[REVIEW]: NemesisPy: A Python package for simulating and retrieving exoplanetary spectra

editorialbot commented 2 months ago

Submitting author: !--author-handle-->@Jingxuan97@JBorrow<!--end-editor-- Reviewers: @shubhagrawal30, @ben-cassese Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/7a225a07b646d233464e0b3a7dd06e98/status.svg)](https://joss.theoj.org/papers/7a225a07b646d233464e0b3a7dd06e98)

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

@shubhagrawal30 & @ben-cassese, 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 @JBorrow 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 @ben-cassese

📝 Checklist for @shubhagrawal30

editorialbot commented 2 months ago

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editorialbot commented 2 months ago

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

OK DOIs

- 10.1088/0004-637X/786/2/154 is OK
- 10.1093/mnras/staa548 is OK
- 10.1093/mnras/staa2219 is OK
- 10.1073/pnas.1304208111 is OK
- 10.3847/1538-4357/aca614 is OK
- 10.1111/j.1365-2966.2007.12353.x is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1093/mnras/staa238 is OK
- 10.1016/j.jqsrt.2007.11.006 is OK
- 10.1029/2023JE007904 is OK
- 10.3847/1538-3881/aad564 is OK
- 10.1029/90JD01945 is OK
- 10.1145/2833157.2833162 is OK
- 10.1111/j.1365-2966.2011.20013.x is OK
- 10.1088/0004-637X/775/2/137 is OK
- 10.3847/2515-5172/acc46a is OK
- 10.1093/mnras/stx1139 is OK
- 10.1088/0004-637X/707/1/24 is OK
- 10.3847/0004-637X/832/1/41 is OK
- 10.1038/nature11611 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1093/mnras/stad2555 is OK

MISSING DOIs

- 10.3847/1538-4357/834/1/50 may be a valid DOI for title: A CONSISTENT RETRIEVAL ANALYSIS OF 10 HOT JUPITERS...
- No DOI given, and none found for title: Simultaneous Retrieval of Phase-Resolved JWST/MIRI...

INVALID DOIs

- None

editorialbot commented 2 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.12 s (432.3 files/s, 85284.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          44            626           1849           7264
TeX                              1             24              0            397
reStructuredText                 4             46             33            109
Markdown                         1              9              0             38
DOS Batch                        1              8              1             26
make                             2              5              7             13
-------------------------------------------------------------------------------
SUM:                            53            718           1890           7847
-------------------------------------------------------------------------------

Commit count by author:

   167  Jingxuan Yang
     1  Jingxuan97
     1  yangj

editorialbot commented 2 months ago

Paper file info:

📄 Wordcount for paper.md is 689

✅ The paper includes a Statement of need section

editorialbot commented 2 months ago

License info:

✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)

editorialbot commented 2 months ago

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

JBorrow commented 2 months ago

Hi @Jingxuan97! Would you please be able to address the missing DOIs in the paper?

ben-cassese commented 2 months ago

Review checklist for @ben-cassese

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/Jingxuan97/nemesispy?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@Jingxuan97) 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?

ben-cassese commented 1 month ago

I've completed my initial review. Excellent package! This is a very useful tool for the community, thanks for open-sourcing your hard work. I've opened a handful of minor issues on the repository itself that shouldn't take long to fix. I've also opened one issue that is my only major blocker right now, which concerns the documentation of the package. More details are included here. Once the documentation is augmented/this issue is resolved, I'd be happy to recommend acceptance. Great work again!

ben-cassese commented 1 month ago

For breadcrumbs, the minor issues are here, here, and here.

Jingxuan97 commented 1 month ago

Hi Ben @ben-cassese, many thanks for the comments!

Jingxuan97 commented 1 month ago

Hi Josh @JBorrow, should I be expecting comments from another reviewer?

JBorrow commented 1 month ago

Yes, @shubhagrawal30 should be making comments at some point shortly; please let me know @shubhagrawal30 if you will need longer than a week or so!

shubhagrawal30 commented 1 month ago

Review checklist for @shubhagrawal30

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/Jingxuan97/nemesispy?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@Jingxuan97) 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?

shubhagrawal30 commented 1 month ago

@Jingxuan97 looks great, only a few minor issues to be flagged:

Issues:

Added a note about community guidelines to the previously added issue#3.
State of the field: issue#5
Functionality documentation: issue#6 (x3)

Some notes:

Performance: paper talks about just-in-time compilation to improve speeds for Bayesian retrieval ---> extensive use of numba jit, so looks good.
previous issues from other reviewer seem to have been taken care of.

P.S. @JBorrow: Generally speaking, I cannot claim to be a good judge of "Does the full list of paper authors seem appropriate and complete?" in Contribution and authorship. Not sure of the expectations, but as an independent reviewer, I have no clue who has worked on this project. I have checked the box, but defer to others including editorial staff.

Jingxuan97 commented 1 month ago

Thank you @shubhagrawal30 https://github.com/shubhagrawal30 for your comments!

On Mon, Jul 8, 2024 at 3:19 PM Shubh Agrawal @.***> wrote:

Only Minor Issues:

Added a note about community guidelines to the previously added issue#3 https://github.com/Jingxuan97/nemesispy/issues/3.

State of the field: issue#5 https://github.com/Jingxuan97/nemesispy/issues/5

Functionality documentation: issue#6 https://github.com/Jingxuan97/nemesispy/issues/6 (x3)

Some notes:

Performance: paper talks about just-in-time compilation to improve speeds for Bayesian retrieval ---> extensive use of numba jit, so looks good.

previous issues from other reviewer seem to have been taken care of.

P.S. @JBorrow https://github.com/JBorrow: Generally speaking, I cannot claim to be a good judge of "Does the full list of paper authors seem appropriate and complete?" in Contribution and authorship. Not sure of the expectations, but as an independent reviewer, I have no clue who has worked on this project. I have checked the box, but defer to others including editorial staff.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6874#issuecomment-2214210019, or unsubscribe https://github.com/notifications/unsubscribe-auth/APJTTQVOUGJ65YHKWQKFVV3ZLKNXNAVCNFSM6AAAAABJEMSEJ6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJUGIYTAMBRHE . You are receiving this because you were mentioned.Message ID: @.***>

Jingxuan97 commented 1 month ago

Hi @shubhagrawal30 and @ben-cassese, I have addressed your comments. Please see the comments under the GitHub issue trackers for detail. Also updating @JBorrow. Thank you kindly for all your efforts!

shubhagrawal30 commented 1 month ago

Very minor additional note on https://github.com/Jingxuan97/nemesispy/issues/6, everything else looks good to go!

ben-cassese commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

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

ben-cassese commented 1 month ago

@Jingxuan97 has addressed all of my concerns!

JBorrow commented 1 month ago

Great! Thank you both for your insightful reviews.

@shubhagrawal30, regarding your question - on smaller projects like this that's less of a concern. When we have, for instance, 20 or so authors, we like to make sure that they all actually contributed to the project.

@shubhagrawal30 please let me know if there is anything outstanding on your end or not.

JBorrow commented 2 weeks ago

Hi @shubhagrawal30 we're just waiting on your final confirmation (a completed checklist) and we can move this paper along. Thanks!

shubhagrawal30 commented 1 week ago

Hi, I am confirming that all issues have been addressed. Thanks!

JBorrow commented 1 week ago

Fantastic, thank you! @Jingxuan97, the next steps are as follows:

I will review the paper to make sure everything is ok. You can expect an automated message to come through letting us know if any DOIs are broken.
You should make a new release of the software and post a source deposit to Zenodo or Figshare.

See here: https://joss.readthedocs.io/en/latest/submitting.html#review-process.

JBorrow commented 1 week ago

@editorialbot generate pdf

JBorrow commented 1 week ago

@editorialbot check references

editorialbot commented 1 week ago

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

OK DOIs

- 10.1088/0004-637X/786/2/154 is OK
- 10.1093/mnras/staa548 is OK
- 10.3847/1538-4357/834/1/50 is OK
- 10.1093/mnras/staa2219 is OK
- 10.1073/pnas.1304208111 is OK
- 10.3847/1538-4357/aca614 is OK
- 10.1111/j.1365-2966.2007.12353.x is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1093/mnras/staa238 is OK
- 10.1016/j.jqsrt.2007.11.006 is OK
- 10.1029/2023JE007904 is OK
- 10.3847/1538-3881/aad564 is OK
- 10.1029/90JD01945 is OK
- 10.1145/2833157.2833162 is OK
- 10.1111/j.1365-2966.2011.20013.x is OK
- 10.1088/0004-637X/775/2/137 is OK
- 10.3847/2515-5172/acc46a is OK
- 10.1093/mnras/stx1139 is OK
- 10.1088/0004-637X/707/1/24 is OK
- 10.3847/0004-637X/832/1/41 is OK
- 10.1038/nature11611 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1093/mnras/stae1427 is OK
- 10.1093/mnras/stad2555 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 week ago

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

JBorrow commented 4 days ago

Hi @Jingxuan97 a reminder that we are awaiting a Zenodo deposit of the final version of the software with the following criteria:

archive names (including order) and title in archive matches those specified in the paper
archive uses the same license as the repo and is OSI approved as open source

We can then proceed to publication with some minor final checks.

openjournals / joss-reviews