[PRE REVIEW]: PySD: System Dynamics Modeling in Python

[editorialbot]

Submitting author: @rogersamso (Roger Samsó)
Repository: https://github.com/JamesPHoughton/pysd/
Branch with paper.md (empty if default branch): paper_pysd
Version: v2.2.4
Editor: @pdebuyl
Reviewers: @blsqr, @andrecieplinski
Managing EiC: Daniel S. Katz

Status

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@rogersamso if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.36 s (255.6 files/s, 76835.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          49           4086           4817          14280
SVG                              1              1              1            909
reStructuredText                19            501            283            699
Jupyter Notebook                 1              0            626            444
make                             2             38              7            183
TeX                              1             12              0            120
Markdown                         4             50              0            115
XML                              7              0              0             79
YAML                             3             13              8             62
SQL                              3              0              0             21
INI                              1              0              0              2
-------------------------------------------------------------------------------
SUM:                            91           4701           5742          16914
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1178

[editorialbot]

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

OK DOIs

- 10.1016/j.rser.2020.110105 is OK
- 10.1088/1748-9326/ac2f62 is OK
- 10.5281/zenodo.5654824 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/j.esr.2020.100582 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/sdr.1474 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/sdr.1695 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.jmsy.2019.10.004 is INVALID because of 'https://doi.org/' prefix

[editorialbot]

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

[danielskatz]

@rogersamso - while we find an editor, you could work on the DOIs that editorialbot flagged. 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. You might also want to proofread the paper, for example, I see some "python"s that should be "Python"s.

[danielskatz]

👋 @pdebuyl - Would you be able to edit this submission?

[danielskatz]

@editorialbot invite @pdebuyl as editor

[editorialbot]

Invitation to edit this submission sent!

[rogersamso]

@editorialbot commands

[rogersamso]

@editorialbot check references

[rogersamso]

@danielskatz why is the bot not doing what I tell it to do?

[rogersamso]

@rogersamso - while we find an editor, you could work on the DOIs that editorialbot flagged. 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. You might also want to proofread the paper, for example, I see some "python"s that should be "Python"s.

done

[danielskatz]

@rogersamso - I'm unsure why @editorialbot is not responding.
@openjournals/dev - github status looks green. Any ideas here?

[pdebuyl]

@editorialbot assign me as editor

[editorialbot]

Assigned! @pdebuyl is now the editor

[pdebuyl]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1016/j.rser.2020.110105 is OK
- 10.1016/j.esr.2020.100582 is OK
- 10.1002/sdr.1474 is OK
- 10.1088/1748-9326/ac2f62 is OK
- 10.1002/sdr.1695 is OK
- 10.5281/zenodo.5654824 is OK
- 10.1016/j.jmsy.2019.10.004 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[pdebuyl]

It might have been a temporary issue with @editorialbot

[pdebuyl]

Question: is it possible to use the package without having any proprietary software? Would there be limitations?

I am looking for reviewers and it is important to know about this. Thanks!

[rogersamso]

Question: is it possible to use the package without having any proprietary software? Would there be limitations?

I am looking for reviewers and it is important to know about this. Thanks!

You don't need any proprietary software installed to use this library. You just need a model built using either Vensim or Stella, which you can read with any text editor. Once the models are translated to Python, using PySD, you use the library to also run them.

You could potentially build the models directly in Python, and only use PySD to run them, though for now this use case is less convenient (e.g. you would need to specify the solving order manually).

In the tests folder there are plenty of Vensim and Stella toy models to play with.

[pdebuyl]

Thank you for the reply.

[pdebuyl]

@editorialbot assign @blsqr as reviewer

[editorialbot]

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

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[pdebuyl]

@editorialbot commands

[editorialbot]

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

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[pdebuyl]

@editorialbot add @blsqr as reviewer

[editorialbot]

@blsqr added to the reviewers list!

[pdebuyl]

@rogersamso I am still looking for a second reviewer, then we can proceed to the review

[blsqr]

Hi everyone! 👋 I'm looking forward to the review process.

[erik-whiting]

Hey @pdebuyl if you're still looking for reviewers, I can volunteer if you can't find anyone. I'm not nearly as qualified as Dr. Sevinchan up there but I have some training in systems engineering. I've also done a couple of reviews for JOSS before so I know the drill. If it's ok with you (and the repo authors of course), I'd be happy to help out.

[rogersamso]

@erik-whiting thanks for your interest in reviewing the paper. We will be very pleased to have you as a reviewer of the manuscript!

[pdebuyl]

Hello @erik-whiting thank you for your interest. I have pending invitations already, which I sent via email. I'll let you know about your participation after I hear from that side.

[pdebuyl]

Hi @rogersamso I am trying out the teacup example. I already have two comments that I believe should be addressed to facilitate the review:

1. In "Basic Usage" there is a statement for print print model.doc(). I gather from that that the docs are not executed for test, but this might cause confusion to new users.
2. Where to find the data file Teacup.mdl ? I did teacup.mdl at https://github.com/SDXorg/test-models but this requires some searching. Also, the plot now includes all parameters by default.

[enekomartinmartinez]

Hi @pdebuyl ,

1. Thank you for pointing that, I have included the output from calling the doc method in the documentation. I have also specified that this output is a pandas.DataFrame
2. I have included a link to the samples folder of test-models
   I have also updated all the dataframes outputs and the plot

[pdebuyl]

@editorialbot add @andrecieplinski as reviewer

[editorialbot]

@andrecieplinski added to the reviewers list!

[pdebuyl]

@erik-whiting thanks for checking on JOSS reviews! I most often try to balance the reviewer duo between software-specific and field-specific knowledge and will keep you in mind if you are interested in further reviewing for JOSS.

[pdebuyl]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #4329.