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[REVIEW]: HinetPy: A Python package for accessing and processing NIED Hi-net seismic data #6840

Closed editorialbot closed 3 months ago

editorialbot commented 4 months ago

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: v0.9.0 Editor: !--editor-->@elbeejay<!--end-editor-- Reviewers: @zhong-yy, @YuYifan2000, @stefanazzz Archive: 10.5281/zenodo.12523911

Status

status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/c59e6f7b6f30aea8a554b7f5687b4f88/status.svg)](https://joss.theoj.org/papers/c59e6f7b6f30aea8a554b7f5687b4f88)

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

@zhong-yy & @YuYifan2000 & @stefanazzz, 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 @elbeejay 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 @zhong-yy

📝 Checklist for @YuYifan2000

📝 Checklist for @stefanazzz

editorialbot commented 4 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 4 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (1948.3 files/s, 196269.3 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 commented 4 months ago

Paper file info:

📄 Wordcount for paper.md is 1204

✅ The paper includes a Statement of need section

editorialbot commented 4 months ago 
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 commented 4 months ago

License info:

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

editorialbot commented 4 months ago

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

elbeejay commented 4 months ago

Hi @zhong-yy, @YuYifan2000, and @stefanazzz - thank you all again for offering to peer-review HinetPy. Hopefully the peer review process ultimately results in the creation of a software tool that is useful to you and your research communities.

Please see the instructions at the top of this issue on how to generate your reviewer checklist and a link to the reviewer guidelines. Do not hesitate to reach out to me if you have any questions about the JOSS review process.

Right now we are asking that reviewers try to complete their reviews in 6 weeks if possible, so by July 16 in this case. Please keep us posted here if you think you will need an extension. I will ask the bot to issue reminders in 3 weeks so we stay aware of this on-going review.

Thanks again, Jay

elbeejay commented 4 months ago

@editorialbot remind @zhong-yy in three weeks

editorialbot commented 4 months ago

Reminder set for @zhong-yy in three weeks

elbeejay commented 4 months ago

@editorialbot remind @YuYifan2000 in three weeks

editorialbot commented 4 months ago

Reminder set for @YuYifan2000 in three weeks

elbeejay commented 4 months ago

@editorialbot remind @stefanazzz in three weeks

editorialbot commented 4 months ago

Reminder set for @stefanazzz in three weeks

YuYifan2000 commented 4 months ago

Review checklist for @YuYifan2000

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

The questions are posted in the issue to the target package: questions

The author have responded to my questions, the review is complete.

seisman commented 4 months ago

@editorialbot generate pdf

editorialbot commented 4 months ago

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

zhong-yy commented 4 months ago

Review checklist for @zhong-yy

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

The paper is well written except that there is a typo in line 38: 24,000 channels should have been 2,400.

elbeejay commented 4 months ago

Awesome, thanks @YuYifan2000 and @zhong-yy for your prompt reviews. The rapid comments and revisions between @YuYifan2000 and @seisman in https://github.com/seisman/HinetPy/issues/117 are exactly how the process is intended to work.

@seisman there's one small note from @zhong-yy at the bottom of his review: "The paper is well written except that there is a typo in line 38: 24,000 channels should have been 2,400." I'm just highlighting it here so you don't miss it!

seisman commented 4 months ago

Thanks @YuYifan2000 and @zhong-yy for the quick reviews.

The paper is well written except that there is a typo in line 38: 24,000 channels should have been 2,400.

Fixed in https://github.com/seisman/HinetPy/commit/4c974054775c10de507afd2876e0ac5d66dce390.

@editorialbot generate pdf

seisman commented 4 months ago

@editorialbot generate pdf

editorialbot commented 4 months ago

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

stefanazzz commented 4 months ago

Review checklist for @stefanazzz

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

stefanazzz commented 4 months ago

chekbox 'performance' and 'automated tests' not applicable. checkbox 'community guidelines' yes to question (2)

seisman commented 4 months ago

@stefanazzz Thanks for your review.

chekbox 'performance' and 'automated tests' not applicable.

The HinetPy package contains many tests at https://github.com/seisman/HinetPy/tree/main/tests. These tests cover 84% of the HinetPy source codes and are automatically executed by GitHub Actions for every change made to the main branch (see https://github.com/seisman/HinetPy/actions/runs/9577487328 for the latest run of the tests).

checkbox 'community guidelines' yes to question (2)

In response to YuYifan2000's reviews (https://github.com/seisman/HinetPy/issues/117), I've added a section to the README file in the main branch:

Feedback and contributions are welcome! Please feel free to open an issue or pull request if you have any suggestions or would like to contribute a feature. For additional information or specific questions, please open an issue directly.

I feel these sentences clarify that users should open issues or pull requests if they want to (1) Contribute to the software, 2) Report issues or problems with the software 3) Seek support.

Is there anything else that you suggest to add?

stefanazzz commented 4 months ago

Hi,

yes that is good. I have no further suggestion, thanks,

On Wed, Jun 19, 2024 at 8:57 AM Dongdong Tian @.***> wrote:

@stefanazzz https://github.com/stefanazzz Thanks for your review.

chekbox 'performance' and 'automated tests' not applicable.

The HinetPy package contains many tests at https://github.com/seisman/HinetPy/tree/main/tests. These tests cover 84% of the HinetPy source codes and are automatically executed by GitHub Actions for every change made to the main branch (see https://github.com/seisman/HinetPy/actions/runs/9577487328 for the latest run of the tests).

checkbox 'community guidelines' yes to question (2)

In response to YuYifan2000's reviews (seisman/HinetPy#117 https://github.com/seisman/HinetPy/issues/117), I've added a section to the README file in the main branch:

Feedback and contributions are welcome! Please feel free to open an issue or pull request if you have any suggestions or would like to contribute a feature. For additional information or specific questions, please open an issue directly.

I feel these sentences clarify that users should open issues or pull requests if they want to (1) Contribute to the software, 2) Report issues or problems with the software 3) Seek support.

Is there anything else that you suggest to add?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6840#issuecomment-2178012588, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKX4DUWKPPGSH57GGOHBMWDZIE2XTAVCNFSM6AAAAABIZLT5TGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNZYGAYTENJYHA . You are receiving this because you were mentioned.Message ID: @.***>

elbeejay commented 4 months ago

@stefanazzz I'd like to ask that you re-read and check off the remaining checkboxes on your checklist if possible. For the cases that are not applicable (such as the "Human and animal research" box, please check it off acknowledging that you saw the box). We like to get reviewers to check off their full checklists just as a measure of accountability for JOSS if we ever need to go back and revisit reviews. Thanks!

stefanazzz commented 4 months ago

all box checked also n/a/ to acknowledge that I saw them . you're welcome

stefanazzz commented 4 months ago

@seisman any chance that similar soft package is available for F-net data soon? thanks

On Wed, Jun 19, 2024 at 8:57 AM Dongdong Tian @.***> wrote:

@stefanazzz https://github.com/stefanazzz Thanks for your review.

chekbox 'performance' and 'automated tests' not applicable.

The HinetPy package contains many tests at https://github.com/seisman/HinetPy/tree/main/tests. These tests cover 84% of the HinetPy source codes and are automatically executed by GitHub Actions for every change made to the main branch (see https://github.com/seisman/HinetPy/actions/runs/9577487328 for the latest run of the tests).

checkbox 'community guidelines' yes to question (2)

In response to YuYifan2000's reviews (seisman/HinetPy#117 https://github.com/seisman/HinetPy/issues/117), I've added a section to the README file in the main branch:

Feedback and contributions are welcome! Please feel free to open an issue or pull request if you have any suggestions or would like to contribute a feature. For additional information or specific questions, please open an issue directly.

I feel these sentences clarify that users should open issues or pull requests if they want to (1) Contribute to the software, 2) Report issues or problems with the software 3) Seek support.

Is there anything else that you suggest to add?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6840#issuecomment-2178012588, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKX4DUWKPPGSH57GGOHBMWDZIE2XTAVCNFSM6AAAAABIZLT5TGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNZYGAYTENJYHA . You are receiving this because you were mentioned.Message ID: @.***>

seisman commented 4 months ago

@stefanazzz The HinetPy package already supports downloading F-net data. The F-net network ID is 0103 and the data are in WIN32 format. If you prefer to download F-net data in MSEED/SEED/SAC format from the F-net website (https://www.fnet.bosai.go.jp/), you can try the FnetPy package. The FnetPy is in its early stages and is not actively maintained, so it may not work as expected. Feel free to open issues in that repository and I'll find time fix them if any.

stefanazzz commented 4 months ago

Oh, that's great that it also supports Fnet (maybe make it more clear in the instructions/paper!). I had a go at Fnetpy earlier but had no luck with that, so I will happily use Hinetpy for that too. Thanks

On Fri, Jun 21, 2024 at 9:27 AM Dongdong Tian @.***> wrote:

@stefanazzz https://github.com/stefanazzz The HinetPy package already supports downloading F-net data. The F-net network ID is 0103 and the data are in WIN32 format. If you prefer to download F-net data in MSEED/SEED/SAC format from the F-net website ( https://www.fnet.bosai.go.jp/), you can try the FnetPy https://github.com/seisman/FnetPy package. The FnetPy is in its early stages and is not actively maintained, so it may not work as expected. Feel free to open issues in that repository and I'll find time fix them if any.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6840#issuecomment-2182263726, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKX4DUVGFQETVTNJAONHVA3ZIPPVVAVCNFSM6AAAAABIZLT5TGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOBSGI3DGNZSGY . You are receiving this because you were mentioned.Message ID: @.***>

elbeejay commented 4 months ago

@stefanazzz looking for your sign-off on the remaining two checkboxes in your checklist for the items "Automated tests" and "Community guidelines" - thanks!

stefanazzz commented 4 months ago

done thanks

elbeejay commented 4 months ago

Many thanks to our reviewers @zhong-yy, @YuYifan2000, and @stefanazzz for taking the time to review this submission and provide their feedback.

@seisman - I will now go over the paper from an editorial perspective, and then provide you with a list of items to complete for me so that we can square away the metadata prior to getting this HinetPy paper published with JOSS.

elbeejay commented 4 months ago

@editorialbot generate pdf

elbeejay commented 4 months ago

@editorialbot check references

editorialbot commented 4 months ago 
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 commented 4 months ago

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

elbeejay commented 4 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

elbeejay commented 4 months ago

@seisman I have a few minor comments on the paper text:

Line 75: Consider rewording to "The key features of HinetPy are:" or "Below the key features of HinetPy are listed:" or something along those lines.

Lines 80-81: Swap the square bracket "[" and "]" for parentheses "(" and ")"

Line 84: Consider rephrasing to something like "Uses multithreading to reduce download and processing times" or "Speeds up the downloading and processing workflow via the use of multithreading"

elbeejay commented 4 months ago

@seisman if you could do the "additional author tasks" in the comment above and let me know what the outcomes are, specifically I need to know if the version has changed and what the archived DOI is. Thanks!

seisman commented 4 months ago

Many thanks to @elbeejay and the three reviewers for handling and reviewing this submission.

Line 75: Consider rewording to "The key features of HinetPy are:" or "Below the key features of HinetPy are listed:" or something along those lines.

Lines 80-81: Swap the square bracket "[" and "]" for parentheses "(" and ")"

Line 84: Consider rephrasing to something like "Uses multithreading to reduce download and processing times" or "Speeds up the downloading and processing workflow via the use of multithreading"

I've made the changes in https://github.com/seisman/HinetPy/pull/120/commits/bd3bf768011a7f154b0c8b1d81d499e08a1ec011.

Double check authors and affiliations (including ORCIDs)

Yes.

Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.

HinetPy 0.9.0 is the release for the paper.

Archive the release on Zenodo/figshare/etc and post the DOI here. Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.

Archived on Zenodo at https://doi.org/10.5281/zenodo.12523911

Make sure that the license listed for the archive is the same as the software license.

Yes, the MIT license.

elbeejay commented 4 months ago

@editorialbot set v0.9.0 as version

editorialbot commented 4 months ago

Done! version is now v0.9.0

elbeejay commented 4 months ago

@editorialbot set 10.5281/zenodo.12523911 as archive

editorialbot commented 4 months ago

Done! archive is now 10.5281/zenodo.12523911

elbeejay commented 4 months ago

@editorialbot recommend-accept

editorialbot commented 4 months ago 
Attempting dry run of processing paper acceptance...
editorialbot commented 4 months ago 
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
elbeejay commented 4 months ago

Awesome thanks @seisman - I've recommended that we accept and publish this paper in JOSS. An editor-in-chief will do one final review of the information and may have minor comments or suggestions.

editorialbot commented 4 months ago

:wave: @openjournals/ese-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5536, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept