[REVIEW]: samgeo: A Python package for segmenting geospatial data with the Segment Anything Model (SAM) #5663

editorialbot · 2023-07-19T05:53:19Z

Submitting author: @giswqs (Qiusheng Wu)
Repository: https://github.com/opengeos/segment-geospatial
Branch with paper.md (empty if default branch):
Version: v0.10.1
Editor: @hugoledoux
Reviewers: @ayoubft, @aazuspan, @SimonMolinsky
Archive: 10.5281/zenodo.8338074

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/74cc80f83debede38c00d12082511aed"><img src="https://joss.theoj.org/papers/74cc80f83debede38c00d12082511aed/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/74cc80f83debede38c00d12082511aed/status.svg)](https://joss.theoj.org/papers/74cc80f83debede38c00d12082511aed)

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

@ayoubft & @aazuspan, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @hugoledoux 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 ✨

Checklists

📝 Checklist for @ayoubft

📝 Checklist for @aazuspan

📝 Checklist for @SimonMolinsky

The text was updated successfully, but these errors were encountered:

editorialbot · 2023-07-19T05:53:21Z

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

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

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editorialbot · 2023-07-19T05:53:51Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (697.4 files/s, 132649.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           8            761            689           2896
Markdown                        13            249              0            482
Jupyter Notebook                 8              0           2401            357
YAML                            12             25             28            332
TeX                              1             13              0            102
Dockerfile                       1              5              0             18
HTML                             1              2              0              9
-------------------------------------------------------------------------------
SUM:                            44           1055           3118           4196
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-07-19T05:53:53Z

Wordcount for paper.md is 512

editorialbot · 2023-07-19T05:53:55Z

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

OK DOIs

- 10.5281/zenodo.4569086 is OK
- 10.21105/joss.03414 is OK
- 10.5281/zenodo.7948229 is OK
- 10.48550/arXiv.2305.08196 is OK
- 10.48550/arXiv.2304.12306 is OK
- 10.48550/arXiv.2304.05750 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-07-19T05:54:40Z

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

aazuspan · 2023-07-19T06:21:23Z

Review checklist for @aazuspan

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 https://github.com/opengeos/segment-geospatial?
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 (@giswqs) 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
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
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?

ayoubft · 2023-07-19T09:49:10Z

Review checklist for @ayoubft

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 https://github.com/opengeos/segment-geospatial?
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 (@giswqs) 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
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
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?

hugoledoux · 2023-07-19T13:19:04Z

@editorialbot add @SimonMolinsky as reviewer

editorialbot · 2023-07-19T13:19:06Z

@SimonMolinsky added to the reviewers list!

giswqs · 2023-07-19T20:51:24Z

@hugoledoux Missing review checklist for reviewer @SimonMolinsky

ayoubft · 2023-07-19T22:43:46Z

Reviewer instructions & questions

@ayoubft & @aazuspan, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:
@editorialbot generate my checklist

@giswqs, actually the reviewer have not yet generated his checklist to start reviewing. Once he will comment the command above, the comment will be edited to the checklist that the reviewer will be crossing each bullet as done.

SimonMolinsky · 2023-07-20T07:28:47Z

Review checklist for @SimonMolinsky

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 https://github.com/opengeos/segment-geospatial?
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 (@giswqs) 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
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
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?

giswqs · 2023-07-22T17:00:47Z

@editorialbot generate pdf

editorialbot · 2023-07-22T17:01:57Z

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

giswqs · 2023-07-25T03:41:35Z

@editorialbot generate pdf

editorialbot · 2023-07-25T03:43:08Z

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

giswqs · 2023-08-17T12:50:52Z

@SimonMolinsky @ayoubft Please let me know if there is any changes I need to make in the repo to faciliate the review. Thank you.

giswqs · 2023-08-22T16:58:01Z

@editorialbot generate pdf

editorialbot · 2023-08-22T16:59:17Z

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

SimonMolinsky · 2023-08-27T21:47:25Z

Hi @giswqs ,

I've created the new (minor) issue in your repository: opengeos/segment-geospatial#179, but it doesn't affect the review. My review is done. Thank you for the excellent tool @giswqs

giswqs · 2023-08-27T22:07:59Z

@SimonMolinsky @aazuspan @ayoubft Thank you all for taking the time to review the submission and providing constructive comments and suggestions. Much appreicated.

@hugoledoux The reviews are now complete.

giswqs · 2023-09-05T13:04:37Z

@hugoledoux Just a gentle reminder that the reviews are complete. Thanks.

hugoledoux · 2023-09-12T11:17:51Z

@editorialbot generate pdf

hugoledoux · 2023-09-12T11:18:26Z

@editorialbot check references

editorialbot · 2023-09-12T11:18:33Z

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

OK DOIs

- 10.5281/zenodo.4569086 is OK
- 10.21105/joss.03414 is OK
- 10.5281/zenodo.7948229 is OK
- 10.48550/arXiv.2305.08196 is OK
- 10.48550/arXiv.2304.12306 is OK
- 10.48550/arXiv.2304.05750 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-09-12T11:19:28Z

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

hugoledoux · 2023-09-12T11:26:49Z

oh wow, I went on holidays 3 weeks and didn't expect that all would be finish!? Thanks to all 3 reviewers!

I just read the paper again and cannot find any typos/mistakes. I wish more submissions to JOSS were like yours @giswqs ❤️

At this point could you:

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 recommending acceptance of the submission.

giswqs · 2023-09-12T12:56:53Z

@hugoledoux I have completed the tasks as requested. Check the links below. Thank you.

Tag release: v0.10.1
DOI: 10.5281/zenodo.8338074

hugoledoux · 2023-09-12T13:36:31Z

@editorialbot set 10.5281/zenodo.8338074 as archive

editorialbot · 2023-09-12T13:36:33Z

Done! archive is now 10.5281/zenodo.8338074

hugoledoux · 2023-09-12T13:36:53Z

@editorialbot set v0.10.1 as version

editorialbot · 2023-09-12T13:36:55Z

Done! version is now v0.10.1

hugoledoux · 2023-09-12T13:36:59Z

@editorialbot recommend-accept

editorialbot · 2023-09-12T13:37:01Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-09-12T13:37:13Z

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

OK DOIs

- 10.5281/zenodo.4569086 is OK
- 10.21105/joss.03414 is OK
- 10.5281/zenodo.7948229 is OK
- 10.48550/arXiv.2305.08196 is OK
- 10.48550/arXiv.2304.12306 is OK
- 10.48550/arXiv.2304.05750 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-09-12T13:38:58Z

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4554, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

giswqs · 2023-09-12T16:31:18Z

@hugoledoux The pdf looks good to me. You can accept it for publication now! Thank you very much for handling the submission and the constructive comments from the reviewers. Appreciated.

kthyng · 2023-09-12T19:58:14Z

@giswqs I'll take over to wrap up your submission now. My steps are:

Check that version was updated
Check that software archive exists, has been input to JOSS, and title and author list look good
Check paper

kthyng · 2023-09-12T20:01:31Z

Ok looks good!

kthyng · 2023-09-12T20:01:36Z

@editorialbot accept

editorialbot · 2023-09-12T20:01:37Z

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

editorialbot · 2023-09-12T20:03:29Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Wu
  given-names: Qiusheng
  orcid: "https://orcid.org/0000-0001-5437-4073"
- family-names: Osco
  given-names: Lucas Prado
  orcid: "https://orcid.org/0000-0002-0258-536X"
doi: 10.5281/zenodo.8338074
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Wu
    given-names: Qiusheng
    orcid: "https://orcid.org/0000-0001-5437-4073"
  - family-names: Osco
    given-names: Lucas Prado
    orcid: "https://orcid.org/0000-0002-0258-536X"
  date-published: 2023-09-12
  doi: 10.21105/joss.05663
  issn: 2475-9066
  issue: 89
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5663
  title: "samgeo: A Python package for segmenting geospatial data with
    the Segment Anything Model (SAM)"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05663"
  volume: 8
title: "samgeo: A Python package for segmenting geospatial data with the
  Segment Anything Model (SAM)"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot · 2023-09-12T20:03:39Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2023-09-12T20:03:40Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.05663 joss-papers#4559
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05663
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kthyng · 2023-09-12T20:10:32Z

Congrats on your new publication @giswqs! Many thanks to editor @hugoledoux and reviewers @ayoubft, @aazuspan, and @SimonMolinsky for your time, hard work, and expertise!!

editorialbot · 2023-09-12T20:10:34Z

🎉🎉🎉 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.05663/status.svg)](https://doi.org/10.21105/joss.05663)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05663">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05663/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05663/status.svg
   :target: https://doi.org/10.21105/joss.05663

This is how it will look in your documentation:

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editorialbot added Dockerfile Python review TeX Track: 6 (ESE) Earth Sciences and Ecology labels Jul 19, 2023

editorialbot assigned hugoledoux Jul 19, 2023

editorialbot mentioned this issue Jul 19, 2023

[PRE REVIEW]: samgeo: A Python package for segmenting geospatial data with the Segment Anything Model (SAM) #5502

Closed

aazuspan mentioned this issue Jul 22, 2023

JOSS review opengeos/segment-geospatial#150

Closed

3 tasks

giswqs mentioned this issue Aug 19, 2023

Improve contributing guidelines opengeos/segment-geospatial#169

Merged

ayoubft mentioned this issue Aug 22, 2023

JOSS Review - @ayoubft opengeos/segment-geospatial#174

Closed

3 tasks

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Sep 12, 2023

editorialbot added accepted published Papers published in JOSS labels Sep 12, 2023

kthyng closed this as completed Sep 12, 2023

[REVIEW]: samgeo: A Python package for segmenting geospatial data with the Segment Anything Model (SAM) #5663

[REVIEW]: samgeo: A Python package for segmenting geospatial data with the Segment Anything Model (SAM) #5663

Comments

editorialbot commented Jul 19, 2023 • edited

Status

Reviewer instructions & questions

Checklists

editorialbot commented Jul 19, 2023

editorialbot commented Jul 19, 2023

editorialbot commented Jul 19, 2023

editorialbot commented Jul 19, 2023

editorialbot commented Jul 19, 2023

aazuspan commented Jul 19, 2023 • edited

Review checklist for @aazuspan

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

ayoubft commented Jul 19, 2023 • edited

Review checklist for @ayoubft

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

hugoledoux commented Jul 19, 2023

editorialbot commented Jul 19, 2023

giswqs commented Jul 19, 2023

ayoubft commented Jul 19, 2023

Reviewer instructions & questions

SimonMolinsky commented Jul 20, 2023 • edited

Review checklist for @SimonMolinsky

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

giswqs commented Jul 22, 2023

editorialbot commented Jul 22, 2023

giswqs commented Jul 25, 2023

editorialbot commented Jul 25, 2023

giswqs commented Aug 17, 2023

giswqs commented Aug 22, 2023

editorialbot commented Aug 22, 2023

SimonMolinsky commented Aug 27, 2023

giswqs commented Aug 27, 2023

giswqs commented Sep 5, 2023

hugoledoux commented Sep 12, 2023

hugoledoux commented Sep 12, 2023

editorialbot commented Sep 12, 2023

editorialbot commented Sep 12, 2023

hugoledoux commented Sep 12, 2023

giswqs commented Sep 12, 2023

hugoledoux commented Sep 12, 2023

editorialbot commented Sep 12, 2023

hugoledoux commented Sep 12, 2023

editorialbot commented Sep 12, 2023

hugoledoux commented Sep 12, 2023

editorialbot commented Sep 12, 2023

editorialbot commented Sep 12, 2023

editorialbot commented Sep 12, 2023

giswqs commented Sep 12, 2023

kthyng commented Sep 12, 2023 • edited

kthyng commented Sep 12, 2023

kthyng commented Sep 12, 2023

editorialbot commented Sep 12, 2023

editorialbot commented Sep 12, 2023

editorialbot commented Sep 12, 2023

editorialbot commented Sep 12, 2023

kthyng commented Sep 12, 2023

editorialbot commented Sep 12, 2023

editorialbot commented Jul 19, 2023 •

edited

aazuspan commented Jul 19, 2023 •

edited

ayoubft commented Jul 19, 2023 •

edited

SimonMolinsky commented Jul 20, 2023 •

edited

kthyng commented Sep 12, 2023 •

edited