[REVIEW]: Museo ToolBox : a python library for remote sensing including a new way to handle rasters.

[whedon]

Submitting author: @nkarasiak (Nicolas Karasiak)
Repository: https://github.com/nkarasiak/MuseoToolBox
Version: v0.13.0
Editor: @kbarnhart
Reviewer: @cmillion, @mollenburger
Archive: 10.5281/zenodo.3759215

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/1f4762d9910093a08034e8f4de441930/status.svg)](https://joss.theoj.org/papers/1f4762d9910093a08034e8f4de441930)

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

@cmillion & @mollenburger, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @cmillion

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 repository url?
• 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 (@nkarasiak) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• 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?

Review checklist for @mollenburger

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 repository url?
• 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 (@nkarasiak) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• 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?

[whedon]

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

⭐ Important ⭐

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:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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

@whedon commands

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

@whedon generate pdf

[whedon]

Attempting to check references...

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

OK DOIs

- 10.3390/rs11212512 is OK
- 10.1111/ecog.02881 is OK
- 10.1016/j.rse.2014.02.015 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👉 Check article proof 📄 👈

[kbarnhart]

👋 @nkarasiak, @cmillion, @mollenburger this is the review thread for the paper. All of our communications will happen here from now on.

All reviewers have checklists at the top of this thread with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#1978 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. I understand that it is late December and many people may be taking vacation and/or spending time away from work. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@kbarnhart) if you have any questions/concerns.

[kbarnhart]

👋 @cmillion, @mollenburger, just a quick reminder to complete your reviews. As always, if you have any questions, please feel free to ping me here.

[kbarnhart]

👋 @cmillion, @mollenburger I wanted to check in to remind you to complete your reviews. As always, if you have any questions, please feel free to ping me here.

[cmillion]

Confirming.

[kbarnhart]

@cmillion thanks for confirming.

[kbarnhart]

👋 @cmillion, @mollenburger A friendly reminder to complete your reviews. If you have an estimated timeline, please let me know.

@mollenburger could you please confirm receipt.

As always, if you have any questions, please feel free to ping me here.

Thank you for being willing to review for JOSS.

[mollenburger]

confirming. I'm working on this today and hope to have it done by the end of the week.

[kbarnhart]

👋 @cmillion, @mollenburger a friendly reminder to complete your reviews.

If you create any issues in the submitted repository, please link to this issue by using /issues/1978

When you are done, please make a note here on this issue indicating your recommendation.

If you have any questions, please let me know.

[kbarnhart]

I wanted to check in to keep this review moving along.

I see that there are open issues in the main repository made by @cmillion, Thank you for making issues there.

This ping is meant as a reminder to the reviewers to make any additional issues that stand in the way of completing the review checklist, and as a reminder to @nkarasiak to address issues.

Thanks again to all for contributing to the JOSS review process.

[kbarnhart]

👋 another message to check in and keep this review moving forward. I see that both @cmillion and @mollenburger have made issues in the main repo (thanks 👍 ). Based on looking at them it appears that some of the issues may need to be addressed before the reviewers can complete their reviews.

@nkarasiak can I ping you to address these issues so the reviewers can complete their reviews.

[nkarasiak]

Of course @kbarnhart, what do I need to do (except addressing the issues) ?
I was preparing my answers (and code/text rewriting) for the reviewers, and a native English speaker is going to proofread my paper.

[kbarnhart]

thanks for the quick reply @nkarasiak. Just addressing the issues is fine.

[kbarnhart]

👋 @nkarasiak I wanted to check in and see if you had an anticipated timeline for addressing the current set of issues.

[nkarasiak]

Hello @kbarnhart. I'm dealing with the issues, and I submitted my library to conda in order to answer to @mollenburger to ease the installation process with gdal but it takes some times...
I didn't forget to answers the issues, I just want to do it the nicest way possible :)
I hope end of next week everything will be adressed.
Kind regards,
Nicolas.

[ooo]

👋 Hey @nkarasiak...

Letting you know, @kbarnhart is currently OOO until Friday, March 20th 2020. ❤️

[kbarnhart]

@nkarasiak thanks for the update. It all sounds good.

Also, sorry for the ooo-bot, I accidentally turned it on trying to demonstrate how to use it for a reviewer (and I haven't yet figured out how to turn it off). I'm not out of the office at all.

[kbarnhart]

@nkarasiak I wanted to check in on this review. Could you provide an update on your progress addressing the current set of issues raised by the reviewers?

[kbarnhart]

@nkarasiak once you have considered nkarasiak/MuseoToolBox/pull/29 and updated the repositories master branch could you:

• Make a tagged release of your software, and indicate 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

[nkarasiak]

Hi @kbarnhart
I updated and published the 0.13.0 version in the master branch :

• The git tagged version is 0.13.0.
• The Zenodo archive version is also 0.13.0 with the DOI 10.5281/zenodo.3759215. Author list, title and ORCID have been added in the archive deposit.

[kbarnhart]

@whedon check references

[whedon]

Reference check summary:

OK DOIs

- 10.2307/2332142 is OK
- 10.3390/rs11212512 is OK
- 10.1111/ecog.02881 is OK
- 10.1016/j.rse.2014.02.015 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[kbarnhart]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[kbarnhart]

@whedon set v0.13.0 as version

[whedon]

OK. v0.13.0 is the version.

[kbarnhart]

@whedon set 10.5281/zenodo.3759215 as archive

[whedon]

OK. 10.5281/zenodo.3759215 is the archive.

[kbarnhart]

@nkarasiak I'm going to move this article to the final stage by notifying the JOSS editors in chief that it is ready to be published. They may or may not have have additional requests of you.

[kbarnhart]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- 10.2307/2332142 is OK
- 10.3390/rs11212512 is OK
- 10.1111/ecog.02881 is OK
- 10.1016/j.rse.2014.02.015 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#1426

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1426, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[arfon]

@whedon accept deposit=true

[arfon]

@whedon commands

[arfon]

@whedon commands

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.01978 joss-papers#1427
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01978
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

[arfon]

@cmillion, @mollenburger - many thanks for your reviews here and to @kbarnhart for editing this one ✨

@nkarasiak - your paper is now accepted into JOSS ⚡🚀💥

[whedon]

🎉🎉🎉 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:
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HTML:
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</a>

reStructuredText:
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This is how it will look in your documentation:

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