[PRE REVIEW]: GeoBO: Python package for Multi-Objective Bayesian Optimisation and Joint Inversion in Geosciences

[whedon]

Submitting author: @sebhaan (Sebastian Haan) Repository: https://github.com/sebhaan/geobo Version: v1.0.0 Editor: @hugoledoux Reviewers: @npetra Managing EiC: Daniel S. Katz

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Author instructions

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

@sebhaan 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).

Editor instructions

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[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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

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

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[whedon]

Reference check summary:

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[danielskatz]

@whedon check repository

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.11 s (319.2 files/s, 103595.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                        10            874              0           3979
HTML                             7            341              0           3772
Python                          12            274            572            992
YAML                             5             90            210            199
TeX                              1              6              0             51
-------------------------------------------------------------------------------
SUM:                            35           1585            782           8993
-------------------------------------------------------------------------------

Statistical information for the repository '2421' was gathered on 2020/07/02.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Seb Haan                         7          1952            106          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Seb Haan                   1846           94.6          0.0               13.54

[jedbrown]

:wave: @sebhaan Could you explain a bit more about related software. Perhaps https://hippylib.github.io/, for example? This would be a good thing to add to your README/documentation as well as the paper.

[arfon]

@whedon query scope

[sebhaan]

👋 @sebhaan Could you explain a bit more about related software. Perhaps https://hippylib.github.io/, for example? This would be a good thing to add to your README/documentation as well as the paper.

@jedbrown Have added a new section about related software (hippylib, Obsidian, and GemPy) to the README and three more references to these bayesian inversion tools in the paper.

[danielskatz]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[danielskatz]

@whedon check references

[whedon]

Reference check summary:

OK DOIs

- 10.21105/joss.00940 is OK

MISSING DOIs

- https://doi.org/10.5194/gmd-12-2941-2019 may be missing for title: Efficiency and robustness in Monte Carlo sampling for 3-D geophysical inversions with Obsidian v0. 1.2: setting up for success
- https://doi.org/10.5194/gmd-12-1-2019 may be missing for title: GemPy 1.0: open-source stochastic geological modeling and inversion

INVALID DOIs

- None

[danielskatz]

@hugoledoux - would you be willing to edit this submission?

[ooo[bot]]

:wave: Hey @danielskatz...

Letting you know, @hugoledoux is currently OOO until Sunday, August 16th 2020. :heart:

[danielskatz]

@whedon invite @hugoledoux as editor

[ooo[bot]]

:wave: Hey @danielskatz...

Letting you know, @hugoledoux is currently OOO until Sunday, August 16th 2020. :heart:

[whedon]

@hugoledoux has been invited to edit this submission.

[ooo[bot]]

:wave: Hey @whedon...

Letting you know, @hugoledoux is currently OOO until Sunday, August 16th 2020. :heart:

[hugoledoux]

@whedon assign me as editor

[whedon]

OK, the editor is @hugoledoux

[hugoledoux]

@jedbrown would you like to review this paper?

[jedbrown]

If needed (quite busy already with JOSS editing), but perhaps @uvilla or @npetra would be available?

[hugoledoux]

I have already asked 2 other persons (on the JOSS reviewers list).

I just saw it was close to your expertise and thought that would be an easy way to recruit the first reviewer! But I understand, let's wait then.

[hugoledoux]

Would @uvilla or @npetra would be available for this review? I didn't get any response from the 2 on the JOSS list, unfortunately.

[uvilla]

Hi Hugo, I’m on a family leave until the end of the semester, and unfortunately I won’t be able to serve as a reviewer for Joss this time around.

I’m looking forward to serve in a future occasion.

Kind regards,

Umberto

On Fri, Sep 18, 2020 at 1:38 AM Hugo Ledoux notifications@github.com wrote:

Would @uvilla https://github.com/uvilla or @npetra https://github.com/npetra would be available for this review? I didn't get any response from the 2 on the JOSS list, unfortunately.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/2421#issuecomment-694686064, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEF5AN6PFIMSD56MLVAOMV3SGL57BANCNFSM4OO7WXHQ .

[npetra]

Hi Hugo (@hugoledoux),

I can help with this review. What is the deadline, etc.?

Best, Noemi

[hugoledoux]

@npetra great. We try to do the reviews <1mo, would that be possible?

I don't know if you've done reviews for JOSS before? If not, you should know that the review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged.

JOSS reviews involve downloading and installing the software, and inspecting the repository and submitted paper for key elements. See https://joss.readthedocs.io/en/latest/review_criteria.html

Editors and reviewers post comments on the Review issue, and authors respond to the comments and improve their submission until acceptance (or withdrawal, if they feel unable to satisfy the review).

Let me know if possible, if not, if you could please propose alternatives that would be great; their github username here (without the "@" so that they don't get automatically the notification).

[hugoledoux]

I’m looking forward to serve in a future occasion.

@uvilla no problem, thanks for getting back to me quickly.

[npetra]

@hugoledoux 1 month should be fine. Thanks for the details. This is the first time I am reviewing for JOSS, will take a look at the review criteria and get back to you if I have questions.

[hugoledoux]

@whedon assign @npetra as reviewer

[whedon]

OK, @npetra is now a reviewer

[hugoledoux]

@npetra super. The actual review is done in another issue, you'll be notified. At the top of the issue there are instructions about what you should do. It's a bit overwhelming at first, so don't hesitate to ask me questions.

You are allowed--and expected!--to interact directly with the authors. You can say "hey this and that doesn't work" and we expect them to fix those. It's a dialogue that goes back and forth.

[hugoledoux]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2690.

[npetra]

@hugoledoux I am ready to submit my review (sorry for the slight delay) but unfortunately it looks like the invite has expired. Is it possible to renew the invite? Thanks!

[hugoledoux]

@whedon re-invite @npetra as reviewer

[whedon]

OK, the reviewer has been re-invited.

@npetra please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations