editorialbot commented 4 months ago

Submitting author: !--author-handle-->@taladjidi@RMeli<!--end-editor-- Reviewers: @Abinashbunty, @obliviateandsurrender Archive: 10.5281/zenodo.12795395

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/e2a6532b5b723a2165bd351e69a1e206/status.svg)](https://joss.theoj.org/papers/e2a6532b5b723a2165bd351e69a1e206)

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

@Abinashbunty & @obliviateandsurrender, 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 @RMeli 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 @Abinashbunty

📝 Checklist for @obliviateandsurrender

editorialbot commented 2 months ago

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

OK DOIs

- 10.21105/joss.01037 is OK
- 10.1038/s41467-018-04534-9 is OK
- 10.1103/RevModPhys.85.299 is OK
- 10.1088/1367-2630/acce5a is OK
- 10.1103/PhysRevA.108.063512 is OK
- 10.1038/s41586-020-2649-2 is OK

MISSING DOIs

- 10.1017/cbo9780511524240.005 may be a valid DOI for title: Bose-Einstein condensation and superfluidity
- No DOI given, and none found for title: Full optical control of quantum fluids of light in...
- No DOI given, and none found for title: CuPy: A NumPy-Compatible Library for NVIDIA GPU Ca...
- No DOI given, and none found for title: Numba: A llvm-based python jit compiler

INVALID DOIs

- None

taladjidi commented 1 month ago

@editorialbot check references

editorialbot commented 1 month ago

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

OK DOIs

- 10.21105/joss.01037 is OK
- 10.1038/s41467-018-04534-9 is OK
- 10.1103/RevModPhys.85.299 is OK
- 10.1088/1367-2630/acce5a is OK
- 10.1103/PhysRevA.108.063512 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1145/2833157.2833162 is OK

MISSING DOIs

- 10.1017/cbo9780511524240.005 may be a valid DOI for title: Bose-Einstein condensation and superfluidity
- No DOI given, and none found for title: CuPy: A NumPy-Compatible Library for NVIDIA GPU Ca...

INVALID DOIs

- 10.5281/zenodo.12698001 is INVALID

taladjidi commented 1 month ago

@editorialbot check references

editorialbot commented 1 month ago

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

OK DOIs

- 10.21105/joss.01037 is OK
- 10.1038/s41467-018-04534-9 is OK
- 10.1103/RevModPhys.85.299 is OK
- 10.5281/zenodo.12698001 is OK
- 10.1088/1367-2630/acce5a is OK
- 10.1103/PhysRevA.108.063512 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1145/2833157.2833162 is OK

MISSING DOIs

- 10.1017/cbo9780511524240.005 may be a valid DOI for title: Bose-Einstein condensation and superfluidity
- No DOI given, and none found for title: CuPy: A NumPy-Compatible Library for NVIDIA GPU Ca...

INVALID DOIs

- None

RMeli commented 1 month ago

@taladjidi I had a look into the missing DOIs and I think they are not available. Can you please confirm that? Thank you.

taladjidi commented 1 month ago

Hi @RMeli , the DOI for the Pitaevskii Stringari works fine on my end, and there is no DOI for Cupy. I did use the official citation provided on their repo though.

RMeli commented 1 month ago

@editorialbot check references

editorialbot commented 1 month ago

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

OK DOIs

- 10.21105/joss.01037 is OK
- 10.1038/s41467-018-04534-9 is OK
- 10.1103/RevModPhys.85.299 is OK
- 10.5281/zenodo.12698001 is OK
- 10.1088/1367-2630/acce5a is OK
- 10.1103/PhysRevA.108.063512 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1145/2833157.2833162 is OK

MISSING DOIs

- 10.1017/cbo9780511524240.005 may be a valid DOI for title: Bose-Einstein condensation and superfluidity
- No DOI given, and none found for title: CuPy: A NumPy-Compatible Library for NVIDIA GPU Ca...

INVALID DOIs

- None

RMeli commented 1 month ago

That's right, the suggested DOI 10.1017/cbo9780511524240.005 does seem to work. I missed this. Can you please add it to the paper.bib?

https://github.com/Quantum-Optics-LKB/NLSE/blob/138f6a8b63f4f0e5a7c0e5c061fb3da328ca531d/paper/paper.bib#L1-L11

taladjidi commented 1 month ago

@editorialbot check references

editorialbot commented 1 month ago

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

OK DOIs

- 10.1017/cbo9780511524240.005 is OK
- 10.21105/joss.01037 is OK
- 10.1038/s41467-018-04534-9 is OK
- 10.1103/RevModPhys.85.299 is OK
- 10.5281/zenodo.12698001 is OK
- 10.1088/1367-2630/acce5a is OK
- 10.1103/PhysRevA.108.063512 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1145/2833157.2833162 is OK

MISSING DOIs

- No DOI given, and none found for title: CuPy: A NumPy-Compatible Library for NVIDIA GPU Ca...

INVALID DOIs

- None

taladjidi commented 1 month ago

That's right, the suggested DOI 10.1017/cbo9780511524240.005 does seem to work. I missed this. Can you please add it to the paper.bib?

https://github.com/Quantum-Optics-LKB/NLSE/blob/138f6a8b63f4f0e5a7c0e5c061fb3da328ca531d/paper/paper.bib#L1-L11

Fixed, sorry I didn't even check that it was in the .bib file at first ... Should be ok now !

RMeli commented 1 month ago

@editorialbot check references

editorialbot commented 1 month ago

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

OK DOIs

- 10.1017/cbo9780511524240.005 is OK
- 10.21105/joss.01037 is OK
- 10.1038/s41467-018-04534-9 is OK
- 10.1103/RevModPhys.85.299 is OK
- 10.5281/zenodo.12698001 is OK
- 10.1088/1367-2630/acce5a is OK
- 10.1103/PhysRevA.108.063512 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1145/2833157.2833162 is OK

MISSING DOIs

- No DOI given, and none found for title: CuPy: A NumPy-Compatible Library for NVIDIA GPU Ca...

INVALID DOIs

- None

RMeli commented 1 month ago

Thanks @taladjidi, LGTM. I'll have final look at everything.

RMeli commented 1 month ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Double check authors and affiliations (including ORCIDs)
Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
Archive the release on Zenodo/figshare/etc and post the DOI here.
Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a pull request)
[x] Check that the archive title, author list, version tag, and the license are correct
[x] Set archive DOI with @editorialbot set <DOI here> as archive
[x] Set version with @editorialbot set <version here> as version
[x] Double check rendering of paper with @editorialbot generate pdf
[x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[x] Recommend acceptance with @editorialbot recommend-accept

taladjidi commented 1 month ago

Hi @RMeli , I uploaded the archive of the last release 2.3.0 on Zenodo DOI : 10.5281/zenodo.12795395. I also changed the license to stronger GNUGPLv3 license. I hope this is OK.

RMeli commented 1 month ago

Thanks @taladjidi, I'll now check all that.

RMeli commented 1 month ago

I also changed the license to stronger GNUGPLv3 license. I hope this is OK.

Yes, this is an OSI-approved license, therefore it is OK.

RMeli commented 1 month ago

@editorialbot generate pdf

RMeli commented 1 month ago

@editorialbot set 2.3.0 as version

editorialbot commented 1 month ago

Done! version is now 2.3.0

RMeli commented 1 month ago

@editorialbot set 10.5281/zenodo.12795395 as archive

editorialbot commented 1 month ago

Done! archive is now 10.5281/zenodo.12795395

editorialbot commented 1 month ago

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

RMeli commented 1 month ago

@taladjidi can you please change the title of the Zenodo archive to match the title of the paper (i.e. remove the version, which is already accounted for by the DOI)? Also, your two co-authors appear as "Contact Persons" and not as authors on Zenodo. Can you please make sure they are in the correct field?

RMeli commented 1 month ago

@editorialbot check references

editorialbot commented 1 month ago

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

OK DOIs

- 10.1017/cbo9780511524240.005 is OK
- 10.21105/joss.01037 is OK
- 10.1038/s41467-018-04534-9 is OK
- 10.1103/RevModPhys.85.299 is OK
- 10.5281/zenodo.12698001 is OK
- 10.1088/1367-2630/acce5a is OK
- 10.1103/PhysRevA.108.063512 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1145/2833157.2833162 is OK

MISSING DOIs

- No DOI given, and none found for title: CuPy: A NumPy-Compatible Library for NVIDIA GPU Ca...

INVALID DOIs

- None

RMeli commented 1 month ago

@taladjidi can you please update the Zenodo metadata to include the full author affiliation (as in the paper)? Thank you.

taladjidi commented 1 month ago

@taladjidi can you please change the title of the Zenodo archive to match the title of the paper (i.e. remove the version, which is already accounted for by the DOI)? Also, your two co-authors appear as "Contact Persons" and not as authors on Zenodo. Can you please make sure they are in the correct field?

Done !

@taladjidi can you please update the Zenodo metadata to include the full author affiliation (as in the paper)? Thank you.

The lab appears as a ROR (research organization registry) entry already, isn't it correct ? When you click on the ROR logo you get the same affiliation as the paper.

RMeli commented 1 month ago

The lab appears as a ROR (research organization registry) entry already, isn't it correct ?

Ah! Thanks for pointing this out. I was just hovering over the author name to see the affiliation. Using "Show affiliation" does indeed show the ROR logo. However, the last author has twice the same org (one of which is not a ROR entry). Would you be able to remove it? Then I think we are good to go. ;)

taladjidi commented 1 month ago

Right all done ! I missed it since it was automatically added ...

RMeli commented 1 month ago

@editorialbot recommend-accept

Many thanks, @taladjidi. Based on the extensive comments from the reviewers, I'm happy to recommend this paper for acceptance! The EiC will now perform the final checks.

Thank you very much again @Abinashbunty and @obliviateandsurrender for the constructive review!

editorialbot commented 1 month ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 month ago

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

OK DOIs

- 10.1017/cbo9780511524240.005 is OK
- 10.21105/joss.01037 is OK
- 10.1038/s41467-018-04534-9 is OK
- 10.1103/RevModPhys.85.299 is OK
- 10.5281/zenodo.12698001 is OK
- 10.1088/1367-2630/acce5a is OK
- 10.1103/PhysRevA.108.063512 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1145/2833157.2833162 is OK

MISSING DOIs

- No DOI given, and none found for title: CuPy: A NumPy-Compatible Library for NVIDIA GPU Ca...

INVALID DOIs

- None

taladjidi commented 1 month ago

@editorialbot recommend-accept

Many thanks, @taladjidi. Based on the extensive comments from the reviewers, I'm happy to recommend this paper for acceptance! The EiC will now perform the final checks.

Thank you very much again @Abinashbunty and @obliviateandsurrender for the constructive review!

Great thank you so much for the very nice review process 👍 I wish all reviews could be like this !

editorialbot commented 1 month ago

:wave: @openjournals/pe-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/5657, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

crvernon commented 1 month ago

🔍 checking out the following:

[x] reviewer checklists are completed or addressed
[x] version set
[x] archive set
[x] archive names (including order) and title in archive matches those specified in the paper
[x] archive uses the same license as the repo and is OSI approved as open source
[x] archive DOI and version match or redirect to those set by editor in review thread
[x] paper is error free - grammar and typos
[x] paper is error free - test links in the paper and bib
[x] paper is error free - refs preserve capitalization where necessary
[x] paper is error free - no invalid refs without justification

crvernon commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

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

crvernon commented 1 month ago

:wave: @taladjidi - great job on this!

I just need you to address the following before I move to accept this one for publication:

[x] Please ensure the title of your Zenodo archive ("NLSE: A python package to solve the non-linear Schrödinger equation") matches the title of your paper ("NLSE: A Python package to solve the nonlinear Schrödinger equation") exactly. Feel free to edit which ever you like to make them match. No need to conduct another release.

In the paper:

[x] LINE 7-8: The phrase "...equation allowing to model the propagation of light..." is missing something. Perhaps it should be stated as "...equation used to model the propagation of light..."
[x] LINE 16: "Numpy" should have a capital "P" in this context to appear as "NumPy"
[x] LINE 17: "Numpy" should have a capital "P" in this context to appear as "NumPy"
[x] LINE 28-29: "...Using an easy to extend object-oriented classes, users..." should read as the following: "...Using easy to extend object-oriented classes, users..." with the removal of "an"
[x] LINE 34: "Cupy" in this context should have a capital "P" and be written as "CuPY"
[x] LINE 35: "Numpy" should have a capital "P" in this context to appear as "NumPy"
[x] LINE 37: "Numpy" should have a capital "P" in this context to appear as "NumPy"
[x] Figure 2 appears in-text before Figure 1. Please configure these so that they appear in order by making the performance figure appear first as Figure 1.
[x] LINE 44: "Numpy" should have a capital "P" in this context to appear as "NumPy"
[x] LINE 47: "This code has been developed initially developed in..." should be written as "This code was initially developed in..."
[x] In the Figure 2 caption, there is a missing space after the period in "...(200 evolution steps).Right..."
[x] LINE 52-53: "...you will need a Julia install to run..." should read "...you will need Julia installed to run..."
[x] LINE 75: "llvm" and "jit" should be written in all capital letters. You can maintain capitalization in your references by placing any content you wish to maintain formatting for in curly brackets in your bib file.
[x] LINE 85: The "e" in "einstein" should be capitalized
[x] LINE 87: The "g" and "p" in "gross--pitaevskii" should be capitalized

Let me know when these changes have been addressed.

taladjidi commented 1 month ago

Hi @crvernon, thanks for the swift takeover ! I just addressed everything you mentioned. I edited all the "nonlinear" without the hyphen to be more consistent with the title. Thanks for the .bib tips I didn't know !

taladjidi commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

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

crvernon commented 1 month ago

Thanks @taladjidi!

I still need you to:

[x] Capitalize the "p" in "python" in your Zenodo archive title

and address:

[x] Figure 2 appears in-text before Figure 1. Please configure these so that they appear in order by making the performance figure appear first as Figure 1.

taladjidi commented 1 month ago

Done, sorry for the figure order !

crvernon commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

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

crvernon commented 1 month ago

@editorialbot accept

openjournals / joss-reviews

[REVIEW]: NLSE: A Python package to solve the nonlinear Schrödinger equation #6607

Status

Reviewer instructions & questions

Checklists

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance