[REVIEW]: MyQueue: Task and workflow scheduling system

whedon commented 5 years ago

Submitting author: @jjmortensen (Jens Jørgen Mortensen) Repository: https://gitlab.com/myqueue/myqueue Version: version-20.1.1 Editor: @danielskatz Reviewer: @gonsie, @marksantcroos Archive: 10.5281/zenodo.3607221

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/33edc00feaacaaaca2bb0e22011bb421"><img src="https://joss.theoj.org/papers/33edc00feaacaaaca2bb0e22011bb421/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/33edc00feaacaaaca2bb0e22011bb421/status.svg)](https://joss.theoj.org/papers/33edc00feaacaaaca2bb0e22011bb421)

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

@gonsie & @marksantcroos, 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.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @danielskatz know.

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

Review checklist for @gonsie

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

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

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@jjmortensen) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

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

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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @marksantcroos

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

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

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@jjmortensen) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

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

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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

danielskatz commented 4 years ago

At this point could you:

[ ] Make a tagged release of your software, and list the version tag of the archived version here.
[ ] Archive the reviewed software in Zenodo or a similar service (e.g. figshare, an institutional repository)
[ ] Check the archival deposit (e.g., in Zenodo) 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.
[ ] Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

jjmortensen commented 4 years ago

The MyQueue version is 20.1.1 and the tag name in the Git repository is "version-20.1.1":

https://gitlab.com/myqueue/myqueue/-/tags/version-20.1.1

I've uploaded an archive to Zenodo:

https://zenodo.org/record/3607221

The DOI is "10.5281/zenodo.3607221".

danielskatz commented 4 years ago

@whedon set version-20.1.1 as version

whedon commented 4 years ago

OK. version-20.1.1 is the version.

danielskatz commented 4 years ago

@whedon set 10.5281/zenodo.3607221 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.3607221 is the archive.

danielskatz commented 4 years ago

@whedon accept

whedon commented 4 years ago

Attempting dry run of processing paper acceptance...

whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.1088/2053-1583/aacfc1 is OK
- 10.1007/10968987_3 is OK
- 10.26434/chemrxiv.9971054.v1 is OK
- 10.1002/cpe.3505 is OK
- https://doi.org/10.1016/j.commatsci.2015.09.013 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 4 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1214

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1214, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

danielskatz commented 4 years ago

👋 @jjmortensen - please merge https://gitlab.com/myqueue/myqueue/merge_requests/51

danielskatz commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

danielskatz commented 4 years ago

@whedon accept

whedon commented 4 years ago

Attempting dry run of processing paper acceptance...

whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.1088/2053-1583/aacfc1 is OK
- 10.1007/10968987_3 is OK
- 10.26434/chemrxiv.9971054.v1 is OK
- 10.1002/cpe.3505 is OK
- https://doi.org/10.1016/j.commatsci.2015.09.013 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 4 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1215

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1215, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

danielskatz commented 4 years ago

@whedon accept deposit=true

whedon commented 4 years ago

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

whedon commented 4 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 4 years ago

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/1216
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01844
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

danielskatz commented 4 years ago

Thanks to @gonsie, @marksantcroos for reviewing! And congratulations to @jjmortensen and coauthors!

whedon commented 4 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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.01844/status.svg)](https://doi.org/10.21105/joss.01844)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01844">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01844/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01844/status.svg
   :target: https://doi.org/10.21105/joss.01844

This is how it will look in your documentation:

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jjmortensen commented 4 years ago

Thanks a lot @danielskatz, @gonsie, @marksantcroos

openjournals / joss-reviews