[REVIEW]: eemont: A Python package that extends Google Earth Engine

whedon commented 3 years ago

Submitting author: @davemlz (David Montero Loaiza) Repository: https://github.com/davemlz/eemont Version: v0.2.0 Editor: @kbarnhart Reviewer: @giswqs, @elbeejay, @patrickcgray Archive: 10.5281/zenodo.4900067

:warning: JOSS reduced service mode :warning:

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

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Markdown: [![status](https://joss.theoj.org/papers/34696c5b62c50898b4129cbbe8befb0a/status.svg)](https://joss.theoj.org/papers/34696c5b62c50898b4129cbbe8befb0a)

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

@giswqs & @elbeejay & @patrickcgray, 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.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @kbarnhart 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 @giswqs

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 (@davemlz) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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: Does the paper have a section titled 'Statement of Need' that clearly states 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 @elbeejay

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 (@davemlz) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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: Does the paper have a section titled 'Statement of Need' that clearly states 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 @patrickcgray

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 (@davemlz) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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: Does the paper have a section titled 'Statement of Need' that clearly states 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 3 years ago

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

:warning: JOSS reduced service mode :warning:

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.

:star: Important :star:

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:

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whedon commented 3 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=1.89 s (96.6 files/s, 32422.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            87          10387            261          22070
JavaScript                      13           2289           2320           8445
SVG                              1              0              0           2671
Python                          17            517           1411           1917
reStructuredText                40            851           1108            910
CSS                              4            181             33            715
Jupyter Notebook                14              0           4682            380
Markdown                         1             20              0             67
TeX                              1              3              0             37
DOS Batch                        1              8              1             26
Rmd                              1             23             40             16
make                             1              4              7              9
INI                              1              1              0              5
YAML                             1              2              5              5
-------------------------------------------------------------------------------
SUM:                           183          14286           9868          37273
-------------------------------------------------------------------------------

Statistical information for the repository 'bfdd8f3f248f5bff15cc1cf9' was
gathered on 2021/04/12.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
U-dmlmont-PC\dmlmont            97         31442          10698          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
U-dmlmont-PC\dmlmont      20744           66.0          2.5               12.84

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

whedon commented 3 years ago

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

OK DOIs

- 10.1016/j.rse.2017.06.031 is OK
- 10.21105/joss.02272 is OK
- 10.21105/joss.02305 is OK

MISSING DOIs

- None

INVALID DOIs

- None

kbarnhart commented 3 years ago

@giswqs, @elbeejay, @patrickcgray - thanks for agreeing to review this submission to JOSS. In the prior comments there is a checklist that you can use to guide you through your review.

We have an automatic reminder set up in two weeks to ask you how the review is going. At present we request that reviewers complete their reviews within 6 weeks. JOSS is trying to be mindful of changes people have experienced due to COVID-19.

As you work through your review, if there are any issues that come up, please make an issue in the eemont repository, and link to this issue (openjournals/joss-reviews/issues/3168). That way most of the discussion can occur on in-repo issues.

If you have any questions, please let me know (tag me here or email krbarnhart@usgs.gov).

kbarnhart commented 3 years ago

/ooo April 15 until April 20

kbarnhart commented 3 years ago

FYI, I will be out of the office from April 15 until April 20. The ooo bot should respond indicating this if you tag me during that time. I will respond to any comments once I return.

whedon commented 3 years ago

:wave: @elbeejay, please update us on how your review is going (this is an automated reminder).

whedon commented 3 years ago

:wave: @patrickcgray, please update us on how your review is going (this is an automated reminder).

whedon commented 3 years ago

:wave: @giswqs, please update us on how your review is going (this is an automated reminder).

elbeejay commented 3 years ago

I've gone though the package and opened up a few issues (#18 and #19 in the eemont repository) where I outline my outstanding questions, concerns, and suggestions regarding this submission.

But overall I think the eemont is a valuable contribution to the Python+Google Earth Engine community, it seems to have picked up a reasonable user-base already and is featured on the GEE developer resources page. Once those 2 outstanding issues are taken care of I will be able to complete the checklist and recommend the eemont software and JOSS paper for publication.

kbarnhart commented 3 years ago

@elbeejay thanks for completing your review and identifying those issues. If @giswqs or @patrickcgray have questions as you work on your reviews, please let me know.

giswqs commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

giswqs commented 3 years ago

I just released geemap v0.8.15, which should help resolve the issue raised in https://github.com/davemlz/eemont/issues/18 regarding the eemont tutorial notebooks.

davemlz commented 3 years ago

Hi to everyone!

Following @elbeejay suggestions (https://github.com/davemlz/eemont/issues/19), I have modified the paper (https://github.com/davemlz/eemont/commit/5e50b13a43ae90a5c8d0a0686ccb74934a426ece) with new sections (including the GEE Community: Developer Resources and the integration with the Earth Engine Plugin for QGIS), benefits of the package (including comparisons with the Earth Engine Python API), and I adjusted it for the State of the Field.

giswqs commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

giswqs commented 3 years ago

@davemlz @kbarnhart I have provided my comments and suggestions at https://github.com/davemlz/eemont/issues/22 and pull request.

kbarnhart commented 3 years ago

@giswqs thank you for providing your review!

@patrickcgray, we are only three weeks into the stated 6-week review period, so no worries if you have not yet been able to start your review. If you have any questions for me when you are able to get to it, please let me know.

kbarnhart commented 3 years ago

A comment for all: I will be in the field all of next week, so will be delayed in my response between May 8 and May 16. I'll address any comments after I return on May 17.

patrickcgray commented 3 years ago

Hi all,

My apologies for my review taking the full six weeks. I've gone through the paper and the repo and have finished my review. I recommend an acceptance and have a few minor comments raised in this issue. I was not able to log in as a reviewer for some reason, but have included my checklist below. @kbarnhart if you're able to resubmit the invite I can log in and take care of fit in the proper format if you'd like. Otherwise everything looks great to me and I think this is a excellent addition to the community.

Review checklist for @patrickcgray

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 (@davemlz) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
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: Does the paper have a section titled 'Statement of Need' that clearly states 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?

kbarnhart commented 3 years ago

@whedon re-invite @patrickcgray as reviewer

whedon commented 3 years ago

OK, the reviewer has been re-invited.

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

kbarnhart commented 3 years ago

@patrickcgray thanks for your review and no problem at all regarding the timeframe.

@davemlz if you have questions for me as you address remaining reviewer comments, please post them here. If not, let me know when you have finished addressing them.

patrickcgray commented 3 years ago

Okay great thanks @kbarnhart! I've now completed the checklist and it all looks good to me pending @davemlz's comments on my issue in the eemont repo.

davemlz commented 3 years ago

Thank you, @kbarnhart and @patrickcgray! I'll work on @patrickcgray comments and let you know when everything is ready!

patrickcgray commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

patrickcgray commented 3 years ago

My comments have been addressed and I think it all looks good!

kbarnhart commented 3 years ago

@davemlz thank you for addressing the reviewer comments.

@patrickcgray thank you for indicating that you think the submission is ready to be accepted.

@elbeejay @giswqs please revisit this review now that the author has finished addressing reviewer comments and indicate whether the authors have addressed all of your concerns. If you think the submission is ready to be accepted, please indicate so in a comment.

@davemlz once all reviewers are satisfied with the submission I will move on to the final steps of the JOSS process.

kbarnhart commented 3 years ago

@whedon check references

whedon commented 3 years ago

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

OK DOIs

- 10.1016/j.rse.2017.06.031 is OK
- 10.21105/joss.02272 is OK
- 10.21105/joss.02305 is OK

MISSING DOIs

- None

INVALID DOIs

- None

elbeejay commented 3 years ago

Looks good to me :+1:

giswqs commented 3 years ago

I would like to make two minor suggestions for the Summary paragraph.

There are e.g. Landsat, Sentinel, MODIS and e.g. Sentinel, Landsat and MODIS. I would suggest making them consistent, such as as e.g., Landsat, Sentinel, MODIS
Google Earth Engine were used three times. Since you already use the acronym GEE for the first one, the other two can be replaced with GEE.

davemlz commented 3 years ago

Thank you, @giswqs!

I have improved the paper with your suggestions! :)

giswqs commented 3 years ago

@davemlz Thanks for your prompt response. @kbarnhart I think the submission is ready to be accepted.

kbarnhart commented 3 years ago

@whedon generate pdf

kbarnhart commented 3 years ago

@whedon check references

whedon commented 3 years ago

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

OK DOIs

- 10.1016/j.rse.2017.06.031 is OK
- 10.21105/joss.02272 is OK
- 10.21105/joss.02305 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

kbarnhart commented 3 years ago

@davemlz I've made two pull requests with very small changes to the text and the .bib file. Please consider these PRs. After you have done so, please test that the article builds correctly here, and presuming it does do the following:

[ ] Make a tagged release of your software, and list the version tag of the archived version here.
[ ] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[ ] 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.

Know also that I'll be out of the office June 3-June 8.

kbarnhart commented 3 years ago

@davemlz FYI, I will be out of the office Thursday June 3-Tuesday June 8.

davemlz commented 3 years ago

Hi, @kbarnhart!

Sorry for the late response, I'll start with it!

davemlz commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

davemlz commented 3 years ago

@whedon check references

whedon commented 3 years ago

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

OK DOIs

- 10.1016/j.rse.2017.06.031 is OK
- 10.21105/joss.02272 is OK
- 10.21105/joss.02305 is OK

MISSING DOIs

- None

INVALID DOIs

- None

davemlz commented 3 years ago

Hi, @kbarnhart!

The package is now in Zenodo:

Tagged release: 0.2.0
Software archived in: Zenodo
List of authors revised.
DOI: 10.5281/zenodo.4900067

kbarnhart commented 3 years ago

@whedon set 10.5281/zenodo.4900067 as archive

openjournals / joss-reviews