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[REVIEW]: DIRECT: Deep Image REConstruction Toolkit #4278

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editorialbot opened this issue Mar 28, 2022 · 65 comments
Closed

[REVIEW]: DIRECT: Deep Image REConstruction Toolkit #4278

editorialbot opened this issue Mar 28, 2022 · 65 comments
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accepted Dockerfile Makefile published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review

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editorialbot commented Mar 28, 2022

Submitting author: @georgeyiasemis (George Yiasemis)
Repository: https://github.com/NKI-AI/direct
Branch with paper.md (empty if default branch): joss-submission
Version: v1.0.1
Editor: @osorensen
Reviewers: @estenhl, @sairamgeethanath
Archive: 10.5281/zenodo.6594702

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/150119fd46692dad9448a26eca669a77"><img src="https://joss.theoj.org/papers/150119fd46692dad9448a26eca669a77/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/150119fd46692dad9448a26eca669a77/status.svg)](https://joss.theoj.org/papers/150119fd46692dad9448a26eca669a77)

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

@estenhl & @sairamgeethanath, 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 @osorensen 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 @estenhl

📝 Checklist for @sairamgeethanath

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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=0.43 s (451.4 files/s, 69344.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         131           3454           4081          12136
SVG                              2              0              0           5849
YAML                            26             22             37           1955
reStructuredText                21            276            514            318
Markdown                         6             81              0            316
TeX                              1             15              0            161
make                             2             27              6             80
TOML                             1              9              4             49
Dockerfile                       1             15              7             45
DOS Batch                        1              8              1             27
-------------------------------------------------------------------------------
SUM:                           192           3907           4650          20936
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 1142

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

OK DOIs

- 10.1109/tmi.2021.3075856 is OK
- 10.1007/978-3-030-59713-9_7 is OK
- 10.1016/j.media.2019.01.005 is OK
- 10.1109/tmi.2018.2799231 is OK
- 10.1002/mrm.27201 is OK
- 10.1109/cvpr46437.2021.00523 is OK
- 10.1088/0031-9155/52/7/r01 is OK
- 10.1109/TIT.2006.871582 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

@estenhl
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estenhl commented Mar 29, 2022

Review checklist for @estenhl

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/NKI-AI/direct?
  • 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 (@georgeyiasemis) 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

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 and who the target audience is?
  • 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?

@sairamgeethanath
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@georgeyiasemis - Could you please let me know if there is a way for me to access the Docker image?

Screen Shot 2022-04-02 at 7 51 35 AM

@georgeyiasemis
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@sairamgeethanath
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@georgeyiasemis Many thanks! If it is not any trouble, could you also please fix the broken link on your documentation page?

@estenhl
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estenhl commented Apr 14, 2022

@editorialbot commands

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Hello @estenhl, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Get a link to the complete list of reviewers
@editorialbot list reviewers

@osorensen
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Thanks for completing your review checklist @estenhl!
@sairamgeethanath, could you please update us on how it is going with your review? Please let me know if there is anything I can help with.

@sairamgeethanath
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@osorensen I will get this done the week after ISMRM (13th May).

@osorensen
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Thanks @sairamgeethanath!

@sairamgeethanath
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sairamgeethanath commented May 13, 2022

Review checklist for @sairamgeethanath

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/NKI-AI/direct?
  • 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 (@georgeyiasemis) 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

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 and who the target audience is?
  • 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?

@sairamgeethanath
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sairamgeethanath commented May 13, 2022

@georgeyiasemis Great job on the package! I thoroughly enjoyed playing with it for a while. However, I could not get your docker to work.Can you please close the Docker issue that @estenhl and I both reported? I will then check off the remaining items.

@georgeyiasemis
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@georgeyiasemis Great job on the package! I thoroughly enjoyed playing with it for a while. However, I could not get your docker to work.Can you please close the Docker issue that @estenhl and I both reported? I will then check off the remaining items.

Thanks a lot @sairamgeethanath 👍 ! Yes we will do that!

@georgeyiasemis
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@georgeyiasemis Great job on the package! I thoroughly enjoyed playing with it for a while. However, I could not get your docker to work.Can you please close the Docker issue that @estenhl and I both reported? I will then check off the remaining items.

@sairamgeethanath The docker issue is fixed!

@sairamgeethanath
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sairamgeethanath commented May 16, 2022 via email

@sairamgeethanath
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@georgeyiasemis I have checked off my list.

@sairamgeethanath
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sairamgeethanath commented May 25, 2022

Review checklist for @sairamgeethanath

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/NKI-AI/direct?
  • 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 (@georgeyiasemis) 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

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 and who the target audience is?
  • 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?

@osorensen
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@editorialbot generate pdf

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

@osorensen
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@georgeyiasemis, the reviewers have now completed their checklists. I will now read through the paper, and get back to you if I have any suggested changes.

In the meantime, 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.

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@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

Check final proof 👉 openjournals/joss-papers#3241

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3241, 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 30, 2022
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Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1117/12.2609876 is OK
- 10.1109/tmi.2021.3075856 is OK
- 10.1007/978-3-030-59713-9_7 is OK
- 10.1016/j.media.2019.01.005 is OK
- 10.1109/tmi.2018.2799231 is OK
- 10.1002/mrm.27201 is OK
- 10.1109/cvpr46437.2021.00523 is OK
- 10.1088/0031-9155/52/7/r01 is OK
- 10.1109/TIT.2006.871582 is OK
- 10.1002/mrm.21391 is OK
- 10.1109/TIT.2005.862083 is OK
- 10.1002/mrm.10171 is OK
- 10.1002/(sici)1522-2594(199911)42:5<952::aid-mrm16>3.0.co;2-s is OK
- 10.1109/msp.2019.2950640 is OK
- 10.48550/ARXIV.2109.08618 is OK

MISSING DOIs

- Errored finding suggestions for "Multi-Coil MRI Reconstruction Challenge – Assessin...", please try later
- Errored finding suggestions for "i-RIM applied to the fastMRI challenge", please try later
- Errored finding suggestions for "fastMRI: An Open Dataset and Benchmarks for Accele...", please try later
- Errored finding suggestions for "Recurrent Variational Network: A Deep Learning Inv...", please try later

INVALID DOIs

- None

@georgeyiasemis
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@editorialbot check references

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

OK DOIs

- 10.1117/12.2609876 is OK
- 10.1109/tmi.2021.3075856 is OK
- 10.48550/ARXIV.2011.07952 is OK
- 10.48550/ARXIV.1910.08952 is OK
- 10.1007/978-3-030-59713-9_7 is OK
- 10.1016/j.media.2019.01.005 is OK
- 10.1109/tmi.2018.2799231 is OK
- 10.1002/mrm.27201 is OK
- 10.1109/cvpr46437.2021.00523 is OK
- 10.48550/ARXIV.1811.08839 is OK
- 10.48550/ARXIV.2111.09639 is OK
- 10.1088/0031-9155/52/7/r01 is OK
- 10.1109/TIT.2006.871582 is OK
- 10.1002/mrm.21391 is OK
- 10.1109/TIT.2005.862083 is OK
- 10.1002/mrm.10171 is OK
- 10.1002/(sici)1522-2594(199911)42:5<952::aid-mrm16>3.0.co;2-s is OK
- 10.1109/msp.2019.2950640 is OK
- 10.48550/ARXIV.2109.08618 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@georgeyiasemis
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@editorialbot generate pdf

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

@danielskatz
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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

- 10.1117/12.2609876 is OK
- 10.1109/tmi.2021.3075856 is OK
- 10.48550/ARXIV.2011.07952 is OK
- 10.48550/ARXIV.1910.08952 is OK
- 10.1007/978-3-030-59713-9_7 is OK
- 10.1016/j.media.2019.01.005 is OK
- 10.1109/tmi.2018.2799231 is OK
- 10.1002/mrm.27201 is OK
- 10.1109/cvpr46437.2021.00523 is OK
- 10.48550/ARXIV.1811.08839 is OK
- 10.48550/ARXIV.2111.09639 is OK
- 10.1088/0031-9155/52/7/r01 is OK
- 10.1109/TIT.2006.871582 is OK
- 10.1002/mrm.21391 is OK
- 10.1109/TIT.2005.862083 is OK
- 10.1002/mrm.10171 is OK
- 10.1002/(sici)1522-2594(199911)42:5<952::aid-mrm16>3.0.co;2-s is OK
- 10.1109/msp.2019.2950640 is OK
- 10.48550/ARXIV.2109.08618 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

Check final proof 👉 openjournals/joss-papers#3244

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3244, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@danielskatz
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👋 @georgeyiasemis - I'm the AEiC on duty this week, and I have a few small changes for the paper before we publish it. Please merge NKI-AI/direct#206 or let me know what you disagree with.

@georgeyiasemis
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👋 @georgeyiasemis - I'm the AEiC on duty this week, and I have a few small changes for the paper before we publish it. Please merge NKI-AI/direct#206 or let me know what you disagree with.

Hi @danielskatz. Thanks for that. Merged it !

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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

- 10.1117/12.2609876 is OK
- 10.1109/tmi.2021.3075856 is OK
- 10.48550/ARXIV.2011.07952 is OK
- 10.48550/ARXIV.1910.08952 is OK
- 10.1007/978-3-030-59713-9_7 is OK
- 10.1016/j.media.2019.01.005 is OK
- 10.1109/tmi.2018.2799231 is OK
- 10.1002/mrm.27201 is OK
- 10.1109/cvpr46437.2021.00523 is OK
- 10.48550/ARXIV.1811.08839 is OK
- 10.48550/ARXIV.2111.09639 is OK
- 10.1088/0031-9155/52/7/r01 is OK
- 10.1109/TIT.2006.871582 is OK
- 10.1002/mrm.21391 is OK
- 10.1109/TIT.2005.862083 is OK
- 10.1002/mrm.10171 is OK
- 10.1002/(sici)1522-2594(199911)42:5<952::aid-mrm16>3.0.co;2-s is OK
- 10.1109/msp.2019.2950640 is OK
- 10.48550/ARXIV.2109.08618 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

Check final proof 👉 openjournals/joss-papers#3247

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3247, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

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@editorialbot accept

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

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🐦🐦🐦 👉 Tweet 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.04278 joss-papers#3248
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04278
  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 30, 2022
@danielskatz
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Congratulations to @georgeyiasemis (George Yiasemis) and co-authors!!

And thanks to @estenhl and @sairamgeethanath for reviewing, and @osorensen for editing!
We couldn't do this without you

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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.04278/status.svg)](https://doi.org/10.21105/joss.04278)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04278">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04278/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04278/status.svg
   :target: https://doi.org/10.21105/joss.04278

This is how it will look in your documentation:

DOI

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