[PRE 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
Managing EiC: Kristen Thyng

Status

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.02 s (1223.3 files/s, 122553.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          10            322            268            991
Markdown                         3            124              0            197
TeX                              1             19              0            154
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            604            373           1728
-------------------------------------------------------------------------------

Commit count by author:

    59	daniloceano
    18	Danilo Couto de Souza

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1063

✅ 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]

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

✅ OK DOIs

- None

🟡 SKIP DOIs

- No DOI given, and none found for title: Life cycle of cyclones and the polar front theory ...
- No DOI given, and none found for title: SciPy 1.0: fundamental algorithms for scientific c...

❌ MISSING DOIs

- 10.1007/978-1-944970-33-8_10 may be a valid DOI for title: Fronts, jet streams and the tropopause
- 10.1175/1520-0493(1993)121<2153:tlcoae>2.0.co;2 may be a valid DOI for title: The life cycle of an extratropical marine cyclone....
- 10.1175/bams-d-16-0261.1 may be a valid DOI for title: When during their life cycle are extratropical cyc...
- 10.1175/mwr3420.1 may be a valid DOI for title: Climatology of cyclone size characteristics and th...
- 10.1175/2008mwr2491.1 may be a valid DOI for title: The spatial distribution and evolution characteris...
- 10.1175/jas-d-13-0267.1 may be a valid DOI for title: The vorticity budgets of North Atlantic winter ext...
- 10.1029/2018gl078977 may be a valid DOI for title: Extratropical cyclone precipitation life cycles: A...
- 10.1029/2018gl078977 may be a valid DOI for title: Extratropical cyclone precipitation life cycles: A...
- 10.1175/jcli-d-16-0697.1 may be a valid DOI for title: Changes in winter North Atlantic extratropical cyc...
- 10.1002/joc.8539 may be a valid DOI for title: New perspectives on South Atlantic storm track thr...
- 10.1007/s00382-019-04778-1 may be a valid DOI for title: The properties and genesis environments of South A...
- 10.21203/rs.3.rs-995499/v1 may be a valid DOI for title: Impact of extratropical cyclone intensity and spee...
- 10.1029/2022ea002482 may be a valid DOI for title: Synoptic Climatology of Subtropical Cyclone Impact...
- 10.3354/cr01651 may be a valid DOI for title: Ocean-Land Atmosphere Model (OLAM) performance for...
- 10.1007/s11069-024-06621-1 may be a valid DOI for title: Extreme rainfall and landslides as a response to h...

❌ INVALID DOIs

- None

[editorialbot]

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

[editorialbot]

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[kthyng]

Welcome back @daniloceano and thanks for your submission! I am looking for some specific items to make sure your submission fits our requirements at a high level (not at the more detailed review level) before moving on to finding an editor or putting this on our waitlist if no relevant editors are available. I'll comment over time as I have a chance to go through them:

• OSI-approved license
• Installation instructions
• Documentation exists at all
• Tests of some sort
• Check paper (make sure compiles, read through, check for length 250-1000 words)
• Substantial scholarly effort
• Clear research application

In the meantime, please take a look at the comments above ⬆️ from the editorialbot to address any DOI, license, or paper issues if you're able (there may not be any), or suggest reviewers. For reviewers, please suggest 5 reviewers from the database listed above or your own (non-conflicted) extended network. Their github handles are most useful to receive but please don't use "@" to reference them since it will prematurely ping them.

[daniloceano]

Hello @kthyng,

Regarding the list of MISSING DOIs, I am a bit confused as the DOIs were provided and direct to the correct papers. Could you please clarify what needs to be done in this case?

As for the reviewers, I would like to suggest the following:

Mattia Almansi
koldunovn
Harald von Waldow
Einara Zahn
amylu00

Best regards,

Danilo

[kthyng]

@daniloceano The note about DOIs is requesting they be present in your .bib file so they come through the references list. I don't see any DOIs in there: https://github.com/daniloceano/CycloPhaser/blob/joss-submission/paper/paper.bib.

[kthyng]

@daniloceano comments:

• I see you have docs that say notes about your software. Do you show what it does somewhere? For example, you process vorticity data: https://cyclophaser.readthedocs.io/en/latest/usage.html#example-processing-vorticity-data-from-era5 but it's hard to understand what exactly your software does without some pictures to support it. Would you consider adding this?
• You have two summaries in your paper
• the in line references have parentheses
• Can the package be used in the northern hemisphere now or just in theory?

[daniloceano]

@kthyng

Thank you for the feedback.

• I have updated the documentation to provide more clarity on what the software does. There is now an Overview section explaining the main purpose of CycloPhaser and a concise description of how it detects cyclone life cycle phases. Additionally, I have added a figure illustrating the CycloPhaser methodology, which visually supports the process of detecting the life cycle stages of cyclones, offering a clearer understanding of the software's capabilities.
• I have deleted the extra summary (oops!)
• I have fixed the inline references and addressed the missing DOIs in the .bib file.
• Regarding Northern Hemisphere support: Yes, CycloPhaser can be used for the Northern Hemisphere as long as the original vorticity series is multiplied by -1 to account for the hemisphere difference in the cyclonic vorticity sign.

[daniloceano]

A quick update: a have also included the information regarding the northern hemisphere on the documentation overview.

[kthyng]

@daniloceano The rest of the docs still need to be updated to say that the software works in the northern hemisphere — they seem to indicate that it doesn't.

[kthyng]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

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[kthyng]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 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
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- 10.1029/2022ea002482 is OK
- 10.3354/cr01651 is OK
- 10.1007/s11069-024-06621-1 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- https://doi.org/10.1175/1520-0493(1922)50<468:JBAHSO>2.0.CO;2 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1038/s41592-019-0686-2 is INVALID because of 'https://doi.org/' prefix

[daniloceano]

@daniloceano The rest of the docs still need to be updated to say that the software works in the northern hemisphere — they seem to indicate that it doesn't.

Thank you for the feedback! I have now updated the documentation to clarify that the software works for both the Southern and Northern Hemispheres.

Additionally, I've also made further improvements to the documentation to ensure clarity and ease of use, and also corrected the wrong DOIs.

I hope the updates address your concerns.

[kthyng]

@editorialbot check references

[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

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[kthyng]

@observingClouds Can you edit this submission?

[kthyng]

@editorialbot invite @observingClouds as editor

[editorialbot]

Invitation to edit this submission sent!

[observingClouds]

@kthyng, happy to take over this submission!

[observingClouds]

@editorialbot assign me as editor

[editorialbot]

Assigned! @observingClouds is now the editor

[observingClouds]

Hi again @daniloceano!
I'll take over from here again and let you know once I have found reviewers and we start the interactive review process.

[observingClouds]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

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[observingClouds]

Hi @daniloceano,
While I am searching for reviewers, could you please:

• check the formatting of the references @bjerknes1922life, @shapiro1990fronts, and @neiman1993life in l. 26, l. 40, l. 66, Fig 1 caption
• add the missing reference in l. 34
• ensure that the references keep their capital letters in the title, {{}} can be used to do this in the references file, e.g. it should be The Vorticity Budgets of North Atlantic Winter Extratropical Cyclone Life Cycles in MERRA Reanalysis and not The vorticity budgets of north atlantic winter extratropical cyclone life cycles in MERRA reanalysis

Thank you!

[daniloceano]

Hi @observingClouds,

Regarding the references, I initially followed the journal guidelines using @citation for direct citations. Since it wasn’t working as expected, I applied a workaround: "Bjerknes et al. (Bjerknes and Solberg 1922), Shapiro and Keyser (Shapiro and Keyser 1990), and Neiman et al. (Neiman and Shapiro 1993)". Would you suggest any alternative, or does this seem like the best approach?

I’ve also addressed the missing references and capitalization issues—everything should be correct now.

Thank you!

[observingClouds]

Hi @daniloceano,
Thanks for your quick response.

Regarding the capitalization of your references, I see now at closer inspection of your paper.bib that the titles are also not capitalized in there. Since that is the source we read the title from, I ask you to adjust the titles their to the version used of the journal. Compare for example your title entry for https://doi.org/10.1175/JAS-D-13-0267.1 with the one on the journals webpage.

In text citations should be created with @author:2001 and those in parenthesis with [@author:2001]. Please note that the ` are only here for better formatting and should not be used in the paper.md. I think that was the issue why it didn't work for you beforehand. Please adjust accordingly.

Thanks!

[daniloceano]

Hi @observingClouds,

Thank you for the clarification. I’ve now followed your suggestion for the in-text citations and adjusted them using the correct format. I’ve also reviewed all the capitalizations in the references and ensured they match the journal’s version, as per your guidance.

Thanks again for your support!

[observingClouds]

@editorialbot generate pdf

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

[editorialbot]

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[observingClouds]

@editorialbot add @freemansw1 as reviewer

[editorialbot]

@freemansw1 added to the reviewers list!

[observingClouds]

@editorialbot add @stella-bourdin as reviewer

[editorialbot]

@stella-bourdin added to the reviewers list!

[observingClouds]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #7363.