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[REVIEW]: f90nml - A Python module for Fortran namelists #1474

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whedon opened this issue May 24, 2019 · 19 comments

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@zbeekman zbeekman

@danielskatz danielskatz

@tclune tclune

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commented May 24, 2019 •
edited by zbeekman

Submitting author: @marshallward (Marshall Ward)
Repository: https://github.com/marshallward/f90nml
Version: v1.1
Editor: @danielskatz
Reviewer: @zbeekman, @tclune
Archive: Pending

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/8ec6def7e9baf878d703fe708855eaa8"><img src="http://joss.theoj.org/papers/8ec6def7e9baf878d703fe708855eaa8/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/8ec6def7e9baf878d703fe708855eaa8/status.svg)](http://joss.theoj.org/papers/8ec6def7e9baf878d703fe708855eaa8)

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

@zbeekman & @tclune, 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 @danielskatz know.

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

Review checklist for @zbeekman

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 (v1.1)?
  • Authorship: Has the submitting author (@marshallward) 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 @tclune

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 (v1.1)?
  • Authorship: Has the submitting author (@marshallward) 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 whedon assigned danielskatz May 24, 2019

@whedon whedon added the review label May 24, 2019

@whedon whedon referenced this issue May 24, 2019

Closed

[PRE REVIEW]: f90nml - A Python module for Fortran namelists #1472

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commented May 24, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @zbeekman, 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
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commented May 24, 2019 

Attempting PDF compilation. Reticulating splines etc...
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commented May 24, 2019

👉 Check article proof 📄 👈

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commented May 24, 2019

👋 @zbeekman, @tclune - we're ready to go ahead with the review in this issue.

And I know @zbeekman won't do anything until May 31...
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commented May 24, 2019

As stated in the first comment in this issue, please carry out your review in this issue by updating the your checklist (above).

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.)

Let me know if you have any problems or questions
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commented May 24, 2019

I can't seem to tick any check boxes
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commented May 24, 2019

Works for me. Of course, I first started checking @zbeekman 's boxes ... But I then unchecked them.
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commented May 24, 2019

Quoting the comment above:

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

I'm sure the first is ok - can you make sure you did the second?
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commented May 24, 2019

I'd accepted already for a previous review. It started working just now. Thanks!

@whedon whedon assigned tclune and zbeekman May 25, 2019

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commented May 31, 2019

I had one minor issue with the installation. 3 different methods are described, but the one that that avoids the requirement for root privileges did not work for me. I have amended a previously closed issue.
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commented May 31, 2019 •
edited

My only other negative comments are:

  • I could not find guidelines for community contributions. OTOH, this is a vanilla GitHub project that should easily work with standard approaches of fork+PR or opening issues.
  • The API documentation appears to be at best partially completed.
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commented May 31, 2019

Thanks very much for the feedback. On the three points:

  • For installation, I'm not able to reproduce the problem you're seeing, including on my work machine where I do not have root access. But we can work through that in marshallward/f90nml#49. (Or perhaps I just ought to remove the explicit setup.py install?)

  • I'll prepare a Contributing guidelines file. (Patches are so infrequent that I haven't had much need for one.)

  • I'll review the API, but could you mention any examples of missing items? I should say that I only consider the Namelist and Parser classes, along with their public functions, as part of the public API. But if there's an expectation to fully document all functions and to integrate them into the documentation, then I'm happy to do that.
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commented May 31, 2019

@marshallward Please disregard my API comment for now. I did not see the Makefile and was just staring at the raw files in the ./doc directory. I'm building the documentation and will update my comment.
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commented May 31, 2019

I retract my comment about the API. Documentation is complete and nicely done. And I thank the author for getting me to actually look at sphinx. I'd heard of it, but never (knowingly) used it before.
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commented Jun 3, 2019

👋 @zbeekman - How is your review coming along?
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commented Jun 3, 2019

👋 @zbeekman - How is your review coming along?

Jumping in now.

This was referenced Jun 3, 2019

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commented Jun 3, 2019

@danielskatz:

Once community/contributing is addressed, I'm happy to check the last checkbox. IMO, the last two issues are not show-stoppers, but I would categorize them as minor changes requested.

I could comment on a number of the boxes that I checked during the review process to document my justification and thought process, if that would be useful. @danielskatz please let me know if you think I should do this and whether or not there are any additional tasks for me, beyond checking off the contributing/community box once upstream provides adequate documentation.

@marshallward Nice work!
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commented Jun 3, 2019

Also, it looks like a lot of climate science tools/packages are using f90nml: https://github.com/marshallward/f90nml/network/dependents very cool!
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commented Jun 4, 2019

@zbeekman:

I could comment on a number of the boxes that I checked during the review process to document my justification and thought process, if that would be useful.

No, you don't need to do this.
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