[REVIEW]: cosasi: Graph Diffusion Source Inference in Python

[editorialbot]

Submitting author: @lucasmccabe (Lucas McCabe)
Repository: https://github.com/lmiconsulting/cosasi/
Branch with paper.md (empty if default branch): joss
Version: v0.0.4-joss
Editor: @danielskatz
Reviewers: @sara-02, @zoometh
Archive: 10.5281/zenodo.7430558

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/2d7b627bb3db796bbd125853bee6e3fb/status.svg)](https://joss.theoj.org/papers/2d7b627bb3db796bbd125853bee6e3fb)

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

@sara-02 & @zoometh, 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 @danielskatz 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 @zoometh

📝 Checklist for @sara-02

[editorialbot]

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]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.07 s (1285.6 files/s, 81991.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          39            538           1246           2257
reStructuredText                38            344            139            403
TeX                              1             11              0            120
JSON                             1              0              0            106
Markdown                         2             64              0            105
YAML                             2              1              4             28
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            85            970           1397           3054
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1008

[editorialbot]

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

OK DOIs

- 10.1109/tit.2011.2158885 is OK
- 10.1007/s10618-015-0435-9 is OK
- 10.1109/ita.2013.6502991 is OK
- 10.1109/icdm.2012.136 is OK
- 10.1007/978-3-031-79285-4 is OK
- 10.1016/j.softx.2022.100988 is OK
- 10.1016/j.softx.2021.100675 is OK
- 10.21105/joss.01731 is OK
- 10.5281/zenodo.4456181 is OK
- 10.18637/jss.v084.i08 is OK
- 10.1007/s11222-007-9033-z is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[danielskatz]

@sara-02 and @zoometh - Thanks for agreeing to review this submission.
This is the review thread for the paper. All of our communications will happen here from now on.

As you can see above, you each should use the command @editorialbot generate my checklist to create your review checklist. @editorialbot commands need to be the first thing in a new comment.

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, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#4894 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if either of you require some more time. We can also use editorialbot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@danielskatz) if you have any questions/concerns.

(And to remind everyone, including myself: @zoometh will start their review in a week or so and @sara-02 will start their review in mid November)

[lucasmccabe]

Hello @danielskatz: I noticed that the version is listed as 0.0.1. Would it be possible to set this to 0.0.3? A few updates were made since the initial submission; these changes are minor, but are listed for transparency in our release log.

Also @sara-02 and @zoometh, if it helps at all regarding the code coverage statement, I included a reference visual in the contributor guide.

Thank you All!

[danielskatz]

@editorialbot set 0.0.3 as version

[editorialbot]

Done! version is now 0.0.3

[danielskatz]

👋 @zoometh - any update on your review? It would be helpful if you can at least create your checklist via using the command @editorialbot generate my checklist. @editorialbot commands need to be the first thing in a new comment.

[zoometh]

I'm a bit overwhelmed these days. I'll start this weekend

[zoometh]

Review checklist for @zoometh

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/lmiconsulting/cosasi/?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@lucasmccabe) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• 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.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• 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

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• 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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• 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?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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?

[lucasmccabe]

Hello @sara-02 and @zoometh - thank you for working on this review during an especially busy season.

I wanted to check in to see if there is anything I can do to facilitate the process. For instance, if it's helpful and appropriate, I can confirm a few of the "general checks" (e.g. whether we conduct animal research).

Thank you for your time!

[danielskatz]

@lucasmccabe - thanks, but as an author, you shouldn't be prompting the reviewers (even if done in a friendly and helpful way), while as editor, I probably should in this case.

[danielskatz]

👋 @sara-02 - is there any update on your review? It would be helpful if you can at least create your checklist via using the command @editorialbot generate my checklist. @editorialbot commands need to be the first thing in a new comment.

[danielskatz]

👋 @zoometh - How is your review coming?

[lucasmccabe]

@lucasmccabe - thanks, but as an author, you shouldn't be prompting the reviewers (even if done in a friendly and helpful way), while as editor, I probably should in this case.

Understood - my apologies!

[sara-02]

Review checklist for @sara-02

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/lmiconsulting/cosasi/?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@lucasmccabe) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• 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.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• 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

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• 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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• 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?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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?

[zoometh]

👋 @zoometh - How is your review coming?

Slowly, due to a large amount of work. I'll continue this end of the week

[sara-02]

@danielskatz @lucasmccabe I am done with reviews from my side, the library loaded smoothly, and the sample code also worked. I have just one minor comment for the documentation. Rest is all good from my side.
The tests are also running smoothly.

[danielskatz]

Thanks @sara-02 !

[lucasmccabe]

Thank you for your review @sara-02! I have updated both the README and the narrative documentation to reflect your recommendation.

[zoometh]

I'm on my way to actually do my review, sorry for the delay

[danielskatz]

@editorialbot set 10.5281/zenodo.7430558 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7430558

[danielskatz]

@editorialbot recommend-accept

I'll proofread this next

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1145/3534678.3539288 is OK
- 10.1109/tit.2011.2158885 is OK
- 10.1007/s10618-015-0435-9 is OK
- 10.1109/ita.2013.6502991 is OK
- 10.1109/icdm.2012.136 is OK
- 10.1007/978-3-031-79285-4 is OK
- 10.1016/j.softx.2022.100988 is OK
- 10.1016/j.softx.2021.100675 is OK
- 10.21105/joss.01731 is OK
- 10.5281/zenodo.4456181 is OK
- 10.18637/jss.v084.i08 is OK
- 10.1007/s11222-007-9033-z is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3796, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

@lucasmccabe - some minor changes are in lmiconsulting/cosasi#3 - please merge this, or let me know what you disagree with, then we can continue the acceptance process

[lucasmccabe]

@danielskatz Thank you for your careful review of the manuscript. These changes make sense, and I've merged them.

[danielskatz]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1145/3534678.3539288 is OK
- 10.1109/tit.2011.2158885 is OK
- 10.1007/s10618-015-0435-9 is OK
- 10.1109/ita.2013.6502991 is OK
- 10.1109/icdm.2012.136 is OK
- 10.1007/978-3-031-79285-4 is OK
- 10.1016/j.softx.2022.100988 is OK
- 10.1016/j.softx.2021.100675 is OK
- 10.21105/joss.01731 is OK
- 10.5281/zenodo.4456181 is OK
- 10.18637/jss.v084.i08 is OK
- 10.18637/jss.v084.i08 is OK
- 10.1007/s11222-007-9033-z is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3797, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

@lucasmccabe - sorry, I now see one more small change I missed the first time - in lmiconsulting/cosasi#4

[lucasmccabe]

@danielskatz Ah, good catch, thanks. I've merged it.

[danielskatz]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04894 joss-papers#3798
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04894
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[danielskatz]

Congratulations to @lucasmccabe (Lucas McCabe)!!

And thanks to @sara-02 and @zoometh for reviewing!
We couldn't do this without you

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.04894/status.svg)](https://doi.org/10.21105/joss.04894)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04894">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04894/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04894/status.svg
   :target: https://doi.org/10.21105/joss.04894

This is how it will look in your documentation:

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[lucasmccabe]

@danielskatz @sara-02 @zoometh Thank you all for your help, review, and suggestions!