[REVIEW]: popkinmocks: mock IFU datacubes for modelling stellar populations and kinematics

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@prashjet@plaplant<!--end-editor-- Reviewers: @apoudel2014, @Jammy2211 Archive: 10.5281/zenodo.7890628

Status

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Markdown: [![status](https://joss.theoj.org/papers/8ac74475656358c47ac2569953c09d6d/status.svg)](https://joss.theoj.org/papers/8ac74475656358c47ac2569953c09d6d)

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

@apoudel2014 & @Jammy2211, 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 @plaplant 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 @apoudel2014

📝 Checklist for @Jammy2211

editorialbot commented 1 year ago

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editorialbot commented 1 year ago

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

OK DOIs

- 10.1137/22M1503002 is OK
- 10.1017/pasa.2020.8 is OK
- 10.1093/mnras/stac1532 is OK
- 10.1093/mnras/stac1531 is OK
- 10.1093/mnras/stz1154 is OK
- 10.1093/mnras/staa1584 is OK
- 10.1093/mnras/stab229 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.28 s (142.2 files/s, 21916.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          17            717           1353           2365
Markdown                         9            339              0            904
YAML                             6              6             17            122
TeX                              1              7              0            107
reStructuredText                 5             58             60             56
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            40           1139           1438           3589
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 654

editorialbot commented 1 year ago

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

plaplant commented 1 year ago

@apoudel2014 @Jammy2211 thanks again for agreeing to review this submission! When you are ready to begin your review, please comment @editorialbot generate my checklist on this issue. As you work your way through the checklist, you may create issues on the GitHub repo for the software being reviewed. Please see the JOSS reviewer guidelines for more information. Let me know if you have any questions!

apoudel2014 commented 1 year ago

Review checklist for @apoudel2014

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/prashjet/popkinmocks?
[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 (@prashjet) 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
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[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?

Jammy2211 commented 1 year ago

Review checklist for @Jammy2211

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/prashjet/popkinmocks?
[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 (@prashjet) 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
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[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?

Jammy2211 commented 1 year ago

All done, I've put up 3 issues on the GitHub which should be straight forward enough to address.

Overall, popkinmocks is an awesome little package with clear docs, easy-to-follow examples and it serves a need and purpose not currently filled elsewhere in the literature.

You may hear from me one day about simulating IFU observations of strong lenses with the tool!

plaplant commented 1 year ago

@Jammy2211 thanks very much for your review!

@prashjet please begin addressing the issues relevant to the review (https://github.com/prashjet/popkinmocks/issues/75, https://github.com/prashjet/popkinmocks/issues/76, https://github.com/prashjet/popkinmocks/issues/77). You can reply to this thread when you feel you've addressed them.

plaplant commented 1 year ago

@apoudel2014 just checking in on how the review is going. As you make your way through the checklist, please update your comment to indicate whether the software addresses the different points or not. Let me know if you have any questions!

apoudel2014 commented 1 year ago

I am working on it. Hopefully I will have something by next week. Will let you know if I have any questions.

Thanks, Amit

On Thu, Apr 6, 2023 at 9:01 AM Paul La Plante @.***> wrote:

@apoudel2014 https://github.com/apoudel2014 just checking in on how the review is going. As you make your way through the checklist, please update your comment to indicate whether the software addresses the different points or not. Let me know if you have any questions!

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/5225#issuecomment-1499296197, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIT5V6DL5P4BNXTLJNDB7HTW73SHNANCNFSM6AAAAAAVR3QMUM . You are receiving this because you were mentioned.Message ID: @.***>

-- Best Regards, Amit Poudel

apoudel2014 commented 1 year ago

I've completed my review and submitted 1 issue on GitHub, which is a minor comment. Regarding the paper, the Popkinmocks package is quite useful, and the paper does an excellent job of presenting the information in a clear and concise manner.

plaplant commented 1 year ago

@apoudel2014 thanks very much for your review!

@prashjet please address the issue relevant to the review (https://github.com/prashjet/popkinmocks/issues/78). You can reply to this thread when you feel it's been addressed.

prashjet commented 1 year ago

Hi all - many thanks for the positive reviews and useful suggestions. The latest merge to the main branch addresses all your comments (except the pypi suggestion, which I will come back to in the future).

@Jammy2211

You may hear from me one day about simulating IFU observations of strong lenses with the tool!

I look forward to it!

prashjet commented 1 year ago

FYI - had some problems with readthedocs updating to the latest release, but sorted now - the latest stable docs are the corrected version

plaplant commented 1 year ago

@prashjet thanks for addressing the reviewers' comments!

@Jammy2211 when you get a chance, please check to make sure all of your initial concerns have been addressed, and update your checklist accordingly. Thanks again for reviewing!

Jammy2211 commented 1 year ago

Done

plaplant commented 1 year ago

@Jammy2211 thanks very much for your review!

@prashjet both reviewers have recommended acceptance of the submission, so we can move forward with the final acceptance checks. If the software has changed in the course of the review, please make a new tagged release of the repository. After that, please archive it (on Zenodo, figshare, or some other long-term hosting platform). Once those are done, please post the version number and DOI of the archive in this thread. Let me know if you have any questions!

plaplant commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

plaplant commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1137/22M1503002 is OK
- 10.1017/pasa.2020.8 is OK
- 10.1093/mnras/stac1532 is OK
- 10.1093/mnras/stac1531 is OK
- 10.1093/mnras/stz1154 is OK
- 10.1093/mnras/staa1584 is OK
- 10.1093/mnras/stab229 is OK
- 10.1111/j.1365-2966.2007.11752.x is OK
- 10.1111/j.1365-2966.2011.18496.x is OK
- 10.1088/2041-8205/764/1/L1 is OK
- 10.1038/s41550-017-0348-1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

prashjet commented 1 year ago

Once those are done, please post the version number and DOI of the archive in this thread. Let me know if you have any questions!

popkinmocks (1.0.1) https://doi.org/10.5281/zenodo.7890628

Thanks!

plaplant commented 1 year ago

@prashjet thank you!

plaplant commented 1 year ago

@editorialbot set 10.5281/zenodo.7890628 as archive

editorialbot commented 1 year ago

Done! archive is now 10.5281/zenodo.7890628

plaplant commented 1 year ago

@editorialbot set v1.0.1 as version

editorialbot commented 1 year ago

Done! version is now v1.0.1

plaplant commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.1137/22M1503002 is OK
- 10.1017/pasa.2020.8 is OK
- 10.1093/mnras/stac1532 is OK
- 10.1093/mnras/stac1531 is OK
- 10.1093/mnras/stz1154 is OK
- 10.1093/mnras/staa1584 is OK
- 10.1093/mnras/stab229 is OK
- 10.1111/j.1365-2966.2007.11752.x is OK
- 10.1111/j.1365-2966.2011.18496.x is OK
- 10.1088/2041-8205/764/1/L1 is OK
- 10.1038/s41550-017-0348-1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:wave: @openjournals/aass-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/4195, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

dfm commented 1 year ago

@prashjet — I've opened a tiny PR to your paper fixing some typographical issues in the bibliography. One last thing I'll need from you: Can you update the Zenodo record metadata (there should be an "Edit" button in the top right corner of this page when you're logged in) so that the title is "popkinmocks: mock IFU datacubes for modelling stellar populations and kinematics" to match the paper? Then I'm happy to continue with publication!

prashjet commented 1 year ago

@dfm - thanks Dan, both just done.

Then I'm happy to continue with publication!

Sweet!

dfm commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

dfm commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.1137/22M1503002 is OK
- 10.1017/pasa.2020.8 is OK
- 10.1093/mnras/stac1532 is OK
- 10.1093/mnras/stac1531 is OK
- 10.1093/mnras/stz1154 is OK
- 10.1093/mnras/staa1584 is OK
- 10.1093/mnras/stab229 is OK
- 10.1111/j.1365-2966.2007.11752.x is OK
- 10.1111/j.1365-2966.2011.18496.x is OK
- 10.1088/2041-8205/764/1/L1 is OK
- 10.1038/s41550-017-0348-1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:wave: @openjournals/aass-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/4201, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

dfm commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

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editorialbot commented 1 year ago

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editorialbot commented 1 year ago

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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/4202
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05225
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

dfm commented 1 year ago

Many thanks to @apoudel2014 and @Jammy2211 for reviewing and to @plaplant for editing! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you!!

@prashjet — Your paper is now accepted and published in JOSS! :zap::rocket::boom:

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