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[REVIEW]: OpenTripPlanner for R #1926

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whedon opened this issue Dec 2, 2019 · 28 comments
Closed

[REVIEW]: OpenTripPlanner for R #1926

whedon opened this issue Dec 2, 2019 · 28 comments
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@whedon whedon commented Dec 2, 2019

Submitting author: @mem48 (Malcolm Morgan)
Repository: https://github.com/ropensci/opentripplanner
Version: v0.2.0
Editor: @danielskatz
Reviewer: @danielskatz
Archive: 10.5281/zenodo.3558311

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/a08bf8a245f529c60daf6c6abfdc0736"><img src="https://joss.theoj.org/papers/a08bf8a245f529c60daf6c6abfdc0736/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/a08bf8a245f529c60daf6c6abfdc0736/status.svg)](https://joss.theoj.org/papers/a08bf8a245f529c60daf6c6abfdc0736)

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

@danielskatz, 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 @danielskatz

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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?
  • Contribution and authorship: Has the submitting author (@mem48) 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 functionality 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

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?
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@whedon whedon commented Dec 2, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @danielskatz it looks like you're currently assigned to review 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

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf
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@whedon whedon commented Dec 2, 2019

Attempting to check references...
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@whedon whedon commented Dec 2, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Dec 2, 2019


OK DOIs

- 10.1016/j.trpro.2018.09.027 is OK
- 10.1007/978-3-642-15775-2_25 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Dec 2, 2019

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@danielskatz danielskatz commented Dec 2, 2019

Note that this submission has been accepted by rOpenSci (ropensci/software-review#295), so this JOSS process is just checking to ensure that JOSS criteria are met.

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@danielskatz danielskatz commented Dec 2, 2019

👋 @mem48 - please merge the changes in ropensci/opentripplanner#41 or let me know which you disagree with.

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@danielskatz danielskatz commented Dec 2, 2019

Also in the second reference in the bib file, I see
booktitle = {Algorithms ? {ESA} 2010},

The ? seems incorrect. Can you check/fix this?

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@mem48 mem48 commented Dec 2, 2019

@danielskatz I've fixed the ? and I also fixed the formatting of the code blocks

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@danielskatz danielskatz commented Dec 2, 2019

@whedon generate pdf

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@whedon whedon commented Dec 2, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Dec 2, 2019

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@danielskatz danielskatz commented Dec 2, 2019

The next steps are to make an archive of the code somewhere, potentially using Zenodo (as described here) or another archive, then let me know both the doi of the archive and the version number of the code, if it has changed. Please also be sure the title and author metadata associated with the archive matches the paper title and authors.

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@mem48 mem48 commented Dec 2, 2019

The DOI of the archive is 10.5281/zenodo.3558311

I've check the title and authors match

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@mem48 mem48 commented Dec 2, 2019

And both the paper and the archive are version 0.2

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@danielskatz danielskatz commented Dec 2, 2019

@whedon set 10.5281/zenodo.3558311 as archive

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@whedon whedon commented Dec 2, 2019

OK. 10.5281/zenodo.3558311 is the archive.

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@danielskatz danielskatz commented Dec 2, 2019

@whedon accept

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@whedon whedon commented Dec 2, 2019

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Dec 2, 2019


OK DOIs

- 10.1016/j.trpro.2018.09.027 is OK
- 10.1007/978-3-642-15775-2_25 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Dec 2, 2019

Check final proof 👉 openjournals/joss-papers#1146

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1146, 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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@danielskatz danielskatz commented Dec 2, 2019

@whedon accept deposit=true

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@whedon whedon commented Dec 2, 2019

Doing it live! Attempting automated processing of paper acceptance...
@whedon whedon added the accepted label Dec 2, 2019
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@whedon whedon commented Dec 2, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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@whedon whedon commented Dec 2, 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#1147
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01926
  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...

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@danielskatz danielskatz commented Dec 2, 2019

Congratulations to @mem48!

@danielskatz danielskatz closed this Dec 2, 2019
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@whedon whedon commented Dec 2, 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.01926/status.svg)](https://doi.org/10.21105/joss.01926)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01926">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01926/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01926/status.svg
   :target: https://doi.org/10.21105/joss.01926

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:

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@mem48 mem48 commented Dec 2, 2019

Thanks @danielskatz

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