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[REVIEW]: SeisModels.jl: A Julia package for models of the Earth's interior #2043

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whedon opened this issue Jan 27, 2020 · 78 comments
Closed

[REVIEW]: SeisModels.jl: A Julia package for models of the Earth's interior #2043

whedon opened this issue Jan 27, 2020 · 78 comments

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@whedon whedon commented Jan 27, 2020

Submitting author: @anowacki (Andy Nowacki)
Repository: https://github.com/anowacki/SeisModels.jl
Version: v1.1.0
Editor: @kbarnhart
Reviewers: @daniellivingston, @joa-quim
Archive: 10.6084/m9.figshare.11993313

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/c2155dd354c1a0a6097003ce2b2b11fe"><img src="https://joss.theoj.org/papers/c2155dd354c1a0a6097003ce2b2b11fe/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/c2155dd354c1a0a6097003ce2b2b11fe/status.svg)](https://joss.theoj.org/papers/c2155dd354c1a0a6097003ce2b2b11fe)

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

@daniellivingston, @fhorrobin, & @joa-quim please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @kbarnhart know.

Please try and complete your review in the next two weeks

Review checklist for @daniellivingston

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

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@anowacki) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • 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?

Review checklist for @fhorrobin

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

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@anowacki) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • 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?

Review checklist for @joa-quim

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

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@anowacki) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • 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?
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@whedon whedon commented Jan 27, 2020

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

⭐️ Important ⭐️

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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@whedon whedon commented Jan 27, 2020

Reference check summary:

OK DOIs

- 10.1111/j.1365-246X.1995.tb03540.x is OK
- 10.1111/j.1365-246X.1991.tb06724.x is OK
- 10.1016/0031-9201(81)90046-7 is OK
- 10.1126/science.1199375 is OK
- 10.1785/gssrl.70.2.154 is OK
- 10.1785/gssrl.81.3.530 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Jan 27, 2020

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@kbarnhart kbarnhart commented Jan 27, 2020

👋 @anowacki, @daniellivingston, @fhorrobin, @joa-quim this is the review thread for the paper. All of our communications will happen here from now on.

All 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 https://github.com/openjournals/joss-reviews/issues/2043 so that a link is created to this thread. This helps create a record of the changes in the repository associated with this review. It also helps me keep track of open/closed issues that remain.

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 2-4 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 (@kbarnhart) if you have any questions/concerns.

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@daniellivingston daniellivingston commented Feb 13, 2020

@anowacki Great package. Does what it claims and does it very well and very elegantly. A minor nitpick and probably a personal taste issue; feel free to ignore.

You write that "[d]ocumentation is available at a dedicated website" without explicitly spelling out the URL. I understand the URL is relatively long (https://anowacki.github.io/SeisModels.jl/stable/), and that embedded hyperlinks mean that spelling out the full address is redundant, but I would still like to see the full path in the document. However, this is a minor thing and perhaps up to personal taste, so I will approve this paper regardless. Just something to think about.

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@daniellivingston daniellivingston commented Feb 13, 2020

Also, in the documentation (https://anowacki.github.io/SeisModels.jl/stable/#How-to-install-1), one finds this:

How to install

SeisModels.jl can be added to your Julia environment like so:

julia> import Pkg; pkg"add https://github.com/anowacki/SeisModels.jl"

This should be changed to match your repo README:

SeisModels.jl can be added to your Julia install like so:

julia> import Pkg; Pkg.add("SeisModels")
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@daniellivingston daniellivingston commented Feb 13, 2020

One of the review guidelines states:

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

Insofar as I can tell, discussions of third-party contributions are limited to this line in your README:

Currently, only three kinds of one-dimensional models are supported, but all model parameterisations and models are acceptable for inclusion. Contributions are welcome.

You may want to add a CONTRIBUTION.md document to the repo root, or just a small paragraph in the README expanding on your contribution process. You can find an over-the-top example of this here: https://reactjs.org/docs/how-to-contribute.html

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@anowacki anowacki commented Feb 13, 2020

I have set up a branch joss-review in which I propose to make the changes before merging them in finally.

@daniellivingston—thank you very much for these helpful suggestions.

Docs website URL

You write that "[d]ocumentation is available at a dedicated website" without explicitly spelling out the URL. […] I would still like to see the full path in the document.

I'm very happy to go along with this and I have updated the manuscript accordingly.

Contribution guidelines

You may want to add a CONTRIBUTION.md document to the repo root, or just a small paragraph in the README expanding on your contribution process.

Thank you for helping me realise this—I had not quite understood the guidelines here, but do now on re-reading them.

I have added a CONTRIBUTING.md file (this filename seems much more common, at least on GirHub and Gitlab repos) to the repo root which hopefully explains things in appropriate detail.

Docs installation instructions

This should be changed to match your repo README:

Thank you for spotting this. I did update the docs a little while ago (in 3c9826ac), but it transpires that the docs stopped building after an earlier commit. I can see that a number of new functions are in fact missing. I will have to investigate this further to work out what has happened.

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@anowacki anowacki commented Feb 13, 2020

@whedon generate pdf from branch joss-review

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@whedon whedon commented Feb 13, 2020

Attempting PDF compilation from custom branch joss-review. Reticulating splines etc...
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@whedon whedon commented Feb 13, 2020

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@anowacki anowacki commented Feb 13, 2020

Docs installation instructions

This should be changed to match your repo README:

Thank you for spotting this. I did update the docs a little while ago (in 3c9826ac), but it transpires that the docs stopped building after an earlier commit. I can see that a number of new functions are in fact missing. I will have to investigate this further to work out what has happened.

Docs are now back up. (The issue was with Travis configuration.)

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@kbarnhart kbarnhart commented Mar 16, 2020

@whedon generate pdf

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@kbarnhart kbarnhart commented Mar 16, 2020

@whedon check references

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@whedon whedon commented Mar 16, 2020

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@whedon whedon commented Mar 16, 2020

Reference check summary:

OK DOIs

- 10.1111/j.1365-246X.1995.tb03540.x is OK
- 10.1111/j.1365-246X.1991.tb06724.x is OK
- 10.1016/0031-9201(81)90046-7 is OK
- 10.1126/science.1199375 is OK
- 10.1785/gssrl.70.2.154 is OK
- 10.1785/gssrl.81.3.530 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@kbarnhart kbarnhart commented Mar 16, 2020

@anowacki I only have a couple of comments. They are meant to improve readability and accessibility for a non-specialist audience.

  • In paragraph 2: Define abbreviations: I think this only means writing out PREM as Preliminary Reference Earth Model. If you are aware of better written out names of the other Earth models, I'd recommend using them, but I suspect they will stay as AK135 and iasp91. I think P-wave and S-wave can stay as is.

  • In paragraph 4: "appropriate formats" is rather unspecific. Could you revise to state which formats are supported.

Once these changes are in the paper, please do the following:

  • Make a tagged release of your software
  • Archive the reviewed software in Zenodo or a similar service (e.g. figshare, an institutional repository)
  • Check the archival deposit (e.g., in Zenodo) has the correct metadata (title and author list exactly the same as on the JOSS paper).
  • Comment here with:
    • The version tag of the archived version
    • the DOI of the archived version

I with then move forward with accepting the submission (I will do some final metadata updating and then pass the submission on to the managing editor in chief who will handle final acceptance and publication).

anowacki added a commit to anowacki/SeisModels.jl that referenced this issue Mar 16, 2020
Update the JOSS paper to address the comments here:

    openjournals/joss-reviews#2043 (comment)
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@anowacki anowacki commented Mar 16, 2020

@whedon generate pdf from branch joss-review

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@whedon whedon commented Mar 16, 2020

Attempting PDF compilation from custom branch joss-review. Reticulating splines etc...
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@whedon whedon commented Mar 16, 2020

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@anowacki anowacki commented Mar 17, 2020

@kbarnhart I have archived v1.1.0 of SeisModels.jl at Figshare with doi 10.6084/m9.figshare.11993313.

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@kbarnhart kbarnhart commented Mar 17, 2020

@whedon set 10.6084/m9.figshare.11993313 as archive

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@whedon whedon commented Mar 17, 2020

OK. 10.6084/m9.figshare.11993313 is the archive.

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@kbarnhart kbarnhart commented Mar 17, 2020

@whedon set v1.1.0 as version

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@whedon whedon commented Mar 17, 2020

OK. v1.1.0 is the version.

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@kbarnhart kbarnhart commented Mar 17, 2020

@whedon accept

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@whedon whedon commented Mar 17, 2020

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Mar 17, 2020

Reference check summary:

OK DOIs

- 10.1111/j.1365-246X.1995.tb03540.x is OK
- 10.1111/j.1365-246X.1991.tb06724.x is OK
- 10.1016/0031-9201(81)90046-7 is OK
- 10.1126/science.1199375 is OK
- 10.1785/gssrl.70.2.154 is OK
- 10.1785/gssrl.81.3.530 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Mar 17, 2020

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

. Check final proof 👉 openjournals/joss-papers#1371

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1371, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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@kbarnhart kbarnhart commented Mar 17, 2020

Nice work @anowacki! Thanks to @daniellivingston and @joa-quim for your reviews.

I've now recommended that this be accepted and handed it off to the JOSS Editors in Chief who handle final processing.

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@arfon arfon commented Mar 17, 2020

@whedon accept deposit=true

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@whedon whedon commented Mar 17, 2020

Doing it live! Attempting automated processing of paper acceptance...
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@whedon whedon commented Mar 17, 2020

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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@whedon whedon commented Mar 17, 2020

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#1372
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02043
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

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@anowacki anowacki commented Mar 17, 2020

Thanks once again, @kbarnhart, @daniellivingston and @joa-quim. The process has been a great pleasure.

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@arfon arfon commented Mar 17, 2020

@daniellivingston, @joa-quim - many thanks for your reviews and to @kbarnhart for editing this submission

@anowacki - your paper is now published in JOSS ⚡️🚀💥

@arfon arfon closed this Mar 17, 2020
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@whedon whedon commented Mar 17, 2020

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.02043/status.svg)](https://doi.org/10.21105/joss.02043)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02043">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02043/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02043/status.svg
   :target: https://doi.org/10.21105/joss.02043

This is how it will look in your documentation:

DOI

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