[REVIEW]: PyStarshade: simulating high-contrast imaging of exoplanets with starshades

[editorialbot]

Submitting author: @xiaziyna (Jamila Taaki)
Repository: https://github.com/xiaziyna/PyStarshade
Branch with paper.md (empty if default branch):
Version: 0.1.8
Editor: @ivastar
Reviewers: @Jashcraf, @ivalaginja, @ecmatthews
Archive: Pending

Status

Status badge code:

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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

@Jashcraf & @ivalaginja, 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 @ivalaginja

📝 Checklist for @Jashcraf

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.98  T=0.05 s (747.1 files/s, 94372.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          25            527           1304           1752
Text                             2            122              0            559
TeX                              1             11              0            105
Markdown                         2             42              0             91
reStructuredText                 4             60             67             46
YAML                             2              6             24             29
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            38            780           1403           2617
-------------------------------------------------------------------------------

Commit count by author:

   169	Jamila Taaki
    70	xiaziyna
    13	ielo

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 598

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

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

✅ OK DOIs

- 10.1117/12.2314407 is OK
- 10.3847/1538-3881/ac45f5 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: SISTER: Starshade Imaging Simulation Toolkit for E...
- No DOI given, and none found for title: Efficient high-order accurate Fresnel diffraction ...
- No DOI given, and none found for title: fresnaq: FRESNel Areal Quadrature
- No DOI given, and none found for title: Introduction to Fourier optics
- No DOI given, and none found for title: Advances in edge diffraction algorithms
- No DOI given, and none found for title: Diffraq: Diffraction with Areal Quadrature
- No DOI given, and none found for title: ExoVista
- No DOI given, and none found for title: EXOSIMS: Exoplanet Open-Source Imaging Mission Sim...

❌ MISSING DOIs

- 10.1364/oe.20.015196 may be a valid DOI for title: Boundary diffraction wave integrals for diffractio...

❌ INVALID DOIs

- None

[editorialbot]

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

[ivastar]

@Jashcraf, @ivalaginja thank you for your willingness to review this submission! Instructions are above. I believe you both have experience reviewing for JOSS before so you know how this works. But please don't hesitate to reach out to me if you have any questions or concerns. We are looking for a first round of reviews if ~3 weeks, so let's say April 10th for this submission. Let me know if you would need more time.

[ivalaginja]

Review checklist for @ivalaginja

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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/xiaziyna/PyStarshade?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@xiaziyna) 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?

[Jashcraf]

Review checklist for @Jashcraf

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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/xiaziyna/PyStarshade?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@xiaziyna) 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?

[ivastar]

@editorialbot add @ecmatthews as reviewer

[editorialbot]

@ecmatthews added to the reviewers list!

[ivastar]

Also welcoming @ecmatthews to the review!

[xiaziyna]

Thank you reviewers!

[ivalaginja]

Just a heads up that I will be submitting my review in the week leading up to 10 April due to other commitments, but I do not see myself needing extra time.

[ivalaginja]

Hi @xiaziyna, thank you for a very nice package! There are not many Python-based packages out there that do optical propagations for starshades, so I see this as a highly valuable contribution to the field!

In the first part of my review, I have focused on the installation process, data management and documentation, for which I have opened the following issues on your repo:

• Installation cleanup xiaziyna/PyStarshade#8
• More information on example scripts xiaziyna/PyStarshade#9
• Remove documentation redundancy xiaziyna/PyStarshade#10

Considering that some of my requested changes could potentially be invasive to your code, I wanted to make sure to post these first. I will continue my review on the other points, but please don't hesitate to reach out if you need any clarifications or further info!

[xiaziyna]

@ivalaginja @Jashcraf thank you both for your careful reviewing / constructive feedback. I will work through these over the next couple of days. I appreciate the time spent on this!

[ivastar]

@xiaziyna pining this thread. Do you have an idea when you might be able to respond to the comments from the reviewers?

[xiaziyna]

@ivastar Unless I am missing some additional comments (?) I believe I have responded to all the issues (Issue 8 requires a second response and some changes which I can address today) - I believe the reviewers are still working on verifying the updated install works. Sorry for not making this clear!

[xiaziyna]

@ivastar I have addressed Issue 8 - thanks!

[ivalaginja]

Hi @xiaziyna, thanks for addressing all my previous issues! I am now continuing to move through the checklist. In doing so, I have identified a couple more things to fix, which I review in the issues below. Sorry that this is so iterative, but I believe it might be easier if I send you what I have already to give you time to have a look while I continue my review.

As always, if something is unclear or doesn't seem to make sense, please do reach out!

• Suggestion: Add .gitignore file to repo xiaziyna/PyStarshade#11
• pytest needed as dependency/requirement xiaziyna/PyStarshade#12
• One of the Bluestein FFT tests fails when run locally xiaziyna/PyStarshade#13
• Requested documentation cleanup xiaziyna/PyStarshade#14
• Requested example notebook cleanup xiaziyna/PyStarshade#15

[ivastar]

@Jashcraf can you continue with the review as well now that the initial issues have been addressed?

[Jashcraf]

Certainly, i'll aim to have it done by the end of the week, thank you!