[REVIEW]: pyndl: Naïve Discriminative Learning in Python

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@derNarr@osorensen<!--end-editor-- Reviewers: @frankier, @jinhangjiang, @VenkteshV Archive: 10.5281/zenodo.7410272

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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

@frankier & @jinhangjiang & @VenkteshV, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @osorensen 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 ✨

Checklists

📝 Checklist for @frankier

📝 Checklist for @VenkteshV

📝 Checklist for @jinhangjiang

osorensen commented 1 year ago

Thanks @frankier, your thorough review is very much appreciated!

Regarding the paper length @derNarr, I think the paper is it is now is fine, because it seems like the large number of references inflates the word count a bit (and a large number of references is in general a good thing).

osorensen commented 1 year ago

Okay! I think the paper is probably a bit too long by JOSS standards now, which is 500-1000 words. (I think a little bit over 1000 words is okay, but it seems like it's probably too much now.) If it were possible to fit things on two pages that might be ideal. I suppose this is an editorial issue and so might be beyond my remit and not quite sure how much this is enforced.

It's possible the plot could be made a bit smaller, which may help with reducing the number of pages (but not the number of words). It might be possible to fit it on a single pane, given that there need only be: ndl (1 job), ndl2 (1 job), ndl2 (2 jobs), pyndl (1 job), pyndl (2 jobs, openMP) pyndl (2 jobs, threading). You may need to move the legend outside the plotting area but it might still save a tiny bit of space.

The acknowledgement is appreciated, but shortening/removing it helps you get to JOSS editorial standards it's fine by me.

I agree that everything in my review has been addressed, and so I recommend that it be accepted, possibly pending some edits to the paper for length.

@frankier could you please tick off the final boxes in your checklist?

osorensen commented 1 year ago

👋 @VenkteshV, could you please let us know if the points raised in your review have been addressed, and if so, tick off the remaining points on your checklist?

frankier commented 1 year ago

Whoops! Done.

VenkteshV commented 1 year ago

wave @VenkteshV, could you please let us know if the points raised in your review have been addressed, and if so, tick off the remaining points on your checklist?

Aplogies. Done!! It is a fine module and apologies for delays from my end. I checked and my comments have been addressed. The documentation is more detailed and the writeup has also been changed incorporating the feedback. Thanks a lot. And aplogies for the delay. I was a bit occupied.

osorensen commented 1 year ago

Big thanks to both of you @frankier and @VenkteshV for your really thorough and helpful reviews!

osorensen commented 1 year ago

@editorialbot generate pdf

osorensen commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

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

OK DOIs

- 10.5334/jors.148 is OK
- 10.21236/ad0241531 is OK
- 10.1016/s0022-2496(02)00016-0 is OK
- 10.1037/a0023851 is OK
- 10.1080/23273798.2021.1954207 is OK
- 10.1017/s0022226719000203 is OK
- 10.3389/fcomm.2020.00017 is OK
- 10.21437/interspeech.2018-2420 is OK
- 10.1111/stan.12134 is OK
- 10.1080/23273798.2020.1815813 is OK
- 10.1515/cog-2021-0006 is OK
- 10.1515/9783110292022-006 is OK
- 10.1371/journal.pone.0174623 is OK
- 10.1037/0003-066x.43.3.151 is OK
- 10.31234/osf.io/prvzq is OK

MISSING DOIs

- None

INVALID DOIs

- None

osorensen commented 1 year ago

@derNarr, I have now read through the final manuscript and find it very well written.

At this point could you:

[ ] Make a tagged release of your software, and list the version tag of the archived version here.
[ ] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[ ] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[ ] Please list the DOI of the archived version here.

I can then move forward with recommending acceptance of the submission.

derNarr commented 1 year ago

@osorensen has the author list to match (also in order)? We have one contributor (Lennart Schneider @sumny), who contributed to pyndl in the beginning but since then has moved on. I talked to him and we agreed that he is no other on the package paper. At the same time I would like to keep him in the author list on Zenodo.

The plan at the moment is to merge the paper branch into the main branch with https://github.com/quantling/pyndl/pull/243 and then publish pyndl version 1.1.1 under the tag v1.1.1, which will be available on Zenodo here https://zenodo.org/record/7364981 .

Depending on your answer I might need to adjust the author list. The title is already corrected to the paper title in the PR.

osorensen commented 1 year ago

@osorensen has the author list to match (also in order)?

@derNarr, having an additional author on the Zenodo archive is fine, but please make sure the title matches.

derNarr commented 1 year ago

tagged release is this one here (tag v1.1.1): https://github.com/quantling/pyndl/releases/tag/v1.1.1
Zenodo link https://zenodo.org/record/7409834
title matches the paper title, authors are all relevant contributors, ordering in the paper and the package as documented on Zenodo differs on purpose
Zenodo DOI for version pyndl 1.1.1 is: 10.5281/zenodo.7409834

Anything missing or incomplete?

osorensen commented 1 year ago

@editorialbot set v1.1.1 as version

editorialbot commented 1 year ago

Done! version is now v1.1.1

osorensen commented 1 year ago

Thanks @derNarr. Could you please edit the title of the Zenodo archive so "pyndl" starts with a lowercase letter, to match the paper title?

osorensen commented 1 year ago

@editorialbot set 10.5281/zenodo.7409834 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7409834

derNarr commented 1 year ago

Sorry, changing the title changed the DOI to 10.5281/zenodo.7410272

The link is now https://zenodo.org/record/7410272

Tag stayed the same, but I removed the tag once and recreated it. (The same for the release, which resulted in having two versions of 1.1.1 now that only differ in the first letter of the title.)

osorensen commented 1 year ago

Thanks!

osorensen commented 1 year ago

@editorialbot set 10.5281/zenodo.7410272 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7410272

osorensen commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3780, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

editorialbot commented 1 year ago

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

OK DOIs

- 10.5334/jors.148 is OK
- 10.21236/ad0241531 is OK
- 10.1016/s0022-2496(02)00016-0 is OK
- 10.1037/a0023851 is OK
- 10.1080/23273798.2021.1954207 is OK
- 10.1017/s0022226719000203 is OK
- 10.3389/fcomm.2020.00017 is OK
- 10.21437/interspeech.2018-2420 is OK
- 10.1111/stan.12134 is OK
- 10.1080/23273798.2020.1815813 is OK
- 10.1515/cog-2021-0006 is OK
- 10.1515/9783110292022-006 is OK
- 10.1371/journal.pone.0174623 is OK
- 10.1037/0003-066x.43.3.151 is OK
- 10.31234/osf.io/prvzq is OK

MISSING DOIs

- None

INVALID DOIs

- None

derNarr commented 1 year ago

To me everything looks good. The links to the archive, the repo and the review are properly set. @osorensen do I have to accept the submission or will you do it?

osorensen commented 1 year ago

@derNarr, the editor in chief will read the paper and make the final decision. This typically takes less than a week.

derNarr commented 1 year ago

Perfect, thanks! I am not in a hurry. :-)

arfon commented 1 year ago

@editorialbot accept

Thanks for your patience folks!

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 1 year ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 1 year ago

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/3814
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04515
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon commented 1 year ago

@frankier, @jinhangjiang, @VenkteshV – many thanks for your reviews here and to @osorensen for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@derNarr – your paper is now accepted and published in JOSS :zap::rocket::boom:

editorialbot commented 1 year ago

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