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[REVIEW]: Pooch: A friend to fetch your data files #1943

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whedon opened this issue Dec 11, 2019 · 52 comments
Closed
38 tasks done

[REVIEW]: Pooch: A friend to fetch your data files #1943

whedon opened this issue Dec 11, 2019 · 52 comments
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@whedon
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@whedon whedon commented Dec 11, 2019

Submitting author: @leouieda (Uieda, L)
Repository: https://github.com/fatiando/pooch
Version: v0.7.1
Editor: @danielskatz
Reviewer: @hmaarrfk, @martindurant
Archive: 10.5281/zenodo.3611376

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/8053e31d2cf8a83007fecbf7b6684e3b"><img src="https://joss.theoj.org/papers/8053e31d2cf8a83007fecbf7b6684e3b/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/8053e31d2cf8a83007fecbf7b6684e3b/status.svg)](https://joss.theoj.org/papers/8053e31d2cf8a83007fecbf7b6684e3b)

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

@hmaarrfk & @martindurant, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @danielskatz know.

Please try and complete your review in the next two weeks

Review checklist for @hmaarrfk

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 repository url?
  • 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 (@leouieda) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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?

Review checklist for @martindurant

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 repository url?
  • 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 (@leouieda) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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?
@whedon
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@whedon whedon commented Dec 11, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @hmaarrfk, @martindurant it looks like you're currently assigned to review this paper 🎉.

Important

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

@whedon
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@whedon whedon commented Dec 11, 2019

Attempting to check references...

@whedon
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@whedon whedon commented Dec 11, 2019

Attempting PDF compilation. Reticulating splines etc...

@whedon
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@whedon whedon commented Dec 11, 2019


OK DOIs

- 10.7717/peerj.453 is OK
- 10.5065/D6WW7G29 is OK
- 10.21105/joss.00957 is OK
- 10.5281/ZENODO.3086002 is OK
- 10.5281/ZENODO.3542092 is OK
- 10.5281/ZENODO.1450596 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@whedon
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@whedon whedon commented Dec 11, 2019

@danielskatz
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@danielskatz danielskatz commented Dec 11, 2019

👋 @hmaarrfk & @martindurant - here we are in the review thread

As I think you know you, your job now is go through the paper and repository and check off boxes in your checklist

Also please be sure to read the prior comments in this issue

@danielskatz
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@danielskatz danielskatz commented Dec 11, 2019

Also, thanks for agreeing to review!

@martindurant
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@martindurant martindurant commented Dec 11, 2019

What is the usual timeframe for this process?

@danielskatz
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@danielskatz danielskatz commented Dec 11, 2019

normally a couple of weeks for the initial passes is requested, but with the December holidays, a bit longer is fine

@martindurant
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@martindurant martindurant commented Jan 2, 2020

Note that the links are not clickable in the github-rendered version of the PDF, only in the download. This is doubtless not a fault of the authors.

I find that the paper does indeed convey that Pooch exists, is and says how and when it might be used. It completes the purpose, therefore, of submitting to JOSS. I am still disappointed by the comparison with the rest of the field and Intake in particular. Obviously, again, I am biased here and perhaps some of the points that follow have more to do with Intake's documentation than with Pooch's, and I do not insist on any changes. However:

  • the library fsspec contains local-file-cache implementations that could be seen as implementing what Pooch does, also by changing only a single line of code. I would argue that it is indeed more flexible, having many file-system backends and allowing for partial downloads of large files. It can also check the source for changes on backends that support checksum or at least write-date metadata, or general cache expiry.
  • Intake does not require you to rewrite any code at all in the simplest case such as the pandas example, but only change one line (pd.read_csv -> intake.open_csv; same arguments) with or without local caching
  • Intake does many other things too, such as read from sources which are not files, from remote servers and services; metadata and visualisation and data-source browsing. In this, I agree that Pooch does one job and does it well.
  • Indeed, Intake and Pooch should have integration points, and I think this is the biggest and saddest missing point. The Pooch registry (which files) and an Intake catalog (how to load which files) clearly have overlap. Pooch could be one way of obtaining files for Intake.
  • At the very least, Pooch may want to investigate fsspec and its backends, to enable downloading from a variety of file stores, not just HTTP/FTP. https://github.com/intake/filesystem_spec/blob/master/fsspec/registry.py#L12

@hmaarrfk
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@hmaarrfk hmaarrfk commented Jan 2, 2020

Looks good. I think a few numbers and facts can be given to accentuate the impact of the paper.

  • Scientific software is also used to "Capture" or "Acquire" data
  • "The usual" -> "One common approach" when talking about smaller datasets.
  • The sentence that describes the challenge with including datasets in the github repo should come before the "Larger datasets [...]" sentence.
  • HTTP -> HTTPS
  • You state that people are recreating the same code, but maybe give a few examples?

Paragraph 2:

  • It isn't clear what the registery holds: local file name, hash, remote file url should be clearly listed.
  • I "minimal dependencies" is the selling point to packagers. The selling point to users is that it is easily installable with standard python distributions PyPi and Conda, and a wide array of python versions (2.7, 3.5->3.8).

Paragraph 3:

  • the functionality to unzip files is understated and should be made more explicit. It probably deserves a paragraph of its own.

Paragraph 4:

  • You should elaborate on what exactly makes intake harder to setup. It seems like Pooch is "files only", while intake is "files + metadata" which is a larger hurdle to overcome.

Paragraph 5:

  • I think you can show off a little bit explaining the motivation in terms of install size this would have on scikit-image. The numbers are listed in the PR

@hmaarrfk
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@hmaarrfk hmaarrfk commented Jan 2, 2020

Truthfully, if pinged, I will accept for JOSS, but I think a few extra words could go a long way.

@danielskatz
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@danielskatz danielskatz commented Jan 2, 2020

Note that the links are not clickable in the github-rendered version of the PDF, only in the download. This is doubtless not a fault of the authors.

Yes, this is a function of GitHub - and some of the links in the paper will not fully work until the paper is closer to being accepted, such as the link to the archived software.

@danielskatz
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@danielskatz danielskatz commented Jan 2, 2020

Thanks @martindurant & @hmaarrfk!

It looks to me like a bit more work would really help this paper, particularly in terms of the state of the field part.

Also, I notice both of you have not checked off the functionality box - Can you let us know what you think is still needed to enable you to check this off?

@hmaarrfk
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@hmaarrfk hmaarrfk commented Jan 2, 2020

I would like a checkbox for Functionality to be incldued in the Software Paper section. My comments mostly refer to that.

@danielskatz
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@danielskatz danielskatz commented Jan 2, 2020

I'm confused by your comment.

The software paper section includes

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?

This is intended to ask if the paper sufficiently describes the functionality of the software at a high-level.

The functionality section includes

Functionality: Have the functional claims of the software been confirmed?

This is intended to ask if the software does what it says it does.

Can you explain what you would like again?

@hmaarrfk
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@hmaarrfk hmaarrfk commented Jan 2, 2020

I guess the question is:

Do you want a deeper discussion of the functionality in the paper for a more technical audience as well?

If so, some of the comments I made refer to that.

@danielskatz
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@danielskatz danielskatz commented Jan 2, 2020

JOSS papers are not intended to be long, and they are really intended to support/introduce the software itself and its documentation, so the paper should be more of a high-level introduction to what the software does, and the software documentation should include the deeper discussion

@danielskatz
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@danielskatz danielskatz commented Jan 6, 2020

@hmaarrfk - To continue our discussion, if the functionality of the software is as claimed, please check off the functionality box. If you have further thoughts on the software paper or documentation, let's talk about them as well.

@danielskatz
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@danielskatz danielskatz commented Jan 6, 2020

👋 @leouieda - I think we are also waiting for you to address some of @martindurant's comments on the state of the field description in the paper. Please let us know how this is going.

@martindurant
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@martindurant martindurant commented Jan 6, 2020

(just to reiterate: my comments were friendly suggestions only, and if the authors decide not to change anything, they are welcome to say so)

@leouieda
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@leouieda leouieda commented Jan 6, 2020

👋 @danielskatz just catching up with notifications from the holidays and will start working on replies/fixes.

@martindurant @hmaarrfk thank you for the reviews! They are all appreciated and I'll provide detailed replies soon.

(just to reiterate: my comments were friendly suggestions only, and if the authors decide not to change anything, they are welcome to say so)

@martindurant your comments are more than welcome and that is precisely why I suggested you as a reviewer 🙂

@leouieda
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@leouieda leouieda commented Jan 7, 2020

the library fsspec contains local-file-cache implementations that could be seen as implementing what Pooch does, also by changing only a single line of code. I would argue that it is indeed more flexible, having many file-system backends and allowing for partial downloads of large files. It can also check the source for changes on backends that support checksum or at least write-date metadata, or general cache expiry.

@martindurant I had seen fsspec while investigating Intake but to be honest, I didn't understand that this is what it does after reading the README or the documentation front page. In hind sight, I should have dug deeper as using fsspec would have simplified some of the work we did on Pooch.

You're right that fsspec is a much more flexible and comprehensive tool and people should definitely use it if they need this flexibility. What Pooch offers is a more limited scope and because of that it's probably easier to understand for non-specialists.

I'll include a section about fsspec in the paper as well.

Intake does not require you to rewrite any code at all in the simplest case such as the pandas example, but only change one line (pd.read_csv -> intake.open_csv; same arguments) with or without local caching

Right, that is what we meant but didn't do a good job in conveying it in the text. Sorry about that. I'll revise this part to make it clear that you only need this for non-standard formats.

Intake does many other things too, such as read from sources which are not files, from remote servers and services; metadata and visualisation and data-source browsing. In this, I agree that Pooch does one job and does it well.

I'll make sure to mention more of this in the text. We should probably also include something like this in the documentation pointing people to Intake if they need these other features.

Indeed, Intake and Pooch should have integration points, and I think this is the biggest and saddest missing point. The Pooch registry (which files) and an Intake catalog (how to load which files) clearly have overlap. Pooch could be one way of obtaining files for Intake.

I completely agree. This has come down to a lack of time on my part to invest in really learning Intake. I'm happy to keep the door open for collaboration but given the time constraints it can't be a priority of mine (but that doesn't mean someone else couldn't take this on).

At the very least, Pooch may want to investigate fsspec and its backends, to enable downloading from a variety of file stores, not just HTTP/FTP. https://github.com/intake/filesystem_spec/blob/master/fsspec/registry.py#L12

Right now, Pooch is pretty much a finished product since it solves the problem we initially set out to solve. But it would make a lot of sense to replace our download code with fsspec in the future and use it as our backend. That way, we can contribute back new backends to fsspec instead.

@danielskatz
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@danielskatz danielskatz commented Jan 17, 2020

@hmaarrfk - your opinion please?

@hmaarrfk
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@hmaarrfk hmaarrfk commented Jan 17, 2020

Just waking up. Good on my end. I was following up in their repo and tracking there progress there 👍

@danielskatz
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@danielskatz danielskatz commented Jan 17, 2020

👋 @leouieda - At this point could you:

  • Make a tagged release of your software, and list the version tag of the archived version here.
  • Archive the reviewed software in Zenodo or a similar service (e.g. figshare, an institutional repository)
  • Check the archival deposit (e.g., in Zenodo) has the correct metadata, this includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it); you may also add the authors' ORCID.
  • Please list the DOI of the archived version here.

I can then move forward with accepting the submission. Please also proofread the submission, including the references, which I will also do.

@leouieda
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@leouieda leouieda commented Jan 17, 2020

@danielskatz will do. Just waiting on any editorial fixes to the paper before releasing and archiving.

@danielskatz
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@danielskatz danielskatz commented Jan 17, 2020

The only things I see are potentially that some of the "python"s in reference titles could be "Python"s instead.

@leouieda
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@leouieda leouieda commented Jan 17, 2020

@whedon generate pdf

@whedon
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@whedon whedon commented Jan 17, 2020

@leouieda
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@leouieda leouieda commented Jan 17, 2020

Should be fixed now. The bibtex was poorly formatted.

@leouieda
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@leouieda leouieda commented Jan 17, 2020

@danielskatz done. Release version 0.7.1 and archive DOI 10.5281/zenodo.3611376

@danielskatz
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@danielskatz danielskatz commented Jan 17, 2020

@whedon set v0.7.1 as version

@whedon
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@whedon whedon commented Jan 17, 2020

OK. v0.7.1 is the version.

@danielskatz
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@danielskatz danielskatz commented Jan 17, 2020

@whedon set 10.5281/zenodo.3611376 as archive

@whedon
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@whedon whedon commented Jan 17, 2020

OK. 10.5281/zenodo.3611376 is the archive.

@danielskatz
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@danielskatz danielskatz commented Jan 17, 2020

@whedon accept

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@whedon whedon commented Jan 17, 2020

Attempting dry run of processing paper acceptance...

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@whedon whedon commented Jan 17, 2020

Reference check summary:

OK DOIs

- 10.7717/peerj.453 is OK
- 10.5065/D6WW7G29 is OK
- 10.21105/joss.00957 is OK
- 10.5281/ZENODO.3086002 is OK
- 10.5281/ZENODO.3542092 is OK
- 10.5281/ZENODO.1450596 is OK
- 10.21105/joss.01450 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@whedon
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@whedon whedon commented Jan 17, 2020

Check final proof 👉 openjournals/joss-papers#1234

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1234, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

@danielskatz
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@danielskatz danielskatz commented Jan 17, 2020

@whedon accept deposit=true

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@whedon whedon commented Jan 17, 2020

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

@whedon
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@whedon whedon commented Jan 17, 2020

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

@whedon
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@whedon whedon commented Jan 17, 2020

🚨🚨🚨 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 👉 openjournals/joss-papers#1235
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01943
  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...

@danielskatz
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@danielskatz danielskatz commented Jan 17, 2020

Thanks to @hmaarrfk & @martindurant for editing!
And congratulations to @leouieda and co-authors!

@whedon
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@whedon whedon commented Jan 17, 2020

🎉🎉🎉 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.01943/status.svg)](https://doi.org/10.21105/joss.01943)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01943">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01943/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01943/status.svg
   :target: https://doi.org/10.21105/joss.01943

This is how it will look in your documentation:

DOI

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

@leouieda
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@leouieda leouieda commented Jan 17, 2020

Thank you @danielskatz @hmaarrfk & @martindurant for all your work!

@whedon whedon added published recommend-accept labels Mar 2, 2020
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