search

pyOpenSci / software-submission

Submit your package for review by pyOpenSci here! If you have questions please post them here: https://pyopensci.discourse.group/
90 stars 33 forks source link

EarthPy: Software Submission for Review #3

Closed lwasser closed 4 years ago

lwasser commented 5 years ago

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: DOI JOSS DOI: DOI Version accepted: v 0.7.5 Date accepted (month/day/year): 11/06/2019

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

Technical checks

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

JOSS Checks - [ ] The package has an **obvious research application** according to JOSS's definition in their [submission requirements](https://joss.readthedocs.io/en/latest/submitting.html#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](https://joss.readthedocs.io/en/latest/submitting.html#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](https://joss.readthedocs.io/en/latest/submitting.html#what-should-my-paper-contain) 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

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 commented 5 years ago

@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 commented 5 years ago

Editor checks:

Editor comments

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

luizirber commented 5 years ago

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

lwasser commented 5 years ago

@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 commented 5 years ago

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

lwasser commented 5 years ago

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

lwasser commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

@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 commented 5 years ago

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

lwasser commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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

HaoZeke commented 4 years ago

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.

luizirber commented 4 years ago

Awesome, thanks @HaoZeke!

So let's get this train rolling: @HaoZeke and @marskar have been assigned, next steps are:

Due date for reviews is 2019-10-25

luizirber commented 4 years ago

Hey all, we have a new potential reviewer! @sgillies responded on Twitter, so I recommend we try either:

I kind of like the three reviewers idea, what do you think @marskar?

lwasser commented 4 years ago

hi colleagues. whoever does review this please note that the clip module is being migrated to geopandas (it fits there better!!) it's underway. but ofcourse if you have implemention comments i'll totally move that over to geopandas in that pr!

luizirber commented 4 years ago

@HaoZeke and @marskar can you please post your reviewer checklist to acknowledge you started?

And @marskar, do you prefer the 3 reviewers approach or moving to another review?

Thanks!

luizirber commented 4 years ago

@HaoZeke @marskar How is it going? Anything I can do to help you with your review?

marskar commented 4 years ago

Hi @luizirber, I think it will be better to stick to 2 reviewers. So my suggestion is to move forward with @HaoZeke and @sgillies as the reviewers. If there is a problem with this, please let me know and I will jump back into the review.

HaoZeke commented 4 years ago

Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

Documentation

The package includes all the following forms of documentation:

Readme requirements The package meets the readme requirements below:

The README should include, from top to bottom:

Functionality

For packages co-submitting to JOSS

Note: Be sure to check this carefully, as JOSS's submission requirements and scope differ from pyOpenSci's in terms of what types of packages are accepted.

The package contains a paper.md matching JOSS's requirements with:

Final approval (post-review)

Estimated hours spent reviewing:

Review Comments

HaoZeke commented 4 years ago

@luizirber. Many apologies for the long wait, I've had a few other reviews to close. I will be happy to finish this in a day or so now!

luizirber commented 4 years ago

Thanks for the feedback, @marskar! Let's proceed with 2 reviewers then.

@sgillies are you still available for this review?

@HaoZeke No worries! Review due date is Oct 25th, and might be postponed depending on @sgillies response. And thanks for posting the reviewer checklist =]

sgillies commented 4 years ago

@luizirber I am. Shall I also copy the checklist into this issue and begin? I have some evening time this week and expect no trouble with the 25 October deadline.

luizirber commented 4 years ago

Cool, thanks @sgillies! Copying the checklist here and you're good to go =]

lwasser commented 4 years ago

you guys rock!! again just a note that the CLIP module is moving to GEOPANDAS:

https://github.com/geopandas/geopandas/pull/1128

but i am open to feedback on it as we move it over if you wish to provide it :)

sgillies commented 4 years ago

Here we go. I'm excited to learn a new process and help out.

Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

Documentation

The package includes all the following forms of documentation:

Readme requirements The package meets the readme requirements below:

The README should include, from top to bottom:

Functionality

For packages co-submitting to JOSS

Note: Be sure to check this carefully, as JOSS's submission requirements and scope differ from pyOpenSci's in terms of what types of packages are accepted.

The package contains a paper.md matching JOSS's requirements with:

Final approval (post-review)

Estimated hours spent reviewing: 6.

Review Comments

I've created issues for review comments and they are collected in https://github.com/earthlab/earthpy/issues/created_by/sgillies.

I'm impressed at the quality of the code, the vignettes, and the documentation. I wish my own projects did as well as earthpy.

@luizirber my review is complete.

luizirber commented 4 years ago

@HaoZeke @sgillies any questions about the process, or any other help I can offer?

sgillies commented 4 years ago

@luizirber the earthpy package has not also been submitted to JOSS correct? I can leave those boxes unchecked?

HaoZeke commented 4 years ago

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

lwasser commented 4 years ago

@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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

@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 commented 4 years ago

Thanks @sgillies!

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

HaoZeke commented 4 years ago

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

luizirber commented 4 years ago

Thanks @HaoZeke!

Label updated, now EarthPy is 6/approved!

luizirber commented 4 years ago

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

To-dos:

For JOSS:

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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

JOSS review is happening here: https://github.com/openjournals/joss-reviews/issues/1869