[PRE REVIEW]: Open and Reproducible Data Science for Earth and Environmental Data: The Intermediate Earth Analytics Online Textbook

[whedon]

Submitting author: @lwasser (Leah Wasser) Repository: https://github.com/earthlab/earth-analytics-intermediate-earth-data-science-textbook Version: release 1.0 Editor: @labarba Reviewers: @cgentemann, @snowman2, @ConorIA Managing EiC: Jordan Gorzalski

:warning: JOSE reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSE 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://jose.theoj.org/papers/7481df300f47a7022e0f30d448c20ff1/status.svg)](https://jose.theoj.org/papers/7481df300f47a7022e0f30d448c20ff1)

Author instructions

Thanks for submitting your paper to JOSE @lwasser. Currently, there isn't an JOSE editor assigned to your paper.

@lwasser if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSE and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

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@whedon commands

[whedon]

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

:warning: JOSE reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSE is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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]

Failed to discover a Statement of need section in paper

[whedon]

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

OK DOIs

- 10.21105/joss.01886 is OK
- 10.5281/zenodo.5203279 is OK
- 10.5281/zenodo.4569086 is OK
- 10.5281/zenodo.5130718 is OK
- 10.5281/zenodo.4657501 is OK
- 10.5281/zenodo.5228063 is OK
- 10.5281/zenodo.5228300 is OK
- 10.1371/journal.pcbi.1005755 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Wordcount for paper.md is 1260

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=5.12 s (40.0 files/s, 83523.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
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Markdown                        94          13989              0          44657
TeX                              1              0              0             85
JSON                             1              0              0             44
YAML                             1              1              4             18
SVG                              2              0              0              2
-------------------------------------------------------------------------------
SUM:                           205         267186          36255         124339
-------------------------------------------------------------------------------

Statistical information for the repository '150bf5d3cbf76b2f1b692835' was
gathered on 2021/09/03.
No commited files with the specified extensions were found.

[whedon]

Failed to discover a valid open source license.

[whedon]

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

[lwasser]

hey @jgorzalski i'm new to this process. it looks like i need to fix a few things in my paper and to add a license file to our repo. should i go ahead and do that before moving on to reviewers? i can do that this week.

[jgorzalski]

Hi Leah,

Yes please! Thank you for moving forward on this - meant to @ you last week but things got away from me. Please let me know if you run into any issues.

On Wed, Sep 8, 2021 at 12:38 PM Leah Wasser @.***> wrote:

hey @jgorzalski https://github.com/jgorzalski i'm new to this process. it looks like i need to fix a few things in my paper and to add a license file to our repo. should i go ahead and do that before moving on to reviewers? i can do that this week.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/jose-reviews/issues/131#issuecomment-915394390, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANJW76XP4VAILXGJHVJZ32LUA6GRJANCNFSM5DMARDJQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

-- Jordan Gorzalski, MSI @. @.>|cell: (202) 617-6024 University of Michigan School of Information*

[lwasser]

ok great - i will work on fixing and will ping you here when i'm done. @jgorzalski can i "ask" whedon to recheck my repository once i and done by tagging @ + whedon with a command?

[jgorzalski]

Thank you! I believe you can ask whedon to generate a PDF to check and make sure everything is generating correctly by saying "generate pdf." For a list of all Whedon commands check out the Docs repo on the site linked here: https://openjournals.readthedocs.io/en/jose/whedon.html

On Wed, Sep 8, 2021 at 1:08 PM Leah Wasser @.***> wrote:

ok great - i will work on fixing and will ping you here when i'm done. @jgorzalski https://github.com/jgorzalski can i "ask" whedon to recheck my repository once i and done by tagging @ + whedon with a command?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/jose-reviews/issues/131#issuecomment-915415832, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANJW76SWIAE54ATGXEMMGU3UA6KB7ANCNFSM5DMARDJQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

-- Jordan Gorzalski, MSI @. @.>|cell: (202) 617-6024 University of Michigan School of Information*

[lwasser]

@jgorzalski thank you. A question about licenses- i read through the JOSE submission requirements and i'm not clear regarding licenses. Right now we have a CC license however we have a Non Commercial and no derivatives version. i'm thinking about moving to a share alike non commercial license but am not sure if that is in scope for JOSE. can you clarify? many thanks.

[jgorzalski]

@lwasser the share alike non commercial license will work for JOSE. Just be sure to put it in its own license file for Whedon. If you're looking for other options for licensing you could check out the papers that have been published through JOSE and click through into their repositories and license files if you've got time and are interested in exploring a bit. Let me know if that helps or you need more info!

[labarba]

@whedon assign me as editor

[whedon]

OK, the editor is @labarba

[labarba]

@lwasser hi! 👋 — did you decide on the license for this material? From the documentation

JOSE submissions must be fully open, under the Open Definition. This means that any text content or graphical objects should be under a Creative Commons license (ideally CC-BY) and code components should be under an OSI-approved license.

[lwasser]

hi there @labarba i've been struggling a bit with the CC-BY. i want to do it but i'm worried about our textbook being sold to a publisher if we do that. is there any way to allow the content to be reused but to avoid any sort of exploitation? i can modify the licenses i just want to do it carefully. i do want this to be reviewed by JOSE and think we are ready for that. i do want others to use it as well. So originally i had it CC-BY-ND-NC but then i thought about CC-BY-NC which aligns with how Hadley wickam published his R book online and i think Jake Vanderplos as well with Python. But it sounds like CC-BYA is the only option for JOSE review. Any thoughts are welcome here.

[labarba]

We say "ideally CC-BY" because that is the most permissive, but any Creative Commons license is accepted.

[lwasser]

ok thank you @labarba i will modify the LICENSE and the paper is easy i just need to add the heading. the content is there. I will ping you once that is done so this can move forward.

[lwasser]

@whedon commands

[whedon]

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

[lwasser]

@whedon check repository

[whedon]

Wordcount for paper.md is 1264

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=1.07 s (191.8 files/s, 398405.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                           106         253196          36251          79533
Markdown                        95          14068              0          44740
TeX                              1              0              0             85
JSON                             1              0              0             44
YAML                             1              1              4             18
SVG                              2              0              0              2
-------------------------------------------------------------------------------
SUM:                           206         267265          36255         124422
-------------------------------------------------------------------------------

Statistical information for the repository '82838bc51305c07fa02b6413' was
gathered on 2021/10/14.
No commited files with the specified extensions were found.

[lwasser]

@whedon generate pdf @whedon check references @labarba i've updated the license file and the paper. i'm trying to get whedon to check things now. please let me know if you need anything else.

[whedon]

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

[lwasser]

i'm also curious - i've updated the license but it's saying CC-BY not CC-BY-NC

![Uploading Screen Shot 2021-10-14 at 4.32.43 PM.png…]()

[labarba]

hi @lwasser 👋 — Given the size of this submission, and mindful of the workload for reviewers, I've come up with the following idea: we define three chunks that are separately reviewed by different people. We assign (say) six reviewers here, but each is only reviewing one-third of the material (by simple agreement in this thread). If you agree, can you suggest the best diving lines between the three chunks?

If you could also pop some names here for suggested reviewers, that would be great (using their GitHub handle but without @-mention).

[lwasser]

hi @labarba I understand. I will come back and suggest reviewers later today as i have a meeting coming up and need to think of people. i'd probably break it up this way:

Part 1 Time Series & API's

• Section 1 - Time Series
• Section 7 - API's and Twitter data
• Section 9 - Data Stories

For this section you'd want someone with some time series data background and pandas

TODO: I will come back and add people once i think about this more. i think this section is more general to anyone with python and pandas and some familiarity with api data access should be able to review this.

---

Part 2 - Spatial data processing

• Section 2 - Vector Data
• Section 3 - Raster Data
• Chapter 4 - Spatial data applications

Here's you'd want someone with geospatial experience but it can be intermediate level. someone from the carpentries. Possible joe jsta or MicheleTobias (MicheleTobias) id say michele may be good because if she can't review for python she probably knows someone who can given she hosts the #gischat thread on twitter.

---

Part 3 - Remote Sensing Data

• Section 5 Spectral remote sensing
• Section 6 Hierarchical data
• Section 8 Workflows

Here you'd want someone with geospatial xarray etc maybe from the pangeo community. I might suggest (but they may be busy) alan snow (snowman2) because we use rioxarray a lot here and that's their package. Another person could be Chelle Gentemann (cgentemann)

[labarba]

Hi Jem @jsta 👋 — I am looking for reviewers for this submission to JOSE (The Journal of Open Source Education). It's a full online textbook, so we want to split it in three parts, and get separate reviewers for each part. The author suggested you might review Part 2. See their post on the issue thread. Might you be able to volunteer a review for us? Thanks for considering it!

[labarba]

Hi @MicheleTobias — I am looking for reviewers for this submission to JOSE (The Journal of Open Source Education): "Open and Reproducible Data Science for Earth and Environmental Data: The Intermediate Earth Analytics Online Textbook" It's fairly large, so we want to split it in three parts, and get separate reviewers for each part. The author suggested you might review Part 2. See their post on the issue thread. Might you be able to volunteer a review for us? (We would appreciate any leads to possible other reviewers: we need six!) Thanks for considering it!

[labarba]

Hi @snowman2 — I am looking for reviewers for this submission to JOSE (The Journal of Open Source Education): "Open and Reproducible Data Science for Earth and Environmental Data: The Intermediate Earth Analytics Online Textbook" It's fairly large, so we want to split it in three parts, and get separate reviewers for each part. The author suggested you might review Part 3. See their post on the issue thread. Might you be able to volunteer a review for us? Thanks for considering it!

[labarba]

Hi Chelle! @cgentemann — I am looking for reviewers for this submission to JOSE (The Journal of Open Source Education): "Open and Reproducible Data Science for Earth and Environmental Data: The Intermediate Earth Analytics Online Textbook" It's fairly large, so we want to split it in three parts, and get separate reviewers for each part. The author suggested you might review Part 3. See their post on the issue thread. Might you be able to volunteer a review for us? Thanks for considering it!

[cgentemann]

@labarba Yes, I volunteer for the review!

[MicheleTobias]

@labarba I'd be happy to review. Just for full disclosure, I'm very qualified to review the concepts and make sure the code works, but I probably wouldn't be able to suggest alternative approaches with the code such as suggesting different functions. I'm a daily R user who is learning python. So let me know if that works for you, or if you'd rather find a different person.

[snowman2]

What is the timeline for the review?

[labarba]

@snowman2 hi! 👋 Thanks for popping in here. Pre-pandemic, we would request reviewers plan for about 3 weeks. In the middle of the pandemic, things stretched over months! Now, we're trying to get back to something like 4 or 5 weeks, if possible.This is a pure volunteer initiative, and we just do our best.

[snowman2]

That sounds like a reasonable timeline. I will take a look and see if I would be a good fit to review when I get time. I am assuming we are reviewing content and not grammar/spelling correct?

[labarba]

hi @snowman2 — thanks for considering it! Have a look at our Review criteria in the docs. And also the section on what the paper should contain. No need to do copy editing, but you can say things like "section 123 has confusing passages... check for typos on section 234" to give the authors revision pointers on these minor issues.

[snowman2]

I see @cgentemann has already agreed to review that section. So, I am thinking that it makes sense for me to focus on the code snippets and @cgentemann can do a more general review. Sound reasonable?

[labarba]

It's standard to have two reviewers per submission. What we're doing here is chunking the one big submission into three sections, with two reviewers per section. It's also natural for some reviewers to focus more in some aspects than others, and that's ok too.

[lwasser]

thank you all ! @labarba i'm struggling to think of two more people to review here. do you have a list of volunteers that i could perhaps have a look at? the first section comprises more general python pandas and api data access skills so it should be the easiest to find reviewers for i'm just spacing on names of people who could do it.

[cgentemann]

@abarciauskas-bgse perhaps you might be able to review section 1 or 2 or recommend someone from dev seed or elsewhere? thanks.

[labarba]

OK, so by my count, we have 3 committed reviewers: @MicheleTobias @cgentemann @snowman2

We need 3 more... I shall persevere!

[labarba]

@lwasser At the top of this thread, you'll find a link to the list of people who signed up to review for JOSE.

[labarba]

hi @cisaacstern 👋 — I am looking for reviewers for this submission to JOSE (The Journal of Open Source Education): "Open and Reproducible Data Science for Earth and Environmental Data: The Intermediate Earth Analytics Online Textbook" It's fairly large, so we want to split it in three parts, and get separate reviewers for each part. We're needing reviewers for Part 1. Might you be able to volunteer a review for us? Thanks for considering it!

[labarba]

hi @raspstephan 👋 — I am looking for reviewers for this submission to JOSE (The Journal of Open Source Education): "Open and Reproducible Data Science for Earth and Environmental Data: The Intermediate Earth Analytics Online Textbook" It's fairly large, so we want to split it in three parts, and get separate reviewers for each part. We're needing reviewers for Part 1. Might you be able to volunteer a review for us? Thanks for considering it!

[raspstephan]

Hi @labarba. Thank you so much for contacting me. This sounds super interesting and I would love to review this but unfortunately I am already behind on a bunch of responsibilities so it would probably not be a good idea to take on another task.

Would it help for me to suggest alternative reviewers?

[cisaacstern]

@labarba, thanks for the opportunity to contribute. Before I commit, could you provide (or link to) a summary of what this specifically entails? Particularly curious about deadlines, scope of work, etc. As part of that, could you help me understand what Part 1, in particular, refers to? I took a look at the textbook repo and it was not immediately apparent. I want to be sure that I feel qualified to review the content of this section.

[labarba]

@raspstephan — Thanks for your reply, and good luck chipping away at the backlog (I know the feeling, eek!). I would certainly appreciate any suggestions for alternative reviewers. Please give us their GitHub handle here, but without @-mention, and we'll invite. (And feel free to unsubscribe to this thread, of course!)

If you think you could be interested to review for JOSE in the future, please consider signing up via our volunteer form 🙏