[REVIEW]: LTPy - Learning tool for Python on Atmospheric Composition

whedon commented 2 years ago

Submitting author: @jwagemann (Julia Wagemann) Repository: https://gitlab.eumetsat.int/eumetlab/atmosphere/atmosphere Version: v1.0 Editor: @ashleefv Reviewer: @djlampert, @BYL4746 Archive: 10.5281/zenodo.7463072

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Review checklist for @djlampert

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSE code of conduct.

General checks

[x] Repository: Is the source for this learning module available at the repository url?
[x] 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)
[x] Version: Does the release version given match the repository release (v1.0)?
[x] Authorship: Has the submitting author (@jwagemann) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

[x] A statement of need: Do the authors clearly state the need for this module and who the target audience is?
[x] Installation instructions: Is there a clearly stated list of dependencies?
[x] Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
[x] 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!)

[x] 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.)
[x] Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
[x] Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
[x] Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
[x] 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

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

Review checklist for @BYL4746

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSE code of conduct.

General checks

[x] Repository: Is the source for this learning module available at the repository url?
[x] 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)
[x] Version: Does the release version given match the repository release (v1.0)?
[x] Authorship: Has the submitting author (@jwagemann) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

[x] A statement of need: Do the authors clearly state the need for this module and who the target audience is?
[x] Installation instructions: Is there a clearly stated list of dependencies?
[x] Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
[x] 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!)

[x] 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.)
[x] Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
[x] Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
[x] Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
[x] 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

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

whedon commented 2 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @djlampert, @BYL4746 it looks like you're currently assigned to review this paper :tada:.

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whedon commented 2 years ago

Wordcount for paper.md is 1457

whedon commented 2 years ago

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

OK DOIs

- 10.2873/011961 is OK
- 10.1080/17538947.2019.1585976 is OK
- 10.1126/science.1197869 is OK
- 10.1016/j.rse.2019.02.016 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 2 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=8.44 s (35.2 files/s, 137446.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Jupyter Notebook               283              1        1127165          31381
Python                           7             93             96            416
Markdown                         2             82              0            205
JSON                             4              0              0            165
TeX                              1              0              0             43
-------------------------------------------------------------------------------
SUM:                           297            176        1127261          32210
-------------------------------------------------------------------------------

Statistical information for the repository 'b928d74120f477e336f7e8c2' was
gathered on 2022/04/15.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Julia Wagemann                   5          1205            453          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
Julia Wagemann              752           62.4          2.0                9.97

whedon commented 2 years ago

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

jwagemann commented 2 years ago

Hi @djlampert and @BYL4746 , thank you for agreeing to review this submission. Since we already submitted it over a year ago, we advanced the training tool quite a bit since then. Hence, I would need to bring the submission to the current status. Would this be possible for me to do in the course of April and I'll ping you again once ready for you to review? I think a revision on my side would make the review process much more efficient.

Thanks, Julia

djlampert commented 2 years ago

Julia, that sounds good. Please make the updates, and when they are complete, ping us again in this thread to re-initiate the review.

Dave

whedon commented 2 years ago

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

whedon commented 2 years ago

:wave: @BYL4746, please update us on how your review is going (this is an automated reminder).

jwagemann commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

PDF failed to compile for issue #172 with the following error:

 /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:456:in `parse': (083703498d520d29fc05b7bb/paper.md): did not find expected key while parsing a block mapping at line 2 column 1 (Psych::SyntaxError)
    from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:456:in `parse_stream'
    from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:390:in `parse'
    from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:277:in `load'
    from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:578:in `block in load_file'
    from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:577:in `open'
    from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:577:in `load_file'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:127:in `load_yaml'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:87:in `initialize'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:38:in `new'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:38:in `set_paper'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:58:in `prepare'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in `run'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in `invoke_command'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in `dispatch'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in `start'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:131:in `<top (required)>'
    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `load'
    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `<main>'

jwagemann commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

PDF failed to compile for issue #172 with the following error:

 /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:456:in `parse': (33e82c00dd187ff773cb6a8a/paper.md): did not find expected key while parsing a block mapping at line 2 column 1 (Psych::SyntaxError)
    from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:456:in `parse_stream'
    from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:390:in `parse'
    from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:277:in `load'
    from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:578:in `block in load_file'
    from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:577:in `open'
    from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:577:in `load_file'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:127:in `load_yaml'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:87:in `initialize'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:38:in `new'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:38:in `set_paper'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:58:in `prepare'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in `run'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in `invoke_command'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in `dispatch'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in `start'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:131:in `<top (required)>'
    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `load'
    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `<main>'

jwagemann commented 2 years ago

@whedon generate paper

whedon commented 2 years ago

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

@whedon commands

jwagemann commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

PDF failed to compile for issue #172 with the following error:

 /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:456:in `parse': (1c5da8e735aa9031df27e167/paper.md): did not find expected key while parsing a block mapping at line 2 column 1 (Psych::SyntaxError)
    from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:456:in `parse_stream'
    from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:390:in `parse'
    from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:277:in `load'
    from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:578:in `block in load_file'
    from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:577:in `open'
    from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:577:in `load_file'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:127:in `load_yaml'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:87:in `initialize'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:38:in `new'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:38:in `set_paper'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:58:in `prepare'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in `run'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in `invoke_command'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in `dispatch'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in `start'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:131:in `<top (required)>'
    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `load'
    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `<main>'

jwagemann commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

jwagemann commented 2 years ago

Hi @djlampert and @BYL4746 , the repository and paper has been updated and is now ready for review. Thanks again for agreeing to review it. Julia

ashleefv commented 2 years ago

Checking in with reviewers @djlampert and @BYL4746, the authors updated version was posted in May. Can we get the review comments back to them in August?

djlampert commented 2 years ago

Hi Ashlee. I believe we can commence the review and get it finished this month. Thank you for the reminder. Dave

ashleefv commented 2 years ago

Checking back in on this. Can you update on the review status @djlampert and @BYL4746 ?

jwagemann commented 2 years ago

Hi @ashleefv , is there an update on the review process? Can I support in any way? Thanks!

djlampert commented 2 years ago

Hi, we have nearly completed the review. I believe I can do final checks today. Sorry for the delay.

Dave

On Wed, Sep 14, 2022, 04:55 Julia Wagemann @.***> wrote:

Hi @ashleefv https://github.com/ashleefv , is there an update on the review process? Can I support in any way? Thanks!

— Reply to this email directly, view it on GitHub https://github.com/openjournals/jose-reviews/issues/172#issuecomment-1246522025, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABRGDOC46VWML4AHVZR7TPTV6GOJPANCNFSM5TRLJWPQ . You are receiving this because you were mentioned.Message ID: @.***>

djlampert commented 2 years ago

I realize we are supposed to make comments in the repository, but since it is not in GitHub and I cannot seem to sign up for an account without an EUMETSAT email address, I will have to make the comment here. The learning objectives stated in the manuscript sound more like activities than outcomes. I suggest the following revision (please feel free to revise further, but ensure that the focus of the objectives are the learning outcomes, not just the activities).

The learning objectives of the LTPy are threefold. By performing the exercises in the LTPy notebooks, learners will: (1) develop a general understanding of available satellite data on atmospheric composition to facilitate data uptake and use, (2) understand how to use atmospheric data through code examples and step-by-step guides on loading, processing, and visualizing these data, and (3) know how to apply satellite data for specific purposes, including X, Y, and Z [please add a bit more detail].

djlampert commented 2 years ago

I don't see a DOI for the first reference (ESA Copernicus 2019 report).

labarba commented 2 years ago

I see that the target repository is on GitLab. Is it not possible for anyone with a Gitlab account to open an issue? We do want to see open issue trackers, so please let us know, @jwagemann.

labarba commented 2 years ago

I can see that the section on Learning Objectives is written to address rather the aims of the LTPy notebooks/course. This needs a bit of re-work, as @djlampert noted above. Writing learning objectives/outcomes is surprisingly hard! For example, learning designers will tell you to avoid the verbs "understand" or "know." They are unhelpful because it's like saying "after learning, you will know." Kind of meaningless. So the trick is to focus clearly on what the learners will be able to do by themselves if they complete the module/course, which is generally expressed by action verbs. So, of example...

At the end of the course, learners will be able to:

find satellite data on atmospheric composition that is relevant to their purposes
load, process, and visualize these data
apply data analysis to different applications

ashleefv commented 2 years ago

Reviewers please disregard the automated email until after the author checks in with the updates they discussed.

On Apr 29, 2022 5:50 PM, whedon @.***> wrote:

👋 @BYL4746https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FBYL4746&data=05%7C01%7Cashleefv%40buffalo.edu%7C27fbff1a416c45be779d08da2a2a46f8%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C637868658309210973%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=0ZK2wP4d9Q47dtlzHtTtnh979MGUwlrYJkZmXsXbDcg%3D&reserved=0, please update us on how your review is going (this is an automated reminder).

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jwagemann commented 2 years ago

Hi - thanks @djlampert and @labarba for your comments. I'll revise the learning objectives next week. Concerning adding some comments to the repository directly as issues: I'll give this as a feedback to the system administrators, but changing this could take a while. Nevertheless, I hope it does not hinder us from publication.

@djlampert have you had additional comments to those you shared above?

djlampert commented 2 years ago

Hi @jwagemann. I have no other comments. We have reviewed the software, and it seems to work fine.

Dave

On Fri, Oct 28, 2022 at 7:42 AM Julia Wagemann @.***> wrote:

Hi - thanks @djlampert https://github.com/djlampert and @labarba https://github.com/labarba for your comments. I'll revise the learning objectives next week. Concerning adding some comments to the repository directly. I'll give this as a feedback to the system administrators, but I hope it does not hinder us from publication.

@djlampert https://github.com/djlampert have you had additional comments to those you shared above?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/jose-reviews/issues/172#issuecomment-1294954191, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABRGDOHKJEBEM5KL5YREW7TWFPC4DANCNFSM5TRLJWPQ . You are receiving this because you were mentioned.Message ID: @.***>

jwagemann commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

jwagemann commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

jwagemann commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

jwagemann commented 2 years ago

Hi @djlampert and @labarba , I re-worked on the learning objectives as suggested and added some references to the paper. Would be great if you could review it another time. Thanks, Julia

djlampert commented 2 years ago

Hi @jwagemann--looks much better to me now. I am fine with the manuscript in this form.

jwagemann commented 2 years ago

Great. Thanks @djlampert for taking the time to reviewing it.

@ashleefv what are now the next steps?

jwagemann commented 1 year ago

Hi @ashleefv @labarba, kind reminder. The reviewers are done with the review. What are the next steps now?

jwagemann commented 1 year ago

HI @ashleefv and @labarba . The review of this submission is finalised. Could we try to bring the submission to publication?Thanks.

ashleefv commented 1 year ago

Thank you for your patience and persistence with this review. I have looked back through all the review notes and read the manuscript. @djlampert has confirmed being "fine with the manuscript in this form", and the other reviewer @BYL4746 raised no concerns on the initial review. I will initiate the acceptance process.

ashleefv commented 1 year ago

@whedon generate pdf

whedon commented 1 year ago

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

ashleefv commented 1 year ago

@whedon check references

whedon commented 1 year ago

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

OK DOIs

- 10.2873/011961 is OK
- 10.1080/17538947.2019.1585976 is OK
- 10.1126/science.1197869 is OK
- 10.1016/j.rse.2019.02.016 is OK
- 10.3390/rs14143359 is OK
- 10.1016/j.cageo.2021.104916 is OK

MISSING DOIs

- None

INVALID DOIs

- None

ashleefv commented 1 year ago

@jwagemann While proofreading, I found a few typos and broken hyperlinks:

In the reference for European Commission - Directorate General for Internal Market Industry, Entrepreneurship and SMES and PwC. (2019), please capitalize February
In the reference for Wagemann, J., Fierli, F., Mantovani, S., Siemen, S., Seeger, B., & Bendix, J. (2022), please capitalize Jupyter
Two references point to broken hyperlinks: European Organisation for the Exploitation of Meteorological Satellites. (2022). Meteosat series | EUMETSAT and Hebden, S. (2020). Plans for a new wave of european satellites. This second one should also have European capitalized.

Please make these requested changes and tag me when they are complete. Then make a Zenodo archive and report the DOI in the review thread.

jwagemann commented 1 year ago

@whedon generate pdf

openjournals / jose-reviews