[REVIEW]: Viash: A meta-framework for building reusable workflow modules

[editorialbot]

Submitting author: @rcannood (Robrecht Cannoodt)
Repository: https://github.com/viash-io/viash
Branch with paper.md (empty if default branch): paper
Version: 0.8.4
Editor: @danielskatz
Reviewers: @wilkinson, @abhishektiwari, @mberacochea
Archive: 10.5281/zenodo.10563479

Status

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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

@wilkinson & @abhishektiwari & @mberacochea, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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@editorialbot generate my checklist

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✨ 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 @mberacochea

📝 Checklist for @wilkinson

[editorialbot]

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Software report:

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-------------------------------------------------------------------------------
Language                     files          blank        comment           code
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SVG                              4              0              0          11803
Markdown                         7           1033              0           2310
YAML                            44             33             19           1444
Bourne Shell                    46            273            219           1392
Python                           8             52             19            144
JavaScript                       1              9              4             65
TeX                              1             11              0             43
R                                1              8             14             40
JSON                             1              1              0             20
Dockerfile                       1              6              7             18
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-------------------------------------------------------------------------------
SUM:                           311           4874           3860          35641
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1872

[editorialbot]

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

OK DOIs

- 10.1093/bioinformatics/bts480 is OK
- 10.1038/s41592-019-0654-x is OK
- 10.1038/s41576-023-00586-w is OK
- 10.15252/msb.20188746 is OK
- 10.1038/s41587-020-0439-x is OK
- 10.1038/nbt.3820 is OK
- 10.5281/ZENODO.4638196 is OK
- 10.5281/ZENODO.4735634 is OK
- 10.1371/journal.pone.0177459 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[danielskatz]

👋 @wilkinson, @abhishektiwari, and @mberacochea - Thanks for agreeing to review this submission.
This is the review thread for the paper. All of our communications will happen here from now on.

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

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

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#6089 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if either of you require some more time. We can also use editorialbot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

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

[abhishektiwari]

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

• 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/viash-io/viash?
• 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 (@rcannood) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[danielskatz]

👋 @wilkinson and @mberacochea - I would appreciate it if you could use the command @editorialbot generate my checklist to create your review checklist, and then check off the CoI and CoC items, to make everything works. @editorialbot commands need to be the first thing in a new comment.

[mberacochea]

Review checklist for @mberacochea

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/viash-io/viash?
• 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 (@rcannood) 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]

@rcannood Please see my initial feedback.

Documentation

Community Guidelines

Please add community guidelines. I also think project will benefit from issue and pull request templates.

Paper

Title

For consistency, I would suggest paper headline to use data pipeline modules and not workflow modules. Everywhere else in the paper and documentation website authors reference Viash as solution for modular data pipelines. Having said that data pipelines are a special type of workflows with major focus on ETL, data cleaning, integration, and preparation for analysis or visualization, so I am also fine using workflow.

State of the field

Current state of the field can be further improved. Given the focus on Bioinformatics related computation/data pipeline frameworks, Viash, and it's counterparts Nextflow, Snakemake, CWL belong to Pipeline as code category. Please consider including Toil in the list as it supports script based pipeline definitions but also supports CWL and WDL. Plus there is other category of frameworks such as Galaxy and KNIME Workbench used by bioinformatics community those rely on UI based drag-n-drop pipeline builders – something worth mentioning here. Similarly, more generic Pipeline as code frameworks such Apache Airflow and Luigi can use standalone executable generated by Viash and used by bioinformatics community.

Suggested improvements (non-blocking)

Given the Viash has broader applicability beyond Bioinformatics particularly MLOps Pipelines, I suggest adding starter using other more generic frameworks such Airflow. In case of Apache Airflow, Airflow BashOperator will works just fine with standalone executable generated by Viash.

Overall comments

I applaud the author's for providing a very frictionless experience. Both Guide and Reference are well documented. I was able to finish everything from installation to functional testing to example in less than an hour. I really liked the use of GitHub template to create a quickstarter. Furthermore, I was able to add new modules on top of existing quickstarter very quickly and run end-to-end pipeline. Finally, it was great to see that authors provided guidance on IDE setup and testing of modules created using Viash.

[wilkinson]

Review checklist for @wilkinson

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/viash-io/viash?
• 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 (@rcannood) 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]

@danielskatz mostly done with my review. Just waiting for @rcannood response on state of field and title before I can mark this review completed from my side.

[danielskatz]

This comment is almost the same as a previous one that I've deleted, but fixes an error I made in tagging.

👋 @wilkinson, @abhishektiwari, @mberacochea, @rcannood - I'm just checking in post-holidays on how this is going.

It looks like @abhishektiwari provided some comments, but I'm unsure if @rcannood has acted on them.

And that @wilkinson and @mberacochea have started reviews, but I'm unsure if there's anything blocking them from making further progress.

Any feedback on status is welcome

[mberacochea]

@rcannood Please see my feedback.

General Comments

The paper is well-written and clearly explains the purpose and functionality of Viash. The authors provide detailed instructions on using the tool to describe modules with it. It is impressive in both the scope and the way it handles the whole process of pipeline writing, from initial module creation to fully functional pipelines using Nextflow.

Documentation

The documentation provided is comprehensive and allowed me to successfully follow the tutorial to create a fully operational pipeline. It consists of a practical tutorial and extensive usage guidelines, as well as documentation on the tool's API. I encountered one minor issue (viash-io/viash#617) which the authors promptly resolved.

Source Code

While I am not familiar with Scala, I was able to understand the high-level logic by reading through the codebase, it is well structured and contains explanatory comments on complex sections.

Generated Nextflow Code

The Nextflow code generated by Viash differs from the canonical style users may be accustomed to in other pipelines. This is not a flaw, but worth noting as it may cause initial confusion. Even though the produced modules are not meant to be modified, the ability to read and modify the code improves the developer experience, specially for the workflow developers. The paper could explore this a bit, as it’s mainly focus on modules and not so much on workflow development.

One question I have - could the custom Nextflow helper methods in Viash be abstracted/pushed into a Nextflow plugin or some kind of library? This question shouldn’t be considered a blocker for this PR.

State of the field

My impression is that Viash provides functionality comparable to nf-core/nf-tools or Snakemake Wrappers, though their approaches are different. Specially around the re-usable modules or components to build pipelines. Nf-core uses a different paradigm but it shares some of concepts with Viash. Explicitly contrasting nf-core/nf-tools - Snakemake Wrappers and Viash would benefit potenial users. The authors may also want to briefly mention OpenPipelines as a repository of Viash modules.

Paper

Applications in Bioinformatics

I don't think Viash is restricted solely to single cell analysis. Based on the underlying technologies, it seems widely applicable in bioinformatics (at least in omics).

In Figure 3, Tables B and C appear inadvertently merged. The authors may want to separate them for clarity

[danielskatz]

👋 @rcannood - there are now two reviewers with comments for you to respond to.

[rcannood]

Thanks @abhishektiwari @mberacochea for your reviews! I'm currently sorting through my post-holiday workload and will go through your valuable feedback ASAP!

[rcannood]

Hey all! I went through the comments I received so far and tried to address each of the reviewers' concerns. Please let me know if you have any further feedback.

@abhishektiwari's comments

Community Guidelines

Please add viash-io/viash#598. I also think project will benefit from issue and pull request templates.

Done, done, and done! Thanks for the suggestion!

Title consistency

For consistency, I would suggest paper headline to use data pipeline modules and not workflow modules. Everywhere else in the paper and documentation website authors reference Viash as solution for modular data pipelines. Having said that data pipelines are a special type of workflows with major focus on ETL, data cleaning, integration, and preparation for analysis or visualization, so I am also fine using workflow.

Good point! For the sake of consistency, I ended up replacing all instances of "pipeline" with "workflow" in viash-io/viash@5029fe0

State of the field

Current state of the field can be further improved. Given the focus on Bioinformatics related computation/data pipeline frameworks, Viash, and it's counterparts Nextflow, Snakemake, CWL belong to Pipeline as code category. Please consider including Toil in the list as it supports script based pipeline definitions but also supports CWL and WDL. Plus there is other category of frameworks such as Galaxy and KNIME Workbench used by bioinformatics community those rely on UI based drag-n-drop pipeline builders – something worth mentioning here. Similarly, more generic Pipeline as code frameworks such Apache Airflow and Luigi can use standalone executable generated by Viash and used by bioinformatics community.

Thanks for this suggestion! I completely rewrote the state of the field in viash-io/viash@6a21f69 . Rather than only compare Viash to Snakemake, Nextflow, CWL and WDL, I instead compare Viash to workflow managers and portability solutions. Based on https://doi.org/10.1038/s41592-021-01254-9, we then discuss the different types of workflow managers (graphical, programmatic, specification-based) and portability solutions (package manager, containerization).

Suggested improvements (non-blocking)

Given the Viash has broader applicability beyond Bioinformatics particularly MLOps Pipelines, I suggest adding starter using other more generic frameworks such Airflow. In case of Apache Airflow, Airflow BashOperator will works just fine with standalone executable generated by Viash.

Thanks for your suggestion, we will definitely take this into account when extending our documentation with different workflow frameworks!

@mberacochea's comments

Generated Nextflow Code

One question I have - could the custom Nextflow helper methods in Viash be abstracted/pushed into a Nextflow plugin or some kind of library? This question shouldn’t be considered a blocker for this PR.

I would really like that! The latest release of Viash already split up the helper functions into separate helper files per function so we can unit test them separately. I would like some of this functionality to be included in a Groovy library so we don't need to include it in every Nextflow module that is generated.

State of the field

My impression is that Viash provides functionality comparable to nf-core/nf-tools or Snakemake Wrappers, though their approaches are different. Specially around the re-usable modules or components to build pipelines. Nf-core uses a different paradigm but it shares some of concepts with Viash. Explicitly contrasting nf-core/nf-tools - Snakemake Wrappers and Viash would benefit potenial users. The authors may also want to briefly mention OpenPipelines as a repository of Viash modules.

Thanks for making the connection with nf-core tools (I think you mean nf-core/modules instead?), Snakemake wrappers and OpenPipelines. I did not include references to these projects in the paper as I felt that creating a repository with reusable commonly used bioinformatics tools goes way beyond the scope of this manuscript.

Applications in bioinformatics

I don't think Viash is restricted solely to single cell analysis. Based on the underlying technologies, it seems widely applicable in bioinformatics (at least in omics).

Good point. I dropped the word "single-cell" in viash-io/viash@874169a

Paper figures

In Figure 3, Tables B and C appear inadvertently merged. The authors may want to separate them for clarity

Thanks, I fixed this in viash-io/viash@758db0f !

[rcannood]

@editorialbot generate pdf

[editorialbot]

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

[danielskatz]

👋 @abhishektiwari & @mberacochea - I look forward to hearing from you about @rcannood's changes

[danielskatz]

👋 @wilkinson - it looks like you are fairly close to done as well. Do the latest changes from @rcannood help you, and if not, what else do you need to complete your review?

[danielskatz]

@editorialbot set 10.5281/zenodo.10563479 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.10563479

[danielskatz]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1093/bioinformatics/bts480 is OK
- 10.1038/s41592-019-0654-x is OK
- 10.1038/s41576-023-00586-w is OK
- 10.15252/msb.20188746 is OK
- 10.1038/s41587-020-0439-x is OK
- 10.1038/nbt.3820 is OK
- 10.5281/ZENODO.4638196 is OK
- 10.1038/s41592-021-01254-9 is OK
- 10.1186/gb-2010-11-8-r86 is OK
- 10.1016/j.jbiotec.2017.07.028 is OK
- 10.5281/ZENODO.4735634 is OK
- 10.1145/3486897 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4947, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

@editorialbot accept

[editorialbot]

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

[editorialbot]

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

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cff-version: "1.2.0"
authors:
- email: robrecht@data-intuitive.com
  family-names: Cannoodt
  given-names: Robrecht
  orcid: "https://orcid.org/0000-0003-3641-729X"
- family-names: Cannoodt
  given-names: Hendrik
  orcid: "https://orcid.org/0000-0002-0032-6719"
- family-names: Schaumont
  given-names: Dries
  orcid: "https://orcid.org/0000-0002-4389-0440"
- family-names: Waldrant
  given-names: Kai
  orcid: "https://orcid.org/0009-0003-8555-1361"
- family-names: Kerckhove
  given-names: Eric Van
  name-particle: de
- family-names: Boschmans
  given-names: Andy
  orcid: "https://orcid.org/0009-0008-8793-4661"
- family-names: Maeyer
  given-names: Dries De
  orcid: "https://orcid.org/0000-0002-1314-3348"
- email: toni@data-intuitive.com
  family-names: Verbeiren
  given-names: Toni
  orcid: "https://orcid.org/0000-0002-7007-6866"
contact:
- email: robrecht@data-intuitive.com
  family-names: Cannoodt
  given-names: Robrecht
  orcid: "https://orcid.org/0000-0003-3641-729X"
- email: toni@data-intuitive.com
  family-names: Verbeiren
  given-names: Toni
  orcid: "https://orcid.org/0000-0002-7007-6866"
doi: 10.5281/zenodo.10563479
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - email: robrecht@data-intuitive.com
    family-names: Cannoodt
    given-names: Robrecht
    orcid: "https://orcid.org/0000-0003-3641-729X"
  - family-names: Cannoodt
    given-names: Hendrik
    orcid: "https://orcid.org/0000-0002-0032-6719"
  - family-names: Schaumont
    given-names: Dries
    orcid: "https://orcid.org/0000-0002-4389-0440"
  - family-names: Waldrant
    given-names: Kai
    orcid: "https://orcid.org/0009-0003-8555-1361"
  - family-names: Kerckhove
    given-names: Eric Van
    name-particle: de
  - family-names: Boschmans
    given-names: Andy
    orcid: "https://orcid.org/0009-0008-8793-4661"
  - family-names: Maeyer
    given-names: Dries De
    orcid: "https://orcid.org/0000-0002-1314-3348"
  - email: toni@data-intuitive.com
    family-names: Verbeiren
    given-names: Toni
    orcid: "https://orcid.org/0000-0002-7007-6866"
  date-published: 2024-01-24
  doi: 10.21105/joss.06089
  issn: 2475-9066
  issue: 93
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6089
  title: "Viash: A meta-framework for building reusable workflow
    modules"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06089"
  volume: 9
title: "Viash: A meta-framework for building reusable workflow modules"

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06089 joss-papers#4948
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06089
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[danielskatz]

Congratulations to @rcannood (Robrecht Cannoodt) and co-authors on your publication!!

And thanks to @wilkinson, @abhishektiwari, and @mberacochea for reviewing!
JOSS depends on volunteers and we couldn't do this without you

[editorialbot]

🎉🎉🎉 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.06089/status.svg)](https://doi.org/10.21105/joss.06089)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06089">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06089/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06089/status.svg
   :target: https://doi.org/10.21105/joss.06089

This is how it will look in your documentation:

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[rcannood]

A big thank you to @abhishektiwari @mberacochea @wilkinson and @danielskatz ! 🙇 🙇 🙇 🙇

I see the names of Eric and Dries are split up incorrectly. Should I create a PR to amend openjournals/joss-papers#4948?

[danielskatz]

Yes, please do

[rcannood]

Hi @danielskatz ! I created openjournals/joss-papers#4949 . Is there somebody I could ask to take a look at this PR? 🙇 Thanks!

[danielskatz]

@rcannood - The files you are trying to change in your PR are automatically generated by JOSS. So please delete this PR, and instead, make changes in your paper source. See https://joss.readthedocs.io/en/latest/submitting.html#names in the JOSS documentation for how to do this.

Let me know when this is done, and I'll redo the generation, so we can check the xml and jats files, then when we are happy, I'll republish those versions.

[rcannood]

Hi @danielskatz! Thanks for your help! I had missed your reply until Arfon pointed it out to me.

I made the necessary changes to the author names in the paper branch at viash-io/viash. Would you be able to regenerate the XML and Jats files?

Thanks you so much for your time! 🙇

[danielskatz]

@editorialbot re-accept

[editorialbot]

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

@editorialbot commands

[danielskatz]

@editorialbot reaccept

[editorialbot]

Rebuilding paper!

[editorialbot]

🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#5004

[danielskatz]

@rcannood - I hope this has fixed the problem - it looks like it did to me.

[rcannood]

Yes -- thank you so much @danielskatz !