[REVIEW]: pypillometry: A Python package for pupillometric analyses #2348

whedon · 2020-06-16T13:50:41Z

Submitting author: @ihrke (Matthias Mittner)
Repository: https://github.com/ihrke/pypillometry
Version: v1.0.0
Editor: @oliviaguest
Reviewers: @samhforbes, @szorowi1, @tjmahr
Archive: 10.5281/zenodo.3925528

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/3b06f4f3d5b703fd99c7e622b7edebe4"><img src="https://joss.theoj.org/papers/3b06f4f3d5b703fd99c7e622b7edebe4/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/3b06f4f3d5b703fd99c7e622b7edebe4/status.svg)](https://joss.theoj.org/papers/3b06f4f3d5b703fd99c7e622b7edebe4)

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

@samhforbes & @szorowi1, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
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 @oliviaguest know.

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

Review checklist for @samhforbes

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

I confirm that I read and will adhere to the JOSS 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 (@ihrke) 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 @szorowi1

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

I confirm that I read and will adhere to the JOSS 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 (@ihrke) 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 @tjmahr

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

I confirm that I read and will adhere to the JOSS 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 (@ihrke) 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?

The text was updated successfully, but these errors were encountered:

whedon · 2020-06-16T13:50:45Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @samhforbes, @szorowi1 it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ 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:

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

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

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

@whedon generate pdf

whedon · 2020-06-16T13:51:11Z

Reference check summary:

OK DOIs

- 10.5334/joc.18 is OK
- 10.1126/science.132.3423.349 is OK
- 10.3758/s13428-020-01374-8 is OK
- 10.1146/annurev.neuro.28.061604.135709 is OK
- 10.3758/cabn.10.2.252 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2020-06-16T13:51:28Z

👉 Check article proof 📄 👈

oliviaguest · 2020-06-16T13:54:06Z

Hi all! 👋 Thank you so much, @samhforbes, @szorowi1, @tjmahr for accepting to review this software package and paper by @ihrke! 😊

Any questions, feedback on the paper, etc., please post here. Any very code-specific questions, suggestions, etc., please use the issues in the code repo and link to them from this thread so we can all keep track of them. 🌸

Thank you again, Sams and Tristan!

oliviaguest · 2020-06-16T15:29:07Z

@whedon add @tjmahr as reviewer

whedon · 2020-06-16T15:29:13Z

OK, @tjmahr is now a reviewer

oliviaguest · 2020-06-22T13:30:10Z

Can @samhforbes, @szorowi1, and @tjmahr give me a rough ETA on their reviews please? ☺️

samhforbes · 2020-06-24T14:27:41Z

Installation instructions: Is there a clearly-stated list of dependencies? Link to more in depth installation instructions for PySTan:
ihrke/pypillometry#4

Example usage and functionality documentation
ideally would have documentation on modelling data. ihrke/pypillometry#1

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
ihrke/pypillometry#2

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?
DOIs need to be included for a number of papers. See ihrke/pypillometry#3

ihrke · 2020-06-25T09:35:27Z

@whedon generate pdf

whedon · 2020-06-25T09:35:50Z

PDF failed to compile for issue #2348 with the following error:

Can't find any papers to compile :-(

oliviaguest · 2020-06-25T10:32:34Z

@whedon generate pdf

whedon · 2020-06-25T10:33:16Z

👉 Check article proof 📄 👈

oliviaguest · 2020-06-26T21:18:46Z

@whedon add @tjmahr as reviewer

whedon · 2020-06-26T21:18:52Z

OK, @tjmahr is now a reviewer

oliviaguest · 2020-06-26T21:19:38Z

@whedon re-invite @tjmahr as reviewer

whedon · 2020-06-26T21:19:41Z

The reviewer already has a pending invite.

@tjmahr please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

whedon · 2020-07-01T15:28:05Z

Attempting dry run of processing paper acceptance...

whedon · 2020-07-01T15:28:50Z

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#1529

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1529, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

oliviaguest · 2020-07-01T15:29:28Z

@ihrke dunno why @whedon ignored me the first time — check final proof please and an EiC will pop by soon and do the deal fully. 🥳

ihrke · 2020-07-01T15:34:30Z

this looks nice, all links in the final PDF are functioning 👍

danielskatz · 2020-07-01T16:52:38Z

@ihrke - can you edit the metadata in the zenodo archive so that the title matches the title of the paper?

danielskatz · 2020-07-01T16:54:34Z

Once you do so, this appears ready to publish

ihrke · 2020-07-02T07:05:58Z

Thanks @danielskatz, I fixed it.

danielskatz · 2020-07-02T12:17:51Z

@whedon accept deposit=true

whedon · 2020-07-02T12:17:54Z

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

whedon · 2020-07-02T12:19:08Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2020-07-02T12:19:08Z

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.02348 joss-papers#1535
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02348
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz · 2020-07-02T12:25:51Z

Thanks to @samhforbes, @szorowi1, @tjmahr for reviewing!
And @oliviaguest for editing!

Congratulations to @ihrke (Matthias Mittner)!!

whedon · 2020-07-02T12:26:08Z

🎉🎉🎉 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.02348/status.svg)](https://doi.org/10.21105/joss.02348)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02348">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02348/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02348/status.svg
   :target: https://doi.org/10.21105/joss.02348

This is how it will look in your documentation:

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

whedon added the review label Jun 16, 2020

whedon assigned oliviaguest Jun 16, 2020

whedon mentioned this issue Jun 16, 2020

[PRE REVIEW]: pypillometry: A Python package for pupillometric analyses #2269

Closed

whedon assigned oliviaguest and unassigned oliviaguest Jun 16, 2020

whedon assigned samhforbes and szorowi1 Jun 16, 2020

whedon assigned oliviaguest, samhforbes and szorowi1 and unassigned szorowi1, oliviaguest and samhforbes Jun 26, 2020

whedon assigned tjmahr Jun 27, 2020

whedon added accepted published Papers published in JOSS labels Jul 2, 2020

danielskatz closed this as completed Jul 2, 2020

oliviaguest mentioned this issue Jul 16, 2020

[REVIEW]: Automated Sleep Stage Scoring Using k-Nearest Neighbors Classifier #2377

Closed

76 tasks

oliviaguest mentioned this issue Aug 31, 2020

[REVIEW]: biopeaks: a graphical user interface for feature extraction from heart- and breathing biosignals #2621

Closed

60 tasks

oliviaguest mentioned this issue Nov 25, 2020

[REVIEW]: Synthia: multi-dimensional synthetic data generation in Python #2863

Closed

40 tasks

oliviaguest mentioned this issue Dec 7, 2020

[REVIEW]: Learning Simulator: A simulation software for animal and human learning #2891

Closed

40 tasks

This was referenced Feb 15, 2021

[REVIEW]: splithalf: robust estimates of split half reliability #3041

Closed

[REVIEW]: fastPLI: A Fiber Architecture Simulation Toolbox for 3D-PLI #3042

Closed

oliviaguest mentioned this issue Apr 12, 2021

[REVIEW]: BIDSonym - a BIDSapp for the pseudo-anonymization of neuroimaging datasets #3169

Closed

60 tasks

oliviaguest mentioned this issue May 10, 2021

[REVIEW]: Fear Learning and Anxiety Response (FLARe): Open-source software for remote human fear conditioning experiments. #3270

Closed

60 tasks

oliviaguest mentioned this issue Aug 30, 2021

[REVIEW]: TE-dependent analysis of multi-echo fMRI with *tedana* #3669

Closed

40 tasks

oliviaguest mentioned this issue Nov 29, 2021

[REVIEW]: BCImat: a Matlab-based framework for Intracortical Brain-Computer Interfaces and their simulation with an artificial spiking neural network #3956

Closed

40 tasks

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

[REVIEW]: pypillometry: A Python package for pupillometric analyses #2348

[REVIEW]: pypillometry: A Python package for pupillometric analyses #2348

whedon commented Jun 16, 2020 •

edited

Loading

whedon commented Jun 16, 2020

whedon commented Jun 16, 2020

whedon commented Jun 16, 2020

oliviaguest commented Jun 16, 2020 •

edited

Loading

oliviaguest commented Jun 16, 2020

whedon commented Jun 16, 2020

oliviaguest commented Jun 22, 2020

samhforbes commented Jun 24, 2020

ihrke commented Jun 25, 2020

whedon commented Jun 25, 2020

oliviaguest commented Jun 25, 2020

whedon commented Jun 25, 2020

oliviaguest commented Jun 26, 2020

whedon commented Jun 26, 2020

oliviaguest commented Jun 26, 2020

whedon commented Jun 26, 2020

whedon commented Jul 1, 2020

whedon commented Jul 1, 2020

oliviaguest commented Jul 1, 2020

ihrke commented Jul 1, 2020

danielskatz commented Jul 1, 2020

danielskatz commented Jul 1, 2020

ihrke commented Jul 2, 2020

danielskatz commented Jul 2, 2020

whedon commented Jul 2, 2020

whedon commented Jul 2, 2020

whedon commented Jul 2, 2020

danielskatz commented Jul 2, 2020

whedon commented Jul 2, 2020

[REVIEW]: pypillometry: A Python package for pupillometric analyses #2348

[REVIEW]: pypillometry: A Python package for pupillometric analyses #2348

Comments

whedon commented Jun 16, 2020 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @samhforbes

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @szorowi1

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @tjmahr

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Jun 16, 2020

whedon commented Jun 16, 2020

whedon commented Jun 16, 2020

oliviaguest commented Jun 16, 2020 • edited Loading

oliviaguest commented Jun 16, 2020

whedon commented Jun 16, 2020

oliviaguest commented Jun 22, 2020

samhforbes commented Jun 24, 2020

ihrke commented Jun 25, 2020

whedon commented Jun 25, 2020

oliviaguest commented Jun 25, 2020

whedon commented Jun 25, 2020

oliviaguest commented Jun 26, 2020

whedon commented Jun 26, 2020

oliviaguest commented Jun 26, 2020

whedon commented Jun 26, 2020

whedon commented Jul 1, 2020

whedon commented Jul 1, 2020

oliviaguest commented Jul 1, 2020

ihrke commented Jul 1, 2020

danielskatz commented Jul 1, 2020

danielskatz commented Jul 1, 2020

ihrke commented Jul 2, 2020

danielskatz commented Jul 2, 2020

whedon commented Jul 2, 2020

whedon commented Jul 2, 2020

whedon commented Jul 2, 2020

danielskatz commented Jul 2, 2020

whedon commented Jul 2, 2020

whedon commented Jun 16, 2020 •

edited

Loading

oliviaguest commented Jun 16, 2020 •

edited

Loading