Devicely: A Python package for reading, timeshifting and writing sensor data

[arianesasso]

Submitting Author: Ariane Sasso (@arianesasso)
All current maintainers: @arianesasso
Package Name: Devicely
One-Line Description of Package: A Python package for reading, timeshifting and writing sensor data
Repository Link: https://github.com/hpi-dhc/devicely
Version submitted: 0.2.5
Editor: @xmnlab
Reviewer 1: @willingc
Reviewer 2: @agricolab
Archive:
JOSS DOI:
Version accepted: v1.1.1
Date accepted (month/day/year): 08/19/2021

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Description

Wearable devices can track a multitude of parameters such as heart rate, body temperature, blood oxygen saturation, acceleration, blood glucose and much more [Kamisalic2018]. Moreover, they are becoming increasingly popular with a steeping increase in market presence in 2020 alone [IDC2020]. Applications for wearable devices varies from tracking cardiovascular risks [Bayoumy2021] to identifying COVID-19 onset [Mishra2020]. Therefore, there is a great need for scientists to easily go through data acquired from different wearables. In order to solve this problem and empower scientists working with biosignals, we developed the devicely package. It represents the data in a science-friendly format and lets scientists focus on what they want: the analysis of biosignals.

Scope

• Please indicate which category or categories this package falls under:
  • Data retrieval
  • Data extraction
  • Data munging
  • Data deposition
  • Reproducibility
  • Geospatial
  • Education
  • Data visualization*

* Please fill out a pre-submission inquiry before submitting a data visualization package. For more info, see notes on categories of our guidebook.

• Explain how the and why the package falls under these categories (briefly, 1-2 sentences):
  We developed this package for scientists to easily go through data acquired from different wearables.

• Who is the target audience and what are scientific applications of this package?
  Scientists working with wearable devices.

• Are there other Python packages that accomplish the same thing? If so, how does yours differ?
  Not to our knowledge.

• If you made a pre-submission enquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted:

Technical checks

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• has an OSI approved license.
• contains a README with instructions for installing the development version.
• includes documentation with examples for all functions.
• contains a vignette with examples of its essential functions and uses.
• has a test suite.
• has continuous integration, such as Travis CI, AppVeyor, CircleCI, and/or others.

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• The package is deposited in a long-term repository with the DOI: 10.5281/zenodo.4661545

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• Yes I am OK with reviewers submitting requested changes as issues to my repo. Reviewers will then link to the issues in their submitted review.

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[lwasser]

hi @arianesasso ! thank you for this submission! i know it's been sitting for a while. I am just catching up and will get back to you regarding next steps!

[lwasser]

this package is definitely in scope for pyopensci review!.

[lwasser]

@arianesasso we are moving on this - we have an editor and reviewers are underway. more to come soon. @xmnlab will be the editor for this package review.

[xmnlab]

@arianesasso @lwasser, adding initial editor checks here.

@arianesasso we are lining up reviewers for your package. When we receive the confirmation I will update the text here with this information.

Editor checks:

• Fit: The package meets criteria for fit and overlap.
• Automated tests: Package has a testing suite and is tested via Travis-CI or another CI service.
• License: The package has an OSI accepted license
• Repository: The repository link resolves correctly
• Archive (JOSS only, may be post-review): The repository DOI resolves correctly
• Version (JOSS only, may be post-review): Does the release version given match the GitHub release (v1.0.0)?

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Editor comments

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Reviewers: @willingc @agricolab

Due date: June. 14th

[xmnlab]

Hi @willingc! @lwasser told me that she has talked to you about reviewing a package for pyopensci! that sounds great!

PyOpenSci contributing guide is here https://www.pyopensci.org/contributing-guide/intro.html

This is the guide specifically for reviewers: https://www.pyopensci.org/contributing-guide/open-source-software-submissions/reviewer-guide.html

This is my first time acting as editor, so I still in the learning curve process :) I have reviewed some packages here so feel free to ping me anytime you need any information or help.

I am waiting for the confirmation of one more reviewer and after that, I will update the schedules for this review.

thank you so much for your support :)

[xmnlab]

Hi @agricolab!

@NickleDave told me you are available to review this package, thank you so much!

PyOpenSci contributing guide is here https://www.pyopensci.org/contributing-guide/intro.html

And this is the guide specifically for reviewers: https://www.pyopensci.org/contributing-guide/open-source-software-submissions/reviewer-guide.html

As I mentioned before, this is my first time acting as an editor, so I still in the learning curve process :) I have reviewed some packages here so feel free to ping me anytime you need any information or help.

I am updating today some information in the first comment in this issue, including the due date for the reviews.

thank you so much for your support!

[xmnlab]

@arianesasso @agricolab @willingc @lwasser

I updated the information here
#37 (comment)

Let me know if I can help in any way! thank you all!

[agricolab]

Looking forward, will start reviewing next week!

[xmnlab]

thank you so much @agricolab, I really appreciate that!

[willingc]

@xmnlab I started last night and made some notes in a gist

[arianesasso]

@arianesasso we are moving on this - we have an editor and reviewers are underway. more to come soon. @xmnlab will be the editor for this package review.

Thank you so much for all your hard work!

[xmnlab]

that sounds great @willingc . thank you so much!

[agricolab]

Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

• As the reviewer I confirm that there are no conflicts of interest for me to review this work (If you are unsure whether you are in conflict, please speak to your editor before starting your review).

Documentation

The package includes all the following forms of documentation:

• A statement of need clearly stating problems the software is designed to solve and its target audience in README
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• Vignette(s) demonstrating major functionality that runs successfully locally
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• Examples for all user-facing functions
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The package meets the readme requirements below:

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The README should include, from top to bottom:

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Package structure should follow general community best-practices. In general please consider:

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Functionality

• Installation: Installation succeeds as documented.
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For packages co-submitting to JOSS

• The package has an obvious research application according to JOSS's definition in their submission requirements.

Note: Be sure to check this carefully, as JOSS's submission requirements and scope differ from pyOpenSci's in terms of what types of packages are accepted.

The package contains a paper.md matching JOSS's requirements with:

• A short summary describing the high-level functionality of the software
• Authors: A list of authors with their affiliations
• A statement of need clearly stating problems the software is designed to solve and its target audience.
• References: with DOIs for all those that have one (e.g. papers, datasets, software).

Final approval (post-review)

• The author has responded to my review and made changes to my satisfaction. I recommend approving this package.

Estimated hours spent reviewing:

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Review Comments

• Some badges are missing (test coverage, repostatus.org)
• Almost all tests failed when running locally on my machine (see Many tests fail when running locally with outdated dependencies hpi-dhc/devicely#19)
• Faros is apparently ignored during CI/ automated tests? When i run it locally, it works, though. Please explain the reason for ignoring it, though, so i can consider whether the item "automated tests" is fullfilled.
• HISTORY/CHANGELOG.md missing in root directory (see https://www.pyopensci.org/contributing-guide/authoring/release.html#history-news-changelog-file)
• A comparison to other packages should be included in the paper.md
• my review is finished, waiting for authors response.

Considering all tests pass when the most recent dependencies are used, and from browsing through the tests, i consider all functionalities and performance claims to be confirmed.

[agricolab]

@xmnlab is this a co-submission to JOSS?

[arianesasso]

@xmnlab is this a co-submission to JOSS?

@agricolab that was our goal :), the paper is in inst/paper.md

[xmnlab]

thanks @arianesasso for the quick response :)

[agricolab]

Dear @arianesasso, i finished my review, looking forward to your response!

[arianesasso]

Dear @arianesasso, i finished my review, looking forward to your response!

Dear @agricolab, thank you so much for reviewing our package! We will go through the comments this week :).

[xmnlab]

thank you so much for your review @agricolab !

[arianesasso]

Dear @agricolab, thanks again for the great review! We added a repostatus.org badge to the repository and will add another one with test coverage (possibly https://github.com/nedbat/coveragepy; other suggestions are welcomed as well). We will fix hpi-dhc/devicely#19. Also, thanks for pointing out the issue with FAROS in CI/tests (we are investigating). More, we will add HISTORY/CHANGELOG.md which is indeed missing in the root directory; and we are currently writing a new section in the paper.md with the comparison to other packages (great point). We will notify everyone when the changes are ready :).

[xmnlab]

@willingc, just a friendly reminder about the review deadline June. 14th (tomorrow). Let me know if you would need extra time to finish your review. thank you so much!

[willingc]

@xmnlab Should be good to wrap up later this evening 👍🏼

[lwasser]

@xmnlab it looks to me like you nailed it! i removed some of the older labels just so it's clear what stage this package is in. this is minor :) but i think we can assume reviewers were found, etc at this point! I'm so so glad the editors guide is clear. i' spent a lot of time on it and know it probably needs fresh eyes to read it but also know i need to work on the maintainer guide next :) so thank you for that feedback!!

I think now we just let JOSS do it's thing. @arianesasso please be sure to reference this issue when submitting to JOSS so we have a clear record of it. Also please make sure there is a paper.md file following all of JOSS' criteria BEFORE you submit there. I do see that my template above doesn't mention the paper.md file does it? I also see that we may want to talk with JOSS about whether they read the paper or we do or both? regardless @xmnlab you did a fantastic job pushing this through the review process!! Thank you. And thank you again to our reviewers @willingc @agricolab . ALL- we are open to any and all feedback as we improve our review processing and documentation.

[willingc]

@lwasser @xmnlab This was the smoothest review process that I have done. Thank you for being so organized. It was a pleasure reviewing with @agricolab too.

Good luck with the project @arianesasso 😄

[agricolab]

Great! Thanks to everyone involved, and good luck with the project!

[arianesasso]

Dear @xmnlab, I think I addressed all of the points till the JOSS submission :). We also released 1.1.0. Thank you for all your effort! Also, thanks for the awesome revision and help from @agricolab @willingc and @lwasser! For us the process was very smooth and interesting! We found all the feedback really helpful to improve the quality of the package ;).

ps: I would like to know more ablout: Move Package to PyOpenSci Organization

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🎉 devicely has been approved by pyOpenSci! Thank you @arianesasso for submitting devicely and many thanks to @willingc and @agricolab for reviewing this package! 😸

There are a few things left to do to wrap up this submission:

• [ x ] Activate Zenodo watching the repo if you haven't already done so.
• [ x ] Tag and create a release to create a Zenodo version and DOI.
• [ x ] Add the badge for pyOpenSci peer-review to the README.md of devicely. The badge should be [![pyOpenSci](https://tinyurl.com/y22nb8up)](https://github.com/pyOpenSci/software-review/issues/issue-number)
• [ x ] Add devicely to the pyOpenSci website. @arianesasso, please open a pr to update this file: to add your package and name to the list of contributors
• [ x ] @arianesasso, @willingc and @agricolab if you have time and are open to being listed on our website, please add yourselves to this file via a pr so we can list you on our website as contributors!

It looks like you would like to submit this package to JOSS. Here are the next steps:

• [ x ] Login to the JOSS website and fill out the JOSS submission form using your Zenodo DOI. When you fill out the form, be sure to mention and link to the approved pyOpenSci review. JOSS will tag your package for expedited review if it is already pyOpenSci approved.
• Wait for a JOSS editor to approve the presubmission (which includes a scope check)
• Once the package is approved by JOSS, you will be given instructions by JOSS about updating the citation information in your README file.
• When the JOSS review is complete, add a comment to your review in the pyOpenSci software-review repo that it has been approved by JOSS.

All -- if you have any feedback for us about the review process please feel free to share it here. We are always looking to improve our process and our documentation in the contributing-guide. We have also been updating our documentation to improve the process so all feedback is appreciated!

PS: Optional - Move Package to PyOpenSci Organization (BETA)

rOpenSci packages often live in the rOpenSci organization. PyOpenSci is still figuring out whether this model fits for the Python community. If you are interested in this option, let us know and we can provide more instructions for that.

[xmnlab]

@arianesasso, that sounds great! thank you so much.

About Move Package to PyOpenSci Organization, I am checking the steps for that I will be back here with this information soon.

thanks!

[xmnlab]

@arianesasso, I have checked it with @lwasser and, for now, PyOpenSci is still figuring out whether this model fits for the Python community.

We are very open to this option, but first, we would need to understand better why authors from the Python community would like to have this option and we can define a protocol for that.

Do you mind explaining to us why you would like to move your package to PyOpenSci organization?

Thank you so much!

[arianesasso]

@xmnlab thanks for checking :). Initially I asked out of curiosity. I guess that one benefit would be for the users looking for particular packages. But I think the listing of the packages in the website already solves that problem :). I could also see a case for researchers producing packages out of an organization and that would like to move them to PyOpenSci. In my case, since I am already part of an organization I guess it wouldn’t make much sense. Thank you 😊!

[xmnlab]

@arianesasso thank you so much for the detailed information. If we decided to move this option forward I will let you know.
thanks!

[lwasser]

hi there @arianesasso !! i am checkin in on this review. Did you end up moving forward with submitting to JOSS to get your cross-ref validated DOI? If you decided against it I am going to close this issue and remove the JOSS tag. If you did - can you kindly send us a link to the JOSS issue? Many thanks.

In the future we do plan to discuss the option of moving repos over to the pyopensci organization in the same way that ropensci does so that input is noted. So far most of our submissions have been happy with remaining in their own organizations but that doesn't mean that all will want to be treated that way.

[arianesasso]

Hi @lwasser, we did publish it on JOSS :). Here is the link: https://joss.theoj.org/papers/10.21105/joss.03679

Thanks for letting us know! For now, we are also ok with having it in our organization.

Cheers!

[lwasser]

oh @arianesasso wonderful. we'd like to reference the issue in JOSS that you published. can you kindly add the link here and then I will close this with the tag "joss approved"? Thank you so much for following up!! We like to keep track of the joss/pyos partnership reviews!!

[arianesasso]

Thank you for following up :).

This is the link: https://joss.theoj.org/papers/10.21105/joss.03679

Does it work for you?

[lwasser]

Thank you @arianesasso i was looking for this guy: openjournals/joss-reviews#3679

It looks like you went through a second review :) that's fine but you didn't need to once accepted here! but that's wonderful that you put in that extra effort!!! Thank you so much I am going to close this issue now!

[arianesasso]

Ah, I see, sorry 🙈 .

Yes, I thought I had to do both. But in the end, I think they were all valuable 😄 .

Thank you again for all your support!

[lwasser]

hey 👋 @arianesasso @willingc @NickleDave @xmnlab @agricolab ! I hope that you are all well. I am reaching out here to all reviewers and maintainers about pyOpenSci now that i am working full time on the project (read more here). We have a survey that we'd like for you to fill out so we can:

🔗 HERE IS THE SURVEY LINK 🔗

1. invite you to our slack channel to participate in our community (if you wish to join - no worries if that is not how you prefer to communicate / participate).
2. Collect information from you about how we can improve our review process and also better serve maintainers.
   The survey should take about 10 minutes to complete depending upon how much you decide to write. This information will help us greatly as we make decisions about how pyOpenSci grows and serves the community. Thank you so much in advance for filling it out.

NOTE: this is different from the form designed for reviewers to sign up to review.
IMPORTANT: If there are other maintainers for this project, please ping them here and ask them to fill out the survey as well. It is important that we ensure packages are supported long term or sunsetted with sufficient communication to users. Thus we will check in with maintainers annually about maintenance.

Thank you in advance for doing this and supporting pyOpenSci.

[lwasser]

Good. morning @willingc @agricolab I know that everyone is super busy BUT if you have just 5-10 minutes to fill our our onboarding / feedback survey for this review i'd greatly appreciate it!! Many thanks in advance for your time. it really helps our organization!
🔗 HERE IS THE SURVEY LINK 🔗