[REVIEW]: Teaspoon: A Python Package for Topological Signal Processing

editorialbot commented 1 month ago

Submitting author: !--author-handle-->@lizliz@hugoledoux<!--end-editor-- Reviewers: @yossibokorbleile, @EduPH Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/fc618a9de406ddbaa64f86ad1d798b9c"><img src="https://joss.theoj.org/papers/fc618a9de406ddbaa64f86ad1d798b9c/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/fc618a9de406ddbaa64f86ad1d798b9c/status.svg)](https://joss.theoj.org/papers/fc618a9de406ddbaa64f86ad1d798b9c)

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 & @EduPH, 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 @hugoledoux 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 @EduPH

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=0.27 s (925.6 files/s, 286646.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            91           5458            360          34440
Python                          60           3399           4221           7637
SVG                              4              1              1           4223
reStructuredText                48           1086            624           2410
Jupyter Notebook                12              0           7246           2085
CSS                              7            224             68           1019
JavaScript                      12            131            221            880
TeX                              2             67              1            652
YAML                             4             10             29            360
Markdown                         8            113              0            348
CSV                              1              0              0            300
TOML                             1              6              0             51
make                             1             14              9             35
-------------------------------------------------------------------------------
SUM:                           251          10509          12780          54440
-------------------------------------------------------------------------------

Commit count by author:

   119  Liz Munch
    62  danielle_barnes
    47  maxchumley
    43  EGR\myersau3
    25  Sarah Tymochko
    24  Firas Khasawneh
    23  Sunia Tanweer
    20  Melih Can Yesilli
    17  Audun Myers
    17  stanweer1
    14  barnesd8
     9  Martin Uray
     8  Elizabeth Munch
     6  Danielle Barnes
     5  Danielle
     4  Kayla Makela
     3  Jesse Berwald
     1  danielle
     1  firas khasawneh
     1  mcanyesilli

editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 1747

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

editorialbot commented 1 month ago

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

✅ OK DOIs

- 10.1051/0004-6361/201629272 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.48550/ARXIV.2110.05266 is OK
- 10.1140/epjds/s13688-023-00379-5 is OK
- 10.1103/physreve.107.034303 is OK
- 10.1063/5.0102421 is OK
- 10.1137/22m1476848 is OK
- 10.48550/ARXIV.2312.02099 is OK
- 10.3934/fods.2024006 is OK
- 10.48550/ARXIV.2212.08295 is OK
- 10.1016/j.precisioneng.2023.05.005 is OK
- 10.1109/icmla.2019.00202 is OK
- 10.3934/fods.2022005 is OK
- 10.1007/s10208-022-09567-7 is OK
- 10.1007/s41468-021-00071-5 is OK
- 10.5281/zenodo.2533369 is OK
- 10.1140/epjds/s13688-017-0109-5 is OK
- 10.4310/HHA.2016.v18.n1.a21 is OK
- 10.48550/arxiv.2204.11080 is OK
- 10.18608/jla.2017.42.6 is OK
- 10.1016/j.physa.2016.06.028 is OK
- 10.1007/s11071-024-09289-1 is OK
- 10.1016/j.probengmech.2024.103634 is OK
- 10.1142/s0219498815500668 is OK
- 10.1109/cvprw59228.2023.00067 is OK
- 10.1109/TPAMI.2018.2885516 is OK
- 10.1109/CVPR.2015.7299106 is OK
- 10.1063/1.4919075 is OK
- 10.1007/s44007-024-00110-4 is OK
- 10.1115/1.4036814 is OK
- 10.1016/s0167-2789(97)00118-8 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Gaps in Globular Cluster Streams: Pal 5 and the Ga...
- No DOI given, and none found for title: Galactic Dynamics: Second Edition
- No DOI given, and none found for title: Fidgit: An ungodly union of GitHub and Figshare
- No DOI given, and none found for title: When Hearts Beat as One – Cardiac Dynamics and Syn...
- No DOI given, and none found for title: Topological Time-Series Classification
- No DOI given, and none found for title: Topological Approaches for Quantifying the Shape o...
- No DOI given, and none found for title: GUDHI: Geometry Understanding in Higher Dimensions
- No DOI given, and none found for title: giotto-tda: A Topological Data Analysis Toolkit fo...
- No DOI given, and none found for title: Dionysus2
- No DOI given, and none found for title: Introduction to the R package TDA
- No DOI given, and none found for title: An Overview of the Topology ToolKit
- No DOI given, and none found for title: Computational Topology for Data Analysis
- No DOI given, and none found for title: Statistical Topological Data Analysis using Persis...
- No DOI given, and none found for title: Persistence Images: A Stable Vector Representation...
- No DOI given, and none found for title: Teaspoon: A comprehensive python package for topol...
- No DOI given, and none found for title: Algebraic Topology

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

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:

yossibokorbleile commented 1 month ago

@editorialbot generate my checklist

editorialbot commented 1 month ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

yossibokorbleile commented 1 month ago

Review checklist for @yossibokorbleile

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/TeaspoonTDA/teaspoon?
[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 (@lizliz) 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?
[ ] 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

[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?

editorialbot commented 1 month ago

Hello @EduPH, 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

EduPH commented 1 month 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/TeaspoonTDA/teaspoon?
[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 (@lizliz) 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.
[ ] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[ ] 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?
[ ] 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)?
[ ] 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 month ago

Hello @lizliz, thank you for such an excellent Python package. I am working on the review and added an issue in the repository about the needed version of the packages.

yossibokorbleile commented 2 weeks ago

Hey @lizliz

I agree with @EduPH that the package looks great! I have found some issues that are preventing me from verifying the functionality. I have created an issue on the repo.

openjournals / joss-reviews