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[PRE REVIEW]: HyperNetX: A Python package for modeling complex network data as hypergraphs #5955

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editorialbot opened this issue Oct 16, 2023 · 55 comments
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[PRE REVIEW]: HyperNetX: A Python package for modeling complex network data as hypergraphs #5955

editorialbot opened this issue Oct 16, 2023 · 55 comments
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@szhorvat @danielskatz @IvanIsCoding
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Makefile pre-review Python TeX Track: 7 (CSISM) Computer science, Information Science, and Mathematics

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editorialbot commented Oct 16, 2023 •
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Submitting author: @brendapraggastis (Brenda Praggastis)
Repository: https://github.com/pnnl/HyperNetX
Branch with paper.md (empty if default branch): paper
Version: v2.0.5
Editor: @danielskatz
Reviewers: @szhorvat, @IvanIsCoding
Managing EiC: Daniel S. Katz

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/97a1ebb3cfc47070c672cb5e6f2c474f"><img src="https://joss.theoj.org/papers/97a1ebb3cfc47070c672cb5e6f2c474f/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/97a1ebb3cfc47070c672cb5e6f2c474f/status.svg)](https://joss.theoj.org/papers/97a1ebb3cfc47070c672cb5e6f2c474f)

Author instructions

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

@brendapraggastis 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:

@editorialbot commands
@editorialbot editorialbot added pre-review Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Oct 16, 2023
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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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Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "," (COMMA) [#<BibTeX::Bibliography data=[15]>, "@", #<BibTeX::Entry >, {:title=>["Phoenix: A Scalable Streaming Hypergraph Analysis Framework"], :author=>["Kurte, Kuldeep and Imam, Neena and Hasan, S M Shamimul and Kannan, Ramakrishnan"], :doi=>["10.1007/978-3-030-71704-9_1"], :url=>["https://www.osti.gov/biblio/1830117"], :journal=>[""], :issn=>["2569--7072"]}, ",", "number", "="]

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.46 s (219.9 files/s, 498668.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          48           2280           5245           5609
Jupyter Notebook                12              0         211574           1108
reStructuredText                21            389            358            818
Markdown                         6            204              0            556
DOS Batch                        1             34              2            227
TeX                              1             24              0            204
YAML                             6             37             29            178
make                             2             34             22             67
INI                              2              4              2             35
TOML                             2              0              0             27
-------------------------------------------------------------------------------
SUM:                           101           3006         217232           8829
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 1210

@danielskatz
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danielskatz commented Oct 16, 2023 •
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👋 @brendapraggastis - note that your paper does not compile. Please follow the example paper and note that you can click on the error above to find out more about it. 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 after making changes to the .md file or when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.

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brendapraggastis commented Oct 16, 2023 via email

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@editorialbot commands

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Hello @brendapraggastis, 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

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# 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

@brendapraggastis
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@editorialbot generate pdf

@brendapraggastis
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@editorialbot check references

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

OK DOIs

- 10.1137/20M1355896 is OK
- 10.1007/978-3-030-71704-9_1 is OK
- 10.21105/joss.05162 is OK
- 10.1101/2023.09.29.560191 is OK

MISSING DOIs

- 10.1007/978-3-030-48478-1_1 may be a valid DOI for title: Hypergraph Analytics of Domain Name System Relationships
- 10.3390/math10050759 may be a valid DOI for title: The application of directed hyper-graphs for analysis of models of information systems
- 10.1109/hipc53243.2021.00045 may be a valid DOI for title: Parallel algorithms for efficient computation of high-order line graphs of hypergraphs
- 10.1109/tvcg.2022.3153895 may be a valid DOI for title: Topological simplifications of hypergraphs
- 10.1140/epjds/s13688-020-00231-0 may be a valid DOI for title: Hypernetwork science via high-order hypergraph walks
- 10.1371/journal.pcbi.1011190 may be a valid DOI for title: HAT: Hypergraph analysis toolbox
- 10.1016/s0924-6509(08)x7007-2 may be a valid DOI for title: Hypergraphs: combinatorics of finite sets
- 10.1186/s12859-021-04197-2 may be a valid DOI for title: Hypergraph models of biological networks to identify genes critical to pathogenic viral response
- 10.1371/journal.pcbi.1011190 may be a valid DOI for title: HAT: Hypergraph analysis toolbox
- 10.1093/comnet/cnad019 may be a valid DOI for title: Hypergraphx: a library for higher-order network analysis
- 10.1007/978-3-030-67318-5_25 may be a valid DOI for title: Hypernetwork Science: From Multidimensional Networks to Computational Topology
- 10.1007/978-3-030-25070-6_9 may be a valid DOI for title: SimpleHypergraphs. jl—novel software framework for modelling and analysis of hypergraphs

INVALID DOIs

- None

@danielskatz
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It looks like it is compiling, at least I see a draft paper on github and it works when I run docker. I’m not sure what to fix. Is there somewhere else to look?

See the error above re the Kurte, Kuldeep entry in the bibtex. And use the commands I suggested - @editorialbot check references to make sure the bibtex is correct, then @editorialbot generate pdf to generate the paper, which won't work until the reference check is ok.

It seems that you are getting this figure out as I'm typing...

@danielskatz
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And if @editorialbot generate pdf fails with no info now that the references can be generated, let me know and I can get help.

@brendapraggastis
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@editorialbot generate pdf

@brendapraggastis
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@danielskatz how can I tell if the generate pdf command was successful? I just get a smiley face.
Also, do I need to do anything else to have the paper reviewed. I read somewhere that I should pick reviewers?

@brendapraggastis
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@editorialbot check references

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

OK DOIs

- 10.1137/20M1355896 is OK
- 10.1007/978-3-030-71704-9_1 is OK
- 10.21105/joss.05162 is OK
- 10.1101/2023.09.29.560191 is OK

MISSING DOIs

- 10.1007/978-3-030-48478-1_1 may be a valid DOI for title: Hypergraph Analytics of Domain Name System Relationships
- 10.3390/math10050759 may be a valid DOI for title: The application of directed hyper-graphs for analysis of models of information systems
- 10.1109/hipc53243.2021.00045 may be a valid DOI for title: Parallel algorithms for efficient computation of high-order line graphs of hypergraphs
- 10.1109/tvcg.2022.3153895 may be a valid DOI for title: Topological simplifications of hypergraphs
- 10.1140/epjds/s13688-020-00231-0 may be a valid DOI for title: Hypernetwork science via high-order hypergraph walks
- 10.1371/journal.pcbi.1011190 may be a valid DOI for title: HAT: Hypergraph analysis toolbox
- 10.1186/s12859-021-04197-2 may be a valid DOI for title: Hypergraph models of biological networks to identify genes critical to pathogenic viral response
- 10.1371/journal.pcbi.1011190 may be a valid DOI for title: HAT: Hypergraph analysis toolbox
- 10.1093/comnet/cnad019 may be a valid DOI for title: Hypergraphx: a library for higher-order network analysis
- 10.1007/978-3-030-67318-5_25 may be a valid DOI for title: Hypernetwork Science: From Multidimensional Networks to Computational Topology
- 10.1007/978-3-030-25070-6_9 may be a valid DOI for title: SimpleHypergraphs. jl—novel software framework for modelling and analysis of hypergraphs

INVALID DOIs

- None

@danielskatz
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@brendapraggastis - normally, you would see a response to the generate pdf command with a link to the PDF, like there is a response for the check references command.

Re the references, please do 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.

@danielskatz
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@openjournals/dev - can you help us figure out why the pdf isn't generating here or returning an error?

@danielskatz
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@brendapraggastis - you can suggest reviewers, but it's the job of the editor to select and find reviewers, based in part on your suggestions. My job is to find an editor, but I won't do that until we have a clear paper and references, as I also do an initial check to make sure your submission is in scope, and I need to see the full submission (the software and the paper) to make an initial decision.

@xuanxu
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xuanxu commented Oct 17, 2023

The compilation of the pdf is failing because there are incorrect values in the metadata of the paper.md file:

0000-0000-0000-0000 is am invalid value for orcid.

@danielskatz
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Thanks @xuanxu - why don't get an error like we used to?

@danielskatz
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@brendapraggastis - please either use actual ORCIDs for all authors, or remove the ORCID line for authors without ORCIDs

@brendapraggastis
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@editorialbot check references

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

OK DOIs

- 10.1007/978-3-030-48478-1_1 is OK
- 10.3390/math10050759 is OK
- 10.1109/hipc53243.2021.00045 is OK
- 10.1109/tvcg.2022.3153895 is OK
- 10.1140/epjds/s13688-020-00231-0 is OK
- 10.1371/journal.pcbi.1011190 is OK
- 10.1016/s0924-6509(09)x7013-3 is OK
- 10.1016/s0924-6509(08)x7007-2 is OK
- 10.1186/s12859-021-04197-2 is OK
- 10.48550/arXiv.2208.03103 is OK
- 10.1093/comnet/cnad019 is OK
- 10.48550/arXiv.2208.06894 is OK
- 10.1007/978-3-030-67318-5_25 is OK
- 10.1137/20M1355896 is OK
- 10.1007/978-3-030-71704-9_1 is OK
- 10.21105/joss.05162 is OK
- 10.1007/978-3-030-25070-6_9 is OK
- 10.1101/2023.09.29.560191 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@danielskatz
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@brendapraggastis - thanks, this all looks good. I'll work on finding an editor now

@danielskatz
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👋 @drvinceknight - would you be willing to edit this submission?

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@editorialbot invite @drvinceknight as editor

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Invitation to edit this submission sent!

@brendapraggastis
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@brendapraggastis - thanks, this all looks good. I'll work on finding an editor now

@danielskatz Thank you so much for your help.

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

OK DOIs

- 10.1007/978-3-030-48478-1_1 is OK
- 10.3390/math10050759 is OK
- 10.1109/hipc53243.2021.00045 is OK
- 10.1109/tvcg.2022.3153895 is OK
- 10.1140/epjds/s13688-020-00231-0 is OK
- 10.1371/journal.pcbi.1011190 is OK
- 10.1016/s0924-6509(09)x7013-3 is OK
- 10.1016/s0924-6509(08)x7007-2 is OK
- 10.1186/s12859-021-04197-2 is OK
- 10.48550/arXiv.2208.03103 is OK
- 10.1093/comnet/cnad019 is OK
- 10.48550/arXiv.2208.06894 is OK
- 10.1007/978-3-030-67318-5_25 is OK
- 10.1137/20M1355896 is OK
- 10.1007/978-3-030-71704-9_1 is OK
- 10.21105/joss.05162 is OK
- 10.1007/978-3-030-25070-6_9 is OK
- 10.1101/2023.09.29.560191 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@danielskatz
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👋 @drvinceknight - ping... (on the request to edit)

@danielskatz
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👋 @drvinceknight - one last ping... (on the request to edit)

@danielskatz
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@brendapraggastis - sorry about the delay. I will edit this submission; I'll assign myself now and start on it soon.

@danielskatz
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@editorialbot assign me as editor

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Assigned! @danielskatz is now the editor

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@brendapraggastis - do you have suggestions for reviewers? If so, 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, or suggestions from outside JOSS are also fine.

@danielskatz
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👋 @IvanIsCoding, @szhorvat, @inakleinbottle - would one or two of you be willing to review this JOSS submission?

@danielskatz
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👋 @TNanukem, @dvysardana, @drj11, @imw - would one or two of you be willing to review this JOSS submission?

@szhorvat
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szhorvat commented Nov 1, 2023 •
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@danielskatz This is within my expertise and I've seen this package before. I think a proper review will take time. This is not a one-afternoon job. I would not be able to get started before Nov 13 (when teaching is over here), and I might take a while to finish ... probably several weeks. If you'd like me to go ahead under these conditions, I think I'd enjoy the review.

@danielskatz
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@szhorvat - thanks, this sounds fine. I'll add you as a reviewer, and once we get one or two more, I'll start the review

@danielskatz
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@editorialbot add @szhorvat as reviewer

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@szhorvat added to the reviewers list!

@IvanIsCoding
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@danielskatz I am available to review the submission. Mind you, this would my first time as a reviewer for JOSS so I would need to spend time reviewing the procedures as well

@danielskatz
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Thanks @IvanIsCoding - I think you have seen this process as an author, so you will be somewhat familiar with it. I'm happy to help answer any questions you have about this (reviewer) side. I'll add you, and we can start the review.

@danielskatz
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@editorialbot add @IvanIsCoding as reviewer

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@IvanIsCoding added to the reviewers list!

@danielskatz
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@editorialbot start review

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OK, I've started the review over in #6016.

@drj11
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drj11 commented Nov 3, 2023

I see you have 2 reviewers now, but i'm happy to be a standby. The suggested reviewers bot is a neat feature!

@danielskatz
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@drj11 - I'm happy to add you as well; I like to have 3 reviewers when I can. See you over in #6016

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