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[REVIEW]: MOTrainer: Distributed Measurement Operator Trainer for Data Assimilation Applications #6591

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editorialbot opened this issue Apr 8, 2024 · 101 comments
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accepted Jupyter Notebook published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review TeX Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning

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editorialbot commented Apr 8, 2024

Submitting author: @rogerkuou (Ou Ku)
Repository: https://github.com/VegeWaterDynamics/motrainer
Branch with paper.md (empty if default branch):
Version: v0.1.7
Editor: @srmnitc
Reviewers: @abhishektiwari, @WarmCyan
Archive: 10.5281/zenodo.13349186

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/0ec1cefe66e3d09476dad0fe3b918c35"><img src="https://joss.theoj.org/papers/0ec1cefe66e3d09476dad0fe3b918c35/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/0ec1cefe66e3d09476dad0fe3b918c35/status.svg)](https://joss.theoj.org/papers/0ec1cefe66e3d09476dad0fe3b918c35)

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

@abhishektiwari & @KwickSilver, 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 @abhishektiwari

📝 Checklist for @KwickSilver

📝 Checklist for @WarmCyan

@editorialbot editorialbot added Jupyter Notebook Python review TeX Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning waitlisted Submissions in the JOSS backlog due to reduced service mode. labels Apr 8, 2024
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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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Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/JSTARS.2014.2325780 is OK
- 10.1080/02723646.2016.1236606 is OK
- 10.5334/jors.148 is OK

MISSING DOIs

- No DOI given, and none found for title: Hydrologic Analysis and Design
- 10.25080/majora-7b98e3ed-013 may be a valid DOI for title: Dask: Parallel Computation with Blocked algorithms...

INVALID DOIs

- https://doi.org/10.1016/j.rse.2022.113116 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.rse.2015.09.009 is INVALID because of 'https://doi.org/' prefix

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1411.9 files/s, 227817.3 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Python                           12            241            331            904
Markdown                         12            179              0            445
Jupyter Notebook                  6              0           4309            298
YAML                              6             17              7            156
TOML                              1             16              6            128
TeX                               1              7              0             76
Bourne Shell                      1             10              5             48
JSON                              4              0              0             47
Bourne Again Shell                1              5              4             11
HTML                              1              2              0              9
--------------------------------------------------------------------------------
SUM:                             45            477           4662           2122
--------------------------------------------------------------------------------

Commit count by author:

   117	rogerkuou
    88	Ou Ku
    37	SarahAlidoost
    22	xushanthu-2014
     1	Meiert Grootes
     1	cpranav93

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Paper file info:

📄 Wordcount for paper.md is 555

✅ The paper includes a Statement of need section

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License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

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

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srmnitc commented Apr 8, 2024

👋🏼 @rogerkuou @abhishektiwari @KwickSilver this is the review thread for the paper. All of our communications will happen here from now on.

As you might know, 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

@srmnitc srmnitc removed the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Apr 11, 2024
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KwickSilver commented Apr 16, 2024 via email

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srmnitc commented Apr 16, 2024

Hi Sarath, Apologies for my delayed response; I haven't been able to start reviewing the journal yet. I plan to begin tomorrow and aim to complete it by the end of this month. Does this timeline work for you? Thanks, Shantanu

On Mon, 8 Apr 2024 at 04:47, Sarath Menon @.> wrote: 👋🏼 @rogerkuou https://github.com/rogerkuou @abhishektiwari https://github.com/abhishektiwari @KwickSilver https://github.com/KwickSilver this is the review thread for the paper. All of our communications will happen here from now on. As you might know, as a reviewer, the first step is to create a checklist for your review by entering @editorialbot https://github.com/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 @. https://github.com/srmnitc ) if you have any questions/concerns, thanks again for the submission, and for thr reviews — Reply to this email directly, view it on GitHub <#6591 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABCUHHJ5AU25RZTRQPVGMKDY4J7VBAVCNFSM6AAAAABF4RFJNSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBSGUZTQOBYGM . You are receiving this because you were mentioned.Message ID: @.***>

@KwickSilver that is fine, thanks for the update!

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srmnitc commented Apr 16, 2024

@abhishektiwari hi! just a short reminder about the review, do you need anything from our side to get started?

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abhishektiwari commented Apr 26, 2024

Review checklist for @abhishektiwari

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/VegeWaterDynamics/motrainer?
  • 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 (@rogerkuou) 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?

@abhishektiwari
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abhishektiwari commented Apr 28, 2024

@rogerkuou Initial feedback,

  1. Update installation instruction as raised here
  2. Provide details on example data generation script here
  3. Add community/contributing guidelines as mentioned here

Once you have fixed these, let us know in comments here so I can verify functional claims.

@rogerkuou
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Thx @abhishektiwari for the feedback! Sorry for the late reply, just came back from a holiday. I will work on them in the coming days, and will let you know when it's done.

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srmnitc commented May 2, 2024

@KwickSilver hi! just a short reminder from my side for the review here.

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@srmnitc Apologies for the delay. Due to competing priorities, I was unable to allocate sufficient time for the review as promptly as I had intended. However, I will commence the review process without further delay.

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KwickSilver commented May 2, 2024

Review checklist for @KwickSilver

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/VegeWaterDynamics/motrainer?
  • 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 (@rogerkuou) 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?

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srmnitc commented May 2, 2024

@srmnitc Apologies for the delay. Due to competing priorities, I was unable to allocate sufficient time for the review as promptly as I had intended. However, I will commence the review process without further delay.

Thanks for your quick reply!

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srmnitc commented May 16, 2024

@rogerkuou just a quick ping to see how the changes are coming along, please dont forget to leave a message here once you are done. Thanks!

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Done! version is now v1.0.7

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srmnitc commented Aug 20, 2024

@rogerkuou thanks a lot for all the changes from your side. Everything looks good to me. I will now pass it on our editor in charge who will finish the rest of the steps.

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srmnitc commented Aug 20, 2024

@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

- 10.1016/j.rse.2022.113116 is OK
- 10.1109/JSTARS.2014.2325780 is OK
- 10.1016/j.rse.2015.09.009 is OK
- 10.1080/02723646.2016.1236606 is OK
- 10.1137/1.9781611970319 is OK
- 10.5334/jors.148 is OK
- 10.25080/majora-7b98e3ed-013 is OK
- 10.1016/j.advwatres.2008.01.001 is OK
- 10.1002/wcc.535 is OK
- 10.1109/MCS.2009.932223 is OK
- 10.3390/rs10101627 is OK
- 10.1175/2007MWR2064.1 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

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👋 @openjournals/dsais-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#5785, 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 Aug 20, 2024
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srmnitc commented Aug 20, 2024

@rogerkuou thanks a lot for all the changes from your side. Everything looks good to me. I will now pass it on our editor in charge who will finish the rest of the steps.

And once again, thanks for your patience too :)

@rogerkuou
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@editorialbot set v1.0.7 as version

Hi @srmnitc sorry for bothering you again, but seems you set the version to v1.0.7. The version I released is v0.1.7. I should have noticed this earlier.

Maybe it can be easily changed? I am not sure if I can use the set version command from editorialbot.

And again, thanks a lot for the editorial work!

@danielskatz
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@editorialbot set v0.1.7 as version

just jumping in with a quick fix...

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Done! version is now v0.1.7

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srmnitc commented Aug 20, 2024

@editorialbot set v0.1.7 as version

just jumping in with a quick fix...

Thanks a lot!

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crvernon commented Aug 22, 2024

🔍 checking out the following:

  • reviewer checklists are completed or addressed
  • version set
  • archive set
  • archive names (including order) and title in archive matches those specified in the paper
  • archive uses the same license as the repo and is OSI approved as open source
  • archive DOI and version match or redirect to those set by editor in review thread
  • paper is error free - grammar and typos
  • paper is error free - test links in the paper and bib
  • paper is error free - refs preserve capitalization where necessary
  • paper is error free - no invalid refs without justification

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@editorialbot generate pdf

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

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crvernon commented Aug 22, 2024

👋 @rogerkuou - I need you to address the following before I can move to accept this one for publication.

  • The title of your Zenodo archive should match the title of your paper exactly. Please edit the metadata in your Zenodo archive to use the title of your paper. No need to conduct another release.

In the paper:

  • Please ensure that capitalization is maintained where necessary in your references. For example in LINE 72, the "e" in "earth" should be capitalized. You can do this in your bib file by using curly brackets around text that you wish to maintain the formatting of.

Let me know once you address these and I will move to accept the paper.

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@editorialbot generate pdf

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

@rogerkuou
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Hi @crvernon, thanks a lot for the review!

The Zenodo repo title and metadata file. Now the title strictly matches the JOSS paper

The reference capitalization has been solved by this PR: VegeWaterDynamics/motrainer#132

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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: Ku
  given-names: Ou
  orcid: "https://orcid.org/0000-0002-5373-5209"
- family-names: Alidoost
  given-names: Fakhereh
  orcid: "https://orcid.org/0000-0001-8407-6472"
- family-names: Shan
  given-names: Xu
  orcid: "https://orcid.org/0000-0002-0569-4326"
- family-names: Chandramouli
  given-names: Pranav
  orcid: "https://orcid.org/0000-0002-7896-2969"
- family-names: Georgievska
  given-names: Sonja
  orcid: "https://orcid.org/0000-0002-8094-4532"
- family-names: Grootes
  given-names: Meiert W.
  orcid: "https://orcid.org/0000-0002-5733-4795"
- family-names: Steele-Dunne
  given-names: Susan
  orcid: "https://orcid.org/0000-0002-8644-3077"
contact:
- family-names: Steele-Dunne
  given-names: Susan
  orcid: "https://orcid.org/0000-0002-8644-3077"
doi: 10.5281/zenodo.13349186
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Ku
    given-names: Ou
    orcid: "https://orcid.org/0000-0002-5373-5209"
  - family-names: Alidoost
    given-names: Fakhereh
    orcid: "https://orcid.org/0000-0001-8407-6472"
  - family-names: Shan
    given-names: Xu
    orcid: "https://orcid.org/0000-0002-0569-4326"
  - family-names: Chandramouli
    given-names: Pranav
    orcid: "https://orcid.org/0000-0002-7896-2969"
  - family-names: Georgievska
    given-names: Sonja
    orcid: "https://orcid.org/0000-0002-8094-4532"
  - family-names: Grootes
    given-names: Meiert W.
    orcid: "https://orcid.org/0000-0002-5733-4795"
  - family-names: Steele-Dunne
    given-names: Susan
    orcid: "https://orcid.org/0000-0002-8644-3077"
  date-published: 2024-08-22
  doi: 10.21105/joss.06591
  issn: 2475-9066
  issue: 100
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6591
  title: "MOTrainer: Distributed Measurement Operator Trainer for Data
    Assimilation Applications"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06591"
  volume: 9
title: "MOTrainer: Distributed Measurement Operator Trainer for Data
  Assimilation Applications"

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.06591 joss-papers#5797
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06591
  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 Aug 22, 2024
@crvernon
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🥳 Congratulations on your new publication @rogerkuou! Many thanks to @srmnitc for editing and @abhishektiwari and @WarmCyan for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

Please consider becoming a reviewer for JOSS if you are not already: https://reviewers.joss.theoj.org/join

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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.06591/status.svg)](https://doi.org/10.21105/joss.06591)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06591">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06591/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06591/status.svg
   :target: https://doi.org/10.21105/joss.06591

This is how it will look in your documentation:

DOI

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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Thanks all for your time and work! @srmnitc @abhishektiwari @WarmCyan @crvernon 🥳

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