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

[whedon]

Submitting author: @egonw (Egon Willighagen)
Repository: https://github.com/egonw/bacting
Version: paper-v3
Editor: @majensen
Reviewer: @Zethson, @arcuri82
Archive: 10.5281/zenodo.4942022

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Reviewers and authors:

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Review checklist for @Zethson

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 (@egonw) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• 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?
• 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 @arcuri82

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 (@egonw) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• 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?
• 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. @Zethson, @arcuri82 it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

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

@whedon generate pdf

[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]

👉 Check article proof 📄 👈

[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: Installation tries to sign with gpg and fails egonw/bacting#8 , which were promptly solved.
2. A question regarding the license: Eclipse Public License 1.0 (EPL-1.0) has been superseded egonw/bacting#9
3. Several issues regarding the community guidelines and documentation: Documentation lacks a few key issues egonw/bacting#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?

[egonw]

2. A question regarding the license: egonw/bacting#9

This one is still open. There are several past Bioclipse developers involved, one of them even passed away. I will not be able to resolve this quickly.

3. Several issues regarding the community guidelines and documentation: egonw/bacting#10

@Zethson, I have isolated some subtasks of egonw/bacting#10 which now have a reply (fixes mostly; see that issue). Thank you for your suggestions.

Additional questions that I have:

1. What do you, @egonw mean with missing progress monitoring? Missing progress bars for called functions?

Indeed. Eclipse (and therefore Bioclipse) has a progress monitoring View (a GUI element) that allows you to see which processes are running in the background. For long running tasks, it would tell the user what they are waiting for. But since Bacting does not have a GUI, I have not ported this functionality yet. I have been thinking about this, but it depends a lot on how it is used. I cannot exclude I will include the progress monitoring in the future, but at this moment this does not have priority.

I'll update the manuscript to be more clear about this.

2. How does Bioeclipse/Bacting compare to BioJava and BioPython?

BioJava is a library that actually has been integrated into (the original) Bioclipse. This week I started porting the functionality. Bioclipse exposes the functionality and makes it interoperable with other libraries by introducing implementation-neutral 'domain objects'.

[egonw]

@egonw - checking in. How are things going?

@majensen, yes, sorry about this. i had to wait until the winter break to start working on the rebuttal. I think I indicated somewhere that I expect to "resubmit" (how does that work?) the manuscript before this Monday. I am tracking progress here: https://github.com/egonw/bacting/projects/1

[majensen]

@egonw Sounds good. Just start back up and I will remove the paused label. We can pick up where we left off.

[majensen]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1093/bioinformatics/btn397 is OK
- 10.5281/zenodo.3950863 is OK
- 10.1186/1471-2105-8-59 is OK
- 10.1186/1471-2105-10-397 is OK
- 10.1186/s13321-017-0220-4 is OK
- 10.1021/ci100384d is OK
- 10.1186/1471-2105-11-5 is OK
- 10.1186/1758-2946-5-14 is OK
- 10.12688/f1000research.12342.1 is OK
- 10.1093/nar/gkx1064 is OK
- 10.6084/m9.figshare.6356027.v1 is OK
- 10.1007/978-3-319-70407-4_36 is OK
- 10.5281/ZENODO.3364510 is OK
- 10.5281/ZENODO.3855084 is OK
- 10.1016/j.csbj.2020.02.023 is OK
- 10.6084/M9.FIGSHARE.12458612 is OK
- 10.1186/s13326-015-0005-5 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#2404

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2404, 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 @egonw, I'm doing some final checks before publishing. The Brenninkmeijer, Mayfield, Rijswijk, Slenter, Spjuth 2009, and Willighagen 2017 references look a bit strange - I think "et al." is included in the bibtex entry somehow. Can you correct those? All authors should be included in the bibtex entries, and then our LaTeX parser can handle truncating the list of authors automatically.

[egonw]

@kyleniemeyer, thank you for catching that. I had not expected Zotero to put et al. in their BibTeX output :( There was a second entry to which this applied and fixed that one too.

When looking at the final proof last night I noticed one sentence that changed in reply to a reviewer comment, but where something seems to have gone wrong. I am changing This means that translation of IFile to String translations in the API do not exist in Bioclipse to This means that the IFile to String translations in the API do not exist in Bioclipse., see egonw/bacting@ff7414c

• make new proof and check changes
• make a new tag paper-v4 for the article in the repo (for the whedon set paper-v4 as version)
• wait for the Zenodo deposit and look up the new DOI on Zenodo (for the whedon set 10.5281/zenodo.494xxxx as archive)

[kyleniemeyer]

@egonw ah sorry for the confusion - I actually meant all six references that began with those first authors...

You do not actually need to update the Zenodo deposit for paper-only changes—you can, if you want, but our focus is on archiving the version of the software that was reviewed, since JOSS archives the paper itself.

[kyleniemeyer]

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[kyleniemeyer]

Actually it looks like all of the references with long author lists have this issue.

[egonw]

Yeah, indeed. I'm sorry about this. Hang on :)

[egonw]

Okay, took a bit of effort, but I exported all references in a different way from Zotero now (next time I'm just going to use citation.js)... I think it should be better now, but also note the ... in the screenshot, which comes from the PDF generation process, I think:

[egonw]

You do not actually need to update the Zenodo deposit for paper-only changes—you can, if you want, but our focus is on archiving the version of the software that was reviewed, since JOSS archives the paper itself.

Okay, that seems to me to contradict earlier instructions by @majensen (all is fine, no problem), but will do without now then. @kyleniemeyer, please do check the references one more time too.

[kyleniemeyer]

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[kyleniemeyer]

@egonw Thanks for your work on that, it now looks good to me. Our paper template does truncate some very long author lists, but includes the final author.

[kyleniemeyer]

@whedon accept

[whedon]

To recommend a paper to be accepted use @whedon recommend-accept

[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.02558 joss-papers#2408
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.02558
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]

Congratulations @egonw on your article's publication in JOSS!

Many thanks to @Zethson and @arcuri82 for reviewing, and @majensen for editing.

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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[egonw]

Congratulations @egonw on your article's publication in JOSS!

Many thanks to @Zethson and @arcuri82 for reviewing, and @majensen for editing.

Thanks everyone for landing this work!

[majensen]

@egonw - great work; @arcuri82 @Zethson really appreciate your help with this submission. We made it under the 1 year mark! Congrats all!