[REVIEW]: New developments in PySDM and PySDM-examples v2: collisional breakup, immersion freezing, dry aerosol composition initialisation, and adaptive time-stepping

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@edejong-caltech@dhhagan<!--end-editor-- Reviewers: @douglowe, @emmasimp Archive: 10.5281/zenodo.7640495

Status

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Markdown: [![status](https://joss.theoj.org/papers/5110170dd97fe1ebf08227881f76bda9/status.svg)](https://joss.theoj.org/papers/5110170dd97fe1ebf08227881f76bda9)

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

@claresinger & @douglowe, 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 @dhhagan 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 @douglowe

📝 Checklist for @emmasimp

editorialbot commented 1 year ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.45 s (917.5 files/s, 63155.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         392           3425           2767          19755
Markdown                         3            185              0           1157
YAML                            11             54             16            387
TeX                              1             38              0            275
JSON                             1              0              0             92
TOML                             1              0              0              2
-------------------------------------------------------------------------------
SUM:                           409           3702           2783          21668
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 1913

editorialbot commented 1 year ago

Failed to discover a Statement of need section in paper

editorialbot commented 1 year ago

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

OK DOIs

- 10.1002/qj.441 is OK
- 10.1145/2833157.2833162 is OK
- 10.5194/npg-24-535-2017 is OK
- 10.5194/gmd-8-1677-2015 is OK
- 10.1175/1520-0469(1967)024<0688:CDGBC>2.0.CO;2 is OK
- 10.5194/acp-18-7313-2018 is OK
- 10.5194/gmd-10-1817-2017 is OK
- 10.21105/joss.00755 is OK
- 10.1029/2018MS001285 is OK
- 10.5194/gmd-13-5119-2020 is OK
- 10.5194/gmd-13-1335-2020 is OK
- 10.1002/2017MS000930 is OK
- 10.5194/gmd-11-3623-2018 is OK
- 10.1007/978-3-030-77964-1_2 is OK
- 10.1002/qj.1913 is OK
- 10.1029/2002JD002673 is OK
- 10.1007/s10546-020-00595-w is OK
- 10.1002/fld.1071 is OK
- 10.1029/2019MS001689 is OK
- 10.21105/joss.02807 is OK
- 10.1038/s41467-019-12982-0 is OK
- 10.1175/JAS3980 is OK
- 10.21105/joss.03219 is OK
- 10.1002/essoar.10510248.1 is OK
- 10.5194/acp-16-2083-2016 is OK
- 10.5194/gmd-13-4107-2020 is OK
- 10.1029/1999JD901161 is OK
- 10.1038/nature22806 is OK
- 10.1126/science.aad4889 is OK
- 10.5194/gmd-9-1455-2016 is OK
- 10.1175/1520-0450(1978)017<0320:ATDPIC>2.0.CO;2 is OK
- 10.1016/0307-904X(84)90088-X is OK
- 10.1017/CBO9781139165389 is OK
- 10.1039/c3fd00035d is OK

MISSING DOIs

- 10.21105/joss.03896 may be a valid DOI for title: PyMPDATA v1: Numba-accelerated implementation of MPDATA with examples in Python, Julia and Matlab

INVALID DOIs

- None

editorialbot commented 1 year ago

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

claresinger commented 1 year ago

@dhhagan Please remove me as a reviewer. I am an author on this paper.

douglowe commented 1 year ago

Review checklist for @douglowe

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/atmos-cloud-sim-uj/PySDM?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@edejong-caltech) 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?

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot remove @claresinger as reviewer

editorialbot commented 1 year ago

@claresinger removed from the reviewers list!

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot add @emmasimp as reviewer

editorialbot commented 1 year ago

@emmasimp added to the reviewers list!

Kevin-Mattheus-Moerman commented 1 year ago

@dhhagan can you check if the reviewers are now properly set? Let me know if you need any help

dhhagan commented 1 year ago

@emmasimp Can you generate your checklist by running "@editorialbot generate my checklist"? Thanks!

dhhagan commented 1 year ago

@dhhagan Please remove me as a reviewer. I am an author on this paper.

Sorry about that mistake!

emmasimp commented 1 year ago

Review checklist for @emmasimp

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/atmos-cloud-sim-uj/PySDM?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@edejong-caltech) 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?

douglowe commented 1 year ago

Apologies for the length of time it has taken for this review.

After looking over the code and paper, I'm happy to report that it looks to be in great shape to me. The paper is well written and describes the new functionality well, the API documentation is easy to find and useful, and the test coverage of the code seems good.

The one thing I would note is that there is not any discussion of the 'state of the field' in this paper. The version 1 paper does list other implementations of these routines, which are also noted in the README document for the code repository. But it would be useful here to have a short note on what extra (if any) open source packages have been added since v1, and if any other software tools have overlapping functionality specifically with the new features described in this paper.

emmasimp commented 1 year ago

Sorry for the delay in getting this review done!

Overall I think the paper and code are very well written. I found the code and documentation easy to understand and get up and running with the model. I wish more software was documented in a way that allowed me to install and run the model within a matter of minutes!

I agree with Doug that the only thing missing is a bit more detail in the paper of how the new features of PySDM v2 fit in to the wider picture of similar models available (or whether or not any exist).

douglowe commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

douglowe commented 1 year ago

Thanks for adding the state of the field section to the paper. It looks good to me now, I'm happy for the paper to be published.

emmasimp commented 1 year ago

I agree with Doug, happy for the paper to be published :)

slayoo commented 1 year ago

Thank you!

One question for the editors we have is how to technically handle the fact that the project has recently moved from github.com/atmos-cloud-sim-uj to github.com/open-atmos. There is a redirect, so the previous link does work, but it would be great to promote the new location on the JOSS website next to the paper. @dhhagan @Kevin-Mattheus-Moerman is there a way to change such piece of metadata? Thanks

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot set github.com/open-atmos as repository

editorialbot commented 1 year ago

Done! repository is now github.com/open-atmos

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:warning: An error happened when generating the pdf.

Kevin-Mattheus-Moerman commented 1 year ago

@slayoo like that ☝️. All should be good. Let us know if the branch should be changed.

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot set https://github.com/open-atmos as repository

editorialbot commented 1 year ago

Done! repository is now https://github.com/open-atmos

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot generate pdf

Kevin-Mattheus-Moerman commented 1 year ago

Looks like it couldn't find paper. Let @dhhagan know where it is found.

editorialbot commented 1 year ago

:warning: An error happened when generating the pdf.

slayoo commented 1 year ago

@editorialbot set https://github.com/open-atmos/PySDM as repository

editorialbot commented 1 year ago

I'm sorry @slayoo, I'm afraid I can't do that. That's something only editors are allowed to do.

claresinger commented 1 year ago

@Kevin-Mattheus-Moerman I think you maybe need to set https://github.com/open-atmos/PySDM as the repository (the whole path, not just the org)

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot set https://github.com/open-atmos/PySDM as repository

editorialbot commented 1 year ago

Done! repository is now https://github.com/open-atmos/PySDM

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

slayoo commented 1 year ago

@editorialbot generate pdf

slayoo commented 1 year ago

(changed my affiliation order from "5,3" to "3,5" + added two commas in the text)

editorialbot commented 1 year ago

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

claresinger commented 1 year ago

@dhhagan @Kevin-Mattheus-Moerman Now that the two reviewers have expressed their approval, can we initiate the next steps in the publication?

claresinger commented 1 year ago

@dhhagan @Kevin-Mattheus-Moerman can you please update us on the next steps needed for publication

slayoo commented 1 year ago

@dhhagan @Kevin-Mattheus-Moerman please update us on the status of this review, thanks!

Kevin-Mattheus-Moerman commented 1 year ago

@slayoo apologies for the delay. It seems @dhhagan might be overlooking these notifications. I'll try to email him. I'll take over as editor if he doesn't respond.

Kevin-Mattheus-Moerman commented 1 year ago

Actually, I'll take it from here.

slayoo commented 1 year ago

Thank you, @Kevin-Mattheus-Moerman

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot generate pdf

openjournals / joss-reviews