[REVIEW]: giotto-deep: A Python Package for Topological Deep Learning

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@matteocao@osorensen<!--end-editor-- Reviewers: @EduPH, @leotrs, @ismailguzel Archive: 10.5281/zenodo.7243721

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/f1f94829081bb7f0f16c48cafe1524d7"><img src="https://joss.theoj.org/papers/f1f94829081bb7f0f16c48cafe1524d7/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/f1f94829081bb7f0f16c48cafe1524d7/status.svg)](https://joss.theoj.org/papers/f1f94829081bb7f0f16c48cafe1524d7)

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

@EduPH & @leotrs & @ismailguzel, 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 @osorensen 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 @EduPH

📝 Checklist for @leotrs

📝 Checklist for @ismailguzel

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:

@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 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.01 s (201.3 files/s, 13287.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                         1             15              0             77
TeX                              1              9              0             74
YAML                             1              1              4             18
-------------------------------------------------------------------------------
SUM:                             3             25              4            169
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 663

editorialbot commented 1 year ago

Failed to discover a valid open source license

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:

editorialbot commented 1 year ago

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

OK DOIs

- None

MISSING DOIs

- 10.1017/9781316671665.004 may be a valid DOI for title: Topological data analysis
- 10.1145/1873951.1874254 may be a valid DOI for title: Torchvision the machine-vision package of torch
- 10.3389/frai.2021.681108 may be a valid DOI for title: A survey of topological machine learning methods

INVALID DOIs

- None

leotrs commented 1 year ago

Review checklist for @leotrs

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/giotto-ai/giotto-deep?
[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 (@matteocao) 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?

EduPH commented 1 year ago

Review checklist for @EduPH

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/giotto-ai/giotto-deep?
[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 (@matteocao) 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?

leotrs commented 1 year ago

Hello @matteocao! The paper has three authors and I see that all three are contributors to the repository. However, there are two contributors that i) are not authors, and ii) have contributed more than one contributor who is an author (at least by GitHub's measures here)

Could you please clarify how authorship was determined for your JOSS submission?

matteocao commented 1 year ago

Dear @leotrs , Thank you for your question. Of the two contributors (that are not authors) you mention, one has joined the efforts very recently and hence has not (yet) contributed to any design/core functionality of the library. The other one, on the other hand, after the initial contributions (1y ago) has completely gone silent and still today we are not able to reach him. This is why we did not include him. Let me know if this answer is satisfactory enough and/or if you have any suggestion on how to best proceed.

To further clarify: @giotto-learn and @matteocao are the same physical person.

leotrs commented 1 year ago

Thanks for the clarification. I think the current author list makes sense. Do consider to add the names of other/past contributors in the acknowledgements section of the paper.

ismailguzel commented 1 year ago

Review checklist for @ismailguzel

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/giotto-ai/giotto-deep?
[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 (@matteocao) 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?

leotrs commented 1 year ago

@matteocao I can see your CI runs pytest on the root directory but wasn't able to find a directory containing a test suite. Could you please point me to it? Thanks!

leotrs commented 1 year ago

@matteocao I see no mention of related/similar software in the current paper. Are there absolutely no other options for using topological techniques in deep learning?

matteocao commented 1 year ago

Dear @leotrs , Thank you for your message.

@matteocao I can see your CI runs pytest on the root directory but wasn't able to find a directory containing a test suite. Could you please point me to it? Thanks!

The unit tests are written per module, meaning that there is a folder called tests in each module folder. Here some examples:

The integration tests (or maybe even callable e2e tests) are the notebookes themselves: all of those in here

We find this way of organising tests reasonable (as opposed to putting all tests in one single folder). Please let us know if this feels reasonable for you as well.

@matteocao I see no mention of related/similar software in the current paper. Are there absolutely no other options for using topological techniques in deep learning?

There are indeed no package that try to do what we do. I would like however to mention the only possibly similar one, though much more limited in scope: https://github.com/MathieuCarriere/perslay. This packages implements one single technique that is topology-flavoured for feed-forward deep networks. Important note: even though we understood the paper (and we did cite such paper) and later were able to reproduce its content, we have not been able to use ay part of this "PersLay" package due to the total lack of documentation and structure. Please feel free to advise on what's the best course of action. Thank you!

leotrs commented 1 year ago

Both responses sound reasonable to me. Thanks.

leotrs commented 1 year ago

I have finished my review and I believe the paper can be accepted as is.

osorensen commented 1 year ago

Thanks a lot for your time and efforts, @leotrs

EduPH commented 1 year ago

Congratulations @matteocao, it is a nice library for the TDA community. I think the paper can be accepted. Just a remark, it would be nice to mention in the paper that previously, people have used TDA libraries such as Gudhi together with deep learning libraries such as scikit-learn, TensorFlow or PyTorch.

ismailguzel commented 1 year ago

I tested the package installation on both Windows and Ubuntu. Good for both platforms, actually. I'm grateful for @matteocao . I also didn't see anything different from what other reviewers had already noted. Finally, my review is completed, and I think the document can be accepted just as it is. It will be a great package for TDA folks.

osorensen commented 1 year ago

Wow! Thanks to all of @EduPH, @leotrs, @ismailguzel for completing your reviews so quickly!

@matteocao, I will now read through the paper a final time, and let you know if I have any suggested changes. In the meantime, could you please

[ ] Make a tagged release of your software, and list the version tag of the archived version here.
[ ] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[ ] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[ ] Please list the DOI of the archived version here.

osorensen commented 1 year ago

@editorialbot generate pdf

osorensen commented 1 year ago

@editorialbot check references

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:

editorialbot commented 1 year ago

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

OK DOIs

- None

MISSING DOIs

- 10.1017/9781316671665.004 may be a valid DOI for title: Topological data analysis
- 10.1145/1873951.1874254 may be a valid DOI for title: Torchvision the machine-vision package of torch
- 10.3389/frai.2021.681108 may be a valid DOI for title: A survey of topological machine learning methods

INVALID DOIs

- None

matteocao commented 1 year ago

Dear @osorensen ,

Thank you for your message. Here the data you asked for:

The tagged release version, as there have not been requests to modify the code nor upgrades for the last 20 days, shall be the v0.0.3: https://github.com/giotto-ai/giotto-deep/releases/tag/v0.0.3
Zenodo DOI:
Zenodo link: https://zenodo.org/record/7243721#.Y1ZKk-xBz64
I doubled checked the data and all is correct.

osorensen commented 1 year ago

Thanks @matteocao

A few comments on the manuscript

On lines 28 and 34 you start a sentence with the word giotto-deep, but on line 39 you write "Giotto-deep" with capital first letter. Please pick one and be consistent.
On line 34 I suggest added a "the" in front of giotto-deep, so it becomes "The giotto-deep architecture ..."
On lines 66-67 and 73, please add DOI to the arXiv references, cf. https://arxiv.org/abs/2206.15195 and https://arxiv.org/abs/1609.08227

Please let me know when this is done, and I can move forward with accepting the publication.

matteocao commented 1 year ago

Dear @osorensen ,

Thank you for your message and for your suggestions. All the changes have been made and the pdf compilation worked. Please let me know if there is anything else I need to do.

Thank you!

osorensen commented 1 year ago

@editorialbot generate pdf

osorensen commented 1 year ago

@editorialbot set v0.0.3 as archive

editorialbot commented 1 year ago

Done! Archive is now v0.0.3

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:

osorensen commented 1 year ago

@editorialbot set 10.5281/zenodo.7243721 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7243721

osorensen commented 1 year ago

@editorialbot set v0.0.3 as version

editorialbot commented 1 year ago

Done! version is now v0.0.3

osorensen commented 1 year ago

@editorialbot set v0.0.3 as version

editorialbot commented 1 year ago

Done! version is now v0.0.3

osorensen commented 1 year ago

@editorialbot set 10.5281/zenodo.7243721 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7243721

osorensen commented 1 year ago

Sorry for all the posts, I mixed up the commands a bit :-)

osorensen commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

:wave: @openjournals/dsais-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/3640, 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

🚨🚨🚨 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/3689
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04846
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

@EduPH, @leotrs, @ismailguzel – many thanks for your reviews here and to @osorensen 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 ✨

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

editorialbot commented 1 year 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:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.04846/status.svg)](https://doi.org/10.21105/joss.04846)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04846">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04846/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04846/status.svg
   :target: https://doi.org/10.21105/joss.04846

This is how it will look in your documentation:

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

openjournals / joss-reviews