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

2. 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

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

Attempting PDF compilation. Reticulating splines etc...

👉 Check article proof 📄 👈

👋 @gonsie, @marksantcroos - as I think you know, we'll do the review here. Your job is to work through the review checklists, checking off items or creating new issues 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.)

If you have any questions or problems, please let me know

Thanks for submission @jjmortensen. I've created some issues in the repo:

• #9 Move license text to LICENSE
• #10 Assert error from mq test
• #11 Ability to kill the daemon?

For the paper, could you include some details on how MyQueue compares with other tools? I think the most relevant tools would come from the workflow tools / managers.

👋 @marksantcroos - how are you doing on your review?

@jjmortensen - fwiw, a long list of workflow tools is in https://github.com/common-workflow-language/common-workflow-language/wiki/Existing-Workflow-systems (and a shorter list is in https://github.com/meirwah/awesome-workflow-engines)

Thanks for the links. I'm familiar with Fireworks and Aiida. Will take a look ...

I've also started my review by going through installation and testing, but got stuck rather quickly.

• #13 system wide installation vs virtual environment
• #14 echo command to create hello.py is wrong in tutorial
• #15 sbatch: unrecognized option '--workdir'

Although I might be biased, these errors do trigger my "yet another workflow system that tries (and fails) to integrate with queuing systems".

Putting this out here for now, will continue the review and edit accordingly.

Thanks for all your comments so far. There is now a version 19.11.1 available on PyPI with some new features and bug-fixes. There is also an updated version of the paper. See:

https://myqueue.readthedocs.io/en/latest/releasenotes.html
https://gitlab.com/myqueue/myqueue/merge_requests/40

When you update the paper, please rebuild it here (using the following whedon command), as I am now going to do

@whedon generate pdf

Attempting PDF compilation. Reticulating splines etc...

👉 Check article proof 📄 👈

This paper is still missing a ‘state of the field’ summary. Comparing MQ to Slurm/PBS is not the right level of comparison. It needs to be compared to other workflow tools.

In addition, the paper mentions that MQ was used to drive a study of 10,000 jobs. Please provide details on that. How did it handle this large number of jobs? What was the job limit enforced by the underlying scheduler? I believe that this may be the real contribution of MQ (rather than just a front end to a scheduler).

👋 @jjmortensen - note that there are some questions/actions for you here.

👋 @marksantcroos - Can you let us know how your review is proceeding? Are you stuck on anything?

We are looking into it ... in the meantime, @gonsie I added a small section on the web-page describing how to work with many jobs:

https://myqueue.readthedocs.io/en/latest/workflows.html#handling-very-many-tasks

@whedon generate pdf

Attempting PDF compilation. Reticulating splines etc...

👉 Check article proof 📄 👈

We have now added a section describing the state of the field, where we compare MyQueue to AiiDA and Fireworks, trying to emphasize what MyQueue can/cannot do. Let us know if you have suggestions for further improvements.

I've worked some more with the software and got something out of it. Will go over the new pdf and report my findings.

@marksantcroos - thanks

@marksantcroos - any update?

@jjmortensen @mortengjerding Thanks for the tool. The principle of having a "local" and optionally per directory queue is an interesting concept. I tried it out for some data crunching I had to do and ultimately managed to get the job done, which is some sign of success :-)

The paper positions adequately (albeit minimally) compared to other tools out there.

I've opened up another issue in the code repo, but that shouldn't block the paper.

@danielskatz I've checked all boxes and accept it as is now.

Thanks @marksantcroos

@gonsie - can I check in with you to get a status of where things are and what you think needs to be done before you can check off your remaining boxes?

I'm still having trouble actually using myqueue. I just filed another issue in the repo:

• #17 Config file documentation is incomplete

In response to the discussion about submitting a large number of tasks...

We are looking into it ... in the meantime, @gonsie I added a small section on the web-page describing how to work with many jobs:

https://myqueue.readthedocs.io/en/latest/workflows.html#handling-very-many-tasks

MyQueue should probably have a sensible default. Unlimited is not a good default. Maybe 1000?

A contributing guide would be nice, but I guess it's not required.

Actually, some guidance for contributors is required, as stated in the Community guidelines review criterion

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

The README needs a fair amount more content, probably take from what's in the docs. Some of the following should be copied:

• A statement of need - What problems is the software designed to solve and who is the target audience
• Installation instructions, including a clearly-stated list of dependencies
• Example usage - or a pointer into the docs that has this
• Functionality documentation - or a pointer into the docs that has this
• Automated tests - or a pointer into the docs that has this
• Community guidelines - clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Basically, the README should give enough info that someone can understand what the software is, how to build it, and what to do if they have problems.

There is a new README now: https://gitlab.com/myqueue/myqueue/

That looks good to me, but I also want to hear @gonsie's opinion

Readme looks good. I'm still working in issue #17 to get mq to actually work for me.

I'll be gone until early January, happy holidays everyone!

Thanks - have a good break!

👋 @gonsie - just a reminder on this once you are back...

The updated readme looks really nice and I've been able to successfully traverse the 'quick start' guide. I'll try to poke around a bit more this week to further test the functionality... but my review is close to being done 👍

My review is complete. Looks great to me, do your thing @danielskatz

@whedon check references

Reference check summary:

OK DOIs

- 10.1088/2053-1583/aacfc1 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

- https://doi.org/10.1007/10968987_3 may be missing for title: SLURM: Simple Linux Utility for Resource Management

INVALID DOIs

- None

@whedon generate pdf

👉 Check article proof 📄 👈

@jjmortensen - it looks like one of your references needs a DOI to be added
Also, please use {}s in the tex to protect the cases (upper, lower) where needed - for example, JSSPP in that reference. Once you've made changed, you can add a new comment here with @whedon generate pdf to generate a new version. I will also proof-read the paper fairly soon.