy link

warrickball commented Jun 12, 2023

Hi @ttricco, if you're happy with the code, the last step is to create a tagged release and archive and upload it to an archiving service like Zenodo or Figshare, then post the version number and archive DOI here so I can attach them to our metadata.

You're welcome to do it however you like but when I once published in JOSS, I followed instructions like these to publish from GitHub to Zenodo. I've never tried it (nor read these docs) but something similar looks possible with Figshare.

@ttricco
Copy link

ttricco commented Jun 13, 2023

@warrickball I've archived Sarracen onto Zenodo. The version is 1.2.1 and archive DOI 10.5281/zenodo.8034448.

Thanks for working through this, and for the time of the two reviewers!

@warrickball
Copy link

warrickball commented Jun 13, 2023

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

  • Double check authors and affiliations (including ORCIDs)
  • Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
  • Archive the release on Zenodo/figshare/etc and post the DOI here.
  • Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
  • Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

  • Read the text of the paper and offer comments/corrections (as either a list or a PR)
  • Check the references in the paper for corrections (e.g. capitalization)
  • Check that the archive title, author list, version tag, and the license are correct
  • Set archive DOI with @editorialbot set <DOI here> as archive
  • Set version with @editorialbot set <version here> as version
  • Double check rendering of paper with @editorialbot generate pdf
  • Specifically check the references with @editorialbot check references and ask author(s) to update as needed
  • Recommend acceptance with @editorialbot recommend-accept

@warrickball
Copy link

Thanks, @ttricco. I notice that the first author in the Zenodo archive is "AndrewHarris709", rather than Andrew Harris as in the JOSS paper. Can you update this in the Zenodo archive?

@warrickball
Copy link

@editorialbot set v1.2.1 as version

@editorialbot
Copy link
Collaborator Author

Done! version is now v1.2.1

@warrickball
Copy link

@editorialbot set 10.5281/zenodo.8034448 as archive

@editorialbot
Copy link
Collaborator Author

Done! archive is now 10.5281/zenodo.8034448

@ttricco
Copy link

ttricco commented Jun 13, 2023

@warrickball Good catch. I've updated the author name (and other metadata) on the zenodo archive.

@warrickball
Copy link

Thanks! Sorry for the back and forth, but one more thing: could you update the license in the Zenodo archive too? Zenodo doesn't detect all possible LICENCE files.

Along the way, I noticed the same issue affected my own JOSS submission about a year ago, which I've now fixed too. 🙃

@ttricco
Copy link

ttricco commented Jun 14, 2023

I noticed that issue last night too when I was fixing the author names. The licence should be correct now.

@warrickball
Copy link

@editorialbot generate pdf

@editorialbot
Copy link
Collaborator Author

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

@warrickball
Copy link

@editorialbot recommend-accept

@editorialbot
Copy link
Collaborator Author

Attempting dry run of processing paper acceptance...

@editorialbot
Copy link
Collaborator Author

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

OK DOIs

- 10.1086/112164 is OK
- 10.1093/mnras/181.3.375 is OK
- 10.1088/0034-4885/68/8/R01 is OK
- 10.1016/j.jcp.2010.12.011 is OK
- 10.1017/pasa.2018.25 is OK
- 10.1093/mnras/stx1643 is OK
- 10.1071/AS07022 is OK
- 10.1088/0067-0049/192/1/9 is OK
- 10.1201/b12985 is OK
- 10.21105/joss.02430 is OK
- 10.21105/joss.01884 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1016/j.jcp.2017.10.024 is OK
- 10.21105/joss.03021 is OK
- 10.1145/2833157.2833162 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@editorialbot
Copy link
Collaborator Author

👋 @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#4311, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Jun 14, 2023
@arfon
Copy link
Member

arfon commented Jun 21, 2023

@editorialbot accept

@editorialbot
Copy link
Collaborator Author

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

@editorialbot
Copy link
Collaborator Author

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: Harris
  given-names: Andrew
- family-names: Tricco
  given-names: Terrence S.
  orcid: "https://orcid.org/0000-0002-6238-9096"
contact:
- family-names: Tricco
  given-names: Terrence S.
  orcid: "https://orcid.org/0000-0002-6238-9096"
doi: 10.5281/zenodo.8034448
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Harris
    given-names: Andrew
  - family-names: Tricco
    given-names: Terrence S.
    orcid: "https://orcid.org/0000-0002-6238-9096"
  date-published: 2023-06-21
  doi: 10.21105/joss.05263
  issn: 2475-9066
  issue: 86
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5263
  title: "Sarracen: a Python package for analysis and visualization of
    smoothed particle hydrodynamics data"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05263"
  volume: 8
title: "Sarracen: a Python package for analysis and visualization of
  smoothed particle hydrodynamics data"

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
Copy link
Collaborator Author

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

@editorialbot
Copy link
Collaborator Author

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

@editorialbot
Copy link
Collaborator Author

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.05263 joss-papers#4332
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05263
  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...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Jun 21, 2023
@arfon
Copy link
Member

arfon commented Jun 21, 2023

@hlim88, @JBorrow – many thanks for your reviews here and to @warrickball 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 ✨

@ttricco – your paper is now accepted and published in JOSS ⚡🚀💥

@arfon arfon closed this as completed Jun 21, 2023
@editorialbot
Copy link
Collaborator Author

🎉🎉🎉 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.05263/status.svg)](https://doi.org/10.21105/joss.05263)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05263">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05263/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05263/status.svg
   :target: https://doi.org/10.21105/joss.05263

This is how it will look in your documentation:

DOI

We need your help!

The 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:

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
accepted published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review Track: 1 (AASS) Astronomy, Astrophysics, and Space Sciences
Projects
None yet
Development

No branches or pull requests

6 participants