[REVIEW]: New developments in PySDM and PySDM-examples v2: collisional breakup, immersion freezing, dry aerosol composition initialisation, and adaptive time-stepping #4968

editorialbot · 2022-11-25T15:40:06Z

Submitting author: @edejong-caltech (Emily de Jong)
Repository: https://github.com/open-atmos/PySDM
Branch with paper.md (empty if default branch):
Version: v2.16
Editor: @dhhagan
Reviewers: @douglowe, @emmasimp
Archive: 10.5281/zenodo.7640495

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/5110170dd97fe1ebf08227881f76bda9"><img src="https://joss.theoj.org/papers/5110170dd97fe1ebf08227881f76bda9/status.svg"></a>
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.
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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

The text was updated successfully, but these errors were encountered:

editorialbot · 2022-11-25T15:40:08Z

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 · 2022-11-25T15:40:11Z

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 · 2022-11-25T15:40:13Z

Wordcount for paper.md is 1913

editorialbot · 2022-11-25T15:40:14Z

Failed to discover a Statement of need section in paper

editorialbot · 2022-11-25T15:41:12Z

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 · 2022-11-25T15:41:40Z

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

claresinger · 2022-11-26T19:37:21Z

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

douglowe · 2022-11-28T10:59:50Z

Review checklist for @douglowe

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/atmos-cloud-sim-uj/PySDM?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
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?
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?

Kevin-Mattheus-Moerman · 2022-12-01T21:26:59Z

@editorialbot remove @claresinger as reviewer

editorialbot · 2022-12-01T21:27:01Z

@claresinger removed from the reviewers list!

Kevin-Mattheus-Moerman · 2022-12-01T21:27:27Z

@editorialbot add @emmasimp as reviewer

editorialbot · 2022-12-01T21:27:29Z

@emmasimp added to the reviewers list!

Kevin-Mattheus-Moerman · 2022-12-01T21:29:09Z

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

dhhagan · 2022-12-08T13:18:41Z

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

dhhagan · 2022-12-08T13:19:04Z

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

Sorry about that mistake!

emmasimp · 2022-12-08T13:23:13Z

Review checklist for @emmasimp

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/atmos-cloud-sim-uj/PySDM?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
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?
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?

douglowe · 2023-01-31T14:25:59Z

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 · 2023-02-03T11:34:47Z

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 · 2023-02-13T16:20:47Z

@editorialbot generate pdf

editorialbot · 2023-02-13T16:22:05Z

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

douglowe · 2023-02-13T16:24:49Z

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 · 2023-02-13T16:30:53Z

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

slayoo · 2023-02-14T16:55:22Z

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 · 2023-03-14T15:37:38Z

@editorialbot set 10.5281/zenodo.7640495 as archive

editorialbot · 2023-03-14T15:37:46Z

Done! Archive is now 10.5281/zenodo.7640495

Kevin-Mattheus-Moerman · 2023-03-14T15:42:24Z

@edejong-caltech @slayoo Would it be okay to make the ZENODO archive author set match that of the current paper? Also can you update the title to match the paper title too? You can manually edit these.
If you can process the author update then there is no issue.

Kevin-Mattheus-Moerman · 2023-03-14T15:42:33Z

@editorialbot generate pdf

editorialbot · 2023-03-14T15:44:17Z

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

slayoo · 2023-03-22T12:44:54Z

If you can process the author update then there is no issue.

Zenodo metadata updated: https://zenodo.org/record/7640495

claresinger · 2023-03-30T17:32:33Z

@Kevin-Mattheus-Moerman ^^ the zenodo metadata has been updated. Please let us know if there is anything else we need to do before the paper can be published. Thank you!

slayoo · 2023-04-06T21:21:06Z

@Kevin-Mattheus-Moerman, @dhhagan, please confirm if there is any further update needed for the paper. Thanks

claresinger · 2023-04-12T16:40:18Z

@Kevin-Mattheus-Moerman @dhhagan Please let us know if anything else is needed for the paper. Thanks.

claresinger · 2023-04-19T13:11:38Z

@Kevin-Mattheus-Moerman Can we get an update on the status of this paper? We would love to have the paper published and be able to close this review!

Kevin-Mattheus-Moerman · 2023-04-19T13:16:31Z

@claresinger @slayoo my sincere apologies for the delay! Because I was not formally assigned as editor here and the "Accept" flag hadn't been added, this dropped off my radar! I will process this now ASAP!

Kevin-Mattheus-Moerman · 2023-04-19T13:16:55Z

@editorialbot recommend accept

editorialbot · 2023-04-19T13:16:56Z

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

Kevin-Mattheus-Moerman · 2023-04-19T13:17:33Z

@editorialbot recommend-accept

editorialbot · 2023-04-19T13:17:35Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-04-19T13:19:05Z

👋 @openjournals/ese-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4141, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

editorialbot · 2023-04-19T13:19:31Z

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
- 10.21105/joss.03896 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
- 10.1029/2022MS002994 is OK
- 10.5194/acp-16-2083-2016 is OK
- 10.5194/gmd-13-4107-2020 is OK
- 10.1029/1999JD901161 is OK
- 10.5194/egusphere-2022-1243 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
- 10.1175/JAS-D-21-0275.1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

Kevin-Mattheus-Moerman · 2023-04-19T13:29:58Z

@editorialbot accept

editorialbot · 2023-04-19T13:29:59Z

Doing it live! Attempting automated processing of paper acceptance...

editorialbot · 2023-04-19T13:32:01Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Jong
  given-names: Emily K.
  name-particle: de
  orcid: "https://orcid.org/0000-0002-5310-4554"
- family-names: Singer
  given-names: Clare E.
  orcid: "https://orcid.org/0000-0002-1708-0997"
- family-names: Azimi
  given-names: Sajjad
  orcid: "https://orcid.org/0000-0002-6329-7775"
- family-names: Bartman
  given-names: Piotr
  orcid: "https://orcid.org/0000-0003-0265-6428"
- family-names: Bulenok
  given-names: Oleksii
  orcid: "https://orcid.org/0000-0003-2272-8548"
- family-names: Derlatka
  given-names: Kacper
  orcid: "https://orcid.org/0000-0003-3137-1288"
- family-names: Dula
  given-names: Isabella
- family-names: Jaruga
  given-names: Anna
  orcid: "https://orcid.org/0000-0003-3194-6440"
- family-names: Mackay
  given-names: J. Ben
  orcid: "https://orcid.org/0000-0001-8677-3562"
- family-names: Ward
  given-names: Ryan X.
  orcid: "https://orcid.org/0000-0003-2317-3310"
- family-names: Arabas
  given-names: Sylwester
  orcid: "https://orcid.org/0000-0003-2361-0082"
doi: 10.5281/zenodo.7640495
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Jong
    given-names: Emily K.
    name-particle: de
    orcid: "https://orcid.org/0000-0002-5310-4554"
  - family-names: Singer
    given-names: Clare E.
    orcid: "https://orcid.org/0000-0002-1708-0997"
  - family-names: Azimi
    given-names: Sajjad
    orcid: "https://orcid.org/0000-0002-6329-7775"
  - family-names: Bartman
    given-names: Piotr
    orcid: "https://orcid.org/0000-0003-0265-6428"
  - family-names: Bulenok
    given-names: Oleksii
    orcid: "https://orcid.org/0000-0003-2272-8548"
  - family-names: Derlatka
    given-names: Kacper
    orcid: "https://orcid.org/0000-0003-3137-1288"
  - family-names: Dula
    given-names: Isabella
  - family-names: Jaruga
    given-names: Anna
    orcid: "https://orcid.org/0000-0003-3194-6440"
  - family-names: Mackay
    given-names: J. Ben
    orcid: "https://orcid.org/0000-0001-8677-3562"
  - family-names: Ward
    given-names: Ryan X.
    orcid: "https://orcid.org/0000-0003-2317-3310"
  - family-names: Arabas
    given-names: Sylwester
    orcid: "https://orcid.org/0000-0003-2361-0082"
  date-published: 2023-04-19
  doi: 10.21105/joss.04968
  issn: 2475-9066
  issue: 84
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 4968
  title: "New developments in PySDM and PySDM-examples v2: collisional
    breakup, immersion freezing, dry aerosol initialization, and
    adaptive time-stepping"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.04968"
  volume: 8
title: "New developments in PySDM and PySDM-examples v2: collisional
  breakup, immersion freezing, dry aerosol initialization, and adaptive
  time-stepping"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot · 2023-04-19T13:32:07Z

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editorialbot · 2023-04-19T13:32:08Z

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editorialbot · 2023-04-19T13:32:09Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04968 joss-papers#4143
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Kevin-Mattheus-Moerman · 2023-04-19T15:20:35Z

@edejong-caltech @claresinger @slayoo congratulations on this publications.

Once again my apologies for the delays this submission encountered!

I would also like to express a special thanks to the reviewers @douglowe and @emmasimp!

editorialbot · 2023-04-19T15:20:37Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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slayoo · 2023-04-19T15:37:59Z

Thank you @Kevin-Mattheus-Moerman, @douglowe & @emmasimp!

editorialbot added Python review TeX Track: 6 (ESE) Earth Sciences and Ecology labels Nov 25, 2022

editorialbot assigned dhhagan Nov 25, 2022

editorialbot mentioned this issue Nov 25, 2022

[PRE REVIEW]: New developments in PySDM and PySDM-examples v2: collisional breakup, immersion freezing, dry aerosol composition initialisation, and adaptive time-stepping #4412

Closed

openjournals deleted a comment from editorialbot Dec 8, 2022

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Apr 19, 2023

editorialbot added accepted published Papers published in JOSS labels Apr 19, 2023

Kevin-Mattheus-Moerman closed this as completed Apr 19, 2023

[REVIEW]: New developments in PySDM and PySDM-examples v2: collisional breakup, immersion freezing, dry aerosol composition initialisation, and adaptive time-stepping #4968

[REVIEW]: New developments in PySDM and PySDM-examples v2: collisional breakup, immersion freezing, dry aerosol composition initialisation, and adaptive time-stepping #4968

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editorialbot commented Nov 25, 2022 • edited

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douglowe commented Nov 28, 2022 • edited

Review checklist for @douglowe

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emmasimp commented Dec 8, 2022 • edited

Review checklist for @emmasimp

Conflict of interest

Code of Conduct

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Functionality

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Software paper

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editorialbot commented Nov 25, 2022 •

edited

douglowe commented Nov 28, 2022 •

edited

emmasimp commented Dec 8, 2022 •

edited