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[REVIEW]: MMM: A C++ library for simulating large herbivores #3631

Closed whedon closed 2 years ago

whedon commented 3 years ago

Submitting author: @wtraylor (Wolfgang Traylor) Repository: https://github.com/wtraylor/modular_megafauna_model Version: v1.1.3 Editor: @diehlpk Reviewers: @dirmeier, @dilawar Archive: 10.5281/zenodo.5779267

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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

@dirmeier & @dilawar, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @diehlpk know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @dirmeier

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @dilawar

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 3 years ago

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

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf
whedon commented 3 years ago

PDF failed to compile for issue #3631 with the following error: 

 Can't find any papers to compile :-(
whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.23 s (964.1 files/s, 234167.1 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
C/C++ Header                     58           4273           4851          17680
C++                              83           1283           1608           7174
SVG                              12              0              0           7161
TOML                             34            763            535           2750
Markdown                         11            565              0           1745
TeX                               1             94              0           1074
CMake                             8            205            231            864
XML                               1              1              0            537
YAML                              5             25             58            452
Rmd                               1             25             29            173
R                                 4             34             51            158
Bourne Again Shell                2             28             18             76
JSON                              1              0              0             44
Bourne Shell                      2              9              5             22
make                              1              5             10              9
Python                            1              3             18              6
--------------------------------------------------------------------------------
SUM:                            225           7313           7414          39925
--------------------------------------------------------------------------------

Statistical information for the repository '6aebd874519ee052772ef905' was
gathered on 2021/08/18.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Unknown                          1             0              2            0.00
Wolfgang Pappa                 131          7195           2472            7.55
Wolfgang Traylor               519         59152          37701           75.65
wolfgangp                       32         16225           5273           16.79

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Wolfgang Pappa             1434           19.9         41.6               46.03
Wolfgang Traylor          34079           57.6         22.3               15.78
wolfgangp                  1383            8.5         43.4               31.60
whedon commented 3 years ago

Failed to discover a valid open source license.

wtraylor commented 3 years ago

@whedon generate pdf from branch joss-paper

whedon commented 3 years ago 
Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...
whedon commented 3 years ago

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

wtraylor commented 3 years ago

Failed to discover a valid open source license.

See https://github.com/openjournals/joss-reviews/issues/3450#issuecomment-874160752

whedon commented 3 years ago

:wave: @dirmeier, please update us on how your review is going (this is an automated reminder).

whedon commented 3 years ago

:wave: @StefanOlin, please update us on how your review is going (this is an automated reminder).

StefanOlin commented 3 years ago

I currently don't have access to a computer where I can compile and run the code, not sure when I'm allowed back in the office, but it won't be this month (September).

Den ons 1 sep. 2021 kl 17:28 skrev whedon @.***>:

👋 @StefanOlin, please update us on how your review is going (this is an automated reminder).

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

-- Stefan Olin Researcher Department of Physical Geography and Ecosystem Science Lund University

@. @.

diehlpk commented 3 years ago

I currently don't have access to a computer where I can compile and run the code, not sure when I'm allowed back in the office, but it won't be this month (September). Den ons 1 sep. 2021 kl 17:28 skrev whedon @.>: … 👋 @StefanOlin, please update us on how your review is going (this is an automated reminder). — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. -- Stefan Olin Researcher Department of Physical Geography and Ecosystem Science Lund University @. @.***

@StefanOlin Thanks for the update.

dirmeier commented 3 years ago

Hello, sorry for the delay. I'll finish the review this weekend.

diehlpk commented 2 years ago

@whedon commands

whedon commented 2 years ago

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

# Re-invite a reviewer (if they can't update checklists)
@whedon re-invite @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Set the software version at the top of the issue e.g.
@whedon set v1.0.1 as version

# Open the review issue
@whedon start review

EDITORIAL TASKS

# All commands can be run on a non-default branch, to do this pass a custom 
# branch name by following the command with `from branch custom-branch-name`.
# For example:

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Remind an author or reviewer to return to a review after a
# certain period of time (supported units days and weeks)
@whedon remind @reviewer in 2 weeks

# Ask Whedon to do a dry run of accepting the paper and depositing with Crossref
@whedon recommend-accept

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

EiC TASKS

# Invite an editor to edit a submission (sending them an email)
@whedon invite @editor as editor

# Reject a paper
@whedon reject

# Withdraw a paper
@whedon withdraw

# Ask Whedon to actually accept the paper and deposit with Crossref
@whedon accept deposit=true
diehlpk commented 2 years ago

@whedon remind @dirmeier in 2 weeks

whedon commented 2 years ago

Reminder set for @dirmeier in 2 weeks

diehlpk commented 2 years ago

@whedon remind @StefanOlin in 2 weeks

whedon commented 2 years ago

Reminder set for @StefanOlin in 2 weeks

dirmeier commented 2 years ago

Ciao @diehlpk, you can find my reviews here: https://github.com/wtraylor/modular_megafauna_model/issues/51, https://github.com/wtraylor/modular_megafauna_model/issues/52

Cheers, S

diehlpk commented 2 years ago

@wtraylor please have a look at these comments. Please ping the reviewer once you are done.

wtraylor commented 2 years ago

@dirmeier Thank you very much for the review. I will get to read and respond to the comments by the end of October, when I am back from vacation.

diehlpk commented 2 years ago

I currently don't have access to a computer where I can compile and run the code, not sure when I'm allowed back in the office, but it won't be this month (September). Den ons 1 sep. 2021 kl 17:28 skrev whedon @.**>: … wave @StefanOlin, please update us on how your review is going (this is an automated reminder). — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. -- Stefan Olin Researcher Department of Physical Geography and Ecosystem Science Lund University @.** @.***

@StefanOlin Thanks for the update.

@StefanOlin Any news from your side?

whedon commented 2 years ago

:wave: @dirmeier, please update us on how your review is going (this is an automated reminder).

diehlpk commented 2 years ago

@dirmeier Thank you very much for the review. I will get to read and respond to the comments by the end of October, when I am back from vacation.

@wtraylor Please let us know once you finished the review.

diehlpk commented 2 years ago

@StefanOlin How is your review going?

diehlpk commented 2 years ago

@wtraylor How is the editing going?

diehlpk commented 2 years ago

@wtraylor Could you might recommend some additional reviewers?

wtraylor commented 2 years ago

How is the editing going?

@diehlpk Thanks for checking in. I have adopted the (minor) changes suggested by @dirmeier.

Could you might recommend some additional reviewers?

I think I have tapped most of my network already, but I will try to come up with other suggestions.

dirmeier commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

PDF failed to compile for issue #3631 with the following error: 

 Can't find any papers to compile :-(
dirmeier commented 2 years ago

@whedon generate pdf from branch joss-paper

whedon commented 2 years ago 
Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...
whedon commented 2 years ago

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

dirmeier commented 2 years ago

Thanks for the updates to code and paper @wtraylor

diehlpk commented 2 years ago

Hi @amadeusine @no @sa501428 @luciorq @dilawar would you be interest to review this paper?

dilawar commented 2 years ago

@diehlpk I am happy to review this work.

diehlpk commented 2 years ago

@whedon add @dilawar as reviewer

whedon commented 2 years ago

OK, @dilawar is now a reviewer

diehlpk commented 2 years ago

@whedon commands

whedon commented 2 years ago

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

# Re-invite a reviewer (if they can't update checklists)
@whedon re-invite @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Set the software version at the top of the issue e.g.
@whedon set v1.0.1 as version

# Open the review issue
@whedon start review

EDITORIAL TASKS

# All commands can be run on a non-default branch, to do this pass a custom 
# branch name by following the command with `from branch custom-branch-name`.
# For example:

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Remind an author or reviewer to return to a review after a
# certain period of time (supported units days and weeks)
@whedon remind @reviewer in 2 weeks

# Ask Whedon to do a dry run of accepting the paper and depositing with Crossref
@whedon recommend-accept

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

EiC TASKS

# Invite an editor to edit a submission (sending them an email)
@whedon invite @editor as editor

# Reject a paper
@whedon reject

# Withdraw a paper
@whedon withdraw

# Ask Whedon to actually accept the paper and deposit with Crossref
@whedon accept deposit=true
diehlpk commented 2 years ago

@whedon remove @StefanOlin as reviewer

whedon commented 2 years ago

OK, @StefanOlin is no longer a reviewer

diehlpk commented 2 years ago

@StefanOlin I removed you as a reviewer, since I have not heard back from you in a while. If you are still interested, I will add you again.

diehlpk commented 2 years ago

@diehlpk I am happy to review this work.

@dilawar Thanks, I added you as the second reviewer.

diehlpk commented 2 years ago

How is the editing going?

@diehlpk Thanks for checking in. I have adopted the (minor) changes suggested by @dirmeier.

Could you might recommend some additional reviewers?

I think I have tapped most of my network already, but I will try to come up with other suggestions.

@wtraylor I found a new reviewer and we seem to be good again.

dilawar commented 2 years ago

MMM is a very high-quality library with an excellent user and API documentation. The repository follows state-of-the-art DevOps. The library is a step towards a critical and hard problem of validating assumptions and discovering missing parameters while modeling a complex system. The library can also serve as a very useful pedagogical tool in Ecology class (I'd have certainly enjoyed seeing some simulations of important ideas).

The author has designed the library to be (C++) user-friendly by choosing a modern build system (CMake). I also appreciate in-source dependencies and choosing an easy-to-read TOML over often used but hardly human-readable XML for user-program interaction.

The CI/CD pipeline is comprehensive. It not only tests for the correctness, but also for memory leaks and lint errors. Tooling is provided for code-formatting.

Contribution guidelines are clear. The author has also set up a social channel (matrix) to engage with the users.

It is heartening to an academic software built with so much care. I wholeheartedly recommend publication of this library.

Following are a few more comments and a question.

diehlpk commented 2 years ago

@dilawar Thanks for the quick review time.

@wtraylor Could you please have a look by Friday, so we can finalize the paper?

wtraylor commented 2 years ago

@whedon generate pdf from branch joss-paper

whedon commented 2 years ago 
Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...