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[REVIEW]: ThermoState: A State manager for Thermodynamics Courses #33

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whedon opened this Issue Oct 15, 2018 · 40 comments

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whedon commented Oct 15, 2018

Submitting author: @bryanwweber (Bryan W. Weber)
Repository: https://github.com/bryanwweber/thermostate
Version: v0.4.1
Editor: @kyleniemeyer
Reviewer: @william-pfalzgraff, @scls19fr
Archive: 10.5281/zenodo.1469771

Status

status

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Markdown: [![status](http://jose.theoj.org/papers/86ddd94292d33a3261a8f1f137a8f9f2/status.svg)](http://jose.theoj.org/papers/86ddd94292d33a3261a8f1f137a8f9f2)

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

@william-pfalzgraff & @scls19fr, 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/jose-reviews/invitations

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

Review checklist for @william-pfalzgraff

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 (v0.4.1)?
  • Authorship: Has the submitting author (@bryanwweber) made substantial 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? (and documentation is sufficient?)
  • 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 the need for this software 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?
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • 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 the need for this software 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 @scls19fr

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 (v0.4.1)?
  • Authorship: Has the submitting author (@bryanwweber) made substantial 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? (and documentation is sufficient?)
  • 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 the need for this software 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?
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • 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 the need for this software 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 commented Oct 15, 2018

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @william-pfalzgraff, 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/jose-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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whedon commented Oct 15, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Oct 15, 2018

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kyleniemeyer commented Oct 15, 2018

👋 @bryanwweber @william-pfalzgraff @scls19fr the review will take place in this issue. Please note the two reviewer checklists above, and you can leave additional review comments here.

You can also leave specific fixes/suggestions/issues as issues in the repo of the submission, just make sure to either mention this issue in those or vice versa so we can see the connection.

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bryanwweber commented Oct 16, 2018

Hi @william-pfalzgraff @scls19fr Thank you for agreeing to review this! In looking at the review issue here, I realized there are no installation instructions in the docs... The easiest way is to install with conda or pip, either of which should work. I think you have to use Python 3.5 or 3.6 because CoolProp is only available for those versions; with pip it has to be 3.5; with conda, you can use my CoolProp package for 3.6 with the following command (that should automatically install CoolProp):

conda install -c bryanwweber thermostate

You also need a channel that has pint if you're using conda; I'd recommend conda-forge. Please let me know if you need help installing so you can check the functionality of the software, and I'll certainly update the docs as part of this review.

Also to be fixed during this review: bryanwweber/thermostate#10 bryanwweber/thermostate#11 bryanwweber/thermostate#12

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scls19fr commented Oct 17, 2018

Hi @bryanwweber ,

Thanks for noticing the lack of install instructions.
Fixing doc could also be a nice improvement that you can probably also achieve.

This project relies on previous work about Python for scientists (Python for Scientific Computing, Python for Scientists and Engineers...) . Maybe you could also cite Matplotlib and Numpy at the very least.
Citing Pint may be more complicated for now according hgrecco/pint#717 but citing it like you did is probably not an issue.
Some of your examples (in the docs folder are using IPython) maybe you can also cite it.
You can probably fix all that before going beyond.

About "Statement of need", my feeling is quite mixed, I noticed that CoolProp have a "State" API also, so I wonder why such a package is not include directly into CoolProp?
But maybe this kind of question is out of the scope of this review.
Anyway giving an usage example with non SI units with both libraries could give readers an interest in using Thermostate instead of using directly Coolprop.

Best regards

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william-pfalzgraff commented Oct 17, 2018

Hi @bryanwweber, thanks for the install instructions. Having detailed install instructions directly int he readme for thermostate would be very helpful.

Do I understand correctly that pip can only be used if I am using python 3.5, and not python 3.6? Link to issue.

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bryanwweber commented Oct 17, 2018

@william-pfalzgraff I think the way to say it is, if you're using pip to install, you must be using Python 3.5 because CoolProp is only available for Python 3.5 from PyPI. If you're using conda, you can use either Python 3.5 or 3.6. Python 3.7 is supported by ThermoState (because ThermoState itself is pure-Python), but binary installers for CoolProp are not yet available for Python 3.7; you can of course build CoolProp yourself and then separately install ThermoState if you wish.

@scls19fr You said

You can probably fix all that before going beyond.

Do you want me to fix these citations in the paper before continuing with the review? I think your comment about the statement of need is quite relevant, and I will respond a bit later 😄

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kyleniemeyer commented Oct 17, 2018

@scls19fr From my perspective, @bryanwweber can work on the issues you have raised while you work through the remaining review items, and then we can return to the paper itself once he revises it. This is meant to be an iterative continuous process.

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bryanwweber commented Oct 19, 2018

@scls19fr @william-pfalzgraff I am updating the ThermoState repository on the jose-paper branch, and in bryanwweber/thermostate#15.

@scls19fr To respond to your "Statement of Need" comment:

  1. I added an example using EE units to the documentation, see bryanwweber/thermostate@71419dc Thank you for that suggestion!
  2. Specifically regarding the PropsSI interface in CoolProp: The typical call to PropsSI looks like
PropsSI('D', 'T', 300.0, 'P', 50000, 'water')

This interface is rather inscrutable to me. I'm pretty sure that you can't use keyword arguments here, so you just have to know that the first argument is the desired output, the next 4 are the input properties, and the last one is the substance. Second, there is not really a way to store a state, say, if you need several properties all at the same input conditions, you need to call PropsSI repeatedly with the same input. (There is a way to store the state in an AbstractState object from CoolProp, but that is part of what they call the "lower-level" interface and requires students to provide more input related to implementation details in CoolProp that I'd rather just not have to tell them about.) Third, ThermoState provides useful error messages if, for instance, a student only specifies one of the two required input properties. Fourth, students can use any unit system, whereas PropsSI requires SI base units (Pa, K, J/kg, etc.). Fifth, because students have to supply units with their input, I can check the dimensions and make sure that the input is suitable, and provide a useful error message if not. Finally, I designed ThermoState to use abbreviations for properties that are used in how I teach the class, e.g., x instead of Q for quality, using specific volume instead of density, etc., which of course again minimizes the overhead in evaluating properties.

I elected not to include all of this justification in the paper because it is already rather long for the purposes of typical JOSS/JOSE papers, and instead, I summarized most of the above by saying

Existing software packages that solve the equation of state for a substance have APIs that are
confusing for students who are learning not only thermodynamics, but Python as well.

As for including it directly in CoolProp, that could certainly be done, but I suspect they would want to make any units-based interface available for all of their interfaces (Matlab, Excel, Python, etc.) and I think adding that to CoolProp is outside the scope of this software.

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scls19fr commented Oct 19, 2018

Thanks @bryanwweber for this very clear explanation!
LGTM when bryanwweber/thermostate#15 will be merged

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william-pfalzgraff commented Oct 19, 2018

One other minor comment/question from me and then likewise LGTM when bryanwweber/thermostate#15 is merged.

My comment/question is about community guidelines. Does posting the project to Github constitute "Clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support" in the sense that third parties could do all of these things through Github? Or is more required, e.g. a statement in the README? @kyleniemeyer, do you have any thoughts?

If there is not already such a statement, it would be nice to add something to the README about how best to contact the author, how to report bugs, that pull requests are welcomed (if they are) etc.

Otherwise, looks good!

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bryanwweber commented Oct 20, 2018

@william-pfalzgraff There are 2 files that cover this: the Contributing instructions and the Contributor Covenant Code of Conduct. I've added a note linking to these files into the README! Thank you! 😄

@kyleniemeyer What should I do now? Do I make a new release of the software incorporating these suggestions?

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kyleniemeyer commented Oct 23, 2018

@whedon generate pdf

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whedon commented Oct 23, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Oct 23, 2018

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kyleniemeyer commented Oct 23, 2018

@bryanwweber I'm going to take a look at your paper now and see if it needs any minor edits. Once you make those (if there are any), then I'll ask you to archive your repo (e.g., in Zenodo) and report the DOI here. Then you'll be done!

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kyleniemeyer commented Oct 23, 2018

@bryanwweber a few paper comments/edits:

  • why is "manager" lowercase in the paper title? Although I personally prefer sentence-case, it looks like you are using title case, so shouldn't that be capitalized?
  • Could you add more-complete affiliation info? (e.g., city, state, country—what you'd typically see in a paper)
  • First paragraph in Statement of Need: I believe "students" needs an apostrophe
  • Second paragraph in Statement of Need: "don't" -> "do not"
  • Third paragraph in Statement of Need: is "utilize" really necessary there? I think "use" would work just fine.
  • In the first code snippet, I'm wondering if you should include where Q_ and State come from. I realize that the repo itself has more-complete use examples, but I think those in the paper would be more useful if they had those extra imports.
  • For the Oliphant reference, if this is a book I believe more details are needed. If this is an electronic-only reference, then we need a DOI or URL.

Finally, this isn't so much an edit but a general question on the package: why did you choose short single-letter abbreviations for properties rather than writing out the names (e.g., T, p vs temperature, pressure)? I would think the latter would be more clear (and thus more Pythonic)... the main benefit I can see is that the variables match those when setting using attributes (e.g., state.Tp = ...).

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bryanwweber commented Oct 23, 2018

@whedon generate pdf

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Attempting PDF compilation. Reticulating splines etc...
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whedon commented Oct 23, 2018

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bryanwweber commented Oct 23, 2018

@kyleniemeyer OK I fixed all your bullets (I think)

To your comment about the syntax, it's because we only ever use abbreviations for the properties in equations in class. I wanted to make the code look as much like a LaTeX equation as I could

LaTeX:

\dot{W}_{cv} = \dot{m}\left(h_1 - h_2\right)

ThermoState:

Wdot_cv = mdot*(st_1.h - st_2.h)

Plus, I think the abbreviations are pretty well standardized, even across fields. Finally, getting the temperature at 12 states (as is common in some more complicated problems) would be a huge pain and quite verbose if you had to type st_X.temperature every time.

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kyleniemeyer commented Oct 23, 2018

@bryanwweber LGTM! And got it, that makes sense.

OK, please archive the entire repo and provide the DOI here.

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kyleniemeyer commented Oct 23, 2018

@labarba This is ready for your attention now

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bryanwweber commented Oct 23, 2018

@kyleniemeyer The doi is 10.5281/zenodo.1469771 🎉

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kyleniemeyer commented Oct 23, 2018

@bryanwweber thanks—I forgot to ping @labarba first (sorry!), so if she has any additional changes you may need to do that again. Stay tuned!

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labarba commented Oct 23, 2018

@bryanwweber The paper has you as the sole author, but the Zenodo archive does not match that. It could be that Zenodo grabbed authors automatically from GitHub commits, and you need to manually edit the entry.

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bryanwweber commented Oct 24, 2018

Thanks @labarba! I changed the Zenodo entry so I'm the sole author there too. Any other places you can see to improve this submission?

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labarba commented Oct 24, 2018

It looks like a great piece of software for teaching thermo and I can't wait to share it with my colleagues!

@labarba labarba added the accepted label Oct 24, 2018

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labarba commented Oct 24, 2018

@whedon set 10.5281/zenodo.1469771 as archive

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whedon commented Oct 24, 2018

OK. 10.5281/zenodo.1469771 is the archive.

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labarba commented Oct 24, 2018

@whedon accept

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whedon commented Oct 24, 2018

Attempting dry run of processing paper acceptance...
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whedon commented Oct 24, 2018

Check final proof 👉 openjournals/jose-papers#1

If the paper PDF and Crossref deposit XML look good in openjournals/jose-papers#1, 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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labarba commented Oct 24, 2018

@whedon accept deposit=true

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whedon commented Oct 24, 2018

Doing it live! Attempting automated processing of paper acceptance...
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whedon commented Oct 24, 2018

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 openjournals/jose-papers#2
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/jose.00033
  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...

@labarba labarba closed this Oct 24, 2018

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whedon commented Oct 24, 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](https://jose.theoj.org/papers/10.21105/jose.00033/status.svg)](https://doi.org/10.21105/jose.00033)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/jose.00033">
  <img src="https://jose.theoj.org/papers/10.21105/jose.00033/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://jose.theoj.org/papers/10.21105/jose.00033/status.svg
   :target: https://doi.org/10.21105/jose.00033

This is how it will look in your documentation:

DOI

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labarba commented Oct 24, 2018

This paper is now published in JOSE !!!

@william-pfalzgraff, @scls19fr — Thank you for your review and being a part in this adventure in new publishing!

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bryanwweber commented Oct 24, 2018

@labarba @kyleniemeyer @william-pfalzgraff @scls19fr Thank you for your help and work getting this paper published!

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