Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[REVIEW]: FRIDGe: Fast Reactor Input Generator #1486

Closed
whedon opened this issue Jun 4, 2019 · 78 comments

Comments

@whedon
Copy link
Collaborator

commented Jun 4, 2019

Submitting author: @ryanstwrt (Ryan Stewart)
Repository: https://github.com/ryanstwrt/FRIDGe
Version: v1.0.1
Editor: @katyhuff
Reviewer: @kellyrowland, @pshriwise
Archive: 10.5281/zenodo.3361822

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/adf3c528083f563d4ac04163315ff90c"><img src="http://joss.theoj.org/papers/adf3c528083f563d4ac04163315ff90c/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/adf3c528083f563d4ac04163315ff90c/status.svg)](http://joss.theoj.org/papers/adf3c528083f563d4ac04163315ff90c)

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

@kellyrowland & @pshriwise, 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 @katyhuff know.

Please try and complete your review in the next two weeks

Review checklist for @kellyrowland

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: v1.0.1
  • Authorship: Has the submitting author (@ryanstwrt) 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 @pshriwise

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: v1.0.1
  • Authorship: Has the submitting author (@ryanstwrt) 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

This comment has been minimized.

Copy link
Collaborator Author

commented Jun 4, 2019

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

This comment has been minimized.

Copy link
Collaborator Author

commented Jun 4, 2019

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jun 4, 2019

@katyhuff

This comment has been minimized.

Copy link
Member

commented Jun 4, 2019

@ryanstwrt The first thing I'd like to note is the image in your paper -- it is too large. Please reduce its width.

@ryanstwrt

This comment has been minimized.

Copy link

commented Jun 4, 2019

@katyhuff Yup, I noticed this when I first uploaded my paper but I wasn't sure if I should update it before it went to you. After I update my document, does it automatically update the article proof so I can check my changes?

@pshriwise

This comment has been minimized.

Copy link

commented Jun 5, 2019

@ryanstwrt during install I got the following error:

error: package directory 'frdige/driver' does not exist

Just a typo it seems. Please find a relevant PR in your repo.

@ryanstwrt

This comment has been minimized.

Copy link

commented Jun 5, 2019

@pshriwise Thanks for the catch! I've merged the changes into the master branch.

@kellyrowland

This comment has been minimized.

Copy link
Collaborator

commented Jun 5, 2019

@ryanstwrt Please see issue #2 in your code repository for a request regarding clearer installation instructions.

@kellyrowland

This comment has been minimized.

Copy link
Collaborator

commented Jun 13, 2019

@pshriwise are you able to test that the EBRII_Driver.i input file generated with the instructions in the README functions correctly as MCNP6 input?

@pshriwise

This comment has been minimized.

Copy link

commented Jun 13, 2019

@kellyrowland I had some trouble too and found that it only worked if I imported the module from the repository rather than from the installed location. I think this is because the required data isn't being installed with the package...

@ryanstwrt I saw that you include package data in the setup.py but I think the preferred method these days is to use a MANIFEST.in file to make sure that data gets included in the package install. More info on that here

The following MANIFEST.in file did the trick for me:

include fridge/data/CotN/*.yaml
include fridge/data/assembly/*.yaml
include fridge/data/materials/*.yaml
include fridge/data/core/*.yaml
include fridge/fridge_input_file/*.yaml
include fridge/mcnp_input_files/*.i
@kellyrowland

This comment has been minimized.

Copy link
Collaborator

commented Jun 13, 2019

Good catch, thanks! I had only tried the import statement in the top repository directory.

@ryanstwrt

This comment has been minimized.

Copy link

commented Jun 14, 2019

@pshriwise I've added the MANIFEST.in file and left include_package_data=True. I've also removed the package_data={...} from the setup.py file. I believe this should address the problem @kellyrowland was experiencing. Thank you for the information on the preferred methodology for including package data. Let me know if the problem persists, and I can take some more time to investigate.

@pshriwise

This comment has been minimized.

Copy link

commented Jun 18, 2019

A few minor edits/suggestions to the paper:

  • "in small scales" → "at reduced scale"
  • "Building simple geometries is a relatively..."
  • "inputes" → "inputs"
  • "(fuel, clad, coolant..." → "(fuel, cladding, coolant..."
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jun 19, 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

@ryanstwrt

This comment has been minimized.

Copy link

commented Jun 19, 2019

@whedon generate pdf

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jun 19, 2019

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jun 19, 2019

@ryanstwrt

This comment has been minimized.

Copy link

commented Jun 19, 2019

@whedon generate pdf

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jun 19, 2019

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jun 19, 2019

@ryanstwrt

This comment has been minimized.

Copy link

commented Jun 19, 2019

@whedon generate pdf

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jun 19, 2019

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jun 19, 2019

@kellyrowland

This comment has been minimized.

Copy link
Collaborator

commented Jul 9, 2019

@ryanstwrt I don't see the MCNP DOI in the latest article proof - it looks like the .bib file was updated with the DOI but the .md file still has the previous reference.

@katyhuff

This comment has been minimized.

Copy link
Member

commented Aug 4, 2019

@labarba Thank you for the ping.

@pshriwise and @kellyrowland Thank you for your reviews -- we couldn't do this without you.

@ryanstwrt Thank you for your submission and for engaging actively in the review process! I have looked over the paper, double-checked all the DOI links, and have conducted a high-level review of the code itself. Thank you for handling my remaining comments.

Everything looks ship-shape to me. At this point, please double-check the paper yourself, review any lingering details in your code/readme/etc., and then make an archive of the reviewed software in Zenodo/figshare/other service. Please be sure that the DOI metadata (title, authors, etc.) matches this JOSS submission. Once that's complete, please update this thread with the DOI of the archive, and I'll move forward with accepting the submission. Until then, now is your moment for final touchups!

@labarba

This comment has been minimized.

Copy link
Member

commented Aug 5, 2019

Before the archive, we will need a new tagged release with all the changes during this review
https://github.com/ryanstwrt/FRIDGe/releases

@ryanstwrt

This comment has been minimized.

Copy link

commented Aug 6, 2019

@whedon generate pdf

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 6, 2019

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 6, 2019

@ryanstwrt

This comment has been minimized.

Copy link

commented Aug 6, 2019

@whedon generate pdf

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 6, 2019

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 6, 2019

@ryanstwrt

This comment has been minimized.

Copy link

commented Aug 6, 2019

I have released a new version of FRIDGe and archived it via Zenodo.
Here is the DOI for the archive: 10.21105/joss.01486
Feel free to let me know if you need anything else.

@arfon

This comment has been minimized.

Copy link
Member

commented Aug 6, 2019

@ryanstwrt - please don't use 10.21105/joss.01486 as the DOI for the archive. This is the DOI that we will use for the JOSS paper.

Please use a Zenodo-issued DOI.

@ryanstwrt

This comment has been minimized.

Copy link

commented Aug 6, 2019

I apologize, I misunderstood. Here is the new DOI: 10.5281/zenodo.3361822

@katyhuff

This comment has been minimized.

Copy link
Member

commented Aug 7, 2019

@whedon set v1.0.1 as version

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 7, 2019

OK. v1.0.1 is the version.

@katyhuff

This comment has been minimized.

Copy link
Member

commented Aug 7, 2019

@whedon set 10.5281/zenodo.3361822 as archive

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 7, 2019

OK. 10.5281/zenodo.3361822 is the archive.

@katyhuff

This comment has been minimized.

Copy link
Member

commented Aug 7, 2019

@whedon generate pdf

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 7, 2019

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 7, 2019

@katyhuff

This comment has been minimized.

Copy link
Member

commented Aug 7, 2019

Thanks again to @ryanstwrt for your submission, and thanks very much to @pshriwise @kellyrowland for your reviews. I think this is ready to accept @openjournals/joss-eics !

@arfon

This comment has been minimized.

Copy link
Member

commented Aug 7, 2019

@whedon accept

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 7, 2019

Attempting dry run of processing paper acceptance...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 7, 2019

Check final proof 👉 openjournals/joss-papers#888

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#888, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
@arfon

This comment has been minimized.

Copy link
Member

commented Aug 7, 2019

@whedon accept deposit=true

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 7, 2019

Doing it live! Attempting automated processing of paper acceptance...

@whedon whedon added the accepted label Aug 7, 2019

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 7, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 7, 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#889
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01486
  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...

@arfon

This comment has been minimized.

Copy link
Member

commented Aug 7, 2019

@kellyrowland, @pshriwise - many thank for your reviews here and to @katyhuff for editing this submission

@ryanstwrt - your paper is now accepted into JOSS ⚡️🚀💥

@arfon arfon closed this Aug 7, 2019

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 7, 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.01486/status.svg)](https://doi.org/10.21105/joss.01486)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01486">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01486/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01486/status.svg
   :target: https://doi.org/10.21105/joss.01486

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:

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
7 participants
You can’t perform that action at this time.