editorialbot commented 3 months ago

Submitting author: !--author-handle-->@petroslk@sappelhoff<!--end-editor-- Reviewers: @PingjunChen, @NetoPedro Archive: 10.5281/zenodo.13838349

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/8587fb20d223790db3cdc903804a398f"><img src="https://joss.theoj.org/papers/8587fb20d223790db3cdc903804a398f/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/8587fb20d223790db3cdc903804a398f/status.svg)](https://joss.theoj.org/papers/8587fb20d223790db3cdc903804a398f)

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

@PingjunChen & @NetoPedro, 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 @sappelhoff 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 @PingjunChen

📝 Checklist for @NetoPedro

editorialbot commented 3 months 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:

@editorialbot commands

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

@editorialbot generate pdf

editorialbot commented 3 months ago

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

OK DOIs

- 10.1007/978-3-030-00934-2_30 is OK
- 10.1109/WACV45572.2020.9093435 is OK
- 10.1038/s41592-020-01018-x is OK
- 10.1016/j.media.2019.101563 is OK
- 10.1038/s41598-017-17204-5 is OK
- 10.3389/fgene.2021.639930 is OK
- 10.1038/ng.2764 is OK
- 10.1200/CCI.18.00157 is OK

MISSING DOIs

- No DOI given, and none found for title: Automatic differentiation in PyTorch
- No DOI given, and none found for title: Scikit-learn: Machine Learning in Python
- No DOI given, and none found for title: The OpenCV Library
- No DOI given, and none found for title: Distilling the knowledge in a neural network
- No DOI given, and none found for title: Teacher-student architecture for knowledge learnin...

INVALID DOIs

- None

editorialbot commented 3 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1153.5 files/s, 141209.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          14            450            669           1194
reStructuredText                 6            315            102            395
Markdown                         3            117              0            259
TeX                              1             14              0            109
Dockerfile                       1             12              9             27
DOS Batch                        1              8              1             26
INI                              1              1              0             18
CSS                              1              3              2             16
YAML                             1              3              0             12
JavaScript                       1              1              1             11
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            31            928            791           2076
-------------------------------------------------------------------------------

Commit count by author:

    20  petroslk
     5  JulienMassonnet
     4  Petros
     2  JonatanBonjour

editorialbot commented 3 months ago

Paper file info:

📄 Wordcount for paper.md is 2202

✅ The paper includes a Statement of need section

editorialbot commented 3 months ago

License info:

✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)

editorialbot commented 3 months ago

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

sappelhoff commented 3 months ago

Hello again! 👋 

@NetoPedro, @PingJunChen

FYI @petroslk

This is the review thread for the paper. All of our higher-level communications will happen here from now on, review comments and discussion can happen in the repository of the project (details below).

📓 Please read the "Reviewer instructions & questions" in the comment from our editorialbot (above).

✅ All reviewers get their own checklist with the JOSS requirements - you generate them as per the details in the editorialbot comment. As you go over the submission, please check any items that you feel have been satisfied.

💻 The JOSS review is different from most other journals: The reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention the link to https://github.com/openjournals/joss-reviews/issues/7022 so that a link is created to this thread. That will also help me to keep track!

❓ Please also feel free to comment and ask questions on this thread if you are unsure about something!

🎯 We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

PingjunChen commented 3 months ago

Review checklist for @PingjunChen

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/choosehappy/HoverFast?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@petroslk) 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?

NetoPedro commented 3 months ago

Review checklist for @NetoPedro

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/choosehappy/HoverFast?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@petroslk) 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?

PingjunChen commented 3 months ago

@sappelhoff The authors have addressed my minor concerns. I believe HoverFast would be a quite useful tool for the computational pathology community, particularly considering its speedy inference compared to Hover-Net. I recommend its acceptance for publication.

sappelhoff commented 2 months ago

Hey @NetoPedro 👋 it's been a while! Do you have any updates on the timeline of completing your review for HoverFast?

NetoPedro commented 2 months ago

Hey @sappelhoff , I intend to finish it this week/weekend!

sappelhoff commented 1 month ago

Hi @NetoPedro this is just a kind reminder to please complete your review :-) it'd be nice to move on with the process! Thanks!

NetoPedro commented 1 month ago

@sappelhoff The authors covered my point, the document is solid and the software brings impressive computational improvements. I too recommend acceptance

sappelhoff commented 1 month ago

Great, thanks a lot @NetoPedro! And thank you again @PingjunChen!

@petroslk we may now go through the final steps.

sappelhoff commented 1 month ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

[x] Double check authors and affiliations (including ORCIDs)
[x] 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.
[x] Archive the release on Zenodo/figshare/etc and post the DOI here.
[x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[x] 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

sappelhoff commented 1 month ago

@petroslk please let me know once you finished your items from the list above: https://github.com/openjournals/joss-reviews/issues/7022#issuecomment-2368183621

I will then work on my final items, and then it's (hopefully) finally time to ship it!

sappelhoff 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

- 10.1007/978-3-030-00934-2_30 is OK
- 10.1109/WACV45572.2020.9093435 is OK
- 10.1038/s41592-020-01018-x is OK
- 10.1016/j.media.2019.101563 is OK
- 10.1038/s41598-017-17204-5 is OK
- 10.3389/fgene.2021.639930 is OK
- 10.7717/peerj.453 is OK
- 10.1038/ng.2764 is OK
- 10.1200/CCI.18.00157 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Automatic differentiation in PyTorch
- No DOI given, and none found for title: The OpenCV Library
- No DOI given, and none found for title: Distilling the knowledge in a neural network
- No DOI given, and none found for title: Teacher-student architecture for knowledge learnin...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

petroslk commented 1 month ago

Hey @sappelhoff

As requested, the release has been archived on Zenodo (DOI: https://doi.org/10.5281/zenodo.13838349 ). I have also checked author names and Orcid IDs for those that provided them. This release is of version 1.0.1 which includes reviewer comments.

Let me know if there anything else I might have missed.

Thanks a lot!

sappelhoff commented 1 month ago

@editorialbot set 10.5281/zenodo.13838349 as archive

editorialbot commented 1 month ago

Done! archive is now 10.5281/zenodo.13838349

sappelhoff commented 1 month ago

@editorialbot set 1.0.1 as version

editorialbot commented 1 month ago

Done! version is now 1.0.1

sappelhoff 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:

sappelhoff commented 1 month ago

Thanks @petroslk! I am recommending this for acceptance. We will need to wait for an associate editor in chief now :-)

sappelhoff commented 1 month ago

@editorialbot recommend-accept

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

- 10.1007/978-3-030-00934-2_30 is OK
- 10.1109/WACV45572.2020.9093435 is OK
- 10.1038/s41592-020-01018-x is OK
- 10.1016/j.media.2019.101563 is OK
- 10.1038/s41598-017-17204-5 is OK
- 10.3389/fgene.2021.639930 is OK
- 10.7717/peerj.453 is OK
- 10.1038/ng.2764 is OK
- 10.1200/CCI.18.00157 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Automatic differentiation in PyTorch
- No DOI given, and none found for title: The OpenCV Library
- No DOI given, and none found for title: Distilling the knowledge in a neural network
- No DOI given, and none found for title: Teacher-student architecture for knowledge learnin...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot commented 1 month 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/5912, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman commented 1 month ago

@petroslk as AEiC for JOSS I will now help to process this submission for acceptance in JOSS. I will now process some final checks:

Checks on repository

[x] Project has OSI approved license
[x] Project features contributing guidelines

Checks on review issue

[x] Review completed
[x] Software license tag listed here matches a tagged release

Checks on archive

[x] Archive listed title and authors matches paper
[x] Archive listed license matches software license
[x] Archive listed version tag matches tagged release (and includes a potential v).

Checks on paper

[x] Checked paper formatting
[x] Check affiliations to make sure country acronyms are not used
[x] Checked reference rendering
[x] Checked if pre-print citations can be updated by published versions
[x] Checked for typos

Kevin-Mattheus-Moerman commented 1 month ago

@editorialbot accept

editorialbot commented 1 month ago

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

editorialbot commented 1 month ago

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

``` cff-version: "1.2.0" authors: - family-names: Liakopoulos given-names: Petros orcid: "https://orcid.org/0009-0005-2015-6795" - family-names: Massonnet given-names: Julien orcid: "https://orcid.org/0009-0004-9515-6100" - family-names: Bonjour given-names: Jonatan orcid: "https://orcid.org/0009-0006-8165-6897" - family-names: Mizrakli given-names: Medya Tekes - family-names: Graham given-names: Simon - family-names: Cuendet given-names: Michel A. - family-names: Seipel given-names: Amanda H. - family-names: Michielin given-names: Olivier - family-names: Merkler given-names: Doron - family-names: Janowczyk given-names: Andrew contact: - family-names: Liakopoulos given-names: Petros orcid: "https://orcid.org/0009-0005-2015-6795" doi: 10.5281/zenodo.13838349 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Liakopoulos given-names: Petros orcid: "https://orcid.org/0009-0005-2015-6795" - family-names: Massonnet given-names: Julien orcid: "https://orcid.org/0009-0004-9515-6100" - family-names: Bonjour given-names: Jonatan orcid: "https://orcid.org/0009-0006-8165-6897" - family-names: Mizrakli given-names: Medya Tekes - family-names: Graham given-names: Simon - family-names: Cuendet given-names: Michel A. - family-names: Seipel given-names: Amanda H. - family-names: Michielin given-names: Olivier - family-names: Merkler given-names: Doron - family-names: Janowczyk given-names: Andrew date-published: 2024-09-26 doi: 10.21105/joss.07022 issn: 2475-9066 issue: 101 journal: Journal of Open Source Software publisher: name: Open Journals start: 7022 title: "HoverFast: an accurate, high-throughput, clinically deployable nuclear segmentation tool for brightfield digital pathology images" type: article url: "https://joss.theoj.org/papers/10.21105/joss.07022" volume: 9 title: "HoverFast: an accurate, high-throughput, clinically deployable nuclear segmentation tool for brightfield digital pathology images" ```

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot commented 1 month ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 1 month 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/5916
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.07022
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman commented 1 month ago

@petroslk congratulations on this JOSS publication!

Thanks for editing @sappelhoff !

And a special thank you to the reviewers: @PingjunChen, @NetoPedro !!

editorialbot commented 1 month ago

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.07022/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.07022/status.svg
   :target: https://doi.org/10.21105/joss.07022

This is how it will look in your documentation:

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openjournals / joss-reviews

[REVIEW]: HoverFast: an accurate, high-throughput, clinically deployable nuclear segmentation tool for brightfield digital pathology images #7022

Status

Reviewer instructions & questions

Checklists

Review checklist for @PingjunChen

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @NetoPedro

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

Checks on repository

Checks on review issue

Checks on archive

Checks on paper