[PRE REVIEW]: HinetPy: A Python package for accessing and processing NIED Hi-net seismic data

[editorialbot]

Submitting author: !--author-handle-->@seisman<!--end-author-handle-- (Dongdong Tian) Repository: https://github.com/seisman/HinetPy Branch with paper.md (empty if default branch): joss-paper Version: 0.8.1 Editor: !--editor-->@elbeejay<!--end-editor-- Reviewers: @zhong-yy, @YuYifan2000, @stefanazzz Managing EiC: Kristen Thyng

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

@seisman if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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[editorialbot]

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

OK DOIs

- 10.1063/1.1854197 is OK
- 10.1038/nature03675 is OK
- 10.1029/2006JB004386 is OK
- 10.1186/BF03353076 is OK
- 10.1088/1749-4699/8/1/014003 is OK
- 10.1002/2014JB011341 is OK
- 10.1016/j.epsl.2005.08.009 is OK
- 10.1038/s41467-017-00229-9 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (1929.6 files/s, 194380.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          16            501           1088           1744
PO File                         23            511            640           1633
reStructuredText                25            327            190            656
YAML                             7             36             25            187
Markdown                         4             47              0            167
TOML                             1             14              3            115
TeX                              1              6              0             88
make                             2             15              8             53
CSV                              1              0              0              5
-------------------------------------------------------------------------------
SUM:                            80           1457           1954           4648
-------------------------------------------------------------------------------

Commit count by author:

   577  Dongdong Tian
    43  dependabot[bot]
     8  TIAN Dongdong
     1  Marius Kriegerowski
     1  Yasu Sawaki

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1204

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[editorialbot]

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

[kthyng]

Hi @seisman and thanks for your submission! I am looking for some specific items to make sure your submission fits our requirements at a high level (not at the more detailed review level) before moving on to finding an editor or putting this on our waitlist if no relevant editors are available. I'll comment over time as I have a chance to go through them:

• [x] Substantial scholarly effort
• [x] Documentation
• [x] Tests of some sort
• [x] Installation instructions
• [x] Clear research application
• [x] Check paper

In the meantime, please take a look at the comments above ⬆️ from the editorialbot to address any DOI, license, or paper issues if you're able, or suggest reviewers.

[kthyng]

@seisman I am going to ping the editorial board to see if this is in scope for JOSS in terms of it being a web client which might not fit. This will take a few weeks, thanks for your patience.

[kthyng]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[kthyng]

Hi @seisman and sorry for the delay in getting back to you. I have a couple of questions.

1. One editor noted: "I notice the paper mentions ObsPy (https://docs.obspy.org/) as a standard package for accessing seismological data. I'd be happier seeing this implemented as an extension to that package, to make the NIED Hi-net data in the paper consistent with the other sources already supported by ObsPy." Is there a possibility of integrating this work into ObsPy fully or more closely, or having it as a sort of extension?
2. I noticed the note in the paper:

   Users must register an account on the NIED Hi-net website for accessing the data and renew the account annually.

Is this account free and automatic or does it need to be manually approved? Would it be possibly to have some test data available long-term for reviewers and for testing purposes that doesn't require an account?

[seisman]

Hi @seisman and sorry for the delay in getting back to you. I have a couple of questions.

No worries. Thank you for considering this submission.

1. One editor noted: "I notice the paper mentions ObsPy (https://docs.obspy.org/) as a standard package for accessing seismological data. I'd be happier seeing this implemented as an extension to that package, to make the NIED Hi-net data in the paper consistent with the other sources already supported by ObsPy." Is there a possibility of integrating this work into ObsPy fully or more closely, or having it as a sort of extension?

In the seismological community, the International Federation of Digital Seismograph Networks (FDSN) defines the FDSN web service interfaces that provide access to data and metadata in seismology. The ObsPy package's obspy.clients.fdsn module provides a Pythonic interface of the FDSN web service, to access seismic data from data centers as long as the data center's web server implements the FDSN web services. As of today, there are already many data centers (https://www.fdsn.org/datacenters/) that support FDSN web services, but NIED Hi-net still doesn't. Accessing seismic data from NIED Hi-net is different from accessing via FDSN web services, so it's impossible to integrate the HinetPy package into ObsPy.

2. I noticed the note in the paper:

Users must register an account on the NIED Hi-net website for accessing the data and renew the account annually.

Is this account free and automatic or does it need to be manually approved? Would it be possibly to have some test data available long-term for reviewers and for testing purposes that doesn't require an account?

Yes, the account is free. Users can register the account by filling out an online form (https://hinetwww11.bosai.go.jp/nied/registration/?LANG=en) and need to wait for a few business days for approval.

The key feature of the HinetPy package is accessing seismic data from NIED Hi-net, so local test data is insufficient for reviewers to evaluate the package. What's more, the NIED Hi-net prohibits any distribution of their data, so an account is required for reviewing the package.

[kthyng]

Hi @seisman. This submission has been a bit tricky to decide on since it is both related to a web application and heavily involves data access (both of which aren't always in scope), but we think it is in scope for JOSS so let's move forward.

[kthyng]

@elbeejay can you edit this submission

[kthyng]

@editorialbot invite @elbeejay as editor

[editorialbot]

Invitation to edit this submission sent!

[elbeejay]

@editorialbot assign @elbeejay as editor

[editorialbot]

Assigned! @elbeejay is now the editor

[elbeejay]

Hi @seisman, thanks for the submission and your answer above provides some of the information reviewers are going to need to have in order to test and evaluate your software. I'm going to be handling the editorial process for your submission going forward; do you have any potential reviewers in mind that you might suggest? This seems like a good opportunity for others in your field to sign up and access data from NIED Hi-net so it definitely will make sense to identify the people who are in the same field to review this work.

If you do have suggestions, please provide their names and github handles here (omit the "@" so they don't get tagged). Thanks!

[seisman]

Thanks for handling the submission.

As for potential reviewers, maybe Yiyuan Zhong (zhong-yy) and Stefan Nielsen (stefanazzz) who opened a series of issues recently.

[elbeejay]

@stefanazzz and @zhong-yy would either of you be interested in reviewing this submission to JOSS titled "HinetPy: A Python package for accessing and processing NIED Hi-net seismic data"? JOSS is an open-source, diamond access software journal. The submitting author, Professor Tian, recommended you both as reviewers as you are users of HinetPy and have submitted issues recently. To provide some additional information about what reviewing will entail, I am providing a summary of the JOSS review process below.

At JOSS we do open checklist-driven reviews; peer-review criteria can be viewed here. This issue is a "pre-review issue" which we use to find peer-reviewers. Once 3 reviewers are found, we will officially start the review in a dedicated GitHub issue. At present we are asking reviewers to complete reviews in 6 weeks, although this can be extended if needed. If you are not able to review but can recommend someone else, please mention them here (in this case please mention their GitHub handle without the "@" symbol).

If you are interested, please take a look at the journal's conflict of interest policy to ensure you do not have a conflict before agreeing to review this submission.

Please do not feel any pressure to accept this review request if you do not have the time or do not feel comfortable reviewing this software package, we appreciate and respect our peer-reviewers' time. If you cannot serve as a reviewer at this time but have a peer, collaborator, student, or colleague who might be available and would be a good fit for this submission, please let me know!

Thanks, Jay

[zhong-yy]

Hi Jay @elbeejay

Thanks for the invitation. I have used HinetPy in a recent project. I am very interested in reviewing this paper.

[elbeejay]

@editorialbot add @zhong-yy as reviewer

Great, thank you! We will officially kick off the review in a separate "review" issue thread once we've found one or two more folks that are willing to serve as reviewers.

[editorialbot]

@zhong-yy added to the reviewers list!

[elbeejay]

Hi @zhuwq0 and @YuYifan2000 - I'm reaching out to ask if either of you would be interested in peer-reviewing HinetPy for the Journal of Open Source Software (JOSS). I saw that you are both geophysicists and have forked the HinetPy repository, so I wanted to ask if you'd be willing to review the software package and associated paper as you are clearly familar with the project as well as the scientific domain.

To provide some additional information about what reviewing will entail, I am providing a summary of the JOSS review process below.

At JOSS we do open checklist-driven reviews; peer-review criteria can be viewed here. This issue is a "pre-review issue" which we use to find peer-reviewers. Once 3 reviewers are found, we will officially start the review in a dedicated GitHub issue. At present we are asking reviewers to complete reviews in 6 weeks, although this can be extended if needed. If you are not able to review but can recommend someone else, please mention them here (in this case please mention their GitHub handle without the "@" symbol).

If you are interested, please take a look at the journal's conflict of interest policy to ensure you do not have a conflict before agreeing to review this submission.

Please do not feel any pressure to accept this review request if you do not have the time or do not feel comfortable reviewing this software package, we appreciate and respect our peer-reviewers' time. If you cannot serve as a reviewer at this time but have a peer, collaborator, student, or colleague who might be available and would be a good fit for this submission, please let me know!

Thanks, Jay

[YuYifan2000]

Hi Jay,

Thanks for reaching out. I am happy to review the HinetPy as I did have experience using it.

Regards,

Yifan

On Jun 3, 2024, at 2:53 PM, J. Hariharan @.***> wrote:

Hi @zhuwq0 https://github.com/zhuwq0 and @YuYifan2000 https://github.com/YuYifan2000 - I'm reaching out to ask if either of you would be interested in peer-reviewing HinetPy for the Journal of Open Source Software (JOSS) https://joss.theoj.org/. I saw that you are both geophysicists and have forked the HinetPy repository, so I wanted to ask if you'd be willing to review the software package and associated paper as you are clearly familar with the project as well as the scientific domain.

To provide some additional information about what reviewing will entail, I am providing a summary of the JOSS review process below.

At JOSS we do open checklist-driven reviews; peer-review criteria can be viewed here https://joss.readthedocs.io/en/latest/review_criteria.html. This issue is a "pre-review issue" which we use to find peer-reviewers. Once 3 reviewers are found, we will officially start the review in a dedicated GitHub issue. At present we are asking reviewers to complete reviews in 6 weeks, although this can be extended if needed. If you are not able to review but can recommend someone else, please mention them here (in this case please mention their GitHub handle without the "@" symbol).

If you are interested, please take a look at the journal's conflict of interest policy https://joss.readthedocs.io/en/latest/reviewer_guidelines.html?#joss-conflict-of-interest-policy to ensure you do not have a conflict before agreeing to review this submission.

Please do not feel any pressure to accept this review request if you do not have the time or do not feel comfortable reviewing this software package, we appreciate and respect our peer-reviewers' time. If you cannot serve as a reviewer at this time but have a peer, collaborator, student, or colleague who might be available and would be a good fit for this submission, please let me know!

Thanks, Jay

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6583#issuecomment-2146190017, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANUESLFODST2W5AE6J35A7LZFTQWPAVCNFSM6AAAAABFZW3IUSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNBWGE4TAMBRG4. You are receiving this because you were mentioned.

[elbeejay]

@editorialbot add @YuYifan2000 as reviewer

Awesome, thanks @YuYifan2000 - we'll start a separate official "review thread" when the formal review process begins and we close this "pre-review" issue

[editorialbot]

@YuYifan2000 added to the reviewers list!

[stefanazzz]

Of course, glad to help with that. I used hynetpy very recently. I wish there was a python equivalent for fnet , too. Please use my work address @.*** Thanks Stefan

On Sat, 1 Jun 2024 at 01:01, J. Hariharan @.***> wrote:

@stefanazzz https://github.com/stefanazzz and @zhong-yy https://github.com/zhong-yy would either of you be interested in reviewing this submission to JOSS titled "HinetPy: A Python package for accessing and processing NIED Hi-net seismic data"? JOSS is an open-source, diamond access software journal. The submitting author, Professor Tian, recommended you both as reviewers as you are users of HinetPy and have submitted issues recently. To provide some additional information about what reviewing will entail, I am providing a summary of the JOSS review process below.

At JOSS we do open checklist-driven reviews; peer-review criteria can be viewed here https://joss.readthedocs.io/en/latest/review_criteria.html. This issue is a "pre-review issue" which we use to find peer-reviewers. Once 3 reviewers are found, we will officially start the review in a dedicated GitHub issue. At present we are asking reviewers to complete reviews in 6 weeks, although this can be extended if needed. If you are not able to review but can recommend someone else, please mention them here (in this case please mention their GitHub handle without the "@" symbol).

If you are interested, please take a look at the journal's conflict of interest policy https://joss.readthedocs.io/en/latest/reviewer_guidelines.html?#joss-conflict-of-interest-policy to ensure you do not have a conflict before agreeing to review this submission.

Please do not feel any pressure to accept this review request if you do not have the time or do not feel comfortable reviewing this software package, we appreciate and respect our peer-reviewers' time. If you cannot serve as a reviewer at this time but have a peer, collaborator, student, or colleague who might be available and would be a good fit for this submission, please let me know!

Thanks, Jay

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6583#issuecomment-2143134099, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKX4DUTFUUUNBVLQCFZXVUDZFEFM7AVCNFSM6AAAAABFZW3IUSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNBTGEZTIMBZHE . You are receiving this because you were mentioned.Message ID: @.***>

[elbeejay]

@editorialbot add @stefanazzz as reviewer.

Hi Stefan - since this is happening through GitHub I believe the notifications are automatically routed through to the email address you have setup with GitHub so I can't control that unfortunately.

[editorialbot]

@stefanazzz added to the reviewers list!

[elbeejay]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6840.