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

Closed editorialbot closed 3 weeks ago

editorialbot commented 1 month ago

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

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

Author instructions

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

@GJHSimmons 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 month 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 month ago

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 commented 1 month ago 
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 commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 1611

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

License info:

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

editorialbot commented 1 month 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 month ago

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 commented 1 month ago

👋 @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 commented 1 month ago

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

danielskatz commented 1 month ago

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 commented 1 month ago

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

danielskatz commented 1 month ago

@editorialbot invite @prashjha as editor

editorialbot commented 1 month ago

Invitation to edit this submission sent!

GJHSimmons commented 1 month ago

@editorialbot check references

editorialbot commented 1 month ago

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 commented 1 month ago

@editorialbot check references

editorialbot commented 1 month ago 
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 commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month 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 month ago

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 commented 1 month ago

@editorialbot check references

editorialbot commented 1 month ago 
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 commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month 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 month ago

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 commented 1 month ago

@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 commented 1 month ago

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 commented 1 month ago

👋 @prashjha

Do you think you could edit this submission?

Just a ping about this...

prashjha commented 1 month ago

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

prashjha commented 1 month ago

@editorialbot assign me as editor

editorialbot commented 1 month ago

Assigned! @prashjha is now the editor

prashjha commented 1 month ago

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

GJHSimmons commented 1 month ago

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 commented 1 month ago

I am available to review this package.

SunnyXu commented 1 month ago

@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 commented 1 month ago

Happy to review as well.

prashjha commented 3 weeks ago

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 commented 3 weeks ago

@editorialbot add @pitmonticone as reviewer

editorialbot commented 3 weeks ago

@pitmonticone added to the reviewers list!

prashjha commented 3 weeks ago

@editorialbot add @SunnyXu as reviewer

editorialbot commented 3 weeks ago

@SunnyXu added to the reviewers list!

prashjha commented 3 weeks ago

@editorialbot start review

editorialbot commented 3 weeks ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/7364.