Joss-reviews: [REVIEW]: The Biddy BDD package

Created on 20 Jan 2019  ·  50Comments  ·  Source: openjournals/joss-reviews

Submitting author: @meolic (Robert Meolic)
Repository: https://github.com/meolic/biddy
Version: v1.8.2
Editor: @brainstorm
Reviewer: @HaoZeke
Archive: 10.5281/zenodo.2561641

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/fc7f571e455ef955d1e5dd271343723f"><img src="http://joss.theoj.org/papers/fc7f571e455ef955d1e5dd271343723f/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/fc7f571e455ef955d1e5dd271343723f/status.svg)](http://joss.theoj.org/papers/fc7f571e455ef955d1e5dd271343723f)

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 instructions & questions

@HaoZeke, 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 @brainstorm know.

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

Review checklist for @HaoZeke

Conflict of interest

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 (v1.8.2)?
  • [x] Authorship: Has the submitting author (@meolic) 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 function 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] 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)?
accepted published recommend-accept review
Source
picture whedon

All 50 comments

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @HaoZeke 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:

watching

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

notifications

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

@whedon commands
whedon picture whedon on 20 Jan 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 20 Jan 2019

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

whedon picture whedon on 20 Jan 2019

@HaoZeke All yours then, thanks!

brainstorm picture brainstorm on 20 Jan 2019

I have improved the first example in the documentation to make the usage of the package more clear. Sorry for these last-minute changes.

meolic picture meolic on 21 Jan 2019

@brainstorm, you're welcome.. I hope to have this finished in a few days.
@meolic, no problem, there may be some more changes, I will open pull requests and link to them as and when required, or discuss them with you here.

Right off the bat, could you please modify the paper.md so as to adhere to the following:

  • [x] Remove the historical review of package changes
  • [x] Remove or reword segments like exciting features and wicked if not used carefully

Beyond that, I would prefer a clearer statment (headings, boldface text etc) detailing the need for the software and the features.

As a style guide, perhaps this JOSS paper would be useful.

Additionally, for changes to paper.md I would not like to open pull requests, so it might be better if I could highlight aspects which need editing, say for example if it is on hackmd.io

HaoZeke picture HaoZeke on 21 Jan 2019

@whedon commands

meolic picture meolic on 21 Jan 2019

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Compile the paper
@whedon generate pdf
whedon picture whedon on 21 Jan 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 21 Jan 2019

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

whedon picture whedon on 21 Jan 2019

@HaoZeke I have made the requested changes. Please check https://hackmd.io/Ii3fJIJmS3iplOQHSCTjHA (i do not know how to use hackmd.io correctly).

meolic picture meolic on 21 Jan 2019

@meolic, thank you. I have also made some changes, please modify the submitted version if they are acceptable. Though it is not mandatory, perhaps an awknowledgment of any support from your institution or other grants might be added.

Meanwhile I will get to the code review.

HaoZeke picture HaoZeke on 22 Jan 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 22 Jan 2019

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

whedon picture whedon on 22 Jan 2019

@whedon generate pdf

meolic picture meolic on 22 Jan 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 22 Jan 2019

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

whedon picture whedon on 22 Jan 2019

@whedon generate pdf

meolic picture meolic on 22 Jan 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 22 Jan 2019

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

whedon picture whedon on 22 Jan 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 22 Jan 2019

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

whedon picture whedon on 22 Jan 2019

@HaoZeke I have updated paper.md. Many thanks for your suggestions, especially for the hint about writing math formulas in the markdown format. I am ready for your comments about the source code and the supplemented documentation (for the instalation it should be enough to read README.md, the complete API is documented in User manual available from biddy.meolic.com).

meolic picture meolic on 22 Jan 2019
👍1

@HaoZeke Do the updates address some of the issues?

brainstorm picture brainstorm on 30 Jan 2019

I have tried to address all of them.

meolic picture meolic on 30 Jan 2019

@brainstorm, yes paper.md is perfect now, I am a bit delayed in my code review however, I will finish by 5th February if that is OK.

HaoZeke picture HaoZeke on 31 Jan 2019
👍1

@brainstorm, I have completed my review. It is compliant with the instructions, and the code is very well documented (along with its usage). There are perhaps more edge cases (on exotic machines) however, even those are easily handled.

I believe the repository and BIDDY adheres to the JOSS guidelines and also that the claims in paper.md are well substantiated.

@meolic thank you for the prompt resolution of all my queries, and for open-sourcing this really well documented and useful software!

I am very sorry for the long delay.

HaoZeke picture HaoZeke on 8 Feb 2019

@whedon check references

brainstorm picture brainstorm on 8 Feb 2019 
Attempting to check references...
whedon picture whedon on 8 Feb 2019

```Reference check summary:

OK DOIs

MISSING DOIs

INVALID DOIs

  • None
    ```
whedon picture whedon on 8 Feb 2019

@meolic Can you please fix the DOI issues?

brainstorm picture brainstorm on 8 Feb 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 8 Feb 2019

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

whedon picture whedon on 8 Feb 2019 
Attempting to check references...
whedon picture whedon on 8 Feb 2019

```Reference check summary:

OK DOIs

MISSING DOIs

  • None

INVALID DOIs

  • None
    ```
whedon picture whedon on 8 Feb 2019

@brainstorm Thank you for this remark. Now, references should be OK.

meolic picture meolic on 8 Feb 2019

@meolic Can you please generate a Zenodo DOI I can set as archive?

brainstorm picture brainstorm on 11 Feb 2019

Done.

DOI

meolic picture meolic on 11 Feb 2019

@whedon set http://doi.org/10.5281/zenodo.2561641 as archive

brainstorm picture brainstorm on 11 Feb 2019

OK. 10.5281/zenodo.2561641 is the archive.

whedon picture whedon on 11 Feb 2019

@whedon accept

brainstorm picture brainstorm on 11 Feb 2019 
Attempting dry run of processing paper acceptance...
whedon picture whedon on 11 Feb 2019

```Reference check summary:

OK DOIs

MISSING DOIs

  • None

INVALID DOIs

  • None
    ```
whedon picture whedon on 11 Feb 2019

@arfon I think we are ready to deposit here ;)

brainstorm picture brainstorm on 11 Feb 2019

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/482

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/482, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

whedon picture whedon on 11 Feb 2019

@whedon accept deposit=true

arfon picture arfon on 12 Feb 2019 
Doing it live! Attempting automated processing of paper acceptance...
whedon picture whedon on 12 Feb 2019

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/483
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01189
  3. If everything looks good, then close this review issue.

  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

    Any issues? notify your editorial technical team...

whedon picture whedon on 12 Feb 2019

@HaoZeke - many thanks for your review and to @brainstorm for editing this submission ✨

@meolic - your paper is now accepted into JOSS :zap::rocket::boom:

arfon picture arfon on 12 Feb 2019
👍1

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.01189/status.svg)](https://doi.org/10.21105/joss.01189)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01189">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01189/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01189/status.svg
   :target: https://doi.org/10.21105/joss.01189

This is how it will look in your documentation:

DOI

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whedon picture whedon on 12 Feb 2019
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