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[PRE REVIEW]: Jupyter Scatter: Interactive Exploration of Large-Scale Datasets #6867

Closed editorialbot closed 1 month ago

editorialbot commented 2 months ago

Submitting author: !--author-handle-->@flekschas<!--end-author-handle-- (Fritz Lekschas) Repository: https://github.com/flekschas/jupyter-scatter/ Branch with paper.md (empty if default branch): joss Version: v0.16.0 Editor: !--editor-->@faroit<!--end-editor-- Reviewers: @xiaohk, @paulbrodersen Managing EiC: Chris Vernon

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status

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HTML: <a href="https://joss.theoj.org/papers/b07b7a67b85b61bf79fa033bd27b2aad"><img src="https://joss.theoj.org/papers/b07b7a67b85b61bf79fa033bd27b2aad/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/b07b7a67b85b61bf79fa033bd27b2aad/status.svg)](https://joss.theoj.org/papers/b07b7a67b85b61bf79fa033bd27b2aad)

Author instructions

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

@flekschas 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

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

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editorialbot commented 2 months 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 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.18 s (396.8 files/s, 113983.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                             4              0              0           4414
Python                          11            853           1322           4023
JavaScript                       5            493             71           2611
Markdown                        19            912              0           2560
Jupyter Notebook                 5              0           1833            305
TeX                              1             23              0            205
YAML                            10             28             10            202
TypeScript                       3             20             12            151
Vuejs Component                  1             19              1            129
TOML                             1             10              2             78
make                             1             20              4             43
SVG                              9              0              0             28
CSS                              1              1              0             12
-------------------------------------------------------------------------------
SUM:                            71           2379           3255          14761
-------------------------------------------------------------------------------

Commit count by author:

   247  Fritz Lekschas
    36  dependabot[bot]
    12  Trevor Manz
     1  Dan Rosén
     1  Kurt McKee
     1  Sehi L'Yi
     1  pablo-gar
editorialbot commented 2 months ago

Paper file info:

📄 Wordcount for paper.md is 1868

✅ The paper includes a Statement of need section

editorialbot commented 2 months ago

License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

editorialbot commented 2 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.05275 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.5281/zenodo.7522322 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.21105/joss.03021 is OK
- 10.48550/ARXIV.1802.03426 is OK
- 10.48550/ARXIV.1312.6114 is OK
- 10.1080/14786440109462720 is OK
- 10.31219/osf.io/puxnf is OK

MISSING DOIs

- 10.1016/j.molcel.2023.06.018 may be a valid DOI for title: Spatial and temporal organization of the genome: C...
- 10.1186/s13059-018-1486-1 may be a valid DOI for title: HiGlass: web-based visual exploration and analysis...
- 10.1038/s41586-022-04718-w may be a valid DOI for title: Extricating human tumour immune alterations from t...
- 10.1016/j.patter.2021.100372 may be a valid DOI for title: New interpretable machine-learning method for sing...
- 10.1038/s41594-022-00892-7 may be a valid DOI for title: Diverse silent chromatin states modulate genome co...
- No DOI given, and none found for title: News category dataset
- No DOI given, and none found for title: Color universal design (cud)-how to make figures a...
- No DOI given, and none found for title: Visualizing Data using t-SNE
- No DOI given, and none found for title: Fashion-MNIST: a Novel Image Dataset for Benchmark...
- No DOI given, and none found for title: Bokeh: Python library for interactive visualizatio...
- No DOI given, and none found for title: Datashader: Accurately Render Even the Largest Dat...
- No DOI given, and none found for title: Traitlets: A Lightweight Traits Like Module
- No DOI given, and none found for title: Anywidget: Jupyter Widgets Made Easy
- No DOI given, and none found for title: GeoNames
- No DOI given, and none found for title: ipywidgets: Interactive Widgets for the Jupyter No...

INVALID DOIs

- None
editorialbot commented 2 months ago

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

flekschas commented 2 months ago

@editorialbot commands

editorialbot commented 2 months ago

Hello @flekschas, 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
flekschas commented 2 months ago

@editorialbot check references

editorialbot commented 2 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.05275 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1016/j.molcel.2023.06.018 is OK
- 10.1186/s13059-018-1486-1 is OK
- 10.1038/s41586-022-04718-w is OK
- 10.1016/j.patter.2021.100372 is OK
- 10.5281/zenodo.7522322 is OK
- 10.1038/s41594-022-00892-7 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.21105/joss.03021 is OK
- 10.48550/ARXIV.1802.03426 is OK
- 10.48550/ARXIV.1312.6114 is OK
- 10.1080/14786440109462720 is OK
- 10.31219/osf.io/puxnf is OK

MISSING DOIs

- No DOI given, and none found for title: News category dataset
- No DOI given, and none found for title: Color universal design (cud)-how to make figures a...
- No DOI given, and none found for title: Visualizing Data using t-SNE
- No DOI given, and none found for title: Fashion-MNIST: a Novel Image Dataset for Benchmark...
- No DOI given, and none found for title: Bokeh: Python library for interactive visualizatio...
- No DOI given, and none found for title: Datashader: Accurately Render Even the Largest Dat...
- No DOI given, and none found for title: Traitlets: A Lightweight Traits Like Module
- No DOI given, and none found for title: Anywidget: Jupyter Widgets Made Easy
- No DOI given, and none found for title: GeoNames
- No DOI given, and none found for title: ipywidgets: Interactive Widgets for the Jupyter No...

INVALID DOIs

- None
flekschas commented 2 months ago

xiaohk

flekschas commented 2 months ago

fil

flekschas commented 2 months ago

paulbrodersen

crvernon commented 2 months ago

@editorialbot invite @faroit as editor

:wave: @faroit - can you take this one on as editor?

editorialbot commented 2 months ago

Invitation to edit this submission sent!

crvernon commented 2 months ago

@editorialbot invite @faroit as editor

Just adding another ping.

@editorialbot invite @faroit as editor

👋 @faroit - can you take this one on as editor?

editorialbot commented 2 months ago

Invitation to edit this submission sent!

faroit commented 2 months ago

@crvernon i'm not sure if I would be a good fit for editing as I am not up-to-date on the data visualization landscape. Nonetheless, I could take over if no one else is available but not before end of june.

crvernon commented 2 months ago

@faroit - thanks for your feedback. At this point, you are the only available editor in this track that has availability (it's been a busy season!). It would be great if you could take this one on and I can provide any help along the way if specific questions come along. Thanks!

flekschas commented 2 months ago

Just to resurface. Here my list of reviewer ideas:

The first two are visualization researchers/engineers. The third one also seems proficient in the visualization and Python space.

crvernon commented 2 months ago

@editorialbot add @faroit as editor

@faroit - I know you are not going to be active in this one until a week from now but I wanted to get it assigned so we can get it out of queue and ready for you when you become available. Thanks!

editorialbot commented 2 months ago

Assigned! @faroit is now the editor

faroit commented 2 months ago

👋 Hi @flekschas, thanks for your submission to JOSS! I will be serving as the editor for this. We'll use this issue to identify reviewers and resolve technical issues.

Regarding this submission, it would be great to have reviewers with domain knowledge who also have experience with visualization software. In addition to your proposals I would like to ask the following potential reviewers

For this, please check the JOSS COI policy and get back to me if i could invite them.

flekschas commented 2 months ago

Thanks @faroit. I don't see any conflict of interest for the reviewers you suggested. However, one small note: I acted as a reviewer for ianhi's recent JOSS paper mpl-interactions: https://joss.theoj.org/papers/10.21105/joss.05651. I don't think this counts as a conflict of interest but I want to mention it anyway.

flekschas commented 1 month ago

@faroit Any updates? :) I know it's summer time but it's been a minute since we submitted the paper. Happy to look for more reviewer candidates if that'd be helpful.

faroit commented 1 month ago

Thanks @faroit. I don't see any conflict of interest for the reviewers you suggested. However, one small note: I acted as a reviewer for ianhi's recent JOSS paper mpl-interactions: https://joss.theoj.org/papers/10.21105/joss.05651. I don't think this counts as a conflict of interest but I want to mention it anyway.

thanks for mentioning that, I would rather tend to treat this as a potential COI, so I would request without that reviewer for now.

faroit commented 1 month ago

👋 @j9ac9k @campagnola @csadorf @xiaohk @fil @paulbrodersen - would any of you be willing to review this submission for JOSS? The JOSS review process takes place on GitHub and focuses on the software and a short paper. We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

The software under review is https://github.com/flekschas/jupyter-scatter

This issue is a "pre-review" issue in which reviewers are assigned. Once sufficient reviewers are recruited we will open a dedicated review issue where the review will take place.

paulbrodersen commented 1 month ago

I am on holiday until July 29th included, but happy to make some time July 30th - Aug 2nd for the first (and hopefully only) round of revisions - if that is timely enough. Either way, at first glance it looks like a pretty cool and useful tool, congratulations!

xiaohk commented 1 month ago

👋 @j9ac9k @campagnola @csadorf @xiaohk @Fil @paulbrodersen - would any of you be willing to review this submission for JOSS? The JOSS review process takes place on GitHub and focuses on the software and a short paper. We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

The software under review is https://github.com/flekschas/jupyter-scatter

This issue is a "pre-review" issue in which reviewers are assigned. Once sufficient reviewers are recruited we will open a dedicated review issue where the review will take place.

Hi @faroit! Happy to review this submission!

paulbrodersen commented 1 month ago

@faroit Back from my holiday and available.

faroit commented 1 month ago

@editorialbot add @xiaohk to reviewers

editorialbot commented 1 month ago

@xiaohk added to the reviewers list!

faroit commented 1 month ago

@editorialbot add @paulbrodersen to reviewers

editorialbot commented 1 month ago

@paulbrodersen added to the reviewers list!

faroit commented 1 month ago

@paulbrodersen @xiaohk 👋 hi and thanks a lot for helping out to review!

faroit commented 1 month ago

@editorialbot start review

editorialbot commented 1 month ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/7059.