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[REVIEW]: ros_control: A generic and simple control framework for ROS #456

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whedon opened this Issue Nov 15, 2017 · 58 comments

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whedon commented Nov 15, 2017

Submitting author: @bmagyar (Bence Magyar)
Repository: https://github.com/ros-controls/joss_paper
Version: 0.12.0
Editor: @danielskatz
Reviewer: @progtologist
Archive: 10.5281/zenodo.1069607

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/8449c6e7b2757d90d7d8451ebecf7fce"><img src="http://joss.theoj.org/papers/8449c6e7b2757d90d7d8451ebecf7fce/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/8449c6e7b2757d90d7d8451ebecf7fce/status.svg)](http://joss.theoj.org/papers/8449c6e7b2757d90d7d8451ebecf7fce)

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 1 questions

@progtologist, please carry out your review in this issue by updating the checklist below (please make sure you're logged in to GitHub). The reviewer guidelines are available here: http://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @danielskatz know.

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: Does the release version given match the GitHub release (0.12.0)?
  • Authorship: Has the submitting author (@bmagyar) 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)?

Reviewer 2 questions

@miguelprada, please carry out your review in this issue by updating the checklist below (please make sure you're logged in to GitHub). The reviewer guidelines are available here: http://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @danielskatz know.

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: Does the release version given match the GitHub release (0.12.0)?
  • Authorship: Has the submitting author (@bmagyar) 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 Nov 15, 2017

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Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @progtologist 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 as 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 commented Nov 15, 2017

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @progtologist 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 as 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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danielskatz Nov 15, 2017

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@progtologist & @miguelprada, please use the two checklists above (one for each of you) to carry out your reviews.

An informal guideline is that we would like your review in 2 weeks, but sooner (or later) are also ok.

The reviewer guidelines are available here: http://joss.theoj.org/about#reviewer_guidelines

Please avoid lengthy details of difficulties in this review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) in this review thread. (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.)

Any questions/concerns, please let me know.

Thanks!!

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danielskatz commented Nov 15, 2017

@progtologist & @miguelprada, please use the two checklists above (one for each of you) to carry out your reviews.

An informal guideline is that we would like your review in 2 weeks, but sooner (or later) are also ok.

The reviewer guidelines are available here: http://joss.theoj.org/about#reviewer_guidelines

Please avoid lengthy details of difficulties in this review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) in this review thread. (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.)

Any questions/concerns, please let me know.

Thanks!!

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miguelprada Nov 15, 2017

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@danielskatz My two first questions already:

First, I might be missing something really obvious here, but I cannot seem to mark the checklist items in the original comment.

Second, the repository listed in the original comment (both in the header and the first item in general checks) is to the contents of the paper, not the software itself. Is this ok?

To be clear, I know where to find the software, I just hesitated when I saw the text

Repository: Is the source code for this software available at the repository url?

with a link pointing to a repo containing just the paper.

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miguelprada commented Nov 15, 2017

@danielskatz My two first questions already:

First, I might be missing something really obvious here, but I cannot seem to mark the checklist items in the original comment.

Second, the repository listed in the original comment (both in the header and the first item in general checks) is to the contents of the paper, not the software itself. Is this ok?

To be clear, I know where to find the software, I just hesitated when I saw the text

Repository: Is the source code for this software available at the repository url?

with a link pointing to a repo containing just the paper.

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danielskatz Nov 15, 2017

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@migueldvb sorry, I need to assign you to this issue, and am working on that.

regarding the second point, you are correct, and the repo should point up one level, not to the paper.

@arfon, help on both of these points is welcome.

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danielskatz commented Nov 15, 2017

@migueldvb sorry, I need to assign you to this issue, and am working on that.

regarding the second point, you are correct, and the repo should point up one level, not to the paper.

@arfon, help on both of these points is welcome.

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First, I might be missing something really obvious here, but I cannot seem to mark the checklist items in the original comment.

@miguelprada - you should have access now (please accept the invite from the openjournals organization).

regarding the second point, you are correct, and the repo should point up one level, not to the paper.

@bmagyar - could you please advise?

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arfon commented Nov 15, 2017

First, I might be missing something really obvious here, but I cannot seem to mark the checklist items in the original comment.

@miguelprada - you should have access now (please accept the invite from the openjournals organization).

regarding the second point, you are correct, and the repo should point up one level, not to the paper.

@bmagyar - could you please advise?

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miguelprada Nov 16, 2017

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First, I might be missing something really obvious here, but I cannot seem to mark the checklist items in the original comment.

@miguelprada - you should have access now (please accept the invite from the openjournals organization).

Accepted the org invite, but I'm still unable to check the items... 😓

May I be doing something wrong? It should be just a matter of clicking on the checkboxes, right? I don't see any other way to edit the original post either.

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miguelprada commented Nov 16, 2017

First, I might be missing something really obvious here, but I cannot seem to mark the checklist items in the original comment.

@miguelprada - you should have access now (please accept the invite from the openjournals organization).

Accepted the org invite, but I'm still unable to check the items... 😓

May I be doing something wrong? It should be just a matter of clicking on the checkboxes, right? I don't see any other way to edit the original post either.

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Accepted the org invite, but I'm still unable to check the items... 😓
Sorry, one more thing. Please accept the invite on this page: https://github.com/openjournals/joss-reviews/invitations

(This usually happens automatically via the API but as we can't handle multiple reviewers automatically yet I have to give you access manually)

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arfon commented Nov 16, 2017

Accepted the org invite, but I'm still unable to check the items... 😓
Sorry, one more thing. Please accept the invite on this page: https://github.com/openjournals/joss-reviews/invitations

(This usually happens automatically via the API but as we can't handle multiple reviewers automatically yet I have to give you access manually)

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miguelprada Nov 16, 2017

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Works now. Thanks @arfon!

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miguelprada commented Nov 16, 2017

Works now. Thanks @arfon!

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progtologist Nov 23, 2017

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@danielskatz can you provide your feedback regarding this issue?

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progtologist commented Nov 23, 2017

@danielskatz can you provide your feedback regarding this issue?

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danielskatz Nov 23, 2017

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As I just wrote in the issue:

JOSS requires a LICENSE or LICENSE.txt file in the root of the repository.

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danielskatz commented Nov 23, 2017

As I just wrote in the issue:

JOSS requires a LICENSE or LICENSE.txt file in the root of the repository.

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progtologist Nov 24, 2017

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Grade: 1) Accept

All minor issues are now resolved as far as I am concerned. The software is research orientated with wide acceptance in the field and is actively developed and maintained.

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progtologist commented Nov 24, 2017

Grade: 1) Accept

All minor issues are now resolved as far as I am concerned. The software is research orientated with wide acceptance in the field and is actively developed and maintained.

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Thanks @progtologist !

@miguelprada , how's your review coming along?

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danielskatz commented Nov 24, 2017

Thanks @progtologist !

@miguelprada , how's your review coming along?

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miguelprada Nov 27, 2017

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I'll issue a grade 2, if only for the missing DOI entries. Will replace it with a 1 once they're in place.

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miguelprada commented Nov 27, 2017

I'll issue a grade 2, if only for the missing DOI entries. Will replace it with a 1 once they're in place.

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miguelprada Nov 27, 2017

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That was quick! Grade: 1 (accept).

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miguelprada commented Nov 27, 2017

That was quick! Grade: 1 (accept).

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Thanks @miguelprada !

@arfon, can I pass this over to you now for the final steps?

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danielskatz commented Nov 27, 2017

Thanks @miguelprada !

@arfon, can I pass this over to you now for the final steps?

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@bmagyar - At this point could you make an archive of the reviewed software packages in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

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arfon commented Nov 27, 2017

@bmagyar - At this point could you make an archive of the reviewed software packages in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

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What would you recommend for gathering up all the package into a tar and submitting for doi?
Zenodo only seems to support repo-wise archiving, figshare seems to be ok with the big tarball.

Should I add a pdf generated by me to the joss-paper repo or will that be generated by them/you?

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bmagyar commented Nov 28, 2017

What would you recommend for gathering up all the package into a tar and submitting for doi?
Zenodo only seems to support repo-wise archiving, figshare seems to be ok with the big tarball.

Should I add a pdf generated by me to the joss-paper repo or will that be generated by them/you?

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What would you recommend for gathering up all the package into a tar and submitting for doi?
Zenodo only seems to support repo-wise archiving, figshare seems to be ok with the big tarball.

My understanding is that both figshare and Zenodo will let you archive a bunch of zip/tar files with them, Zenodo just has a cleaner/more automated approach if you're archiving a single repository.

Should I add a pdf generated by me to the joss-paper repo or will that be generated by them/you?

That will be done by us. We just just need you to supply us with the archive DOI for the software that has been reviewed as part of this submission.

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arfon commented Nov 30, 2017

What would you recommend for gathering up all the package into a tar and submitting for doi?
Zenodo only seems to support repo-wise archiving, figshare seems to be ok with the big tarball.

My understanding is that both figshare and Zenodo will let you archive a bunch of zip/tar files with them, Zenodo just has a cleaner/more automated approach if you're archiving a single repository.

Should I add a pdf generated by me to the joss-paper repo or will that be generated by them/you?

That will be done by us. We just just need you to supply us with the archive DOI for the software that has been reviewed as part of this submission.

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bmagyar Dec 2, 2017

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Thanks for the comments @arfon !

Here is the link to the archive: https://zenodo.org/record/1069607

DOI

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bmagyar commented Dec 2, 2017

Thanks for the comments @arfon !

Here is the link to the archive: https://zenodo.org/record/1069607

DOI

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danielskatz Dec 4, 2017

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@whedon set 10.5281/zenodo.1069607 as archive

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danielskatz commented Dec 4, 2017

@whedon set 10.5281/zenodo.1069607 as archive

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OK. 10.5281/zenodo.1069607 is the archive.

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whedon commented Dec 4, 2017

OK. 10.5281/zenodo.1069607 is the archive.

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Attempting PDF compilation. Reticulating splines etc...
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whedon commented Dec 4, 2017

Attempting PDF compilation. Reticulating splines etc...
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https://github.com/openjournals/joss-papers/blob/joss.00456/joss.00456/10.21105.joss.00456.pdf
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whedon commented Dec 4, 2017

https://github.com/openjournals/joss-papers/blob/joss.00456/joss.00456/10.21105.joss.00456.pdf
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Hey @arfon

  1. In the PDF, the "repository" link on the left points to the paper repo (https://github.com/ros-controls/joss_paper) rather than the high-level set of repos (https://github.com/ros-controls) I understand why this is the case, but in this unusual paper describing a set of repos, this link should probably be changed manually.
  2. Also in the PDF, the archive link seems wrong - it seems to point to the code repo, not to the zenodo archive...
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danielskatz commented Dec 4, 2017

Hey @arfon

  1. In the PDF, the "repository" link on the left points to the paper repo (https://github.com/ros-controls/joss_paper) rather than the high-level set of repos (https://github.com/ros-controls) I understand why this is the case, but in this unusual paper describing a set of repos, this link should probably be changed manually.
  2. Also in the PDF, the archive link seems wrong - it seems to point to the code repo, not to the zenodo archive...
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OK, I can fix that up.

Also in the PDF, the archive link seems wrong - it seems to point to the code repo, not to the zenodo archive...

I'm not sure it currently links to anything. This link is only made in the final version of the paper.

Assuming both of the above are fixed up, is this paper good to accept? If so, I can do the final pieces.

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arfon commented Dec 4, 2017

OK, I can fix that up.

Also in the PDF, the archive link seems wrong - it seems to point to the code repo, not to the zenodo archive...

I'm not sure it currently links to anything. This link is only made in the final version of the paper.

Assuming both of the above are fixed up, is this paper good to accept? If so, I can do the final pieces.

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let's wait until ros-controls/joss_paper#28 is merged, which fixes some bib issues and also includes a note about a correct URL that @bmagyar needs to find (as I can't find the right one)

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danielskatz commented Dec 4, 2017

let's wait until ros-controls/joss_paper#28 is merged, which fixes some bib issues and also includes a note about a correct URL that @bmagyar needs to find (as I can't find the right one)

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@whedon generate pdf

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danielskatz commented Dec 4, 2017

@whedon generate pdf

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Attempting PDF compilation. Reticulating splines etc...
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whedon commented Dec 4, 2017

Attempting PDF compilation. Reticulating splines etc...
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@arfon - any idea what got stuck here? Reticulation of splines is usually such a quick operation...

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danielskatz commented Dec 4, 2017

@arfon - any idea what got stuck here? Reticulation of splines is usually such a quick operation...

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anyhow, once this works, I think we are good to accept this one.

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danielskatz commented Dec 4, 2017

anyhow, once this works, I think we are good to accept this one.

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@arfon - any idea what got stuck here? Reticulation of splines is usually such a quick operation...

I think Heroku might be doing some platform maintenance right now (I'm seeing some weird behaviour elsewhere). I'll do some digging.

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arfon commented Dec 4, 2017

@arfon - any idea what got stuck here? Reticulation of splines is usually such a quick operation...

I think Heroku might be doing some platform maintenance right now (I'm seeing some weird behaviour elsewhere). I'll do some digging.

@arfon arfon added the accepted label Dec 4, 2017

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@progtologist - many thanks for your review here and to @danielskatz for editing this submission

@bmagyar - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00456 ⚡️ 🚀 💥

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arfon commented Dec 4, 2017

@progtologist - many thanks for your review here and to @danielskatz for editing this submission

@bmagyar - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00456 ⚡️ 🚀 💥

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Also, thanks for @miguelprada for his review.

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danielskatz commented Dec 4, 2017

Also, thanks for @miguelprada for his review.

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graiola Dec 5, 2017

Hello, I am @graiola, one of the authors.
First of all, I would like to thank you all for your efforts in making this publication possible.
By looking at the resulting pdf I noticed that the markdown list has not been correctly transformed (look at the robot section). Is it possible to fix it? Thanks in advance.

graiola commented Dec 5, 2017

Hello, I am @graiola, one of the authors.
First of all, I would like to thank you all for your efforts in making this publication possible.
By looking at the resulting pdf I noticed that the markdown list has not been correctly transformed (look at the robot section). Is it possible to fix it? Thanks in advance.

@danielskatz danielskatz reopened this Dec 5, 2017

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@arfon - if you look at https://github.com/ros-controls/joss_paper/blob/master/paper.md you will see a section

Robots using ros_control

that has a list of bullets. In the version at the DOI, "ros_control" is in a too-small font, and in both the version at the DOI and the PDF, the bullets have been lost.

Can you fix these?

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danielskatz commented Dec 5, 2017

@arfon - if you look at https://github.com/ros-controls/joss_paper/blob/master/paper.md you will see a section

Robots using ros_control

that has a list of bullets. In the version at the DOI, "ros_control" is in a too-small font, and in both the version at the DOI and the PDF, the bullets have been lost.

Can you fix these?

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Looks like Pandoc is really fussy about whitespace around the list. I've fixed it up in ros-controls/joss_paper#29

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arfon commented Dec 5, 2017

Looks like Pandoc is really fussy about whitespace around the list. I've fixed it up in ros-controls/joss_paper#29

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@arfon - The PR has been merged - can you regenerate the paper now?

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danielskatz commented Dec 5, 2017

@arfon - The PR has been merged - can you regenerate the paper now?

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@arfon - The PR has been merged - can you regenerate the paper now?

Yes, I've regenerated it.

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arfon commented Dec 5, 2017

@arfon - The PR has been merged - can you regenerate the paper now?

Yes, I've regenerated it.

@arfon arfon closed this Dec 5, 2017

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both the version at the DOI and the PDF still look not correct to me. Am I missing something? Maybe I'm getting a cached version?

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danielskatz commented Dec 5, 2017

both the version at the DOI and the PDF still look not correct to me. Am I missing something? Maybe I'm getting a cached version?

@danielskatz danielskatz reopened this Dec 5, 2017

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screen shot 2017-12-05 at 10 45 26 am

screen shot 2017-12-05 at 11 03 05 am

Yep, I think you must be getting a cached versions? See the screenshot of the PDF view and the website.

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arfon commented Dec 5, 2017

screen shot 2017-12-05 at 10 45 26 am

screen shot 2017-12-05 at 11 03 05 am

Yep, I think you must be getting a cached versions? See the screenshot of the PDF view and the website.

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ok, thanks.

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danielskatz commented Dec 5, 2017

ok, thanks.

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