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[REVIEW]: Neuropsydia.py: A Python Module for Creating Experiments, Tasks and Questionnaires #259

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whedon opened this Issue May 12, 2017 · 21 comments

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whedon commented May 12, 2017

Submitting author: @DominiqueMakowski (Dominique Makowski)
Repository: https://github.com/neuropsychology/Neuropsydia.py/
Version: 1.0.4
Editor: @arokem
Reviewer: @cMadan
Archive: 10.5281/zenodo.1048777

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/e39d331f658d0501382853ff46bc9776"><img src="http://joss.theoj.org/papers/e39d331f658d0501382853ff46bc9776/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/e39d331f658d0501382853ff46bc9776/status.svg)](http://joss.theoj.org/papers/e39d331f658d0501382853ff46bc9776)

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 questions

Conflict of interest

  • As the reviewer I confirm that there are no conflicts of interest for me to review this work (such as being a major contributor to the software).

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?
  • Version: Does the release version given match the GitHub release (1.0.4)?
  • Authorship: Has the submitting author (@DominiqueMakowski) made major contributions to the software?

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: Have any performance claims of the software been confirmed?

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 function 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

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g. papers, datasets, software)?
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whedon May 12, 2017

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Hello human, I'm @whedon. I'm here to help you with some common editorial tasks for JOSS. @cMadan it looks like you're currently assigned as the reviewer for 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 as reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all JOSS 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
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whedon commented May 12, 2017

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks for JOSS. @cMadan it looks like you're currently assigned as the reviewer for 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 as reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all JOSS 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
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cMadan May 12, 2017

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@DominiqueMakowski - I just did a quick first pass at going through the JOSS reviewer questions, but not yet testing the functionality of the software itself. There are a few things I noticed that need to be addressed, and I will continue and test the code itself within a few days.

Version - You list the software as being version 1.0.4 in the repo, but haven't minted a 'release' in Github to go with this. If someone wanted to specifically run version 1.0.4 in the future, this wouldn't be possible. Also, JOSS will later require you to archive the accepted version of the software in an archival repository (such as Zenodo or figshare), but that isn't necessary yet.

Documentation - the API documentation link in the README is listed as http://neuropsydia.readthedocs.io/en/master/documentation.html, but this appears to only be a skeleton document. In the paper, the link is http://neuropsydia.readthedocs.io/en/latest/documentation.html, which does have content. These should both be linked to the same complete document.

References - DOIs are currently missing.

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cMadan commented May 12, 2017

@DominiqueMakowski - I just did a quick first pass at going through the JOSS reviewer questions, but not yet testing the functionality of the software itself. There are a few things I noticed that need to be addressed, and I will continue and test the code itself within a few days.

Version - You list the software as being version 1.0.4 in the repo, but haven't minted a 'release' in Github to go with this. If someone wanted to specifically run version 1.0.4 in the future, this wouldn't be possible. Also, JOSS will later require you to archive the accepted version of the software in an archival repository (such as Zenodo or figshare), but that isn't necessary yet.

Documentation - the API documentation link in the README is listed as http://neuropsydia.readthedocs.io/en/master/documentation.html, but this appears to only be a skeleton document. In the paper, the link is http://neuropsydia.readthedocs.io/en/latest/documentation.html, which does have content. These should both be linked to the same complete document.

References - DOIs are currently missing.

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arokem Jun 11, 2017

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@DominiqueMakowski : have you had a chance to address the comments that @cMadan made?

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arokem commented Jun 11, 2017

@DominiqueMakowski : have you had a chance to address the comments that @cMadan made?

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DominiqueMakowski Jun 19, 2017

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@arokem I plan to address them by the end of the week. Sorry for the delay!

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DominiqueMakowski commented Jun 19, 2017

@arokem I plan to address them by the end of the week. Sorry for the delay!

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DominiqueMakowski Jun 23, 2017

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Dear @arokem, sorry for the long answer, and thanks a lot to @cMadan for his first comments.

Version - You list the software as being version 1.0.4 in the repo, but haven't minted a 'release' in Github to go with this. If someone wanted to specifically run version 1.0.4 in the future, this wouldn't be possible. Also, JOSS will later require you to archive the accepted version of the software in an archival repository (such as Zenodo or figshare), but that isn't necessary yet.

That has been done. We created a 1.0.4 release on github.

Documentation - the API documentation link in the README is listed as http://neuropsydia.readthedocs.io/en/master/documentation.html, but this appears to only be a skeleton document. In the paper, the link is http://neuropsydia.readthedocs.io/en/latest/documentation.html, which does have content. These should both be linked to the same complete document.

We replaced the wrong links with the correct one.

References - DOIs are currently missing.

This has been modified here accordingly.

Again, thanks a lot and sorry for the delay.

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DominiqueMakowski commented Jun 23, 2017

Dear @arokem, sorry for the long answer, and thanks a lot to @cMadan for his first comments.

Version - You list the software as being version 1.0.4 in the repo, but haven't minted a 'release' in Github to go with this. If someone wanted to specifically run version 1.0.4 in the future, this wouldn't be possible. Also, JOSS will later require you to archive the accepted version of the software in an archival repository (such as Zenodo or figshare), but that isn't necessary yet.

That has been done. We created a 1.0.4 release on github.

Documentation - the API documentation link in the README is listed as http://neuropsydia.readthedocs.io/en/master/documentation.html, but this appears to only be a skeleton document. In the paper, the link is http://neuropsydia.readthedocs.io/en/latest/documentation.html, which does have content. These should both be linked to the same complete document.

We replaced the wrong links with the correct one.

References - DOIs are currently missing.

This has been modified here accordingly.

Again, thanks a lot and sorry for the delay.

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arokem Jul 10, 2017

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@cMadan : any more thoughts here?

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arokem commented Jul 10, 2017

@cMadan : any more thoughts here?

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cMadan Jul 13, 2017

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@arokem - Sorry, I was traveling/on vacation. I will get back to this within the next few days.

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cMadan commented Jul 13, 2017

@arokem - Sorry, I was traveling/on vacation. I will get back to this within the next few days.

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cMadan Jul 21, 2017

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I tried the first example (go/no-go) and got a blank screen--will follow-up with issues in their repo.

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cMadan commented Jul 21, 2017

I tried the first example (go/no-go) and got a blank screen--will follow-up with issues in their repo.

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arokem Jul 23, 2017

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Thanks - ping me here when things are resolved, with pointers to the relevant issues. Thanks again!

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arokem commented Jul 23, 2017

Thanks - ping me here when things are resolved, with pointers to the relevant issues. Thanks again!

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arokem Oct 8, 2017

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Any progress here? @DominiqueMakowski / @cMadan? Have the issues previously identified been resolved?

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arokem commented Oct 8, 2017

Any progress here? @DominiqueMakowski / @cMadan? Have the issues previously identified been resolved?

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For some reason I can't get it to work on my Mac laptop, though someone else was able to get it to work on their Mac. Since I tried this last, I've moved to another uni (and generally been busy)... I will try the package on a Windows machine next week.

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cMadan commented Oct 11, 2017

For some reason I can't get it to work on my Mac laptop, though someone else was able to get it to work on their Mac. Since I tried this last, I've moved to another uni (and generally been busy)... I will try the package on a Windows machine next week.

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@arokem I was able to test the package fine on a Windows 10 PC and it worked great. Also, as mentioned last time another person has had it work on a Mac, so we can leave that debugging for another time. The package does what's supposed to do, is well documented, and the paper seems to be in order. I recommend the submission be accepted at JOSS.

@DominiqueMakowski, sorry for the delay in testing it further!

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cMadan commented Nov 10, 2017

@arokem I was able to test the package fine on a Windows 10 PC and it worked great. Also, as mentioned last time another person has had it work on a Mac, so we can leave that debugging for another time. The package does what's supposed to do, is well documented, and the paper seems to be in order. I recommend the submission be accepted at JOSS.

@DominiqueMakowski, sorry for the delay in testing it further!

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arokem Nov 14, 2017

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Great! @DominiqueMakowski : could you please create an archive (e.g., on zenodo) of the final version of the software and share the DOI here?

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arokem commented Nov 14, 2017

Great! @DominiqueMakowski : could you please create an archive (e.g., on zenodo) of the final version of the software and share the DOI here?

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DominiqueMakowski Nov 14, 2017

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@cMadan Thanks a lot for all your suggestions and comments.

@arokem , the DOI is the following: 10.5281/zenodo.1048777

DOI

Thank you for your work!

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DominiqueMakowski commented Nov 14, 2017

@cMadan Thanks a lot for all your suggestions and comments.

@arokem , the DOI is the following: 10.5281/zenodo.1048777

DOI

Thank you for your work!

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arokem Nov 14, 2017

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@whedon set 10.5281/zenodo.1048777 as archive

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arokem commented Nov 14, 2017

@whedon set 10.5281/zenodo.1048777 as archive

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whedon Nov 14, 2017

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OK. 10.5281/zenodo.1048777 is the archive.

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whedon commented Nov 14, 2017

OK. 10.5281/zenodo.1048777 is the archive.

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arokem Nov 14, 2017

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@arfon : I believe this paper can now be published.

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arokem commented Nov 14, 2017

@arfon : I believe this paper can now be published.

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DominiqueMakowski Nov 21, 2017

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@arokem Should I do something more?

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DominiqueMakowski commented Nov 21, 2017

@arokem Should I do something more?

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arokem Nov 24, 2017

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No. I believe this is in @arfon's hands for the final call.

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arokem commented Nov 24, 2017

No. I believe this is in @arfon's hands for the final call.

@arfon arfon added the accepted label Nov 27, 2017

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@cMadan - many thanks for your review here and to @arokem for editing this one

@DominiqueMakowski - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00259 ⚡️ 🚀 💥

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arfon commented Nov 27, 2017

@cMadan - many thanks for your review here and to @arokem for editing this one

@DominiqueMakowski - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00259 ⚡️ 🚀 💥

@arfon arfon closed this Nov 27, 2017

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DominiqueMakowski Nov 27, 2017

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@cMadan @arokem @arfon Many thanks to the reviewers and editors!

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DominiqueMakowski commented Nov 27, 2017

@cMadan @arokem @arfon Many thanks to the reviewers and editors!

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