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[REVIEW]: FlexWing-ROM: A matlab framework for data-driven reduced-order modeling of flexible wings #4211

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editorialbot opened this issue Feb 28, 2022 · 79 comments
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accepted GLSL Matlab published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials

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editorialbot commented Feb 28, 2022

Submitting author: @urban-fasel (Urban Fasel)
Repository: https://github.com/urban-fasel/FlexWingROM
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @Kevin-Mattheus-Moerman
Reviewers: @omtazi, @Kevin-Mattheus-Moerman
Archive: 10.5281/zenodo.7419465

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/70cc0af28cda2015132999136ce38eee"><img src="https://joss.theoj.org/papers/70cc0af28cda2015132999136ce38eee/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/70cc0af28cda2015132999136ce38eee/status.svg)](https://joss.theoj.org/papers/70cc0af28cda2015132999136ce38eee)

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

@oriolcg & @omtazi, 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 @Kevin-Mattheus-Moerman 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 @omtazi

📝 Checklist for @Kevin-Mattheus-Moerman

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Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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=1.58 s (365.0 files/s, 92679.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
MATLAB                         520           7153          15352         106601
HTML                            37           1792           3627           9769
Markdown                         7            130              0            445
XSLT                             1             64             25            311
TeX                              1             30              0            277
GLSL                             2             15              7            155
XML                              5             12             28            118
CSS                              1             14              0             57
YAML                             1              0              0             11
-------------------------------------------------------------------------------
SUM:                           575           9210          19039         117744
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 1430

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

OK DOIs

- 10.1017/S0962492902000077 is OK
- 10.1146/annurev.fluid.37.061903.175743 is OK
- 10.1016/j.jcp.2017.02.027 is OK
- 10.2514/3.55530 is OK
- 10.1117/12.776137 is OK
- 10.1016/j.paerosci.2012.06.001 is OK
- 10.1017/jfm.2013.163 is OK
- 10.2514/1.J055193 is OK

MISSING DOIs

- 10.1088/1361-665x/aa7c87 may be a valid DOI for title: Aerostructural optimization of a morphing wing for airborne wind energy applications
- 10.2514/1.j059621 may be a valid DOI for title: Concurrent Design and Flight Mission Optimization of Morphing Airborne Wind Energy Wings
- 10.1098/rspa.2020.0079 may be a valid DOI for title: Data-driven nonlinear aeroelastic models of morphing wings for control
- 10.1002/rnc.3586 may be a valid DOI for title: A method to construct reduced-order parameter-varying models
- 10.1016/j.ast.2021.106821 may be a valid DOI for title: The balanced mode decomposition algorithm for data-driven LPV low-order models of aeroservoelastic systems
- 10.1145/800186.810616 may be a valid DOI for title: A two-dimensional interpolation function for irregularly-spaced data
- 10.2514/1.j052715 may be a valid DOI for title: Aero-structural optimization of three-dimensional adaptive wings with embedded smart actuators
- 10.2514/1.j058019 may be a valid DOI for title: Reduced-order dynamic model of a morphing airborne wind energy aircraft
- 10.1242/jeb.204.12.2073 may be a valid DOI for title: Shape, flapping and flexion: wing and fin design for forward flight
- 10.1038/35089071 may be a valid DOI for title: Spanwise flow and the attachment of the leading-edge vortex on insect wings
- 10.1126/science.1142281 may be a valid DOI for title: Bat flight generates complex aerodynamic tracks
- 10.2514/1.36694 may be a valid DOI for title: Aeromechanics of membrane wings with implications for animal flight

INVALID DOIs

- None

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

@Kevin-Mattheus-Moerman
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@oriolcg, @omtazi this is where the review takes place. Here are our review guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html.

Once you are ready you may post the following comment here (on its own, no other text): @editorialbot generate my checklist

This will create a checklist for you that will guide you through the process. In essence you will test the software and review the short paper and go through the checklist.

Please do not hesitate to contact me if you have any questions.

Thanks again for your help!

@omtazi
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omtazi commented Mar 7, 2022

Review checklist for @omtazi

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/urban-fasel/FlexWingROM?
  • 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 (@urban-fasel) 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?

@Kevin-Mattheus-Moerman
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@oriolcg thanks again for your help with this review. Let me know if you have any questions. Are you able to start the review process too? You can call @editorialbot generate my checklist to get a list like shown ☝️, this will guide you through the review process. Thanks!

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@oriolcg 👋 let me know if I can help.

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oriolcg commented Apr 9, 2022

Review checklist for @oriolcg

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/urban-fasel/FlexWingROM?
  • 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 (@urban-fasel) 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?

@oriolcg
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oriolcg commented Apr 9, 2022

@Kevin-Mattheus-Moerman, where do I post comments on the review? Directly to the repository?

@Kevin-Mattheus-Moerman
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@oriolcg apologies for the slow response. You can comment on small ish things here but if they are larger issues I recommend you open an issue on the project repository on that and then link to it here. Let me know if you have any other questions.

@Kevin-Mattheus-Moerman
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@oriolcg, @omtazi thanks again for your help here. Can you provide an update on review progress? Thanks.

@omtazi
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omtazi commented May 5, 2022

@oriolcg, @omtazi thanks again for your help here. Can you provide an update on review progress? Thanks.

Sorry for the late response, I've been a bit busy lately. I'm hoping to be done by next week on the review

@omtazi
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omtazi commented May 13, 2022

Hello @Kevin-Mattheus-Moerman @oriolcg , I'm having trouble running the example1 and example2 codes. I get the following message when I run example2_NACA6418_unsteadyFSI.m . Do you have this too ?

`Unable to resolve the name 'parallel.Settings'.

Error in Assembly/adjust_parallel_settings (line 26)
ps = parallel.Settings;

Error in Assembly/set.parallelized (line 22)
adjust_parallel_settings(self);

Error in Assembly (line 16)
self.parallelized = false;

Error in runYetAnotherFEcode (line 147)
PlateAssembly = Assembly(myMesh);

Error in generateWingModelStructure (line 1374)
[M,K,wP] = runYetAnotherFEcode(wingProperties, wingDesign);

Error in example2_NACA6418_unsteadyFSI (line 46)
wingModelStructure = generateWingModelStructure(wingDesign,simParam);`

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@urban-fasel can you help @omtazi to address this issue? ☝️

@urban-fasel
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Hi @Kevin-Mattheus-Moerman, yes! And sorry for not directly replying to the issue.

Hi @omtazi, the issue is related to the "yetAnotherFEcode" that we use to build the FE model of the wing. This package uses the "Parallel Computing Toolbox". If you install the toolbox, you should be able to run the code.

In case other toolboxes are missing, the required toolboxes for e.g. example2 can be found and printed in the command line like this:
[~,pList] = matlab.codetools.requiredFilesAndProducts('example2_NACA6418_unsteadyFSI.m');
{pList.Name}'

I hope this helps and please let me know if you still get the error message.

@Kevin-Mattheus-Moerman
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@omtazi can you test this approach ☝️

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@omtazi 👋

1 similar comment
@Kevin-Mattheus-Moerman
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@omtazi 👋

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oriolcg commented Jun 25, 2022

@urban-fasel , I get the following error when executing the code:

  Control System Toolbox
  DSP System Toolbox
  Model Predictive Control Toolbox
  Signal Processing Toolbox

Error in generate_gramian (line 19)
            sys = ss(A_aIODMDc,B_aIODMDc,C_aIODMDc,D_aIODMDc,0.006);

Error in Obtain_BMD_model (line 67)
    [W_o, W_c] = generate_gramian(Snapshot(:,:,k), Snapshot_input(:,:,k), V0, type_string_gram, loadGramians, rankMax, simInput);

Error in ROMsim (line 33)
        ROMs = Obtain_BMD_model(Snapshot, Snapshot_input, V0, type_string, rankROM.rankMaxBMD, simInput);

Error in ROM (line 119)
ROMsim(V0,rankROM,type_string,dT,iTest,simInput,simOutFULL);

Error in MAIN (line 187)
    ROM(paramFSI);

Please, state in the README the required toolbox that should be installed before executing

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oriolcg commented Jun 25, 2022

@editorialbot generate pdf

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

@Kevin-Mattheus-Moerman
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@omtazi @frederickgosselin can you please start the review process? Thanks

@Kevin-Mattheus-Moerman
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@oriolcg thanks again for your help here. I see you encountered a "missing toolboxes" type of error. Can you install those and proceed or is this an obstacle?

@urban-fasel please do add toolbox requirements to the README.

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@editorialbot generate pdf

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

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Kevin-Mattheus-Moerman commented Dec 9, 2022

@urban-fasel thanks for processing those changes. All looks good now. At this point the review is finished and both reviewers have recommended accept. Next, before we can proceed to formal acceptance, please can you work on the following:

  • Please archive a copy of the reviewed software on ZENODO and report back here with the DOI. You can archive a copy manually, but some find these automated steps useful.

Next ensure that the following ZENODO aspects are correct (you may need to manually edit these):

  • Ensure that the title matches that of the JOSS paper
  • Ensure that the author set and author order matches that of the JOSS paper
  • Ensure that the license listed is the same as for the reviewed software (the default is other(open) so check this).
  • We recommend that you add ORCID information for authors

Finally:

  • Please ensure that you have a tagged release on GitHub which is the same as the reviewed software and the same as the archived software on ZENODO.
  • Please report the release/version tag here. Currently the review here lists v1.0.0, please let me know if that is updated e.g. as part of the steps shown here. You can alter it as you wish as long as what we assign for this review (I can update it when you tell me to do so) matches a labelled release on your repository as well as the version shown on ZENODO.

Let me know if you have any questions.

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@Kevin-Mattheus-Moerman I archived a copy of the software to ZENODO. The DOI is 10.5281/zenodo.7419465. The tagged release is v1.0.0. Thanks again for your review!

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@editorialbot set 10.5281/zenodo.7419465 as archive

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Done! Archive is now 10.5281/zenodo.7419465

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@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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👋 @openjournals/bcm-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#3789, 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 Dec 11, 2022
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Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1017/S0962492902000077 is OK
- 10.1146/annurev.fluid.37.061903.175743 is OK
- 10.1016/j.jcp.2017.02.027 is OK
- 10.2514/3.55530 is OK
- 10.1117/12.776137 is OK
- 10.1016/j.paerosci.2012.06.001 is OK
- 10.1017/jfm.2013.163 is OK
- 10.2514/1.J055193 is OK

MISSING DOIs

- 10.1088/1361-665x/aa7c87 may be a valid DOI for title: Aerostructural optimization of a morphing wing for airborne wind energy applications
- 10.2514/1.j059621 may be a valid DOI for title: Concurrent Design and Flight Mission Optimization of Morphing Airborne Wind Energy Wings
- 10.1098/rspa.2020.0079 may be a valid DOI for title: Data-driven nonlinear aeroelastic models of morphing wings for control
- 10.1002/rnc.3586 may be a valid DOI for title: A method to construct reduced-order parameter-varying models
- 10.1016/j.ast.2021.106821 may be a valid DOI for title: The balanced mode decomposition algorithm for data-driven LPV low-order models of aeroservoelastic systems
- 10.1145/800186.810616 may be a valid DOI for title: A two-dimensional interpolation function for irregularly-spaced data
- 10.2514/1.j052715 may be a valid DOI for title: Aero-structural optimization of three-dimensional adaptive wings with embedded smart actuators
- 10.2514/1.j058019 may be a valid DOI for title: Reduced-order dynamic model of a morphing airborne wind energy aircraft
- 10.2514/1.j061518 may be a valid DOI for title: Data-driven unsteady aeroelastic modeling for control
- 10.1242/jeb.204.12.2073 may be a valid DOI for title: Shape, flapping and flexion: wing and fin design for forward flight
- 10.1038/35089071 may be a valid DOI for title: Spanwise flow and the attachment of the leading-edge vortex on insect wings
- 10.1126/science.1142281 may be a valid DOI for title: Bat flight generates complex aerodynamic tracks
- 10.2514/1.36694 may be a valid DOI for title: Aeromechanics of membrane wings with implications for animal flight

INVALID DOIs

- None

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@urban-fasel can you check those potentially missing DOI's? ☝️ You can call @editorialbot check references to check them

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@editorialbot check references

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

OK DOIs

- 10.1088/1361-665X/aa7c87 is OK
- 10.2514/1.J059621 is OK
- 10.1137/15M1013857 is OK
- 10.1098/rspa.2020.0079 is OK
- 10.1002/rnc.3586 is OK
- 10.1016/j.ast.2021.106821 is OK
- 10.5281/zenodo.4011282 is OK
- 10.1017/CBO9780511810329 is OK
- 10.1061/JMCEA3.0000098 is OK
- 10.2514/3.44330 is OK
- 10.1145/800186.810616 is OK
- 10.2514/1.J052715 is OK
- 10.2514/1.J058019 is OK
- 10.3929/ethz-b-000428849 is OK
- 10.1017/S0962492902000077 is OK
- 10.1146/annurev.fluid.37.061903.175743 is OK
- 10.1016/j.jcp.2017.02.027 is OK
- 10.2514/3.55530 is OK
- 10.1117/12.776137 is OK
- 10.1016/j.paerosci.2012.06.001 is OK
- 10.1017/jfm.2013.163 is OK
- 10.2514/1.J055193 is OK
- 10.2514/1.J061518 is OK
- 10.1242/jeb.204.12.2073 is OK
- 10.1038/35089071 is OK
- 10.1126/science.1142281 is OK
- 10.2514/1.36694 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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@Kevin-Mattheus-Moerman I just updated the bib file, all DOIs are ok now.

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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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🐘🐘🐘 👉 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.04211 joss-papers#3792
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04211
  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 Dec 12, 2022
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@openjournals/dev hmm the DOI does not resolve yet. Can you see what's wrong?

@danielskatz
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The DOI resolves for me, but the PDF is not available

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The PDF is now working for me too

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@danielskatz thanks. Yes it looks good now. I usually wait until the PDF is there too. It did take an awful lot longer than usual.

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@urban-fasel congratulations on this publication in JOSS!

@omtazi thank you for reviewing this work!

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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.04211/status.svg)](https://doi.org/10.21105/joss.04211)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04211">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04211/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04211/status.svg
   :target: https://doi.org/10.21105/joss.04211

This is how it will look in your documentation:

DOI

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