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

whedon commented 4 years ago

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

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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

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

Make sure you're logged in to your GitHub account
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

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

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: Do the authors clearly state 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 @olivertomic

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

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: Do the authors clearly state 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 @greglandrum

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

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[ ] 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?
[ ] 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).
[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

[ ] 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 commented 4 years ago

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 :tada:.

:star: Important :star:

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 😿

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whedon commented 4 years ago

Attempting to check references...

whedon commented 4 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 4 years ago


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 commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

csoneson commented 4 years ago

👋@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 commented 4 years ago

@whedon remind @olivertomic in 6 weeks

whedon commented 4 years ago

Reminder set for @olivertomic in 6 weeks

csoneson commented 4 years ago

👋@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 commented 4 years ago

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 commented 4 years ago

👋 @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 commented 4 years ago

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

csoneson commented 4 years ago

@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 commented 4 years ago

@whedon add @greglandrum as reviewer

whedon commented 4 years ago

OK, @greglandrum is now a reviewer

greglandrum commented 4 years ago

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

csoneson commented 4 years ago

@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 commented 4 years ago

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

olivertomic commented 4 years ago

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 commented 4 years ago

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

olivertomic commented 4 years ago

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

csoneson commented 4 years ago

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

@olivertomic - did you have a chance to start your review of this submission?

olivertomic commented 4 years ago

@csoneson - starting today.

Sulstice commented 4 years ago

@csoneson I updated per some of the requests from @greglandrum so there should be updates to some of the initial README and installation instructions. Please let me know if it isn't clear and I can help with the installation (would prove useful in the docs).

csoneson commented 4 years ago

@olivertomic - any update on your review?

@csoneson - starting today.

csoneson commented 4 years ago

@olivertomic - please update us on the status of your review.

olivertomic commented 4 years ago

@csoneson In progress. Please see the checked boxes above.

arfon commented 4 years ago

Dear authors and reviewers

We wanted to notify you that in light of the current COVID-19 pandemic, JOSS has decided to suspend submission of new manuscripts and to handle existing manuscripts (such as this one) on a "best efforts basis". We understand that you may need to attend to more pressing issues than completing a review or updating a repository in response to a review. If this is the case, a quick note indicating that you need to put a "pause" on your involvement with a review would be appreciated but is not required.

Thanks in advance for your understanding.

Arfon Smith, Editor in Chief, on behalf of the JOSS editorial team.

arfon commented 4 years ago

:wave: @floux, @olivertomic, @greglandrum, just a friendly check-in to see how things are going with your reviews?

Sulstice commented 4 years ago

@arfon I have a blocker on oliver temporarily with a dependency issue on the package that we discovered last week. I need to apply a fix ASAP to the package. Sorry about the delay (had a lot of craziness happening with corona for work)

olivertomic commented 4 years ago

@arfon I am in touch with @Sulstice regarding examples of how to run the software. Work in progress. :-)

arfon commented 4 years ago

👍 thanks for the updates @Sulstice and @olivertomic.

arfon commented 4 years ago

:wave: @Sulstice, @olivertomic, @greglandrum - today we reopened JOSS for new submissions and are checking in on our existing reviews. Do you think you might be able to wrap up this discussion and review in the next 2-3 weeks?

Sulstice commented 4 years ago

Yes! I am making a little more interactive examples of how to use Cocktail Shaker per as @olivertomic suggestions (i.e juptyer notebooks or a gitpod) I am aiming for this saturday may 23rd (free time) to wrap that up.

I believe I tackled nearly all the issues attached with the repo filed from both greg and oliver and should be good to go unless I missed something (please let me know!).

Sulstice commented 4 years ago

I added jupyter notebook examples for each of the apis with some more documentation into how it works with examples. I also added a litle ascii cinema in the README file for a quick visibility so someone can see if they would like to pip install it prior.

If there is anything else let me know!

csoneson commented 4 years ago

Just checking in here - @Sulstice, do I interpret your message above correctly in that you have addressed the issues raised by the reviewers and are ready for a re-review?

Sulstice commented 4 years ago

Yep I am ready for a re-review!

csoneson commented 4 years ago

Great - @olivertomic, @greglandrum, could you please have a look at the updated submission and let us know what you think? Thanks!

olivertomic commented 4 years ago

I am happy to approve the paper for publication. @Sulstice , and @csoneson . Just a minor change would be requried in paper.md itself.

The text says: ´Cocktail Shaker´ consists of four major class objects available to the user: PeptideMolecule, CocktailShaker, and FileWriter.´

However, only three are mentioned.

@Sulstice , thank you for the collaboration and implementation of suggestions.

Sulstice commented 4 years ago

Yes you are definitely right, kind of an artifact of time of submission and me updating the modules. I will fix that later today!

@olivertomic done!

olivertomic commented 4 years ago

Excellent @Sulstice ! I am happy to recommend publication of the paper.

csoneson commented 4 years ago

@greglandrum - could you give us an update on the status of your review? Thanks!

csoneson commented 4 years ago

Ping @greglandrum

@greglandrum - could you give us an update on the status of your review? Thanks!

csoneson commented 4 years ago

👋 @Sulstice - in order to move this review process forward, I have decided to invite a fourth reviewer, who has agreed to take a first look shortly (thanks @richardjgowers!)

csoneson commented 4 years ago

@whedon add @richardjgowers as reviewer

whedon commented 4 years ago

OK, @richardjgowers is now a reviewer

csoneson commented 4 years ago

@whedon remove @floux as reviewer

whedon commented 4 years ago

OK, @floux is no longer a reviewer

Sulstice commented 4 years ago

@richardjgowers Let me know if there is anything I need to do!

richardjgowers commented 4 years ago

@Sulstice the comment before about mentioning 4 classes but then listing 3 of them is still valid.

openjournals / joss-reviews