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[REVIEW]: AMLTK: A Modular AutoML Toolkit in Python #6367

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editorialbot opened this issue Feb 17, 2024 · 71 comments
Closed

[REVIEW]: AMLTK: A Modular AutoML Toolkit in Python #6367

editorialbot opened this issue Feb 17, 2024 · 71 comments
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accepted just 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 Feb 17, 2024

Submitting author: @eddiebergman (Edward Bergman)
Repository: https://github.com/automl/amltk
Branch with paper.md (empty if default branch): joss-paper
Version: v1.12.1
Editor: @JBorrow
Reviewers: @gomezzz, @woznicak, @hirzel
Archive: 10.5281/zenodo.13309537

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/63a52e26b9e3bb3cfb7e028df69d6fe5"><img src="https://joss.theoj.org/papers/63a52e26b9e3bb3cfb7e028df69d6fe5/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/63a52e26b9e3bb3cfb7e028df69d6fe5/status.svg)](https://joss.theoj.org/papers/63a52e26b9e3bb3cfb7e028df69d6fe5)

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

@gomezzz & @woznicak & @hirzel, 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 @JBorrow 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 @gomezzz

📝 Checklist for @hirzel

📝 Checklist for @woznicak

@editorialbot editorialbot added just 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 Feb 17, 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 1.88  T=0.22 s (765.3 files/s, 134583.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         110           4948           6589          12376
Markdown                        34            955              0           2762
SVG                             11              6             10            967
YAML                             8             31             13            527
HTML                             5             48              0            268
TOML                             1             30             14            266
TeX                              1             17              0            133
CSS                              1             17              6             87
-------------------------------------------------------------------------------
SUM:                           171           6052           6632          17386
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 1189

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

OK DOIs

- None

MISSING DOIs

- 10.1109/tpami.2021.3067763 may be a valid DOI for title: Auto-Pytorch: Multi-Fidelity MetaLearning for Efficient and Robust AutoDL
- 10.21105/joss.01132 may be a valid DOI for title: GAMA: Genetic Automated Machine Learning Assistant
- 10.1007/s10994-022-06200-0 may be a valid DOI for title: Naive automated machine learning
- 10.1145/2908812.2908918 may be a valid DOI for title: Evaluation of a Tree-based Pipeline Optimization Tool for Automating Data Science
- 10.1371/journal.pdig.0000276 may be a valid DOI for title: AutoPrognosis 2.0: Democratizing Diagnostic and Prognostic Modeling in Healthcare with Automated Machine Learning

INVALID DOIs

- None

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

@gomezzz
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gomezzz commented Feb 18, 2024

Review checklist for @gomezzz

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/automl/amltk?
  • 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 (@eddiebergman) 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?

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JBorrow commented Feb 28, 2024

Hi @eddiebergman, there seem to be some missing references in your paper. Would you be able to fix those and re-generate the PDF? Please include a valid DOI for all references (indeed 10.1109/TPAMI.2021.3067763 is the correct one for your first reference).

@eddiebergman
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eddiebergman commented Feb 29, 2024

@JBorrow Apologies, I missed that this was required in the paper.bib. I've included a doi for all entries where I could find one. Is there any command to have the bot re-check this?

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JBorrow commented Feb 29, 2024

@editorialbot check references

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

OK DOIs

- 10.48550/arXiv.2003.06505 is OK
- 10.48550/arxiv.2207.12560 is OK
- 10.1109/tpami.2021.3067763 is OK
- 10.1007/978-3-030-05318-5 is OK
- 10.1007/978-3-030-67670-4_39 is OK
- 10.21105/joss.01132 is OK
- 10.48550/arxiv.2206.03493 is OK
- 10.48550/arxiv.1908.06756 is OK
- 10.1007/s10994-022-06200-0 is OK
- 10.1145/3292500.3330701 is OK
- 10.1007/978-3-030-05318-5_4 is OK
- 10.1145/2908812.2908918 is OK
- 10.1371/journal.pdig.0000276 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@JBorrow
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JBorrow commented Feb 29, 2024

All looks good now @eddiebergman, thank you.

@gomezzz
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gomezzz commented Mar 4, 2024

(starting to go through the checklist now)
@eddiebergman The paper has a fairly long author list and I believe JOSS has somewhat more restrictive authorship criteria. Could you clarify the contributions of the authors who did not contribute significantly to the code (deduced from here https://github.com/automl/amltk/graphs/contributors)?

@eddiebergman
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Hi @gomezzz,

The contributions are as follows:

  • Myself (Eddie/Edward), Lennart and Aron contributed directly to the code:
    • Aron had put a lot of work in making sure this library could be used to reconstruct the pipelines of AutoSklearn and contributing issues and design
    • Lennart has been invaluable with reviewing every (at least reviewable) PR and discussin features and API design. Unfortunately PR review is not listed in the contributions graph.
  • Matthias/Katharina are the original authors of Auto-Sklearn and have been vital for consulting on the technical details of implementation when it comes to interfacing w/ various aspects of Automated Machine Learning, including but not limited to Optimization, Evaluation and Meta-Learning.
  • Amir has been one of the earliest forms of quality assurance we have gotten, i.e. he is a user of the tool for his own research projects and has been giving feedback on what does and doesn't work with suggestions.
  • Sarah maintains DeepCave and SMAC and we are working on having these tools interop more seamlessly. She has also volunteered to contribute visualizations, once ready, and maintenance to the tool in the long term.
  • Frank and Marius have been invaluable in terms of scope, design and desiderata of the project in the larger landscape of AutoML as well as giving strategic feedback on prioritization.

Please let me know if I can further clarify any of these points :)

@gomezzz
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gomezzz commented Mar 7, 2024

Thanks @eddiebergman for the details. I am not sure how this interacts with the authorship guidelines of JOSS and if all these are sufficient for authorship. I have no strong opinions on the matter, I'll check the box and maybe @JBorrow can decide on this aspect if there remains any uncertainty.

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JBorrow commented Mar 15, 2024

Hi @gomezzz, thank you. I will raise this with the editorial board shortly.

In other news, I will be out on vacation until the 24th, so please do not expect any responses before then.

@hirzel
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hirzel commented Mar 20, 2024

Review checklist for @hirzel

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/automl/amltk?
  • 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 (@eddiebergman) 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?

@hirzel
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hirzel commented Mar 20, 2024

Hi, I read through the paper and the Readme, tried the "pip install", and poked around in the repo as needed to answer the questions in the checklist. Overall, this seems like a nice package. Thank you for submitting it!

A couple of suggestions that could make this even better:

  • Performance: The paper does not report any experimental results. On the other hand, the first claimed contribution is "(a) Enabling systematic comparison". Such comparison is only meaningful if AMLTK has competitive performance. Therefore, I encourage you to report some numbers.

  • Architecture: The paper does not contain any architecture diagram. I would assume such a diagram could show how pipelines, search space, optimizers, and schedulers interact. Adding a diagram would help readers more quickly grasp the functionality, and might also be helpful for users and contributors.

  • Novelty: I was looking for novel claims in the paper, but if they are there, I missed them. Perhaps novelty is not the aim here, taking a backseat to the well-engineered implementation of known concepts? On the other hand, if there is novelty, you should consider pointing it out explicitly.

Finally, I was wondering if the paper should cite Lale. I hesitate to bring this up, because I am one of the Lale authors. However, I do believe it is quite relevant here for multiple reasons. The first example in the Readme illustrates a >> combinator for pipeline composition, which Lale also provides. The paper emphasizes AMLTK's support for multiple optimizers, which Lale also provides (see Section 4 of the NeurIPS paper). Also, the authors chose me as a reviewer in part because Lale is close related work for AMLTK. That said, if you decide not to cite the Lale paper here, I am fine with that.

@arfon arfon removed the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Mar 24, 2024
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JBorrow commented Mar 25, 2024

Hi @woznicak, have you had a chance to start on your review yet?

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JBorrow commented Aug 13, 2024

@editorialbot set https://zenodo.org/records/13309538 as archive

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That doesn't look like a valid DOI value

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JBorrow commented Aug 13, 2024

@editorialbot set 10.5281/zenodo.13309537 as archive

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Done! archive is now 10.5281/zenodo.13309537

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JBorrow commented Aug 13, 2024

@editorialbot set v1.12.1 as version

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Done! version is now v1.12.1

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JBorrow commented Aug 13, 2024

@editorialbot generate pdf

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

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JBorrow commented Aug 13, 2024

@editorialbot recommend-accept

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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

- 10.48550/arXiv.2003.06505 is OK
- 10.48550/arXiv.2007.04074 is OK
- 10.48550/arxiv.2207.12560 is OK
- 10.1109/tpami.2021.3067763 is OK
- 10.1007/978-3-030-05318-5 is OK
- 10.1007/978-3-030-67670-4_39 is OK
- 10.21105/joss.01132 is OK
- 10.48550/arxiv.2206.03493 is OK
- 10.48550/arxiv.1908.06756 is OK
- 10.1007/s10994-022-06200-0 is OK
- 10.1145/3292500.3330701 is OK
- 10.1007/978-3-030-05318-5_4 is OK
- 10.1145/2908812.2908918 is OK
- 10.1371/journal.pdig.0000276 is OK

MISSING DOIs

- No DOI given, and none found for title: Efficient and Robust Automated Machine Learning
- No DOI given, and none found for title: SMAC3: A Versatile Bayesian Optimization Package f...
- No DOI given, and none found for title: FLAML: A fast and lightweight automl library
- No DOI given, and none found for title: Pipeline Combinators for Gradual AutoML
- No DOI given, and none found for title: H2O AutoML: Scalable Automatic Machine Learning

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#5763, 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 Aug 13, 2024
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@editorialbot generate pdf

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crvernon commented Aug 14, 2024

🔍 checking out the following:

  • reviewer checklists are completed or addressed
  • version set
  • archive set
  • archive names (including order) and title in archive matches those specified in the paper
  • archive uses the same license as the repo and is OSI approved as open source
  • archive DOI and version match or redirect to those set by editor in review thread
  • paper is error free - grammar and typos
  • paper is error free - test links in the paper and bib
  • paper is error free - refs preserve capitalization where necessary
  • paper is error free - no invalid refs without justification

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

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crvernon commented Aug 14, 2024

👋 @eddiebergman - I just need you to address the following before I can accept this for publication:

  • The paper title and the Zenodo archive title must match exactly. Please edit the Zenodo archive's metadata to reflect this.

In the paper:

  • LINE 130 and 133: "bayesian" should have a capital "B". Formatting can be maintained in the bib file by using curly brackets around the characters you wish to maintain the formatting of.

Thanks

@eddiebergman
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Hi @crvernon, the issues have been addressed!

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@editorialbot generate pdf

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

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@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: Bergman
  given-names: Edward
  orcid: "https://orcid.org/0009-0003-4390-7614"
- family-names: Feurer
  given-names: Matthias
  orcid: "https://orcid.org/0000-0001-9611-8588"
- family-names: Bahram
  given-names: Aron
  orcid: "https://orcid.org/0009-0002-8896-2863"
- family-names: Balef
  given-names: Amir Rezaei
  orcid: "https://orcid.org/0000-0002-6882-0051"
- family-names: Purucker
  given-names: Lennart
  orcid: "https://orcid.org/0009-0001-1181-0549"
- family-names: Segel
  given-names: Sarah
  orcid: "https://orcid.org/0009-0005-2966-266X"
- family-names: Lindauer
  given-names: Marius
  orcid: "https://orcid.org/0000-0002-9675-3175"
- family-names: Hutter
  given-names: Frank
  orcid: "https://orcid.org/0000-0002-2037-3694"
- family-names: Eggensperger
  given-names: Katharina
  orcid: "https://orcid.org/0000-0002-0309-401X"
contact:
- family-names: Bergman
  given-names: Edward
  orcid: "https://orcid.org/0009-0003-4390-7614"
- family-names: Feurer
  given-names: Matthias
  orcid: "https://orcid.org/0000-0001-9611-8588"
- family-names: Lindauer
  given-names: Marius
  orcid: "https://orcid.org/0000-0002-9675-3175"
- family-names: Hutter
  given-names: Frank
  orcid: "https://orcid.org/0000-0002-2037-3694"
- family-names: Eggensperger
  given-names: Katharina
  orcid: "https://orcid.org/0000-0002-0309-401X"
doi: 10.5281/zenodo.13309537
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Bergman
    given-names: Edward
    orcid: "https://orcid.org/0009-0003-4390-7614"
  - family-names: Feurer
    given-names: Matthias
    orcid: "https://orcid.org/0000-0001-9611-8588"
  - family-names: Bahram
    given-names: Aron
    orcid: "https://orcid.org/0009-0002-8896-2863"
  - family-names: Balef
    given-names: Amir Rezaei
    orcid: "https://orcid.org/0000-0002-6882-0051"
  - family-names: Purucker
    given-names: Lennart
    orcid: "https://orcid.org/0009-0001-1181-0549"
  - family-names: Segel
    given-names: Sarah
    orcid: "https://orcid.org/0009-0005-2966-266X"
  - family-names: Lindauer
    given-names: Marius
    orcid: "https://orcid.org/0000-0002-9675-3175"
  - family-names: Hutter
    given-names: Frank
    orcid: "https://orcid.org/0000-0002-2037-3694"
  - family-names: Eggensperger
    given-names: Katharina
    orcid: "https://orcid.org/0000-0002-0309-401X"
  date-published: 2024-08-14
  doi: 10.21105/joss.06367
  issn: 2475-9066
  issue: 100
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6367
  title: "AMLTK: A Modular AutoML Toolkit in Python"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06367"
  volume: 9
title: "AMLTK: A Modular AutoML Toolkit in Python"

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.06367 joss-papers#5767
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06367
  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 Aug 14, 2024
@crvernon
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🥳 Congratulations on your new publication @eddiebergman! Many thanks to @JBorrow for editing and @gomezzz, @woznicak, and @hirzel for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

Please consider becoming a reviewer for JOSS if you are not already: https://reviewers.joss.theoj.org/join

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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.06367/status.svg)](https://doi.org/10.21105/joss.06367)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06367">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06367/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06367/status.svg
   :target: https://doi.org/10.21105/joss.06367

This is how it will look in your documentation:

DOI

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accepted just 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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