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[REVIEW]: multipers: Multiparameter Persistence for Machine Learning #6773

Open editorialbot opened 4 months ago

editorialbot commented 4 months ago

Submitting author: !--author-handle-->@DavidLapous<!--end-author-handle-- (David Loiseaux) Repository: https://github.com/DavidLapous/multipers Branch with paper.md (empty if default branch): Version: v2.0.0 Editor: !--editor-->@RMeli<!--end-editor-- Reviewers: @yossibokorbleile, @peekxc Archive: Pending

Status

status

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HTML: <a href="https://joss.theoj.org/papers/73e33046702c27dbb1cc76841e7d5fba"><img src="https://joss.theoj.org/papers/73e33046702c27dbb1cc76841e7d5fba/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/73e33046702c27dbb1cc76841e7d5fba/status.svg)](https://joss.theoj.org/papers/73e33046702c27dbb1cc76841e7d5fba)

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

@yossibokorbleile & @peekxc, 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 @RMeli 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 @yossibokorbleile

📝 Checklist for @peekxc

editorialbot commented 4 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:

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editorialbot commented 4 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.21 s (952.8 files/s, 310802.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C/C++ Header                   115           5232           6255          33181
Python                          46           1352           1993           7552
Cython                          13            295            609           1455
Jupyter Notebook                13              0           5445            929
TeX                              1             22              0            320
YAML                             2             12             31            146
Markdown                         2             40              0            127
reStructuredText                 3             54             74             42
JSON                             1              0              0             30
TOML                             1              1              0             14
make                             1              6              7             10
Bourne Shell                     2              0              0              9
-------------------------------------------------------------------------------
SUM:                           200           7014          14414          43815
-------------------------------------------------------------------------------

Commit count by author:

   154  David Loiseaux
    46  DavidLapous
editorialbot commented 4 months ago

Paper file info:

📄 Wordcount for paper.md is 1321

🔴 Failed to discover a Statement of need section in paper

editorialbot commented 4 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.48550/arXiv.2203.14289 is OK
- 10.21105/joss.05022 is OK
- 10.1137/20M1353605 is OK
- 10.48550/arxiv.2303.14040 is OK
- 10.1137/1.9781611977561.ch3 is OK
- 10.1137/1.9781611977912.173 is OK
- 10.1007/978-3-662-44199-2_28 is OK
- 10.48550/arXiv.2206.02026 is OK
- 10.1137/1.9781611976472.16 is OK
- 10.48550/arXiv.2005.09048 is OK
- 10.48550/arXiv.1512.00180 is OK
- 10.4230/LIPIcs.SoCG.2022.19 is OK
- 10/gtt7dq is OK

MISSING DOIs

- No DOI given, and none found for title: GRIL: A \2\-Parameter Persistence Based Vectorizat...
- No DOI given, and none found for title: GUDHI
- No DOI given, and none found for title: A Framework for Fast and Stable Representations of...
- No DOI given, and none found for title: Multiparameter Persistence Landscapes
- No DOI given, and none found for title: POT: Python Optimal Transport
- No DOI given, and none found for title: Kernel Operations on the GPU, with Autodiff, witho...
- No DOI given, and none found for title: PyTorch: An Imperative Style, High-Performance Dee...
- No DOI given, and none found for title: Stable Vectorization of Multiparameter Persistent ...
- No DOI given, and none found for title: Scikit-Learn: Machine Learning in Python
- No DOI given, and none found for title: Differentiability and Convergence of Filtration Le...

INVALID DOIs

- None
editorialbot commented 4 months ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

editorialbot commented 4 months ago

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

yossibokorbleile commented 4 months ago

Review checklist for @yossibokorbleile

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

peekxc commented 4 months ago

Review checklist for @peekxc

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

RMeli commented 3 months ago

👋 @DavidLapous, @peekxc, and @yossibokorbleile

I hope everything is going well. Could you all provide a short few sentences/bullet points on how things are going with this review?

Thanks and keep up the great work!

yossibokorbleile commented 3 months ago

@RMeli 👋👋👋

I am little behind where I had hoped to be, but it's going well. I am on holidays until July 1, and am aiming to finish the review by July 15.

RMeli commented 3 months ago

@yossibokorbleile great, thanks for letting us know!

RMeli commented 3 months ago

👋 @DavidLapous, @peekxc, and @yossibokorbleile

I hope your review is processing well. Could you all provide a short few sentences on how things are going and if there are any blockers?

Many thanks!

yossibokorbleile commented 3 months ago

@RMeli its going well! I just need to finish testing the installation and functionality, and read the documentation.

RMeli commented 3 months ago

Thanks for the update @yossibokorbleile!

peekxc commented 3 months ago

@RMeli I am also working on reviewing the docs and running the software. Unfortunately, the dependencies for this project are quite extensive; I currently cannot obtain a valid dependency resolution for the package

yossibokorbleile commented 3 months ago

@RMeli I can second what @peekxc has said, resolving the dependencies is not an easy task, and I haven't succeeded yet.

DavidLapous commented 3 months ago

👋 @RMeli @peekxc @yossibokorbleile Thanks for taking the time to review this!

I'm curious of what's failing on your end for the installation. If you're not using windows (which is not supported, cf DavidLapous/multipers#6), a pip install multipers tqdm matplotlib with python>=3.10 should pass all the tests, and notebooks parts that do not require external libraries. There was also very recently a major numpy upgrade (which was unlocked with Gudhi 3.10 in the dependencies), for which I need to make a release, with recompiled binaries (cf. DavidLapous/multipers@bca4ac3). I'll do that in a minute.

Could you open an issue / email me if you still have an issue there ?

RMeli commented 3 months ago

Hi all, thank you very much for all the updates. @peekxc and @yossibokorbleile, please do open issues in the repository (and please link this issue) if you encounter issues so that @DavidLapous can track them and take care of them. I'll also have a look at the installation procedure.

yossibokorbleile commented 3 months ago

@RMeli @DavidLapous I have managed to get multipers installed now using pip (still unsure what the initial issue was, but a fresh environment sorted it all out). I will leave checking compilation from source to @peekxc

yossibokorbleile commented 3 months ago

@RMeli @DavidLapous I have created the issue https://github.com/DavidLapous/multipers/issues/13 which is about Mac M1/M2/... support. I can test the functionality on a Linux environment, but this will delay the day I can finish this review by.

RMeli commented 2 months ago

I have managed to get multipers installed now using pip (still unsure what the initial issue was, but a fresh environment sorted it all out).

I'm glad this worked out in the end!

yossibokorbleile commented 2 months ago

Hiiiiiiiii @RMeli

Managed to finish testing what I wanted to test.

RMeli commented 2 months ago

Thank you for the update and for completing the checklist @yossibokorbleile.

@peekxc how are things going with your review? Please let me know if I can be of any help.

RMeli commented 1 month ago

Hi @peekxc, I hope you are well. How are things going with this review? Would you mind sharing a few lines describing the progress?

Many thanks.

RMeli commented 3 weeks ago

Hi @peekxc, I haven't heard from you in a long while. How is the review going? Is there any problem preventing you to continue/complete the review? Please let me know if this is the case, so that we can proceed accordingly. Many thanks.

peekxc commented 2 weeks ago

Hey @RMeli, sorry I've been a bit busy of late. I spent a couple hours this morning and have managed to reproduce the notebooks and look a bit more through the package. I'm filling some additional issues now that I think should be met before proceeding.

RMeli commented 2 weeks ago

Thank you for the update @peekxc.

RMeli commented 1 week ago

Hi @peekxc and @DavidLapous, how is this progressing?

DavidLapous commented 1 week ago

Hey @RMeli,
@peekxc found some issues that I will fix in the next release (DavidLapous/multipers#18 and DavidLapous/multipers#19) they involve the documentation website, so I cannot update this now (to match the current version). We currently are merging some Gudhi upstream files, which require some testing for a proper stable release. Edit: Commit DavidLapous/multipers@1f4a76f1a74b526cb2dcbae2400249ef49c35a9b should have fixed both issues.

DavidLapous commented 1 week ago

The latest release should have fixed these issues. I've also updated the website accordingly. I've also put the repo on zenodo; with the DOI: DOI

RMeli commented 6 days ago

Thanks @DavidLapous! @peekxc how is the review proceeding?

peekxc commented 3 days ago

Hi @RMeli, I've now finished my review and all of the issues I've created have been addressed.

RMeli commented 3 days ago

@peekxc thank you for completing the review! @DavidLapous I'll now start the final checks on my side.