[REVIEW]: SleepPy: A python package for sleep analysis from accelerometer data

whedon commented 5 years ago

Submitting author: @elyiorgos (Yiorgos Christakis) Repository: https://github.com/elyiorgos/sleeppy Version: 0.2.21 Editor: @lheagy Reviewers: @eskofier, @ikarosilva, @nhejazi Archive: 10.5281/zenodo.3572581

Status

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Markdown: [![status](https://joss.theoj.org/papers/fad54455272cbb33a611cfb93b758480/status.svg)](https://joss.theoj.org/papers/fad54455272cbb33a611cfb93b758480)

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

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

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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 @lheagy know.

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

Review checklist for @eskofier

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: 0.2.21
[x] Authorship: Has the submitting author (@elyiorgos) 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)?

Review checklist for @ikarosilva

Conflict of interest

[ ] 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: 0.2.21
[x] Authorship: Has the submitting author (@elyiorgos) 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)?

Review checklist for @nhejazi

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: 0.2.21
[x] Authorship: Has the submitting author (@elyiorgos) 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)?

whedon commented 4 years ago

Attempting to check references...

whedon commented 4 years ago


OK DOIs

- 10.1152/japplphysiol.00421.2014 is OK
- 10.1371/journal.pone.0142533 is OK
- 10.1371/journal.pone.0160644 is OK
- 10.1093/sleep/15.5.461 is OK
- 10.1038/s41598-018-31266-z is OK
- 10.5281/zenodo.1051064 is OK

MISSING DOIs

- None

INVALID DOIs

- None

elyiorgos commented 4 years ago

Hi @lheagy,

Based on the above passing I went ahead and made a new release (0.2.21) and archived it at zenodo with DOI: 10.5281/zenodo.3572581

I made sure the title of the archive matches the title of the paper and that the authors of the archive match the authors of the paper.

Please let me know if everything looks good and if there's anything else for me to take care of. Thank you!

Best, Yiorgos

lheagy commented 4 years ago

Excellent, thanks @elyiorgos! and apologies for my delay - I was at the AGU conference last week and was a bit overloaded.

This looks good. Many thanks @eskofier, @ikarosilva, @nhejazi for your review 🎉

lheagy commented 4 years ago

@whedon set 10.5281/zenodo.3572581 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.3572581 is the archive.

lheagy commented 4 years ago

@whedon set 0.2.21 as version

whedon commented 4 years ago

OK. 0.2.21 is the version.

lheagy commented 4 years ago

:wave: @openjournals/joss-eics, this submission is ready fo final checks!

arfon commented 4 years ago

@whedon accept

whedon commented 4 years ago

Attempting dry run of processing paper acceptance...

whedon commented 4 years ago


OK DOIs

- 10.1152/japplphysiol.00421.2014 is OK
- 10.1371/journal.pone.0142533 is OK
- 10.1371/journal.pone.0160644 is OK
- 10.1093/sleep/15.5.461 is OK
- 10.1038/s41598-018-31266-z is OK
- 10.5281/zenodo.1051064 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 4 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1182

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1182, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

arfon commented 4 years ago

@whedon accept deposit=true

whedon commented 4 years ago

Doing it live! Attempting automated processing of paper acceptance...

whedon commented 4 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 4 years ago

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1183
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01663
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

arfon commented 4 years ago

@eskofier, @ikarosilva, @nhejazi - many thanks for your reviews here and to @lheagy for editing this submission ✨

Also, special congratulations to @lheagy for editing her final JOSS paper. Thanks for all of efforts @lheagy making JOSS the success it is!

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

arfon commented 4 years ago

I'm going to keep this issue upon for a while until the PDF is resolving on GitHub pages...

arfon commented 4 years ago

I'm going to keep this issue upon for a while until the PDF is resolving on GitHub pages...

Update - looks like this is working now.

whedon commented 4 years ago

: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](https://joss.theoj.org/papers/10.21105/joss.01663/status.svg)](https://doi.org/10.21105/joss.01663)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01663">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01663/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01663/status.svg
   :target: https://doi.org/10.21105/joss.01663

This is how it will look in your documentation:

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