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[PRE REVIEW]: Teaspoon: A Python Package for Topological Signal Processing #7145

Open editorialbot opened 2 weeks ago

editorialbot commented 2 weeks ago

Submitting author: !--author-handle-->@lizliz<!--end-author-handle-- (Elizabeth Munch) Repository: https://github.com/TeaspoonTDA/teaspoon Branch with paper.md (empty if default branch): joss-paper Version: 1.5.7 Editor: !--editor-->@hugoledoux<!--end-editor-- Reviewers: !--reviewers-list-->@yossibokorbleile<!--end-reviewers-list-- Managing EiC: Daniel S. Katz

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Markdown: [![status](https://joss.theoj.org/papers/fc618a9de406ddbaa64f86ad1d798b9c/status.svg)](https://joss.theoj.org/papers/fc618a9de406ddbaa64f86ad1d798b9c)

Author instructions

Thanks for submitting your paper to JOSS @lizliz. Currently, there isn't a JOSS editor assigned to your paper.

@lizliz if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

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editorialbot commented 2 weeks ago

Hello human, 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 2 weeks ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.27 s (923.8 files/s, 285913.5 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             64              1            627
YAML                             4             10             29            360
Markdown                         8            108              0            337
CSV                              1              0              0            300
TOML                             1              6              0             51
make                             1             14              9             35
-------------------------------------------------------------------------------
SUM:                           251          10501          12780          54404
-------------------------------------------------------------------------------

Commit count by author:

   117  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 2 weeks ago

Paper file info:

📄 Wordcount for paper.md is 1448

✅ The paper includes a Statement of need section

editorialbot commented 2 weeks ago

License info:

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

editorialbot commented 2 weeks 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

🟡 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...

❌ MISSING DOIs

- 10.1109/cvprw59228.2023.00067 may be a valid DOI for title: TopFusion: Using Topological Feature Space for Fus...
- 10.1109/tpami.2018.2885516 may be a valid DOI for title: Persistence paths and signature features in topolo...
- 10.1109/cvpr.2015.7299106 may be a valid DOI for title: A Stable Multi-Scale Kernel for Topological Machin...
- 10.1063/1.4919075 may be a valid DOI for title: Time lagged ordinal partition networks for capturi...
- 10.1007/s44007-024-00110-4 may be a valid DOI for title: Delay parameter selection in permutation entropy u...
- 10.1115/1.4036814 may be a valid DOI for title: Reliable estimation of minimum embedding dimension...
- 10.1016/s0167-2789(97)00118-8 may be a valid DOI for title: Practical method for determining the minimum embed...

❌ INVALID DOIs

- None
editorialbot commented 2 weeks ago

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

danielskatz commented 2 weeks ago

👋 @hugoledoux - do you think you you could edit this submission?

danielskatz commented 2 weeks ago

@editorialbot invite @hugoledoux as editor

editorialbot commented 2 weeks ago

Invitation to edit this submission sent!

danielskatz commented 2 weeks ago

👋 @lizliz - thanks for your submission. While we look for an editor, you could work on the possibly missing DOIs that editorialbot suggests, but note that some may be incorrect. Please feel free to make changes to your .bib file, then use the command @editorialbot check references to check again, and the command @editorialbot generate pdf when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.

Also, I wonder if the readme and/or the paper could use a little more information about this software for the general developer community (non-topology people)?

editorialbot commented 2 weeks ago

Five most similar historical JOSS papers:

TDApplied: An R package for machine learning and inference with persistence diagrams Submitting author: @shaelebrown Handling editor: @mahfuz05062 (Active) Reviewers: @EduPH, @peekxc Similarity score: 0.7275

TDAstats: R pipeline for computing persistent homology in topological data analysis Submitting author: @rrrlw Handling editor: @leeper (Retired) Reviewers: @corybrunson Similarity score: 0.7173

Ripser.py: A Lean Persistent Homology Library for Python Submitting author: @sauln Handling editor: @arokem (Retired) Reviewers: @lmcinnes Similarity score: 0.7080

flowTorch - a Python library for analysis and reduced-order modeling of fluid flows Submitting author: @AndreWeiner Handling editor: @Kevin-Mattheus-Moerman (Active) Reviewers: @akaptano, @JaroslavHron, @salrm8, @hkjeldsberg Similarity score: 0.7054

TimeSeriesClustering: An extensible framework in Julia Submitting author: @holgerteichgraeber Handling editor: @danielskatz (Active) Reviewers: @jgoldfar, @ahwillia Similarity score: 0.6988

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

hugoledoux commented 2 weeks ago

@editorialbot assign @hugoledoux as editor

editorialbot commented 2 weeks ago

Assigned! @hugoledoux is now the editor

lizliz commented 2 weeks ago

Excellent, thanks for the very fast feedback! We will work on updating the DOIs and expanding the intro a bit, hopefully in the next few days.

lizliz commented 2 weeks ago

@editorialbot check references

editorialbot commented 2 weeks 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
hugoledoux commented 1 week ago

@lizliz I'm the editor in charge of your paper, and things were a bit slow with the new academic year but now I'm looking for potential reviewers. Could you please look in our database of reviewers (https://reviewers.joss.theoj.org/) and suggest here 4-5 potential good ones, or someone else you think would be a good fit? Please remove their "@" from their github username to not ping them unnecessarily.

hariharanragothaman commented 5 days ago

@hugoledoux - I would like to participate and review this paper. Can I get assigned to review this please? Thanks in advance.

saaikrishnan commented 5 days ago

@hugoledoux Can I please get assigned to review this ? Thank you in advance.

lizliz commented 5 days ago

Hi folks! Apologies for the delay, the beginning of the semester is also throwing me for a loop.

Thank you to those who have offered to review. I will include some additional options, although I have a potential conflict of interest with some which i've noted, so you can decide what is appropriate.

Also I will note that since the original submission, we have added a bit more content to the introduction in response to @danielskatz's comments. I am working on adding some more content to the readme as well, as requested. Please do let me know if there is additional editing needed and/or if that's not what you were thinking of.

hugoledoux commented 4 days ago

@editorialbot add @yossibokorbleile as reviewer

editorialbot commented 4 days ago

@yossibokorbleile added to the reviewers list!