[REVIEW]: pyveg: A Python package for analysing the time evolution of patterned vegetation using Google Earth Engine

[whedon]

Submitting author: @samvanstroud (Samuel Van Stroud)
Repository: https://github.com/alan-turing-institute/monitoring-ecosystem-resilience
Version: 1.1.0
Editor: @usethedata
Reviewers: @arbennett , @usethedata
Archive: 10.5281/zenodo.4281273

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/929c21011e8fbcaeca6b1255fdf04d5d"><img src="https://joss.theoj.org/papers/929c21011e8fbcaeca6b1255fdf04d5d/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/929c21011e8fbcaeca6b1255fdf04d5d/status.svg)](https://joss.theoj.org/papers/929c21011e8fbcaeca6b1255fdf04d5d)

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

@arbennett , 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 @usethedata know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @arbennett

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

• 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?
• Contribution and authorship: Has the submitting author (@samvanstroud) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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?

Review checklist for @usethedata

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

• 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?
• Contribution and authorship: Has the submitting author (@samvanstroud) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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?

[whedon]

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

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ 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:

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

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

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[whedon]

Reference check summary:

OK DOIs

- 10.1098/rsos.160443 is OK
- 10.1111/gcb.14059 is OK
- 10.1073/pnas.0802430105 is OK
- 10.1103/PhysRevE.71.056103 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[usethedata]

👋 @arbennett -- any update on your review?

[arbennett]

@usethedata thanks for the reminder! I am working on the review now!

[arbennett]

👋 Hi @samvanstroud - thanks for developing pyveg, I think it sounds like a very nice tool for processing GEE vegetation data. However, in reviewing this I came across a few difficulties that I think need to be addressed before accepting this for publication. I have opened a few issues on the monitoring-ecosystem-resilience for organization. Here is a list:

• - Example configuration doesn't seem to run through
• - Tutorial notebook errors
• - Documenting core functionality
• - Documenting configuration
• - Allow user configuration of coordinates

[crangelsmith]

👋Hi @arbennett , thank you for your comments and issues, they are very relevant and some where already in our to-do list! @nbarlowATI and I will be working through these issues in the next couple of weeks and keep you updated.

[usethedata]

@crangelsmith -- Thanks for the comment. I'm thinking I'll do the second review, as I'd like to dig into this work more carefully than I have so far, as it relates to some of what I do in my day job.

[usethedata]

@whedon add @usethedata as reviewer

[whedon]

OK, @usethedata is now a reviewer

[labarba]

hi 👋 – @arbennett , @usethedata: it looks like this review needs attention? The last movement is from over six weeks ago. Can you give us an update on your timeline for this? Thanks!

[arbennett]

hi @labarba - I submitted my review on July 27 with some outstanding issues in being able to run some of the code. It looks like there has been recent development on the repo, but I haven't been updated on whether we should give another round of reviews.

[crangelsmith]

hi @labarba @arbennett, sorry for the silence. We have been working hard on the project, implementing the review comments but also in general development in view for a science paper we are also aiming to publish.

We are planning to do a PR to master this week, which will include the implementation of the comments from @arbennett. But also, the code has evolved a bit, and we would like to add a couple of more authors to the paper, to acknowledge the work some new members have done in the last couple of months. Is it ok to update the paper with this new info (authors + a couple of sentences about the new functionalities)?

[usethedata]

@crangelsmith Sorry to have been absent, but end of fiscal year stuff was pretty hectic. I would say you should go ahead and revise the paper. Let me take a look at the changes in the code from what @arbennett has already review and decide how best to proceed with the review.

[usethedata]

@crangelsmith Just checking -- what is the timeline for your updates? I see that you've merged the issue that's related to @arbennett comments, but it looks like the paper hasn't been updated. No worries, just asking about the timeline.

[crangelsmith]

Hi @usethedata, sorry for the slow updates. Currently we are in a transition moment for this project, the RSE funded time has finished (that is me, @nbarlowATI and @samvanstroud) and we have handed over the finalisation of the project to the researchers in Exeter (@jbuxt, @caboulton and @jabrams23). We will all keep working on getting this paper published but at different capacities.

I think the new version of the paper will be merged into master imminently, but I will let @jbuxt confirm.

[jbuxt]

Hello @usethedata apologies for the delay in merging the paper into the master. It should all be up to date now, please do let me know if there are any comments/questions.

[usethedata]

@arbennett -- can you go through and complete your review?

@jbuxt @crangelsmith -- I expect to work through my review over the weekend. Normally, I don't review papers I edit, but this one is of particular interest to my day job. I'll be working on this over the weekend.

[usethedata]

@whedon check references

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1098/rsos.160443 is OK
- 10.1111/gcb.14059 is OK
- 10.1073/pnas.0802430105 is OK
- 10.1103/PhysRevE.71.056103 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[usethedata]

@samvanstroud (and team):

1. Looking at the repository, I'm seeing version 1.0 as the current release, with a date of March 2020. I don't know if you want to tag at 1.0.1 or something similar to note the changes made since this review started. Please confirm what you want for the version number for the paper and either let me know you're going with 1.0 or set up the new release/tag and let me know that.
2. When you have that, please create a deposit at Zenodo and post back here with the DOI that they give you.

Regards,
Bruce

[usethedata]

I confirm I have no further editorial changes to make to the paper itself.

[crangelsmith]

Hi @usethedata,

1. Looking at the repository, I'm seeing version 1.0 as the current release, with a date of March 2020. I don't know if you want to tag at 1.0.1 or something similar to note the changes made since this review started. Please confirm what you want for the version number for the paper and either let me know you're going with 1.0 or set up the new release/tag and let me know that.

Yes, we decided to move to version v1.1.0, this is now tagged and updated on the repo.

2. When you have that, please create a deposit at Zenodo and post back here with the DOI that they give you.

Done, this is the DOI they provide: 10.5281/zenodo.4281273

Thank you and @arbennett for all your work reviewing this paper!!!

[usethedata]

@whedon set 1.1.0 as version

[whedon]

OK. 1.1.0 is the version.

[usethedata]

@whedon set 10.5281/zenodo.4281273 as archive

[whedon]

OK. 10.5281/zenodo.4281273 is the archive.

[usethedata]

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[usethedata]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#1931

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1931, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1098/rsos.160443 is OK
- 10.1111/gcb.14059 is OK
- 10.1073/pnas.0802430105 is OK
- 10.1103/PhysRevE.71.056103 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[danielskatz]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02483 joss-papers#1932
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02483
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[danielskatz]

Congratulations to @samvanstroud (Samuel Van Stroud) and co-authors!!

And thanks to @arbennett for reviewing, and @usethedata for reviewing/editing!

[whedon]

🎉🎉🎉 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.02483/status.svg)](https://doi.org/10.21105/joss.02483)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02483">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02483/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02483/status.svg
   :target: https://doi.org/10.21105/joss.02483

This is how it will look in your documentation:

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:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss