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[REVIEW]: Phobos: A tool for creating complex robot models #1326

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whedon opened this issue Mar 16, 2019 · 90 comments
Closed

[REVIEW]: Phobos: A tool for creating complex robot models #1326

whedon opened this issue Mar 16, 2019 · 90 comments
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@whedon whedon commented Mar 16, 2019

Submitting author: @Amudtogal (Simon Reichel)
Repository: https://github.com/dfki-ric/phobos
Version: v1.0.1
Editor: @gkthiruvathukal
Reviewer: @CameronDevine, @trallard
Archive: 10.5281/zenodo.3581101

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/9bcd3fc6d5050983951e0f579bca07bf"><img src="http://joss.theoj.org/papers/9bcd3fc6d5050983951e0f579bca07bf/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/9bcd3fc6d5050983951e0f579bca07bf/status.svg)](http://joss.theoj.org/papers/9bcd3fc6d5050983951e0f579bca07bf)

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) 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

@CameronDevine & @trallard, 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/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @gkthiruvathukal know.

Please try and complete your review in the next two weeks

Review checklist for @CameronDevine

Conflict of interest

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?
  • Version: v1.0.1
  • Authorship: Has the submitting author (@Amudtogal) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @trallard

Conflict of interest

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?
  • Version: v1.0.1
  • Authorship: Has the submitting author (@Amudtogal) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
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@whedon whedon commented Mar 16, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @CameronDevine, it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐️ Important ⭐️

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:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

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

@whedon commands
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@whedon whedon commented Mar 16, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Mar 16, 2019

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@CameronDevine CameronDevine commented Mar 23, 2019

@Amudtogal Looking through the repository I didn't find any tests or other ways to check if the software is operating correctly (See Automated tests section of the checklist above).

I also opened an issue (dfki-ric/phobos#179) about some issues in the Wiki.

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@Amudtogal Amudtogal commented Mar 26, 2019

@CameronDevine I will fix the issues in the wiki soon. Sorry for the delay, I had some issues with my computer...

The issue with tests for Phobos has been discussed for a long time. Setting up tests for a Blender addon is a cumbersome process (see dfki-ric/phobos#121). For now, we decided that the additional effort maintaining a CI environment for Phobos is not really worth the trouble. This will be revisited, if we can actually see a growing user base and can also nail down real testing scenarios for the different operators.

Does this make sense, or do you think the tests are absolutely necessary? I'd be ready to discuss this further :)

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@CameronDevine CameronDevine commented Mar 26, 2019

@Amudtogal I don't think tests are absolutely necessary. However, I do think it wouldn't be too hard to add in a limited number of tests. For example, calculateBoxInertia, writeURDFGeometry, and similar functions could be tested without installing blender in a test environment.

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@gkthiruvathukal gkthiruvathukal commented Mar 26, 2019

I agree with @CameronDevine. In software engineering, we often refer to these tests as model tests. That is, the part of your code that perhaps isn't entangled with the user interface. If there are patterns being used (e.g. Model-View-Controller) you might be able to focus on the model part. The methods @CameronDevine showed strongly suggest this possibility as the code is independent of Blender per se.

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@CameronDevine CameronDevine commented Apr 2, 2019

I opened two more issues today, dfki-ric/phobos#180 and dfki-ric/phobos#181. Both of these issue relate to a minor difficulties I experienced while configuring Phobos.

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@Amudtogal Amudtogal commented Apr 16, 2019

I have just closed these issues.
Furthermore, I added the model tests to our agenda. Do you expect us to finish the test before advancing the publication?

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@gkthiruvathukal gkthiruvathukal commented Apr 21, 2019

@CameronDevine, have the issues you reported all been addressed satisfactorily?
@trallard Do you have any additional input on this submission?

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@CameronDevine CameronDevine commented Apr 21, 2019

@gkthiruvathukal The only outstanding item for me is the lack of automated tests. Since neither automated or manual tests are provided I do not yet feel comfortable checking that item off.

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@gkthiruvathukal gkthiruvathukal commented May 2, 2019

@Amudtogal I am seeing that we (or I, more precisely) did not respond to your question about model tests. Sorry for the delay as it has been a busy ending to my academic year here.

Can you please add some basic model tests so we can check off the last box? I'd feel a lot better if there were at least a few tests, which would establish a basis for more expanded testing at a later date. As soon as you can take care of this and @CameronDevine gets a final look, I can proceed.

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@trallard trallard commented May 4, 2019

HI sorry for taking so long @gkthiruvathukal AND @Amudtogal from my part the thing missing as well is that corresponding to the tests.

I believe some model tests would be essential even if to have a baseline of the software performance / behaviour at the current state.

Apart from that I do not see any major issues or blockers

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@gkthiruvathukal gkthiruvathukal commented May 8, 2019

Thanks, @trallard.
@Amudtogal, based on the feedback from the reviewers--and my own relatively strong opinions about the need for tests--please act upon this input so we can proceed to the next steps.

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@Amudtogal Amudtogal commented May 8, 2019

@gkthiruvathukal sorry for responding so late, too. The same academic madness is happening here right now :)
I will work on the tests as soon as I can find some spare time. When I am done, I will come back to you.
Thank you for the reviews and help you have been providing!

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@gkthiruvathukal gkthiruvathukal commented May 19, 2019

@Amudtogal Just a nudge here. Any update on tests?

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@gkthiruvathukal gkthiruvathukal commented Jun 3, 2019

@Amudtogal Please update on when you will be able to work on some tests.

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@Amudtogal Amudtogal commented Jun 4, 2019

I am planning to start the tests within the next three weeks. Next weekend there is a big event I am part of, which has been devouring my spare time... When it is over, I can shift my focus back to coding...

Sorry for delaying this whole process (I don't want to waste your time)! Is there a time limit I need to consider or can I pursue this plan?
Thanks again for your patience!

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@danielskatz danielskatz commented Jun 18, 2019

@whedon remind @Amudtogal in 2 weeks

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@whedon whedon commented Jun 18, 2019

Reminder set for @Amudtogal in 2 weeks

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@gkthiruvathukal gkthiruvathukal commented Jun 18, 2019

@danielskatz Thanks for setting the reminder.

@Amudtogal Please try to work on this as soon as you can. Even if you can get some initial tests in place, this would be satisfactory and allow us to move to the next steps.

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@trallard trallard commented Jul 1, 2019

Hi folks, I am just checking how this is going and if you need any help with the review

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@Amudtogal Amudtogal commented Jul 1, 2019

Hi folks,
a short update on my progress:

I have setup a Travis CI, which runs and installs Phobos and is able to run different tests from the test folder.
https://travis-ci.org/Amudtogal/phobos
Right now, all these changes sit on my fork on github (https://github.com/Amudtogal/phobos), as there are still some minor issues to be resolved before I can merge it into the master:

  • proper error code propagation from the test files to the Travis commandline (otherwise the build never fails)
  • fix the current tests (I wrote a bunch of tests which do not rely on any of the Blender functionality)

Let me know whether you think this is promising or you expected something else :)
Have a nice week,
Simon

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@gkthiruvathukal gkthiruvathukal commented Jul 1, 2019

@trallard Thanks for checking in! We definitely can use your help with the remaining work on this review. Would you be willing to take a look at @Amudtogal's updates for Travis CI/testing? If it is on the right track, I think we can move toward acceptance pretty soon.

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@CameronDevine CameronDevine commented Jul 1, 2019

@gkthiruvathukal, I will take a look at this as well.

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@whedon whedon commented Jan 7, 2020

No archive DOI set. Exiting...

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@danielskatz danielskatz commented Jan 7, 2020

@whedon set 10.5281/zenodo.3581101 as archive

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@whedon whedon commented Jan 7, 2020

OK. 10.5281/zenodo.3581101 is the archive.

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@danielskatz danielskatz commented Jan 7, 2020

@whedon set v1.0.1 as version

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@whedon whedon commented Jan 7, 2020

OK. v1.0.1 is the version.

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@danielskatz danielskatz commented Jan 7, 2020

@whedon accept

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@whedon whedon commented Jan 7, 2020

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Jan 7, 2020

Reference check summary:

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Jan 7, 2020

Check final proof 👉 openjournals/joss-papers#1203

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1203, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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@danielskatz danielskatz commented Jan 7, 2020

👋 @arfon - note that ref 2 in the xml has the same problem as we've seen before with an incomplete URL...
This is otherwise ready for accepting.

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@arfon arfon commented Jan 7, 2020

OK thanks @danielskatz. Let's accept here and I'll fix post publication.

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@danielskatz danielskatz commented Jan 7, 2020

@whedon accept deposit=true

@whedon whedon added the accepted label Jan 7, 2020
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@whedon whedon commented Jan 7, 2020

Doing it live! Attempting automated processing of paper acceptance...
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@whedon whedon commented Jan 7, 2020

PDF failed to compile for issue #1326 with the following error:

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@danielskatz danielskatz commented Jan 7, 2020

@whedon accept deposit=true

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@whedon whedon commented Jan 7, 2020

Doing it live! Attempting automated processing of paper acceptance...
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@whedon whedon commented Jan 7, 2020

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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@whedon whedon commented Jan 7, 2020

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#1204
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01326
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

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@danielskatz danielskatz commented Jan 7, 2020

Thanks to @CameronDevine & @trallard for reviewing!
And to @gkthiruvathukal for editing!
And congratulations to @Amudtogal and co-authors!

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@danielskatz danielskatz commented Jan 7, 2020

👋 @arfon - can you fix the XML, and then close this?

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@kthyng kthyng commented Jan 7, 2020

@danielskatz I'm worried that I am missing problems in the XML when finishing up submissions. What do you see that is incorrect?

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@danielskatz danielskatz commented Jan 7, 2020

see line 89 of the XML in https://github.com/openjournals/joss-papers/pull/1204/files where the "https" is missing at the start of the URL

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@kthyng kthyng commented Jan 7, 2020

How did you find that? Were you looking for that type of error in particular? I have been only checking the first few lines for name and title.

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@danielskatz danielskatz commented Jan 7, 2020

just through scanning the XML to see if everything looks ok - sorry I can't be more helpful

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@Amudtogal Amudtogal commented Jan 7, 2020

Thanks everyone!
Just checking back:
The Zenodo Archive is currently a draft, I have not published it, because I was not sure, whether I should put any information about the Journal into the Zenodo form...

We reached the final stage:

  • Make a tagged release of your software, and list the version tag of the archived version here.
    Where can I do this? The release tag is 1.0.1 "Capricious Choutengan"
  • Archive the reviewed software in Zenodo
  • Check the Zenodo deposit has the correct metadata, this includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it); you may also add the authors' ORCID.
  • List the Zenodo DOI of the archived version here. 10.5281/zenodo.3581101

I haven't published the Zenodo archive yet, as there are a few options I could fill in (e.g. the Journal section). Just give me a call what I shall do with it and I can get it online!

Shall I go online or fill in this stuff:
joss

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@arfon arfon commented Jan 7, 2020

👋 @arfon - can you fix the XML, and then close this?

This is fixed.

@Amudtogal - I don't think you need to put the journal information into this form.

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@Amudtogal Amudtogal commented Jan 7, 2020

In that case,
🎆 🍾 🎆

Thank you so much for your time and effort! I am glad, this went through and excited to maybe meet some of you one day!

@arfon arfon closed this Jan 7, 2020
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@whedon whedon commented Jan 7, 2020

🎉🎉🎉 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.01326/status.svg)](https://doi.org/10.21105/joss.01326)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01326">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01326/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01326/status.svg
   :target: https://doi.org/10.21105/joss.01326

This is how it will look in your documentation:

DOI

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