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[REVIEW]: GaitPy: An Open-Source Python Package for Gait Analysis Using an Accelerometer on the Lower Back #1778

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whedon opened this issue Oct 2, 2019 · 35 comments
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@whedon whedon commented Oct 2, 2019

Submitting author: @matt002 (Matthew Czech)
Repository: https://github.com/matt002/GaitPy
Version: v1.0
Editor: @arfon
Reviewer: @finsberg, @abhishektha
Archive: 10.5281/zenodo.3528115

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/a2233c9e27db0b6625dc56a3f7363875"><img src="https://joss.theoj.org/papers/a2233c9e27db0b6625dc56a3f7363875/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/a2233c9e27db0b6625dc56a3f7363875/status.svg)](https://joss.theoj.org/papers/a2233c9e27db0b6625dc56a3f7363875)

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

@finsberg & @abhishektha, 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.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @arfon know.

Please try and complete your review in the next two weeks

Review checklist for @finsberg

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

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 (@mdc007) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 @abhishektha

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

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 (@mdc007) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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?
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@whedon whedon commented Oct 2, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @finsberg, @abhishektha it looks like you're currently assigned to review this paper 🎉.

⭐️ Important ⭐️

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:

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  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

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

@whedon generate pdf
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@whedon whedon commented Oct 2, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Oct 2, 2019

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@arfon arfon commented Nov 1, 2019

@finsberg, @abhishektha - it looks like you've both made good progress on your reviews. Could I ask whether you're close to making a recommendation to accept here?

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@finsberg finsberg commented Nov 1, 2019

@arfon I am still not able to install this software using pip (see matt002/GaitPy#9). When this issue is fixed I will recommend acceptance.

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@abhishektha abhishektha commented Nov 1, 2019

@arfon I just have a few more things to check off, will have it done this weekend!

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@finsberg finsberg commented Nov 1, 2019

@arfon I am done with my review, and can recommend GaitPy for publication in JOSS.

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@arfon arfon commented Nov 1, 2019

@arfon I am done with my review, and can recommend GaitPy for publication in JOSS.

👍 many thanks @finsberg!

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@abhishektha abhishektha commented Nov 3, 2019

@arfon I am done with my review as well and can recommend GaitPy for publication. Its a very cool package, I was able to run some of my own IMU data through it and it did a great job predicting initial and final contact times.

I did notice that one of the references was missing its DOI in the paper, I put a pull request in the repository to hopefully fit it: matt002/GaitPy#18

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@arfon arfon commented Nov 3, 2019

@whedon generate pdf

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@whedon whedon commented Nov 3, 2019

Attempting PDF compilation. Reticulating splines etc...
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@arfon arfon commented Nov 3, 2019

@whedon check references

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@whedon whedon commented Nov 3, 2019

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@whedon whedon commented Nov 3, 2019

Attempting to check references...
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@whedon whedon commented Nov 3, 2019


OK DOIs

- 10.1016/j.gaitpost.2012.02.019 is OK
- 10.1016/S0966-6362(02)00190-X is OK
- 10.1109/TBME.2003.812189 is OK
- 10.1109/JBHI.2015.2419317 is OK
- 10.1016/j.gaitpost.2014.07.007 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.1016/j.cll.2010.01.003.Lyme is INVALID
@arfon arfon referenced this issue Nov 3, 2019
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@arfon arfon commented Nov 3, 2019

@mdc007 - I've also fixed a DOI in your paper here: matt002/GaitPy#19 and made some general improvements to the paper here: matt002/GaitPy#20

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@arfon arfon commented Nov 3, 2019

@finsberg, @abhishektha - many thanks for your reviews here!

@mdc007 - please let us know when you've had a chance to incorporate the updates from myself and @abhishektha.

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@arfon arfon commented Nov 3, 2019

@whedon check references

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@whedon whedon commented Nov 3, 2019

Attempting to check references...
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@whedon whedon commented Nov 3, 2019


OK DOIs

- 10.1016/j.gaitpost.2012.02.019 is OK
- 10.1016/S0966-6362(02)00190-X is OK
- 10.1016/j.gaitpost.2011.03.024 is OK
- 10.1109/TBME.2003.812189 is OK
- 10.1109/JBHI.2015.2419317 is OK
- 10.1023/A:1010933404324 is OK
- 10.1016/j.gaitpost.2014.07.007 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@matt002 matt002 commented Nov 3, 2019

@arfon @finsberg @abhishektha I have incorporated the above mentioned updates. Thank you all very much for your review and edits. The paper and package are much improved following the review process.

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@arfon arfon commented Nov 3, 2019

@matt002 - At this point could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

  • The title of the archive is the same as the JOSS paper title
  • That the authors of the archive are the same as the JOSS paper authors

I can then move forward with accepting the submission.

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@matt002 matt002 commented Nov 4, 2019

@arfon I made a new release (1.6.0) and archived the software in Zenodo with DOI: 10.5281/zenodo.3528115

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@arfon arfon commented Nov 4, 2019

@whedon set 10.5281/zenodo.3528115 as archive

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@whedon whedon commented Nov 4, 2019

OK. 10.5281/zenodo.3528115 is the archive.

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@arfon arfon commented Nov 4, 2019

@whedon accept

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@whedon whedon commented Nov 4, 2019

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Nov 4, 2019


OK DOIs

- 10.1016/j.gaitpost.2012.02.019 is OK
- 10.1016/S0966-6362(02)00190-X is OK
- 10.1016/j.gaitpost.2011.03.024 is OK
- 10.1109/TBME.2003.812189 is OK
- 10.1109/JBHI.2015.2419317 is OK
- 10.1023/A:1010933404324 is OK
- 10.1016/j.gaitpost.2014.07.007 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Nov 4, 2019

Check final proof 👉 openjournals/joss-papers#1085

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1085, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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@arfon arfon commented Nov 4, 2019

@whedon accept deposit=true

@whedon whedon added the accepted label Nov 4, 2019
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@whedon whedon commented Nov 4, 2019

Doing it live! Attempting automated processing of paper acceptance...
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@whedon whedon commented Nov 4, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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@whedon whedon commented Nov 4, 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 👉 openjournals/joss-papers#1086
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01778
  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...

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@arfon arfon commented Nov 4, 2019

@finsberg, @abhishektha - many thanks for your reviews here

@matt002 - your paper is now accepted into JOSS ⚡️🚀💥

@arfon arfon closed this Nov 4, 2019
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@whedon whedon commented Nov 4, 2019

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

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

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.01778/status.svg)](https://doi.org/10.21105/joss.01778)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01778">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01778/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01778/status.svg
   :target: https://doi.org/10.21105/joss.01778

This is how it will look in your documentation:

DOI

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