[REVIEW]: ObsPlus: A Pandas Centric ObsPy Expansion Pack

whedon commented 3 years ago

Submitting author: @d-chambers (Derrick Chambers) Repository: https://github.com/niosh-mining/obsplus Version: v0.1.0 Editor: @leouieda Reviewer: @seisman, @ThomasLecocq Archive: 10.5281/zenodo.4544008

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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

@seisman & @ThomasLecocq, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ 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 ✨

Review checklist for @seisman

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@d-chambers) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

Review checklist for @ThomasLecocq

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@d-chambers) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

whedon commented 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @seisman, @ThomasLecocq it looks like you're currently assigned to review this paper :tada:.

: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.

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whedon commented 3 years ago

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

OK DOIs

-  10.25080/Majora-92bf1922-00a  is OK

MISSING DOIs

- 10.1088/1749-4699/8/1/014003 may be a valid DOI for title: ObsPy: A bridge for seismology into the scientific Python ecosystem

INVALID DOIs

- None

whedon commented 3 years ago

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

leouieda commented 3 years ago

👋 @d-chambers @seisman @ThomasLecocq this is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread 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 openjournals/joss-reviews#2236 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 reviews to be completed within about 4 weeks. Please let me know if any of you require some more time. We can also use @whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me here (@leouieda) or email me privately if you have any questions/concerns.

leouieda commented 3 years ago

@d-chambers please have a look at the missing DOI report from Whedon above and add the missing DOIs to your BibTex file.

d-chambers commented 3 years ago

@leouieda my apologies, I missed this last request. I just added the correct DOI to the Bib Tex file.

leouieda commented 3 years ago

Hi @ThomasLecocq @seisman just checking in on the status of this review 🙂 Let me know if you have any questions or concerns.

seisman commented 3 years ago

Sorry for forgetting this paper. I'll review it in the following week.

leouieda commented 3 years ago

Thank you for the update @seisman 🙂

leouieda commented 3 years ago

👋🏼 Hi @seisman @ThomasLecocq just checking in to see how things are going with the reviews. It would be nice to get some progress on this soon but let me know if you require more time (we’re all living in strange times).

seisman commented 3 years ago

Hi @leouieda, sorry for the delay. I'm a little too busy with job interviews and preparing for AGU meeting recently. I may have more time in December.

leouieda commented 3 years ago

@seisman thanks for the update. I realize that the earlier than usual AGU deadlines are causing problems. Good luck on the job interviews and let me know when you have some more time.

@d-chambers apologies for the unusually long delays with this paper. I really appreciate your patience in these strange times we live in 😞

d-chambers commented 3 years ago

Hi @leouieda,

No worries, I understand the circumstances.

leouieda commented 3 years ago

Hi @seisman @ThomasLecocq are there any updates on this review?

seisman commented 3 years ago

I'll start to review the submission in the following week.

arfon commented 3 years ago

:wave: @ThomasLecocq @leouieda happy new year! Just checking in here on the status of this review?

calum-chamberlain commented 3 years ago

Sorry to pester, but @leouieda are the any updates on this? I'm keen to have this out so that I can cite it for some upcoming papers for which ObsPlus had been very useful!

ThomasLecocq commented 3 years ago

It's all good for me

d-chambers commented 3 years ago

I would love to get this wrapped up soon. I addressed all of @seisman's comments thus far, but I am happy to make any additional improvements that might be required.

seisman commented 3 years ago

I reviewed the original v0.1.0 version. It's good for me.

ThomasLecocq commented 3 years ago

I can't check the boxes above, but I have no further remarks other than the citation for Pandas seem buggy in the latest rendered PDF. Other than that, it's good to go

danielskatz commented 3 years ago

@whedon re-invite @ThomasLecocq as reviewer

whedon commented 3 years ago

OK, the reviewer has been re-invited.

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

danielskatz commented 3 years ago

This should let you check the boxes

ThomasLecocq commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

PDF failed to compile for issue #2696 with the following error:

 Error reading bibliography file paper.bib:
(line 7, column 9):
unexpected "Y"
expecting space, ",", white space or "}"
Looks like we failed to compile the PDF

ThomasLecocq commented 3 years ago

All 🟢 for me, just the missing Pandas citation in the PDF available above.

d-chambers commented 3 years ago

Ok the pdf now compiles and I think the citation looks correct.

@whedon generate pdf

danielskatz commented 3 years ago

@whedon generate pdf

(whedon commands need to be on the first line of a comment)

whedon commented 3 years ago

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

ThomasLecocq commented 3 years ago

All good now!

kyleniemeyer commented 3 years ago

Hi @d-chambers, I'm the AEIC on duty this week, and stepping in here to help get this past the finish line. It looks like the reviewers have both recommended this for acceptance.

Some final steps needed:

[x] Your article is missing a Statement of Need section, which is a required element of JOSS papers. You may be able to just move some existing text into that section.
[x] Once you've made that change, you can archive your software repository (e.g., on Zenodo) and provide the DOI here.

d-chambers commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

d-chambers commented 3 years ago

Current-version DOI: http://doi.org/10.5281/zenodo.4544008

All-version DOI: http://doi.org/10.5281/zenodo.3228432

d-chambers commented 3 years ago

ok @kyleniemeyer, let me know if anything else is required. Also, thanks for your work on JOSS :smile:

kyleniemeyer commented 3 years ago

Thanks @d-chambers - can you clean up the author list on the current-version Zenodo record to match that of the paper?

d-chambers commented 3 years ago

Done. My apologies for not doing it originally, I am new to Zenodo.

kyleniemeyer commented 3 years ago

@whedon set 10.5281/zenodo.4544008 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4544008 is the archive.

kyleniemeyer commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

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

OK DOIs

-  10.1088/1749-4699/8/1/014003  is OK
- 10.25080/Majora-92bf1922-00a is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 3 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2237

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2237, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

kyleniemeyer commented 3 years ago

@d-chambers sorry, looks like I missed something - the QuakeML reference is actually missing some key citation details, including a few authors, the volume (54) and number (1), and DOI: 10.4401/ag-4874

Can you add these?

d-chambers commented 3 years ago

Ok, I have added the volume, number and DOI.

The missing authors issue is interesting. The authors are included in the bib but don't show up in the PDF. Same issue for the ObsPy reference. I will dig into it more.

kyleniemeyer commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

d-chambers commented 3 years ago

Sorry haven't merged the changes to master yet, still trying to figure out why the middle authors aren't showing.

kyleniemeyer commented 3 years ago

Ah, I think the issue related to the commas in the author fields.

For the ObsPy reference, it should be {Krischer, L. and Megies, T. and Barsch, R. and Beyreuther, M. and Lecocq, T. and Caudron, C. and Wassermann, J.} (you want "and" rather than commas between the authors)

Also, you also do not need brackets around all the surnames, except in uncommon cases.

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