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[REVIEW]: PressureDrop.jl: Pressure traverses for oil & gas wells #1642

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whedon opened this issue Aug 12, 2019 · 92 comments
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@whedon whedon commented Aug 12, 2019

Submitting author: @jnoynaert (Jared Noynaert)
Repository: https://github.com/jnoynaert/PressureDrop.jl
Version: v1.0.1
Editor: @oliviaguest
Reviewer: @wkearn, @mancellin
Archive: 10.5281/zenodo.3529746

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/06b3959e7319a94468e572edac33e0f4"><img src="https://joss.theoj.org/papers/06b3959e7319a94468e572edac33e0f4/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/06b3959e7319a94468e572edac33e0f4/status.svg)](https://joss.theoj.org/papers/06b3959e7319a94468e572edac33e0f4)

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

@wkearn & @mancellin, 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 @oliviaguest know.

Please try and complete your review in the next two weeks

Review checklist for @wkearn

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 (v1.0.1)?
  • Authorship: Has the submitting author (@jnoynaert) 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 @mancellin

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 (v1.0.1)?
  • Authorship: Has the submitting author (@jnoynaert) 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 whedon commented Aug 12, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @wkearn, @mancellin 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:

  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

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

@whedon generate pdf
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@whedon whedon commented Aug 12, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Aug 12, 2019

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@oliviaguest oliviaguest commented Aug 12, 2019

👋@wkearn, @mancellin — This is where the action happens. You both have a review checklist to work your way through. Feel free to post questions here and open review issues in the submission repository.

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@labarba labarba commented Aug 12, 2019

Hi everybody! If you open a new issue in the submission repository, it's nice if you link to this very issue thread here, so we get a cross-link from GitHub.

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@oliviaguest oliviaguest commented Aug 12, 2019

[ @labarba thanks for all the help so far ]

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@jnoynaert jnoynaert commented Aug 29, 2019

@whedon generate pdf

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@whedon whedon commented Aug 29, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Aug 29, 2019

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@jnoynaert jnoynaert commented Aug 29, 2019

@whedon generate pdf

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@whedon whedon commented Aug 29, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Aug 29, 2019

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@mancellin mancellin commented Aug 30, 2019

PressureDrop.jl is a specialized tool to model the pressure profile in oil and gas wells.
The code can be installed and tested easily using Julia package manager. It is well documented and the code behaved as documented when I tried it.

Some comments and suggestions have been discussed there: jnoynaert/PressureDrop.jl#3.

Overall, I can recommend the paper for publication.

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@oliviaguest oliviaguest commented Sep 7, 2019

@mancellin thank you so much!

@wkearn could you give us a status update for your review?

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@wkearn wkearn commented Sep 11, 2019

@oliviaguest Sorry for the delay, I plan to finish my review this afternoon.

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@oliviaguest oliviaguest commented Sep 11, 2019

@wkearn Fantastic and thank you. 😊

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@wkearn wkearn commented Sep 18, 2019

Sorry, again, for taking so long with my review.

This package looks great! It is definitely designed with a specialized audience in mind, but the code is very clearly documented, and someone with experience using these kinds of models will, I think, have no problem running the models and analyzing the output.

I have a few minor suggestions that I will add to jnoynaert/PressureDrop.jl/issues/3 but otherwise I am happy to recommend this paper for publication.

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@oliviaguest oliviaguest commented Sep 19, 2019

@labarba what is the next step, please? 😊 Do we wait for the suggestions (see comment just above mine) to be discussed because doing anything else at the moment?

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@labarba labarba commented Sep 19, 2019

@wkearn You said "otherwise" you're happy to recommend publication. Thus, we wait for you to confirm that your minor suggestion is addressed, and you are satisfied.

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@oliviaguest oliviaguest commented Oct 2, 2019

@wkearn just a quick reminder to report back if/when you can — thanks. 😄

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@jnoynaert jnoynaert commented Oct 7, 2019

Sorry, I haven't had a chance to get back and make those documentation changes yet. I should have some spare time this week to finish them.

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@oliviaguest oliviaguest commented Oct 17, 2019

@jnoynaert any updates? 👍

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@jnoynaert jnoynaert commented Oct 18, 2019

@oliviaguest finally pushed this and tagged Will in the original issue

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@danielskatz danielskatz commented Nov 2, 2019

👋 @jnoynaert & @oliviaguest - what's the status of this now?

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@oliviaguest oliviaguest commented Nov 4, 2019

@whedon generate pdf

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@oliviaguest oliviaguest commented Nov 7, 2019

Ah, yes! Thanks! @openjournals/joss-eics 👋

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@kyleniemeyer kyleniemeyer commented Nov 8, 2019

Hi @jnoynaert, just a few things before I finalize acceptance:

  1. In the newest Zenodo record (10.5281/zenodo.3529746, I believe), can you fix the title to match that of the paper?

  2. One of our paper requirements is

A summary describing the high-level functionality and purpose of the software for a diverse, non-specialist audience.

Can you edit the introduction to make it a bit more accessible to a more general audience?

  1. Also, a number of the older references are missing information:
  • Payne:1979 reference: missing doi={10.2118/6874-PA}, volume=31, number=9
  • Ramey:1962 reference: missing doi={10.2118/96-PA}, volume=14, number=4
  • Griffith:1961 reference: missing doi={10.1115/1.3682268}, volume=83, number=3, pages={307--318}`
  • Beggs:1973 reference: missing doi={10.2118/4007-PA}, volume=25, number=5
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@jnoynaert jnoynaert commented Nov 8, 2019

@whedon generate pdf

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@jnoynaert jnoynaert commented Nov 8, 2019

@whedon commands

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@whedon whedon commented Nov 8, 2019

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

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

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

# Ask Whedon to check the references for missing DOIs
@whedon check references

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@jnoynaert jnoynaert commented Nov 8, 2019

@whedon generate pdf

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@whedon whedon commented Nov 8, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Nov 8, 2019

PDF failed to compile for issue #1642 with the following error:

Error reading bibliography ./paper.bib (line 18, column 3):
unexpected "d"
expecting space, ",", white space or "}"
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

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@jnoynaert jnoynaert commented Nov 8, 2019

@whedon generate pdf

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@whedon whedon commented Nov 8, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Nov 8, 2019

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@jnoynaert jnoynaert commented Nov 8, 2019

@whedon check references

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@whedon whedon commented Nov 8, 2019

Attempting to check references...
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@whedon whedon commented Nov 8, 2019


OK DOIs

- 10.1115/1.3682268 is OK
- 10.2118/4007-PA is OK
- 10.2118/6874-PA is OK
- 10.2118/96-PA is OK
- 10.1115/1.3227845 is OK
- 10.5281/zenodo.593105 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@kyleniemeyer kyleniemeyer commented Nov 8, 2019

@whedon set 10.5281/zenodo.3529746 as archive

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@whedon whedon commented Nov 8, 2019

OK. 10.5281/zenodo.3529746 is the archive.

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@jnoynaert jnoynaert commented Nov 8, 2019

@kyleniemeyer

  • updated title @ doi.org/10.5281/zenodo.3529746)
  • added references and verified the last DOI-less citation does not have one available (at least a reasonably discoverable one, at any rate)
  • added two introductory paragraphs to clarify a bit for people not working in that field
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@kyleniemeyer kyleniemeyer commented Nov 8, 2019

@jnoynaert ok, looks good! The introduction is much better.

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@kyleniemeyer kyleniemeyer commented Nov 8, 2019

@whedon accept

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@whedon whedon commented Nov 8, 2019

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Nov 8, 2019


OK DOIs

- 10.1115/1.3682268 is OK
- 10.2118/4007-PA is OK
- 10.2118/6874-PA is OK
- 10.2118/96-PA is OK
- 10.1115/1.3227845 is OK
- 10.5281/zenodo.593105 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Nov 8, 2019

Check final proof 👉 openjournals/joss-papers#1095

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1095, 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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@kyleniemeyer kyleniemeyer commented Nov 8, 2019

@whedon accept deposit=true

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@whedon whedon commented Nov 8, 2019

Doing it live! Attempting automated processing of paper acceptance...
@whedon whedon added the accepted label Nov 8, 2019
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@whedon whedon commented Nov 8, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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@whedon whedon commented Nov 8, 2019

🚨🚨🚨 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#1096
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01642
  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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@kyleniemeyer kyleniemeyer commented Nov 8, 2019

Congrats @jnoynaert on your article's publication in JOSS!

Many thanks to @wkearn and @mancellin for reviewing, and @oliviaguest for editing this submission.

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@whedon whedon commented Nov 8, 2019

🎉🎉🎉 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.01642/status.svg)](https://doi.org/10.21105/joss.01642)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01642">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01642/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01642/status.svg
   :target: https://doi.org/10.21105/joss.01642

This is how it will look in your documentation:

DOI

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