[REVIEW]: scarplet: A Python package for topographic template matching and diffusion dating

Question

[REVIEW]: scarplet: A Python package for topographic template matching and diffusion dating

Closed this issue 6 years ago · 49 comments

Submitting author: @rmsare (Robert Sare)
Repository: https://github.com/rmsare/scarplet
Version: 0.1.0
Editor: @kthyng
Reviewer: @fclubb, @mcflugen
Archive: 10.5281/zenodo.1492786

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/2a23987d6f629b4be281de912f66db69"><img src="http://joss.theoj.org/papers/2a23987d6f629b4be281de912f66db69/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/2a23987d6f629b4be281de912f66db69/status.svg)](http://joss.theoj.org/papers/2a23987d6f629b4be281de912f66db69)

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

@fclubb & @mcflugen, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
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 @kthyng know.

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

Review checklist for @fclubb

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: Does the release version given match the GitHub release (0.1.0)?
Authorship: Has the submitting author (@rmsare) 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 @mcflugen

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: Does the release version given match the GitHub release (0.1.0)?
Authorship: Has the submitting author (@rmsare) 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)?

Answer 1 · 2018-11-05T17:32:59.000Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @fclubb, it looks like you're currently assigned as the reviewer for this paper 🎉.

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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:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

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@whedon commands

Answer 2 · 2018-11-05T17:33:00.000Z

Attempting PDF compilation. Reticulating splines etc...

Answer 3 · 2018-11-05T17:33:31.000Z

👉 Check article proof 📄 👈

Answer 4 · 2018-11-05T19:52:18.000Z

@kthyng and reviewers - thanks for this! I am tagging co-author @gehilley in case he would like to follow the review.

Answer 5 · 2018-11-06T19:02:59.000Z

@rmsare Nice work 👍I think this is great.

I submitted a couple issues to your repository that address most of the items on our checklist. There are only a couple of other things.

Things to do:

Fix installation issues (stgl/scarplet#59)
Fix examples (stgl/scarplet#60)
Fix gdal_merge import problem (stgl/scarplet#61)
Add Statement of Need to the documentation
Add DOIs to the references in paper.md

I think that's it for now.

Answer 6 · 2018-11-07T14:12:45.000Z

@mcflugen Thank you for the thorough review and your work on the conda recipe! I will dig into this and hope to address your comments and implement changes by Monday.

Answer 7 · 2018-11-08T09:31:45.000Z

Hi @rmsare, thanks for submitting this, the package looks really useful. Here are some notes/comments, which I think are mostly similar those that @mcflugen mentioned.

Installation and functionality

Installation worked for me with pip but I couldn't get the code to run due to issues with gdal (stgl/scarplet#62). I think it would be better to have an environment file so that the gdal install is already taken care of, or do a conda package as was already suggested.
Examples: it wasn't immediately clear to me that the example data was included within the GitHub repository, as I had just done a pip install. I have added a comment to the issue that @mcflugen opened.
The data for the channel network example is not provided within the GitHub repo so I couldn't test this example. Would need to test this to check all of the functionality of the software.

Software paper

I think the software paper needs to include DOIs with the references.

Documentation

Readme file could contain a clearer statement of need.

Answer 8 · 2018-11-10T02:17:58.000Z

@whedon generate pdf

Answer 9 · 2018-11-10T02:18:00.000Z

Attempting PDF compilation. Reticulating splines etc...

Answer 10 · 2018-11-10T02:18:31.000Z

👉 Check article proof 📄 👈

Answer 11 · 2018-11-10T16:54:34.000Z

Thanks for your comments @fclubb and @mcflugen.

The example issues have been addressed in some of the PRs above. I've also clarified the statement of need in the README and added DOIs to the paper.

A conda recipe has been submitted that should take care of install problems. I will give it a few days to get into review, and follow up if necessary.

It seems like the best course of action is cutting a new version after I fully address your reviews, and I will release and increment the paper/recipe versions then.

Please let me know if you have any other thoughts or issues.

Answer 12 · 2018-11-17T16:22:31.000Z

Just a quick check in, @rmsare — looks like you are working on some things, but just want to be sure I'm correct.

Answer 13 · 2018-11-17T17:38:38.000Z

@kthyng Thanks for the follow up.

I believe I have addressed the points raised so far by both reviewers. Just to clarify, the following changes have been made:

Add DOIs to paper
Add statement of need to README
Refactor example data access
Clarify how to run examples and access sample data in both README and docs
Change call to a GDAL binary based on @mcflugen's code review
Submit package to conda-forge

The remaining issues should be solved once the conda package is accepted. At that point I think @fclubb will be able to install without GDAL problems and verify functionality.

Unfortunately that package review is blocking for now. Please let me know if there's anything I can do in the meantime.

Answer 14 · 2018-11-20T18:14:41.000Z

@whedon commands

Answer 15 · 2018-11-20T18:14:44.000Z

Here are some things you can ask me to do:

# List Whedon's capabilities
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Answer 16 · 2018-11-21T08:34:10.000Z

Hi @rmsare, I have checked the changes that you made and I am happy with submission - I have checked off all the points in my checklist. Nice work!

Answer 17 · 2018-11-21T19:18:10.000Z

@rmsare Yep, looks good to me too! 🎉

Answer 18 · 2018-11-21T20:05:53.000Z

Thanks to you both for your help and reviews. This submission was a good learning experience for me.

Answer 19 · 2018-11-21T20:06:04.000Z

@whedon generate pdf

Answer 20 · 2018-11-21T20:06:06.000Z

Attempting PDF compilation. Reticulating splines etc...

Answer 21 · 2018-11-21T20:06:29.000Z

👉 Check article proof 📄 👈

Answer 22 · 2018-11-21T20:15:05.000Z

@whedon generate pdf

Answer 23 · 2018-11-21T20:15:08.000Z

Attempting PDF compilation. Reticulating splines etc...

Answer 24 · 2018-11-21T20:15:31.000Z

👉 Check article proof 📄 👈

Answer 25 · 2018-11-21T20:26:20.000Z

Several multi-author references are being formatted incorrectly. The landlab reference is correct (Hobley, et al., 2017) but others are not.

I'm not sure what the problem is here, as the author lists are all in the same style in paper.bib and use "and" to separate authors. @kthyng (or @arfon), is this a known issue with whedon?

Answer 26 · 2018-11-21T20:28:18.000Z

The Zenodo archive of the latest release is 10.5281/zenodo.1492786

Answer 27 · 2018-11-21T22:06:25.000Z

I'm not sure what the problem is here, as the author lists are all in the same style in paper.bib and use "and" to separate authors. @kthyng (or @arfon), is this a known issue with whedon?

I think you need to separate authors with commas from memory.

Answer 28 · 2018-11-21T22:06:41.000Z

Feel free to try tweaking the bibtex and compiling here.

Answer 29 · 2018-11-21T22:50:18.000Z

@whedon generate pdf

Answer 30 · 2018-11-21T22:50:21.000Z

Attempting PDF compilation. Reticulating splines etc...

Answer 31 · 2018-11-21T22:50:42.000Z

👉 Check article proof 📄 👈

Answer 32 · 2018-11-21T22:56:11.000Z

@whedon generate pdf

Answer 33 · 2018-11-21T22:56:14.000Z

Attempting PDF compilation. Reticulating splines etc...

Answer 34 · 2018-11-21T22:56:39.000Z

👉 Check article proof 📄 👈

Answer 35 · 2018-11-21T23:19:56.000Z

I'm happy with the formatting as is.

This comes up in other JOSS papers, too, like 10.21105/joss.00979.

(One fix might be to use the natbib package to format citations when compiling the paper. But this looks like it is not compatible with whedon's current use of pandoc.citeproc)

Answer 36 · 2018-11-25T02:50:17.000Z

The Zenodo archive of the latest release is 10.5281/zenodo.1492786

@kthyng - are we ready to accept this submission?

Answer 37 · 2018-11-26T21:36:41.000Z

One more thing:
@rmsare it looks like you have no co-author on your zenodo archive, but you have one on this JOSS submission. Presumably they should match, in which case can you edit the metadata for the zenodo entry?

Answer 38 · 2018-11-26T21:52:34.000Z

@kthyng, thank you for catching that. I've updated the Zenodo archive to add @gehilley as co-author and note relevant funding sources

Answer 39 · 2018-11-26T22:09:22.000Z

Great! We're ready to move forward then @arfon.

Answer 40 · 2018-11-26T22:09:36.000Z

@whedon set 10.5281/zenodo.1492786 as archive

Answer 41 · 2018-11-26T22:09:39.000Z

OK. 10.5281/zenodo.1492786 is the archive.

Answer 42 · 2018-11-27T00:27:08.000Z

@whedon accept

Answer 43 · 2018-11-27T00:27:11.000Z

Attempting dry run of processing paper acceptance...

Answer 44 · 2018-11-27T00:27:37.000Z

Check final proof 👉 openjournals/joss-papers#84

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#84, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

Answer 45 · 2018-11-27T00:29:21.000Z

@whedon accept deposit=true

Answer 46 · 2018-11-27T00:29:24.000Z

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

Answer 47 · 2018-11-27T00:30:00.000Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#85
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01066
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

Answer 48 · 2018-11-27T00:32:50.000Z

@fclubb, @mcflugen - many thanks for your reviews here and to @kthyng for editing this submission ✨

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

Answer 49 · 2018-11-27T00:32:53.000Z

🎉🎉🎉 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](http://joss.theoj.org/papers/10.21105/joss.01066/status.svg)](https://doi.org/10.21105/joss.01066)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01066">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01066/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01066/status.svg
   :target: https://doi.org/10.21105/joss.01066

This is how it will look in your documentation:

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