[REVIEW]: PyAutoGalaxy: Open-Source Multiwavelength Galaxy Structure & Morphology

[editorialbot]

Submitting author: @Jammy2211 (James Nightingale)
Repository: https://github.com/Jammy2211/PyAutoGalaxy
Branch with paper.md (empty if default branch):
Version: 2023.1.15.1
Editor: @christinahedges
Reviewers: @alexandergagliano, @sloneil
Archive: 10.5281/zenodo.7546915

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/ff0397c0c3837bc963e757f844f2a2b6/status.svg)](https://joss.theoj.org/papers/ff0397c0c3837bc963e757f844f2a2b6)

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

@alexandergagliano & @sloneil, 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 @christinahedges 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 @sloneil

📝 Checklist for @alexandergagliano

[editorialbot]

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

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.40 s (708.6 files/s, 148260.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         158           9355           7218          24116
JSON                            39              0              0          12603
TeX                              3             35              0           1370
reStructuredText                30           1036           1145           1217
INI                             49            109              0           1068
Markdown                         3             30              0            211
YAML                             3              8              3            108
-------------------------------------------------------------------------------
SUM:                           285          10573           8366          40693
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1685

[editorialbot]

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

OK DOIs

- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.3847/1538-4365/aaee8c is OK
- 10.21105/joss.00024 is OK
- 10.1093/mnras/staa278 is OK
- 10.1086/670067 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1145/2833157.2833162 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.21105/joss.02550 is OK
- 10.1111/j.1365-2966.2009.14548.x is OK
- 10.1051/0004-6361/201322971 is OK
- 10.3390/jimaging4030051 is OK
- 10.5281/zenodo.3936959 is OK
- 10.21105/joss.00433 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1016/j.physletb.2019.134871 is OK
- 10.1088/0004-637X/757/1/82 is OK
- 10.1088/0004-637X/811/1/20 is OK
- 10.1111/j.1365-2966.2011.19726.x is OK
- 10.1093/mnras/stu305 is OK
- 10.1093/mnras/sty021 is OK
- 10.1088/0004-637X/703/1/L51 is OK
- 10.1093/mnras/stu1316 is OK
- 10.1093/mnras/stu413 is OK
- 10.1093/mnras/stv1455 is OK
- 10.1093/mnras/sty1264 is OK
- 10.1093/mnras/stz2220 is OK
- 10.1088/0004-637X/800/2/94 is OK
- 10.1093/mnras/stx483 is OK
- 10.1088/0004-637X/690/1/670 is OK
- 10.1111/j.1365-2966.2008.14005.x is OK
- 10.1093/mnras/stu943 is OK
- 10.1088/0004-637X/800/1/18 is OK
- 10.1126/science.1185759 is OK
- 10.1093/mnras/stu1395 is OK
- 10.1093/mnras/staa2740 is OK
- 10.1016/j.dark.2018.11.002 is OK
- 10.3847/0004-637X/826/2/112 is OK
- 10.1093/mnras/sts633 is OK
- 10.1086/340952 is OK
- 10.1093/mnras/stw3039 is OK
- 10.1088/0004-637X/799/2/226 is OK
- 10.1088/0067-0049/203/2/24 is OK
- 10.1093/mnras/stu632 is OK
- 10.1007/978-3-319-19378-6_16 is OK
- 10.3847/1538-4357/836/1/115 is OK
- 10.1111/j.1365-2966.2012.20450.x is OK
- 10.1007/978-94-007-5609-0_2 is OK
- 10.1093/mnras/stx2707 is OK
- 10.1086/592836 is OK
- 10.1016/S0370-1573(02)00134-5 is OK
- 10.3847/1538-4357/ab1846 is OK
- 10.1016/j.physrep.2014.02.009 is OK
- 10.1086/143018 is OK
- 10.21105/joss.02825 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[christinahedges]

@Jammy2211, @alexandergagliano, @sloneil – This is the review thread for thePyAutoGalaxy paper. Please don't hesitate to message me here if you have questions (use @christinahedges). ✉️

Please read the "Reviewer instructions & questions" in the first comment above to get started. If you get lost, you can also see the reviewer guidelines. You will have to generate your review "checklist" by adding the comment @editorialbot generate my checklist to this thread.

To review for JOSS ,@alexandergagliano and @sloneil will step through that checklist for PyAutoGalaxy and assess the package. As you go over the submission, please check any items that you feel have been satisfied. If you are concerned about a requirement, please discuss it here on this thread 🧵 . Feel free to post about questions/concerns as they come up as you go through your review. Discussion between the authors/reviewers and myself is encouraged!

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 this issue (#4475) so that a link is created to this thread (and I can keep an eye on what is happening).

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule. When you're finished with your checklist, leave a comment and @ me to let everyone know your review is complete.

[christinahedges]

@alexandergagliano, @sloneil just checking in, please let me know if you have any issues with starting the review!

[christinahedges]

@alexandergagliano, @sloneil it seems like you haven't been able to start the review yet, and we kicked off the review close to 4 weeks ago. Can you check in and let us know how you're getting on?

[sloneil]

Review checklist for @sloneil

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/Jammy2211/PyAutoGalaxy?
• 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 (@Jammy2211) 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?
• welcome.py line 128: 'scritps' should be 'scripts'
• Functionality: Have the functional claims of the software been confirmed?
• InversionPlotter notebook and GalaxyPlotter notebook uses variable mask_2ded_grid_2d that is not defined. Should this be masked_grid2d?
• tutorial_7_scale_dataset, the line 'background_level = ag.preprocess.background_noise_map_via_edges_of_image_from(
  image=image, no_edges=2
  )[0]' has 'image' undefined. Should this be 'image_2d'?
• The chapter_4_pixelizations and chapter_4_inversions seem to have exactly the same notebooks in them. Are these intended to be different sets of tutorials?
• 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?
• mainly compares to how it expands and builds on previous softwares
• 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?

[alexandergagliano]

@christinahedges thanks for the check-in -- it's taken a little time to get this wrapped up but I'll be sure to finalize the checklist by the end of this week at the latest.

[alexandergagliano]

Review checklist for @alexandergagliano

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/Jammy2211/PyAutoGalaxy?
• 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 (@Jammy2211) 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?
• Issues open at #32, #33 and #35.
• The starting walkthrough at https://pyautogalaxy.readthedocs.io/en/latest/overview/overview_1_galaxies.html imports autogalaxy as al but then uses it as ag.
• In tutorial_5_fitting.ipynb, it looks like the plotted mask just contains pixels along an annulus and not all pixels outside of it to the edges of the image. Why is this?
• In tutorial_5_fitting.ipynb, Fitting (incorrect fit), if I change the center for the model light profile to something extreme like centre=(5., 3.), the resultant plots do not change. Slightly below this, the print("New Likelihood:") line should read print(fit_very_bad.log_likelihood) instead of print(fit.log_likelihood).
• "we assume the imaging data consists of independent Gaussian noise in every image pixel." Is this required? Would it be possible to include a non-uniform noise model in the fitting procedure? I could imagine this would be useful for considering the contributions of e.g., a massive neighboring galaxy off-image.
• How do you ensure convergence of the Dynesty runs?
• parametric_to_inversion.ipynb: result_1_list = search.fit(model=model, analysis=analysis) should be changed to result_1_list = search_1.fit(model=model, analysis=analysis).
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)
• No performance claims found.

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• The description of the code is great! The target audience is a little more unclear -- maybe a few science questions that would benefit the software could be given at https://pyautogalaxy.readthedocs.io/en/latest/index.html#?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Dependencies are listed here without versions -- are any version-specific?
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• The link in "An overview of PyAutoGalaxy’s core features can be found in the overview section of the readthedocs." is a broken link!
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Tutorial 5 is titled Tutorial 8 and Tutorial 6 is titled Tutorial 9.
• I really appreciate the thoroughness of the documentation, and the presentation of the core functionality in such a straightforward and pedagogical manner.
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Tests are provided and verified at #31.
• 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
• The readme contains information for reporting issues and seeking support but not contributing. This should be added.

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?
• Commentary on other packages not found.
• 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?
• Software references appear here but should be moved to the References header of the paper. I can't find any paper references.

[alexandergagliano]

@christinahedges My review is complete. There are some outstanding remaining comments about updating references and a statement on the state of the field, but none are major and it looks like the software comments have all been addressed.

[arfon]

👋 @Jammy2211 – how are you getting along making your updates based on the reviewer feedback?

[Jammy2211]

Got overwhemed with deadlines this month, things finally clear up this week so will get them sorted!

[Jammy2211]

I have respond to all comments and fixed them on the project master branches.

A pip release will follow in the next week or so, we are doing a big switch to automated build servers so trying not to rock the boat with a release until everything is fully tested.

[dfm]

@alexandergagliano, @sloneil, @Jammy2211 — Hi folks, I wanted to check in here because we're recently switched to a "tracks" model here at JOSS and I'm now the managing editor of the track where this submission has been assigned. It looks like there hasn't been much activity on this review in a while - can you update me on what the status is and if there are any blockers in place that I can help with? Thanks!

[alexandergagliano]

@dfm @Jammy2211 has addressed all my comments, I'm totally on board with this moving forward!

[sloneil]

It's fine with me as well!

[dfm]

@Jammy2211 — It looks like the only one that is actually used is the ISBN for the "Python Reference Manual" (a citation that I'd probably just remove…). While you're at it, can you also take a look at the Sersic (1968) reference too? It looks like it got mangled somewhere.

Otherwise, yes - I think it's fine to remove any other ISBN entries!

[Jammy2211]

Pushed fixes which I hope sorts everything now.

[dfm]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

The paper's PDF and metadata files generation produced some warnings that could prevent the final paper to be published. Please fix them before the end of the review process:

L_{\rm IR}\sim\sim\sim5\sim\times10^{12}
       ^
unexpected control sequence \rm
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

\sigma_{\rm r}\lesssim
            ^
unexpected control sequence \rm
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

\Sigma_{\rm SFR}
            ^
unexpected control sequence \rm
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

\Sigma_{\rm SFR}
            ^
unexpected control sequence \rm
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

[editorialbot]

👋 @openjournals/aass-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#3904, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[editorialbot]

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

OK DOIs

- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.3847/1538-4365/aaee8c is OK
- 10.21105/joss.00024 is OK
- 10.1093/mnras/staa278 is OK
- 10.1086/670067 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1145/2833157.2833162 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.21105/joss.02550 is OK
- 10.1111/j.1365-2966.2009.14548.x is OK
- 10.1051/0004-6361/201322971 is OK
- 10.3390/jimaging4030051 is OK
- 10.5281/zenodo.3936959 is OK
- 10.21105/joss.00433 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1016/j.physletb.2019.134871 is OK
- 10.1088/0004-637X/757/1/82 is OK
- 10.1088/0004-637X/811/1/20 is OK
- 10.1111/j.1365-2966.2011.19726.x is OK
- 10.1093/mnras/stu305 is OK
- 10.1093/mnras/sty021 is OK
- 10.1088/0004-637X/703/1/L51 is OK
- 10.1093/mnras/stu1316 is OK
- 10.1093/mnras/stu413 is OK
- 10.1093/mnras/stv1455 is OK
- 10.1093/mnras/sty1264 is OK
- 10.1093/mnras/stz2220 is OK
- 10.1088/0004-637X/800/2/94 is OK
- 10.1093/mnras/stx483 is OK
- 10.1088/0004-637X/690/1/670 is OK
- 10.1111/j.1365-2966.2008.14005.x is OK
- 10.1093/mnras/stu943 is OK
- 10.1088/0004-637X/800/1/18 is OK
- 10.1126/science.1185759 is OK
- 10.1093/mnras/stu1395 is OK
- 10.1093/mnras/staa2740 is OK
- 10.1016/j.dark.2018.11.002 is OK
- 10.3847/0004-637X/826/2/112 is OK
- 10.1093/mnras/sts633 is OK
- 10.1086/340952 is OK
- 10.1093/mnras/stw3039 is OK
- 10.1088/0004-637X/799/2/226 is OK
- 10.1088/0067-0049/203/2/24 is OK
- 10.1093/mnras/stu632 is OK
- 10.1007/978-3-319-19378-6_16 is OK
- 10.3847/1538-4357/836/1/115 is OK
- 10.1111/j.1365-2966.2012.20450.x is OK
- 10.1007/978-94-007-5609-0_2 is OK
- 10.1093/mnras/stx2707 is OK
- 10.1086/592836 is OK
- 10.1016/S0370-1573(02)00134-5 is OK
- 10.3847/1538-4357/ab1846 is OK
- 10.1016/j.physrep.2014.02.009 is OK
- 10.1086/143018 is OK
- 10.21105/joss.02825 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[Jammy2211]

PR merged and proofs look good to me!

[dfm]

@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

- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.3847/1538-4365/aaee8c is OK
- 10.21105/joss.00024 is OK
- 10.1093/mnras/staa278 is OK
- 10.1086/670067 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1145/2833157.2833162 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.21105/joss.02550 is OK
- 10.1111/j.1365-2966.2009.14548.x is OK
- 10.1051/0004-6361/201322971 is OK
- 10.3390/jimaging4030051 is OK
- 10.5281/zenodo.3936959 is OK
- 10.21105/joss.00433 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1016/j.physletb.2019.134871 is OK
- 10.1088/0004-637X/757/1/82 is OK
- 10.1088/0004-637X/811/1/20 is OK
- 10.1111/j.1365-2966.2011.19726.x is OK
- 10.1093/mnras/stu305 is OK
- 10.1093/mnras/sty021 is OK
- 10.1088/0004-637X/703/1/L51 is OK
- 10.1093/mnras/stu1316 is OK
- 10.1093/mnras/stu413 is OK
- 10.1093/mnras/stv1455 is OK
- 10.1093/mnras/sty1264 is OK
- 10.1093/mnras/stz2220 is OK
- 10.1088/0004-637X/800/2/94 is OK
- 10.1093/mnras/stx483 is OK
- 10.1088/0004-637X/690/1/670 is OK
- 10.1111/j.1365-2966.2008.14005.x is OK
- 10.1093/mnras/stu943 is OK
- 10.1088/0004-637X/800/1/18 is OK
- 10.1126/science.1185759 is OK
- 10.1093/mnras/stu1395 is OK
- 10.1093/mnras/staa2740 is OK
- 10.1016/j.dark.2018.11.002 is OK
- 10.3847/0004-637X/826/2/112 is OK
- 10.1093/mnras/sts633 is OK
- 10.1086/340952 is OK
- 10.1093/mnras/stw3039 is OK
- 10.1088/0004-637X/799/2/226 is OK
- 10.1088/0067-0049/203/2/24 is OK
- 10.1093/mnras/stu632 is OK
- 10.1007/978-3-319-19378-6_16 is OK
- 10.3847/1538-4357/836/1/115 is OK
- 10.1111/j.1365-2966.2012.20450.x is OK
- 10.1007/978-94-007-5609-0_2 is OK
- 10.1093/mnras/stx2707 is OK
- 10.1086/592836 is OK
- 10.1016/S0370-1573(02)00134-5 is OK
- 10.3847/1538-4357/ab1846 is OK
- 10.1016/j.physrep.2014.02.009 is OK
- 10.1086/143018 is OK
- 10.21105/joss.02825 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/aass-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#3912, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[dfm]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 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.04475 joss-papers#3913
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04475
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...

[dfm]

Many thanks to @alexandergagliano and @sloneil for reviewing and to @christinahedges for editing! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you!!

@Jammy2211 — Your paper is now accepted and published in JOSS! ⚡🚀💥

[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.04475/status.svg)](https://doi.org/10.21105/joss.04475)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04475">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04475/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04475/status.svg
   :target: https://doi.org/10.21105/joss.04475

This is how it will look in your documentation:

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