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[REVIEW]: pendsim: Developing, Simulating, and Visualizing Feedback Controlled Inverted Pendulum Dynamics #168

Closed whedon closed 1 year ago

whedon commented 2 years ago

Submitting author: @rland93 (Mike Sutherland) Repository: https://github.com/EASEL-UCI/pendsim Version: v1.2 Editor: @moorepants Reviewer: @cooperrc, @repagh Archive: 10.5281/zenodo.7603937

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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

@cooperrc & @repagh, 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
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/jose-reviews/invitations

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

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @repagh

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 2 years ago

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

:warning: JOSS reduced service mode :warning:

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whedon commented 2 years ago

Wordcount for paper.md is 1049

whedon commented 2 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.12 s (228.9 files/s, 82072.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           9            264            586            919
Jupyter Notebook                 6              0           6920            386
Markdown                         2             65              0            124
reStructuredText                 4             82             98            101
TeX                              1              2              0             29
DOS Batch                        1              8              1             26
make                             1              5              7             16
YAML                             1              6             10             14
CSS                              1              1              0              8
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            27            433           7622           1626
-------------------------------------------------------------------------------

Statistical information for the repository '1da1f6afba6c0cc2ccd739dd' was
gathered on 2022/04/01.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Mike Sutherland                 19          2585           2036           29.12
ms                              23          5399           4472           62.21
rland93                          6           954            422            8.67

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
Mike Sutherland            1690           65.4          2.5                8.46
rland93                      79            8.3          3.6               41.77
whedon commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1515/9781400828739 is OK
- 10.1109/MCSE.2007.55 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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:

moorepants commented 2 years ago

@cooperrc, @repagh, and @rland93 welcome to the review issue. For the reviewers please read through the above information. I was wrong in the other thread on the timeline, it seems that 6 weeks is the recommended due date. Note that JOSE reviews are a bit different than most academic journal reviews in that they are open here on Github and there can be a conversation among the reviewers, editors, and authors to arrive a final version that meets the standards for publication. You all can start the review when you'd like and I'll jump in to answer questions or help things move along. Thanks again for volunteering your time and expertise!

moorepants commented 2 years ago

@whedon remind @reviewer in 4 weeks

whedon commented 2 years ago

Reminder set for @reviewer in 4 weeks

moorepants commented 2 years ago

Also I believe this submission is the second type we accept "open-source software, created as educational technology or infrastructure" (see https://openjournals.readthedocs.io/en/jose/submitting.html). @rland93, is that correct?

whedon commented 2 years ago

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

whedon commented 2 years ago

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

moorepants commented 2 years ago

@cooperrc and @repagh can we get an update on the status of your reviews? I see that @repagh has worked through his checklist. Do we expect completion of the first reviews within the 6 weeks deadline? Thanks -- Jason

cooperrc commented 2 years ago

@cooperrc and @repagh can we get an update on the status of your reviews? I see that @repagh has worked through his checklist. Do we expect completion of the first reviews within the 6 weeks deadline? Thanks -- Jason

Thanks for checking in @moorepants. I'm getting back to this today. I'll get my initial thoughts down this week (4/25-4/29). Will have my review done within the 6-week timeframe (before May 13)

cooperrc commented 2 years ago

I added an issue (closed) and two PRs to the pendsim repo.

My review is as follows:

The package and the paper are excellent. The one spot that seems to be lacking is a clear path to extend the package (maybe another section for developers). In the paper, @rland93 says the user can implement any control policy with a new class. It would be great to see how to create the new class and how/if the new class could be added to the current repository of controller algorithms.

Another minor note, the ## Example Notebooks could be added to the documentation Tutorials for more in-depth examples.

rland93 commented 2 years ago

Will work on implementing these changes this week. Details:

https://github.com/rland93/pendsim/issues/15 https://github.com/rland93/pendsim/issues/16 https://github.com/rland93/pendsim/issues/17

Thanks!

repagh commented 2 years ago

Here is my review:

Review for "pendsim: Developing, Simulating, and Visualizing Feedback Controlled Inverted Pendulum Dynamics"

This paper presents a package for simulation and control of an inverted pendulum, targeted at use in education

moorepants commented 2 years ago

@repagh and @cooperrc thank you both for the reviews.

@rland93 I see that there is one checkbox missing on both lists above "community guidelines" and both reviewers have left their comments here or on issues on your repository. Please address the issues and when ready you can provide a response here to each reviewer. Let me know if you have any questions. Feel free to interact with the reviewers here also.

moorepants commented 2 years ago

@rland93 Can you provide an update on your status in addressing the feedback?

moorepants commented 2 years ago

@rland93 Just checking in again here. Can you provide an update on your status in addressing the feedback?

labarba commented 2 years ago

@moorepants — I received an email from David A. Copp saying Mike Sutherland (@rland93) has been incommunicado for several months, and if he can be swapped as corresponding author to finish up this submission.

moorepants commented 2 years ago

David Copp is currently listed as a co-author on the paper. Although, I do not see any contributions from him in the pendsim repository: https://github.com/rland93/pendsim/graphs/contributors. We would need his github handle to swap him out, of course.

EASEL-UCI commented 2 years ago

Hello, this is David Copp. I appreciate the feedback and will happily finish up this submission.

moorepants commented 2 years ago

Hi David. The review is present here and as issues on your repository. Any outstanding items on the checklists above and all PRs/issues on your repository need to be addressed as well as providing a response to the reviewers' comments.

moorepants commented 2 years ago

Hi @EASEL-UCI, do you plan to complete this paper? We have not heard from you for about a month.

EASEL-UCI commented 2 years ago

Yes, definitely. I apologize for the delay. I will need to fork the original repository and make changes there. Will it be an issue to change this submission's repository to the new forked repository?

moorepants commented 2 years ago

Will it be an issue to change this submission's repository to the new forked repository?

I suspect we will be able to fix that. @labarba can you comment?

labarba commented 2 years ago

I don't remember dealing with a change in target repo. @openjournals/dev – can you confirm whether we can edit the submission repository?

arfon commented 2 years ago

You can yes but I'll need to edit it in the database too. What's the new repo?

labarba commented 2 years ago

TY, @arfon. @EASEL-UCI : please report here the URL of the fork you will use for completing this review.

EASEL-UCI commented 2 years ago

TY, @arfon. @EASEL-UCI : please report here the URL of the fork you will use for completing this review.

Excellent. Thank you. Please use https://github.com/EASEL-UCI/pendsim

arfon commented 2 years ago

Updated.

EASEL-UCI commented 2 years ago

@whedon generate pdf

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:

EASEL-UCI commented 2 years ago

@whedon generate pdf

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:

EASEL-UCI commented 2 years ago

The following changes were made:

@cooperrc: Thank you for your feedback and the excellent proposed changes. I believe we have addressed your comments, but if not or if you have other comments or concerns, please let me know.

@repagh: Thank you for your helpful feedback and for catching errors. Please find our responses to your comments below.

This is the only Python package I am aware of that allows for design, analysis, and visualization of control and estimation algorithms for an inverted pendulum system. Moreover, the example notebooks cover multiple algorithms, whereas other projects may focus solely on PID control, for example. We also added a tutorial on how to create a custom control algorithm (https://rland93.github.io/pendsim/customctl.html).

Regarding how to use this in teaching, you make an excellent point. We added the following paragraph in the Example Usage section to briefly describe how this package can be used in education, and we added an example assignment notebook. The emphasis here is on augmenting in-class activities or in-lab hardware experiments rather than serving as the sole instructional material on a topic. For example, there are many excellent online resources for learning PID control; we do not try to replicate those. Instead we aim to provide a sandbox that students can easily use to gain experience tuning a PID controller, visualizing the results, and reflecting on the process.

"This design-test-visualize sequence also allows instructors to introduce students to new topics and create interactive assignments that can augment theoretical class discussions and hardware experiments. Thus, pendsim may be naturally used in engineering courses related to dynamics and control that are taught in any format, including in-person, hybrid, and online settings. An example PID Controller Design Assignment notebook is available to show how students may use pendsim in a course assignment."

moorepants commented 2 years ago

@EASEL-UCI, thanks for the update.

@cooperrc and @repagh, can you now review the updates and see if it satisfies your concerns? If so or if not, you can comment here with approval for publishing or requests for more adjustments. Please finalize the checklists above if those are now complete.

cooperrc commented 2 years ago

My comments and suggestions were addressed and satisfies any concerns I had.

Thank you for your contribution @EASEL-UCI !

repagh commented 2 years ago

Looks fine. I like the additional example to the pendsim repository. Thanks for the contribution!

moorepants commented 2 years ago

@EASEL-UCI I see some math rendering errors here: image https://rland93.github.io/pendsim/customctl.html#Model-Predictive-Control-(MPC)

Maybe a pass through to check for these things is worthwhile.

moorepants commented 2 years ago

@whedon set v1.1.0 as version

whedon commented 2 years ago

OK. v1.1.0 is the version.

moorepants commented 2 years ago

@whedon check references

moorepants commented 2 years ago

@whedon check repository

whedon commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1515/9781400828739 is OK
- 10.1109/MCSE.2007.55 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 2 years ago

Wordcount for paper.md is 1111

whedon commented 2 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.07 s (404.0 files/s, 162147.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           9            270            580            939
Jupyter Notebook                 8              0           7984            564
Markdown                         2             62              0            184
YAML                             1              9             10             44
reStructuredText                 2             25             22             37
TeX                              1              2              0             29
DOS Batch                        1              8              1             26
make                             1              5              7             16
CSS                              1              1              0              8
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            27            382           8604           1850
-------------------------------------------------------------------------------

Statistical information for the repository '4b2bd083c821b41ef8f29cb7' was
gathered on 2022/10/10.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Mike Sutherland                 19          2585           2036           29.00
ms                              23          5399           4472           61.95
rland93                          9           997            445            9.05

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
Mike Sutherland            1681           65.0          9.3                8.51
rland93                     108           10.8          6.3               25.00
moorepants commented 2 years ago

@whedon generate pdf

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:

moorepants commented 2 years ago

There isn't an issues tab on the new repository so I'll leave some things here. The old repository is still referenced in many places, for example: image Do you plan to update these?