EarthPy: Software Submission for Review

[lwasser]

Submitting Author: Leah Wasser (@lwasser)
All current maintainers: (@lwasser, @nkorinek, @mbjoseph, @joemcglinchy, @jlpalomino)
Package Name: earthpy
One-Line Description of Package: A package built to support working with spatial data using open source python
Repository Link: https://github.com/earthlab/earthpy
Version submitted: 0.7
Editor: @luizirber
Reviewer 1: @HaoZeke
Reviewer 2: @sgillies
Archive:
JOSS DOI:
Version accepted: v 0.7.5
Date accepted (month/day/year): 11/06/2019

---

• Paste the full DESCRIPTION file inside a code block below:

Python is a generic programming language designed to support many different applications. Because of this, many commonly performed spatial tasks for science including plotting and working with spatial data take many steps of code. EarthPy takes advantage of functionality developed for raster data (rasterio) and vector data (geopandas) and simplifies the code needed to :

    Stack raster bands from data such as Landsat into an easy to use numpy array
    Work with masks to set bad pixels such a those covered by clouds and cloud-shadows to NA (mask_pixels())
    Plot rgb (color), color infrared and other 3 band combination images (plot_rgb())
    View histograms of sets of raster
    Create discrete (categorical) legends

EarthPy also has an io module that allows users to

    Quickly access pre-created datasubsets used in the earth-analytics courses hosted on www.earthdatascience.org
    Download other datasets that they may want to use in their workflows.

Scope

• Please indicate which category or categories this package falls under:
  • Data retrieval
  • Data extraction
  • Data munging
  • Data deposition
  • Reproducibility
  • Geospatial
  • Education
  • Data visualization*

* Please fill out a pre-submission inquiry before submitting a data visualization package. For more info, see this section of our guidebook.

• Explain how the and why the package falls under these categories (briefly, 1-2 sentences):
  This package wraps around rasterio and geopandas to make working with geospatial data easier.

• Who is the target audience and what are scientific applications of this package?
  The target audience is people working with different types of raster and vector data in python. There are many operations that are often repeated by users that require a lot of code. This package simplifies these operations so users can quickly explore their data.

• Are there other Python packages that accomplish the same thing? If so, how does yours differ?
  Not that we know of! this is why we created this package.

• If you made a pre-submission enquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted:

Technical checks

For details about the pyOpenSci packaging requirements, see our packaging guide. Confirm each of the following by checking the box. This package:

• does not violate the Terms of Service of any service it interacts with.
• has an OSI approved license
• contains a README with instructions for installing the development version.
• includes documentation with examples for all functions.
• contains a vignette with examples of its essential functions and uses.
• has a test suite.
• has continuous integration, such as Travis CI, AppVeyor, CircleCI, and/or others.

Publication options

• Do you wish to automatically submit to the Journal of Open Source Software? If so:

JOSS Checks

• The package has an obvious research application according to JOSS's definition in their submission requirements. Be aware that completing the pyOpenSci review process does not guarantee acceptance to JOSS. Be sure to read their submission requirements (linked above) if you are interested in submitting to JOSS.
• The package is not a "minor utility" as defined by JOSS's submission requirements: "Minor ‘utility’ packages, including ‘thin’ API clients, are not acceptable." pyOpenSci welcomes these packages under "Data Retrieval", but JOSS has slightly different criteria.
• The package contains a paper.md matching JOSS's requirements with a high-level description in the package root or in inst/.
• The package is deposited in a long-term repository with the DOI:

Note: Do not submit your package separately to JOSS

Code of conduct

• I agree to abide by pyOpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

P.S. Have feedback/comments about our review process? Leave a comment here

NOTE: I am actually not sure what research application means according to Joss!! may followup with Arfon on this.

[lwasser]

@luizirber as the editor for this package, will you please ping the reviewers and give them a 3 week deadline to perform the review?

[luizirber]

Editor checks:

• Fit: The package meets criteria for fit and overlap.
• Automated tests: Package has a testing suite and is tested via Travis-CI or another CI service.
  • Travis and AppVeyor
• License: The package has an OSI accepted license
  • yes, BSD 3-Clause
• Repository: The repository link resolves correctly
• Archive (JOSS only, may be post-review): The repository DOI resolves correctly
• Version (JOSS only, may be post-review): Does the release version given match the GitHub release (v1.0.0)?

---

Editor comments

---

Reviewer: @HaoZeke
Reviewer: @sgillies
Due date: 2019-10-25

[luizirber]

@lwasser I don't have permission to change labels in this issue, but ready for review (past editor checks and reviewer assignment)

[lwasser]

@luizirber !! i Just made you an admin for this repo so you should have permissions now. Please let me know if you don't!! And thank you for letting me know and for being willing to serve as an editor!!

[luizirber]

Hi @kysolvik and @carsonfarmer! Anything I can do to help you with your reviews? Next steps are:

• Post this template in a comment here: https://www.pyopensci.org/dev_guide/appendices/templates#review-template
• Follow the template and https://www.pyopensci.org/dev_guide/peer_review/reviewer_guide.html for you review.

[lwasser]

our docs are building again too - yay! they were down due to a RTD issue. thank you @luizirber

[lwasser]

hey guys @carsonfarmer @luizirber -- wanted to followup on here. @kysolvik pointed out that there is a potential conflict of interest here given Kylen has worked for me and i'm not sure if that would apply with @carsonfarmer as well given we were both a part of earth lab for some time. we may need to reassign reviewers. @luizirber i tried to ping you on slack but am not sure if you saw it! just want to ensure this review moves forward given we definitely need to swap out atleast one reviewer!! i was wondering if @leouieda could do it instead of @kysolvik and kylen could do one of martin's submissions as one idea. but very open to thoughts.

[luizirber]

Good point, I reset the reviewers and changed the label back to seeking reviewers.

If @leouieda agree to review this one, maybe @marskar would like to be a reviewer? It is a geospatial submission, but since @leouieda can cover the specific area I think it is good to have someone with a distinct expertise taking a look too.

@marskar @leouieda what do you think?

[lwasser]

@luizirber i think we have confirmation as of today from @marskar and @leouieda that they are willing to work on reviewing earthpy!! i'll find someone else for nbless :)

[luizirber]

Hi @leouieda and @marskar! You've been assigned, next steps are:

• Post this template in a comment here: https://www.pyopensci.org/dev_guide/appendices/templates#review-template
• Follow the template and https://www.pyopensci.org/dev_guide/peer_review/reviewer_guide.html for you review.

[lwasser]

hello there @luizirber @leouieda @marskar just checking in to see where this review is now?? i've bumped the version of earthpy up a few times since submitting so if the review hasn't started i might update the version here. and if it has and you guys have questions, please say the word!

[marskar]

Hi @lwasser,
Let's work with the latest version.
I have a bio (not geo) background, so maybe @leouieda could address the science behind earthpy first and I will read his review and then follow up with more general packaging advice (testing, docs, etc.). Does that sound like a good plan?

[lwasser]

hey team. i thijnk we might need to regroup on this review! given there has been no activity here. i suggest we reassign everything: editor, and reviewers. @luizirber i feel like you are super busy and don't have time. i'm wondering if @marskar or someone else might want to serve as the editor and we can find two new reviewers then! i have one reviewer in mind who's using this package for lessons for the carpentries!! let me know what you guys think. a package review shouldn't sit for this long!

many thanks!

[marskar]

Hi @lwasser, I am happy to serve as editor. In my opinion, the more, the merrier in terms of reviewers. Earth science is not my field, though I am happy to learn. It would be excellent if we could have involve the reviewer you mentioned, the one with experience using EarthPy!

[lwasser]

ok let's try that! this review has been stale for a while so i'd like to see it move forward. @rbavery was one person i thought might be able to review for us. Ryan would you be game for that? but if not, can you suggest 1 or 2 people? We could also ask around (Twitter maybe??) to find some else that has time and can make our 3 week review window!

[xmnlab]

I don't have any experience with EarthPy but I have some experience with GIS ... let me know if I can help in any way.

[lwasser]

thank you @xmnlab because earthpy is something i worked on, i'm trying hard to stand back from the review :) but it is a spatial library! it's designed to make exploring spatial data a bit easier. it has wrappers around rasterio and geopandas. you just did a (great) review and i know you are wrapping that up. i'll step back and will let @marskar decide on what he'd like to do as editor :) @marskar if you have any questions about the review / editor process please do say the word as well. we can also chat on thursday. Thank you both for stepping up. i think people are just very busy and i totally get that!!

[lwasser]

@luizirber it sounds like @HaoZeke might be available to review this as well.

[HaoZeke]

Yup, @luizirber and @lwasser, I'd be happy to review this one here and later for JOSS once it's been written up and submitted there as well.

[HaoZeke]

Yeah I believe it is not for consideration there since there's no `paper.md` either..

[lwasser]

@sgillies @HaoZeke we'd like to submit to JOSS but i've never been through that process before and this is my first time having a package reviewed. So i was going to complete this initial review with pyopensci and then if all goes well, ask for things to be pushed along to JOSS. i need to contact arfon again about how that works. I believe that the JOSS reviewers look at the paper.md. @luizirber do you know given your experience with JOSS?? if you need the paper now i can begin working on it!! i can ask @leouieda if you guys don't know. i just need more info :)

[HaoZeke]

Well I've reviewed seven papers for joss and if you set up a paper.md I'd be happy to serve as a reviewer when you submit there as well. I'm not sure how the transfer works though. via Newton Mail [https://cloudmagic.com/k/d/mailapp?ct=pa&cv=10.0.25&pv=6.0.1&source=email_footer_2]

[lwasser]

ok thank you @HaoZeke i will dig into the joss part. This is the first package that will move on to JOSS. it needs to pass pyopensci review first however. I will do a bit of research on that document and will get back to you guys soon!! in the meantime i'm working on comments and issues from this review and are so appreciative of everything suggested so far!!

[lwasser]

ok i am working my way through @sgillies comments and issues which are all great -- THANK YOU!! @HaoZeke do you have a review for us coming? i didn't see your review template as filled out.

in the meantime we will have a paper.md file pushed in the next few days for JOSS!!

[HaoZeke]

Hi @luizirber. I have completed my review, and I am satisfied with the code both in terms of functionality as well as documentation and reproducibility. I am not much of a geologist, but I am certain such a well crafted tool will be of much use to the community. I recommend this for endorsement. Also @lwasser, thank you for your patience. I would be willing to review this submission when you submit it to JOSS as well.

[luizirber]

Hello all,

thanks for the reviews @sgillies and @HaoZeke! I see that the only item missing in both your checklist is the final approval (and the JOSS parts), so I think this is ready to be approved (if you don't have any other concerns).

[lwasser]

awesome. just a note that

1. we will not address the issue associated with the clip modules as that is moving to geopandas and we are working on the PR there. we will however integrate sean's suggestions in that PR!
2. we were going to implement logging but after some discussion with @sgillies we decided that this might not be necessary for earthpy. so if everyone is on board, i think we are in good shape. I do have the joss paper in the repo now AND it's passing all of the JOSS whedon tests. so when i get the final approval here, i'll submit it to JOSS. i am more than happy however to address any other items if need be !!!

[sgillies]

@lwasser went above and beyond in responding to my review comments. I've checked off the last box. Thanks for letting me get involved, I found the process and documentation quite interesting and well done.

[luizirber]

Thanks @sgillies!

@HaoZeke, any final comments before we move to approved?

[HaoZeke]

Thank you for asking. I think the documentation is great and it's ready to go further without any issues. Great work.

[luizirber]

Thanks @HaoZeke!

Label updated, now EarthPy is 6/approved!

[luizirber]

Approved! Thanks @lwasser for submitting and @HaoZeke and @sgillies for your reviews! 😸

To-dos:

• Transfer the repo to our "pyOpenSci" GitHub organization under "Settings" in your repo. I have invited you to a team that should allow you to do so. You'll be made admin once you do.
• Fix any links in badges for CI and coverage to point to the pyOpenSci URL. For Appveryor projects, you should still use your personal Appveyor account. After transfer of your repo to the "pyOpenSci" GitHub organization the badge should be [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/pyOpenSci/pkgname?branch=master&svg=true)](https://ci.appveyor.com/project/individualaccount/pkgname).

For JOSS:

• Activate Zenodo watching the repo
• Tag and create a release so as to create a Zenodo version and DOI
• Submit to JOSS using the Zenodo DOI. We will tag it for expedited review.

We've started putting together a gitbook with our best practice and tips, this chapter starts the 3rd section that's about guidance for after onboarding. Please tell us what could be improved, the corresponding repo is here.

[luizirber]

and this approval template might need some tweaks, since we are not asking repos to be moved to pyopensci... But the JOSS items are relevant!

[lwasser]

oh yay !! ok @luizirber that's a great idea to update the template. whatever suggestions you have would be awesome!!

I will create a release and submit to JOSS next. @arfon told me to just link to this issue as documentation that we are approved by pyopensci. You may know more than me on this but i'll submit it first and will report back here in this issue. Please let me know if you have any suggestions!!

@HaoZeke and @sgillies thank you AGAIN for your reviews. i think we made some great improvements to earthpy through this process.

[lwasser]

JOSS review is happening here: openjournals/joss-reviews#1869

[lwasser]

this has also been approved!! so closing the issue!! yay!