[PRE REVIEW]: hetGPy: Heteroskedastic Gaussian Process Modeling in Python

[editorialbot]

Submitting author: @davidogara (David O’Gara)
Repository: https://github.com/davidogara/hetGPy
Branch with paper.md (empty if default branch):
Version: v1.1
Editor: @matthewfeickert
Reviewers: @Edenhofer, @DanWaxman
Managing EiC: Chris Vernon

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/795d74e35cd3aec6f63ad6832c247f90"><img src="https://joss.theoj.org/papers/795d74e35cd3aec6f63ad6832c247f90/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/795d74e35cd3aec6f63ad6832c247f90/status.svg)](https://joss.theoj.org/papers/795d74e35cd3aec6f63ad6832c247f90)

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.11 s (936.2 files/s, 441612.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              1              0             39           4938
Python                          48           1126           1769           4167
C++                              3            223             84            994
Jupyter Notebook                14              0          31826            869
CSV                             12              0              0            772
TeX                              1             41              0            462
R                                2             40            205            119
Markdown                         3             49              0             95
reStructuredText                13             34             70             49
YAML                             2              6              8             46
DOS Batch                        1              8              1             26
TOML                             1             10              0             19
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           102           1541          34009          12565
-------------------------------------------------------------------------------

Commit count by author:

   284	David O'Gara
     9	Mickaël Binois
     1	Lia Schattner

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1056

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU Lesser General Public License v2.1 (Check here for OSI approval)

[editorialbot]

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

✅ OK DOIs

- 10.1371/journal.pcbi.1009149 is OK
- 10.18637/jss.v098.i13 is OK
- 10.1002/adts.202300147 is OK
- 10.1098/rsos.210506 is OK
- 10.1126/science.abm4247 is OK
- 10.1080/10618600.2018.1458625 is OK
- 10.1080/00401706.2018.1469433 is OK
- 10.48550/arXiv.2002.01321 is OK
- 10.1016/j.epidem.2021.100535 is OK
- 10.1038/s41467-021-27486-z is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.48550/arXiv.1912.01703 is OK
- 10.1145/2049662.2049669 is OK
- 10.1002/9780470770801 is OK
- 10.1007/s00158-013-0919-4 is OK
- 10.7717/peerj-cs.1516 is OK
- 10.21105/joss.04455 is OK
- 10.1111/j.2517-6161.1985.tb01327.x is OK
- 10.1287/opre.1090.0754 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1137/0916069 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Bayesian Optimization
- No DOI given, and none found for title: Surrogates: Gaussian Process Modeling, Design and ...
- No DOI given, and none found for title: Modeling and Simulation in Python: An Introduction...
- No DOI given, and none found for title: Scikit-learn: Machine Learning in Python
- No DOI given, and none found for title: BoTorch: A Framework for Efficient Monte-Carlo Bay...
- No DOI given, and none found for title: GPyTorch: Blackbox Matrix-Matrix Gaussian Process ...
- No DOI given, and none found for title: Virtual Library of Simulation Experiments: Test Fu...
- No DOI given, and none found for title: GPflow: A Gaussian Process Library using TensorFlo...
- No DOI given, and none found for title: reticulate: Interface to ’Python’

❌ MISSING DOIs

- 10.1201/9781003226581 may be a valid DOI for title: Modeling and Simulation in Python

❌ INVALID DOIs

- None

[editorialbot]

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

[editorialbot]

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⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[crvernon]

@editorialbot invite @matthewfeickert as editor

👋 @matthewfeickert - can you take this one on as editor? Thanks!

[editorialbot]

Invitation to edit this submission sent!

[matthewfeickert]

@editorialbot assign @matthewfeickert as editor

[editorialbot]

Assigned! @matthewfeickert is now the editor

[matthewfeickert]

(I'm currently traveling for a work conference so I will be delayed a few days on finding reviewers.)

[matthewfeickert]

👋 @Bobby-Huggins You've been identified as a potential good reviewer for this submission. Would you be willing to review it? For an overview of what reviewing for JOSS is like please see the Reviewing for JOSS documentation: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html Please read this while considering the request to become a reviewer.

If you are interested in reviewing we would like reviewers to aim to have their preliminary reviews (not fully finished!) completed within 3-4 weeks. We understand that everyone is busy and so even if you are interested your schedule might prohibit you from accepting this review at this time. If you have any questions please feel free to ask me. I would be happy to discuss them with you.

[matthewfeickert]

@editorialbot add @Edenhofer as reviewer

[editorialbot]

@Edenhofer added to the reviewers list!

[Bobby-Huggins]

Hi @matthewfeickert, thanks for reaching out and yes I am willing to review.

[Bobby-Huggins]

@matthewfeickert Whoops, should have checked the full author list first, but I am actually in the process of joining Roman Garnett's lab here at WashU, so this is probably a conflict of interest?

[matthewfeickert]

I am actually in the process of joining Roman Garnett's lab here at WashU, so this is probably a conflict of interest?

Thanks for checking this in advance @Bobby-Huggins. Yes, if you have already joined the lab and are currently working with Roman then this would hit the JOSS Conflict of Interest Policy. Though if you haven't yet formally started work and you wouldn't join the lab until you're already well into the review then I think this would be okay.

[Bobby-Huggins]

I am actually in the process of joining Roman Garnett's lab here at WashU, so this is probably a conflict of interest?

Thanks for checking this in advance @Bobby-Huggins. Yes, if you have already joined the lab and are currently working with Roman then this would hit the JOSS Conflict of Interest Policy. Though if you haven't yet formally started work and you wouldn't join the lab until you're already well into the review then I think this would be okay.

I suppose it's borderline: I have not yet formally started in the lab but we are informally collaborating at the moment. I think it would be best to find another reviewer if possible, if only to avoid even the appearance of impropriety.

[matthewfeickert]

@editorialbot add @DanWaxman as reviewer

[editorialbot]

@DanWaxman added to the reviewers list!

[matthewfeickert]

We now have the minimum two reviewers required, so I'll go ahead and start the review. Additional reviewers are very welcome so if other potential reviewers I contacted would be interested in helping I can add you to the review after it has started.

[matthewfeickert]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #7518.