Joss-reviews: [REVIEW]: pd-parser: A tool for Matching Photodiode Deflection Events to Time-Stamped Events

[whedon]

Submitting author: @alexrockhill (Alexander Rockhill)
Repository: https://github.com/alexrockhill/pd-parser
Version: v0.3
Editor: @oliviaguest
Reviewers: @rougier, @rly, @libertyh
Archive: 10.5281/zenodo.4122049

:warning: JOSS reduced service mode :warning:

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

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Markdown: [![status](https://joss.theoj.org/papers/5ca2ad9880e4606376bb8d69321e7aea/status.svg)](https://joss.theoj.org/papers/5ca2ad9880e4606376bb8d69321e7aea)

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

@rougier & @rly, 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
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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @oliviaguest know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @rougier

Conflict of interest

• [x] 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

• [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] Contribution and authorship: Has the submitting author (@alexrockhill) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [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] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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 @libertyh

Conflict of interest

• [x] 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

• [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] Contribution and authorship: Has the submitting author (@alexrockhill) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [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] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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 @rly

Conflict of interest

• [x] 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

• [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] Contribution and authorship: Has the submitting author (@alexrockhill) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [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] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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?

[whedon]

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

:warning: JOSS reduced service mode :warning:

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.

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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 😿

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

@whedon generate pdf

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1038/sdata.2016.44 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.1038/sdata.2018.110 is OK
- 10.1038/s41597-019-0104-8 is OK
- 10.1038/s41597-019-0105-7 is OK
- 10.21105/joss.01896 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[oliviaguest]

Hey 👋 @rougier, @rly, @libertyh: this is where the review will take place. Please make sure to read the instructions above.

For any and all things worthy of discussion or comment, use this issue right here — so drop comments or questions for me, the author, etc., here. For any very code-specific things please feel free to start an issue on the repo of the code itself (if appropriate!) and link back to it from here. For an example of how this process plays out feel free to skim previous reviews, such as: #2285 and #2348. ☺️

[oliviaguest]

@whedon add @libertyh as reviewer

[whedon]

OK, @libertyh is now a reviewer

[oliviaguest]

@whedon generate pdf

[whedon]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[oliviaguest]

Hey @rougier, @rly, @libertyh — when you get a chance can you give me an ETA for your reviews, please?

[rly]

@oliviaguest I'll have this done by October 8.

[rougier]

Same here, thanks for the reminder !

[libertyh]

I should be done by Oct 8 as well, thanks!

[oliviaguest]

@whedon remind @rly in 9 days

[whedon]

Reminder set for @rly in 9 days

[oliviaguest]

@whedon remind @libertyh in 9 days

[whedon]

Reminder set for @libertyh in 9 days

[oliviaguest]

@whedon remind @rougier in 9 days

[whedon]

Reminder set for @rougier in 9 days

[rougier]

@oliviaguest I'm jealous of whedon (I'm the reminder bot for ReScience...)

[oliviaguest]

@rougier it's so cute — see: https://joss.readthedocs.io/en/latest/whedon.html

[rougier]

@guest I can do all these command on ReScience (just replace whedon by rougier)...

@alexrockhill I'started testing your software and opened an issue on your repo. You already addressed one of my issue, could you have a look at the new one?

[oliviaguest]

@rougier can you link to any relevant issues here please, so we can all have them organised and accessible? 😊

[rougier]

Sure, here is is: https://github.com/alexrockhill/pd-parser/issues/1. And I realized my second post was not not posted.

[rly]

Hi @alexrockhill, I have reviewed your software and paper. Overall, the software and paper look good. There were a few issues to address, as per the JOSS paper guidelines/rubric. I created a few issues in your repo:
https://github.com/alexrockhill/pd-parser/issues/2
https://github.com/alexrockhill/pd-parser/issues/3
https://github.com/alexrockhill/pd-parser/issues/4

Suggestions:
https://github.com/alexrockhill/pd-parser/issues/5

[rly]

@alexrockhill has addressed all of my concerns and, in my view, has met all of the review criteria. I would be happy to discuss this paper with the other reviewers when they are ready.

[rougier]

the two provided examples are now working properly on my machine. I think it would be nice to have these exampls tests alongside the pd_parser such that you can type pd_parser.test() to check everything's ok. And/or you could also have very simple unittests that would help you spotting discrepancies in the API. Apart from these minor points, I'm satisfied with the submission.

[alexrockhill]

the two provided examples are now working properly on my machine. I think it would be nice to have these exampls tests alongside the pd_parser such that you can type pd_parser.test() to check everything's ok. And/or you could also have very simple unittests that would help you spotting discrepancies in the API. Apart from these minor points, I'm satisfied with the submission.

Good idea, I added unit tests for the examples to make sure they run with this commit https://github.com/alexrockhill/pd-parser/commit/9086579ba5ca615bc9a2d9e03ede3c406c780073. They don't check whether they look right, the only way to do that is by eye, but you can run pytest and it will test everything including the examples now as described in the contributing guidelines https://github.com/alexrockhill/pd-parser/blob/master/CONTRIBUTING.md.

[libertyh]

I've also started my review and left some comments about the README and the paper text so far as issues in the pd-parser repo. @oliviaguest I think I may need to be re-invited to the repo (sorry!!) in order to complete the checklist. Will link to my issues in a bit when complete!

[oliviaguest]

@whedon re-invite @libertyh as reviewer

[whedon]

OK, the reviewer has been re-invited.

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

[oliviaguest]

No worries, @libertyh. With respect to your feedback please link to all issues you have opened here in this thread, so we can all easily take a look — ta!

[whedon]

:wave: @rougier, please update us on how your review is going.

[whedon]

:wave: @libertyh, please update us on how your review is going.

[rougier]

Good bot ! I forgot to check one box and I just remember I had a question about co-authors. They do not seem to have commited anything in the repo. @alexrockhill Could you explain their role ?

[alexrockhill]

Good bot ! I forgot to check one box and I just remember I had a question about co-authors. They do not seem to have commited anything in the repo. @alexrockhill Could you explain their role ?

Dr. Raslan and Dr. Swann have actively supervised, reviewed and given high-level direction of both the software package and the physical setup for data collection that is used in the example data and discussed in the paper. And helped write and edit the paper.

Thanks for bringing that up to clarify!

[libertyh]

Hi everyone! Thanks @alexrockhill for starting to address my comments. I'm including the issues I opened here:

alexrockhill/pd-parser#6
alexrockhill/pd-parser#7
alexrockhill/pd-parser#8

Most of these have to do with clarifications to the usage of pd-parser so that it's as easy as possible for your end users to get started. I was able to get the code to work on my machine with the jupyter notebook examples. Happy to discuss when everyone is ready.

[alexrockhill]

Just pinging this thread to keep things moving forward.

[rly]

Everything looks good on my end. The new example mentioned in https://github.com/alexrockhill/pd-parser/issues/7 looks good too. @alexrockhill I would encourage you to git tag the new version and make a new release both on PyPI and on GitHub.

Pending that, I think that the tool and paper are both suitable for publication on JOSS.

[libertyh]

Looks good to me too, I agree with @rly that following the new release this is acceptable for publication in JOSS.

[alexrockhill]

Ok, releasing 0.3 now!

[alexrockhill]

@whedon set 0.3 as version

[whedon]

I'm sorry @alexrockhill, I'm afraid I can't do that. That's something only editors are allowed to do.

[alexrockhill]

Oops, I guess @oliviaguest has to do that.

[alexrockhill]

Here's the DOI for the 0.3 release as well http://doi.org/10.5281/zenodo.4122049

[oliviaguest]

@whedon set v0.3 as version

[whedon]

OK. v0.3 is the version.

[oliviaguest]

@alexrockhill can you change the title of the zenodo repo to match the title of your paper, please? ☺️

[oliviaguest]

@whedon check references

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1038/sdata.2016.44 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.1038/sdata.2018.110 is OK
- 10.1038/s41597-019-0104-8 is OK
- 10.1038/s41597-019-0105-7 is OK
- 10.21105/joss.01896 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[oliviaguest]

@whedon set 10.5281/zenodo.4122049 as archive

[whedon]

OK. 10.5281/zenodo.4122049 is the archive.

[oliviaguest]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1038/sdata.2016.44 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.1038/sdata.2018.110 is OK
- 10.1038/s41597-019-0104-8 is OK
- 10.1038/s41597-019-0105-7 is OK
- 10.21105/joss.01896 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1851

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1851, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[alexrockhill]

@alexrockhill can you change the title of the zenodo repo to match the title of your paper, please? ☺️

Fixed!

Yay thank you all for the review, it was a very positive and helpful experience!

[kyleniemeyer]

@alexrockhill Hi there, I am the EIC on duty this week doing some final checks before publishing. There are just a few things I noticed:

• Can you break up the text of your article into paragraphs? Right now it sort of looks like a wall of text in each section.
• Can you add your co-authors to the Zenodo archive? That author list should match the paper as well.

[alexrockhill]

Thanks for the copy editing, @kyleniemeyer, those suggested changes have been implemented!

[kyleniemeyer]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1038/sdata.2016.44 is OK
- 10.3389/fnins.2013.00267 is OK
- 10.1038/sdata.2018.110 is OK
- 10.1038/s41597-019-0104-8 is OK
- 10.1038/s41597-019-0105-7 is OK
- 10.21105/joss.01896 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1854

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1854, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[kyleniemeyer]

@alexrockhill looks good, thanks!

[kyleniemeyer]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/1855
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02674
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...

[kyleniemeyer]

Congrats @alexrockhill on your article's publication in JOSS!

Many thanks to @rougier, @rly, and @libertyh for reviewing this, and @oliviaguest for editing.

[whedon]

: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.02674/status.svg)](https://doi.org/10.21105/joss.02674)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02674">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02674/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02674/status.svg
   :target: https://doi.org/10.21105/joss.02674

This is how it will look in your documentation:

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[oliviaguest]

@rougier, @rly, @libertyh thank you for all your hard work and congratulations to @alexrockhill! 😊

[alexrockhill]

Thank you Nicolas, Ryan and Liberty for a super helpful review and Olivia for editing!! And Kyle for copy editing! 😊