[REVIEW]: commensurability: a Python package for classifying astronomical orbits based on their toroid volume

editorialbot commented 3 months ago

Submitting author: !--author-handle-->@ilikecubesnstuff@dfm<!--end-editor-- Reviewers: @nstarman, @TomWagg Archive: Pending

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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

@nstarman & @TomWagg, 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 @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 ✨

Checklists

📝 Checklist for @nstarman

📝 Checklist for @TomWagg

editorialbot commented 3 months ago

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editorialbot commented 3 months ago

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

OK DOIs

- 10.1093/mnras/staa3202 is OK
- 10.21105/joss.00388 is OK
- 10.1093/mnras/sty2672 is OK
- 10.1088/0067-0049/216/2/29 is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.1145/235815.235821 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.3847/1538-4357/ace976 is OK
- 10.1109/MCSE.2007.55 is OK

MISSING DOIs

- No DOI given, and none found for title: SuperFreq: Numerical determination of fundamental ...
- No DOI given, and none found for title: Hierarchical Data Format, version 5

INVALID DOIs

- None

dfm commented 3 months ago

@nstarman, @TomWagg — This is the review thread for the paper. All of our correspondence will happen here from now on. Thanks again for agreeing to participate!

👉 Please read the "Reviewer instructions & questions" in the first comment above, and generate your checklists by commenting @editorialbot generate my checklist on this issue ASAP. 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. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#7009 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is 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 please try to make a start ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule. Please get your review started as soon as possible!

editorialbot commented 3 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1390.7 files/s, 149978.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          18            450            830           1646
Markdown                        16            390              0            906
YAML                             5             17             12            192
TeX                              1             11              0            160
TOML                             1              7              0             70
INI                              1              4              0             19
JavaScript                       1              1              0             15
CSS                              1              3              0             12
-------------------------------------------------------------------------------
SUM:                            44            883            842           3020
-------------------------------------------------------------------------------

Commit count by author:

    76  ilikecubesnstuff
     3  michael-petersen
     1  Subhadeep Sarkar

editorialbot commented 3 months ago

Paper file info:

📄 Wordcount for paper.md is 1230

✅ The paper includes a Statement of need section

editorialbot commented 3 months ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

editorialbot commented 3 months ago

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

nstarman commented 3 months ago

Review checklist for @nstarman

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/ilikecubesnstuff/commensurability?
[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 (@ilikecubesnstuff) 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.
[ ] 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?
[ ] 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?
[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).
[ ] 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?
[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)?
[ ] 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?

TomWagg commented 3 months ago

Review checklist for @TomWagg

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/ilikecubesnstuff/commensurability?
[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 (@ilikecubesnstuff) 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.
[ ] 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?
[ ] 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?
[ ] 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?
[ ] 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?

nstarman commented 2 months ago

Hi @ilikecubesnstuff! I would love to continue reviewing, but https://github.com/ilikecubesnstuff/commensurability/issues/18 is a blocker to exactly reproducing the results. If you could post a fix in that Issue thread, even before merging a full PR, that would be appreciated. Thanks!

ilikecubesnstuff commented 2 months ago

Hi @nstarman, thank you for letting me know! I will respond to the issue later today. However, I will be very busy over the next 2 weeks, so I cannot guarantee any pull requests until September at least.

If any further issues block your review progress, feel free to notify me and I will respond ASAP!

dfm commented 1 month ago

@ilikecubesnstuff — I wanted to check in to see how things are going with your work responding to the comments from @nstarman and @TomWagg. Let us know what the status is - thanks!

ilikecubesnstuff commented 1 month ago

Hi all, I got extremely busy moving countries over September. I can continue working on this codebase now. Thank you for checking in!

The last time I opened this, my Agama installation was causing issues with my examples and automated tests. I plan to update the code to use Agama's latest version. However, in the interest of time, I can temporarily deprecate Agama support and remake the relevant documentation/examples with one of the other galactic dynamics packages if that is preferable.

Thank you for the additional issues @TomWagg, I will look through them shortly.

ilikecubesnstuff commented 1 month ago

The last time I opened this, my Agama installation was causing issues with my examples and automated tests. I plan to update the code to use Agama's latest version. However, in the interest of time, I can temporarily deprecate Agama support and remake the relevant documentation/examples with one of the other galactic dynamics packages if that is preferable.

I have isolated the version of Agama with which my examples were written (commit hash 0c5993d). I can specify this commit hash in the README and relevant parts of the documentation - I'm not sure how else to work with Agama's versioning. 😅

ilikecubesnstuff commented 1 month ago

Addressing ilikecubesnstuff/commensurability#18, I have created a joss version of the docs hosted at https://commensurability.readthedocs.io/en/joss/.

This should contain any documentation changes in the joss branch (until it is merged into main).

dfm commented 1 week ago

@ilikecubesnstuff, @nstarman, @TomWagg — Hi all! I'm just stopping by to check in on the review. It looks like @ilikecubesnstuff has made some progress on responding to feedback so it would be great if everyone could check back in to see where everything stands at this point. Thanks everyone!!

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