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[REVIEW]: MoFEM: An open source, parallel finite element library #1441

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whedon opened this issue May 9, 2019 · 15 comments

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@whedon
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commented May 9, 2019

Submitting author: @likask (Lukasz Kaczmarczyk)
Repository: https://bitbucket.org/likask/mofem-cephas
Version: v0.8.22
Editor: @jedbrown
Reviewer: @tjhei, @chrisrichardson, @Kevin-Mattheus-Moerman, @vijaysm
Archive: Pending

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/43d9625e5ed28d5c493bfc0fae6d8215"><img src="http://joss.theoj.org/papers/43d9625e5ed28d5c493bfc0fae6d8215/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/43d9625e5ed28d5c493bfc0fae6d8215/status.svg)](http://joss.theoj.org/papers/43d9625e5ed28d5c493bfc0fae6d8215)

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

@tjhei & @chrisrichardson, @Kevin-Mattheus-Moerman, & @vijaysm, 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 @jedbrown know.

Please try and complete your review in the next two weeks

Review checklist for @tjhei

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 (v0.8.22)?
  • Authorship: Has the submitting author (@likask) 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 @chrisrichardson

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 (v0.8.22)?
  • Authorship: Has the submitting author (@likask) 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 @Kevin-Mattheus-Moerman

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 (v0.8.22)?
  • Authorship: Has the submitting author (@likask) 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 @vijaysm

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 (v0.8.22)?
  • Authorship: Has the submitting author (@likask) 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

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commented May 9, 2019

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

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commented May 9, 2019

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

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commented May 9, 2019

@jedbrown

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commented May 9, 2019

@tjhei @chrisrichardson @Kevin-Mattheus-Moerman 👋 Welcome and thanks for agreeing to review! The comments from @whedon above outline the review process, which takes place in this thread (possibly with issues filed in the MoFem repository). I'll be watching this thread if you have any questions.

@likask

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commented May 9, 2019

Thank you all for agreeing to spend some time on this. Making life easier, to kick start installation, you can use docker & spack as follows:

git clone --recurse-submodules https://bitbucket.org/likask/mofem-cephas.git mofem-cephas
cd mofem-cephas
docker build -t spack_mofem_build --force-rm=true --file=Dockerfile-spack-mofem-testing .

@chrisrichardson

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commented May 15, 2019

@whedon commands

@whedon

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commented May 15, 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

@chrisrichardson

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commented May 15, 2019

@likask - https://bitbucket.org/likask/mofem-cephas/src/joss/media/paper.md seems not to work. Is this the correct URL anyway?

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commented May 15, 2019

@chrisrichardson Hello, I had to move paper to the directory visible by whedon to generate PDF. You will find it here https://bitbucket.org/likask/mofem-cephas/src/master/joss/paper.md

See here to view compiled PDF

@chrisrichardson

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commented May 17, 2019

@likask - it seems like something must be wrong though. The URL is supposed to point at the software, not the paper?

Repository: Is the source code for this software available at the repository url?

@arfon

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commented May 17, 2019

@whedon generate pdf

@whedon

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commented May 17, 2019

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

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commented May 17, 2019

@likask - it seems like something must be wrong though. The URL is supposed to point at the software, not the paper?

I've updated the URL for the software at the top of the review issue.

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commented May 17, 2019

@likask

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commented May 17, 2019

@arfon Thank you.

@chrisrichardson Source for a master branch is here. Alternatively, you can browse in doxygen generated web-pages here.

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