Joss-reviews: [REVIEW]: bit: a git-based tool for the management of code and data

[whedon]

Submitting author: @jorgeboucas (Jorge Boucas)
Repository: https://github.com/mpg-age-bioinformatics/bit
Version: 0.1.1
Editor: @acabunoc
Reviewer: @dvalters, @paulklemm
Archive: Pending

Status

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Markdown: [![status](http://joss.theoj.org/papers/3714b0dbb3e3e5acb4277537d7093dee/status.svg)](http://joss.theoj.org/papers/3714b0dbb3e3e5acb4277537d7093dee)

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) 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 1 instructions & questions

@dvalters, 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.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @acabunoc know.

### Conflict of interest

• [x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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] Version: Does the release version given match the GitHub release (0.1.1)?
• [x] Authorship: Has the submitting author (@jorgeboucas) 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?
• [ ] 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).
• [ ] 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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [ ] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Reviewer 2 instructions & questions

@paulklemm, 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.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @acabunoc know.

### Conflict of interest

• [x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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] Version: Does the release version given match the GitHub release (0.1.1)?
• [x] Authorship: Has the submitting author (@jorgeboucas) 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?
• [ ] 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).
• [ ] 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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
• [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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @dvalters it looks like you're currently assigned as the reviewer for 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 😿

To fix this do the following two things:

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

1. 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

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

https://github.com/openjournals/joss-papers/blob/joss.00549/joss.00549/10.21105.joss.00549.pdf

[acabunoc]

@dvalters & @paulklemm -- I duplicated the reviewer checklist so you should each have your own list to check off. thanks & let me know if you have any questions!

[arfon]

@dvalters & @paulklemm - friendly reminder to get to this review when you get a chance.

[dvalters]

Hi @jorgeboucas, I've raised a few issues in the issue tracker in the submission's github repository (see linked issues above). My other comments so far are:

1. Documentation is a bit sparse - there is a 'man page' style usage guide in the README.md file, which I think might meet the minimum requirements for documentation (@acabunoc?) but I could not find any separate documentation linked for the software. (My impression is that JOSS submissions should have separate documentation pages _in addition_ to a high-level overview in the README file, but please correct me if I'm wrong @acabunoc)

2. No tests per se. There are examples of usage in the README.md file, but again, these are fairly limited, and I'm not sure they are sufficient under the JOSS guidelines:

Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?

1. No community guidelines present.

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

I will continue with the testing of the software functionality once https://github.com/mpg-age-bioinformatics/bit/issues/6 is fixed (or I have done something wrong in the setup, let me know 😄)

A nice utility, hope to see it reach publication in JOSS once the issues are resolved.

[arfon]

@paulklemm - please carry out your review here when you get a chance?

@jorgeboucas - also, please take a look at @dvalters' comments and provide feedback.

[arfon]

:wave: how are we getting along here? @dvalters, @paulklemm - it looks like you're reviews aren't complete yet but also we've not heard back from @jorgeboucas.

[dvalters]

@arfon ready to proceed, but https://github.com/mpg-age-bioinformatics/bit/issues/6 question needs resolved before I can test the software

[paulklemm]

Also ready to proceed, require issue https://github.com/mpg-age-bioinformatics/bit/issues/8 to be solved to test the software.

[arfon]

@jorgeboucas - how are we getting along here?

[arfon]

Hi @jorgeboucas - are you still interested in pursuing this publication in JOSS?

[arfon]

@acabunoc, @dvalters, @paulklemm - I'm sorry to say that we're going to have to close this review. I've been unable to get hold of @jorgeboucas over the past few months and so I have to assume he's no longer interested in pursuing this publication.

My apologies for any time wasted here.