Joss-reviews: [REVIEW]: Bacting: a next generation, command line version of Bioclipse

[whedon]

Submitting author: @egonw (Egon Willighagen)
Repository: https://github.com/egonw/bacting
Version: 0.0.11
Editor: @majensen
Reviewer: @Zethson, @arcuri82
Archive: Pending

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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

@Zethson & @arcuri82, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ 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 ✨

Review checklist for @Zethson

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 (@egonw) 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

• [ ] 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?
• [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).
• [ ] 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?
• [ ] 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?
• [ ] 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 @arcuri82

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 (@egonw) 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

• [ ] 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

• [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.
• [ ] 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

• [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?
• [ ] 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)?
• [ ] 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. @Zethson, @arcuri82 it looks like you're currently assigned to review this paper :tada:.

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[whedon]

PDF failed to compile for issue #2558 with the following error:

Can't find any papers to compile :-(

[majensen]

@whedon generate pdf from branch devel/0.0.13

[whedon]

Attempting PDF compilation from custom branch devel/0.0.13. Reticulating splines etc...

[whedon]

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

[Zethson]

Hi,

this is the first time that I am reviewing for JOSS, so feel free to tell me if I am doing something wrong.

1. I identified an issue with the installation instructions: https://github.com/egonw/bacting/issues/8 , which were promptly solved.
2. A question regarding the license: https://github.com/egonw/bacting/issues/9
3. Several issues regarding the community guidelines and documentation: https://github.com/egonw/bacting/issues/10

Additional questions that I have:

1. What do you, @egonw mean with missing progress monitoring? Missing progress bars for called functions?
2. How does Bioeclipse/Bacting compare to BioJava and BioPython?

The paper is well written and I am looking forward to your answers!
Great work.

Thank you!
Cheers

[majensen]

Looks good to me @Zethson - onward!

[egonw]

Regarding the license question, I also replied in the issue tracker, but here copy it here for convenience: There is a lot of code being reused, a good bit of which has not been written by me, but other Bioclipse developers. I cannot change the license. But I like the suggestion and will look into the (dis)advantages and discuss those with all original authors.

[majensen]

Hi @arcuri82 - just checking in. Have you had a chance to start looking at this work?
Thanks.

[arcuri82]

Hi @majensen - unfortunately haven't had time to start yet :( but hopefully should be able to start next week

[egonw]

@arcuri82, that sounds fine. I have not been able to work on the package this week anyway.

[arcuri82]

I made a first set of comments.
However, there is one thing I would like to get clarified. The program is written Java, but, its intended usage seems for Groovy. I do not know Groovy. And unfortunately I do not have the time to learn a new programming language just for doing a review. If all examples are going to be only in Groovy, I am not sure I can really try out this software, and give a proper review. But, asking examples/tutorials in Java for a program that is meant to be used mainly in Groovy would likely be unfair to the author.

[majensen]

@egonw can you comment regarding @arcuri82 's concern?

[egonw]

Yes, I can and will. Right now, I'm swamped in university year start and project mid terms reviews. I have some ideas, some take a bit more time to work out. Other things I have to try and see how they work out. I have created a project on GitHub to work out ideas the reviewers gave, towards the rebuttal/revision: https://github.com/egonw/bacting/projects/1?add_cards_query=is%3Aopen

I will report back here when making progress. @arcuri82 wrote "first set of comments" and I will also monitor things here if more feedback comes one.

[kthyng]

@egonw Totally understand the trouble with the start of the academic year! As the rotating associate editor in chief this week, I am going to pause this submission while we wait for your responses to start. This is for bookkeeping purposes and can be removed whenever you are ready to move forward. Thanks!

[majensen]

@egonw - how are things? Just checking in.

[majensen]

@egonw - checking in. How are things going?