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[REVIEW]: Moran Pycess: a Python package to simulate Moran processes driven by game theory #2643

Closed whedon closed 4 years ago

whedon commented 4 years ago

Submitting author: @AngryMaciek (Maciej Bak) Repository: https://github.com/AngryMaciek/angry-moran-simulator Version: 1.0.0 Editor: @majensen Reviewer: @xin-huang, @tkchafin Archive: 10.5281/zenodo.4114143

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Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@xin-huang & @tkchafin, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @xin-huang

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @tkchafin

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 4 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @xin-huang, @tkchafin it looks like you're currently assigned to review this paper :tada:.

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whedon commented 4 years ago

PDF failed to compile for issue #2643 with the following error:

Can't find any papers to compile :-(

majensen commented 4 years ago

@whedon generate pdf from branch paper

whedon commented 4 years ago 
Attempting PDF compilation from custom branch paper. Reticulating splines etc...
whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

xin-huang commented 4 years ago

The authors implemented a python package to perform simulation with different evolutionary strategies under Moran process. This is an interesting simulator in population biology, because there are very few user-friendly simulators for evolutionary game currently. After testing this package and reading the paper, I have several concerns on the documentation and software paper. I have opened some issues (https://github.com/AngryMaciek/angry-moran-simulator/issues/5 and https://github.com/AngryMaciek/angry-moran-simulator/issues/6) in the repository. Because I do not have computers with MacOS and TravisCI cannot make python builds on MacOS. I cannot verify the installation and performance on MacOS.

tkchafin commented 4 years ago

[Review complete] The authors have provided a flexible and user-friendly software to generate simulations under several different scenarios from evolutionary game theory. I was able to verify functionality of the simulated processes and built-in plotting functions under MacOS, after minor changes to the documented installation instructions provided by the authors. After completing my review, I would recommend publication of this contribution in JOSS after completing several necessary revisions, which are aimed primarily at increasing clarity of the communications associated with this package (both software paper and documentation), and making installation/ plotting easier for the user. These are summarized below, and in greater detail as Issues on the software github page.

Software paper: Major issues (per checklist) are currently: 1) The lack of a non-specialist summary statement; and 2) There are many inconsistencies in the writing that make me suggest the authors go back through more carefully to edit for clarity and language). For example, “EES” vs “ESS” is not consistent, and several other instances (i.e. “A population consists of individuals…” rather than “Population is created by individuals…”) where the quality of writing could be improved. These problems are listed in more detail over at issue #9(https://github.com/AngryMaciek/angry-moran-simulator/issues/9).

Documentation/ Functionality: There are 2 major issues here that I think should be corrected prior to publication: 1) The installation was not initially successful (on MacOS) without first manually relaxing the version constraints specified in the .yml file. I suspect that these constraints are overly specific, which for me created conflicts when creating the environment in conda; and 2) Documentation for the plotting functions is insufficient. A third issue (which I consider minor) is that - per the checklist - the documentation should also contain a statement of need. These are also added as issues #7 (https://github.com/AngryMaciek/angry-moran-simulator/issues/7) and #8 (https://github.com/AngryMaciek/angry-moran-simulator/issues/8)

majensen commented 4 years ago

Wow @xin-huang and @tkchafin, you may have set some kind of record. Thanks very much.

rozmanowna commented 4 years ago

@whedon generate pdf from branch paper

whedon commented 4 years ago 
Attempting PDF compilation from custom branch paper. Reticulating splines etc...
whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

rozmanowna commented 4 years ago

@whedon generate pdf from branch paper

whedon commented 4 years ago 
Attempting PDF compilation from custom branch paper. Reticulating splines etc...
whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

xin-huang commented 4 years ago

Hi @majensen I have checked off all the items on the checklist. The authors already addressed my concerns. I have no further comments.

majensen commented 4 years ago

Thanks @xin-huang - so @AngryMaciek I will look for https://github.com/AngryMaciek/angry-moran-simulator/issues/7 to be addressed and @tkchafin to then tick the final box on that review. I'll then proceed with editorial checks. Thanks all!

AngryMaciek commented 4 years ago

Dear @majensen , I believe we have addressed all of the suggestions raised by the reviewers :)

(CC @rozmanowna @tkchafin @xin-huang )

majensen commented 4 years ago

@whedon generate pdf from branch paper

whedon commented 4 years ago 
Attempting PDF compilation from custom branch paper. Reticulating splines etc...
majensen commented 4 years ago

@whedon check references from branch paper

whedon commented 4 years ago 
Attempting to check references... from custom branch paper
whedon commented 4 years ago

PDF failed to compile for issue #2643 with the following error:

sh: 0: getcwd() failed: No such file or directory pandoc: 10.21105.joss.02643.pdf: openBinaryFile: does not exist (No such file or directory) Looks like we failed to compile the PDF

whedon commented 4 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1017/S0305004100033193 is OK
- 10.1017/CBO9780511806292 is OK
- 10.1016/j.jocs.2019.101067 is OK
- 10.5281/zenodo.3980654 is OK
- 10.1155/2007/18636 is OK
- 10.1038/nature07921 is OK
- 10.1137/15M1044825 is OK
- 10.1038/380240a0 is OK

MISSING DOIs

- None

INVALID DOIs

- None
majensen commented 4 years ago

@openjournals/dev - please see error in compilation at https://github.com/openjournals/joss-reviews/issues/2643#issuecomment-699695148 - I was able to use https://whedon.theoj.org successfully.

majensen commented 4 years ago

Proof generated by whedon.theoj.org

arfon commented 4 years ago

@whedon check references from branch paper

whedon commented 4 years ago 
Attempting to check references... from custom branch paper
whedon commented 4 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1017/S0305004100033193 is OK
- 10.1017/CBO9780511806292 is OK
- 10.1016/j.jocs.2019.101067 is OK
- 10.5281/zenodo.3980654 is OK
- 10.1155/2007/18636 is OK
- 10.1038/nature07921 is OK
- 10.1137/15M1044825 is OK
- 10.1038/380240a0 is OK

MISSING DOIs

- None

INVALID DOIs

- None
arfon commented 4 years ago

@whedon generate pdf from branch paper

whedon commented 4 years ago 
Attempting PDF compilation from custom branch paper. Reticulating splines etc...
whedon commented 4 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

AngryMaciek commented 4 years ago

Dear Editors, Should we now make a zenodo submission ourselves, or... (?)

majensen commented 4 years ago

You can do that if you wish @AngryMaciek. I will have a pull request for you with a number of suggested changes. Apologies for the delay, thanks for your patience.

AngryMaciek commented 4 years ago

@majensen Then there is no need now, I will wait until I merge your suggestions.

majensen commented 4 years ago

will get to this by Thursday - thanks @AngryMaciek

majensen commented 4 years ago

@AngryMaciek please have a look at the suggestions in the PR (and assoc. comments).

I would also like to see an example run in the paper that exemplifies stochastic effects. One example might be to show that if an invading population is small enough, it can disappear frequently (i.e., among many replicate simulations) even if it uses an ESS. Probably (just guessing) the fitness benefit has to exceed 1/N more or less to get a high probability of establishment. (This is also a test of the software - if a rare invader never disappears over multiple replicates, there is probably a code issue.) thanks

majensen commented 4 years ago

@whedon generate pdf from branch paper

whedon commented 4 years ago 
Attempting PDF compilation from custom branch paper. Reticulating splines etc...
whedon commented 4 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

AngryMaciek commented 4 years ago

We have just included the most recent changes in the branch paper of the repository.

AngryMaciek commented 4 years ago

@whedon generate pdf from branch paper

whedon commented 4 years ago 
Attempting PDF compilation from custom branch paper. Reticulating splines etc...
whedon commented 4 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

majensen commented 4 years ago

@AngryMaciek I think things look quite good. Can you now create your archive, making sure that the archive title and authors are the same as those on the paper? Once that's done, please provide the archive DOI in this thread. Then I will attempt the spell summoning the editors-in-chief. thanks!

AngryMaciek commented 4 years ago

@majensen

We have merged branch paper to master and removed the former. We have submitted the code to zenodo: https://doi.org/10.5281/zenodo.4114143

Good luck with the spellcasting! (∩｀-´)⊃━☆ﾟ.*･｡ﾟ

majensen commented 4 years ago

@whedon set 10.5281/zenodo.4114143 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.4114143 is the archive.

majensen commented 4 years ago

@whedon set 1.0.0 as version

whedon commented 4 years ago

OK. 1.0.0 is the version.

majensen commented 4 years ago

@whedon accept