[REVIEW]: x11docker - Run GUI applications in Docker containers #1349

whedon · 2019-03-25T14:25:16Z

Submitting author: @mviereck (Martin Viereck)
Repository: https://github.com/mviereck/x11docker
Version: v5.6.0
Editor: @arfon
Reviewer: @yxliang01, @sgyzetrov, @1138-4eb
Archive: 10.5281/zenodo.2658749

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/7ff985f2699880f77b86209b98c0d98d"><img src="http://joss.theoj.org/papers/7ff985f2699880f77b86209b98c0d98d/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/7ff985f2699880f77b86209b98c0d98d/status.svg)](http://joss.theoj.org/papers/7ff985f2699880f77b86209b98c0d98d)

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

@yxliang01 & @sgyzetrov & @1138-4eb, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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

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

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @yxliang01

Review based on mviereck/x11docker@56de629

Conflict of interest

As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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?
Version: v5.6.0
Authorship: Has the submitting author (@mviereck) 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 @sgyzetrov

Conflict of interest

As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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?
Version: v5.6.0
Authorship: Has the submitting author (@mviereck) 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 @1138-4eb

Conflict of interest

As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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?
Version: v5.6.0
Authorship: Has the submitting author (@mviereck) 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)?

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

whedon · 2019-03-25T14:25:20Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @yxliang01, 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:

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

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

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

@whedon commands

whedon · 2019-03-25T14:25:24Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-03-25T14:25:48Z

👉 Check article proof 📄 👈

arfon · 2019-03-25T14:27:31Z

@yxliang01, @sgyzetrov, @1138-4eb - please carry out your review in this issue by updating the checklist above and giving feedback in this issue. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Any questions/concerns please let me know.

sgyzetrov · 2019-03-25T15:45:39Z

@whedon check references

whedon · 2019-03-25T15:45:42Z

Attempting to check references...

whedon · 2019-03-25T15:45:47Z


OK DOIs

- 10.1145/2723872.2723882 is OK
- 10.1145/2889160.2891057 is OK
- 10.2218/ijdc.v12i2.509 is OK
- 10.1093/bioinformatics/btw120 is OK
- 10.25080/Majora-4af1f417-011 is OK
- 10.1007/s10816-015-9272-9 is OK
- 10.11588/heibooks.285.377 is OK

MISSING DOIs

- None

INVALID DOIs

- None

yxliang01 · 2019-03-25T16:16:37Z

Noted. Currently, I would schedule starting review on Wednesday.

EDIT: @arfon I would say it might be better to include @gflofst though since all three of us have more or less contributed to this paper.

mviereck · 2019-03-25T17:20:30Z

Thanks at all of you for your interest and help!

I've opened a ticket for discussion of paper.md here: mviereck/x11docker#137
Feel free to open further tickets for each point to discuss.

eine · 2019-03-25T17:31:59Z

I have finished reviewing the checklist. There are three items which I'd like to explain:

Conflict of interest

See #1346 (comment)

[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.

Dependencies are clearly-stated, and there are plenty of info messages to tell the user when some are missing. There is no explicit list, tho. I.e., the user must check how a specific package is installed in a host. Nonetheless, I think that an automated package management would unnecessarily complicate this project.

@arfon, according to Bad (not acceptable): Reliance on other software not listed by the authors, should I uncheck this item?

[ ] 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

There are no guidelines at all. Words 'contribute'/'contributor' are not found in the repo. This is because it is a single man project, so most of the contributions are not direct code modifications.

However, it is easy to report issues or problems and to get support. The author is very responsive, and most issues are attended and solved within hours or days. PRs are also handled fast.

Should I cross off this item?

Regarding #1346 (comment), the suggestions still apply, and have been copied to mviereck/x11docker#137. But none of them is a stopper for approval. Those are just suggestions that can opinionatedly improve the quality of the paper.

mviereck · 2019-03-25T18:42:22Z

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

There are no guidelines at all.

I have added some notes about issues, contributing and support in README.md: https://github.com/mviereck/x11docker#contact

eine · 2019-03-25T19:25:55Z

I have added some notes about issues, contributing and support in README.md

Review updated accordingly.

mviereck · 2019-03-26T17:16:36Z

@whedon generate pdf

whedon · 2019-03-26T17:16:38Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-03-26T17:17:17Z

👉 Check article proof 📄 👈

mviereck · 2019-03-26T17:20:07Z

I've made some careful adjustments in paper.md. (diff)

sgyzetrov · 2019-03-26T18:23:51Z

I'm almost finished reviewing the software (and software documentation) part and going to start the paper itself soon. For the software (and software documentation) part, I have raised a few issues in mviereck/x11docker#137

sgyzetrov · 2019-03-27T16:14:25Z

I have gone through the paper, and it looks good to me. Some wording could be enhanced but since the author's ideas are clear-stated, this is more of a cherry-on-top thing.

Two newly raised issues:

Reference for jupyter seems broken in pdf submission (e.g. jupyter notebooks (al., 2018)), maybe consider using the recommended bibtex entry from here, see bib file here. @mviereck please look into it.
It would be nice to keep the citation with one consistent style (e.g. Rechert et al., 2017,Emsley & De Roure (2018) >> Rechert et al., 2017; Emsley & De Roure, 2018)

One remaining issue:
mviereck/x11docker#137 (comment)

mviereck · 2019-03-27T17:11:31Z

@whedon generate pdf

whedon · 2019-03-27T17:11:33Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-03-27T17:12:07Z

👉 Check article proof 📄 👈

mviereck · 2019-03-27T17:22:47Z

Some wording could be enhanced but since the author's ideas are clear-stated, this is more of a cherry-on-top thing.

Suggestions (or a PR) are quite appreciated!

Reference for jupyter seems broken in pdf submission

fixed.

It would be nice to keep the citation with one consistent style

done.

One remaining issue: mviereck/x11docker#137 (comment)

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?

I've added a note about target audience in paper.md.

One point is still open:

Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.

As long as it is a recommendation ("ideally"), I won't do the major task of automated package management.
Instead, I will provide a table with package names for a number of popular distributions. This makes it easier to find the matching package for each recommended dependency. I am currently working on it.

sgyzetrov · 2019-03-28T13:08:15Z

@whedon check references

whedon · 2019-03-28T13:08:17Z

Attempting to check references...

whedon · 2019-03-28T13:08:21Z


OK DOIs

- 10.1145/2723872.2723882 is OK
- 10.1145/2889160.2891057 is OK
- 10.2218/ijdc.v12i2.509 is OK
- 10.1093/bioinformatics/btw120 is OK
-  10.25080/Majora-4af1f417-011  is OK
- 10.1007/s10816-015-9272-9 is OK
- 10.11588/heibooks.285.377 is OK

MISSING DOIs

- None

INVALID DOIs

- None

sgyzetrov · 2019-03-29T06:33:58Z

Instead, I could provide a table with package names for a number of popular distributions. This makes it easier to find the matching package for each recommended dependency.

mviereck/x11docker@d699254 looks good enough to me! Since all issues have been addressed, I move to recommend this paper for acceptance.

arfon · 2019-03-29T06:59:23Z

@whedon generate pdf

arfon · 2019-04-29T10:24:44Z

OK great!

@yxliang01, @sgyzetrov, @1138-4eb - could you confirm you're happy with the updates from @mviereck? If so, I think we're ready to accept this submission into JOSS.

sgyzetrov · 2019-04-29T11:18:14Z

The new release looks good, for now I do not have newly raised issues.

eine · 2019-04-29T15:48:43Z

LGTM.

yxliang01 · 2019-04-29T18:57:18Z

This paper looks good to me for acceptance.

This comment is valid for mviereck/x11docker@56de629 This is however invalid for new updates on the paper.

arfon · 2019-05-01T17:30:43Z

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

mviereck · 2019-05-02T21:22:47Z

I have archived x11docker at Zenodo: https://zenodo.org/record/2658749

Viereck, Martin. (2019, May 2). x11docker: Run GUI applications in Docker containers (Version v5.6.0). Zenodo. http://doi.org/10.5281/zenodo.2658749

The archived files are the identical to x11docker release v5.6.0 at github: https://github.com/mviereck/x11docker/releases/tag/v5.6.0

arfon · 2019-05-03T01:30:25Z

@whedon set 10.5281/zenodo.2658749 as archive

whedon · 2019-05-03T01:30:28Z

OK. 10.5281/zenodo.2658749 is the archive.

arfon · 2019-05-03T01:30:35Z

@whedon accept

whedon · 2019-05-03T01:30:38Z

Attempting dry run of processing paper acceptance...

whedon · 2019-05-03T01:30:50Z

PDF failed to compile for issue #1349 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/1349 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in collect!'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/processor.rb:57:in find_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:73:in compile' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:116:in <top (required)>'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

arfon · 2019-05-03T01:31:12Z

@whedon accept

whedon · 2019-05-03T01:31:15Z

Attempting dry run of processing paper acceptance...

whedon · 2019-05-03T01:31:32Z


OK DOIs

- 10.1145/2723872.2723882 is OK
- 10.1145/2889160.2891057 is OK
- 10.2218/ijdc.v12i2.509 is OK
- 10.1093/bioinformatics/btw120 is OK
-  10.25080/Majora-4af1f417-011  is OK
- 10.1007/s10816-015-9272-9 is OK
- 10.11588/heibooks.285.377 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2019-05-03T01:32:02Z


OK DOIs

- 10.1145/2723872.2723882 is OK
- 10.1145/2889160.2891057 is OK
- 10.2218/ijdc.v12i2.509 is OK
- 10.1093/bioinformatics/btw120 is OK
-  10.25080/Majora-4af1f417-011  is OK
- 10.1007/s10816-015-9272-9 is OK
- 10.11588/heibooks.285.377 is OK

MISSING DOIs

- None

INVALID DOIs

- None

arfon · 2019-05-03T01:40:25Z

@whedon accept

whedon · 2019-05-03T01:40:28Z

Attempting dry run of processing paper acceptance...

whedon · 2019-05-03T01:41:26Z

Check final proof 👉 openjournals/joss-papers#655

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#655, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

whedon · 2019-05-03T01:41:44Z


OK DOIs

- 10.1145/2723872.2723882 is OK
- 10.1145/2889160.2891057 is OK
- 10.2218/ijdc.v12i2.509 is OK
- 10.1093/bioinformatics/btw120 is OK
-  10.25080/Majora-4af1f417-011  is OK
- 10.1007/s10816-015-9272-9 is OK
- 10.11588/heibooks.285.377 is OK

MISSING DOIs

- None

INVALID DOIs

- None

arfon · 2019-05-03T01:42:50Z

@whedon accept deposit=true

whedon · 2019-05-03T01:42:53Z

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

whedon · 2019-05-03T01:43:36Z

🚨🚨🚨 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.01349 joss-papers#656
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01349
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

arfon · 2019-05-03T01:45:27Z

@yxliang01, @sgyzetrov, @1138-4eb - many thanks for your reviews here ✨

@mviereck - your paper is now accepted into JOSS ⚡🚀💥

whedon · 2019-05-03T01:45:30Z

🎉🎉🎉 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](http://joss.theoj.org/papers/10.21105/joss.01349/status.svg)](https://doi.org/10.21105/joss.01349)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01349">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01349/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01349/status.svg
   :target: https://doi.org/10.21105/joss.01349

This is how it will look in your documentation:

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: http://joss.theoj.org/reviewer-signup.html
Making a small donation to support our running costs here: https://numfocus.salsalabs.org/donate-to-joss

mviereck · 2019-05-03T07:59:16Z

Great!

Much thanks for all your friendly help and work, @arfon, @yxliang01, @sgyzetrov, @1138-4eb ! 👍 👍 👍

:-)

whedon assigned arfon Mar 25, 2019

whedon added the review label Mar 25, 2019

whedon mentioned this issue Mar 25, 2019

[PRE REVIEW]: x11docker - Run GUI applications in Docker containers #1346

Closed

openjournals deleted a comment from whedon May 3, 2019

whedon added the accepted label May 3, 2019

arfon closed this as completed May 3, 2019

whedon added published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. labels Mar 2, 2020

[REVIEW]: x11docker - Run GUI applications in Docker containers #1349

[REVIEW]: x11docker - Run GUI applications in Docker containers #1349

Comments

whedon commented Mar 25, 2019 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @yxliang01

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @sgyzetrov

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @1138-4eb

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Mar 25, 2019

whedon commented Mar 25, 2019

whedon commented Mar 25, 2019

arfon commented Mar 25, 2019

sgyzetrov commented Mar 25, 2019

whedon commented Mar 25, 2019

whedon commented Mar 25, 2019

yxliang01 commented Mar 25, 2019 • edited Loading

mviereck commented Mar 25, 2019

eine commented Mar 25, 2019 • edited Loading

mviereck commented Mar 25, 2019

eine commented Mar 25, 2019

mviereck commented Mar 26, 2019

whedon commented Mar 26, 2019

whedon commented Mar 26, 2019

mviereck commented Mar 26, 2019

sgyzetrov commented Mar 26, 2019 • edited Loading

sgyzetrov commented Mar 27, 2019

mviereck commented Mar 27, 2019

whedon commented Mar 27, 2019

whedon commented Mar 27, 2019

mviereck commented Mar 27, 2019 • edited Loading

sgyzetrov commented Mar 28, 2019

whedon commented Mar 28, 2019

whedon commented Mar 28, 2019

sgyzetrov commented Mar 29, 2019

arfon commented Mar 29, 2019

arfon commented Apr 29, 2019

sgyzetrov commented Apr 29, 2019

eine commented Apr 29, 2019

yxliang01 commented Apr 29, 2019

arfon commented May 1, 2019

mviereck commented May 2, 2019

arfon commented May 3, 2019

whedon commented May 3, 2019

arfon commented May 3, 2019

whedon commented May 3, 2019

whedon commented May 3, 2019

arfon commented May 3, 2019

whedon commented May 3, 2019

whedon commented May 3, 2019

whedon commented May 3, 2019

arfon commented May 3, 2019

whedon commented May 3, 2019

whedon commented May 3, 2019

whedon commented May 3, 2019

arfon commented May 3, 2019

whedon commented May 3, 2019

whedon commented May 3, 2019

arfon commented May 3, 2019

whedon commented May 3, 2019

mviereck commented May 3, 2019

whedon commented Mar 25, 2019 •

edited

Loading

yxliang01 commented Mar 25, 2019 •

edited

Loading

eine commented Mar 25, 2019 •

edited

Loading

sgyzetrov commented Mar 26, 2019 •

edited

Loading

mviereck commented Mar 27, 2019 •

edited

Loading