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[PRE REVIEW]: pyPLNmodels: A Python package to analyse multivariate high-dimensional count data #6965

Closed editorialbot closed 5 days ago

editorialbot commented 1 week ago

Submitting author: !--author-handle-->@bastien-mva<!--end-author-handle-- (Bastien Batardiere) Repository: https://github.com/PLN-team/pyPLNmodels.git Branch with paper.md (empty if default branch): joss Version: 0.0.78 Editor: !--editor-->@likeajumprope<!--end-editor-- Reviewers: @LingfengLuo0510, @mrazomej Managing EiC: Chris Vernon

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status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/1f6f471f36670700a9d70ccd03654038"><img src="https://joss.theoj.org/papers/1f6f471f36670700a9d70ccd03654038/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/1f6f471f36670700a9d70ccd03654038/status.svg)](https://joss.theoj.org/papers/1f6f471f36670700a9d70ccd03654038)

Author instructions

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

@bastien-mva 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.

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editorialbot commented 1 week 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 1 week ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (705.1 files/s, 171888.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          30           1380           3087           6043
CSV                             10              0              0           1948
Markdown                         3             87              0            360
R                                2             30              9            171
TeX                              1             12              0             83
YAML                             2              8             17             79
Jupyter Notebook                 1              0           1026             64
TOML                             1              6              8             53
DOS Batch                        1              8              1             26
reStructuredText                 7             13             56             17
Bourne Shell                     1              2              0             13
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            60           1550           4211           8866
-------------------------------------------------------------------------------

Commit count by author:

   631  bastien-mva
    11  Julien Chiquet
     9  Jean-Benoist Leger
     1  Joon Kwon
editorialbot commented 1 week ago

Paper file info:

📄 Wordcount for paper.md is 1747

✅ The paper includes a Statement of need section

editorialbot commented 1 week ago

License info:

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

editorialbot commented 1 week ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3389/fevo.2021.588292 is OK
- 10.5281/zenodo.5765804 is OK
- 10.1093/biomet/76.4.643 is OK

MISSING DOIs

- No DOI given, and none found for title: PyTorch: An Imperative Style, High-Performance Dee...
- 10.25080/majora-92bf1922-011 may be a valid DOI for title: statsmodels: Econometric and statistical modeling ...
- 10.1214/18-aoas1177 may be a valid DOI for title: Variational inference for probabilistic Poisson PC...
- No DOI given, and none found for title: gllvm - Fast analysis of multivariate abundance da...
- No DOI given, and none found for title: Zero-inflation in the Multivariate Poisson Lognorm...
- No DOI given, and none found for title: The NLopt nonlinear-optimization package

INVALID DOIs

- None
editorialbot commented 1 week ago

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

editorialbot commented 1 week ago

Five most similar historical JOSS papers:

Pyglmnet: Python implementation of elastic-net regularized generalized linear models Submitting author: @jasmainak Handling editor: @arokem (Retired) Reviewers: @professoralkmin, @ryEllison Similarity score: 0.7138

PyNM: a Lightweight Python implementation of Normative Modeling Submitting author: @harveyaa Handling editor: @dfm (Active) Reviewers: @smkia, @saigerutherford Similarity score: 0.7068

SiSyPHE: A Python package for the Simulation of Systems of interacting mean-field Particles with High Efficiency Submitting author: @antoinediez Handling editor: @pdebuyl (Active) Reviewers: @lorenzo-rovigatti, @junghans Similarity score: 0.7025

Groupyr: Sparse Group Lasso in Python Submitting author: @richford Handling editor: @galessiorob (Active) Reviewers: @janfreyberg, @JonathanReardon, @rougier Similarity score: 0.7001

DeepOF: a Python package for supervised and unsupervised pattern recognition in mice motion tracking data Submitting author: @lucasmiranda42 Handling editor: @emdupre (Active) Reviewers: @cellistigs, @edeno Similarity score: 0.6972

⚠️ 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.

Bastien-mva commented 1 week ago

@editorialbot commands

editorialbot commented 1 week ago

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

@editorialbot commands

Bastien-mva commented 1 week ago

@editorialbot commands

editorialbot commented 1 week ago

Hello @Bastien-mva, 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
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# Check the references of the paper for missing DOIs
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@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers
Bastien-mva commented 1 week ago

@editorialbot check repository

editorialbot commented 1 week ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (700.4 files/s, 169699.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          30           1380           3087           6043
CSV                             10              0              0           1948
Markdown                         3             67              0            290
R                                2             30              9            171
TeX                              1             12              0             83
YAML                             2              8             17             79
Jupyter Notebook                 1              0           1026             64
TOML                             1              6              8             53
DOS Batch                        1              8              1             26
reStructuredText                 7             13             56             17
Bourne Shell                     1              2              0             13
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            60           1530           4211           8796
-------------------------------------------------------------------------------

Commit count by author:

   632  bastien-mva
    11  Julien Chiquet
     9  Jean-Benoist Leger
     1  Joon Kwon
editorialbot commented 1 week ago

Paper file info:

📄 Wordcount for paper.md is 1106

✅ The paper includes a Statement of need section

editorialbot commented 1 week ago

License info:

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

Bastien-mva commented 1 week ago

At-mentioning co-authors here: @jchiquet @joon-kwon

Here is a non-exhaustive list of potential reviewers from the JOSS reviewers google sheet (coauthors, please feel free to add more in this thread):

Bastien-mva commented 1 week ago

@editorialbot check repository

editorialbot commented 1 week ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (703.7 files/s, 170455.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          30           1380           3087           6043
CSV                             10              0              0           1948
Markdown                         3             65              0            289
R                                2             30              9            171
TeX                              1             12              0             83
YAML                             2              8             17             79
Jupyter Notebook                 1              0           1026             64
TOML                             1              6              8             53
DOS Batch                        1              8              1             26
reStructuredText                 7             13             56             17
Bourne Shell                     1              2              0             13
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            60           1528           4211           8795
-------------------------------------------------------------------------------

Commit count by author:

   633  bastien-mva
    11  Julien Chiquet
     9  Jean-Benoist Leger
     1  Joon Kwon
editorialbot commented 1 week ago

Paper file info:

📄 Wordcount for paper.md is 1092

✅ The paper includes a Statement of need section

editorialbot commented 1 week ago

License info:

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

Bastien-mva commented 1 week ago

@editorialbot check repository

editorialbot commented 1 week ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (700.1 files/s, 169563.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          30           1380           3087           6043
CSV                             10              0              0           1948
Markdown                         3             65              0            288
R                                2             30              9            171
TeX                              1             12              0             83
YAML                             2              8             17             79
Jupyter Notebook                 1              0           1026             64
TOML                             1              6              8             53
DOS Batch                        1              8              1             26
reStructuredText                 7             13             56             17
Bourne Shell                     1              2              0             13
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            60           1528           4211           8794
-------------------------------------------------------------------------------

Commit count by author:

   634  bastien-mva
    11  Julien Chiquet
     9  Jean-Benoist Leger
     1  Joon Kwon
editorialbot commented 1 week ago

Paper file info:

📄 Wordcount for paper.md is 1070

✅ The paper includes a Statement of need section

editorialbot commented 1 week ago

License info:

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

Bastien-mva commented 1 week ago

@editorialbot check references

editorialbot commented 1 week ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3389/fevo.2021.588292 is OK
- 10.5281/zenodo.5765804 is OK
- 10.1093/biomet/76.4.643 is OK

MISSING DOIs

- No DOI given, and none found for title: PyTorch: An Imperative Style, High-Performance Dee...
- 10.25080/majora-92bf1922-011 may be a valid DOI for title: statsmodels: Econometric and statistical modeling ...
- 10.1214/18-aoas1177 may be a valid DOI for title: Variational inference for probabilistic Poisson PC...
- No DOI given, and none found for title: gllvm - Fast analysis of multivariate abundance da...
- No DOI given, and none found for title: Zero-inflation in the Multivariate Poisson Lognorm...
- No DOI given, and none found for title: The NLopt nonlinear-optimization package

INVALID DOIs

- None
Bastien-mva commented 1 week ago

@editorialbot check references

editorialbot commented 1 week ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3389/fevo.2021.588292 is OK
- 10.25080/majora-92bf1922-011 is OK
- 10.5281/zenodo.5765804 is OK
- 10.1093/biomet/76.4.643 is OK
- 10.1214/18-aoas1177 is OK

MISSING DOIs

- No DOI given, and none found for title: PyTorch: An Imperative Style, High-Performance Dee...
- No DOI given, and none found for title: gllvm - Fast analysis of multivariate abundance da...
- No DOI given, and none found for title: Zero-inflation in the Multivariate Poisson Lognorm...
- No DOI given, and none found for title: The NLopt nonlinear-optimization package

INVALID DOIs

- None
crvernon commented 6 days ago

@editorialbot invite @likeajumprope as editor

👋 @likeajumprope - do you want to take this one on as editor?

editorialbot commented 6 days ago

Invitation to edit this submission sent!

likeajumprope commented 6 days ago

Invitation to edit this submission sent!

sure!

likeajumprope commented 6 days ago

@editorialbot assign @likeajumprope as editor

editorialbot commented 6 days ago

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

@editorialbot commands

likeajumprope commented 6 days ago

@editorialbot commands

editorialbot commented 6 days ago

Hello @likeajumprope, here are the things you can ask me to do:


# List all available commands
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# Add to this issue's reviewers list
@editorialbot add @username as reviewer

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@editorialbot list editors

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@editorialbot remind @reviewer in 2 weeks

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@editorialbot generate my checklist

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likeajumprope commented 6 days ago

@editorialbot assign @likeajumprope as editor

editorialbot commented 6 days ago

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

@editorialbot commands

likeajumprope commented 6 days ago

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

@editorialbot commands

what am I doing wrong haha can you assign me @crvernon?

crvernon commented 6 days ago

@editorialbot assign @likeajumprope as editor

I believe only editors in chief can run assignments on a name (even if it is your own). You have to actually run:

@editorialbot assign me as editor

No problem though, I've got you on this one. And thanks!

editorialbot commented 6 days ago

Assigned! @likeajumprope is now the editor

likeajumprope commented 5 days ago

Hi @LingfengLuo0510 👋 - would you be interested in taking on this paper for review?

likeajumprope commented 5 days ago

Hi @mayer79 👋 would you be interested in taking on this paper for review?

likeajumprope commented 5 days ago

Hi @mrazomej 👋 would you be interested in taking this paper on for review?

LingfengLuo0510 commented 5 days ago

Hi @LingfengLuo0510 👋 - would you be interested in taking on this paper for review?

Thanks! Yes I am interested.

likeajumprope commented 5 days ago

Hi @LingfengLuo0510 👋 - would you be interested in taking on this paper for review?

Thanks! Yes I am interested.

perfect thanks!!

likeajumprope commented 5 days ago

@editorialbot add @LingfengLuo0510 as reviewer

editorialbot commented 5 days ago

@LingfengLuo0510 added to the reviewers list!

mrazomej commented 5 days ago

Hi @mrazomej 👋 would you be interested in taking this paper on for review?

Yes, I'm interested. Count me in!

likeajumprope commented 5 days ago

@editorialbot add @mrazomej as reviewer

likeajumprope commented 5 days ago

@editorialbot add @mrazomej as reviewer