[REVIEW]: Diff_classifier: Parallelization of multi-particle tracking video analyses #989

whedon · 2018-09-30T18:12:40Z

Submitting author: @ccurtis7 (Chad Curtis)
Repository: https://github.com/ccurtis7/diff_classifier
Version: v0.1-beta
Editor: @cMadan
Reviewer: @stsievert
Archive: 10.5281/zenodo.2631862

Status

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

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

Review checklist for @stsievert

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

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?
Version: v0.1-beta
Authorship: Has the submitting author (@ccurtis7) 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.
- see MAINT: resolve install depedencies (and add note to install master) Nance-Lab/diff_classifier#18
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)?

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

whedon · 2018-09-30T18:12:43Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @stsievert it looks like you're currently assigned as the reviewer for this paper 🎉.

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whedon · 2018-09-30T18:12:43Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-09-30T18:13:15Z

👉 Check article proof 📄 👈

cMadan · 2018-09-30T18:14:46Z

@stsievert, let me know if you have any questions!

ccurtis7 · 2018-11-05T19:21:15Z

@stsievert, I wanted to find out how the review is coming along, and if there is anything you need from me. Thanks!

stsievert · 2018-11-13T05:19:25Z

Thanks for the reminder @ccurtis7. I've started it, and will try to finish it this week. My apologies for the delay.

stsievert · 2018-11-25T03:12:14Z

@ccurtis7 could you add DOIs for first 4 papers in papers.bib? i.e., the Chenouard:2014 reference should have a DOI of https://doi.org/10.1038/nmeth.2808.

ccurtis7 · 2019-01-07T15:55:05Z

I forgot to mention that I went and updated the papers.bib file as requested.

ccurtis7 · 2019-01-07T15:56:45Z

@stsievert I hope you had a good winter break! I noticed that you have checked everything except installation and performance. I believe I have addressed all the issues you brought up.

Let me know if I can do anything else to finish up!

stsievert · 2019-01-09T04:10:01Z

Thanks for the ping @ccurtis7, and my apologies for the excessive delay.

I think this paper is coming to an acceptable state. Past the issues/PRs I've filed, I think the only blocker is verification of the CloudKnot parallelization claims. I'll try to do that this weekend.

cMadan · 2019-02-12T23:25:54Z

@ccurtis7 and @stsievert, how are things progressing? Thanks!

stsievert · 2019-02-13T02:57:15Z

Thanks for checking in. I’ve found a couple issues in CloudKnot, specifically on some dependencies (see Nance-Lab/diff_classifier#28 for some more detail). @ccurtis7 has resolved that issue, and I need to check the notebook again.

I don’t think I would have accepted the version of diff_classifier as submitted. I think now it’s closer to being ready.

cMadan · 2019-02-13T03:36:29Z

@stsievert, looks like things are moving along then. Thank you for the update!

ccurtis7 · 2019-02-13T03:41:57Z

Hey @cMadan, @stsievert has really given some great help on improving the quality of the package, and I've tried to be as prompt as possible in addressing issues. As he mentioned, I think there's only one last double check of the parallelization demo notebook, and it should be good to go.

stsievert · 2019-03-03T20:35:46Z

I think diff_classifier is almost ready for acceptance. Here's a quick summary of the changes since the v0.1-alpha tag:

Clean dependencies on Fiji, an image processing library (No Fiji installation does not raise an error Nance-Lab/diff_classifier#22, No Fiji means infinite download loop in diff_classifier_demo.ipynb Nance-Lab/diff_classifier#30)
Clean confusion on Python 2/3 decadency on remote/local machines with Cloudknot (resolved in Checking Cloudknot functionality Nance-Lab/diff_classifier#28 (comment))
Cleaning usage with pip: MAINT: resolve install depedencies (and add note to install master) Nance-Lab/diff_classifier#18

Here are all the commits since the v0.1-alpha tag: Nance-Lab/diff_classifier@V0.1-alpha...master

cMadan · 2019-03-10T20:37:27Z

@stsievert, thanks for the detailed update! It's good to see things moving along :)

stsievert · 2019-03-31T21:59:15Z

This review is complete! This software package is ready for acceptance. One question:

Significant changes have been made since the initial submission (some changes are in #989 (comment)). I feel there should be a new release for this – I wouldn't have accepted 0.1-alpha, but I'm willing to accept the master branch now. How should this be resolved?

cMadan · 2019-04-03T15:41:36Z

@stsievert, perfect, thank you for confirming! Thanks for highlighting this difference :). After I do a final pass of the submission, I will ask @ccurtis7 to mint a new release and archive the code (@ccurtis7, wait until I do a final pass though!) and this will then be the version that is accepted.

@ccurtis7, sit tight for now and I will let you know how the last steps proceed shortly.

ccurtis7 · 2019-04-03T15:44:23Z

Thanks @cMadan! And thanks @stsievert for all your hard work through the review!

cMadan · 2019-04-07T17:02:23Z

@ccurtis7, everything look good and I'm almost ready to accept. Can you mint a new release that includes the changes from the review process? I also need a DOI for an archived version of the code (i.e., from Zenodo or figshare).

ccurtis7 · 2019-04-07T17:15:27Z

@cMadan, I have minted a new release, v0.1-beta, and the DOI is 10.5281/zenodo.2631862

cMadan · 2019-04-08T23:55:47Z

@whedon set v0.1-beta as version

whedon · 2019-04-08T23:55:51Z

OK. v0.1-beta is the version.

cMadan · 2019-04-08T23:56:00Z

@whedon set 10.5281/zenodo.2631862 as archive

whedon · 2019-04-08T23:56:04Z

OK. 10.5281/zenodo.2631862 is the archive.

cMadan · 2019-04-08T23:56:45Z

@whedon accept

whedon · 2019-04-08T23:56:47Z

Attempting dry run of processing paper acceptance...

whedon · 2019-04-08T23:58:01Z


OK DOIs

- 10.1049/ip-rsn:20045064 is OK
- 10.1038/nmeth.2808 is OK
- 10.1016/j.ymeth.2016.09.016 is OK
- 10.1016/j.jconrel.2015.10.021 is OK
- 10.5281/zenodo.1413740 is OK
-  10.25080/Majora-4af1f417-001  is OK

MISSING DOIs

- None

INVALID DOIs

- None

cMadan · 2019-04-09T00:01:21Z

@ccurtis7, it looks like a recent change broke the paper.md (or bib)

ccurtis7 · 2019-04-09T02:47:51Z

@whedon generate pdf

whedon · 2019-04-09T02:47:53Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-04-09T02:48:24Z

👉 Check article proof 📄 👈

ccurtis7 · 2019-04-09T02:50:10Z

Hmmm, it appears that whedon has changed how it treats Latex characters in the title. Previously, I had to type diff\_classifier for it to render correctly, but now I no longer have to warn it with a \. I can just type diff_classifier. I have updated the file in my master branch accordingly.

Do I have to generate another release, or is the paper.md file in the master branch OK @cMadan?

cMadan · 2019-04-09T18:02:40Z

@ccurtis7, yes, I know you previously had the \, but you're right that this functionality has changed now. whedon is it's own software package that's being improved over time, so I suppose these things can happen. There's no need to generate a new release for this.

cMadan · 2019-04-09T18:02:53Z

@whedon accept

whedon · 2019-04-09T18:02:55Z

Attempting dry run of processing paper acceptance...

whedon · 2019-04-09T18:03:03Z


OK DOIs

- 10.1049/ip-rsn:20045064 is OK
- 10.1038/nmeth.2808 is OK
- 10.1016/j.ymeth.2016.09.016 is OK
- 10.1016/j.jconrel.2015.10.021 is OK
- 10.5281/zenodo.2631862 is OK
- 10.25080/Majora-4af1f417-001 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2019-04-09T18:03:22Z

Check final proof 👉 openjournals/joss-papers#610

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#610, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

cMadan · 2019-04-09T18:06:05Z

@openjournals/joss-eics, I think we're all set to accept here!

labarba · 2019-04-09T21:01:56Z

@ccurtis7 — Since we will have the Zenodo archive DOI on the front page of the paper, as part of the metadata shown in the margin note, we don't include a citation to it or mention it in the paper. Can you delete that?

And while you're at it, please edit:

"principle component analysis" >> principal
add comms after "e.g."

ccurtis7 · 2019-04-09T21:13:57Z

@whedon generate pdf

whedon · 2019-04-09T21:14:00Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-04-09T21:14:33Z

👉 Check article proof 📄 👈

ccurtis7 · 2019-04-09T21:15:46Z

I have made the requested changes @labarba, thank you.

labarba · 2019-04-10T00:00:34Z

@whedon accept

whedon · 2019-04-10T00:00:37Z

Attempting dry run of processing paper acceptance...

whedon · 2019-04-10T00:01:10Z

Check final proof 👉 openjournals/joss-papers#611

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#611, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

whedon · 2019-04-10T00:01:16Z


OK DOIs

- 10.1049/ip-rsn:20045064 is OK
- 10.1038/nmeth.2808 is OK
- 10.1016/j.ymeth.2016.09.016 is OK
- 10.1016/j.jconrel.2015.10.021 is OK
- 10.25080/Majora-4af1f417-001 is OK

MISSING DOIs

- None

INVALID DOIs

- None

labarba · 2019-04-10T00:02:34Z

@whedon accept deposit=true

whedon · 2019-04-10T00:02:36Z

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

whedon · 2019-04-10T00:03:29Z

🚨🚨🚨 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.00989 joss-papers#612
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.00989
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

labarba · 2019-04-10T00:05:30Z

Congratulations, @ccurtis7, your JOSS paper is published!

Sincere thanks to the editor: @cMadan, and reviewer: @stsievert — Merci, gracias, danke 🙏

whedon · 2019-04-10T00:05:51Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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whedon assigned cMadan Sep 30, 2018

whedon added the review label Sep 30, 2018

whedon mentioned this issue Sep 30, 2018

[PRE REVIEW]: Diff_classifier: Parallelization of multi-particle tracking video analyses #939

Closed

whedon added the accepted label Apr 10, 2019

labarba closed this as completed Apr 10, 2019

whedon added published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. labels Mar 2, 2020

[REVIEW]: Diff_classifier: Parallelization of multi-particle tracking video analyses #989

[REVIEW]: Diff_classifier: Parallelization of multi-particle tracking video analyses #989

Comments

whedon commented Sep 30, 2018 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @stsievert

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Sep 30, 2018

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cMadan commented Sep 30, 2018

ccurtis7 commented Nov 5, 2018

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