[REVIEW]: Ocellaris: an exactly incompressible DG FEM solver for free surface flows

[whedon]

Submitting author: @TormodLandet (Tormod Landet)
Repository: https://bitbucket.org/ocellarisproject/ocellaris
Version: v2019.0.2
Editor: @labarba
Reviewer: @inducer, @piyueh
Archive: 10.5281/zenodo.2601988

Status

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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

@inducer & @piyueh, 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 @labarba know.

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

Review checklist for @inducer

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: v2019.0.2
• Authorship: Has the submitting author (@TormodLandet) 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 @piyueh

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: v2019.0.2
• Authorship: Has the submitting author (@TormodLandet) 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. @inducer, 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:

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

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

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[labarba]

👋 @inducer, @piyueh —
Thank you for agreeing to review for JOSS: we couldn't do this without you 🙏

This is where the action happens. You both have a reviewer checklist at the top of this thread. Work your way through that, and feel free to ask questions here and to open issues in the submission repository as needed.

The JOSS review process

[TormodLandet]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[piyueh]

@labarba @TormodLandet Regarding the question "Version: Does the release version given match the GitHub release (2019.0.1)?", should I only review this specific version? Or should I review the master branch? It appears there are some new commits in the repository after the commit that is tagged with 2019.0.1.

[TormodLandet]

I have worked on updating the documentation since the release. There should not be any code changes as far as I remember. I can release 2019.0.2 with the current changes if that is preferable. The only change since 2019.0.1 is extending and moving the documentation to www.ocellaris.org and working on the JOSS paper.

[labarba]

As the review proceeds, the author will make changes, so commits will accrue. But your review should be on the master branch, unless the author requests that we work on a separate branch for the whole review. What we don't want, though, is to confuse reviewers with more than one branch active in review.

[piyueh]

OK, I'll review the master branch

[inducer]

Here's a marked-up copy of the paper. I've raised a number of concerns.

On the code end (for now):

• https://bitbucket.org/ocellarisproject/ocellaris/issues/9/joss-lid-driven-cavity-example-crashes
• https://bitbucket.org/ocellarisproject/ocellaris/issues/8/joss-unclosed-file-warning

Other things:

• Also noticed that two references are missing DOIs.
• I couldn't find specific community guidelines (see review checklist) in the docs.