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

[editorialbot]

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

Status

Status badge code:

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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 @trichter

📝 Checklist for @ThomasLecocq

[editorialbot]

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[editorialbot]

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]

Paper file info:

📄 Wordcount for paper.md is 1331

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

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]

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

[crvernon]

👋 @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 #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]

👋 @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]

👋 @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]

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

[trichter]

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

[crvernon]

@editorialbot add @trichter as reviewer

Excellent! Thanks @trichter!

[editorialbot]

@trichter added to the reviewers list!

[trichter]

Review checklist for @trichter

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/swiss-seismological-service/DUGseis?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@mrosskopf) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[trichter]

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]

@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]

Review checklist for @ThomasLecocq

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/swiss-seismological-service/DUGseis?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@mrosskopf) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[crvernon]

👋 @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]

👋 @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]

@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:

• Line 47: Please clarify the format of the station metadata, on first reading I thought it had to be in ASDF format.
• I checked the Community Guidelines box because IMO it is pretty clear how to contribute or ask for help (open issues, create PRs, e.t.c), but technically this box asks for more. Maybe add a section in the readme?

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

[crvernon]

👋 @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]

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]

👋 @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]

@editorialbot add @erexer as reviewer

[editorialbot]

@erexer added to the reviewers list!

[jessepisel]

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

[crvernon]

@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]

@jessepisel added to the reviewers list!