editorialbot commented 1 year ago

Submitting author: !--author-handle-->@stevenshave@richardjgowers<!--end-editor-- Reviewers: @hannahbaumann, @exs-cbouy Archive: 10.6084/m9.figshare.24477184.v1

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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 commented 1 year ago

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

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editorialbot commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

Wordcount for paper.md is 1453

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:

exs-cbouy commented 1 year ago

Review checklist for @exs-cbouy

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/JustinYKC/FEPOPS?
[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 (@stevenshave) 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?

exs-cbouy commented 1 year ago

@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 commented 1 year ago

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

stevenshave commented 1 year ago

@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 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:

stevenshave commented 1 year ago

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 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:

exs-cbouy commented 1 year ago

Thank you @stevenshave for this open-source version of FEPOPS and the benchmark with commonly used fingerprints, I believe this will be a useful 3D representation for a variety of use cases, as it becomes more widely available to the public.

@richardjgowers All my comments have been addressed and my checklist is complete, LGTM!

Kevin-Mattheus-Moerman commented 1 year ago

@hannahbaumann thanks for agreeing to review this JOSS submission. Are you able to get started on your review?

hannahbaumann commented 1 year ago

Review checklist for @hannahbaumann

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/JustinYKC/FEPOPS?
[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 (@stevenshave) 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?

stevenshave commented 1 year ago

Thank you for your review @hannahbaumann , we believe we have addressed all comments and fixed the installation issue in the new 1.8.1 OpenFEPOPS release which is now on pypi.

Best, Steve

stevenshave 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:

hannahbaumann commented 11 months ago

@richardjgowers All my comments have been addressed and my checklist is complete!

richardjgowers commented 11 months ago

@editorialbot set v1.8.2 as version

editorialbot commented 11 months ago

Done! version is now v1.8.2

richardjgowers commented 11 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

[x] Double check authors and affiliations (including ORCIDs)
[x] 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.
[x] Archive the release on Zenodo/figshare/etc and post the DOI here.
[x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[x] Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

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

richardjgowers commented 11 months ago

Hi @stevenshave we're onto the final checklist above. Can you make a zenodo/figshare release of 1.8.2 and post the DOI here?

richardjgowers commented 11 months ago

@editorialbot check references

editorialbot commented 11 months ago

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

stevenshave commented 11 months ago

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 commented 11 months ago

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

editorialbot commented 11 months ago

That doesn't look like a valid DOI value

richardjgowers commented 11 months ago

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

editorialbot commented 11 months ago

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

@editorialbot commands

richardjgowers commented 11 months ago

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

editorialbot commented 11 months ago

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

richardjgowers commented 11 months ago

@editorialbot recommend-accept

editorialbot commented 11 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 11 months ago

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 commented 11 months ago

:wave: @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4759, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman commented 11 months ago

@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:

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

Comments/recommendations (not required):

[x] 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.
[x] 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 commented 11 months ago

@editorialbot generate pdf

editorialbot commented 11 months ago

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

stevenshave commented 11 months ago

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 commented 11 months ago

@editorialbot generate pdf

editorialbot commented 11 months ago

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

Kevin-Mattheus-Moerman commented 11 months ago

@stevenshave thanks that all looks good now then.

Kevin-Mattheus-Moerman commented 11 months ago

@editorialbot accept

editorialbot commented 11 months ago

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

editorialbot commented 11 months ago

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 commented 11 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 11 months ago

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/4770
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05763
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

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openjournals / joss-reviews

[REVIEW]: OpenFEPOPS: A Python implementation of the FEPOPS molecular similarity technique #5763

Status

Reviewer instructions & questions

Checklists

Review checklist for @exs-cbouy

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @hannahbaumann

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance