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[REVIEW]: SCAS dashboard: A tool to intuitively and interactively analyze Slurm cluster usage #6017

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editorialbot opened this issue Nov 3, 2023 · 113 comments
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accepted CSS published Papers published in JOSS Python R recommend-accept Papers recommended for acceptance in JOSS. review Track: 7 (CSISM) Computer science, Information Science, and Mathematics

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editorialbot commented Nov 3, 2023

Submitting author: @wathom (Thomas W.)
Repository: https://github.com/Bioinformatics-Munich/scas_dashboard
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @danielskatz
Reviewers: @aturner-epcc, @phargogh
Archive: 10.5281/zenodo.10064783

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/c87682f0b4f5fa6e7615d5a5b16370f0"><img src="https://joss.theoj.org/papers/c87682f0b4f5fa6e7615d5a5b16370f0/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/c87682f0b4f5fa6e7615d5a5b16370f0/status.svg)](https://joss.theoj.org/papers/c87682f0b4f5fa6e7615d5a5b16370f0)

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

@editorialbot editorialbot added CSS Python R review Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Nov 3, 2023
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Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

@editorialbot commands

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

@editorialbot generate pdf

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Software report:

github.com/AlDanial/cloc v 1.88  T=2.31 s (14.7 files/s, 1937.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                                5            437            272           1429
Python                          13            280            349           1037
Markdown                         4             59              0            300
YAML                             3              7              8            126
TeX                              1              4              0             46
Dockerfile                       3             22             19             42
CSS                              1              3              0             14
Bourne Shell                     3              1              2             10
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                            34            813            650           3005
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 1500

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Failed to discover a Statement of need section in paper

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Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/10968987_3 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@danielskatz
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@aturner-epcc, @apjez, and @verolero86 - Thanks for agreeing to review this submission.
This is the review thread for the paper. All of our communications will happen here from now on.

As you can see above, you each should use the command @editorialbot generate my checklist to create your review checklist. @editorialbot commands need to be the first thing in a new comment.

As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

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.

Please feel free to ping me (@danielskatz) if you have any questions/concerns.

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@wathom - To fix the editorialbot complaint about not finding a Statement of need section, I'm suggesting some changes to how section headings are formatted in Bioinformatics-Munich/scas_dashboard#1 - this is what JOSS papers typically use, and I don't think it makes any difference to the formatted PDF, other than that I've promoted the conclusions header to a 1st level heading. If this seems ok, please merge it.

@wathom
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wathom commented Nov 3, 2023

Dear @danielskatz - many thanks, I merged the pull request.

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wathom commented Nov 3, 2023

@editorialbot generate pdf

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@danielskatz
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👋 @aturner-epcc, @apjez, and @verolero86, if you could please create your checklist typing: @editorialbot generate my checklist, and check off the two items (code of conduct and COIs), I would appreciate it.

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apjez commented Nov 6, 2023

Review checklist for @apjez

Conflict of interest

  • 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

General checks

  • Repository: Is the source code for this software available at the https://github.com/Bioinformatics-Munich/scas_dashboard?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • 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?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • 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.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • 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

  • 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 functionality 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

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • 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?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • 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?

@aturner-epcc
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aturner-epcc commented Nov 7, 2023

Review checklist for @aturner-epcc

Conflict of interest

  • 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

General checks

  • Repository: Is the source code for this software available at the https://github.com/Bioinformatics-Munich/scas_dashboard?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • 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?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • 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.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • 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

  • 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 functionality 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

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • 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?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • 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
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👋 @verolero86, if you could please create your checklist typing: @editorialbot generate my checklist, and check off the two items (code of conduct and COIs), I would appreciate it.

@danielskatz
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👋 @aturner-epcc and @apjez, how are things coming along in your reviews?

@verolero86
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verolero86 commented Nov 22, 2023

Review checklist for @verolero86

Conflict of interest

  • 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

General checks

  • Repository: Is the source code for this software available at the https://github.com/Bioinformatics-Munich/scas_dashboard?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • 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?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • 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.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • 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

  • 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 functionality 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

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • 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?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • 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
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👋 @aturner-epcc, @apjez, and @verolero86, I just wanted to check in with you to see how your reviews are coming, and if there's anything blocking your progress I can help with.

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aturner-epcc commented Dec 5, 2023

@wathom I see an failure using the installation instructions provided right at the start.

Build and start containers

Build images an run docker-compose to start the containers (nginx, frontend, backend, postgres):
To build: docker compose build

~/temp/joss/scas_dashboard/docker main                                                                                                                                                                          3.9.16 anaconda3 aturner@MBP-AT
❯ docker compose build
[+] Building 1.3s (3/3) FINISHED                                                                                                                                                                                           docker:desktop-linux
 => [scas-backend internal] load build definition from Dockerfile                                                                                                                                                                          0.0s
 => => transferring dockerfile: 1.32kB                                                                                                                                                                                                     0.0s
 => [scas-backend internal] load .dockerignore                                                                                                                                                                                             0.0s
 => => transferring context: 2B                                                                                                                                                                                                            0.0s
 => ERROR [scas-backend internal] load metadata for docker.io/rocker/shiny:4.0.5                                                                                                                                                           1.2s
------
 > [scas-backend internal] load metadata for docker.io/rocker/shiny:4.0.5:
------
failed to solve: rocker/shiny:4.0.5: no match for platform in manifest sha256:4e68438dc5a553b440e148ba04832007a6949361c4c9796c042599a7b2444285: not found

Am I doing something wrong or missing a step?

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aturner-epcc commented Dec 5, 2023

@wathom The link to the API documentation seems invalid. It is listed as: https://yourserver.edu/docs/ (this does not exist) Ah! just a minute. Is this only available when you have the framework running? Can the API docs be hosted in such a way that they are accessible without having to run the service?

@aturner-epcc
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@wathom As well as the two issues above, I think the following items are missing from the submission (happy to be pointed at them if I have missed them):

State of the field: Do the authors describe how this software compares to other commonly-used packages?

I see mention of integration with tools like Graphana but expcted to see notes on how this compares to other commonly used tools in this area such as OpenXDMoD and Open OnDemand.

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

This does not seem to really be present other than "Submit an issue". What level of support can be expected (e.g. this is not funded so we will do our best in our spare time)? Are there any contribution guidelines or coding styles that need to be adhered to? What level of information is required for Issues or PRs?

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wathom commented Dec 8, 2023

Dear @aturner-epcc,
Many thanks for your comments, we will address them.
The API documentation is now available also here: https://bioinformatics-munich.github.io/scas_dashboard_api_documentation and the link has been added to the readme.

@wathom
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wathom commented Dec 8, 2023

@wathom I see an failure using the installation instructions provided right at the start.

Build and start containers

Build images an run docker-compose to start the containers (nginx, frontend, backend, postgres):
To build: docker compose build

~/temp/joss/scas_dashboard/docker main                                                                                                                                                                          3.9.16 anaconda3 aturner@MBP-AT
❯ docker compose build
[+] Building 1.3s (3/3) FINISHED                                                                                                                                                                                           docker:desktop-linux
 => [scas-backend internal] load build definition from Dockerfile                                                                                                                                                                          0.0s
 => => transferring dockerfile: 1.32kB                                                                                                                                                                                                     0.0s
 => [scas-backend internal] load .dockerignore                                                                                                                                                                                             0.0s
 => => transferring context: 2B                                                                                                                                                                                                            0.0s
 => ERROR [scas-backend internal] load metadata for docker.io/rocker/shiny:4.0.5                                                                                                                                                           1.2s
------
 > [scas-backend internal] load metadata for docker.io/rocker/shiny:4.0.5:
------
failed to solve: rocker/shiny:4.0.5: no match for platform in manifest sha256:4e68438dc5a553b440e148ba04832007a6949361c4c9796c042599a7b2444285: not found

Am I doing something wrong or missing a step?

@aturner-epcc Is this error still present, unfortunatley I can't reproduce it on my platforms.

@wathom
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wathom commented May 9, 2024

@editorialbot generate pdf

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

@editorialbot commands

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wathom commented May 9, 2024

@editorialbot generate pdf

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@danielskatz
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👋 @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.

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wathom commented May 10, 2024

Dear @danielskatz,

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@editorialbot set v1.0.0 as version

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Done! version is now v1.0.0

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@editorialbot set 10.5281/zenodo.10064783 as archive

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Done! archive is now 10.5281/zenodo.10064783

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@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/10968987_3 is OK
- 10.1109/MCSE.2015.68 is OK
- 10.21105/joss.00622 is OK

MISSING DOIs

- No DOI given, and none found for title: SLURM Dashboard
- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: shiny: Web Application Framework for R
- No DOI given, and none found for title: shinydashboard: Create Dashboards with ’Shiny’

INVALID DOIs

- None

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👋 @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5340, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label May 10, 2024
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@editorialbot accept

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

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Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Walzthoeni
  given-names: Thomas
  orcid: "https://orcid.org/0009-0009-3995-709X"
- family-names: Singiali
  given-names: Bom Bahadur
- family-names: Rayner
  given-names: N. William
  orcid: "https://orcid.org/0000-0003-0510-4792"
- family-names: Casale
  given-names: Francesco Paolo
- family-names: Feest
  given-names: Christoph
  orcid: "https://orcid.org/0000-0002-0772-7267"
- family-names: Marr
  given-names: Carsten
  orcid: "https://orcid.org/0000-0003-2154-4552"
- family-names: Wachsmann
  given-names: Alf
  orcid: "https://orcid.org/0000-0002-7736-3059"
contact:
- family-names: Walzthoeni
  given-names: Thomas
  orcid: "https://orcid.org/0009-0009-3995-709X"
doi: 10.5281/zenodo.10064783
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Walzthoeni
    given-names: Thomas
    orcid: "https://orcid.org/0009-0009-3995-709X"
  - family-names: Singiali
    given-names: Bom Bahadur
  - family-names: Rayner
    given-names: N. William
    orcid: "https://orcid.org/0000-0003-0510-4792"
  - family-names: Casale
    given-names: Francesco Paolo
  - family-names: Feest
    given-names: Christoph
    orcid: "https://orcid.org/0000-0002-0772-7267"
  - family-names: Marr
    given-names: Carsten
    orcid: "https://orcid.org/0000-0003-2154-4552"
  - family-names: Wachsmann
    given-names: Alf
    orcid: "https://orcid.org/0000-0002-7736-3059"
  date-published: 2024-05-10
  doi: 10.21105/joss.06017
  issn: 2475-9066
  issue: 97
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6017
  title: "SCAS dashboard: A tool to intuitively and interactively
    analyze Slurm cluster usage"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06017"
  volume: 9
title: "SCAS dashboard: A tool to intuitively and interactively analyze
  Slurm cluster usage"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

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🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06017 joss-papers#5341
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06017
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

@editorialbot editorialbot added accepted published Papers published in JOSS labels May 10, 2024
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Congratulations to @wathom (Thomas W.) and co-authors on your publication!!

And thanks to @aturner-epcc and @phargogh for reviewing this work!
JOSS depends on volunteers and wouldn't be successful without your efforts

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🎉🎉🎉 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](https://joss.theoj.org/papers/10.21105/joss.06017/status.svg)](https://doi.org/10.21105/joss.06017)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06017">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06017/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06017/status.svg
   :target: https://doi.org/10.21105/joss.06017

This is how it will look in your documentation:

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@wathom
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wathom commented May 10, 2024

Great, many thanks to the editor @danielskatz and the reviewers @aturner-epcc and @phargogh

@arfon
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arfon commented May 13, 2024

@editorialbot reaccept

(Nothing to see here, just re-accepting this to make sure the JATS output are in the correct format)

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Rebuilding paper!

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⚠️ Couldn't update published paper. An error happened.

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