[REVIEW]: PiSCAT: A Python Package for Interferometric Scattering Microscopy

whedon commented 2 years ago

Submitting author: !--author-handle-->@po60nani@emdupre<!--end-editor-- Reviewers: @ziatdinovmax, @aquilesC Archive: 10.5281/zenodo.6389882

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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

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

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Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@po60nani) 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: Does the paper have a section titled 'Statement of Need' that clearly states 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 @aquilesC

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@po60nani) 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: Does the paper have a section titled 'Statement of Need' that clearly states 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?

editorialbot commented 2 years ago

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

emdupre commented 2 years ago

Thank you, @po60nani.

Please let us know, @aquilesC, if these edits are in line with what you were expecting. Please let me know, too, if my explanation helped to clarify your questions !

aquilesC commented 2 years ago

Thanks a lot @emdupre for your explanation, and @po60nani for the updated manuscript.

I have checked the text and marked all the ticks for the review process as completed. I think the work is ready to be published.

emdupre commented 2 years ago

Thank you, @aquilesC ! Confirming that I've spoken to @ziatdinovmax via email, who has also confirmed that he's happy to recommend PiSCAT for publication in JOSS. Thank you both for your thoughtful reviews !

I'll perform a few last checks now, but at this point, @po60nani, could you please:

[x] Make a tagged release of your software, and list the version tag of the archived version here.
[x] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[x] Check the archival deposit (e.g., in Zenodo) has the correct metadata (e.g., the JOSS paper and software archive have the same title and author listing)
[x] List the DOI of the archived version here.

I can then move forward with accepting the submission :rocket:

emdupre commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.1103/PhysRevLett.93.037401 is OK
- 10.1021/acs.nanolett.9b01822 is OK
- 10.1007/978-3-030-21722-8 is OK
- 10.1088/1361-6463/ac2f68 is OK
- 10.1038/ncomms5495 is OK
- 10.1021/acs.nanolett.8b02240 is OK
- 10.1364/OE.401374 is OK
- 10.5281/zenodo.4682814 is OK
- 10.3847/1538-3881/aabc4f is OK

MISSING DOIs

- None

INVALID DOIs

- None

po60nani commented 2 years ago

Thank you @emdupre. We updated the repository:

Make a tagged release of your software, and list the version tag of the archived version here. PiSCAT version 0.1.23 (link)
Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository) Done!
Check the archival deposit (e.g., in Zenodo) has the correct metadata (e.g., the JOSS paper and software archive have the same title and author listing) Done! Here you can find the Zendo
List the DOI of the archived version here.

emdupre commented 2 years ago

Thank you, @po60nani ! So, to confirm, 10.5281/zenodo.6389882 is the archive for the latest release. I will only associate one DOI with the JOSS publication, so please let me know if the other, earlier archive has non-overlapping information.

On the archive itself, a few formatting requests:

[x] Could you please update the title of the archive to match the software paper ? Currently, the archive title appears cut-off (i.e., is missing the term "microscopy" compared to the software paper).
[x] Similarly, could you confirm the author listing in the software archive ? The first two authors are differently listed between the two objects (e.g., the first author is Houman in the software archive and Houman Mirzaalian Dastjerdi in the software paper).

These edits can be made directly on the archived version, without minting a new DOI ! A guide is available here.

emdupre commented 2 years ago

@editorialbot set 0.1.23 as version

editorialbot commented 2 years ago

Done! version is now 0.1.23

emdupre commented 2 years ago

@editorialbot set 10.5281/zenodo.6389882 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.6389882

po60nani commented 2 years ago

@emdupre, I apologize for the mistakes; they have been corrected.

emdupre commented 2 years ago

Thank you for the quick corrections ! I'm now happy to recommend PiSCAT to the EIC team for publication, and I just want to add my congratulations to you on such an impressive effort !

emdupre commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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

OK DOIs

- 10.1103/PhysRevLett.93.037401 is OK
- 10.1021/acs.nanolett.9b01822 is OK
- 10.1007/978-3-030-21722-8 is OK
- 10.1088/1361-6463/ac2f68 is OK
- 10.1038/ncomms5495 is OK
- 10.1021/acs.nanolett.8b02240 is OK
- 10.1364/OE.401374 is OK
- 10.5281/zenodo.4682814 is OK
- 10.3847/1538-3881/aabc4f is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

: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/3097

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3097, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

kyleniemeyer commented 2 years ago

Hi @po60nani, I'm doing some final checks before publishing. Just a few things:

in the statement of need section, could you change "e.g" to "e.g.," ?
The journal name in the Dastjerdi et al. reference looks off, could you correct that?

po60nani commented 2 years ago

Hi, @kyleniemeyer. I fixed the problems.

kyleniemeyer commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

kyleniemeyer commented 2 years ago

@po60nani thanks—but unfortunately there is another issue that I missed, the Astropy paper is missing the journal name (we see this a lot because .bib files often have journal name macros that our system doesn't interpret). Could you fix that too?

po60nani commented 2 years ago

@kyleniemeyer, Thank you, I fixed it.

po60nani commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

kyleniemeyer commented 2 years ago

@editorialbot accept

editorialbot commented 2 years ago

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

editorialbot commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 2 years 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/3107
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04024
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer commented 2 years ago

Congratulations @po60nani on your article's publication in JOSS!

Many thanks to @ziatdinovmax and @aquilesC for reviewing this, and @emdupre for editing.

editorialbot commented 2 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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