[REVIEW]: OpenFEPOPS: A Python implementation of the FEPOPS molecular similarity technique

[editorialbot]

Submitting author: @stevenshave (Steven Shave)
Repository: https://github.com/JustinYKC/FEPOPS
Branch with paper.md (empty if default branch):
Version: v1.8.2
Editor: @richardjgowers
Reviewers: @hannahbaumann, @exs-cbouy
Archive: 10.6084/m9.figshare.24477184.v1

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/b4ab6027d3eca941ca7b3ffc70e636d8"><img src="https://joss.theoj.org/papers/b4ab6027d3eca941ca7b3ffc70e636d8/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/b4ab6027d3eca941ca7b3ffc70e636d8/status.svg)](https://joss.theoj.org/papers/b4ab6027d3eca941ca7b3ffc70e636d8)

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

@hannahbaumann & @exs-cbouy, 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 @richardjgowers 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 @exs-cbouy

📝 Checklist for @hannahbaumann

[editorialbot]

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:

@editorialbot commands

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

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (543.1 files/s, 77300.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          14            304            918           1251
Jupyter Notebook                 1              0            653            287
Markdown                         3             55              0            185
TeX                              1             11              0            123
YAML                             3              2              4             90
TOML                             1              6              0             50
reStructuredText                 4             36             54             44
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            29            426           1637           2065
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

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

OK DOIs

- 10.1016/j.jmgm.2007.02.005 is OK
- 10.1021/jm049654z is OK
- 10.1002/9783527665143.ch10 is OK
- 10.1016/j.drudis.2011.02.011 is OK
- 10.1111/j.1476-5381.2010.01127.x is OK
- 10.1186/s13321-020-00444-5 is OK
- 10.1021/ci050296y is OK
- 10.1021/jm300687e is OK
- 10.1186/1758-2946-4-27 is OK
- 10.1016/j.eswa.2008.01.039 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Wordcount for paper.md is 1453

[editorialbot]

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

[exs-cbouy]

Review checklist for @exs-cbouy

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/JustinYKC/FEPOPS?
• 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 (@stevenshave) 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?

[exs-cbouy]

@richardjgowers as a reviewer am I supposed to rerun the benchmarking notebook (as it would qualify as "original results") and make sure that the results are the same, or is making sure that the notebook is runnable enough? It's quite slow to run (but the notebook works).

[richardjgowers]

@exs-cbouy yes if you could rerun the notebook in the repo and verify the results, i.e. a manual notebook regression test

[stevenshave]

@richardjgowers as a reviewer am I supposed to rerun the benchmarking notebook (as it would qualify as "original results") and make sure that the results are the same, or is making sure that the notebook is runnable enough? It's quite slow to run (but the notebook works).

Hi @exs-cbouy , thank you very much for your in depth review. We are working on addressing all points. As for rerunning the notebook, this has been refactored somewhat in addressing your comments. The most up to date version in the development branch (not yet merged to main) would be the best to use, available here: https://github.com/JustinYKC/FEPOPS/blob/7b929a16dc1eadfa1f4abfd4e80a4c2a7982cad9/Explore_DUDE_diversity_set.ipynb

In addition, pre-generated FEPOPS database files for the DUDE diversity set are available here: https://doi.org/10.6084/m9.figshare.23951445.v3 which will massively speedup running the notebook. These new descriptors have been generated after addressing your point on feature scaling before k-medoid clustering and so differ from earlier versions.

Once we have addressed all changes on the development branch we will merge to main and notify all here.

Many thanks,
Steve

[stevenshave]

@editorialbot generate pdf

[editorialbot]

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

[stevenshave]

Hi @richardjgowers and @exs-cbouy, we have now addressed the raised issues and released a new version of OpenFEPOPS (v.1.8.0) which includes bugfixes and updates to functionality, online documentation and the manuscript.
Many thanks,
Steve

[stevenshave]

@editorialbot generate pdf

[editorialbot]

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

[stevenshave]

Hi @richardjgowers, I've just added the 1.8.2 source archive to figshare under the URL:
https://doi.org/10.6084/m9.figshare.24477184.v1

and DOI:
10.6084/m9.figshare.24477184.v1

Many thanks to you and the reviewers for progressing this!
Steve

[richardjgowers]

@editorialbot set 10.6084/m9.figshare.24477184.v1 as archive

[editorialbot]

That doesn't look like a valid DOI value

[richardjgowers]

@editorialbot pretty please set https://doi.org/10.6084/m9.figshare.24477184.v1 as archive

[editorialbot]

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

@editorialbot commands

[richardjgowers]

@editorialbot set https://doi.org/10.6084/m9.figshare.24477184.v1 as archive

[editorialbot]

Done! archive is now 10.6084/m9.figshare.24477184.v1

[richardjgowers]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1016/j.jmgm.2007.02.005 is OK
- 10.1021/jm049654z is OK
- 10.1002/9783527665143.ch10 is OK
- 10.1016/j.drudis.2011.02.011 is OK
- 10.1111/j.1476-5381.2010.01127.x is OK
- 10.1186/s13321-020-00444-5 is OK
- 10.1021/ci050296y is OK
- 10.1021/jm300687e is OK
- 10.1186/1758-2946-4-27 is OK
- 10.1016/j.eswa.2008.01.039 is OK
- 10.1021/ci970431 is OK
- 10.1021/ci990307l is OK
- 10.1016/0040-4020(80)80168-2 is OK
- 10.1016/j.patrec.2005.10.010 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/bcm-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#4759, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[Kevin-Mattheus-Moerman]

@stevenshave as the AEiC on this track I will now help to process the final steps. I have checked the repository, this review, the paper, and the archive link. Most seems in order. However I have the below points that require your attention:

On the paper:

• Both British English (e.g. neighbouring) and American English (e.g. featurization) are used. Please correct to be consistent.
• Check spelling for totalling, which should perhaps be totaling.

Comments/recommendations (not required):

• Your affiliations are currently (nearly) full postal addresses. However, if you prefer to shorten this you may do so, e.g. to simply have the format , <University/Institute/Company>, , . In other words, you may, if you like, leave out street/building names and postal/zip codes.
• For your first reference (K-means++ the advantages of careful seeding) you may consider adding a url entry in your bib file e.g. to: https://dl.acm.org/doi/abs/10.5555/1283383.1283494 (looks like their DOI does not resolve but this url does).

[stevenshave]

@editorialbot generate pdf

[editorialbot]

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

[stevenshave]

Hi @Kevin-Mattheus-Moerman, many thanks for your work on this.

I have now standardised to British English, replacing featurization with featurisation. I looked into the totalling vs totaling and it seems unclear, with both being acceptable, but have gone with your suggestion of totaling. I discovered another typo of "fingeprint" which has now been corrected.

After a brief discussion with coauthors, one would strongly prefer keeping the addresses as prescribed by our departments for use in publishing. I hope that it is OK if these remain as they are.

I have added the suggested URL to the Arthur 2007 reference, which now appears correctly.

My thanks to all reviewers and editors for the work you have all contributed to this, it has been a great experience!

Best,
Steve

[Kevin-Mattheus-Moerman]

@editorialbot generate pdf

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@stevenshave thanks that all looks good now then.

[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: Chen
  given-names: Yan-Kai
  orcid: "https://orcid.org/0000-0001-7161-9503"
- family-names: Houston
  given-names: Douglas R.
  orcid: "https://orcid.org/0000-0002-3469-1546"
- family-names: Auer
  given-names: Manfred
  orcid: "https://orcid.org/0000-0001-8920-3522"
- family-names: Shave
  given-names: Steven
  orcid: "https://orcid.org/0000-0001-6996-3663"
contact:
- family-names: Shave
  given-names: Steven
  orcid: "https://orcid.org/0000-0001-6996-3663"
doi: 10.6084/m9.figshare.24477184.v1
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Chen
    given-names: Yan-Kai
    orcid: "https://orcid.org/0000-0001-7161-9503"
  - family-names: Houston
    given-names: Douglas R.
    orcid: "https://orcid.org/0000-0002-3469-1546"
  - family-names: Auer
    given-names: Manfred
    orcid: "https://orcid.org/0000-0001-8920-3522"
  - family-names: Shave
    given-names: Steven
    orcid: "https://orcid.org/0000-0001-6996-3663"
  date-published: 2023-11-09
  doi: 10.21105/joss.05763
  issn: 2475-9066
  issue: 91
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5763
  title: "OpenFEPOPS: A Python implementation of the FEPOPS molecular
    similarity technique"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05763"
  volume: 8
title: "OpenFEPOPS: A Python implementation of the FEPOPS molecular
  similarity technique"

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.05763 joss-papers#4770
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05763
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...

[stevenshave]

I see that the paper is now live!

I have added a CITATION.cff to the repository and GitHub has picked it up, enabling the "Cite this repository" link/button.

Again, my thanks to the reviewers for the in depth reviews which forced me to rethink many things and also become more proficient at github, and to the editors for making this such a good experience. We will be looking in the future to improve the speed of the technique with some compiled rust to replace performance critical sections and increase the utility of OpenFEPOPS.

Best wishes,
Steve

[Kevin-Mattheus-Moerman]

Congratulations on this JOSS publication @stevenshave

Thanks for editing @richardjgowers

And a special thanks to the reviewers: @hannahbaumann, @exs-cbouy

[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:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.05763/status.svg)](https://doi.org/10.21105/joss.05763)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05763">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05763/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05763/status.svg
   :target: https://doi.org/10.21105/joss.05763

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:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss