[REVIEW]: OpenCADD-KLIFS: A Python package to fetch kinase data from the KLIFS database

whedon commented 2 years ago

Submitting author: @dominiquesydow (Dominique Sydow) Repository: https://github.com/volkamerlab/opencadd Version: v1.0.1 Editor: @richardjgowers Reviewer: @ojeda-e, @andrewtarzia, @mcs07 Archive: 10.5281/zenodo.6065555

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Review checklist for @ojeda-e

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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

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General checks

[x] Repository: Is the source code for this software available at the repository url?
[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 (@dominiquesydow) 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

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 and who the target audience is?
[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?

Review checklist for @andrewtarzia

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
[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 (@dominiquesydow) 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

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 and who the target audience is?
[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?

Review checklist for @mcs07

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
[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 (@dominiquesydow) 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

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 and who the target audience is?
[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?

whedon commented 2 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @ojeda-e, @andrewtarzia, @mcs07 it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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whedon commented 2 years ago

PDF failed to compile for issue #3951 with the following error:

 Can't find any papers to compile :-(

dominiquesydow commented 2 years ago

@whedon generate pdf from branch joss-paper

whedon commented 2 years ago

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...

whedon commented 2 years ago

PDF failed to compile for issue #3951 with the following error:

 Can't find any papers to compile :-(

dominiquesydow commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

PDF failed to compile for issue #3951 with the following error:

 Can't find any papers to compile :-(

arfon commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

whedon commented 2 years ago

:wave: @andrewtarzia, please update us on how your review is going (this is an automated reminder).

whedon commented 2 years ago

:wave: @ojeda-e, please update us on how your review is going (this is an automated reminder).

whedon commented 2 years ago

:wave: @mcs07, please update us on how your review is going (this is an automated reminder).

andrewtarzia commented 2 years ago

Just an update - mostly done. Aiming to read the paper and test the code on Friday, fingers crossed.

ojeda-e commented 2 years ago

Update: Currently clarifying some points about the installation instructions, which I expect to be solved in the next few days. Then will review functionality and read the paper.

mcs07 commented 2 years ago

To update: I am currently testing the functionality. General checks, installation, documentation - all looks good. I have added some additional comments and suggestions about the manuscript in https://github.com/volkamerlab/opencadd/issues/133.

whedon commented 2 years ago

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

dominiquesydow commented 2 years ago

@whedon generate pdf from branch joss-review-issues-133-134

whedon commented 2 years ago

Attempting PDF compilation from custom branch joss-review-issues-133-134. Reticulating splines etc...

whedon commented 2 years ago

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

andrewtarzia commented 2 years ago

I have completed my review of this work and am happy for it to be accepted. Great work by the authors!!

ojeda-e commented 2 years ago

I finished my review of OpenCADD-KLIFS. All my comments were addressed by @dominiquesydow and I'm happy to recommend this work for publication!

mcs07 commented 2 years ago

Sorry for the delay - I have now finished my review, and I am also happy to recommend acceptance.

dominiquesydow commented 2 years ago

Thank you, @ojeda-e, @andrewtarzia, and @mcs07, for all your input on the manuscript and the documentation!

I have updated the documentation "Statement of need" with the updated manuscript version - and merged PR https://github.com/volkamerlab/opencadd/pull/135.

Will generate the manuscript one more time from the master branch now, to check if everything works after the merge.

dominiquesydow commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

richardjgowers commented 2 years ago

@whedon check references

whedon commented 2 years ago

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

OK DOIs

- 10.1038/s41573-021-00195-4 is OK
- 10.1016/bs.armc.2017.08.001 is OK
- 10.1093/nar/gkaa895 is OK
- 10.1021/jm400378w is OK
- 10.21105/joss.00279 is OK
- 10.1093/nar/gky1075 is OK
- 10.3390/molecules23040908 is OK
- 10.1021/acs.jcim.6b00686 is OK
- 10.1002/cmdc.201700754 is OK
- 10.5281/zenodo.3509134 is OK

MISSING DOIs

- 10.2307/j.ctt1ffjkfp.36 may be a valid DOI for title: bravado

INVALID DOIs

- None

richardjgowers commented 2 years ago

@dominiquesydow looks like we're good to go. Can you make a tagged release of the software (e.g. via zenodo)? I think it might be easiest to archive the entire package rather than worry about splitting out this module. (The DOI suggestion seems to be for a poem, top marks for effort though Whedon!)

dominiquesydow commented 2 years ago

Hi @richardjgowers, thanks!

I have tagged a new release of the (full) opencadd repository - waiting for it to sync with our zenodo entry. I have contacted zenodo support already and will ping you again once this is solved.

The DOI suggestion seems to be for a poem, top marks for effort though Whedon!

I love this! :D

EDIT: Submitted issue to zenodo GH repo on 20220113: https://github.com/zenodo/zenodo/issues/2281

dominiquesydow commented 2 years ago

Hi @richardjgowers,

Good news - the opencadd zenodo entry is finally updated to the latest opencadd release 🥳 https://zenodo.org/record/6065555

Please let me know if there is anything else for me to do. Thank you!

richardjgowers commented 2 years ago

@whedon set 10.5281/zenodo.6065555 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.6065555 is the archive.

richardjgowers commented 2 years ago

@whedon set v1.0.1 as version

whedon commented 2 years ago

OK. v1.0.1 is the version.

richardjgowers commented 2 years ago

@whedon recommend-accept

whedon commented 2 years ago

Attempting dry run of processing paper acceptance...

whedon commented 2 years ago

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

OK DOIs

- 10.1038/s41573-021-00195-4 is OK
- 10.1016/bs.armc.2017.08.001 is OK
- 10.1093/nar/gkaa895 is OK
- 10.1021/jm400378w is OK
- 10.21105/joss.00279 is OK
- 10.1093/nar/gky1075 is OK
- 10.3390/molecules23040908 is OK
- 10.1021/acs.jcim.6b00686 is OK
- 10.1002/cmdc.201700754 is OK
- 10.5281/zenodo.3509134 is OK

MISSING DOIs

- 10.2307/j.ctt1ffjkfp.36 may be a valid DOI for title: bravado

INVALID DOIs

- None

whedon commented 2 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2953

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2953, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

danielskatz commented 2 years ago

@dominiquesydow - please update the metadata (title, authors) in your zenodo repository so that it matches the paper

danielskatz commented 2 years ago

@dominiquesydow - I've also suggested a few minor changes in the paper in https://github.com/volkamerlab/opencadd/pull/140

dominiquesydow commented 2 years ago

@dominiquesydow - I've also suggested a few minor changes in the paper in volkamerlab/opencadd#140

Thank you, I just merged the suggested changes.

dominiquesydow commented 2 years ago

@dominiquesydow - please update the metadata (title, authors) in your zenodo repository so that it matches the paper

I have a quick question regarding this. The zenodo repository covers the whole OpenCADD package, while this paper covers only one module of OpenCADD (i.e., OpenCADD-KLIFS). If I changed the zenodo repo's title and author list to this paper's title and author list, it would not reflect the full content of OpenCADD and the work other people have done for previous versions of OpenCADD anymore. Would it be possible to not synchronise in this case?

danielskatz commented 2 years ago

Ok, that makes sense. Thanks for the explanation.

danielskatz commented 2 years ago

@whedon recommend-accept

whedon commented 2 years ago

Attempting dry run of processing paper acceptance...

whedon commented 2 years ago

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

OK DOIs

- 10.1038/s41573-021-00195-4 is OK
- 10.1016/bs.armc.2017.08.001 is OK
- 10.1093/nar/gkaa895 is OK
- 10.1021/jm400378w is OK
- 10.21105/joss.00279 is OK
- 10.1093/nar/gky1075 is OK
- 10.3390/molecules23040908 is OK
- 10.1021/acs.jcim.6b00686 is OK
- 10.1002/cmdc.201700754 is OK
- 10.5281/zenodo.3509134 is OK

MISSING DOIs

- 10.2307/j.ctt1ffjkfp.36 may be a valid DOI for title: bravado

INVALID DOIs

- None

whedon commented 2 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2972

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2972, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

danielskatz commented 2 years ago

@whedon accept deposit=true

whedon commented 2 years ago

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

whedon commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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