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[REVIEW]: PyGeoPressure: Geopressure Prediction in Python #992

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whedon opened this Issue Oct 2, 2018 · 25 comments

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whedon commented Oct 2, 2018

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

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/9b2dfdf4e60f236e1387bca03e3d8394"><img src="http://joss.theoj.org/papers/9b2dfdf4e60f236e1387bca03e3d8394/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/9b2dfdf4e60f236e1387bca03e3d8394/status.svg)](http://joss.theoj.org/papers/9b2dfdf4e60f236e1387bca03e3d8394)

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) 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

@WalBytes & @JesperDramsch, 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.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

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

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)?
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whedon Oct 2, 2018

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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 🎉.

⭐️ 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 😿

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whedon commented Oct 2, 2018

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 🎉.

⭐️ 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:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

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

@whedon commands
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Attempting PDF compilation. Reticulating splines etc...
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whedon commented Oct 2, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Oct 2, 2018

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JesperDramsch Oct 4, 2018

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@whedon commands

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JesperDramsch commented Oct 4, 2018

@whedon commands

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Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Compile the paper
@whedon generate pdf

🚧 🚧 🚧 Experimental Whedon features 🚧 🚧 🚧

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

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whedon commented Oct 4, 2018

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Compile the paper
@whedon generate pdf

🚧 🚧 🚧 Experimental Whedon features 🚧 🚧 🚧

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

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JesperDramsch Oct 5, 2018

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

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JesperDramsch commented Oct 5, 2018

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

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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!

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WalBytes commented Oct 5, 2018

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!

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whimian Oct 6, 2018

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

whimian commented Oct 6, 2018

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

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@whedon generate pdf

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JesperDramsch commented Oct 6, 2018

@whedon generate pdf

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Attempting PDF compilation. Reticulating splines etc...
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whedon commented Oct 6, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Oct 6, 2018

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WalBytes commented Oct 6, 2018

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kthyng Oct 8, 2018

Excellent @JesperDramsch and @WalBytes!

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

kthyng commented Oct 8, 2018

Excellent @JesperDramsch and @WalBytes!

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

@kthyng kthyng added the accepted label Oct 8, 2018

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whimian Oct 9, 2018

@JesperDramsch and @WalBytes Many thanks for the review!

whimian commented Oct 9, 2018

@JesperDramsch and @WalBytes Many thanks for the review!

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whimian Oct 9, 2018

@kthyng Thank you for all your assistance.

DOI for the latest release is 10.5281/zenodo.1452001

whimian commented Oct 9, 2018

@kthyng Thank you for all your assistance.

DOI for the latest release is 10.5281/zenodo.1452001

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kthyng Oct 9, 2018

@whedon set 10.5281/zenodo.1452001 as archive

kthyng commented Oct 9, 2018

@whedon set 10.5281/zenodo.1452001 as archive

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whedon Oct 9, 2018

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OK. 10.5281/zenodo.1452001 is the archive.

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whedon commented Oct 9, 2018

OK. 10.5281/zenodo.1452001 is the archive.

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kthyng Oct 9, 2018

hey @arfon we have another accepted paper here!!

kthyng commented Oct 9, 2018

hey @arfon we have another accepted paper here!!

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arfon Oct 9, 2018

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@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 ⚡️ 🚀 💥

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arfon commented Oct 9, 2018

@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 ⚡️ 🚀 💥

@arfon arfon closed this Oct 9, 2018

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🎉🎉🎉 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](http://joss.theoj.org/papers/10.21105/joss.00992/status.svg)](https://doi.org/10.21105/joss.00992)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.00992">
  <img src="http://joss.theoj.org/papers/10.21105/joss.00992/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.00992/status.svg
   :target: https://doi.org/10.21105/joss.00992

This is how it will look in your documentation:

DOI

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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whedon commented Oct 9, 2018

🎉🎉🎉 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](http://joss.theoj.org/papers/10.21105/joss.00992/status.svg)](https://doi.org/10.21105/joss.00992)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.00992">
  <img src="http://joss.theoj.org/papers/10.21105/joss.00992/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.00992/status.svg
   :target: https://doi.org/10.21105/joss.00992

This is how it will look in your documentation:

DOI

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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whimian Oct 11, 2018

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?

whimian commented Oct 11, 2018

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?

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arfon Oct 11, 2018

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

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arfon commented Oct 11, 2018

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

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whimian Oct 12, 2018

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

whimian commented Oct 12, 2018

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

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arfon commented Oct 12, 2018

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whimian commented Oct 14, 2018

Thanks. @arfon

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