[REVIEW]: CycloPhaser: A Python Package for Detecting Extratropical Cyclone Life Cycles

[editorialbot]

Submitting author: @daniloceano (Danilo Couto de Souza)
Repository: https://github.com/daniloceano/CycloPhaser
Branch with paper.md (empty if default branch): joss-submission
Version: 1.8.1
Editor: @observingClouds
Reviewers: @freemansw1, @stella-bourdin
Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/fc6ccda843aaedbf2d813473b7a561e0/status.svg)](https://joss.theoj.org/papers/fc6ccda843aaedbf2d813473b7a561e0)

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

@freemansw1 & @stella-bourdin, 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 @observingClouds 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 @freemansw1

📝 Checklist for @stella-bourdin

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.02 s (1233.6 files/s, 124131.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          10            322            268            991
Markdown                         3            121              0            195
TeX                              1             19              0            171
reStructuredText                 7             95             84            143
YAML                             3             32             13            142
CSV                              1              0              0             66
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            27            601            373           1743
-------------------------------------------------------------------------------

Commit count by author:

    67	daniloceano
    18	Danilo Couto de Souza

[editorialbot]

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

✅ OK DOIs

- 10.1175/1520-0493(1922)50<468:JBAHSO>2.0.CO;2 is OK
- 10.1007/978-1-944970-33-8_10 is OK
- 10.1175/1520-0493(1993)121<2153:tlcoae>2.0.co;2 is OK
- 10.1175/bams-d-16-0261.1 is OK
- 10.1175/mwr3420.1 is OK
- 10.1175/2008mwr2491.1 is OK
- 10.1175/jas-d-13-0267.1 is OK
- 10.1029/2018gl078977 is OK
- 10.1175/jcli-d-16-0697.1 is OK
- 10.1002/joc.8539 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1007/s00382-019-04778-1 is OK
- 10.21203/rs.3.rs-995499/v1 is OK
- 10.1029/2022ea002482 is OK
- 10.3354/cr01651 is OK
- 10.1007/s11069-024-06621-1 is OK
- 10.1007/s00382-005-0065-9 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 921

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

[editorialbot]

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

[observingClouds]

👋🏼 @daniloceano @freemansw1 @stella-bourdin this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains 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#7363 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 reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@observingClouds ) if you have any questions/concerns.

[freemansw1]

Review checklist for @freemansw1

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/daniloceano/CycloPhaser?
• 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 (@daniloceano) 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?

[stella-bourdin]

Review checklist for @stella-bourdin

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/daniloceano/CycloPhaser?
• 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 (@daniloceano) 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?

[stella-bourdin]

Hi,
Thank you for your submission. I have gone through the paper and ran the documented test. Here are my comments on some points of the review checklists, besides functionality issues raised as issues on the repo itself (links above).

General checks

Authorship

Only the first author appear in the commits. Please make sure that authorship follows journal guidelines. I am aware these can include author that did not directly committed into the code, and that you are responsible for the choice of final author list, so this is just a reminder.

Documentation

Statement of need

Procedure overview page is great. I would suggest making a similar one for the statement of need (which I supposed can be a copy of the statement of need in the paper).

Example provided

Besides functionality issues, here are some more comments regarding the example:

• A brief introduction to what is done in this example would be appreciated. In particular, what is the data that is loaded. Help us understand what we are doing here.
• For the output figure, please precise what the different zeta variables correspond to
• In the legend, the residual is green like decay instead of grey.

API

• Must the series argument in determine_period be in a specific unit? In any case, I recommend specifying whether or not in the documentation of the function.

Paper

Summary, statement of need and state of the field

Very clear and well written

Features

I suggest adding a first paragraph about what are the input requirements to give context.
Current paragraph 1 lacks clarity, but it would be helped by adding a first paragraph as suggested above.
Current paragraph 2: I suggest citing the paper from the top of the paragraph. e.g. "Thresholds for phase detection were rigorously calibrated in Couto de Souza et al. (2024) using a representative set of cyclone tracks, ensuring accurate phase identification while filtering out noise."
Current paragraph 3: It is not clear whether the user can actually plug in an SLP or wind time series and it would work just as well, or whether it would require additional adaptations.

I will next go through a more thorough testing of the code functionalities, and test other data.
Stella

[daniloceano]

@stella-bourdin, thank you for your thorough review. Below, I will address your comments and the steps I have taken to address them:

---

Authorship

• Comment: Only the first author appears in the commits. Please make sure that authorship follows journal guidelines. I am aware that these can include authors that did not directly commit to the code, so this is just a reminder.

• Response: I appreciate the reminder. I was the only one working directly on the code, but the other researchers involved contributed significantly to the conceptualization of the algorithm, provided datasets, and collaborated with me in checking the outputs. Their contributions were essential for ensuring that the package produces realistic and useful results.

---

Documentation

Statement of Need

• Comment: The procedure overview page is great. I would suggest making a similar one for the statement of need (which can be a copy from the paper).

• Response: I have now added a Statement of Need section in the documentation, following the suggestion.

Example Provided

• Comment: A brief introduction to what is done in the example would be appreciated. In particular, explain what data is loaded and clarify what we are doing here.

• Response: A brief introduction explaining the dataset used and the purpose of the example has been added to the Usage section of the documentation.

• Comment: For the output figure, please clarify what the different zeta variables correspond to.

• Response: I simplified the output by removing the extra zeta variables in the figure for better clarity.

• Comment: In the legend, the residual phase is green like decay instead of grey.

• Response: The color for the residual phase has been updated to grey as originally intended.

---

I am currently working on the remaining issues you raised in the repository and will continue to address them one by one. Once all the adjustments are complete, I will notify you and provide the updated code and paper.

Thank you again for your invaluable feedback. I look forward to continuing to improve the paper and the package based on your suggestions.

Best regards,
Danilo