[REVIEW]: PyView: A general purpose tool for analyzing calcium imaging data

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@ajkswamy@csoneson<!--end-editor-- Reviewers: @adamltyson, @Yannan-Chen Archive: 10.12751/g-node.ezh5w2

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/9f066476240ca7b5f36805676f19d169/status.svg)](https://joss.theoj.org/papers/9f066476240ca7b5f36805676f19d169)

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

@adamltyson & @Yannan-Chen, 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 @csoneson 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 @adamltyson

📝 Checklist for @Yannan-Chen

editorialbot commented 1 year ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

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

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editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.38 s (406.7 files/s, 78202.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         137           6080           8304          12596
HTML                             2             36              4            274
TeX                              1             20              0            255
YAML                             5              1              4            171
Markdown                         2             41              0            104
Jupyter Notebook                 1              0           1386             92
IDL                              1             12              4             32
SVG                              4              0              0              4
-------------------------------------------------------------------------------
SUM:                           153           6190           9702          13528
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

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

OK DOIs

- 10.7554/elife.61834 is OK
- 10.3389/fninf.2016.00006 is OK
- 10.1016/j.jneumeth.2009.06.031 is OK
- 10.1111/ejn.12558 is OK
- 10.1038/8144 is OK
- 10.1201/9781420039429.ch13 is OK
- 10.7554/elife.38173 is OK
- 10.1152/physiol.00032.2007 is OK
- 10.3389/fncel.2018.00128 is OK
- 10.1109/cvprw.2016.78 is OK
- 10.1038/srep21841 is OK
- 10.1007/s00359-017-1209-1 is OK
- 10.1007/s00441-020-03385-5 is OK
- 10.1016/j.conb.2018.11.004 is OK
- 10.1016/j.cmpb.2019.104991 is OK
- 10.1371/journal.pcbi.1005526 is OK
- 10.1046/j.1460-9568.1999.00826.x is OK
- 10.1038/nmeth.2019 is OK
- 10.1016/j.bpj.2017.09.040 is OK
- 10.1016/j.neuroimage.2014.04.041 is OK
- 10.1186/1471-2105-14-s18-s4 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

Wordcount for paper.md is 2603

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:

csoneson commented 1 year ago

👋🏼 @ajkswamy, @adamltyson, @Yannan-Chen - this is the review thread for the submission. All our communications will happen here from now on.

Please check the post at the top of the issue for instructions on how to generate your own review checklist. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues directly in the software repository. If you do so, please mention this thread so that a link is created (and I can keep an eye on what is happening). Please also feel free to comment and ask questions in this thread. It is often easier to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

Please feel free to ping me (@csoneson) if you have any questions or concerns. Thanks!

adamltyson commented 1 year ago

Review checklist for @adamltyson

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 https://github.com/galizia-lab/pyview?
[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 (@ajkswamy) 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
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
[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?

ajkswamy commented 1 year ago

Hello @csoneson @adamltyson @Yannan-Chen

Thanks for organizing the review process and agreeing to review our submission!

A quick update: thanks to @adamltyson's issue, we have now migrated PyView to Python 3.10 and made a new release. We request you to use this release when reviewing.

We are looking forward to your issues, comments, questions and reviews!

Thanks!

Yannan-Chen commented 1 year ago

Review checklist for @Yannan-Chen

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 https://github.com/galizia-lab/pyview?
[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 (@ajkswamy) 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
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
[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?

adamltyson commented 1 year ago

Hey @ajkswamy, as I play with the software, I'm going to raise issues on anything that I come across. Just letting you know that some of these will likely be personal preference, or may not affect the software from a user's point of view (e.g. https://github.com/galizia-lab/pyview/issues/23). Don't feel like all of these must be addressed for the JOSS submission, so feel free to close/ignore these.

adamltyson commented 1 year ago

The paper itself looks good. It may be nice to cite the suite2p pre-print for consistency (e.g. the CaImAn paper is cited).

adamltyson commented 1 year ago

Hey @ajkswamy, I saw that you added a tutorial PDF. The software is much, much easier to understand now. Considering how much work has gone into this software, and it's broad functionality, it would be a shame if it's not used by more people. I would recommend documenting everything as comprehensively as the tutorial, and make it as easy to find for new users as possible.

However, there are very few tools that couldn't do with a bit more documentation (including all of mine!), so considering the installation procedure is also much improved, I'm now happy to recommend acceptance! :tada: cc @csoneson.

csoneson commented 1 year ago

Thank you @adamltyson!

Yannan-Chen commented 1 year ago

Hi @csoneson , In this submission, the authors provide a software offering a wide range of features for working with calcium imaging data interactively. The tool is user-friendly and easy to install, with clear and straightforward documentation. Overall, I’m happy to recommend this tool to be accepted by JOSS!

csoneson commented 1 year ago

Thank you @Yannan-Chen!

@ajkswamy - as both reviewers have given their ok, I'll take a quick look through the submission as well, and get back to you with the next steps.

csoneson commented 1 year ago

@editorialbot generate pdf

csoneson commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.7554/elife.61834 is OK
- 10.3389/fninf.2016.00006 is OK
- 10.1016/j.jneumeth.2009.06.031 is OK
- 10.1111/ejn.12558 is OK
- 10.1038/8144 is OK
- 10.1201/9781420039429.ch13 is OK
- 10.7554/elife.38173 is OK
- 10.1152/physiol.00032.2007 is OK
- 10.3389/fncel.2018.00128 is OK
- 10.1109/cvprw.2016.78 is OK
- 10.1038/srep21841 is OK
- 10.1007/s00359-017-1209-1 is OK
- 10.1007/s00441-020-03385-5 is OK
- 10.1016/j.conb.2018.11.004 is OK
- 10.1016/j.cmpb.2019.104991 is OK
- 10.1371/journal.pcbi.1005526 is OK
- 10.1046/j.1460-9568.1999.00826.x is OK
- 10.1038/nmeth.2019 is OK
- 10.1016/j.bpj.2017.09.040 is OK
- 10.1016/j.neuroimage.2014.04.041 is OK
- 10.1186/1471-2105-14-s18-s4 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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:

csoneson commented 1 year ago

Hi @ajkswamy - sorry for the delay. I had a quick look through the paper, and at the moment it is a bit too long for JOSS standards. In particular, see here:

The paper should be between 250-1000 words. Authors submitting papers significantly longer than 1000 words may be asked to reduce the length of their paper.

Your paper currently:

Wordcount for paper.md is 2603

Can you see if you can bring the paper a bit closer to the suggested length? In particular some of the technical content could perhaps be moved to the documentation, and I think some of the non-technical sections can be made more concise without losing too much information. Thanks!

ajkswamy commented 1 year ago

@csoneson Thanks for the message. We are looking into it and it might take a week or two. I will update you here once we are done revising the manuscript.

ajkswamy commented 1 year ago

@csoneson Thanks again for your suggestions. We have accordingly revised the manuscript to bring down the word count to ~1600 words. Here is summary of changes:

the section "Architecture: Data processing" has been drastically shortened by moving content to the wiki
the sections "Statement of Need" and "Conclusion" have been considerably shortened to remove phrasing and details that were somewhat redundant.

Please have a look and let me know if any further changes are needed to the manuscript, the code repo or its wiki. Thanks!

csoneson commented 1 year ago

@editorialbot generate pdf

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:

csoneson commented 1 year ago

Thanks @ajkswamy - this looks good! I made a PR with some small modifications, please check and merge if you agree.

The next steps then are:

[x] Make a tagged release of the software, and list the version tag of the archived version here.
[x] Archive the reviewed software in Zenodo or a similar service
[x] Check that the archival deposit (e.g., in Zenodo) has the correct metadata. In particular, the title and author list should be identical to those of the paper. You can also add the authors' ORCID.
[x] Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

ajkswamy commented 1 year ago

Hi @csoneson. Thanks for your PR with improvements to the manuscript. We have accepted the PR and made a new release: v1.3.

The same version of the code has been archived with G-Node Infrastructure services (GIN): https://doi.org/10.12751/g-node.ezh5w2

csoneson commented 1 year ago

@editorialbot generate pdf

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:

csoneson commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.7554/elife.61834 is OK
- 10.3389/fninf.2016.00006 is OK
- 10.1016/j.jneumeth.2009.06.031 is OK
- 10.1111/ejn.12558 is OK
- 10.1038/8144 is OK
- 10.1201/9781420039429 is OK
- 10.7554/elife.38173 is OK
- 10.1152/physiol.00032.2007 is OK
- 10.3389/fncel.2018.00128 is OK
- 10.1109/cvprw.2016.78 is OK
- 10.1038/srep21841 is OK
- 10.1007/s00359-017-1209-1 is OK
- 10.1007/s00441-020-03385-5 is OK
- 10.1016/j.conb.2018.11.004 is OK
- 10.1016/j.cmpb.2019.104991 is OK
- 10.1371/journal.pcbi.1005526 is OK
- 10.1046/j.1460-9568.1999.00826.x is OK
- 10.1038/nmeth.2019 is OK
- 10.1016/j.bpj.2017.09.040 is OK
- 10.1016/j.neuroimage.2014.04.041 is OK
- 10.1186/1471-2105-14-s18-s4 is OK

MISSING DOIs

- None

INVALID DOIs

- None

csoneson commented 1 year ago

@editorialbot set 1.3 as version

editorialbot commented 1 year ago

Done! version is now 1.3

csoneson commented 1 year ago

@editorialbot set 10.12751/g-node.ezh5w2 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.12751/g-node.ezh5w2

csoneson commented 1 year ago

Thanks @ajkswamy - this looks good to me. I'm going to hand over to the track EiC for the final steps. Thanks for submitting to JOSS!

csoneson commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.7554/elife.61834 is OK
- 10.3389/fninf.2016.00006 is OK
- 10.1016/j.jneumeth.2009.06.031 is OK
- 10.1111/ejn.12558 is OK
- 10.1038/8144 is OK
- 10.1201/9781420039429 is OK
- 10.7554/elife.38173 is OK
- 10.1152/physiol.00032.2007 is OK
- 10.3389/fncel.2018.00128 is OK
- 10.1109/cvprw.2016.78 is OK
- 10.1038/srep21841 is OK
- 10.1007/s00359-017-1209-1 is OK
- 10.1007/s00441-020-03385-5 is OK
- 10.1016/j.conb.2018.11.004 is OK
- 10.1016/j.cmpb.2019.104991 is OK
- 10.1371/journal.pcbi.1005526 is OK
- 10.1046/j.1460-9568.1999.00826.x is OK
- 10.1038/nmeth.2019 is OK
- 10.1016/j.bpj.2017.09.040 is OK
- 10.1016/j.neuroimage.2014.04.041 is OK
- 10.1186/1471-2105-14-s18-s4 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:wave: @openjournals/bcm-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/3952, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

arfon commented 1 year ago

@editorialbot accept

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/3990
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04936
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

@adamltyson, @Yannan-Chen – many thanks for your reviews here and to @csoneson 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 ✨

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

editorialbot commented 1 year ago

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HTML:
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</a>

reStructuredText:
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   :target: https://doi.org/10.21105/joss.04936

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ajkswamy commented 1 year ago

@adamltyson @Yannan-Chen Thanks for taking the time to review our software and manuscript. Your input has helped improve them a lot!

@csoneson @arfon Thanks for a great editorial process and the opportunity to publish in JOSS. It was the most transparent and the best structured review process I have experienced!

openjournals / joss-reviews