[REVIEW]: Educational resources to accelerate the analysis of remote sensing data using cloud resources with Xarray

[editorialbot]

Submitting author: @e-marshall (Emma Marshall)
Repository: https://github.com/e-marshall/JOSE_tutorials_submission
Branch with paper.md (empty if default branch):
Version: n/a
Editor: @kls2177
Reviewers: @mikemorris12, @r-ford, @dcamron
Archive: Pending
Paper kind: learning module

Status

Status badge code:

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Markdown: [![status](https://jose.theoj.org/papers/35519017bbfdfeafc070263cbeee4f26/status.svg)](https://jose.theoj.org/papers/35519017bbfdfeafc070263cbeee4f26)

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

@mikemorris12 & @r-ford & @dcamron, 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://openjournals.readthedocs.io/en/jose/reviewer_guidelines.html. Any questions/concerns please let @kls2177 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 @r-ford

📝 Checklist for @dcamron

📝 Checklist for @mikemorris12

[editorialbot]

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:

@editorialbot generate pdf

[editorialbot]

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "pages" (NAME) [#<BibTeX::Bibliography data=[1]>, "@", #<BibTeX::Entry >, {:title=>["Toward the Geoscience Paper of the Future: Best practices for documenting and sharing research from data to software to provenance"], :volume=>["3"], :issn=>["2333-5084, 2333-5084"], :url=>["https://agupubs.onlinelibrary.wiley.com/doi/10.1002/2015EA000136"], :doi=>["10.1002/2015EA000136"], :number=>["10"], :journal=>["Earth and Space Science"], :author=>["Gil, Yolanda and David, Cédric H. and Demir, Ibrahim and Essawy, Bakinam T. and Fulweiler, Robinson W. and Goodall, Jonathan L. and Karlstrom, Leif and Lee, Huikyo and Mills, Heath J. and Oh, Ji‐Hyun and Pierce, Suzanne A. and Pope, Allen and Tzeng, Mimi W. and Villamizar, Sandra R. and Yu, Xuan"], :year=>["2016"], :month=>[:oct]}, ",", "p"]

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.98  T=0.01 s (419.1 files/s, 47359.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                              1             23              0            242
Markdown                         2             19              0             55
-------------------------------------------------------------------------------
SUM:                             3             42              0            297
-------------------------------------------------------------------------------

Commit count by author:

    42	Emma Marshall
     8	e-marshall
     1	Jessica Scheick

[editorialbot]

⚠️ An error happened when generating the pdf.

[editorialbot]

Paper file info:

⚠️ Wordcount for paper.md is 1577

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🔴 License found: Creative Commons Zero v1.0 Universal (Not OSI approved)

[kls2177]

Hello @mikemorris12, @r-ford, @dcamron,

Thank you again for agreeing to review. We are now ready to go!

Please complete the above checklists and then provide your specific review comments as issues to the submitted repo. Here is an example of a nicely organized review.

If you have any questions about the process, please refer to the JOSE docs. If you don't find what you are looking for in these docs, feel free to connect with me.

Thanks!

Karen

[r-ford]

Review checklist for @r-ford

Conflict of interest

• As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• I confirm that I read and will adhere to the JOSE code of conduct.

General checks

• Repository: Is the source for this learning module available at the https://github.com/e-marshall/JOSE_tutorials_submission?
• License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
• Version: Does the release version given match the repository release?
• Authorship: Has the submitting author (@e-marshall) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

• A statement of need: Do the authors clearly state the need for this module and who the target audience is?
• Installation instructions: Is there a clearly stated list of dependencies?
• Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

• Learning objectives: Does the module make the learning objectives plainly clear? (We don't require explicitly written learning objectives; only that they be evident from content and design.)
• Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
• Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
• Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
• Instructional design: Is the instructional design deliberate and apparent? For example, exploit worked-example effects; effective multi-media use; low extraneous cognitive load.

JOSE paper

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Does the paper clearly state the need for this module and who the target audience is?
• Description: Does the paper describe the learning materials and sequence?
• Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
• Could someone else teach with this module, given the right expertise?
• Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[r-ford]

It looks like there is a typo in the .bib file preventing the pdf from generating.

[e-marshall]

so sorry about that! Just fixed

[r-ford]

@editorialbot generate pdf

[editorialbot]

⚠️ An error happened when generating the pdf.

[r-ford]

Guess that wasn't the issue! Based on the error, my guess is that there is an issue with the affiliations. Can affiliations include links?

[e-marshall]

thank you @r-ford ! Sorry about that! I'm not sure if i'm allowed to engage with editorial bot or not, do you know if its okay if I run 'generate pdf' to check ?

[r-ford]

thank you @r-ford ! Sorry about that! I'm not sure if i'm allowed to engage with editorial bot or not, do you know if its okay if I run 'generate pdf' to check ?

I'm new to the JOSE review process, but it seems fine in the documentation.

[r-ford]

@editorialbot generate pdf

[editorialbot]

⚠️ An error happened when generating the pdf.

[e-marshall]

I'll take a look at this right now

[e-marshall]

@editorialbot generate pdf

[editorialbot]

⚠️ An error happened when generating the pdf.

[e-marshall]

@editorialbot generate pdf

[editorialbot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

[e-marshall]

@editorialbot generate pdf

[editorialbot]

⚠️ An error happened when generating the pdf.

[e-marshall]

@editorialbot generate pdf

[editorialbot]

⚠️ An error happened when generating the pdf.

[mikemorris12]

Hi @e-marshall, I'm looking forward to reviewing your work! Since each attempt to generate the PDF adds new messages to this thread (and we're all emailed each time), I suggest debugging the PDF generation using the tips on this page of the JOSS docs. I've previously published in JOSE and I used the GitHub Action tool described in the linked page to auto-compile a sample PDF upon each update to the GitHub repository.

[e-marshall]

Hey @mikemorris12 , thank you so much! I'm really sorry for all the spamming, first time trying to figure a lot of these things out! I was just looking into running this locally. i'll update when I have done that and resolved issues

[e-marshall]

@editorialbot generate pdf

[editorialbot]

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

[e-marshall]

the issues should be fixed now, thank you @mikemorris12 for pointing me toward the gh action, apologies to everyone for the emails and thank you so much for taking the time to review!

[dcamron]

Review checklist for @dcamron

Conflict of interest

• As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• I confirm that I read and will adhere to the JOSE code of conduct.

General checks

• Repository: Is the source for this learning module available at the https://github.com/e-marshall/JOSE_tutorials_submission?
• License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
• Version: Does the release version given match the repository release?
• Authorship: Has the submitting author (@e-marshall) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

• A statement of need: Do the authors clearly state the need for this module and who the target audience is?
• Installation instructions: Is there a clearly stated list of dependencies?
• Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

• Learning objectives: Does the module make the learning objectives plainly clear? (We don't require explicitly written learning objectives; only that they be evident from content and design.)
• Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
• Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
• Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
• Instructional design: Is the instructional design deliberate and apparent? For example, exploit worked-example effects; effective multi-media use; low extraneous cognitive load.

JOSE paper

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Does the paper clearly state the need for this module and who the target audience is?
• Description: Does the paper describe the learning materials and sequence?
• Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
• Could someone else teach with this module, given the right expertise?
• Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[mikemorris12]

Review checklist for @mikemorris12

Conflict of interest

• As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• I confirm that I read and will adhere to the JOSE code of conduct.

General checks

• Repository: Is the source for this learning module available at the https://github.com/e-marshall/JOSE_tutorials_submission?
• License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
• Version: Does the release version given match the repository release?
• Authorship: Has the submitting author (@e-marshall) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

• A statement of need: Do the authors clearly state the need for this module and who the target audience is?
• Installation instructions: Is there a clearly stated list of dependencies?
• Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

• Learning objectives: Does the module make the learning objectives plainly clear? (We don't require explicitly written learning objectives; only that they be evident from content and design.)
• Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
• Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
• Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
• Instructional design: Is the instructional design deliberate and apparent? For example, exploit worked-example effects; effective multi-media use; low extraneous cognitive load.

JOSE paper

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Does the paper clearly state the need for this module and who the target audience is?
• Description: Does the paper describe the learning materials and sequence?
• Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
• Could someone else teach with this module, given the right expertise?
• Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[mikemorris12]

Hi @e-marshall, thanks for submitting these resources to JOSE. I think each of them provide useful information and teach practical programming skills for working with climate data. The purpose of each of the two guidebooks is clear, and the manuscript contains all of the necessary information about the submission.

However, I have several comments about the way the software is archived, the styles of writing and code, and some bugs I found when testing the code. I've got a few general comments here, as well as issues I've opened in each of the GitHub repositories. These comments must be addressed before the submission can be accepted.

Overall Comments

• All the submission materials should be in a single repository, instead of 3 separate ones. The submission repository doesn’t contain any of the code for either tutorial. This will make version tracking and archiving more straightforward. @kls2177, please correct me if this isn't required, but it seems to violate the "Repository" checklist item.
• The manuscript is too long. It is well over the requested length of 1000 words.
• Some of the citations in the paper are missing DOIs (e.g. Kluyver et al. 2016). Double check that you can find the DOI for each cited source.
• The repositories are missing licenses and version information.

The issues with specific comments about each tutorial and section are linked below:

ITS_LIVE Tutorial

• General Comments
• Comments about Software and Data section.
• Comments about Individual Glacier Data Inspection.
• Comments about Individual Glacier Surface Velocity Analysis.
• Comments about Region-Scale Glacier Analysis.

Sentinel-1 RTC Tutorial

• General Comments
• Comments about Software and Data.
• Comments about Data Cleaning and Organization.
• Comments about ASF GDAL VRT Approach.
• Comments about ASF-processed RTC Data Inspection.
• Comments about RTC Dataset Comparison.
• Comments about Applied example: RTC time series analysis.
• Comments about Appendices.

[kls2177]

Hi @mikemorris12, this is a good question about the repository materials. This is the first time I have seen multiple repositories, so I will follow-up.

In addition, multiple jupyterbooks is unusual as well. Combining the tutorials into one jupyterbook with an overarching narrative would be helpful for learners and educators.

[e-marshall]

thank you @mikemorris12 ! I'm working on addressing your comments and I'll update this thread once I've finished. I'll also work on combining the tutorials into a single book and repo

[r-ford]

Thanks @e-marshall for taking the time to develop these resources. I overall found the two tutorials practical and well-motivated. My main concern is about the reproducibility of the environment/code, which is essential if the goal is for these tutorials to be usable by other instructors. Since it seems like there will be some restructuring of the repositories, I will leave my specific comments as issues in the submitted repository instead of the two content repositories.

Comments on the general checks

• Repository: There are two tutorials, which are linked in the submitted repository. Is there any issue with this? (Already discussed above)
• License: The tutorial repositories do not have licenses.
• Version: No version is given in the submission. Having two repositories for the content may cause issues with versioning.
• Authorship: Both content repositories have visible contributions from Emma Marshall, Scott Henderson, and Deepak Cherian, while Emma Marshall and Jessica Scheick have contributed to the submitted repository (the paper).

Specific comments

• RF JOSE review: general + paper e-marshall/JOSE_tutorials_submission#12
• RF JOSE review: ITS_LIVE e-marshall/JOSE_tutorials_submission#13
• RF JOSE review: Sentinel-1 RTC e-marshall/JOSE_tutorials_submission#14