[REVIEW]: Learning Simulator: A simulation software for animal and human learning

whedon commented 3 years ago

Submitting author: @markusrobertjonsson (Markus Jonsson) Repository: https://github.com/learningsimulator/learningsimulator Version: v1.0.1 Editor: @oliviaguest Reviewers: @themkar, @CatarauCorina Archive: 10.5281/zenodo.4544535

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Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/3987c9eb5e1e31414be3f320eed9303f"><img src="https://joss.theoj.org/papers/3987c9eb5e1e31414be3f320eed9303f/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/3987c9eb5e1e31414be3f320eed9303f/status.svg)](https://joss.theoj.org/papers/3987c9eb5e1e31414be3f320eed9303f)

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

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

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @oliviaguest 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 @themkar

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@markusrobertjonsson) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @CatarauCorina

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@markusrobertjonsson) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

oliviaguest commented 3 years ago

@whedon generate pdf

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:

oliviaguest commented 3 years ago

@whedon remove @jkbye as reviewer

whedon commented 3 years ago

OK, @jkbye is no longer a reviewer

oliviaguest commented 3 years ago

@markusrobertjonsson can you please create an archive for the software (on Zenodo, figshare, etc.) and post the DOI here? 😊

oliviaguest commented 3 years ago

@whedon check references

whedon commented 3 years ago

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

OK DOIs

- 10.1109/MCSE.2007.55 is OK
- 10.1098/rsos.160734 is OK
- 10.1111/j.1751-0813.2010.00653.x is OK
- 10.1016/s0899-9007(98)00192-0 is OK
- 10.4324/9780203803509 is OK
- 10.1109/tsmcc.2012.2218595 is OK
- 10.1101/446906 is OK
- 10.1098/rsos.180778 is OK
- 10.1098/rsos.161011 is OK
- 10.3758/brm.40.2.442 is OK
- 10.3758/lb.38.1.1 is OK
- 10.1016/j.cmpb.2012.02.004 is OK
- 10.3758/brm.41.1.29 is OK
- 10.3758/brm.40.2.435 is OK
- 10.1109/adprl.2009.4927542 is OK
- 10.1016/s0019-9958(77)90354-0 is OK
- 10.3758/s13423-020-01749-0 is OK

MISSING DOIs

- 10.1007/978-0-387-44956-2_12 may be a valid DOI for title: A mathematical model for simple learning

INVALID DOIs

- None

oliviaguest commented 3 years ago

@markusrobertjonsson and fix the DOIs (you can run the same command as me to check them). ☺️

markusrobertjonsson commented 3 years ago

@whedon check references

whedon commented 3 years ago

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

OK DOIs

- 10.1109/MCSE.2007.55 is OK
- 10.1098/rsos.160734 is OK
- 10.1111/j.1751-0813.2010.00653.x is OK
- 10.1016/s0899-9007(98)00192-0 is OK
- 10.4324/9780203803509 is OK
- 10.1109/tsmcc.2012.2218595 is OK
- 10.1101/446906 is OK
- 10.1098/rsos.180778 is OK
- 10.1098/rsos.161011 is OK
- 10.3758/brm.40.2.442 is OK
- 10.3758/lb.38.1.1 is OK
- 10.1016/j.cmpb.2012.02.004 is OK
- 10.3758/brm.41.1.29 is OK
- 10.3758/brm.40.2.435 is OK
- 10.1037/h0054388 is OK
- 10.1109/adprl.2009.4927542 is OK
- 10.1016/s0019-9958(77)90354-0 is OK
- 10.3758/s13423-020-01749-0 is OK

MISSING DOIs

- None

INVALID DOIs

- None

markusrobertjonsson commented 3 years ago

@oliviaguest I added the repo to Zenodo. The DOI is 10.5281/zenodo.4544535.

oliviaguest commented 3 years ago

@whedon check repository

oliviaguest commented 3 years ago

@whedon set 10.5281/zenodo.4544535 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4544535 is the archive.

oliviaguest commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=1.08 s (107.8 files/s, 39777.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          54           3189           6778          10109
JavaScript                      10           2311           2347           8544
HTML                            43            405              0           7350
CSS                              3            234             44            917
Markdown                         2             76              0            326
TeX                              1             34              7            302
Lisp                             1              3             24             46
YAML                             1              5              4             43
DOS Batch                        1              8              1             27
make                             1              4              6             10
-------------------------------------------------------------------------------
SUM:                           117           6269           9211          27674
-------------------------------------------------------------------------------

Statistical information for the repository '3b7733eeeba18e148f188832' was
gathered on 2021/02/22.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Learning Simulator -             1             1              1            0.00
Markus Jonsson                 111         53557          17954           99.94
drghirlanda                      3            35              9            0.06

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
Learning Simulator -          1          100.0          1.0                0.00
Markus Jonsson            33334           62.2         10.7               11.29
Stefano Ghirlanda            21          100.0         20.1                4.76

oliviaguest commented 3 years ago

@markusrobertjonsson can you change the title on zenodo to match the title of your JOSS submission please?

whedon commented 3 years ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2106

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2106, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

oliviaguest commented 3 years ago

@whedon set v1.0.1 as version

whedon commented 3 years ago

OK. v1.0.1 is the version.

whedon commented 3 years ago

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

OK DOIs

- 10.1109/MCSE.2007.55 is OK
- 10.1098/rsos.160734 is OK
- 10.1111/j.1751-0813.2010.00653.x is OK
- 10.1016/s0899-9007(98)00192-0 is OK
- 10.4324/9780203803509 is OK
- 10.1109/tsmcc.2012.2218595 is OK
- 10.1101/446906 is OK
- 10.1098/rsos.180778 is OK
- 10.1098/rsos.161011 is OK
- 10.3758/brm.40.2.442 is OK
- 10.3758/lb.38.1.1 is OK
- 10.1016/j.cmpb.2012.02.004 is OK
- 10.3758/brm.41.1.29 is OK
- 10.3758/brm.40.2.435 is OK
- 10.1037/h0054388 is OK
- 10.1109/adprl.2009.4927542 is OK
- 10.1016/s0019-9958(77)90354-0 is OK
- 10.3758/s13423-020-01749-0 is OK

MISSING DOIs

- None

INVALID DOIs

- None

oliviaguest commented 3 years ago

@whedon generate pdf

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:

markusrobertjonsson commented 3 years ago

@oliviaguest The title on Zenodo is now changed to match the JOSS submission.

kthyng commented 3 years ago

Hi @markusrobertjonsson! I'll be helping to finalize your publication. Can you also update the metadata on your Zenodo archive so that the author list matches your JOSS paper?

kthyng commented 3 years ago

@markusrobertjonsson Your paper looks great and everything will be in order once I hear back from you about the author list. Thanks!

markusrobertjonsson commented 3 years ago

@kthyng Thanks. The author list on Zenodo is now correct.

kthyng commented 3 years ago

@whedon accept deposit=true

whedon commented 3 years ago

Doing it live! Attempting automated processing of paper acceptance...

whedon commented 3 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 3 years ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/2110
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02891
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kthyng commented 3 years ago

Congratulations to @markusrobertjonsson on your new publication! Many thanks to editor @oliviaguest and to reviewers @themkar and @CatarauCorina — this literally couldn't occur without you! 🎉

(will wait to close this issue until the doi resolves)

whedon commented 3 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.02891/status.svg)](https://doi.org/10.21105/joss.02891)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02891">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02891/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02891/status.svg
   :target: https://doi.org/10.21105/joss.02891

This is how it will look in your documentation:

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