editorialbot commented 1 month ago

Submitting author: !--author-handle-->@EtienneCmb@jbytecode<!--end-editor-- Reviewers: @pitmonticone, @ClaudMor Archive: 10.5281/zenodo.14046562

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/cdae325c0d48fdcb8c09802b7744554f"><img src="https://joss.theoj.org/papers/cdae325c0d48fdcb8c09802b7744554f/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/cdae325c0d48fdcb8c09802b7744554f/status.svg)](https://joss.theoj.org/papers/cdae325c0d48fdcb8c09802b7744554f)

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

@pitmonticone & @ClaudMor, 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 @jbytecode 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 @pitmonticone

📝 Checklist for @ClaudMor

editorialbot commented 1 month 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 1 month ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (1510.4 files/s, 157635.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          45           1100           1853           2572
SVG                              1              0              0            729
TeX                              2             50              0            502
reStructuredText                14            187            144            207
YAML                             5             28             11            123
Markdown                         2             18              0             72
HTML                             2              6              1             48
DOS Batch                        1              8              1             26
TOML                             1              1              0             16
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            74           1402           2017           4304
-------------------------------------------------------------------------------

Commit count by author:

   144  EtienneCmb
    66  Dishie2498
    10  Pierre Robiglio
     9  Mattehub
     7  Onur Ates
     7  dependabot[bot]
     3  Matteo NERI
     2  Andrea Brovelli
     1  Christian Ferreyra
     1  Etienne Combrisson

editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 781

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

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

✅ OK DOIs

- 10.1103/PhysRevE.100.032305 is OK
- 10.1038/s41593-022-01070-0 is OK
- 10.3390/e21090869 is OK
- 10.1103/PhysRevResearch.5.013025 is OK
- 10.1038/s41567-021-01371-4 is OK
- 10.1523/ENEURO.0052-18.2018 is OK
- 10.1016/j.nbd.2022.105918 is OK
- 10.1089/brain.2020.0982 is OK
- 10.7554/eLife.92938 is OK
- 10.21105/joss.01081 is OK
- 10.21105/joss.00738 is OK
- 10.21105/joss.01609 is OK
- 10.1371/journal.pcbi.1006343 is OK
- 10.1016/j.tics.2023.11.005 is OK
- 10.1103/PhysRevResearch.5.013025 is OK
- 10.1103/PhysRevE.91.052802 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Towards an extended taxonomy of information dynami...
- No DOI given, and none found for title: Nonnegative decomposition of multivariate informat...
- No DOI given, and none found for title: Beyond normal: On the evaluation of mutual informa...
- No DOI given, and none found for title: An information-theoretic approach to hypergraph ps...
- No DOI given, and none found for title: Estimation of Shannon differential entropy: An ext...

❌ MISSING DOIs

- 10.4135/9781412959384.n229 may be a valid DOI for title: A mathematical theory of communication

❌ INVALID DOIs

- None

editorialbot commented 1 month ago

License info:

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

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:

jbytecode commented 1 month ago

Dear @pitmonticone, @ClaudMor

You can start by creating your task lists. Each list will contain several tasks.

As you complete each task, you can check off the corresponding checkbox. Since the review process for JOSS is interactive, you are encouraged to engage with the author, other reviewers, and the editor throughout. You can open issues and submit pull requests in the target repository. Please include the URL of this page in those interactions, so we can keep track of activities outside of the platform.

To generate your task list, simply type:

@editorialbot generate my checklist

Thank you in advance.

pitmonticone commented 1 month ago

Review checklist for @pitmonticone

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/brainets/hoi?
[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 (@EtienneCmb) 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?

pitmonticone commented 1 month ago

@editorialbot commands

editorialbot commented 1 month ago

Hello @pitmonticone, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

ClaudMor commented 1 month ago

Review checklist for @ClaudMor

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/brainets/hoi?
[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 (@EtienneCmb) 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?

pitmonticone commented 1 month ago

I have finished my review:

jbytecode commented 1 month ago

@pitmonticone - Thank you for your review, opened issues, and pull requests.

@EtienneCmb - Could you please consider the review items and apply them? Please ping us here when you've done with them. Thank you in advance!

EtienneCmb 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

- 10.1103/PhysRevE.100.032305 is OK
- 10.1038/s41593-022-01070-0 is OK
- 10.3390/e21090869 is OK
- 10.1103/PhysRevResearch.5.013025 is OK
- 10.1038/s41567-021-01371-4 is OK
- 10.1002/j.1538-7305.1948.tb01338.x is OK
- 10.1523/ENEURO.0052-18.2018 is OK
- 10.1016/j.nbd.2022.105918 is OK
- 10.1089/brain.2020.0982 is OK
- 10.7554/eLife.92938 is OK
- 10.21105/joss.01081 is OK
- 10.21105/joss.00738 is OK
- 10.21105/joss.01609 is OK
- 10.1371/journal.pcbi.1006343 is OK
- 10.1016/j.tics.2023.11.005 is OK
- 10.1103/PhysRevResearch.5.013025 is OK
- 10.1103/PhysRevE.91.052802 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Towards an extended taxonomy of information dynami...
- No DOI given, and none found for title: Nonnegative decomposition of multivariate informat...
- No DOI given, and none found for title: Beyond normal: On the evaluation of mutual informa...
- No DOI given, and none found for title: An information-theoretic approach to hypergraph ps...
- No DOI given, and none found for title: Estimation of Shannon differential entropy: An ext...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

EtienneCmb 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:

pitmonticone commented 4 weeks ago

I have finished my review:

Review Issues

Review PRs

All the issues I opened have been resolved and all the PRs I opened have been merged.

I recommend this paper for acceptance.

ClaudMor commented 4 weeks ago

Hi @jbytecode,

The authors have satisfied all my issues and I believe the package represents a valid contribution. I invite the authors to update the performance claims as agreed here and recommend acceptance.

jbytecode commented 4 weeks ago

@pitmonticone , @ClaudMor - Great! Thank you.

@EtienneCmb - It seems we have one more issue to solve and we can go forward after you've done with them. Please ping me when you are ready to go. Thank you in advance.

EtienneCmb commented 4 weeks ago

Yes indeed @jbytecode, I'll try to do it quickly. I would like to thank @pitmonticone and @ClaudMor for their very insightful comments and and commits

EtienneCmb commented 3 weeks ago

Hi @jbytecode, I solved the remaining issue. I'll let @ClaudMor confirm. Thank you.

jbytecode commented 3 weeks ago

@EtienneCmb - Thank you.

@ClaudMor - Could you please update your review? Thank you in advance.

ClaudMor commented 3 weeks ago

Hi @jbytecode and @EtienneCmb,

I confirm I now get the expected plots.

jbytecode commented 3 weeks 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
[ ] Recommend acceptance with @editorialbot recommend-accept

jbytecode commented 3 weeks ago

@editorialbot check references

editorialbot commented 3 weeks ago

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

✅ OK DOIs

- 10.1103/PhysRevE.100.032305 is OK
- 10.1038/s41593-022-01070-0 is OK
- 10.3390/e21090869 is OK
- 10.1103/PhysRevResearch.5.013025 is OK
- 10.1038/s41567-021-01371-4 is OK
- 10.1002/j.1538-7305.1948.tb01338.x is OK
- 10.1523/ENEURO.0052-18.2018 is OK
- 10.1016/j.nbd.2022.105918 is OK
- 10.1089/brain.2020.0982 is OK
- 10.7554/eLife.92938 is OK
- 10.21105/joss.01081 is OK
- 10.21105/joss.00738 is OK
- 10.21105/joss.01609 is OK
- 10.1371/journal.pcbi.1006343 is OK
- 10.1016/j.tics.2023.11.005 is OK
- 10.1103/PhysRevResearch.5.013025 is OK
- 10.1103/PhysRevE.91.052802 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Towards an extended taxonomy of information dynami...
- No DOI given, and none found for title: Nonnegative decomposition of multivariate informat...
- No DOI given, and none found for title: Beyond normal: On the evaluation of mutual informa...
- No DOI given, and none found for title: An information-theoretic approach to hypergraph ps...
- No DOI given, and none found for title: Estimation of Shannon differential entropy: An ext...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

jbytecode commented 3 weeks ago

@editorialbot generate pdf

editorialbot commented 3 weeks ago

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

EtienneCmb commented 3 weeks ago

Hi @jbytecode,

[x] Authors and affiliations are correct
[x] We released the version 0.0.5
[x] Zenodo's DOI : 10.5281/zenodo.14046562
[x] I checked title, authors and license file, all of them match those in the JOSS paper

jbytecode commented 3 weeks ago

@editorialbot set v0.0.5 as version

editorialbot commented 3 weeks ago

Done! version is now v0.0.5

jbytecode commented 3 weeks ago

@editorialbot set 10.5281/zenodo.14046562 as archive

editorialbot commented 3 weeks ago

Done! archive is now 10.5281/zenodo.14046562

jbytecode commented 3 weeks ago

@EtienneCmb - I've just sent a pull request. This PR includes some minor changes in both the manuscript and the bibliography. Could you please review the PR and merge it? Thank you in advance.

https://github.com/brainets/hoi/pull/75

EtienneCmb commented 3 weeks ago

Hi @jbytecode, thanks for the PR, I merged it !

jbytecode commented 3 weeks ago

@editorialbot check references

editorialbot commented 3 weeks ago

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

✅ OK DOIs

- 10.1103/PhysRevE.100.032305 is OK
- 10.1038/s41593-022-01070-0 is OK
- 10.3390/e21090869 is OK
- 10.1103/PhysRevResearch.5.013025 is OK
- 10.1038/s41567-021-01371-4 is OK
- 10.1002/j.1538-7305.1948.tb01338.x is OK
- 10.1523/ENEURO.0052-18.2018 is OK
- 10.1016/j.nbd.2022.105918 is OK
- 10.1089/brain.2020.0982 is OK
- 10.7554/eLife.92938 is OK
- 10.21105/joss.01081 is OK
- 10.21105/joss.00738 is OK
- 10.21105/joss.01609 is OK
- 10.1371/journal.pcbi.1006343 is OK
- 10.1016/j.tics.2023.11.005 is OK
- 10.1103/PhysRevResearch.5.013025 is OK
- 10.1103/PhysRevE.91.052802 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Towards an extended taxonomy of information dynami...
- No DOI given, and none found for title: Nonnegative decomposition of multivariate informat...
- No DOI given, and none found for title: Beyond normal: On the evaluation of mutual informa...
- No DOI given, and none found for title: An information-theoretic approach to hypergraph ps...
- No DOI given, and none found for title: Estimation of Shannon differential entropy: An ext...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

jbytecode commented 3 weeks ago

@editorialbot generate pdf

editorialbot commented 3 weeks ago

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

jbytecode commented 3 weeks ago

@EtienneCmb - The paper and the bibliography now look good to me. Please perform one more proof-reading of the paper. Please tell me if there is any issue. Thank you in advance.

EtienneCmb commented 3 weeks ago

@jbytecode the draft looks correct indeed 👍

jbytecode commented 3 weeks ago

@editorialbot check references

editorialbot commented 3 weeks ago

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

✅ OK DOIs

- 10.1103/PhysRevE.100.032305 is OK
- 10.1038/s41593-022-01070-0 is OK
- 10.3390/e21090869 is OK
- 10.1103/PhysRevResearch.5.013025 is OK
- 10.1038/s41567-021-01371-4 is OK
- 10.1002/j.1538-7305.1948.tb01338.x is OK
- 10.1523/ENEURO.0052-18.2018 is OK
- 10.1016/j.nbd.2022.105918 is OK
- 10.1089/brain.2020.0982 is OK
- 10.7554/eLife.92938 is OK
- 10.21105/joss.01081 is OK
- 10.21105/joss.00738 is OK
- 10.21105/joss.01609 is OK
- 10.1371/journal.pcbi.1006343 is OK
- 10.1016/j.tics.2023.11.005 is OK
- 10.1103/PhysRevResearch.5.013025 is OK
- 10.1103/PhysRevE.91.052802 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Towards an extended taxonomy of information dynami...
- No DOI given, and none found for title: Nonnegative decomposition of multivariate informat...
- No DOI given, and none found for title: Beyond normal: On the evaluation of mutual informa...
- No DOI given, and none found for title: An information-theoretic approach to hypergraph ps...
- No DOI given, and none found for title: Estimation of Shannon differential entropy: An ext...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

jbytecode commented 3 weeks ago

@editorialbot generate pdf

editorialbot commented 3 weeks ago

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

jbytecode commented 3 weeks ago

@editorialbot recommend-accept

editorialbot commented 3 weeks ago

Attempting dry run of processing paper acceptance...

editorialbot commented 3 weeks ago

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

✅ OK DOIs

- 10.1103/PhysRevE.100.032305 is OK
- 10.1038/s41593-022-01070-0 is OK
- 10.3390/e21090869 is OK
- 10.1103/PhysRevResearch.5.013025 is OK
- 10.1038/s41567-021-01371-4 is OK
- 10.1002/j.1538-7305.1948.tb01338.x is OK
- 10.1523/ENEURO.0052-18.2018 is OK
- 10.1016/j.nbd.2022.105918 is OK
- 10.1089/brain.2020.0982 is OK
- 10.7554/eLife.92938 is OK
- 10.21105/joss.01081 is OK
- 10.21105/joss.00738 is OK
- 10.21105/joss.01609 is OK
- 10.1371/journal.pcbi.1006343 is OK
- 10.1016/j.tics.2023.11.005 is OK
- 10.1103/PhysRevResearch.5.013025 is OK
- 10.1103/PhysRevE.91.052802 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Towards an extended taxonomy of information dynami...
- No DOI given, and none found for title: Nonnegative decomposition of multivariate informat...
- No DOI given, and none found for title: Beyond normal: On the evaluation of mutual informa...
- No DOI given, and none found for title: An information-theoretic approach to hypergraph ps...
- No DOI given, and none found for title: Estimation of Shannon differential entropy: An ext...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot commented 3 weeks ago

:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.

ID ref-scagliariniU003A2023 already defined

openjournals / joss-reviews

[REVIEW]: High-performance estimation of Higher-Order Interactions from multivariate data #7360

Status

Reviewer instructions & questions

Checklists

Review checklist for @pitmonticone

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @ClaudMor

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