[REVIEW]: PySDM v1: particle-based cloud modelling package for warm-rain microphysics and aqueous chemistry

[whedon]

Submitting author: @piotrbartman (Piotr Bartman)
Repository: https://github.com/atmos-cloud-sim-uj/PySDM.git
Branch with paper.md (empty if default branch):
Version: v1.27
Editor: @dhhagan
Reviewers: @darothen, @josephhardinee
Archive: 10.5281/zenodo.6321270

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Review checklist for @josephhardinee

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 repository url?
• 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 (@piotrbartman) 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

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 and who the target audience is?
• 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?

Review checklist for @darothen

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 repository url?
• 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 (@piotrbartman) 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

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 and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @jwuttke, @darothen it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

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[whedon]

PDF failed to compile for issue #3219 with the following error:

 Can't find any papers to compile :-(

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.41 s (534.1 files/s, 31905.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         212           2053           1184           7548
SVG                              1              0             19           1402
Jupyter Notebook                 3              0            207            336
Markdown                         1             38              0            280
YAML                             4             20              4            112
-------------------------------------------------------------------------------
SUM:                           221           2111           1414           9678
-------------------------------------------------------------------------------


Statistical information for the repository 'ee5fa7f3802655beaf36d792' was
gathered on 2021/04/26.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Anna Jaruga                      1             3              1            0.01
Bartosz Piasecki                 1            42             23            0.08
Michael                         18           443            170            0.80
Michaeldz36                     37          2661           2424            6.64
Piotr Bartman                   10            14             19            0.04
Sylwester Arabas               417         11939           7609           25.54
piotrbartman                    61          2072           2853            6.44
prbartman                      438         26379          19740           60.27
tehAgitto                        4            84             51            0.18

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Bartosz Piasecki             30           71.4          5.1                0.00
Michael                     289           65.2         15.1               10.03
Sylwester Arabas           4438           37.2          3.2                4.35
piotrbartman               6011          290.1          9.3                7.97
tehAgitto                    42           50.0          4.5                2.38

[slayoo]

@whedon generate pdf from branch JOSS

[whedon]

Attempting PDF compilation from custom branch JOSS. Reticulating splines etc...

[whedon]

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

[darothen]

Review - @darothen

PySDM is a new open-source package for particle-resolved modeling of the physics and chemistry of cloud and aerosol microphysics. It provides high-performance reference implementations of state-of-the-science process models in a flexible, highly-configurable package that is relatively easy to manipulate and modify to suit a wide variety of cloud and aerosol modeling tasks. It also ships with a back-end for running certain processes on GPUs, although this functionality does not seem to be fully implemented for all configurations which a user may seek to leverage.

Overall this is a high quality and valuable contribution to the field. Many researchers leverage simple box and parcel models for critical work into fundamental aerosol/cloud microphysics, and PySDM provides extremely useful tooling for exploring this domain and for replicating the results of other researchers. However, the library is lacking in documentation, both formally (in clearly defining the complex structure of the objects which comprise the code and how they interact) and informally (through docstrings and other comments/annotations in the code which may allow users to better understand arguments to key functions and how to manipulate and extend them). At present, the authors provide a nice "Hello world" example with some prose on how to configure it, as well as a basic section on package structure and API. But a more comprehensive listing of the arguments, attributes, and parameters that the user should know about in order to configure or extend this example would go a very long way to promote practical usability.

I would encourage the authors to improve or augment this documentation before the final publication of this software paper. However, in all other aspects I find this to be a comprehensive and uniquely valuable software contribution to the cloud and aerosol microphysical modeling community and an ideal candidate for publication in JOSS.

Please note the handful of detailed comments below on specific changes necessary to meet JOSS standards.

General Checks

• Two authors on the paper (Grzegorz Lazarski and Aleksandra Talar) do not seem to appear as contributors to the repo and aren't listed in "Author Contributions." I don't really believe there is any issue here - for long-incubated software projects like this with lots of research interfaces there have to be many contributors over time! But I do want to note this for the editors.

Functionality

• A simple install recipe using PyPI is provided, but given the capability to run on the GPU a conda-forge recipe or something which can help readers understand requirements - or provide a turnkey installation with necessary dependencies - would be very helpful! (Issue 494)

• Installation using the documented instructions misses out on installing pystrict, a required dependency (Issue/PR 495)

Documentation

• The automated tests seem to work out of the box, but the smoke tests seem to take a very long time to run. Even one of the unit tests (namely attributes/chemistry/test_pH.py) took a disproportionate amount of time compared to the others. Please note that I was not able to run the GPU tests as I did not have immediate access to a GPU-powered machine.

• While there is extensive, excellent demonstration and example code available from the authors in related, clearly-linked repositories, the API documentation leaves much to be desired. There is a high degree of customizability and configuration exposed to the user, but very little in the way of curated documentation for the APIs and data structures in the software, or docstrings and annotations. As a motivating example, consider the spectra module; in this module, a nice base class for building probability distributions is exposed, but there are no docstrings describing the required and optional arguments for either the base class or any of the sub-classes which implement it. An effort to improve the documentation with basic docstrings for all the core methods and functionality would greatly improve the quality of the software and the user experience when adapting it for a specialized research task. Ideally, a simple Sphinx-based documentation for the key API and configurations exposed to users would follow very plainly from such an effort, greatly improving the ease of access of the software.

• Community / contribution guidelines are not provided with the repo; the JOSS reviewer guidelines suggest that such documentattion should clearly indicate how third-parties may contribute to the software, report issues, and seek support should they need to do so.

Software Paper

• The software paper does not include a section which explicitly explains a "Statement of Need." However, I do believe that the prose in the paper covers this topic with the necessary detail. I will defer to the editors whether a stand-alone "Statement of Need" section is required to meet JOSS guidelines.

• It's much appreciated that the authors include links to open source software which attempts to tackle subsets of the broad functionality that PySDM provides. I would strongly encourage the author to include a brief discussion of each package (particularly pyrcel and PyBox) and compare/contrast the unique or improved functionalities of PySDM relative to each. My take (as the author of one of those libraries, pyrcel!) is that PySDM offers a substantial improvement over each in terms of the breadth of calculations and science/research that can be performed with it as well as the cleanliness of its interface and design for future improvements and extensions. These are all very positive things for PySDM and I would strongly encourage the authors to lean into the fantastic work here to promote the capabilities and utility of their library relative to the competition!

[slayoo]

@darothen, on behalf of all authors, let me thank for the feedback!

Let me just address one comment right away:

Two authors on the paper (Grzegorz Lazarski and Aleksandra Talar) do not seem to appear as contributors to the repo and aren't listed in "Author Contributions." I don't really believe there is any issue here - for long-incubated software projects like this with lots of research interfaces there have to be many contributors over time! But I do want to note this for the editors.

GŁ's (@Golui) and AT's (@aleksandratal) contributions were subject to refactors during which we've not preserved commit authorship, yet these can be traced back, e.g., here: open-atmos/PySDM#157 & open-atmos/PySDM#142 Both are mentioned in the "Author Contributions" section:

Thanks!

[slayoo]

@whedon generate pdf from branch JOSS

[whedon]

Attempting PDF compilation from custom branch JOSS. Reticulating splines etc...

[slayoo]

@whedon generate pdf from branch JOSS

This was just to reflect an API change within one of the code snippets presented in the text:
open-atmos/PySDM@ca4d821

[whedon]

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

[whedon]

👋 @jwuttke, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @darothen, please update us on how your review is going (this is an automated reminder).

[darothen]

@dhhagan Just checking in here - anything immediately needed from me here?

@slayoo please let me know if there are any PRs or other updates I've missed.

[slayoo]

We are almost done with preparing a release and will soon after post here a point-by-point reply to the review detailing how the points were addressed in the release. Thanks, S.

[dhhagan]

@darothen Thanks for checking in -> you should be good for now. Just waiting on the other reviewer and updated/patches from the authors before any next steps are needed. Thanks for checking in!

[dhhagan]

@jwuttke Can you please update us on the status of your review? Thanks!

[piotrbartman]

@whedon generate pdf from branch JOSS

[whedon]

Attempting PDF compilation from custom branch JOSS. Reticulating splines etc...

[dhhagan]

@whedon reming @jwuttke in 1 day

[whedon]

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

@whedon commands

[dhhagan]

@whedon remind @jwuttke in 1 day

[arfon]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03219 joss-papers#3168
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03219
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[arfon]

@darothen, @josephhardinee – many thanks for your reviews here and to @dhhagan for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@piotrbartman – your paper is now accepted and published in JOSS ⚡🚀💥

[editorialbot]

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

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The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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[slayoo]

@arfon Thank you!
In the final paper page that one is redirected to by using the DOI the author list is full of unescaped HTML non-braking space:

Is it possible to do correct it?
Thanks

[arfon]

@slayoo - please remove all of the &nsbp; characters and I'll re-deposit the paper.

[piotrbartman]

@dhhagan @darothen @josephhardinee @arfon @slayoo Thank you all! 🎉🎉🎉

[slayoo]

@slayoo - please remove all of the &nsbp; characters and I'll re-deposit the paper.

Removed: open-atmos/PySDM@cf59297

(note, we have changed the branch name from master to main)

Thank you, @arfon!

[arfon]

@editorialbot re-accept

[editorialbot]

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

@editorialbot commands

[arfon]

@editorialbot reaccept

[editorialbot]

Rebuilding paper!

[editorialbot]

🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#3173

[slayoo]

Thank you, @arfon!

[arfon]

👍 looks like this is now fixed. Closing.

[editorialbot]

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.03219/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03219/status.svg
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This is how it will look in your documentation:

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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