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[REVIEW]: PyBADS: Fast and robust black-box optimization in Python #5694

Closed editorialbot closed 7 months ago

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@GurjeetSinghSangra<!--end-author-handle-- (Gurjeet Singh) Repository: https://github.com/acerbilab/pybads Branch with paper.md (empty if default branch): joss-submission Version: 1.0.4 Editor: !--editor-->@rkurchin<!--end-editor-- Reviewers: @jungtaekkim, @vankesteren Archive: 10.5281/zenodo.10696782

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Markdown: [![status](https://joss.theoj.org/papers/bebd124ad9238299fc24d33973c675c8/status.svg)](https://joss.theoj.org/papers/bebd124ad9238299fc24d33973c675c8)

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

@max-little & @gaxler, 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 @rkurchin 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 @jungtaekkim

📝 Checklist for @vankesteren

editorialbot commented 1 year ago

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 commented 1 year ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.13 s (822.4 files/s, 94431.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          59           1244           1575           5501
TeX                              2             86             16            730
INI                              4             14              0            376
reStructuredText                21            188             96            308
YAML                             6             24              5            210
Markdown                         5             78              0            183
Jupyter Notebook                 5              0           1234            140
TOML                             1              9              3             56
DOS Batch                        1             10              1             39
make                             1              6             11             18
CSS                              1              1              0              9
-------------------------------------------------------------------------------
SUM:                           106           1660           2941           7570
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 1 year ago

Wordcount for paper.md is 1580

editorialbot commented 1 year ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.05428 is OK
- 10.1145/3544489 is OK
- 10.23915/distill.00026 is OK
- 10.21105/joss.00024 is OK

MISSING DOIs

- 10.1007/s10898-012-9951-y may be a valid DOI for title: Derivative-free optimization: a review of algorithms and comparison of software implementations
- 10.1109/tte.2022.3218341 may be a valid DOI for title: Topology Comparison and Sensitivity Analysis of Fuel Cell Hybrid Systems for Electric Vehicles
- 10.1016/j.petsci.2022.06.016 may be a valid DOI for title: Well production optimization using streamline features-based objective function and Bayesian adaptive direct search algorithm
- 10.1101/2021.03.11.434913 may be a valid DOI for title: On the generality and cognitive basis of base-rate neglect
- 10.1016/j.jmapro.2021.02.052 may be a valid DOI for title: A novel energy partition model for belt grinding of Inconel 718
- 10.1016/j.jeem.2020.102317 may be a valid DOI for title: The impact of wildfires on the recreational value of heathland: A discrete factor approach with adjustment for on-site sampling
- 10.1137/040603371 may be a valid DOI for title: Mesh Adaptive Direct Search Algorithms for Constrained Optimization
- 10.1109/wsc.2006.323088 may be a valid DOI for title: Adaptation of the UOBYQA algorithm for noisy functions
- 10.1137/080716980 may be a valid DOI for title: OrthoMADS: A deterministic MADS instance with orthogonal directions
- 10.1007/s10589-020-00249-0 may be a valid DOI for title: Stochastic mesh adaptive direct search for blackbox optimization using probabilistic estimates
- 10.1038/s41586-023-06124-2 may be a valid DOI for title: Expertise increases planning depth in human gameplay
- 10.1101/500413 may be a valid DOI for title: Causal inference in the multisensory brain
- 10.1038/s41593-019-0453-9 may be a valid DOI for title: Optimal policy for multi-alternative decisions
- 10.1038/s41562-019-0804-2 may be a valid DOI for title: Quantum reinforcement learning during human decision-making
- 10.1016/j.cub.2019.04.067 may be a valid DOI for title: Simple Acoustic Features Can Explain Phoneme-Based Predictions of Cortical Responses to Speech
- 10.1016/j.jmapro.2020.07.018 may be a valid DOI for title: A new method to achieve dynamic heat input monitoring in robotic belt grinding of Inconel 718
- 10.3390/en14030626 may be a valid DOI for title: Interpretation of Gas/Water Relative Permeability of Coal Using the Hybrid Bayesian-Assisted History Matching: New Insights
- 10.1109/jproc.2015.2494218 may be a valid DOI for title: Taking the Human Out of the Loop: A Review of Bayesian Optimization
- 10.1016/j.anucene.2020.108046 may be a valid DOI for title: Application of Kriging and Variational Bayesian Monte Carlo method for improved prediction of doped UO2 fission gas release
- 10.1007/s40857-022-00277-2 may be a valid DOI for title: Application of Dual-Source Modal Dispersion and Variational Bayesian Monte Carlo Method for Local Geoacoustic Inversion in Weakly Range-Dependent Shallow Water
- 10.3390/pharmaceutics14040749 may be a valid DOI for title: Interrogating and Quantifying In Vitro Cancer Drug Pharmacodynamics via Agent-Based and Bayesian Monte Carlo Modelling
- 10.1162/neco_a_01127 may be a valid DOI for title: Adaptive Gaussian Process Approximation for Bayesian Inference with Expensive Likelihood Functions
- 10.1214/20-ba1200 may be a valid DOI for title: Parallel Gaussian Process Surrogate Bayesian Inference with Noisy Likelihood Evaluations
- 10.1016/0378-3758(91)90002-v may be a valid DOI for title: Bayes–Hermite quadrature

INVALID DOIs

- None
editorialbot commented 1 year ago

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

rkurchin commented 1 year ago

Reviewers @max-little and @gaxler, please let me know if you have any questions about how to get started on your reviews!

@GurjeetSinghSangra, at some point be sure to address those missing DOI's that got flagged above.

GurjeetSinghSangra commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

GurjeetSinghSangra commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

rkurchin commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/s10898-012-9951-y is OK
- 10.1109/TTE.2022.3218341 is OK
- 10.1016/j.petsci.2022.06.016 is OK
- 10.1101/2021.03.11.434913 is OK
- 10.1016/j.jmapro.2021.02.052 is OK
- 10.1016/j.jeem.2020.102317 is OK
- 10.1137/040603371 is OK
- 10.1109/wsc.2006.323088 is OK
- 10.1137/080716980 is OK
- 10.1007/s10589-020-00249-0 is OK
- 10.21105/joss.05428 is OK
- 10.1145/3544489 is OK
- 10.1038/s41586-023-06124-2 is OK
- 10.1016/j.neuron.2019.03.043 is OK
- 10.1038/s41593-019-0453-9 is OK
- 10.1038/s41562-019-0804-2 is OK
- 10.1016/j.cub.2019.04.067 is OK
- 10.1016/j.jmapro.2020.07.018 is OK
- 10.3390/en14030626 is OK
- 10.1109/JPROC.2015.2494218 is OK
- 10.23915/distill.00026 is OK
- 10.1016/j.anucene.2020.108046 is OK
- 10.1007/s40857-022-00277-2 is OK
- 10.3390/pharmaceutics14040749 is OK
- 10.1162/neco_a_01127 is OK
- 10.1214/20-ba1200 is OK
- 10.1016/0378-3758(91)90002-V is OK
- 10.21105/joss.00024 is OK

MISSING DOIs

- None

INVALID DOIs

- None
rkurchin commented 1 year ago

👋 Hi reviewers @max-little and @gaxler, just checking in again on this!

rkurchin commented 1 year ago

👋 Hi again @max-little and @gaxler, any updates on when you'll be able to start your reviews?

rkurchin commented 1 year ago

@max-little and @gaxler, are you still able to review this submission to JOSS?

gaxler commented 1 year ago

Review checklist for @gaxler

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

rkurchin commented 1 year ago

Thanks for getting things started here, @gaxler! Checking in with @max-little again... 🔔

rkurchin commented 1 year ago

Sent an email to @max-little to check in; if I don't get a response in a few days I'll find a replacement reviewer.

(link to pre-review for my own reference here so I don't re-ask the same people who already said no: https://github.com/openjournals/joss-reviews/issues/5544 )

rkurchin commented 1 year ago

👋 @jungtaekkim, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

jungtaekkim commented 1 year ago

Hi @rkurchin, I am willing to review this submission. Please add me as a reviewer.

rkurchin commented 1 year ago

@editorialbot add @jungtaekkim as reviewer

editorialbot commented 1 year ago

@jungtaekkim added to the reviewers list!

rkurchin commented 1 year ago

@jungtaekkim, let me know if you need any further guidance on how to get your review started! Take a look at the first comment in the issue for some initial information.

jungtaekkim commented 1 year ago

Review checklist for @jungtaekkim

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

rkurchin commented 12 months ago

@gaxler and @jungtaekkim, checking in on review progress here! You should feel free to open issues etc. in the project repo as part of your review; if you do so, please link back to this issue for easy tracking.

rkurchin commented 11 months ago

Hi, pinging reviewers @gaxler and @jungtaekkim again!

rkurchin commented 11 months ago

@editorialbot remove @max-little as reviewer

editorialbot commented 11 months ago

@max-little removed from the reviewers list!

jungtaekkim commented 11 months ago

@rkurchin I am sorry for the delay. I will upload my review as soon as possible.

rkurchin commented 11 months ago

Checking in with reviewers @gaxler and @jungtaekkim – any sense when you'll be able to finish working through your checklists?

jungtaekkim commented 11 months ago

I left the review on the PyBADS codebase and the paper.

Please see the following issues:

I will update my checklist if they are resolved or answered.

jungtaekkim commented 11 months ago

@editorialbot generate pdf

editorialbot commented 11 months ago

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

jungtaekkim commented 11 months ago

@rkurchin I am sorry for the late review. My concerns and questions have been resolved, so I updated my checklist. Please let me know if there is a further step.

GurjeetSinghSangra commented 11 months ago

@editorialbot generate pdf

editorialbot commented 11 months ago

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

rkurchin commented 11 months ago

Thanks @jungtaekkim, if you're happy to recommend publication than we're all set there.

@gaxler, any updates on the rest of your review?

rkurchin commented 10 months ago

(Sent @gaxler an email to check in about review)

GurjeetSinghSangra commented 10 months ago

Dear editor @gaxler, I trust this message finds you well. We appreciate the time and effort invested by you and the reviewers thus far; however, it has come to our attention that one of the assigned reviewers has not responded or continued with the review process. We understand the busy schedule and work commitments of reviewers, nevertheless receiving feedback impacts our work and deadlines. We kindly ask for your assistance in prioritising and concluding the review process. We know that finding competent and reliable reviewers is a difficult task, and we truly appreciate your effort and collaboration. Thank you for your understanding and prompt attention to this matter. Best regards, Gurjeet

rkurchin commented 10 months ago

Hi @GurjeetSinghSangra, I'm the editor here – apologies for the troubles seeing this one through; it may not be much consolation, but this is the most dramatic case I've ever handled of reviewers ghosting mid-review. I will work on finding another reviewer for this submission ASAP!

rkurchin commented 10 months ago

@editorialbot remove @gaxler as reviewer

editorialbot commented 10 months ago

@gaxler removed from the reviewers list!

rkurchin commented 10 months ago

👋 @vankesteren and/or @tmigot, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

tmigot commented 10 months ago

Dear editor @rkurchin , unfortunately I am not available for the upcoming monthes, so I prefer to decline the invitation. Best, Tangi

rkurchin commented 10 months ago

👋 @sarats, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

lacerbi commented 9 months ago

If we can help in any way to speed up the process please let us know @rkurchin, e.g. by proposing potential reviewers. Since it's been quite a while since our first submission, if a reviewer doesn't reply positively within a few days I'd suggest we move on with other reviewers until someone can take the task. Thanks for your support!

sarats commented 9 months ago

Sorry @rkurchin I'm presently on extended vacation, can't get this done in a timely manner and it won't be fair given the extensive delays incurred in this case already.

rkurchin commented 9 months ago

@lacerbi I'd certainly be open to other reviewer suggestions at this point!

GurjeetSinghSangra commented 9 months ago

Hello @rkurchin, I would like to suggest the following most relevant reviewers I found on the JOSS web-search.

I haven't tagged them, as I don't want to spam their emails all at once.

rkurchin commented 9 months ago

Hey @sgbaird, you were invited to review this one in pre-review and were bandwidth-constrained at the time, but as that was ~5 months ago and you seemed interested and clearly qualified, would you be willing to step in as a second reviewer here?