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[REVIEW]: DUGseis: A Python Package for Real-Time and Post-Processing of Picoseismicity #6768

Open editorialbot opened 5 months ago

editorialbot commented 5 months ago

Submitting author: !--author-handle-->@mrosskopf<!--end-author-handle-- (Martina Rosskopf) Repository: https://github.com/swiss-seismological-service/DUGseis Branch with paper.md (empty if default branch): Version: v0.3 Editor: !--editor-->@crvernon<!--end-editor-- Reviewers: @trichter, @erexer, @jessepisel Archive: Pending

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/d6852782d77b87a4f45a0c2058d056c6"><img src="https://joss.theoj.org/papers/d6852782d77b87a4f45a0c2058d056c6/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/d6852782d77b87a4f45a0c2058d056c6/status.svg)](https://joss.theoj.org/papers/d6852782d77b87a4f45a0c2058d056c6)

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

@ThomasLecocq, 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 @crvernon 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 @ThomasLecocq

📝 Checklist for @trichter

📝 Checklist for @erexer

📝 Checklist for @jessepisel

editorialbot commented 5 months 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 5 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.13 s (973.9 files/s, 192128.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          71           2479           3313          10703
SQL                              1            189              0           2016
Qt                               3              0              0           1558
XML                             15              0              0           1159
Markdown                        13            304              0           1016
YAML                            13             80            180            675
TeX                              1             10              0             97
TOML                             1              6              1             70
C                                1             40             54             61
DOS Batch                        1              8              1             26
make                             1              4              7              9
SVG                              1              0              0              1
-------------------------------------------------------------------------------
SUM:                           122           3120           3556          17391
-------------------------------------------------------------------------------

Commit count by author:

    50  Lion Krischer
    22  mrosskopf
    22  vlinus
    19  virginie
    10  Linvill
     7  LiSedZh
     6  memeier
     1  Thomas Haag
     1  mschwar
editorialbot commented 5 months ago

Paper file info:

📄 Wordcount for paper.md is 1331

✅ The paper includes a Statement of need section

editorialbot commented 5 months ago

License info:

🟡 License found: Other (Check here for OSI approval)

editorialbot commented 5 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.5880/GFZ.2.4.2020.003 is OK
- 10.1016/j.ascom.2015.06.004 is OK
- 10.5281/zenodo.10054611 is OK
- 10.5281/zenodo.10598393 is OK
- 10.5281/zenodo.10728558 is OK
- 10.1785/gssrl.81.3.530 is OK
- 10.3390/s23063315 is OK
- 10.5194/se-13-301-2022 is OK
- 10.5194/se-11-627-2020 is OK

MISSING DOIs

- No DOI given, and none found for title: Picoseismic response of hectometer-scale fracture ...

INVALID DOIs

- None
editorialbot commented 5 months ago

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

crvernon commented 5 months ago

👋 @mrosskopf and @ThomasLecocq - This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/6768 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

crvernon commented 5 months ago

👋 @kwinkunks - Would you be willing to review this submission to 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

crvernon commented 5 months ago

:wave: @meghanrjones - Would you be willing to review this submission to 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

crvernon commented 5 months ago

👋 @jlarsen-usgs - I know this one is a little bit outside of your interest area, but would you consider reviewing it? Thanks!

trichter commented 5 months ago

@crvernon Sorry to come back to this so late. I can take over the second review.

crvernon commented 5 months ago

@editorialbot add @trichter as reviewer

Excellent! Thanks @trichter!

editorialbot commented 5 months ago

@trichter added to the reviewers list!

trichter commented 5 months ago

Review checklist for @trichter

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

trichter commented 5 months ago

I have a conflict of interest with the last author of this submission. We are both long-time contributors to the obspy package. I request this COI to be waived.

crvernon commented 5 months ago

@trichter - as long as you and the author have not collaborated on this current submission, I believe it is OK to waive this COI since the "obspy" package has so many contributors.

ThomasLecocq commented 5 months ago

Review checklist for @ThomasLecocq

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

crvernon commented 5 months ago

:wave: @mrosskopf, @ThomasLecocq, @trichter - I'm glad to see this review rolling along. Could @ThomasLecocq and @trichter provide a short update to how things are going here in this thread?

Thanks!

crvernon commented 5 months ago

👋 @mrosskopf, @ThomasLecocq, @trichter - I'm glad to see this review rolling along. Could @ThomasLecocq and @trichter provide a short update to how things are going here in this thread?

Thanks!

👋 @mrosskopf, @ThomasLecocq, @trichter - Just following up on the above.

trichter commented 4 months ago

@crvernon Sorry for the delay, I had to find a long enough time slot for the review.

I've finished my review. The submission looks good to me.

I have two minor issues:

My other comments have been addressed in the issues. The new points in the open issue are minor.

crvernon commented 4 months ago

:wave: @ThomasLecocq - Just checking in to see how things are going. Can you give a time estimate to when you may be able to complete your review? Thanks!

mrosskopf commented 4 months ago

Thank you @trichter for your review. I adjusted the two minor issues in the paper and readme. I will also work on the suggestions you gave in the open issue in the next days.

crvernon commented 4 months ago

👋 @jessepisel - Would you be willing to review this submission to 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

crvernon commented 4 months ago

@editorialbot add @erexer as reviewer

editorialbot commented 4 months ago

@erexer added to the reviewers list!

jessepisel commented 4 months ago

Hi @crvernon I would be happy to review. What does the timeline look like for reviews at this time?

crvernon commented 4 months ago

@editorialbot add @jessepisel as reviewer

Great @jessepisel! How about sometime within the next two weeks. You can generate your review checklist using:

@editorialbot generate my checklist

Thanks so much!

editorialbot commented 4 months ago

@jessepisel added to the reviewers list!

erexer commented 3 months ago

Review checklist for @erexer

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

erexer commented 3 months ago

@editorialbot generate pdf

editorialbot commented 3 months ago

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

mrosskopf commented 3 months ago

Hello @crvernon, sadly, this review is not really moving forward. Is there a way to speed it up somehow? This paper will be part of my PhD so it would be great to have it done soonish since it was published already beginning of February. Until it is published, is there a way to cite this paper, because it does not have a DOI yet? It would be needed since other papers submitted later were already accepted. Thanks already for your efforts!

crvernon commented 3 months ago

Unfortunately @mrosskopf, we are bound by the time by which the reviewers can complete their reviews. Since this paper has not yet been accepted for publication, the only citation that can be issued is the following one without a formal DOI:

Rosskopf et al. (in review). DUGseis: A Python package for real-time and post-processing of picoseismicity. Journal of Open Source Software, 0(0), 4 6768.

I can move forward with my portion of this review once we have at least 2 reviewers sign off - having completed all of their checkboxes. To that measure...

@trichter, @erexer, @jessepisel please provide an update as to when you will be able to finish your review of this work so that we may move it forward.

trichter commented 3 months ago

I finished my review, see above.

crvernon commented 3 months ago

Yes sorry @trichter I accidentally included you in that comment. Many thanks!

erexer commented 3 months ago

@crvernon I'll get on it this week!

erexer commented 3 months ago

@mrosskopf can you say more about the author list? I see Martina Rosskopf, Virginie Durand, Linus Villiger, Joseph Doetsch, Anne Obermann, and Lion Krischer listed as authors on the paper, and only four of those folks listed as contributors in the repo. (not sure who seismotologist is)

mrosskopf commented 3 months ago

@erexer - Sure, I am guessing the four you are referring to are Virginie Durand, Linus Villiger, Lion Krischer and me. We worked together on bringing DUGseis to the state where it is now. Anne Obermann is a seismologist and my PhD supervisor, so she gave input on the software itself and helped with the paper. Joseph Doetsch was a main contributor on an earlier version of DUGseis which was used as a starting point for the current version. I hope I answered your question. Let me know if there is anything else.

jessepisel commented 2 months ago

Review checklist for @jessepisel

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

jessepisel commented 2 months ago

Hi @crvernon I got the package installed and up and running this past week. I opened a couple of minor issues that the authors have fixed. I have completed my review and checklist at this time. It would be good to see more test coverage for the package at some point down the line, but the current tests have sufficient coverage. It looks like the only bit to sort out is the additional contributions from other authors raised earlier in the review process. Once that is complete, this is all done on my side.

crvernon commented 2 months ago

@editorialbot remove @ThomasLecocq from reviewers

editorialbot commented 2 months ago

@ThomasLecocq removed from the reviewers list!

crvernon commented 2 months ago

@erexer could you post an update about what is left to address from your side of things? Thanks!

erexer commented 2 months ago

@crvernon working through the paper checklist, still need to confirm functionality and documentation. Thanks for the reminder.

erexer commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

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

erexer commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

:warning: An error happened when generating the pdf.

erexer commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

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