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[PRE REVIEW]: giotto-deep: A Python Package for Topological Deep Learning #4828

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editorialbot opened this issue Oct 7, 2022 · 35 comments
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[PRE REVIEW]: giotto-deep: A Python Package for Topological Deep Learning #4828

editorialbot opened this issue Oct 7, 2022 · 35 comments
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pre-review TeX Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning waitlisted Submissions in the JOSS backlog due to reduced service mode.

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editorialbot commented Oct 7, 2022 •
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Submitting author: @matteocao (Matteo Caorsi)
Repository: https://github.com/giotto-ai/giotto-deep
Branch with paper.md (empty if default branch): paper
Version: v0.0.3
Editor: @osorensen
Reviewers: @EduPH, @leotrs, @ismailguzel
Managing EiC: Kevin M. Moerman

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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)

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

@matteocao if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

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 editorialbot added pre-review Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning labels Oct 7, 2022
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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

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.02 s (181.4 files/s, 11971.8 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

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Wordcount for paper.md is 663

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Failed to discover a valid open source license

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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

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@Kevin-Mattheus-Moerman
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@matteocao the above lines of code counts seem very low ☝️ can you clarify what the submission to be reviewed entails? Is it just the content over at https://github.com/giotto-ai/giotto-deep or is there other content/repos too?

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@editorialbot check repository

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.01 s (385.0 files/s, 25407.6 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

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Wordcount for paper.md is 663

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Failed to discover a valid open source license

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Dear @Kevin-Mattheus-Moerman ,

Thank you for your comments.

If I understand your question correctly, I would say that the editorialbot is not counting properly: it is excluding all the files with .py extension as well as .ipynb which form the core of the library (thousands of lines). Furthermore, there are k8 yaml files not considered either.
The license is the standard AGPLv3, which is also not discovered by the editorialbot apparently.

Finally, the library code is in the main branch of https://github.com/giotto-ai/giotto-deep , while the paper is in the paper branch.
Please let me know if this clarifies the submission content.

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arfon commented Oct 9, 2022

Here's the output of cloc on the main branch:

 cloc giotto-deep/
     198 text files.
     196 unique files.                                          
      21 files ignored.

github.com/AlDanial/cloc v 1.86  T=0.19 s (1007.1 files/s, 119234.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         119           1991           3403           7959
Jupyter Notebook                18              0           5264           1894
YAML                            15             18             13            491
Markdown                         5             84              0            313
reStructuredText                19            161            101            250
JSON                             3              0              0             61
Dockerfile                       3             17             10             36
DOS Batch                        1              8              1             26
SVG                              2              0              0             17
make                             1              4              7              9
HTML                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                           187           2283           8799          11057
-------------------------------------------------------------------------------

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arfon commented Oct 9, 2022

@matteocao - thanks for your submission to JOSS. We're currently managing a large backlog of submissions and the editor most appropriate for your area is already rather busy.

For now, we will need to waitlist this paper and process it as the queue reduces. Thanks for your patience!

@arfon arfon added the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Oct 9, 2022
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kthyng commented Oct 10, 2022

Hi @osorensen! Could you edit this submission?

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kthyng commented Oct 10, 2022

@editorialbot invite @osorensen as editor

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Invitation to edit this submission sent!

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@editorialbot assign @osorensen as editor

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Assigned! @osorensen is now the editor

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@editorialbot generate pdf

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

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👋 @ismailguzel @leotrs @EduPH @Annielytix, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

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EduPH commented Oct 11, 2022

Hello, I'm available.

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@editorialbot add @EduPH as reviewer

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@EduPH added to the reviewers list!

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leotrs commented Oct 11, 2022

Yes.

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@editorialbot add @leotrs as reviewer

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@leotrs added to the reviewers list!

@ismailguzel
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Yes. It will be my pleasure. Thank you.

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osorensen commented Oct 11, 2022 •
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@editorialbot add @ismailguzel as reviewer

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

@editorialbot commands

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@editorialbot add @ismailguzel as reviewer

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@ismailguzel added to the reviewers list!

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@editorialbot start review

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OK, I've started the review over in #4846.

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