[PRE REVIEW]: Psymple: A Python package for complex systems modelling #7221

editorialbot · 2024-09-13T11:06:54Z

Submitting author: @GJHSimmons (George Simmons)
Repository: https://github.com/casasglobal-org/psymple/
Branch with paper.md (empty if default branch): joss-review
Version: v0.3.4
Editor: @prashjha
Reviewers: @pitmonticone, @SunnyXu
Managing EiC: Daniel S. Katz

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/10eda7c95b9676b0d9fe1a8dd3ea2cb7/status.svg)](https://joss.theoj.org/papers/10eda7c95b9676b0d9fe1a8dd3ea2cb7)

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editorialbot · 2024-09-13T11:06:56Z

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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editorialbot · 2024-09-13T11:07:17Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.06 s (1249.9 files/s, 163596.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          30           1169           1755           3846
Markdown                        32            629              0           1319
YAML                             6             25              9            320
TeX                              1             24              0            266
TOML                             1              2              3             24
JavaScript                       1              1              0             18
INI                              1              2              0             12
-------------------------------------------------------------------------------
SUM:                            72           1852           1767           5805
-------------------------------------------------------------------------------

Commit count by author:

   111	George Simmons
    16	Georg Osang
     1	Georg Os

editorialbot · 2024-09-13T11:07:18Z

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

✅ OK DOIs

- 10.1016/B978-0-12-809633-8.02390-6 is OK
- 10.1098/rspb.2019.1916 is OK
- 10.1007/s10668-023-03698-9 is OK
- 10.4204/EPTCS.372.14 is OK
- 10.4204/eptcs.380.5 is OK
- 10.1093/icb/icy018 is OK
- 10.7717/peerj-cs.103 is OK
- 10.1007/s10340-023-01610-y is OK
- 10.1186/s12302-020-00406-6 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: AlgebraicDynamics.jl
- No DOI given, and none found for title: The climatic factor in Australian grassland ecolog...
- No DOI given, and none found for title: The Ecology of \emphAphis craccivora Koch and Subt...

❌ MISSING DOIs

- 10.1016/0304-3800(80)90048-4 may be a valid DOI for title: Simulation of ecological processes

❌ INVALID DOIs

- https://doi.org/10.1146/annurev.ecolsys.110308.120159 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1111/j.1461-0248.2008.01277.x is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1111/1749-4877.12618 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/S0304-3800(99)00144-1 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1111/j.1461-0248.2010.01479.x is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/S0921-8009(97)00103-1 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1111/j.1365-2699.2011.02659.x is INVALID because of 'https://doi.org/' prefix
- 10.1079/9781800621459.0004 is INVALID
- 10.1079/9781800621459.0015 is INVALID

editorialbot · 2024-09-13T11:07:23Z

Paper file info:

📄 Wordcount for paper.md is 1611

✅ The paper includes a Statement of need section

editorialbot · 2024-09-13T11:07:26Z

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

editorialbot · 2024-09-13T11:08:23Z

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

editorialbot · 2024-09-13T11:09:07Z

Five most similar historical JOSS papers:

PySD: System Dynamics Modeling in Python
Submitting author: @rogersamso
Handling editor: @pdebuyl (Active)
Reviewers: @blsqr, @sixpearls
Similarity score: 0.7383

Simframe: A Python Framework for Scientific Simulations
Submitting author: @stammler
Handling editor: @taless474 (Retired)
Reviewers: @schruste, @lucaferranti
Similarity score: 0.7098

SimuPy: A Python framework for modeling and simulating dynamical systems
Submitting author: @sixpearls
Handling editor: @cMadan (Retired)
Reviewers: @demotu
Similarity score: 0.7092

py-pde: A Python package for solving partial differential equations
Submitting author: @david-zwicker
Handling editor: @xuanxu (Active)
Reviewers: @celliern, @mstimberg
Similarity score: 0.7087

DE-Sim: an object-oriented, discrete-event simulation tool for data-intensive modeling of complex systems in Python
Submitting author: @artgoldberg
Handling editor: @danielskatz (Active)
Reviewers: @gonsie, @carothersc, @yadudoc
Similarity score: 0.7052

⚠️ 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 · 2024-09-13T11:19:58Z

👋 @GJHSimmons - thanks for your submission. While I look for an editor, you could work on the incorrectly formatted and 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 · 2024-09-13T11:21:18Z

Also, JOSS papers typically don't use addresses in the affiliations, just institutions and countries.

danielskatz · 2024-09-13T11:23:28Z

Finally, your paper is a bit long. JOSS suggests 250-1000 words, and your paper is a little over 1600. Is there anything you can remove, perhaps pointing to documentation or the repository instead?

danielskatz · 2024-09-13T11:24:35Z

👋 @prashjha - Do you think you could edit this submission?

danielskatz · 2024-09-13T11:24:45Z

@editorialbot invite @prashjha as editor

editorialbot · 2024-09-13T11:24:47Z

Invitation to edit this submission sent!

GJHSimmons · 2024-09-16T08:52:31Z

@editorialbot check references

editorialbot · 2024-09-16T08:52:57Z

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "publisher" (NAME) [#<BibTeX::Bibliography data=[20]>, "@", #<BibTeX::Entry >, {:author=>["de Wit, C. and Goudrian, J."], :title=>["Simulation of ecological processes"], :edition=>["2"], :year=>["1978"], :doi=>["10.1016/0304-3800(80)90048-4"]}]

GJHSimmons · 2024-09-16T08:56:24Z

@editorialbot check references

editorialbot · 2024-09-16T08:56:44Z

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

✅ OK DOIs

- 10.1016/B978-0-12-809633-8.02390-6 is OK
- 10.1146/annurev.ecolsys.110308.120159 is OK
- 10.1111/j.1461-0248.2008.01277.x is OK
- 10.1098/rspb.2019.1916 is OK
- 10.1111/1749-4877.12618 is OK
- 10.1007/s10668-023-03698-9 is OK
- 10.1016/S0304-3800(99)00144-1 is OK
- 10.4204/EPTCS.372.14 is OK
- 10.4204/eptcs.380.5 is OK
- 10.1111/j.1461-0248.2010.01479.x is OK
- 10.1093/icb/icy018 is OK
- 10.7717/peerj-cs.103 is OK
- 10.1007/s10340-023-01610-y is OK
- 10.1186/s12302-020-00406-6 is OK
- 10.1016/S0921-8009(97)00103-1 is OK
- 10.1111/j.1365-2699.2011.02659.x is OK
- 10.1016/0304-3800(80)90048-4 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: AlgebraicDynamics.jl
- No DOI given, and none found for title: The climatic factor in Australian grassland ecolog...
- No DOI given, and none found for title: The Ecology of \emphAphis craccivora Koch and Subt...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- 10.1079/9781800621459.0004 is INVALID
- 10.1079/9781800621459.0015 is INVALID

GJHSimmons · 2024-09-16T09:04:09Z

@editorialbot generate pdf

editorialbot · 2024-09-16T09:05:35Z

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

editorialbot · 2024-09-16T09:06:32Z

Five most similar historical JOSS papers:

PySD: System Dynamics Modeling in Python
Submitting author: @rogersamso
Handling editor: @pdebuyl (Active)
Reviewers: @blsqr, @sixpearls
Similarity score: 0.7334

Simframe: A Python Framework for Scientific Simulations
Submitting author: @stammler
Handling editor: @taless474 (Retired)
Reviewers: @schruste, @lucaferranti
Similarity score: 0.7068

SimuPy: A Python framework for modeling and simulating dynamical systems
Submitting author: @sixpearls
Handling editor: @cMadan (Retired)
Reviewers: @demotu
Similarity score: 0.7051

py-pde: A Python package for solving partial differential equations
Submitting author: @david-zwicker
Handling editor: @xuanxu (Active)
Reviewers: @celliern, @mstimberg
Similarity score: 0.7045

DE-Sim: an object-oriented, discrete-event simulation tool for data-intensive modeling of complex systems in Python
Submitting author: @artgoldberg
Handling editor: @danielskatz (Active)
Reviewers: @gonsie, @carothersc, @yadudoc
Similarity score: 0.7020

⚠️ 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.

GJHSimmons · 2024-09-16T09:28:05Z

@editorialbot check references

editorialbot · 2024-09-16T09:28:20Z

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

✅ OK DOIs

- 10.1016/B978-0-12-809633-8.02390-6 is OK
- 10.1146/annurev.ecolsys.110308.120159 is OK
- 10.1111/j.1461-0248.2008.01277.x is OK
- 10.1098/rspb.2019.1916 is OK
- 10.1111/1749-4877.12618 is OK
- 10.1007/s10668-023-03698-9 is OK
- 10.1016/S0304-3800(99)00144-1 is OK
- 10.4204/EPTCS.372.14 is OK
- 10.4204/eptcs.380.5 is OK
- 10.1111/j.1461-0248.2010.01479.x is OK
- 10.1093/icb/icy018 is OK
- 10.7717/peerj-cs.103 is OK
- 10.1007/s10340-023-01610-y is OK
- 10.1186/s12302-020-00406-6 is OK
- 10.1016/S0921-8009(97)00103-1 is OK
- 10.1111/j.1365-2699.2011.02659.x is OK
- 10.1079/9781800621459.0000 is OK
- 10.1079/9781800621459.0000 is OK
- 10.1016/0304-3800(80)90048-4 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: AlgebraicDynamics.jl
- No DOI given, and none found for title: The climatic factor in Australian grassland ecolog...
- No DOI given, and none found for title: The Ecology of \emphAphis craccivora Koch and Subt...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

GJHSimmons · 2024-09-16T09:28:21Z

@editorialbot generate pdf

editorialbot · 2024-09-16T09:29:59Z

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

editorialbot · 2024-09-16T09:30:42Z

Five most similar historical JOSS papers:

PySD: System Dynamics Modeling in Python
Submitting author: @rogersamso
Handling editor: @pdebuyl (Active)
Reviewers: @blsqr, @sixpearls
Similarity score: 0.7386

py-pde: A Python package for solving partial differential equations
Submitting author: @david-zwicker
Handling editor: @xuanxu (Active)
Reviewers: @celliern, @mstimberg
Similarity score: 0.7094

SimuPy: A Python framework for modeling and simulating dynamical systems
Submitting author: @sixpearls
Handling editor: @cMadan (Retired)
Reviewers: @demotu
Similarity score: 0.7062

DE-Sim: an object-oriented, discrete-event simulation tool for data-intensive modeling of complex systems in Python
Submitting author: @artgoldberg
Handling editor: @danielskatz (Active)
Reviewers: @gonsie, @carothersc, @yadudoc
Similarity score: 0.7057

Simframe: A Python Framework for Scientific Simulations
Submitting author: @stammler
Handling editor: @taless474 (Retired)
Reviewers: @schruste, @lucaferranti
Similarity score: 0.7041

⚠️ 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.

GJHSimmons · 2024-09-16T09:31:33Z

@danielskatz Thank you for proceeding quickly.

I've fixed DOIs and affiliations. Flagging that two chapters (here and here) have stated but inactivated DOIs. I've fallen back to the full book which has an active DOI.

I'll need some deeper advice on paper length. I understand the 'description' section is unusual, but contains important citations for how the package was built which don't belong in the statement of need or documentation. How is this usually handled for JOSS articles?

danielskatz · 2024-09-16T11:59:22Z

I'll need some deeper advice on paper length. I understand the 'description' section is unusual, but contains important citations for how the package was built which don't belong in the statement of need or documentation. How is this usually handled for JOSS articles?

I'm not sure if this will help you or not, but might be worth remembering that the paper is for users of the software, whether end users or developers. And if you can't do anything, perhaps reviewers will have suggestions later in the process.

Also, as a side note, if you are going to say "see Author", you should encode this in markdown as "see @author", not "see [@author]" The latter (using the []s) is just for parenthetical references.

danielskatz · 2024-09-18T06:00:51Z

👋 @prashjha

Do you think you could edit this submission?

Just a ping about this...

prashjha · 2024-09-18T20:10:03Z

Thank you for the invitation to edit, @danielskatz. Happy to help.

prashjha · 2024-09-18T20:10:12Z

@editorialbot assign me as editor

editorialbot · 2024-09-18T20:10:15Z

Assigned! @prashjha is now the editor

prashjha · 2024-09-18T20:12:31Z

Hello @GJHSimmons, could you please look at the JOSS reviewer database and suggest a few names who can review your submission?

GJHSimmons · 2024-09-24T12:41:57Z

Hi @prashjha, thank you for agreeing to edit! I've done a quick search and got some ideas for reviewers, both for the mathematical/systems context and the ecological background context, depending on what you think is needed. Let me know if you need more suggestions.

Complex systems, mathematics context
@pitmonticone
@SunnyXu

Ecological or biological flavoured modelling/dynamic systems context
@JoanyMarino
@chenyangkang
@gartavanis
@chaypaterson

pitmonticone · 2024-09-24T20:21:11Z

I am available to review this package.

SunnyXu · 2024-09-25T02:41:58Z

@GJHSimmons Thanks for considering me as a reviewer.
@prashjha I am available to review this work with a background of biological complex systems. Hope to have your consideration.

gartavanis · 2024-09-27T21:09:24Z

Happy to review as well.

prashjha · 2024-10-17T22:14:21Z

Dear @pitmonticone, @SunnyXu, and @gartavanis: thank you for your interest. We need two reviewers, so I will select the two based on the response order.

prashjha · 2024-10-17T22:14:30Z

@editorialbot add @pitmonticone as reviewer

editorialbot · 2024-10-17T22:14:32Z

@pitmonticone added to the reviewers list!

prashjha · 2024-10-17T22:14:40Z

@editorialbot add @SunnyXu as reviewer

editorialbot · 2024-10-17T22:14:42Z

@SunnyXu added to the reviewers list!

prashjha · 2024-10-17T22:14:46Z

@editorialbot start review

editorialbot · 2024-10-17T22:14:50Z

OK, I've started the review over in #7364.

editorialbot added pre-review Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Sep 13, 2024

editorialbot added Python TeX labels Sep 13, 2024

editorialbot assigned prashjha Sep 18, 2024

editorialbot assigned pitmonticone Oct 17, 2024

editorialbot assigned SunnyXu Oct 17, 2024

editorialbot closed this as completed Oct 17, 2024

[PRE REVIEW]: Psymple: A Python package for complex systems modelling #7221

[PRE REVIEW]: Psymple: A Python package for complex systems modelling #7221

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