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[PRE REVIEW]: ConleyDynamics.jl: A Julia package for multivector dynamics on Lefschetz complexes #7543

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editorialbot opened this issue Dec 2, 2024 · 37 comments
Open

[PRE REVIEW]: ConleyDynamics.jl: A Julia package for multivector dynamics on Lefschetz complexes #7543

editorialbot opened this issue Dec 2, 2024 · 37 comments
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Julia Mathematica pre-review TeX Track: 7 (CSISM) Computer science, Information Science, and Mathematics

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editorialbot commented Dec 2, 2024 •
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Submitting author: @almost6heads (Thomas Wanner)
Repository: https://github.com/almost6heads/ConleyDynamics.jl
Branch with paper.md (empty if default branch):
Version: v0.1.0
Editor: @drvinceknight
Reviewers: Pending
Managing EiC: Daniel S. Katz

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/e08afdaceec945d759cd412ac3c3bd84"><img src="https://joss.theoj.org/papers/e08afdaceec945d759cd412ac3c3bd84/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/e08afdaceec945d759cd412ac3c3bd84/status.svg)](https://joss.theoj.org/papers/e08afdaceec945d759cd412ac3c3bd84)

Author instructions

Thanks for submitting your paper to JOSS @almost6heads. Currently, there isn't a JOSS editor assigned to your paper.

@almost6heads 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 Dec 2, 2024
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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:

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.08 s (1419.5 files/s, 181584.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                        19            894              0           4484
Julia                           75           1837           2597           3429
TeX                              5             70              6            538
YAML                             5              6              8            133
TOML                             3              5              0             40
CSS                              1              0              0             17
Bourne Shell                     1              0              0              6
SVG                              1              0              0              1
-------------------------------------------------------------------------------
SUM:                           110           2812           2611           8648
-------------------------------------------------------------------------------

Commit count by author:

   233	Thomas Wanner

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Paper file info:

📄 Wordcount for paper.md is 1880

✅ The paper includes a Statement of need section

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License info:

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

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

✅ OK DOIs

- 10.1007/s10208-020-09444-1 is OK
- 10.1137/141000671 is OK
- 10.1137/23M1562469 is OK
- 10.1007/s00454-010-9303-y is OK
- 10.1007/PL00004638 is OK
- 10.1006/aima.1997.1650 is OK
- 10.1007/s41468-021-00073-3 is OK
- 10.3934/jcd.2016002 is OK
- 10.1007/s41468-022-00102-9 is OK
- 10.1016/j.cnsns.2021.106226 is OK
- 10.1016/j.jde.2021.10.001 is OK
- 10.1137/140971075 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Diskrete Räume
- No DOI given, and none found for title: Polygonal approximation of flows
- No DOI given, and none found for title: Isolated Invariant Sets and the Morse Index
- No DOI given, and none found for title: JuliaGraphs/Graphs.jl: an optimized graphs package...
- No DOI given, and none found for title: GUDHI User and Reference Manual
- No DOI given, and none found for title: Computational Homology
- No DOI given, and none found for title: Algebraic Topology
- No DOI given, and none found for title: Conley index
- No DOI given, and none found for title: Connection Matrices in Combinatorial Topological D...
- No DOI given, and none found for title: Elements of Algebraic Topology
- No DOI given, and none found for title: Finding attracting sets using combinatorial multiv...
- No DOI given, and none found for title: Global dynamics via multivector fields on Lefschet...
- No DOI given, and none found for title: ConleyDynamics.jl: A Julia package for multivector...

❌ MISSING DOIs

- 10.1016/b978-044452208-5/50049-1 may be a valid DOI for title: Computational Topology
- 10.1090/s0002-9947-1989-0978368-7 may be a valid DOI for title: The connection matrix theory for Morse decompositi...
- 10.1007/978-1-4939-9063-4 may be a valid DOI for title: A Basic Course in Algebraic Topology
- 10.1007/s10208-016-9330-z may be a valid DOI for title: Conley-Morse-Forman theory for combinatorial multi...

❌ INVALID DOIs

- None

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

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Five most similar historical JOSS papers:

DynamicalBilliards.jl: An easy-to-use, modular and extendable Julia package for Dynamical Billiard systems in two dimensions.
Submitting author: @Datseris
Handling editor: @kyleniemeyer (Active)
Reviewers: @ahwillia
Similarity score: 0.7251

ComplexRegions.jl: A Julia package for regions in the complex plane
Submitting author: @tobydriscoll
Handling editor: @drvinceknight (Active)
Reviewers: @dlfivefifty, @dpsanders
Similarity score: 0.7063

DREiMac: Dimensionality Reduction with Eilenberg-MacLane Coordinates
Submitting author: @LuisScoccola
Handling editor: @fabian-s (Active)
Reviewers: @mtsch, @raphaelreinauer
Similarity score: 0.7037

SyntheticEddyMethod.jl: A Julia package for the creation of inlet flow conditions for LES
Submitting author: @carlodev
Handling editor: @philipcardiff (Active)
Reviewers: @atzberg, @akshaysridhar
Similarity score: 0.6997

ModeCouplingTheory.jl: A solver for mode-coupling-theory-like integro-differential equations
Submitting author: @IlianPihlajamaa
Handling editor: @mstimberg (Active)
Reviewers: @epspebble, @dawbarton
Similarity score: 0.6997

⚠️ 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.

@danielskatz
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👋 @almost6heads - Thanks for your submission. It appears a bit long, about 1900 words, while JOSS typically expects 250-1000. Is there anything you can move to the repo or documentation and just point to or summarize in the paper?

In addition, 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.

@danielskatz
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Also, I see in the README

Currently, this repository does not allow any outside contributors. But if you are interested in getting involved, let me know!

This will need to be changed for JOSS to something more welcoming, as described in https://joss.readthedocs.io/en/latest/review_criteria.html#community-guidelines

@almost6heads
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@danielskatz I have added guideline for contributing to the project.
Also, possible reviewers might be: pitmonticone, DanielVandH, avik-pal, LuisScoccola.

I will work on the missing DOIs, and will try to shorten the paper as soon as I can. Thanks!

@danielskatz
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@almost6heads - please ping me when you are ready for this to move forward.

@almost6heads
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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/s10208-020-09444-1 is OK
- 10.1137/141000671 is OK
- 10.1137/23M1562469 is OK
- 10.1007/s00454-010-9303-y is OK
- 10.1007/PL00004638 is OK
- 10.1006/aima.1997.1650 is OK
- 10.1007/s41468-021-00073-3 is OK
- 10.3934/jcd.2016002 is OK
- 10.1007/s41468-022-00102-9 is OK
- 10.1016/j.cnsns.2021.106226 is OK
- 10.1016/j.jde.2021.10.001 is OK
- 10.1137/140971075 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Diskrete Räume
- No DOI given, and none found for title: Polygonal approximation of flows
- No DOI given, and none found for title: Isolated Invariant Sets and the Morse Index
- No DOI given, and none found for title: JuliaGraphs/Graphs.jl: an optimized graphs package...
- No DOI given, and none found for title: GUDHI User and Reference Manual
- No DOI given, and none found for title: Computational Homology
- No DOI given, and none found for title: Algebraic Topology
- No DOI given, and none found for title: Conley index
- No DOI given, and none found for title: Connection Matrices in Combinatorial Topological D...
- No DOI given, and none found for title: Elements of Algebraic Topology
- No DOI given, and none found for title: Finding attracting sets using combinatorial multiv...
- No DOI given, and none found for title: Global dynamics via multivector fields on Lefschet...
- No DOI given, and none found for title: ConleyDynamics.jl: A Julia package for multivector...

❌ MISSING DOIs

- 10.1016/b978-044452208-5/50049-1 may be a valid DOI for title: Computational Topology
- 10.1090/s0002-9947-1989-0978368-7 may be a valid DOI for title: The connection matrix theory for Morse decompositi...
- 10.1007/978-1-4939-9063-4 may be a valid DOI for title: A Basic Course in Algebraic Topology
- 10.1007/s10208-016-9330-z may be a valid DOI for title: Conley-Morse-Forman theory for combinatorial multi...

❌ INVALID DOIs

- None

@almost6heads
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@editorialbot check references

@editorialbot
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Collaborator Author 

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

✅ OK DOIs

- 10.1007/s10208-020-09444-1 is OK
- 10.1137/141000671 is OK
- 10.1016/j.topol.2006.04.033 is OK
- 10.1137/23M1562469 is OK
- 10.1007/s00454-010-9303-y is OK
- 10.1007/PL00004638 is OK
- 10.1006/aima.1997.1650 is OK
- 10.2307/2001142 is OK
- 10.1007/s41468-021-00073-3 is OK
- 10.1007/b97315 is OK
- 10.3934/jcd.2016002 is OK
- 10.1007/s41468-022-00102-9 is OK
- 10.1007/978-1-4939-9063-4 is OK
- 10.1007/s10208-016-9330-z is OK
- 10.1016/j.cnsns.2021.106226 is OK
- 10.1016/j.jde.2021.10.001 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Isolated Invariant Sets and the Morse Index
- No DOI given, and none found for title: JuliaGraphs/Graphs.jl: an optimized graphs package...
- No DOI given, and none found for title: GUDHI User and Reference Manual
- No DOI given, and none found for title: Algebraic Topology
- No DOI given, and none found for title: Conley index
- No DOI given, and none found for title: Connection Matrices in Combinatorial Topological D...
- No DOI given, and none found for title: Elements of Algebraic Topology
- No DOI given, and none found for title: Finding attracting sets using combinatorial multiv...
- No DOI given, and none found for title: Global dynamics via multivector fields on Lefschet...
- No DOI given, and none found for title: ConleyDynamics.jl: A Julia package for multivector...

❌ MISSING DOIs

- 10.1007/978-3-540-33259-6_7 may be a valid DOI for title: Computational Topology: An Introduction

❌ INVALID DOIs

- None

@almost6heads
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@danielskatz I am almost ready to move forward, but do have one question: I located three of the missing DOIs, but there is still one labeled as missing. The problem is that this book does not have a DOI, but there is an unrelated paper with the same title that does. How can I deal with that?
Other than that, the paper has been shortened.

@almost6heads
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@editorialbot generate pdf

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

@editorialbot
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Five most similar historical JOSS papers:

DynamicalBilliards.jl: An easy-to-use, modular and extendable Julia package for Dynamical Billiard systems in two dimensions.
Submitting author: @Datseris
Handling editor: @kyleniemeyer (Active)
Reviewers: @ahwillia
Similarity score: 0.7538

WorldDynamics.jl: A Julia Package for Developing and Simulating Integrated Assessment Models
Submitting author: @aurorarossi
Handling editor: @fraukewiese (Active)
Reviewers: @ranocha, @StanczakDominik, @miguelraz
Similarity score: 0.7464

DREiMac: Dimensionality Reduction with Eilenberg-MacLane Coordinates
Submitting author: @LuisScoccola
Handling editor: @fabian-s (Active)
Reviewers: @mtsch, @raphaelreinauer
Similarity score: 0.7453

IndividualDisplacements.jl: a Julia package to simulate and study particle displacements within the climate system
Submitting author: @gaelforget
Handling editor: @kthyng (Active)
Reviewers: @milankl, @visr
Similarity score: 0.7427

HOODESolver.jl: A Julia package for highly oscillatory problems
Submitting author: @pnavaro
Handling editor: @vissarion (Active)
Reviewers: @ranocha, @HaoZeke
Similarity score: 0.7400

⚠️ 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.

@danielskatz
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@danielskatz I am almost ready to move forward, but do have one question: I located three of the missing DOIs, but there is still one labeled as missing. The problem is that this book does not have a DOI, but there is an unrelated paper with the same title that does. How can I deal with that?

you can just ignore it - that's what I meant when I wrote that not all suggestions would be correct.

Other than that, the paper has been shortened.

Thanks.

@danielskatz
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@editorialbot check repository

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.08 s (1452.3 files/s, 183104.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                        20            895              0           4423
Julia                           75           1837           2597           3429
TeX                              5             68              6            524
YAML                             5              6              8            133
TOML                             3              5              0             40
CSS                              1              0              0             17
Bourne Shell                     1              0              0              6
SVG                              1              0              0              1
-------------------------------------------------------------------------------
SUM:                           111           2811           2611           8573
-------------------------------------------------------------------------------

Commit count by author:

   235	Thomas Wanner

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Paper file info:

📄 Wordcount for paper.md is 1000

✅ The paper includes a Statement of need section

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License info:

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

@danielskatz danielskatz removed the paused label Dec 2, 2024
@danielskatz
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@drvinceknight - Would you be willing to edit this submission?

@danielskatz
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@editorialbot invite @drvinceknight as editor

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Invitation to edit this submission sent!

@danielskatz
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And note that the author suggested some possible reviewers in #7543 (comment)

@drvinceknight
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@editorialbot assign me as editor

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Assigned! @drvinceknight is now the editor

@danielskatz
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👋 @drvinceknight - can you get this started please?

@drvinceknight
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Hi @pitmonticone, @DanielVandH, @avik-pal, @LuisScoccola I'm pinging you to ask if you would be able to assist with reviewing this submissions to JOSS (The Journal of Open Source Software).

JOSS publishes articles about open source research software. The submission I'd like you to review is titled: “ ConleyDynamics.jl: A Julia package for multivector dynamics on Lefschetz complexes”. You can find more information at the top of this Github issue.

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.

@DanielVandH
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Hi @drvinceknight - unfortunately I will not be available to review this. Thanks.

@avik-pal
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Hi @drvinceknight, I don't have the relevant background to review this. Thanks!

@pitmonticone
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Hi @drvinceknight, unfortunately I won't be able to review for the next few months.

@LuisScoccola
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Hi @drvinceknight; I know the reviewing process is supposed to be quick for this venue, and unfortunately I cannot take any more reviewing commitments for the next couple of months.

@drvinceknight
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Thanks @DanielVandH, @avik-pal, @pitmonticone and @LuisScoccola.

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