[REVIEW]: SCAS dashboard: A tool to intuitively and interactively analyze Slurm cluster usage

editorialbot commented 10 months ago

Submitting author: !--author-handle-->@wathom@danielskatz<!--end-editor-- Reviewers: @aturner-epcc, @phargogh Archive: 10.5281/zenodo.10064783

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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

@aturner-epcc & @apjez & @verolero86, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @danielskatz know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @aturner-epcc

aturner-epcc commented 6 months ago

@wathom Thanks for the updated manuscript. @danielskatz All checkboxes ticked now.

danielskatz commented 6 months ago

👋 @wscullin - would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html (Two of my three reviewers seem to have vanished, and I need at least two reviews to move this forward.)

danielskatz commented 6 months ago

Thanks @wscullin - I didn't get a notification for your reaction, so missed this until now, but will assume your 👍 means you are willing, so I will add you now

danielskatz commented 6 months ago

@editorialbot add @wscullin as reviewer

editorialbot commented 6 months ago

@wscullin added to the reviewers list!

danielskatz commented 6 months ago

👋 @wscullin, your review will be checklist based. You will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

As you go over the submission, please check any items that you feel have been satisfied. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#6017 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if either of you require some more time. We can also use editorialbot (our bot) to set automatic reminders if you know you'll be away for a known period of time.Any questions/concerns please let @danielskatz know.

danielskatz commented 6 months ago

👋 @wscullin - if you can go ahead and generate your checklist as above, and then at least check off the COI and CoC items, I would appreciate it, in part to make sure all the permissions are working ok.

danielskatz commented 6 months ago

👋 @wscullin - if you can go ahead and generate your checklist as above, and then at least check off the COI and CoC items, I would appreciate it, in part to make sure all the permissions are working ok.

danielskatz commented 5 months ago

👋 @wscullin - if you can go ahead and generate your checklist as above, and then at least check off the COI and CoC items, I would appreciate it, in part to make sure all the permissions are working ok.

danielskatz commented 5 months ago

👋 @wscullin - one last ping before I look for another reviewer - I do still hope you have time to do this though

danielskatz commented 5 months ago

We have another reviewer who has agreed to review this, so I'm going to add him, and remove the reviewers who haven't appeared...

danielskatz commented 5 months ago

@editorialbot add @phargogh as reviewer

editorialbot commented 5 months ago

@phargogh added to the reviewers list!

danielskatz commented 5 months ago

@editorialbot remove @wscullin as reviewer

editorialbot commented 5 months ago

@wscullin removed from the reviewers list!

danielskatz commented 5 months ago

@editorialbot remove @apjez as reviewer

editorialbot commented 5 months ago

@apjez removed from the reviewers list!

danielskatz commented 5 months ago

@editorialbot remove verolero86 as reviewer

editorialbot commented 5 months ago

I can't add that reviewer: verolero86 is not a username

danielskatz commented 5 months ago

👋 @phargogh, thanks for agreeing to review this.

Your review will be checklist based. You will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

As you go over the submission, please check any items that you feel have been satisfied. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#6017 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if either of you require some more time. We can also use editorialbot (our bot) to set automatic reminders if you know you'll be away for a known period of time.Any questions/concerns please let @danielskatz know.

danielskatz commented 5 months ago

@editorialbot remove @verolero86 as reviewer

editorialbot commented 5 months ago

@verolero86 removed from the reviewers list!

phargogh commented 5 months ago

Review checklist for @phargogh

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 https://github.com/Bioinformatics-Munich/scas_dashboard?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@wathom) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[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 5 months ago

Thanks for getting started so quickly @phargogh

danielskatz commented 5 months ago

👋 @phargogh - how is your review coming along? Is there anything blocking you from making more progress?

phargogh commented 5 months ago

Thanks for the ping @danielskatz ! Still in progress and I believe I'll have more to report back on in the next day or two.

danielskatz commented 4 months ago

@phargogh - just checking on this again...

phargogh commented 4 months ago

Thanks @danielskatz , and I'm sorry all for the delay.

@danielskatz I see that other JOSS papers have a specific References section of the paper in addition to Acknowledgements. This paper has an explicit Acknowledgements section that includes the references. Is this a normal format for listing references for JOSS?

phargogh commented 4 months ago

@wathom I noticed that your CONTRIBUTIONS.md file makes reference to GitLab quite a number of times, yet the code for this repo is hosted here on GitHub. There are a few other minor differences of language, like that GitLab uses Merge Requests instead of Pull Requests. To avoid any confusion here, perhaps it'd be worth updating the language to be consistent with GitHub?

danielskatz commented 4 months ago

Thanks @phargogh for catching this. The paper needs to have a References header added at the end, so that the JOSS processsing that adds the actual references at the end of paper will fill them in under this header, not the Acknowledgements one.

@wathom - please see the example paper and change your paper to fix this.

Thanks @danielskatz , and I'm sorry all for the delay.

@danielskatz I see that other JOSS papers have a specific References section of the paper in addition to Acknowledgements. This paper has an explicit Acknowledgements section that includes the references. Is this a normal format for listing references for JOSS?

wathom commented 4 months ago

Many thanks @phargogh for reviewing the paper. Dear @danielskatz, I changed the CONTRIBUTIONS.md and the paper.md files accordingly.

wathom commented 4 months ago

@editorialbot generate pdf

editorialbot commented 4 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

phargogh commented 4 months ago

@wathom thanks for the changes. The proof looks complete now, with the correct references header, and I see the updates in the contribution guidelines doc now refer to github instead of gitlab. I think it's fine to leave references to "merge requests", since folks familiar with either platform should understand well enough.

@danielskatz all boxes are now checked. Is there anything else I need to do?

danielskatz commented 4 months ago

Thanks @phargogh - no, nothing more is needed from you

danielskatz commented 4 months ago

@wathom - at this point, I'll proofread the paper and let you know the next steps. This might take me a little bit due to some other activities.

danielskatz commented 4 months ago

@wathom - I'm suggesting some small changes to the paper in https://github.com/Bioinformatics-Munich/scas_dashboard/pull/3 Please merge this or let me know what you disagree with, then we can finish the process.

wathom commented 4 months ago

Dear @danielskatz, many thanks for proofreading the paper, I merged the changes.

wathom commented 4 months ago

@editorialbot generate pdf

editorialbot commented 4 months ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

wathom commented 4 months ago

@editorialbot generate pdf

editorialbot commented 4 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

danielskatz commented 4 months ago

👋 @wathom - 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.

wathom commented 4 months ago

Dear @danielskatz,

The tagged release on Github is v1.0.0 (https://github.com/Bioinformatics-Munich/scas_dashboard/tree/v1.0.0)
Archive on Zenodo: https://zenodo.org/records/10064783
The Doi of the archived version is:

danielskatz commented 4 months ago

@editorialbot set v1.0.0 as version

editorialbot commented 4 months ago

Done! version is now v1.0.0

danielskatz commented 4 months ago

@editorialbot set 10.5281/zenodo.10064783 as archive

editorialbot commented 4 months ago

Done! archive is now 10.5281/zenodo.10064783

danielskatz commented 4 months ago

@editorialbot recommend-accept

editorialbot commented 4 months ago

Attempting dry run of processing paper acceptance...

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