[REVIEW]: pymdp: A Python library for active inference in discrete state spaces #4098

whedon · 2022-01-25T00:57:50Z

Submitting author: @conorheins (Conor Heins)
Repository: https://github.com/infer-actively/pymdp
Branch with paper.md (empty if default branch): master
Version: v0.0.5
Editor: @emdupre
Reviewers: @seankmartin, @patrickmineault
Archive: 10.5281/zenodo.6484849

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Markdown: [![status](https://joss.theoj.org/papers/a6362c8d3e0c953d8ce832664a32f66b/status.svg)](https://joss.theoj.org/papers/a6362c8d3e0c953d8ce832664a32f66b)

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Review checklist for @seankmartin

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General checks

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Contribution and authorship: Has the submitting author (@conorheins) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
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

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

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
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 @patrickmineault

✨ 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

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

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

General checks

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

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
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

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

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
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?

The text was updated successfully, but these errors were encountered:

whedon · 2022-01-25T00:57:53Z

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

⚠️ JOSS reduced service mode ⚠️

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.

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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 · 2022-01-25T00:58:02Z

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.16 s (396.3 files/s, 143004.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          30           1995           1963           4615
Jupyter Notebook                11              0           9723           1496
MATLAB                           9            558            790           1406
Markdown                         2             94              0            234
YAML                             2             10             10             42
reStructuredText                 8             29             40             36
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            64           2698          12534           7864
-------------------------------------------------------------------------------


Statistical information for the repository '0f55aadd4137f41905c03063' was
gathered on 2022/01/25.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Alexander Kiefer                 2             5              3            0.01
Beren                            4           193             54            0.32
Brennan Klein                    1             1              1            0.00
Conor Heins                     87          8074           2193           13.16
alec-tschantz                   55          8626           6334           19.18
arun                             3            88             73            0.21
conorheins                     237         26192          26172           67.13

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
Alexander Kiefer              5          100.0          6.5                0.00
Beren                        13            6.7         20.0               15.38
alec-tschantz              1245           14.4         18.4               12.21
arun                         13           14.8         11.6                0.00
conorheins                 7297           27.9          7.3                9.09

whedon · 2022-01-25T00:58:03Z

PDF failed to compile for issue #4098 with the following error:

 Can't find any papers to compile :-(

emdupre · 2022-01-25T00:59:23Z

@whedon generate pdf from branch paper_branch

whedon · 2022-01-25T00:59:25Z

Attempting PDF compilation from custom branch paper_branch. Reticulating splines etc...

whedon · 2022-01-25T00:59:55Z

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

emdupre · 2022-01-25T01:00:11Z

@whedon check references from branch paper_branch

whedon · 2022-01-25T01:00:14Z

Attempting to check references... from custom branch paper_branch

whedon · 2022-01-25T01:00:51Z

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

OK DOIs

- 10.1371/journal.pone.0006421 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1162/neco_a_01354 is OK
- 10.1080/17588928.2015.1020053 is OK
- 10.1038/s41598-018-38246-3 is OK
- 10.1561/2200000001 is OK
- 10.1167/jov.20.4.12 is OK
- 10.1038/ncomms14218 is OK
- 10.3390/e22050552 is OK
- 10.1162/neco.1992.4.3.415 is OK
- 10.1016/j.neuroimage.2004.07.041 is OK
- 10.1080/01621459.2017.1285773 is OK
- 10.1126/science.1238406 is OK
- 10.1007/s00422-012-0512-8 is OK
- 10.1016/j.tics.2011.11.018 is OK
- 10.1162/neco_a_01357 is OK
- 10.1109/IJCNN48605.2020.9207382 is OK
- 10.1016/0166-2236(83)90190-X is OK
- 10.1523/JNEUROSCI.11-03-00641.1991 is OK
- 10.1162/NECO_a_00912 is OK
- 10.3390/e21030257 is OK
- 10.3389/frobt.2019.00020 is OK
- 10.1007/s00422-018-0785-7 is OK
- 10.1371/journal.pcbi.1007805 is OK
- 10.1109/ICASSP40776.2020.9054364 is OK
- 10.1016/B978-0-12-372560-8.X5000-1 is OK
- 10.1038/nrn2787 is OK
- 10.1016/j.jmp.2020.102447 is OK
- 10.1016/S0004-3702(98)00023-X is OK
- 10.1162/neco_a_01351 is OK
- 10.1093/cercor/bhu159 is OK
- 10.1016/j.drugalcdep.2020.108208 is OK
- 10.1503/jpn.200032 is OK
- 10.31234/osf.io/b4jm6 is OK
- 10.1016/j.neuroimage.2008.02.054 is OK
- 10.1016/j.jmp.2020.102348 is OK
- 10.1007/978-3-030-64919-7_1 is OK
- 10.1016/j.neubiorev.2016.06.022 is OK
- 10.1162/neco.1995.7.5.889 is OK
- 10.1037/13536-000 is OK
- 10.1016/j.neunet.2021.05.010 is OK
- 10.1109/LRA.2021.3090015 is OK
- 10.1016/B978-0-323-88506-5.50066-8 is OK
- 10.1007/s00422-019-00805-w is OK
- 10.3390/e23020198 is OK
- 10.1080/10407413.2021.1965480 is OK
- 10.1098/rsif.2013.0475 is OK
- 10.7554/eLife.41703 is OK
- 10.1162/neco_a_00999 is OK

MISSING DOIs

- 10.1162/neco_a_01427 may be a valid DOI for title: Chance-Constrained Active Inference
- 10.1017/s0140525x19001353 may be a valid DOI for title: Generative models as parsimonious descriptions of sensorimotor loops
- 10.7551/mitpress/7111.003.0009 may be a valid DOI for title: Perceptions as hypotheses
- 10.31234/osf.io/2rzu5 may be a valid DOI for title: Active inference, selective attention, and the cocktail party problem
- 10.1016/j.schres.2021.07.032 may be a valid DOI for title: Everything is connected: Inference and attractors in delusions
- 10.31234/osf.io/bsuh8 may be a valid DOI for title: Long-term stability of computational parameters during approach-avoidance conflict in a transdiagnostic psychiatric patient sample

INVALID DOIs

- None

emdupre · 2022-01-25T01:02:10Z

Hi everyone 👋 Thanks again for agreeing to review this submission ! The review will take place in this issue.

Whenever possible, please open relevant issues on the linked software repository (and cross-link them with this issue) rather than discussing them here. This helps to make sure that feedback is translated into actionable items to improve the software.

If you aren't sure how to get started, please see the Reviewing for JOSS guide -- and, of course, feel free to ping me with any questions !

seankmartin · 2022-01-25T12:00:42Z

Cool, thanks!
I should be able to get to doing the review fairly soon

seankmartin · 2022-01-25T12:01:15Z

@whedon commands

whedon · 2022-01-25T12:01:34Z

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

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

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

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

# 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

seankmartin · 2022-02-01T22:34:50Z

I'm in progress with the review.
I've raised a non-blocking issue about some missing API documentation here infer-actively/pymdp#67.
The paper is missing an explicit summary section, which I think should be added.
Will post a final update after checking functionality!

seankmartin · 2022-02-01T22:38:39Z

@whedon remind @seankmartin in 4 days

whedon · 2022-02-01T22:38:42Z

I'm sorry @seankmartin, I'm afraid I can't do that. That's something only editors are allowed to do.

patrickmineault · 2022-02-02T17:14:20Z

I'm going to wait until @seankmartin completes a first pass until I look at this.

emdupre · 2022-02-02T18:13:51Z

@whedon remind @seankmartin in 3 days

whedon · 2022-02-02T18:13:54Z

Reminder set for @seankmartin in 3 days

emdupre · 2022-02-02T18:15:18Z

@seankmartin I've set the reminder :) Thanks for starting on this and cross-linking the opened issue !

whedon · 2022-02-05T18:13:56Z

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

whedon · 2022-02-08T00:58:07Z

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

whedon · 2022-02-08T00:58:07Z

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

editorialbot · 2022-05-02T18:10:22Z

Done! branch is now master

emdupre · 2022-05-02T18:10:33Z

@editorialbot check references

editorialbot · 2022-05-02T18:10:44Z

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

OK DOIs

- 10.1371/journal.pone.0006421 is OK
- 10.1162/neco_a_01427 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1162/neco_a_01354 is OK
- 10.1080/17588928.2015.1020053 is OK
- 10.1038/s41598-018-38246-3 is OK
- 10.1561/2200000001 is OK
- 10.1167/jov.20.4.12 is OK
- 10.1038/ncomms14218 is OK
- 10.3390/e22050552 is OK
- 10.1162/neco.1992.4.3.415 is OK
- 10.1016/j.neuroimage.2004.07.041 is OK
- 10.1080/01621459.2017.1285773 is OK
- 10.1126/science.1238406 is OK
- 10.1007/s00422-012-0512-8 is OK
- 10.1016/j.tics.2011.11.018 is OK
- 10.1162/neco_a_01357 is OK
- 10.1109/IJCNN48605.2020.9207382 is OK
- 10.1016/0166-2236(83)90190-X is OK
- 10.1523/JNEUROSCI.11-03-00641.1991 is OK
- 10.1162/NECO_a_00912 is OK
- 10.3390/e21030257 is OK
- 10.3389/frobt.2019.00020 is OK
- 10.1007/s00422-018-0785-7 is OK
- 10.1371/journal.pcbi.1007805 is OK
- 10.1109/ICASSP40776.2020.9054364 is OK
- 10.1016/B978-0-12-372560-8.X5000-1 is OK
- 10.1038/nrn2787 is OK
- 10.1016/j.jmp.2020.102447 is OK
- 10.1016/S0004-3702(98)00023-X is OK
- 10.1162/neco_a_01351 is OK
- 10.1093/cercor/bhu159 is OK
- 10.1016/j.drugalcdep.2020.108208 is OK
- 10.1503/jpn.200032 is OK
- 10.1016/j.jmp.2021.102632 is OK
- 10.1016/j.neuroimage.2008.02.054 is OK
- 10.1016/j.jmp.2020.102348 is OK
- 10.1007/978-3-030-64919-7_1 is OK
- 10.1016/j.ijar.2018.11.002 is OK
- 10.1098/rstb.1980.0090 is OK
- 10.1016/j.neubiorev.2016.06.022 is OK
- 10.1162/neco.1995.7.5.889 is OK
- 10.1037/13536-000 is OK
- 10.1007/978-3-030-93736-2_48 is OK
- 10.1016/j.neunet.2021.05.010 is OK
- 10.1109/LRA.2021.3090015 is OK
- 10.1016/B978-0-323-88506-5.50066-8 is OK
- 10.1007/s00422-019-00805-w is OK
- 10.3390/e23020198 is OK
- 10.1080/10407413.2021.1965480 is OK
- 10.1098/rsif.2013.0475 is OK
- 10.7554/eLife.41703 is OK
- 10.1162/neco_a_00999 is OK
- 10.1016/j.neubiorev.2021.09.038 is OK
- 10.1016/j.schres.2021.07.032 is OK
- 10.1038/s41598-021-91308-x is OK

MISSING DOIs

- 10.3389/fpsyg.2022.855074 may be a valid DOI for title: Enactive-Dynamic Social Cognition and Active Inference

INVALID DOIs

- None

emdupre · 2022-05-02T18:16:16Z

Thank you, @conorheins ! I have one last reference request, since the included Hipólito reference was published in Frontiers over the weekend. Can you please update this reference to:

@article{hipolito2021enactive,
author = {Hip{\'o}lito, In{\^e}s and van Es, Thomas},
title = {Enactive-Dynamic Social Cognition and Active Inference},
journal = {Frontiers in Psychology},
volume = {13},
year = {2022},
url = {https://www.frontiersin.org/article/10.3389/fpsyg.2022.855074},
doi = {10.3389/fpsyg.2022.855074},
issn = {1664-1078}
}

conorheins · 2022-05-02T18:25:04Z

Hi @emdupre , I removed that reference as well as several others that weren't used here (some of them were left over from the arxiv version). Thanks

emdupre · 2022-05-02T18:28:11Z

@editorialbot check references

editorialbot · 2022-05-02T18:28:18Z

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

OK DOIs

- 10.1371/journal.pone.0006421 is OK
- 10.1162/neco_a_01427 is OK
- 10.1162/neco_a_01354 is OK
- 10.1080/17588928.2015.1020053 is OK
- 10.1038/s41598-018-38246-3 is OK
- 10.1016/j.neuroimage.2004.07.041 is OK
- 10.1007/s00422-012-0512-8 is OK
- 10.1016/j.tics.2011.11.018 is OK
- 10.1162/neco_a_01357 is OK
- 10.1109/IJCNN48605.2020.9207382 is OK
- 10.1162/NECO_a_00912 is OK
- 10.3390/e21030257 is OK
- 10.3389/frobt.2019.00020 is OK
- 10.1007/s00422-018-0785-7 is OK
- 10.1371/journal.pcbi.1007805 is OK
- 10.1109/ICASSP40776.2020.9054364 is OK
- 10.1016/B978-0-12-372560-8.X5000-1 is OK
- 10.1038/nrn2787 is OK
- 10.1016/j.jmp.2020.102447 is OK
- 10.1016/S0004-3702(98)00023-X is OK
- 10.1162/neco_a_01351 is OK
- 10.1093/cercor/bhu159 is OK
- 10.1016/j.drugalcdep.2020.108208 is OK
- 10.1503/jpn.200032 is OK
- 10.1016/j.jmp.2021.102632 is OK
- 10.1016/j.neuroimage.2008.02.054 is OK
- 10.1016/j.jmp.2020.102348 is OK
- 10.1007/978-3-030-64919-7_1 is OK
- 10.1016/j.ijar.2018.11.002 is OK
- 10.1098/rstb.1980.0090 is OK
- 10.1016/j.neubiorev.2016.06.022 is OK
- 10.1162/neco.1995.7.5.889 is OK
- 10.1037/13536-000 is OK
- 10.1007/978-3-030-93736-2_48 is OK
- 10.1016/j.neunet.2021.05.010 is OK
- 10.1109/LRA.2021.3090015 is OK
- 10.1016/B978-0-323-88506-5.50066-8 is OK
- 10.1007/s00422-019-00805-w is OK
- 10.3390/e23020198 is OK
- 10.1080/10407413.2021.1965480 is OK
- 10.1098/rsif.2013.0475 is OK
- 10.7554/eLife.41703 is OK
- 10.1162/neco_a_00999 is OK
- 10.1016/j.neubiorev.2021.09.038 is OK
- 10.1016/j.schres.2021.07.032 is OK
- 10.1038/s41598-021-91308-x is OK

MISSING DOIs

- None

INVALID DOIs

- None

emdupre · 2022-05-02T18:33:24Z

@openjournals/joss-eics, this is ready for final review !

kyleniemeyer · 2022-05-04T17:15:00Z

@editorialbot recommend-accept

editorialbot · 2022-05-04T17:15:02Z

Attempting dry run of processing paper acceptance...

editorialbot · 2022-05-04T17:15:12Z

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

OK DOIs

- 10.1371/journal.pone.0006421 is OK
- 10.1162/neco_a_01427 is OK
- 10.1162/neco_a_01354 is OK
- 10.1080/17588928.2015.1020053 is OK
- 10.1038/s41598-018-38246-3 is OK
- 10.1016/j.neuroimage.2004.07.041 is OK
- 10.1007/s00422-012-0512-8 is OK
- 10.1016/j.tics.2011.11.018 is OK
- 10.1162/neco_a_01357 is OK
- 10.1109/IJCNN48605.2020.9207382 is OK
- 10.1162/NECO_a_00912 is OK
- 10.3390/e21030257 is OK
- 10.3389/frobt.2019.00020 is OK
- 10.1007/s00422-018-0785-7 is OK
- 10.1371/journal.pcbi.1007805 is OK
- 10.1109/ICASSP40776.2020.9054364 is OK
- 10.1016/B978-0-12-372560-8.X5000-1 is OK
- 10.1038/nrn2787 is OK
- 10.1016/j.jmp.2020.102447 is OK
- 10.1016/S0004-3702(98)00023-X is OK
- 10.1162/neco_a_01351 is OK
- 10.1093/cercor/bhu159 is OK
- 10.1016/j.drugalcdep.2020.108208 is OK
- 10.1503/jpn.200032 is OK
- 10.1016/j.jmp.2021.102632 is OK
- 10.1016/j.neuroimage.2008.02.054 is OK
- 10.1016/j.jmp.2020.102348 is OK
- 10.1007/978-3-030-64919-7_1 is OK
- 10.1016/j.ijar.2018.11.002 is OK
- 10.1098/rstb.1980.0090 is OK
- 10.1016/j.neubiorev.2016.06.022 is OK
- 10.1162/neco.1995.7.5.889 is OK
- 10.1037/13536-000 is OK
- 10.1007/978-3-030-93736-2_48 is OK
- 10.1016/j.neunet.2021.05.010 is OK
- 10.1109/LRA.2021.3090015 is OK
- 10.1016/B978-0-323-88506-5.50066-8 is OK
- 10.1007/s00422-019-00805-w is OK
- 10.3390/e23020198 is OK
- 10.1080/10407413.2021.1965480 is OK
- 10.1098/rsif.2013.0475 is OK
- 10.7554/eLife.41703 is OK
- 10.1162/neco_a_00999 is OK
- 10.1016/j.neubiorev.2021.09.038 is OK
- 10.1016/j.schres.2021.07.032 is OK
- 10.1038/s41598-021-91308-x is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-05-04T17:16:25Z

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

Check final proof 👉 openjournals/joss-papers#3194

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3194, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

kyleniemeyer · 2022-05-04T17:26:43Z

Hi @conorheins, I'm the AEIC on duty this week doing some final checks.

In your article, can you remove the explicit arXiv URL from the end of the statement of need section? The citation you included is sufficient and includes the URL.

Similarly, the article already links to the software repository, so I think you should remove the URL pointing to that in the same paragraph. If you really want to keep a link in the text, perhaps just make the word "repository" a hyperlink like [repository](https://github.com/infer-actively/pymdp).

In the Introduction first paragraph, can you wrap "e.g." with commas, like "... in, e.g., psychophysics ...". Similarly, please add a comma after "e.g." in later uses.

It looks like the Parr et al. 2020 article from Cerebral Cortex is missing a DOI, can you check if one is available?

-removed github URL from statement of need section -wrapped e.g.'s in commas -added doi to parr2020prefrontal citation In response to: openjournals/joss-reviews#4098 (comment)

conorheins · 2022-05-04T21:25:42Z

Hi @kyleniemeyer, thanks for the final checks. I have made the changes you requested, let me know if anything else needs fixing.

kyleniemeyer · 2022-05-04T21:29:59Z

@editorialbot generate pdf

editorialbot · 2022-05-04T21:31:14Z

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

kyleniemeyer · 2022-05-04T21:33:03Z

@editorialbot accept

editorialbot · 2022-05-04T21:33:05Z

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

editorialbot · 2022-05-04T21:35:02Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2022-05-04T21:35:03Z

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.04098 joss-papers#3198
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04098
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer · 2022-05-04T21:56:21Z

Congratulations @conorheins on your article's publication in JOSS! (Conor Heins)

Many thanks to @seankmartin and @patrickmineault for reviewing this, and @emdupre for editing.

editorialbot · 2022-05-04T21:56:22Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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.04098/status.svg)](https://doi.org/10.21105/joss.04098)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04098">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04098/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04098/status.svg
   :target: https://doi.org/10.21105/joss.04098

This is how it will look in your documentation:

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conorheins · 2022-05-04T22:20:59Z

Thanks very much (on behalf of all the authors) for the great news, and thank you again @seankmartin and @patrickmineault for your helpful reviews. And finally many thanks @emdupre for all your help/patience during the review process!

whedon added Matlab Python review labels Jan 25, 2022

whedon assigned emdupre Jan 25, 2022

whedon mentioned this issue Jan 25, 2022

[PRE REVIEW]: pymdp: A Python library for active inference in discrete state spaces #4067

Closed

whedon assigned seankmartin and patrickmineault Jan 26, 2022

editorialbot added accepted published Papers published in JOSS labels May 4, 2022

kyleniemeyer closed this as completed May 4, 2022

editorialbot mentioned this issue Sep 27, 2023

[PRE REVIEW]: PAM: Population Activity Modeller #5845

Closed

editorialbot mentioned this issue Aug 7, 2024

[PRE REVIEW]: MDPSolver: An Efficient Solver for Markov Decision Processes #7084

Open

editorialbot mentioned this issue Sep 20, 2024

[PRE REVIEW]: madupite: A High-Performance Distributed Solver for Large-Scale Markov Decision Processes #7247

Closed

[REVIEW]: pymdp: A Python library for active inference in discrete state spaces #4098

[REVIEW]: pymdp: A Python library for active inference in discrete state spaces #4098

Comments

whedon commented Jan 25, 2022 • edited by editorialbot Loading

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