[REVIEW]: Cocktail Shaker: An open source drug expansion and enumeration library for peptides

[whedon]

Submitting author: @Sulstice (Suliman Sharif)
Repository: https://github.com/Sulstice/cocktail-shaker
Version: 1.1.8
Editor: @csoneson
Reviewers: @olivertomic, @richardjgowers
Archive: 10.5281/zenodo.3981540

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/c2e1d3c408a5729d832b34ac680d6305"><img src="https://joss.theoj.org/papers/c2e1d3c408a5729d832b34ac680d6305/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/c2e1d3c408a5729d832b34ac680d6305/status.svg)](https://joss.theoj.org/papers/c2e1d3c408a5729d832b34ac680d6305)

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

@floux & @olivertomic, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @csoneson know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @richardjgowers

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 (@Sulstice) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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 @olivertomic

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 (@Sulstice) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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 @greglandrum

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 (@Sulstice) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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. @floux, @olivertomic it looks like you're currently assigned to review this paper 🎉.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf

[whedon]

Attempting to check references...

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

OK DOIs

- 10.1111/cbdd.12055 is OK
- 10.4155/tde.13.104 is OK
- 10.1093/nargab/lqz004 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👉 Check article proof 📄 👈

[csoneson]

👋@floux, @olivertomic - thanks for accepting to review this submission. This is where the review happens! Please see the instructions in the first post above, and don't hesitate to ping me if you have questions.

@Sulstice - please have a look at the reviewer checklists above. If you notice something missing from your submission, you can add it already now to simplify the review process.

[csoneson]

@whedon remind @olivertomic in 6 weeks

[whedon]

Reminder set for @olivertomic in 6 weeks

[csoneson]

👋@floux - just checking in on your review. Do you have an estimate of when you think you'll be able to provide some feedback for @Sulstice? Of course, don't hesitate to ping me if you have questions.

[csoneson]

I have sent three follow-up emails to @floux but not received any reply. At this point, I will therefore start looking for a replacement reviewer for this submission.

[csoneson]

👋 @greglandrum - would you be interested in reviewing this submission for the Journal of Open Source Software (JOSS)?

Cocktail Shaker: An open source drug expansion and enumeration library for peptides

Cocktail Shaker is a python package for exploring, expanding, and synthesizing chemical peptide data, operating within the RDKit platform.

Software: https://github.com/Sulstice/cocktail-shaker
Short accompanying paper: https://github.com/openjournals/joss-papers/blob/joss.01992/joss.01992/10.21105.joss.01992.pdf

JOSS reviews are performed openly on GitHub and are based on a checklist that can be found here: https://joss.readthedocs.io/en/latest/review_checklist.html
Additional information about reviewing for JOSS is available via https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

[greglandrum]

@csoneson - Sure; I can give this a try.

[csoneson]

@greglandrum - brilliant, thank you! I will add you as a reviewer and add a checklist for you in the first post above (there are also some additional instructions). Don't hesitate to ping me if you have any questions.

[csoneson]

@whedon add @greglandrum as reviewer

[whedon]

OK, @greglandrum is now a reviewer

[greglandrum]

@csoneson - just to confirm: should I directly complete the checklist above or make a copy in a comment?

[csoneson]

@greglandrum Please directly fill the checklist in the first post above so that we have a summary in one place.
You can then comment on individual items/aspects in separate comments (or open issues in the software repository and just mention them here).

[whedon]

👋 @olivertomic, please update us on how your review is going.

[olivertomic]

I must admit that I am not sure any longer whether I am supposed to review the manuscript or not. 4 days ago whedon assigned me and then unassigned me and I interpreted this as being out. Or is it the other way around?

[danielskatz]

Yes, you should - the action @whedon took was, in the process of adding a reviewer, to unassign you than to reassign you.

[olivertomic]

OK, thanks for the update. I plan to start reviewing within a weeks time.

[Sulstice]

Alright, should be done! does that all work out?

[csoneson]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[csoneson]

@whedon set 10.5281/zenodo.3981540 as archive

[whedon]

OK. 10.5281/zenodo.3981540 is the archive.

[csoneson]

@whedon set 1.1.8 as version

[whedon]

OK. 1.1.8 is the version.

[csoneson]

Looks good! I'll hand over to the AEiC on duty for the final steps.

[csoneson]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- 10.1111/cbdd.12055 is OK
- 10.4155/tde.13.104 is OK
- 10.1093/nargab/lqz004 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#1640

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1640, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[kyleniemeyer]

Hi @Sulstice, I'm doing some final review steps—can you add more info to the RDKit citation? It looks like you can add either a DOI for the most recent version (10.5281/zenodo.3981263), or for all versions (10.5281/zenodo.591637)

[Sulstice]

@kyleniemeyer Done :) I added the DOI for all versions and in the docs a RDKit 2019.09.1+ -> ran tests on latest RDKit 2020 release and passing.

Should be good to go!

[kyleniemeyer]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[kyleniemeyer]

@Sulstice thanks! looks good

[kyleniemeyer]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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.01992 joss-papers#1646
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01992
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...

[kyleniemeyer]

Congrats @Sulstice on your article's publication in JOSS!

Many thanks to @olivertomic and @richardjgowers for reviewing this, and @csoneson for editing.

[whedon]

🎉🎉🎉 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.01992/status.svg)](https://doi.org/10.21105/joss.01992)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01992">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01992/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01992/status.svg
   :target: https://doi.org/10.21105/joss.01992

This is how it will look in your documentation:

We need your help!

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://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

[Sulstice]

Thank you guys! @csoneson you really helped make this process pretty simple!