[PRE REVIEW]: rfsed: Receiver function analysis and dealing with sediment effects

[editorialbot]

Submitting author: @akinremisa (Stephen Akinremi)
Repository: https://github.com/akinremisa/rfsed
Branch with paper.md (empty if default branch):
Version: v0.1.7
Editor: @elbeejay
Reviewers: @paudetseis, @alistairboyce11
Managing EiC: Kristen Thyng

Status

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Author instructions

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

@akinremisa 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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Software report:

github.com/AlDanial/cloc v 1.88  T=0.15 s (379.4 files/s, 98949.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                              5              0              0           5613
Python                          44            797           2918           5054
YAML                             3              9             12            134
Markdown                         2             47              0            103
JSON                             1             18              0             82
TeX                              1              0              0             73
TOML                             1              0              0              7
-------------------------------------------------------------------------------
SUM:                            57            871           2930          11066
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

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

OK DOIs

- 10.21105/joss.01808 is OK
- 10.1785/0120120290 is OK
- 10.1785/0220220288 is OK
- 10.1002/2014JB011610 is OK
- 10.1029/1999jb900322 is OK

MISSING DOIs

- None

INVALID DOIs

- underreview is INVALID

[editorialbot]

Wordcount for paper.md is 529

[editorialbot]

Failed to discover a Statement of need section in paper

[editorialbot]

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

[editorialbot]

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[kthyng]

Hi @akinremisa and thanks for your submission! We have a backlog of submissions so I will add this to our waitlist. In the meantime, please suggest 5 reviewers from the database listed above or your own (non-conflicted) extended network. Their github handles are most useful to receive but please don't use "@" to reference them since it will prematurely ping them. Also please check out the other notifications from the editorial bot above. I see that you have very light docs that reference examples but the examples are all scripts — typically there would be notebooks or a hosted readthedocs version of examples/tutorials. Have you considered that sort of thing?

Thanks for your patience.

[akinremisa]

Hi @kthyng
Thank you for initiating the review of the manuscript and software I submitted.

Is it compulsory to add a section on "Statement of need" in the paper?

[kthyng]

Is it compulsory to add a section on "Statement of need" in the paper?

Yes: https://joss.readthedocs.io/en/latest/submitting.html#what-should-my-paper-contain

[akinremisa]

@kthyng
Here is a list of the handles of suggested reviewers:
trichter
paudetseis
xumi1993
jenndrei
schaefferaj
PyGLImER

[akinremisa]

@kthyng, I have remade the example files into notebooks to fit the requirements. Also, I have added a "Statement of need" section to the manuscript to make it complete. Thank you.

[kthyng]

@akinremisa — notebooks are not a requirement for your docs for JOSS but I suggested it since typically with notebooks or markdown in hosted docs, users are better able to understand, set up, and use your software properly. It looks like you dumped the contents of the .py files into .ipynb files but there is no explanation of how to use them or what they do, unless I missed some overview that does explain it all. In any case, reviewers will dig deeper into your repository to see what changes should be made and any changes could be made at that point instead.

[akinremisa]

@akinremisa — notebooks are not a requirement for your docs for JOSS but I suggested it since typically with notebooks or markdown in hosted docs, users are better able to understand, set up, and use your software properly. It looks like you dumped the contents of the .py files into .ipynb files but there is no explanation of how to use them or what they do, unless I missed some overview that does explain it all. In any case, reviewers will dig deeper into your repository to see what changes should be made and any changes could be made at that point instead.

Thank you again @kthyng. I now modified the notebooks to include the explanations on how to use them, while I wait for the reviewers' comments.

[kthyng]

@elbeejay Now that you are about done with another submission, can you take this one on?

[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]

@editorialbot generate pdf

[elbeejay]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.21105/joss.01808 is OK
- 10.1785/0120120290 is OK
- 10.1785/0220220288 is OK
- 10.1002/2014JB011610 is OK
- 10.1029/1999jb900322 is OK

MISSING DOIs

- None

INVALID DOIs

- underreview is INVALID

[editorialbot]

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

[elbeejay]

@akinremisa thanks for suggesting potential reviewers. I've just read over the paper and scanned through the repository and am going to start the search for reviewers, please have some patience as we go through this process to find folks that'll be able to provide high quality reviews.

[elbeejay]

Hello @trichter and @paudetseis, I'm reaching out to ask if you would be able to review the JOSS submission "rfsed: Receiver function analysis and dealing with sediment effects"

I am aware you both have experience publishing your work in JOSS, so I believe you'll be familiar with the process. I believe this submission aligns well with your subject-matter expertise, and would appreciate your reviews if you have the time.

Please let me know and reach out if you have any questions. Thanks!

[trichter]

Hello, Thank you for considering me as reviewer. Unfortunately, I have to decline because of time constraints.

[elbeejay]

Hi @PeterMakus and @xumi1993, I'm reaching out to ask if you'd be interested in reviewing this submission for JOSS titled "rfsed: Receiver function analysis and dealing with sediment effects". As you both have experience in Python and in seismology, I thought you'd be able to provide quality reviews of this submission.

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.

Thanks again for taking a moment to consider this, feel free to contact me if you have any questions about the JOSS review process. 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! If interested we can figure out how to set up a "co-review" for a colleague of yours that is a more junior or inexperienced member of the community.

Let me know, thanks.
Jay

[paudetseis]

Hi @elbeejay - sorry for my late response. I can review this submission.

[elbeejay]

@editorialbot add @paudetseis as reviewer

No problem, thank you @paudetseis!

[editorialbot]

@paudetseis added to the reviewers list!

[xumi1993]

Thank you for the peer review invitation, however, due to time constraints, I am unable to accept at this time.

[elbeejay]

No problem @trichter and @xumi1993 - thank you both for responding.

[elbeejay]

@rbeucher, I'm reaching out to ask if you'd be interested in reviewing this submission for JOSS titled "rfsed: Receiver function analysis and dealing with sediment effects". From what I can tell you have experience in the field of geodynamics and are comfortable programming in Python. I know you've also taken part in the JOSS review process as both a reviewer and as an author. Please take a look at this article and let us know if you are able and willing to serve as a peer-reviewer.

Thanks again for taking a moment to consider this, feel free to contact me if you have any questions about the JOSS review process. 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! If interested we can figure out how to set up a "co-review" for a colleague of yours that is a more junior or inexperienced member of the community.

Let me know, thanks.
Jay

[PeterMakus]

Hi @elbeejay ,
Thank you for the invitation to review. Unfortunately, I will have to decline due to time constraints.
Best wishes

[elbeejay]

@sannecottaar and @bobmyhill I'm reaching out to ask if you'd be interested in reviewing the submission "rfsed: Receiver function analysis and dealing with sediment effects" for JOSS. I expect you're both familiar with JOSS and our publication process from your recent publication on the BurnMan toolkit. Please take a look at this submission and let us know here if you'd be able to provide a review, thanks!

[rbeucher]

That would have been great but I can't at the moment...sorry

[sannecottaar]

Sorry, I can't take this on at the moment. Please consider Alistair Boyce alistairboyce11

[bobmyhill]

I don't think I count as an expert in the field, so I shouldn't review by JOSS guidelines. But here are a couple of things that I noticed:

• rf is published on PyPI - is there a reason you copy the code here? It is almost always better to add existing modules as dependencies.
• SeisPy is also published on PyPI. If you've modified the code because it needs correcting or improving, why not submit a PR to the SeisPy team? SeisPy is actively maintained.
• The environment.yml file is very restrictive. If everyone required exact versions of every dependency as done here, it would be very hard to set up multi-module python environments.
• The structure of the repo is unusual - tests and examples aren't normally stored in the src directory. Typically, module structure looks something like
  project/
  ├ package/
  ├ ├ init.py
  ├ ├ code1.py
  ├ ├ code2.py
  ├ examples/
  ├ tests/
  ├ ├ init.py
  ├ ├ test1.py
  ├ setup.py

[elbeejay]

Thanks all. @bobmyhill I think those are all reasonable questions, appreciate you taking a look.

@akinremisa you don't have to address them now, but we will re-post those questions in the review issue so that you can consider and respond.

[elbeejay]

Hi @alistairboyce, I'm reaching out to ask if you'd be interested in reviewing this submission for JOSS titled "rfsed: Receiver function analysis and dealing with sediment effects". You were recommended by Sanne Cottaar (@ sannecottaar) as a good fit for this submission.

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.

Thanks again for taking a moment to consider this, feel free to contact me if you have any questions about the JOSS review process. 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

[elbeejay]

Whoops, just realizing I didn't properly tag @alistairboyce11 above.

[alistairboyce11]

Hi @elbeejay, I am happy to take this on and will aim to turn it around in 6 weeks as requested. This is my first review of this type so I will try my best to follow the best practice guidelines provided.

Alistair

[elbeejay]

@editorialbot add @alistairboyce11 as reviewer

Sounds good, thanks Alistair! And no worries, please feel free to reach out anytime during the process if you have any questions.

[editorialbot]

@alistairboyce11 added to the reviewers list!

[elbeejay]

All, we will be starting our review in a separate issue which should mean those who are not signed up to be reviewers, or are not the submitting author will stop getting notifications. Thank you all for your responses and general helpfulness.

@bobmyhill - I will be relaying your comments in the official review issue as I do believe they warrent responses, if not revisions. Thank you for taking the time to provide them.

[elbeejay]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #6612.