[REVIEW]: orbitize! v3: Orbit-fitting for the High-contrast Imaging Community

editorialbot commented 1 month ago

Submitting author: !--author-handle-->@sblunt@ivastar<!--end-editor-- Reviewers: @Yiting206265, @DTCupcakes Archive: Pending

Status

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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

@Yiting206265 & @DTCupcakes, 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 @ivastar 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 @Yiting206265

📝 Checklist for @DTCupcakes

editorialbot commented 1 month ago

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editorialbot commented 1 month ago

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

OK DOIs

- 10.3847/1538-3881/ab6663 is OK
- 10.3847/1538-3881/acf5cc is OK
- 10.3847/1538-3881/ac042e is OK
- 10.3847/1538-3881/ab1d66 is OK
- 10.3847/1538-3881/ab76c6 is OK
- 10.3847/2515-5172/ac151d is OK
- 10.3847/2515-5172/acdc29 is OK
- 10.3847/2515-5172/ac61d8 is OK
- 10.1093/mnras/staa278 is OK
- 10.3847/1538-3881/ab5b92 is OK
- 10.3847/1538-3881/ad06b7 is OK
- 10.1088/1538-3873/128/968/102001 is OK
- 10.3847/1538-4365/abf93c is OK
- 10.1051/0004-6361/202141889 is OK
- 10.3847/1538-3881/ab5b11 is OK
- 10.5281/zenodo.8102085 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 month ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.62 s (188.4 files/s, 611796.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          48           2202           2959           6855
Jupyter Notebook                15              0         360443           1385
D                                4              0              0            595
reStructuredText                20            233            142            375
CSV                             13              0              0            346
TeX                              1             33              0            270
Markdown                         5             58              0            256
YAML                             4             16              7            104
C                                1             27             33             75
CUDA                             2             15             27             53
Cython                           1             11             22             32
DOS Batch                        1              8              1             27
make                             1              4              6             10
-------------------------------------------------------------------------------
SUM:                           116           2607         363640          10383
-------------------------------------------------------------------------------

Commit count by author:

   344  Sarah Blunt
   309  sblunt
   209  Henry Ngo
   159  Jason Wang
    87  Rob685
    44  isabelangelo
    27  tirthsurti
    24  vighnesh-nagpal
    23  Devin Cody
    16  devincody
    13  Jorge
    13  Rob De Rosa
    13  Sofia Covarrubias
    11  Mireya-A
     9  Malena Rice
     7  Roberto Tejada
     5  Adam J. R. W. Smith
     5  Lea Hirsch
     4  Rodrigo F
     3  jruffio
     2  Robert De Rosa
     2  Rodrigo
     2  Rodrigo Ferrer Chávez
     2  Ryan Rubenzahl
     1  Arya Das
     1  Hannah Gallamore
     1  Jason Wnag
     1  Logan Pearce
     1  Michael Poon
     1  Mireya Arora
     1  MissingBrainException
     1  Tomas Stolker
     1  Ubuntu
     1  Will Thompson
     1  malenarice

editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 1257

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

License info:

🟡 License found: Other (Check here for OSI approval)

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:

ivastar commented 1 month ago

@Yiting206265 & @DTCupcakes welcome to the review of orbitize!. See the instructions above on generating the review checklist. We'd like the first round of reviews completed by mid-June. Please don't hesitate to reach out to me if you have any questions.

sblunt commented 1 month ago

Thanks for reviewing everyone!! I just wanted to make you aware of something— I’m currently locked out of my pypi account, so the version of orbitize on pypi is not 3.0.0. I’ll update the pypi release as soon as I can regain access to my account!

Yiting206265 commented 1 month ago

Review checklist for @Yiting206265

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/sblunt/orbitize?
[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 (@sblunt) 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?

DTCupcakes commented 1 month ago

Review checklist for @DTCupcakes

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/sblunt/orbitize?
[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 (@sblunt) 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?
[ ] 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?

DTCupcakes commented 1 month ago

I've noticed that there's some authors in the author list of the original AJ paper that are missing from this paper. Specifically

Isabel Angelo
Henry Ngo
James Graham
Logan Pearce
Malena Rice

Is there a reason why this is the case?

DTCupcakes commented 1 month ago

When running the first cell in the HGCA tutorial I get an "InconsistentTableError". Is this an issue with orbitize? I'm not familiar with the Hipparcos-Gaia backend.

sblunt commented 3 weeks ago

Hey @DTCupcakes! Thanks for reviewing for us. Two things:

This JOSS paper is meant to cover additions to the code between v1 and v3, while the original AJ paper covered additions to the code up to v1. So, the folks who you listed contributed to v1 but did not contribute subsequently.
Do you have v3 installed? I'm having this super annoying issue where I'm locked out of my pypi account and can't make v3 pip installable, but if you follow the most up-to-date installation instructions, you should be able to install v3. If you do have v3 installed and you're still getting the error, let me know!

ivastar commented 3 weeks ago

@Yiting206265 checking the status of your review. Are you satisfied with the submission as it is? Please let us know if you have any recommendations for improvements or you are happy to recommend for publication as submitted.

Yiting206265 commented 3 weeks ago

@Yiting206265 checking the status of your review. Are you satisfied with the submission as it is? Please let us know if you have any recommendations for improvements or you are happy to recommend for publication as submitted.

I have reviewed the source code and the paper carefully and found no functional or contextual issues. I am satisfied with the submission as it stands. As long as the PyPI version issue is fixed, I am happy to recommend publication as submitted !

DTCupcakes commented 3 weeks ago

@sblunt I checked the version of orbitize in the Jupyter notebook and it is v3. I've simply copied and pasted the code from the tutorials into the notebook cells, so is it possible I could have missed something?

sblunt commented 2 weeks ago

Hm, ok! I'm not sure. I can't reproduce the error on my machine. Two follow up questions:

1) Did you follow the instructions to obtain the data (this section of the tutorial), and did you run into any issues with that?

2) Can you send the full error?

sblunt commented 2 weeks ago

Also-- are you getting errors with any other tutorials?

ivastar commented 1 week ago

I think @DTCupcakes is travelling, I hope they respond when they return.

openjournals / joss-reviews