[REVIEW]: NOMAD CAMELS: Configurable Application for Measurements, Experiments and Laboratory Systems #6371

editorialbot · 2024-02-19T09:03:56Z

Submitting author: @lapmk (Michael Krieger)
Repository: https://github.com/FAU-LAP/NOMAD-CAMELS
Branch with paper.md (empty if default branch): JOSS-paper
Version: 1.0.2
Editor: @srmnitc
Reviewers: @NicolasCARPi, @ktahar
Archive: 10.5281/zenodo.10793952

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/3c9738d23ab6b6a366c795dbb9538bcd/status.svg)](https://joss.theoj.org/papers/3c9738d23ab6b6a366c795dbb9538bcd)

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

@NicolasCARPi & @ktahar, 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 @srmnitc 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 @NicolasCARPi

📝 Checklist for @ktahar

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

editorialbot · 2024-02-19T09:03:59Z

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:

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

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editorialbot · 2024-02-19T09:04:03Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.24 s (564.8 files/s, 130095.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          98           4112           5126          12900
Qt                              20              0              0           3930
SVG                              7            678              5           3139
Markdown                         3             66              0            346
TeX                              1             19              0            264
YAML                             3              4             55            159
DOS Batch                        1              0              0             32
TOML                             1              4              0             25
-------------------------------------------------------------------------------
SUM:                           134           4883           5186          20795
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2024-02-19T09:04:04Z

Wordcount for paper.md is 1336

editorialbot · 2024-02-19T09:04:44Z

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

OK DOIs

- 10.21105/joss.05388 is OK
- 10.52825/cordi.v1i.376 is OK
- 10.6028/jres.117.010 is OK
- 10.1038/467753a is OK
- 10.1080/08940886.2019.1608121 is OK
- 10.1038/s41586-022-04501-x is OK
- 10.1557/mrs.2018.208 is OK
- 10.1107/S1600576714027575 is OK
- 10.1088/2515-7639/ab13bb is OK
- 10.1016/0168-9002(94)91577-6 is OK
- 10.52825/cordi.v1i.283 is OK
- 10.1038/sdata.2016.18 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2024-02-19T09:05:05Z

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

srmnitc · 2024-02-19T09:05:27Z

👋🏼 @lapmk @NicolasCARPi @ktahar this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains 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, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#REVIEW_NUMBER 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 any 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 (@srmnitc ) if you have any questions/concerns, thanks again for the submission, and for thr reviews

lapmk · 2024-02-19T10:09:51Z

On behalf of all co-authors: @NicolasCARPi and @ktahar, thank you very much for your willingness and precious time to review our manuscript. Thanks a lot also to @srmnitc for editing our submission. We look forward to your comments and are happy to answer your questions.

NicolasCARPi · 2024-02-19T17:08:14Z

Review checklist for @NicolasCARPi

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

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 https://github.com/FAU-LAP/NOMAD-CAMELS?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@lapmk) 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?

NicolasCARPi · 2024-02-19T17:11:25Z

it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

Good to know. I was going for the other way around, but I agree with this approach!

ktahar · 2024-02-20T16:47:37Z

Review checklist for @ktahar

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

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 https://github.com/FAU-LAP/NOMAD-CAMELS?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@lapmk) 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?

lapmk · 2024-02-21T12:52:18Z

Hi @NicolasCARPi and @ktahar. First of all, thank you very much for digging so deeply into our NOMAD CAMELS code. This is extremely helpful and will lead to significant improvements. We really appreciate your input.
Just to let you know, we've released v1.0.0 yesterday afternoon which comes with several improvements and fixes. We will do our best to implement your suggestions and remarks promptly. These can immediately be viewed in the development branch. We plan to release smaller patches throughout the review process.

NicolasCARPi · 2024-02-29T21:14:05Z

@editorialbot generate pdf

editorialbot · 2024-02-29T21:15:43Z

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

NicolasCARPi · 2024-03-04T23:18:47Z

Hello everyone,

My checklist is done. All my remarks were promptly and adequately addressed by the dev team. Looks good to me!

srmnitc · 2024-03-05T07:22:45Z

Thanks @NicolasCARPi. @lapmk I see that some of the issues are still open, could you please close them if they have been addressed already?

srmnitc · 2024-03-05T07:24:57Z

Hi @ktahar, hope everything is going well! Are there any issues still open from your side to check the remaining boxes?

srmnitc · 2024-03-07T17:52:43Z

@editorialbot set 1.0.2 as version

editorialbot · 2024-03-07T17:52:45Z

Done! version is now 1.0.2

srmnitc · 2024-03-07T17:53:09Z

@editorialbot generate pdf

editorialbot · 2024-03-07T17:54:18Z

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

srmnitc · 2024-03-07T17:55:19Z

@editorialbot check references

editorialbot · 2024-03-07T17:55:41Z

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

OK DOIs

- 10.21105/joss.05388 is OK
- 10.52825/cordi.v1i.376 is OK
- 10.6028/jres.117.010 is OK
- 10.1038/467753a is OK
- 10.1080/08940886.2019.1608121 is OK
- 10.1038/s41586-022-04501-x is OK
- 10.1557/mrs.2018.208 is OK
- 10.1107/S1600576714027575 is OK
- 10.1088/2515-7639/ab13bb is OK
- 10.1016/0168-9002(94)91577-6 is OK
- 10.52825/cordi.v1i.283 is OK
- 10.1038/sdata.2016.18 is OK

MISSING DOIs

- No DOI given, and none found for title: NOMAD CAMELS Documentation
- No DOI given, and none found for title: PyMoDAQ
- No DOI given, and none found for title: PyVISA
- No DOI given, and none found for title: FAIRmat NeXus Proposal
- No DOI given, and none found for title: DFG Positionspapier: Förderung von Informationsinf...
- No DOI given, and none found for title: pip documentation V23.3.1
- No DOI given, and none found for title: Bluesky Project
- No DOI given, and none found for title: EPICS - Experimental Physics and Industrial Contro...
- No DOI given, and none found for title: CAMELS_drivers: instrument implementation for CAME...
- No DOI given, and none found for title: SweepMe! - A multi-tool measurement software

INVALID DOIs

- None

srmnitc · 2024-03-07T17:58:47Z

@editorialbot recommend-accept

editorialbot · 2024-03-07T17:58:50Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-03-07T17:59:18Z

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

OK DOIs

- 10.21105/joss.05388 is OK
- 10.52825/cordi.v1i.376 is OK
- 10.6028/jres.117.010 is OK
- 10.1038/467753a is OK
- 10.1080/08940886.2019.1608121 is OK
- 10.1038/s41586-022-04501-x is OK
- 10.1557/mrs.2018.208 is OK
- 10.1107/S1600576714027575 is OK
- 10.1088/2515-7639/ab13bb is OK
- 10.1016/0168-9002(94)91577-6 is OK
- 10.52825/cordi.v1i.283 is OK
- 10.1038/sdata.2016.18 is OK

MISSING DOIs

- No DOI given, and none found for title: NOMAD CAMELS Documentation
- No DOI given, and none found for title: PyMoDAQ
- No DOI given, and none found for title: PyVISA
- No DOI given, and none found for title: FAIRmat NeXus Proposal
- No DOI given, and none found for title: DFG Positionspapier: Förderung von Informationsinf...
- No DOI given, and none found for title: pip documentation V23.3.1
- No DOI given, and none found for title: Bluesky Project
- No DOI given, and none found for title: EPICS - Experimental Physics and Industrial Contro...
- No DOI given, and none found for title: CAMELS_drivers: instrument implementation for CAME...
- No DOI given, and none found for title: SweepMe! - A multi-tool measurement software

INVALID DOIs

- None

editorialbot · 2024-03-07T18:00:05Z

👋 @openjournals/pe-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#5100, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

srmnitc · 2024-03-07T18:00:59Z

@lapmk Thank you for the submission, I have now passed it on to our EiCs who will take care of the rest of the process. Thanks for responding promptly to all reviewer issues and making the changes.

@NicolasCARPi @ktahar once again, thanks for the taking your time to review and provide feedback!

lapmk · 2024-03-07T18:08:09Z

@srmnitc Thank you very much for taking care of our submission as editor. This review process was really a pleasure, and also gave our software a boost. Thank you all for your time!

kyleniemeyer · 2024-03-08T22:42:32Z

Hi @lapmk, I made a few edits to the paper via FAU-LAP/NOMAD-CAMELS#73, could you review and merge?

lapmk · 2024-03-09T12:59:34Z

@editorialbot generate pdf

editorialbot · 2024-03-09T13:00:48Z

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

lapmk · 2024-03-09T13:06:49Z

Hi @lapmk, I made a few edits to the paper via FAU-LAP/NOMAD-CAMELS#73, could you review and merge?

@kyleniemeyer Thank you very much for your edits. Merged. I understand that you didn't like the examples places in parentheses, however, I would prefer to keep references separate from words in the text if this is acceptable. Thus, I made two minor changes in lines 17-18 and 58 in the compiled manuscript. Is this fine with you?

kyleniemeyer · 2024-03-11T14:34:30Z

@lapmk I think that looks good.

kyleniemeyer · 2024-03-11T14:34:37Z

@editorialbot accept

editorialbot · 2024-03-11T14:34:40Z

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

editorialbot · 2024-03-11T14:41:17Z

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: Fuchs
  given-names: Alexander D.
  orcid: "https://orcid.org/0000-0003-1896-9242"
- family-names: Lehmeyer
  given-names: Johannes A. F.
  orcid: "https://orcid.org/0000-0003-2041-9987"
- family-names: Junkes
  given-names: Heinz
  orcid: "https://orcid.org/0000-0002-0218-4873"
- family-names: Weber
  given-names: Heiko B.
  orcid: "https://orcid.org/0000-0002-6403-9022"
- family-names: Krieger
  given-names: Michael
  orcid: "https://orcid.org/0000-0003-1480-9161"
contact:
- family-names: Krieger
  given-names: Michael
  orcid: "https://orcid.org/0000-0003-1480-9161"
doi: 10.5281/zenodo.10793952
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Fuchs
    given-names: Alexander D.
    orcid: "https://orcid.org/0000-0003-1896-9242"
  - family-names: Lehmeyer
    given-names: Johannes A. F.
    orcid: "https://orcid.org/0000-0003-2041-9987"
  - family-names: Junkes
    given-names: Heinz
    orcid: "https://orcid.org/0000-0002-0218-4873"
  - family-names: Weber
    given-names: Heiko B.
    orcid: "https://orcid.org/0000-0002-6403-9022"
  - family-names: Krieger
    given-names: Michael
    orcid: "https://orcid.org/0000-0003-1480-9161"
  date-published: 2024-03-11
  doi: 10.21105/joss.06371
  issn: 2475-9066
  issue: 95
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6371
  title: "NOMAD CAMELS: Configurable Application for Measurements,
    Experiments and Laboratory Systems"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06371"
  volume: 9
title: "NOMAD CAMELS: Configurable Application for Measurements,
  Experiments and Laboratory Systems"

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.

editorialbot · 2024-03-11T14:41:20Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-03-11T14:41:21Z

🚨🚨🚨 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.06371 joss-papers#5115
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06371
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer · 2024-03-11T15:33:33Z

Congratulations @lapmk on your article's publication in JOSS! Please consider signing up as a reviewer if you haven't already.

Many thanks to @NicolasCARPi and @ktahar for reviewing this, and @srmnitc for editing.

editorialbot · 2024-03-11T15:33:35Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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reStructuredText:
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lapmk · 2024-03-11T16:04:57Z

Congratulations @lapmk on your article's publication in JOSS! Please consider signing up as a reviewer if you haven't already.

Many thanks to @NicolasCARPi and @ktahar for reviewing this, and @srmnitc for editing.

@kyleniemeyer Thank you very much on behalf of all co-authors! And I've just signed up as a reviewer for JOSS ;-)

Again, many thanks to all and see you next time! @srmnitc @NicolasCARPi @ktahar

editorialbot added Batchfile Python review TeX Track: 3 (PE) Physics and Engineering labels Feb 19, 2024

editorialbot assigned srmnitc Feb 19, 2024

editorialbot mentioned this issue Feb 19, 2024

[PRE REVIEW]: NOMAD CAMELS: Configurable Application for Measurements, Experiments and Laboratory Systems #6204

Closed

NicolasCARPi mentioned this issue Feb 19, 2024

Why two LICENSE file? (LICENSE and LICENSE.txt) FAU-LAP/NOMAD-CAMELS#59

Closed

This was referenced Feb 19, 2024

Installation issue FAU-LAP/NOMAD-CAMELS#60

Closed

Incorrect user data directory FAU-LAP/NOMAD-CAMELS#62

Closed

Improper error handling FAU-LAP/NOMAD-CAMELS#61

Closed

This was referenced Feb 20, 2024

Test fails / test procedure is not documented FAU-LAP/NOMAD-CAMELS#65

Closed

Hard-coded paths of developer's PC? FAU-LAP/NOMAD-CAMELS#66

Closed

NicolasCARPi mentioned this issue Feb 29, 2024

Missing CONTRIBUTING.md FAU-LAP/NOMAD-CAMELS#70

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Mar 7, 2024

editorialbot added accepted published Papers published in JOSS labels Mar 11, 2024

kyleniemeyer closed this as completed Mar 11, 2024

editorialbot mentioned this issue Sep 7, 2024

[PRE REVIEW]: QuDAP: an Open Source Software for Quantum Materials Characterization #7194

Closed

[REVIEW]: NOMAD CAMELS: Configurable Application for Measurements, Experiments and Laboratory Systems #6371

[REVIEW]: NOMAD CAMELS: Configurable Application for Measurements, Experiments and Laboratory Systems #6371

Comments

editorialbot commented Feb 19, 2024 • edited Loading

Status

Reviewer instructions & questions

Checklists

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lapmk commented Feb 19, 2024

NicolasCARPi commented Feb 19, 2024 • edited Loading

Review checklist for @NicolasCARPi

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

NicolasCARPi commented Feb 19, 2024

ktahar commented Feb 20, 2024 • edited Loading

Review checklist for @ktahar

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

lapmk commented Feb 21, 2024

NicolasCARPi commented Feb 29, 2024

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srmnitc commented Mar 7, 2024 • edited Loading

lapmk commented Mar 7, 2024

kyleniemeyer commented Mar 8, 2024

lapmk commented Mar 9, 2024

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editorialbot commented Feb 19, 2024 •

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srmnitc commented Mar 7, 2024 •

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