[REVIEW]: flowerMD: Flexible Library of Organic Workflows and Extensible Recipes for Molecular Dynamics

[editorialbot]

Submitting author: @marjanalbouye (Marjan Albooyeh)
Repository: https://github.com/cmelab/flowerMD
Branch with paper.md (empty if default branch):
Version: 1.1.1
Editor: @lucydot
Reviewers: @LIVazquezS, @abhishektiwari
Archive: 10.5281/zenodo.10215501

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/75c5135b3e0eb1b561a89783ce949067/status.svg)](https://joss.theoj.org/papers/75c5135b3e0eb1b561a89783ce949067)

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

@csadorf & @LIVazquezS & @abhishektiwari, 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 @lucydot 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 @abhishektiwari

📝 Checklist for @LIVazquezS

[editorialbot]

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.25 s (316.5 files/s, 85731.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                              7              1             29          11175
Python                          41            859           1228           4772
TeX                              1             15              0            244
Jupyter Notebook                 4              0           2362            229
Markdown                         3             44              2            195
YAML                             8             16             14            194
reStructuredText                13             71            104             56
DOS Batch                        1              8              1             26
make                             1              4              7              9
INI                              1              0              0              4
-------------------------------------------------------------------------------
SUM:                            80           1018           3747          16904
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gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1191

[editorialbot]

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

OK DOIs

- 10.1038/s41524-022-00906-4 is OK
- 10.1080/00268976.2020.1742938 is OK
- 10.21105/joss.01831 is OK
- 10.1063/1.2978177 is OK
- 10.1021/ct0502864 is OK
- 10.1016/j.commatsci.2019.109363 is OK
- 10.1038/s41467-021-27627-4 is OK
- 10.1021/acs.jcim.3c00081 is OK
- 10.1021/acs.macromol.8b00011 is OK
- 10.1007/978-981-10-1128-3_5 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.5281/zenodo.8370982 is OK
- 10.1088/1361-651X/ab6a44 is OK
- 10.1126/sciadv.abg9763 is OK
- 10.1063/1.470016 is OK
- 10.3390/polym13132162 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[abhishektiwari]

Review checklist for @abhishektiwari

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/cmelab/flowerMD?
• 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 (@marjanalbouye) 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?

[LIVazquezS]

Review checklist for @LIVazquezS

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/cmelab/flowerMD?
• 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 (@marjanalbouye) 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?

[erjank]

@lucydot , a possible perceived COI is that @csadorf and I had the same PhD advisor. I graduated from that lab in 2012, years before @csadorf joined and we have not worked together.

[lucydot]

Hi @erjank - thanks for flagging up. Given the timeframe, it is okay 👍

[abhishektiwari]

@mbarzegary Please see my initial comments.

General checks

Contribution and authorship

Can you provide more details on Eric Jankowski contributions to paper or software?

Software paper

Reference

Incorrect reference to HOOMD-blue paper at line 8 and 28, should be pointing to anderson2020hoomd as included in paper.bib file.

Quality of writing

A few typos

— macromolecular not macrmolecular
— because not becuase

Suggested improvements

— A lot of deprecation warnings due to use of older numpy interfaces. Worth making sure there is path to latest behaviour. E.g. — Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future.
— Provide pip package to make installation. I believe authors already working on it.
— There is potential to use directed acyclic graphs (DAG) execution for workflow recipes. Worth exploring a few examples using Airflow or likes.

Overall

I truly enjoyed reviewing this paper. Everything from installation to functional testing to tutorial, I was able to finish within few hours. Kudos to authors for providing a very frictionless experience. Tutorial cover variety of well documented use cases. Package APIs are well documented and include type hints at parameters level. More importantly, package is structured in a way which encourage extensibility.

[chrisjonesBSU]

@abhishektiwari Thank you for the review and suggestions!

• The spelling and citation errors have been fixed by PR #86.
• Unfortunately, I'm fairly certain that the deprecation errors come from other packages that are dependencies for flowermd and have been an ongoing issue for a while. Regardless, we'll give it another pass-through!
• Eric Jankowski is the PI of our research lab, providing guidance on the direction and development. He also was heavily involved in writing and editing of the paper.md file.
• We will prioritize finishing conda and pip packages this week.
• Thank you for the DAG suggestion. I see there are a lot of resources out there for implementing these; we'll be sure to check them out!

[LIVazquezS]

Dear Authors,

Here are some of my thoughts.

General Checks

Example Usage

I enjoyed the examples given by the authors. However, the quality of them needs to be improved.

• In the tutorials, the authors repeatedly refer the user to the source code of the different classes for examples (i.e. Pack and Lattice). That should not be the case. Examples of using the different classes should be available in the documentation or the tutorial.
• In tutorial 2, The authors provide examples of how to create a custom molecule. In example 4, they mentioned that a custom molecule can be defined through a class. The authors should give a concrete example of the required attributes of that class and how to define the molecule instead of just referring to the source code.
• I found it very good that you can define your force field using .xml files. However, I think the authors need to specify how the .xml file should be constructed or re-direct the interested user to a reference with that information.
• The authors mentioned in their statement of need that other tools can not be used for modelling complex processes. Then, they cited two examples: fusion welding and surface wetting. In the tutorials, only the first is described. Do the authors intend to add a new module for surface wetting in the future, or have they already done so? I recommend either adding a tutorial for surface wetting (which will increase the value of this contribution) or rewriting the sentence.

Community Guidelines

The authors provided simple and concise instructions for contributing to their code. However, I did not find options to report problems with the code or ask for help if needed.

Software paper

References

The reference to HOOMD-Blue needs to be rendered correctly.

Suggested improvements

• There are a few depreciation warnings that the authors should consider to avoid future problems.
• The examples need to be improved as described before.
• Functionalities of the code need to be described in the documentation so as not to force the user to go to the source code. If I understand correctly, the goal of this code is to reduce cognitive and programming loads from the user. That is impossible if the user needs to go to the source code for examples.
• I strongly recommend to create a pip or anaconda package.
• I recommend the authors finish their paper with suggestions for possible extensions to their code by taking advantage of the modularity of it.

Overall

This code can become a powerful tool for the simulations of complex systems from construction, force field specification, and running simulations almost automatically but without falling into a black box approach. I applaud the author's effort to make the code modular so that every step is understandable and reproducible. Complementary to this is the structure of the software, which promotes its extension and further applicability. Nevertheless, considerable improvements to documentation and tutorials should be made to improve user-friendliness.

Other questions

• Can the authors make their CG parametrization approach compatible with established CG force fields such as MARTINI or SIRAH?

[marjanalbooyeh]

@editorialbot generate pdf

[editorialbot]

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

[marjanalbooyeh]

@LIVazquezS Thank you for the review and suggestions.

Example Usage:

• We have updated the tutorials in this PR, providing additional descriptions and guidelines on creating subclasses for force fields and molecules. Tutorial 2 includes code examples for using both the Pack and Lattice classes.

• Direct references to the source code have been removed. Instead, we've added links to our documentation, which comprehensively covers details of classes and functions.

• A link to the .xml forcefield format has been added to Section 2 of Tutorial 2.

• We have initiated the development of the surface wetting module for flowerMD. You can track the progress in this PR. Upon completion of implementation and testing, we'll provide a tutorial explaining the new functionalities.

Community Guidelines:

• A new section has been added to our contribution guidelines for questions and comments. This section also includes instructions for bug reports and code contributions.

Suggested Improvements:

• As mentioned earlier, unfortunately, many of the deprecation warnings stem from packages in flowerMD dependencies. We are actively addressing the ones caused by our code.

• flowerMD's documentation includes descriptions of functions and classes. This documentation has been linked in the README and paper.

• We have already initiated the process of creating the conda package in this PR on conda-forge staged-recipes. Once the package is published, we will update the installation guidelines.

Other Questions:

Thank you for the suggestion regarding the CG force fields. While we haven't directly worked with MARTINI or SIRAH, we will make sure to explore them. However, supporting those CG force fields is currently beyond the scope of flowerMD.

[lucydot]

Thank you @LIVazquezS and @abhishektiwari for your thorough and prompt reviews - if you happy that all of your acceptance-blockers are addressed (?) please complete tick-boxes (if not already done so).

@csadorf have you started your review? As we have had two thorough reviews which are largely in agreement, I am happy to publish without a third reviewer - that said, if you are part way through please feel free to complete so that your reviewer contribution can be recognised on the publication. We aim to have the review process complete in 4-5 weeks, so you have a couple of weeks remaining for review.

[abhishektiwari]

@lucydot Review and checklist is completed from my side.

[chrisjonesBSU]

The anaconda package for flowermd is done as of this morning. You can see it here and the conda-forge feedstock repo here.

@marjanAlbouye and I looked into making a pip package as well. A big chunk of the dependencies for flowermd are only available on anaconda and don't have pip packages in pypi. From what we understand, this might complicate the process of making a pip package for flowermd. Marjan found poetry which I think can help with that. We'll keep it a goal to have a pip package at some point, but it may be a bit before we can get to that.

[LIVazquezS]

@marjanAlbouye and @chrisjonesBSU Thanks for your prompt reply. The examples look much better. I will be looking forward to the surface-wetting module.

@lucydot The authors addressed my comments, and I completed the checklist.

[lucydot]

Thank you @LIVazquezS and @abhishektiwari for signing off on your reviews -

@marjanAlbouye @chrisjonesBSU we are onto the final stages of the review process now ✨ I will ask editorial-bot to generate a post-review checklist. You will not be able to tick off the items, but please let me know when each is complete.

[lucydot]

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

• Double check authors and affiliations (including ORCIDs)
• Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
• Archive the release on Zenodo/figshare/etc and post the DOI here.
• Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

• Read the text of the paper and offer comments/corrections (as either a list or a PR)
• Check the references in the paper for corrections (e.g. capitalization)
• Check that the archive title, author list, version tag, and the license are correct
• Set archive DOI with @editorialbot set <DOI here> as archive
• Set version with @editorialbot set <version here> as version
• Double check rendering of paper with @editorialbot generate pdf
• Specifically check the references with @editorialbot check references and ask author(s) to update as needed
• Recommend acceptance with @editorialbot recommend-accept

[lucydot]

@editorialbot generate pdf

[marjanalbooyeh]

@lucydot please let us know if there's anything left to do on our side. Thanks!

[Kevin-Mattheus-Moerman]

@editorialbot set 1.1.1 as version

[editorialbot]

Done! version is now 1.1.1

[Kevin-Mattheus-Moerman]

@marjanAlbouye as AEiC I will now help to process final steps. I have check the paper, this review, the archive link, and your repository. Most seems in order, however, I do have the below point that requires your attention.

On the paper:

• It looks like this should be added as the DOI for the below reference: 10.1371/journal.pcbi.1005659

Eastman, P., Swails, J., Chodera, J. D., McGibbon, R. T., Zhao, Y., Beauchamp, K. A., Wang,
L.-P., Simmonett, A. C., Harrigan, M. P., Stern, C. D., & others. (2017). OpenMM
7: Rapid development of high performance algorithms for molecular dynamics. PLoS
Computational Biology, 13(7), e1005659.

[marjanalbooyeh]

@editorialbot generate pdf

[editorialbot]

⚠️ An error happened when generating the pdf.

[marjanalbooyeh]

@editorialbot generate pdf

[editorialbot]

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

[marjanalbooyeh]

@Kevin-Mattheus-Moerman Thanks for noticing the missing DOI. We fixed it, it should be good now.

[Kevin-Mattheus-Moerman]

@editorialbot accept

[editorialbot]

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

[editorialbot]

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: Albooyeh
  given-names: Marjan
  orcid: "https://orcid.org/0009-0001-9565-3076"
- family-names: Jones
  given-names: Chris
  orcid: "https://orcid.org/0000-0002-6196-5274"
- family-names: Barrett
  given-names: Rainier
  orcid: "https://orcid.org/0000-0002-5728-9074"
- family-names: Jankowski
  given-names: Eric
  orcid: "https://orcid.org/0000-0002-3267-1410"
contact:
- family-names: Jankowski
  given-names: Eric
  orcid: "https://orcid.org/0000-0002-3267-1410"
doi: 10.5281/zenodo.10215501
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Albooyeh
    given-names: Marjan
    orcid: "https://orcid.org/0009-0001-9565-3076"
  - family-names: Jones
    given-names: Chris
    orcid: "https://orcid.org/0000-0002-6196-5274"
  - family-names: Barrett
    given-names: Rainier
    orcid: "https://orcid.org/0000-0002-5728-9074"
  - family-names: Jankowski
    given-names: Eric
    orcid: "https://orcid.org/0000-0002-3267-1410"
  date-published: 2023-12-15
  doi: 10.21105/joss.05989
  issn: 2475-9066
  issue: 92
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5989
  title: "FlowerMD: Flexible Library of Organic Workflows and Extensible
    Recipes for Molecular Dynamics"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05989"
  volume: 8
title: "FlowerMD: Flexible Library of Organic Workflows and Extensible
  Recipes for Molecular Dynamics"

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]

🐘🐘🐘 👉 Toot 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.05989 joss-papers#4844
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05989
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...

[marjanalbooyeh]

On behalf of the authors of flowerMD, I would like to thank the reviewers and editors for all the helpful comments and suggestions. This was a great learning experience for us. Thank you!

[Kevin-Mattheus-Moerman]

@editorialbot remove @csadorf as reviewer

[editorialbot]

@csadorf removed from the reviewers list!

[Kevin-Mattheus-Moerman]

@editorialbot re-accept

[editorialbot]

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

@editorialbot commands

[Kevin-Mattheus-Moerman]

@editorialbot reaccept

[editorialbot]

Rebuilding paper!

[editorialbot]

🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#4846

[Kevin-Mattheus-Moerman]

@marjanAlbouye congratulations on this JOSS publication! 🎄 🎁

Thanks for editing @lucydot! And a special thanks to the reviewers: @LIVazquezS, @abhishektiwari !

[editorialbot]

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

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[lucydot]

@csadorf removed from the reviewers list!

@Kevin-Mattheus-Moerman, a quick note to say that @csadorf had to withdraw for personal reasons. They communicated this to me before the paper was in accepted for publication; I managed to drop the ball on it. Thanks for catching.