[REVIEW]: rgee: An R package for interacting with Google Earth Engine

whedon commented 4 years ago

Submitting author: @csaybar (Cesar Luis Aybar Camacho) Repository: https://github.com/r-spatial/rgee Version: v1.0.0 Editor: @hugoledoux Reviewers: @appelmar, @gena, @jhollist Archive: 10.5281/zenodo.3947571

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Review checklist for @appelmar

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@csaybar) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 @gena

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@csaybar) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 @jhollist

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@csaybar) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 4 years ago

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

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whedon commented 4 years ago

Reference check summary:

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.1016/j.rse.2017.06.031 may be missing for title: Google Earth Engine: Planetary-scale geospatial analysis for everyone
- https://doi.org/10.1038/sdata.2017.191 may be missing for title: TerraClimate, a high-resolution global dataset of monthly climate and climatic water balance from 1958–2015

INVALID DOIs

- None

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

hugoledoux commented 4 years ago

@whedon add @jhollist as reviewer

whedon commented 4 years ago

OK, @jhollist is now a reviewer

csaybar commented 4 years ago

@whedon commands

whedon commented 4 years ago

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

csaybar commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

hugoledoux commented 4 years ago

👋 @appelmar @gena @jhollist I was wondering if you need any help/instructions at this point or if I can help?

jhollist commented 4 years ago

@hugoledoux thanks for the reminder on this. I am all set, just need to clone myself! Hoping to work on the review this week.

gena commented 4 years ago

Same here. I will write a review over the weekend or beginning of the next week.

appelmar commented 4 years ago

Same here, too. I'll finish the review next week at the latest.

hugoledoux commented 4 years ago

@whedon add @gena as reviewer

whedon commented 4 years ago

OK, @gena is now a reviewer

jhollist commented 4 years ago

@csaybar Really nice job! I have posted a new issue on your repo (https://github.com/r-spatial/rgee/issues/68) with some more detailed review comments. Any questions, let me know.

csaybar commented 4 years ago

@whedon generate pdf from branch JOSS

whedon commented 4 years ago

Attempting PDF compilation from custom branch JOSS
. Reticulating splines etc...

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

jhollist commented 4 years ago

@hugoledoux and @csaybar I have completed the checklist and the edits (https://github.com/r-spatial/rgee/pull/69) made in response to my review (https://github.com/r-spatial/rgee/issues/68) all look great. Again, really nice job on this package.

csaybar commented 4 years ago

Thank @jhollist for your comments and suggestions :). They were addressed here r-spatial/rgee#69

appelmar commented 4 years ago

Great work @csaybar. Please find my detailed review with some minor comments in a separate issue in your repo (see r-spatial/rgee#70). Let me know if you have questions.

appelmar commented 4 years ago

@hugoledoux I can't fill out the checklist in this issue, did I miss something?

danielskatz commented 4 years ago

I can't fill out the checklist in this issue, did I miss something?

As stated at the top:

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

If these don't solve the problem, ping again

appelmar commented 4 years ago

Thanks @danielskatz. I am logged in but I might have missed to accept the invitation when this issue was started, now getting "Sorry, we couldn't find that repository invitation. It is possible that the invitation was revoked or that you are not logged into the invited account.". Could you invite me again? Sorry for the inconvenience.

danielskatz commented 4 years ago

@whedon re-invite @appelmar as reviewer

whedon commented 4 years ago

OK, the reviewer has been re-invited.

@appelmar please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

gena commented 4 years ago

I've added my review https://github.com/r-spatial/rgee/issues/72, it's short, not a lot to add to other reviews.

csaybar commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

csaybar commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

hugoledoux commented 4 years ago

@csaybar has https://github.com/r-spatial/rgee/issues/72 been completely solved? It seems yes but you left it open. It seems all reviewers are happy now, and if this issue is closed then we can move towards acceptance and the final steps.

csaybar commented 4 years ago

Hi @hugoledoux sorry for the late reply. We are waiting for the response of @appelmar (r-spatial/rgee#70)!.

appelmar commented 4 years ago

No need to wait, all good from my side!

csaybar commented 4 years ago

@appelmar @gena @jhollist Thank you very much for your time and support in reviewing rgee. I appreciate it!. @hugoledoux all issues were solved we will happy to continue with the submission process.

hugoledoux commented 4 years ago

@whedon check references

whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.1016/j.rse.2017.06.031 is OK
- 10.1002/wics.147 is OK

MISSING DOIs

- None

INVALID DOIs

- None

hugoledoux commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

hugoledoux commented 4 years ago

@csaybar there's a glitch with your PDF, see this:

CleanShot 2020-07-15 at 08 03 01@2x

Something goes wrong with a function name with "$ and it doesn't escape, I think you should modify at l.45

("$getInfo")

=>

`($getInfo)`

hugoledoux commented 4 years ago

also, shouldn't the reference to mapview be the package/website? I tried to find the paper, but couldn't in 2min, while the website is complete, informative, etc. If you want to stick to the paper at EGU, please provide a DOI

hugoledoux commented 4 years ago

@csaybar the 3 reviewers recommend acceptance, and I'm happy to say that we're reaching the end of the review!

At this point could you:

[x] Fix the 2 issues I pointed above
[x] Make a tagged release of your software, and list the version tag of the archived version here.
[x] Archive the reviewed software in Zenodo or a similar service (e.g. figshare, an institutional repository)
[x] Check the archival deposit (e.g., in Zenodo) has the correct metadata, this includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it); you may also add the authors' ORCID.

Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

csaybar commented 4 years ago

Dear @hugoledoux thanks for the fast response. I've made the requested changes.

I changed ("$getInfo") by ("\$getInfo") the problem will be fixed now. With respect to the citation to mapview we now refer to the R package manual instead of the publication in EGU.
rgee v.0.5.0.
rgee is archived in zenodo here.

csaybar commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

hugoledoux commented 4 years ago

@csaybar I am confused, you have a v1.0.0 release, but also you made one for v.0.5.0? Your releases have 2 options for one repository? This is new to me, and rather confusing... Can you shed some light on why that is?

csaybar commented 4 years ago

Hi @hugoledoux, after submitting rgee version 0.5.0 to JOSS I was making some additional changes that were reflected in new versions of rgee. Version 1.0.0 has all the changes made to pass the issues pointed out by the reviewers. However, I was not sure which version should be used if version 0.5.0 or 1.0.0. Sorry if this is a bit confusing.

hugoledoux commented 4 years ago

ah right, then if you released v1.0.0 based on all reviews than it should be v.1.0.0 for JOSS, this is a nice outcome too.

Could you make a new Zenodo release (pointing to v1.0.0) and list the DOI here please?

csaybar commented 4 years ago

@hugoledoux I've made the requested changes.

Archived rgee v.1.0.0 in Zenodo here.
rgee v.1.0.0 Zenodo citation: Cesar Aybar, Qiusheng Wu, Lesly Bautista, Roy Yali, & Antony Barja. (2020, July 14). rgee: An R package for interacting with Google Earth Engine (Version v.1.0.0). Zenodo. http://doi.org/10.5281/zenodo.3945409

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