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[REVIEW]: Contextualized: Heterogeneous Modeling Toolbox #6469

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editorialbot opened this issue Mar 12, 2024 · 82 comments
Closed

[REVIEW]: Contextualized: Heterogeneous Modeling Toolbox #6469

editorialbot opened this issue Mar 12, 2024 · 82 comments
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accepted HTML 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 Mar 12, 2024

Submitting author: @cnellington (Caleb Ellington)
Repository: https://github.com/cnellington/Contextualized
Branch with paper.md (empty if default branch): joss
Version: v0.2.8
Editor: @fabian-s
Reviewers: @holl-, @pescap
Archive: 10.5281/zenodo.11130703

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/eff44b075cc108df6151e5123975115f"><img src="https://joss.theoj.org/papers/eff44b075cc108df6151e5123975115f/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/eff44b075cc108df6151e5123975115f/status.svg)](https://joss.theoj.org/papers/eff44b075cc108df6151e5123975115f)

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

@holl- & @pescap, 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 @fabian-s 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 @holl-

📝 Checklist for @pescap

@editorialbot editorialbot added HTML 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 Mar 12, 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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Software report:

github.com/AlDanial/cloc v 1.90  T=0.12 s (680.9 files/s, 263179.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          44            903           1525           3951
Jupyter Notebook                16              0          22839           1264
CSS                              1             23             17            510
HTML                             1              7            110            348
Markdown                         7             60              0            196
TeX                              2             12              0            172
YAML                             5             18             33            121
CSV                              1              0              0            109
JavaScript                       1              9              2            109
TOML                             1              4              0             43
reStructuredText                 2             16             52              8
Bourne Shell                     2              0              0              4
SVG                              1              0              0              1
-------------------------------------------------------------------------------
SUM:                            84           1052          24578           6836
-------------------------------------------------------------------------------

Commit count by author:

   210	Caleb Ellington
   142	Ben Lengerich
    52	cnellington
    16	wtt102
     9	Andrea Rubbi
     5	juwayni lucman
     3	aaron10l
     2	PaulCCCCCCH
     1	Jannik Deuschel

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Paper file info:

📄 Wordcount for paper.md is 862

✅ The paper includes a Statement of need section

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License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

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

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

OK DOIs

- 10.48550/arXiv.2310.07918 is OK
- 10.48550/arXiv.2310.11340 is OK
- 10.1101/2023.12.01.569658 is OK
- 10.1016/j.jbi.2022.104086 is OK
- 10.1609/aaai.v34i03.5693 is OK

MISSING DOIs

- No DOI given, and none found for title: Varying-coefficient models
- No DOI given, and none found for title: Contextual Explanation Networks
- No DOI given, and none found for title: NOTMAD: Estimating Bayesian Networks with Sample-S...
- 10.1101/2020.06.25.20140053 may be a valid DOI for title: Discriminative Subtyping of Lung Cancers from Hist...
- No DOI given, and none found for title: Personalized Survival Prediction with Contextual E...

INVALID DOIs

- None

@fabian-s
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👋🏼 hi @cnellington @holl- @pescap -- this is the review thread for the paper. All of our communications will happen here from now on.

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

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#6469 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 (@fabian-s) if you have any questions/concerns.

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@cnellington: while we wait for the reviews, please take a look at the missing DOIs above and see what's what.

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@editorialbot generate pdf

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

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@editorialbot commands

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Hello @cnellington, 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

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

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

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

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

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

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

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@editorialbot check references

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

OK DOIs

- 10.1016/j.jbi.2022.104086 is OK
- 10.1609/aaai.v34i03.5693 is OK
- 10.48550/arXiv.2310.11340 is OK
- 10.1101/2023.12.01.569658 is OK
- 10.48550/arXiv.2111.01104 is OK
- 10.1111/j.2517-6161.1993.tb01939.x is OK
- 10.48550/arXiv.1705.10301 is OK
- 10.1101/2020.06.25.20140053 is OK
- 10.48550/arXiv.1801.09810 is OK
- 10.48550/arXiv.2310.07918 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@holl-
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holl- commented Mar 16, 2024

Review checklist for @holl-

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/cnellington/Contextualized?
  • 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 (@cnellington) 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?

@holl-
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holl- commented Mar 16, 2024

@cnellington From the GitHub statistics, Ben Lengerich @blengerich has contributed the most to the library, at least in terms of lines of code. Why isn't he first author? Also Eric Xing is not on the list of contributors on GitHub. Did he actually contribute to the software?

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cnellington commented Mar 16, 2024

@holl- I authored the majority of our core Python packages under contextualized/, but out codebase also contains many .ipynb files for our documentation, website, and tutorials built with jupyter-book. @blengerich, in addition to making many contributions to our code codebase, also spearheaded our website/documentation efforts, and also did a large amount of standardized style formatting with black on our codebase. The line count differences are mainly due to the differences in .ipynb and .py file types, a few reorganizations of large notebook files into new directories, and automated formatting of large swathes of the codebase.

Notebook inflation examples:

Style formatting inflation:

Eric P. Xing is my PhD advisor, and Manolis Kellis is @blengerich's postdoc advisor. While they have not made direct contributions to the code, they have been essential in supporting and directing the software development.

@holl-
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holl- commented Mar 16, 2024

@cnellington Okay, that's fine, then. 👍

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holl- commented Mar 16, 2024

@cnellington I have some comments for your easy demo notebook, see this issue

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holl- commented Mar 18, 2024

@cnellington Looking at your test setup, it seems that baselines/tests.py is not being run.
The following files have less than 85% coverage. Is there a good reason for this? Otherwise, could you add more tests?

Module statements missing coverage
contextualized\analysis\effects.py 206 190 8%
contextualized\analysis\embeddings.py 67 59 12%
contextualized\analysis\accuracy_split.py 39 33 15%
contextualized\baselines\networks.py 178 135 24%
contextualized\easy\ContextualizedNetworks.py 97 71 27%
contextualized\analysis\pvals.py 31 22 29%
contextualized\analysis\utils.py 6 3 50%
contextualized\dags\losses.py 32 14 56%
contextualized\easy\ContextualGAM.py 9 4 56%
contextualized\modules.py 105 43 59%
contextualized\dags\graph_utils.py 102 27 74%
contextualized\utils.py 22 5 77%
contextualized\dags\lightning_modules.py 152 27 82%

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holl- commented Mar 18, 2024

@cnellington Your paper is missing an overview of the State of the field. In the 'Statement of need', could you add more concrete motivation for using this library and relate it to existing software solutions (incl. appropriate references)?

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

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fabian-s commented May 8, 2024

@editorialbot set 10.5281/zenodo.11130703 as archive

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Done! archive is now 10.5281/zenodo.11130703

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fabian-s commented May 8, 2024

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

  • Double check authors and affiliations (including ORCIDs)
  • Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
  • Archive the release on Zenodo/figshare/etc and post the DOI here.
  • Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
  • Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

  • Read the text of the paper and offer comments/corrections (as either a list or a pull request)
  • Check that the archive title, author list, version tag, and the license are correct
  • Set archive DOI with @editorialbot set <DOI here> as archive
  • Set version with @editorialbot set <version here> as version
  • Double check rendering of paper with @editorialbot generate pdf
  • Specifically check the references with @editorialbot check references and ask author(s) to update as needed
  • Recommend acceptance with @editorialbot recommend-accept

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fabian-s commented May 8, 2024

@editorialbot set v0.2.8 as version

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Done! version is now v0.2.8

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fabian-s commented May 8, 2024

@editorialbot generate pdf

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fabian-s commented May 8, 2024

@editorialbot check references

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

OK DOIs

- 10.1016/j.jbi.2022.104086 is OK
- 10.1609/aaai.v34i03.5693 is OK
- 10.48550/arXiv.2310.11340 is OK
- 10.1101/2023.12.01.569658 is OK
- 10.48550/arXiv.2111.01104 is OK
- 10.1111/j.2517-6161.1993.tb01939.x is OK
- 10.48550/arXiv.1705.10301 is OK
- 10.1101/2020.06.25.20140053 is OK
- 10.48550/arXiv.1801.09810 is OK
- 10.48550/arXiv.2310.07918 is OK
- 10.1214/aos/1017939139 is OK
- 10.1016/j.isci.2019.03.021 is OK
- 10.1080/01621459.2021.2000866 is OK
- 10.1093/bioinformatics/btr239 is OK
- 10.1214/09-AOAS308 is OK
- 10.1198/106186008X319331 is OK

MISSING DOIs

- No DOI given, and none found for title: partykit: A Modular Toolkit for Recursive Partytio...

INVALID DOIs

- None

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

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fabian-s commented May 8, 2024

@editorialbot recommend-accept

re missing DOI for "partykit":
this is a JMLR publication that does not have a DOI

many thanks again to @holl- and @pescap for their reviews and congrats to @cnellington and coauthors!

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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.jbi.2022.104086 is OK
- 10.1609/aaai.v34i03.5693 is OK
- 10.48550/arXiv.2310.11340 is OK
- 10.1101/2023.12.01.569658 is OK
- 10.48550/arXiv.2111.01104 is OK
- 10.1111/j.2517-6161.1993.tb01939.x is OK
- 10.48550/arXiv.1705.10301 is OK
- 10.1101/2020.06.25.20140053 is OK
- 10.48550/arXiv.1801.09810 is OK
- 10.48550/arXiv.2310.07918 is OK
- 10.1214/aos/1017939139 is OK
- 10.1016/j.isci.2019.03.021 is OK
- 10.1080/01621459.2021.2000866 is OK
- 10.1093/bioinformatics/btr239 is OK
- 10.1214/09-AOAS308 is OK
- 10.1198/106186008X319331 is OK

MISSING DOIs

- No DOI given, and none found for title: partykit: A Modular Toolkit for Recursive Partytio...

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#5319, 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 8, 2024
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fabian-s commented May 8, 2024

@editorialbot recommend-accept

re missing DOI for "partykit": this is a JMLR publication that does not have a DOI

many thanks again to @holl- and @pescap for their reviews and congrats to @cnellington and coauthors!

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crvernon commented May 8, 2024

👋 I am the AEiC for the Data Science, Artificial Intelligence, and Machine Learning (DSAIS) track of JOSS submissions. This is a very clean submission and made my job easy in this case! Thank you! I am pushing this through to publication.

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crvernon commented May 8, 2024

@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: Ellington
  given-names: Caleb N.
  orcid: "https://orcid.org/0000-0001-7029-8023"
- family-names: Lengerich
  given-names: Benjamin J.
  orcid: "https://orcid.org/0000-0001-8690-9554"
- family-names: Lo
  given-names: Wesley
- family-names: Alvarez
  given-names: Aaron
- family-names: Rubbi
  given-names: Andrea
- family-names: Kellis
  given-names: Manolis
- family-names: Xing
  given-names: Eric P.
contact:
- family-names: Ellington
  given-names: Caleb N.
  orcid: "https://orcid.org/0000-0001-7029-8023"
- family-names: Lengerich
  given-names: Benjamin J.
  orcid: "https://orcid.org/0000-0001-8690-9554"
doi: 10.5281/zenodo.11130703
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Ellington
    given-names: Caleb N.
    orcid: "https://orcid.org/0000-0001-7029-8023"
  - family-names: Lengerich
    given-names: Benjamin J.
    orcid: "https://orcid.org/0000-0001-8690-9554"
  - family-names: Lo
    given-names: Wesley
  - family-names: Alvarez
    given-names: Aaron
  - family-names: Rubbi
    given-names: Andrea
  - family-names: Kellis
    given-names: Manolis
  - family-names: Xing
    given-names: Eric P.
  date-published: 2024-05-08
  doi: 10.21105/joss.06469
  issn: 2475-9066
  issue: 97
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6469
  title: "Contextualized: Heterogeneous Modeling Toolbox"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06469"
  volume: 9
title: "Contextualized: Heterogeneous Modeling Toolbox"

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.06469 joss-papers#5320
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06469
  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 8, 2024
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crvernon commented May 8, 2024

Congratulations on your new publication @cnellington! Many thanks to @fabian-s for an excellent job editing and @holl- and @pescap for your time, hard work, and expertise in reviewing!! JOSS wouldn't be able to function nor succeed without your efforts.

@crvernon crvernon closed this as completed May 8, 2024
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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.06469/status.svg)](https://doi.org/10.21105/joss.06469)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06469">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06469/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06469/status.svg
   :target: https://doi.org/10.21105/joss.06469

This is how it will look in your documentation:

DOI

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