[PRE REVIEW]: BayesO: A Bayesian optimization framework in Python

[editorialbot]

Submitting author: !--author-handle-->@jungtaekkim<!--end-author-handle-- (Jungtaek Kim) Repository: https://github.com/jungtaekkim/bayeso Branch with paper.md (empty if default branch): joss-paper Version: v0.5.4 Editor: !--editor-->@drvinceknight<!--end-editor-- Reviewers: @salrm8, @thomaspinder Managing EiC: George K. Thiruvathukal

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Markdown: [![status](https://joss.theoj.org/papers/201781ebd4110e9d58c66626f84e9d4a/status.svg)](https://joss.theoj.org/papers/201781ebd4110e9d58c66626f84e9d4a)

Author instructions

Thanks for submitting your paper to JOSS @jungtaekkim. Currently, there isn't a JOSS editor assigned to your paper.

@jungtaekkim if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.01 s (384.3 files/s, 58672.3 lines/s)
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Language                     files          blank        comment           code
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TeX                              1             28              0            226
Markdown                         1             30              0            151
YAML                             1              1              4             18
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SUM:                             3             59              4            395
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gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1049

[editorialbot]

Failed to discover a valid open source license

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[editorialbot]

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

OK DOIs

- None

MISSING DOIs

- 10.1109/jproc.2015.2494218 may be a valid DOI for title: Taking the human out of the loop: A review of Bayesian optimization
- 10.1007/978-3-319-23871-5_3 may be a valid DOI for title: Bayesian optimization for materials design
- 10.1038/s41586-021-03213-y may be a valid DOI for title: Bayesian reaction optimization as a tool for chemical synthesis
- 10.1007/s10994-021-05949-0 may be a valid DOI for title: Bayesian Optimization with Approximate Set Kernels
- 10.1007/978-3-030-56485-8_3 may be a valid DOI for title: Random forests
- 10.2307/2332286 may be a valid DOI for title: On the likelihood that one unknown probability exceeds another in view of the evidence of two samples
- 10.1007/s10898-005-2454-3 may be a valid DOI for title: Global optimization of stochastic black-box systems via sequential kriging meta-models
- 10.2172/204262 may be a valid DOI for title: A limited memory algorithm for bound constrained optimization
- 10.1007/bf00941892 may be a valid DOI for title: Lipschitzian optimization without the Lipschitz constant

INVALID DOIs

- None

[jungtaekkim]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[jungtaekkim]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[arfon]

Repository stats for default branch:

cloc bayeso/
     194 text files.
     175 unique files.                                          
      32 files ignored.

github.com/AlDanial/cloc v 1.96  T=0.13 s (1339.7 files/s, 226784.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
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Python                          94           2914           2674          11632
SVG                             22              4              4           9803
Jupyter Notebook                 5              0            517            361
reStructuredText                39            300            806            186
Markdown                         2             44              0            126
YAML                             4             17             27            109
Text                             5              2              0             29
DOS Batch                        1              8              1             27
Bourne Shell                     1              0              0             10
make                             1              4              6             10
INI                              1              0              0              2
-------------------------------------------------------------------------------
SUM:                           175           3293           4035          22295
-------------------------------------------------------------------------------

[arfon]

@jungtaekkim – could you please merge the default branch for this repository to the joss-paper branch please?

[arfon]

@jungtaekkim - thanks for your submission to JOSS. We're currently managing a large backlog of submissions and the editor most appropriate for your area is already rather busy.

For now, we will need to waitlist this paper and process it as the queue reduces. Thanks for your patience!

[jungtaekkim]

@arfon Can I merge a joss-paper branch with a working branch (0.5.4)? My paper describes the working branch and it is not merged to a main branch yet. I am planning to merge it after a review process of JOSS.

Okay, I am looking forward to starting a review process for our paper soon.

[arfon]

Yes, feel free to merge!

[arfon]

@editorialbot invite @drvinceknight as editor

:wave: @drvinceknight – would you be willing to edit this submission for JOSS?

[editorialbot]

Invitation to edit this submission sent!

[drvinceknight]

@editorialbot assign me as editor

[editorialbot]

Assigned! @drvinceknight is now the editor

[drvinceknight]

@jungtaekkim thanks for your patience with this.

If you could, would you be able to take a look at the list of potential reviewers here https://bit.ly/joss-reviewers and suggest a few people who you feel would be suitable to review.

[jungtaekkim]

@drvinceknight

I suggest some potential reviewers seba-1511, torressa, jdreo.

[drvinceknight]

@seba-1511 @torressa @jdreo I am pinging you to ask if you would be able to assist with reviewing this submissions to JOSS (The Journal of Open Source Software).

JOSS publishes articles about open source research software. The submission I'd like you to review is titled: “BayesO: A Bayesian optimization framework in Python”. You can find more information at the top of this Github issue.

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.

[seba-1511]

Hello @drvinceknight, unfortunately I won't have bandwidth for reviews until August. I'd be happy to assist then, but hope you can find a replacement earlier than that.

[torressa]

Sorry this is not my area of expertise unfortunately. Looks super cool and pretty well established

[drvinceknight]

Thanks @seba-1511 and @torressa.

[drvinceknight]

@mattpitkin @malmaud @thomaspinder @salrm8 I am pinging you to ask if you would be able to assist with reviewing this submissions to JOSS (The Journal of Open Source Software).

JOSS publishes articles about open source research software. The submission I'd like you to review is titled: “BayesO: A Bayesian optimization framework in Python”. You can find more information at the top of this Github issue.

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.

[salrm8]

@drvinceknight I would be happy to review this submission.

[drvinceknight]

Thanks @salrm8!

[drvinceknight]

@editorialbot add @salrm8 as reviewer

[editorialbot]

@salrm8 added to the reviewers list!

[drvinceknight]

@thomaspinder (sorry for the "re"ping but this does seem right in your area of expertise) @jmp75 @BenWinchester I am pinging you to ask if you would be able to assist with reviewing this submissions to JOSS (The Journal of Open Source Software).

JOSS publishes articles about open source research software. The submission I'd like you to review is titled: “BayesO: A Bayesian optimization framework in Python”. You can find more information at the top of this Github issue.

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.

[thomaspinder]

Hi @drvinceknight - I can review this.

[drvinceknight]

@editorialbot add @thomaspinder as reviewer

[editorialbot]

@thomaspinder added to the reviewers list!

[drvinceknight]

Thanks @thomaspinder.

[drvinceknight]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/5320.