[REVIEW]: PyGeoPressure: Geopressure Prediction in Python

[whedon]

Submitting author: @whimian (Hao Yu)
Repository: https://github.com/whimian/pyGeoPressure
Version: v0.1.8
Editor: @kthyng
Reviewer: @WalBytes, @JesperDramsch
Archive: 10.5281/zenodo.1452001

Status

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Reviewers and authors:

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Reviewer instructions & questions

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

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The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @kthyng know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @WalBytes

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• I confirm that I read and will adhere to the JOSS 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?
• Version: Does the release version given match the GitHub release (v0.1.8)?
• Authorship: Has the submitting author (@whimian) 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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @JesperDramsch

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• I confirm that I read and will adhere to the JOSS 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?
• Version: Does the release version given match the GitHub release (v0.1.8)?
• Authorship: Has the submitting author (@whimian) 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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @WalBytes, it looks like you're currently assigned as the reviewer for this paper 🎉.

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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 😿

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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[JesperDramsch]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

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# Compile the paper from a custom git branch
@whedon generate pdf from branch custom-branch-name

[JesperDramsch]

Good to go from my side @kthyng. It's a very nice package. Works as described and is well documented. Pleasure to review.

[GeoscienceSoftware]

Very useful package. The software functions as described. A minor revision in the second line of the paper; the author can re-word as follows: "The pore fluid pressure affects the physical properties of reservoir rocks, hence predicted pore pressure is a key input when building the geomechanical model of a reservoir. "
Good to go!

[whimian]

@WalBytes I've revised the paper in the latest commit.

[JesperDramsch]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[GeoscienceSoftware]

Awesome! Good to go from my side @kthyng <https://github.com/kthyng>.

…

On Oct 6, 2018 1:19 AM, "whedon" ***@***.***> wrote: 👉 Check article proof 📄 👈 <https://github.com/openjournals/joss-papers/blob/joss.00992/joss.00992/10.21105.joss.00992.pdf> — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#992 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/APJLejAjdXx9A7noDxZoWrEwyPNKSxtrks5uiEuIgaJpZM4XEOpF> .

[kthyng]

Excellent @JesperDramsch and @WalBytes!

Nice work @whimian! Please create an archive (on Zenodo, figshare, or other) and post the archive DOI in this issue.

[whimian]

@JesperDramsch and @WalBytes Many thanks for the review!

[whimian]

@kthyng Thank you for all your assistance.

DOI for the latest release is 10.5281/zenodo.1452001

[kthyng]

@whedon set 10.5281/zenodo.1452001 as archive

[whedon]

OK. 10.5281/zenodo.1452001 is the archive.

[kthyng]

hey @arfon we have another accepted paper here!!

[arfon]

@WalBytes, @JesperDramsch - many thanks for your reviews here and to @kthyng for editing this submission ✨

@whimian - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00992 ⚡ 🚀 💥

[whedon]

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

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HTML:
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reStructuredText:
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[whimian]

hey @kthyng,

There is something wrong with the author name .

My family name is "Yu", But it's "Hao" on the paper.

Could you please correct the author name?

[arfon]

@whimian - please change the order in your paper.md and we can recompile the paper.

[whimian]

@arfon I've changed the author name in paper.md, please recompile it.

[arfon]

OK that should be updated now.

[whimian]

Thanks. @arfon