[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

:warning: JOSE reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSE is currently operating in a "reduced service mode".

Status

Status badge code:

HTML: <a href="https://jose.theoj.org/papers/8837ff3532dcb8f1fd59fa77a6c7b8a4"><img src="https://jose.theoj.org/papers/8837ff3532dcb8f1fd59fa77a6c7b8a4/status.svg"></a>
Markdown: [![status](https://jose.theoj.org/papers/8837ff3532dcb8f1fd59fa77a6c7b8a4/status.svg)](https://jose.theoj.org/papers/8837ff3532dcb8f1fd59fa77a6c7b8a4)

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

@djlampert & @BYL4746, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/jose-reviews/invitations

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

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 1 year ago

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

jwagemann 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:

jwagemann commented 1 year ago

Hi @ashleefv - I made the required changes. I realised that capitalisation of words in the title is per default disabled. Hence, now all titles should have the correct spelling as in the titles of the publication.

Let me know if you require anything further from my side. Thank you.

ashleefv commented 1 year ago

I concur that the references are now corrected with functioning links.

Please make a Zenodo archive and report the DOI in the review thread. https://zenodo.org/ This is required to set the archive for the manuscript, prior to acceptance.

Ashlee N. Ford Versypt, Ph.D. (she, her, hers) Associate Professor, Department of Chemical and Biological Engineering Affiliated Faculty, Department of Engineering Education, Department of Biomedical Engineering, and Institute for Artificial Intelligence and Data Science University at Buffalo, The State University of New York 507 Furnas Hall, Buffalo, NY 14260 @.*** http://www.cbe.buffalo.edu/fordversypt

From: Julia Wagemann @.> Sent: Sunday, December 18, 2022 5:02 AM To: openjournals/jose-reviews @.> Cc: Ashlee Ford Versypt @.>; Mention @.> Subject: Re: [openjournals/jose-reviews] [REVIEW]: LTPy - Learning tool for Python on Atmospheric Composition (Issue #172)

Hi @ashleefvhttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fashleefv&data=05%7C01%7Cashleefv%40buffalo.edu%7C3ff8ea39eadc4e91334108dae0def076%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638069545363416361%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=1CtUcvP%2F8G%2B0OUx5%2FedG%2FoW260RV0F%2B8DNOMIL%2BwZWY%3D&reserved=0 - I made the required changes. I realised that capitalisation of words in the title is per default disabled. Hence, now all titles should have the correct spelling as in the titles of the publication.

Let me know if you require anything further from my side. Thank you.

— Reply to this email directly, view it on GitHubhttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fopenjournals%2Fjose-reviews%2Fissues%2F172%23issuecomment-1356762527&data=05%7C01%7Cashleefv%40buffalo.edu%7C3ff8ea39eadc4e91334108dae0def076%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638069545363416361%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=plKDj8wrjh%2B1%2BcNgENkevNmKCAsf1v9B2qDrpLgfwXc%3D&reserved=0, or unsubscribehttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FADAP4NXR35YM266VGNQSXF3WN3OKLANCNFSM5TRLJWPQ&data=05%7C01%7Cashleefv%40buffalo.edu%7C3ff8ea39eadc4e91334108dae0def076%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638069545363416361%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=WkG7buhJX0%2BDayCxh%2BO%2F9mzYH3uWIivOGKr7kUlYv2I%3D&reserved=0. You are receiving this because you were mentioned.Message ID: @.***>

jwagemann commented 1 year ago

Hi @ashleefv ,

archive made on Zenodo:

ashleefv commented 1 year ago

@whedon set 10.5281/zenodo.7463072 as archive

whedon commented 1 year ago

OK. 10.5281/zenodo.7463072 is the archive.

ashleefv commented 1 year ago

@openjournals/joss-eics paper is ready to be accepted.

danielskatz commented 1 year ago

👋 @ashleefv - the next step is for you to use the command @editorialbot recommend-accept and then to make sure it works, and to check the produced files - this command will produce the message you gave above, which typically you won't type manually

danielskatz commented 1 year ago

oops, sorry, this is a JOSE paper, not a JOSS one - please ignore my comment above

danielskatz commented 1 year ago

In this case, you probably need to ping a JOSE EiC, not a JOSS one

danielskatz commented 1 year ago

Also, if this was in JOSS, you would need to get the version string of the archived software, and use the command @editorialbot set version_string as version though I don't know if this is the same in JOSE

ashleefv commented 1 year ago

Sorry for the confusion JOSS editors, I was following the instructions from https://openjournals.readthedocs.io/en/jose/editing.html. It seems that several times JOSS is mentioned instead of JOSE.

@openjournals/jose-eics paper is ready to be accepted.

danielskatz commented 1 year ago

Thanks @ashleefv - I've suggested changes to the docs in https://github.com/openjournals/docs/pull/6 which might fix this, but @openjournals/jose-eics should check this

ashleefv commented 1 year ago

@labarbahttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Flabarba&data=05%7C01%7Cashleefv%40buffalo.edu%7Ca9ed369aa9594766436508dae494cc20%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638073624980164186%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Xwkn98snMUcF8R1%2FM7qapPUQZzROdTTPDWhDx8DlLe8%3D&reserved=0 I believe this submission is ready to accept.

Ashlee N. Ford Versypt, Ph.D. (she, her, hers) Associate Professor, Department of Chemical and Biological Engineering Affiliated Faculty, Department of Engineering Education, Department of Biomedical Engineering, and Institute for Artificial Intelligence and Data Science University at Buffalo, The State University of New York 507 Furnas Hall, Buffalo, NY 14260 @.*** http://www.cbe.buffalo.edu/fordversypt

From: Ashlee Ford Versypt @.> Sent: Tuesday, December 20, 2022 6:47 PM To: openjournals/jose-reviews @.> Cc: Ashlee Ford Versypt @.>; Your activity @.> Subject: Re: [openjournals/jose-reviews] [REVIEW]: LTPy - Learning tool for Python on Atmospheric Composition (Issue #172)

Sorry for the confusion JOSS editors, I was following the instructions from https://openjournals.readthedocs.io/en/jose/editing.html https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fopenjournals.readthedocs.io%2Fen%2Fjose%2Fediting.html&data=05%7C01%7Cashleefv%40buffalo.edu%7Ca3ba24dd76f540ae5b6a08dae2e47f5c%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638071768269270812%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=nWoTIjdVq6XYCXsvhE3kbYnrTQValje6Uvi%2BFPJRbvk%3D&reserved=0. It seems that several times JOSS is mentioned instead of JOSE.

@openjournals/jose-eicshttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Forgs%2Fopenjournals%2Fteams%2Fjose-eics&data=05%7C01%7Cashleefv%40buffalo.edu%7Ca3ba24dd76f540ae5b6a08dae2e47f5c%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638071768269270812%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=0WO51r0CAHqmJMMk%2Fll%2BbSuLJJIGKT9nrfsjApRrv8k%3D&reserved=0 paper is ready to be accepted.

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labarba commented 1 year ago

Thank you, @danielskatz – merged, and updated deprecated bits

labarba commented 1 year ago

@ashleefv : please run @whedon recommend-accept to move this to my queue – thanks! 🙏

ashleefv commented 1 year ago

@whedon recommend-accept

On Dec 24, 2022 7:33 AM, "Lorena A. Barba" @.***> wrote:

@ashleefvhttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fashleefv&data=05%7C01%7Cashleefv%40buffalo.edu%7Cc4338eb75ef342a2231808dae5b379f6%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638074856251135616%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Bf6BOmJcaytxgQERCWO3qgPAeGskVAUwFpvSfNYWp40%3D&reserved=0 : please run @whedon recommend-accept to move this to my queue – thanks! 🙏

— Reply to this email directly, view it on GitHubhttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fopenjournals%2Fjose-reviews%2Fissues%2F172%23issuecomment-1364531012&data=05%7C01%7Cashleefv%40buffalo.edu%7Cc4338eb75ef342a2231808dae5b379f6%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638074856251135616%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=EM5dLGb%2B1%2Bna2jm%2BJ42XiscAx6QYX%2FFmHGd2vXCyYak%3D&reserved=0, or unsubscribehttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FADAP4NRU7UZW3ZF7XEDCZVDWO33TNANCNFSM5TRLJWPQ&data=05%7C01%7Cashleefv%40buffalo.edu%7Cc4338eb75ef342a2231808dae5b379f6%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638074856251135616%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=%2FS6iUyWcYIQ%2BVtINSUdSii2xhiuzfTSXAc2zMCCZmfc%3D&reserved=0. You are receiving this because you were mentioned.Message ID: @.***>

whedon commented 1 year ago

Attempting dry run of processing paper acceptance...

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

whedon commented 1 year ago

:wave: @openjournals/jose-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/openjournals/jose-papers/pull/112

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/jose-papers/pull/112, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

ashleefv commented 1 year ago

@labarba This is my first editorial role. Do I take the next/last step or is this your responsibility?

ashleefv commented 1 year ago

@labarba This is my first editorial role. Do I take the next/last step or is this your responsibility?

labarba commented 1 year ago

hi @ashleefv – thanks for the bump! 👊 This is now on my queue to take through the finish line (and I see it in my dashboard). I'm just a little backed up! 😬

jwagemann commented 1 year ago

Hi @ashleefv and @labarba , wanted to check in here. Let me know if I can support you with the last step of getting the paper published. Thanks.

labarba commented 1 year ago

I notice that @djlampert 's checklist is missing two items to check (learning objectives, and references), but that in a comment he approved of the revisions. I will proceed to add the check marks to leave the review complete.

labarba commented 1 year ago

For the Learning Objectives, did you mean them to display as a bulleted list? With * instead of - to start each line, currently it does not render as a list. See: https://gitlab.eumetsat.int/eumetlab/atmosphere/atmosphere/-/blob/master/paper.md?plain=1#L53

labarba commented 1 year ago

While you are looking into that detail, reconsider the wording "multi-disciplined" on L53: should it be "multi-disciplinary"? ("disciplined" means marked by or possessing discipline). Also reconsider the wording "due to the diverse ways of data structures." What do you mean here?

On L80, you have a repetition: "more than more than 1000 learners"

jwagemann commented 1 year ago

Excellent - thanks @labarba . I'll make these modifications right now.

jwagemann 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:

jwagemann commented 1 year ago

Hi @labarba not sure about the best way to format a bullet list - if I use '-', it is not rendered as list in the pdf generated by whedon, but on Gitlab. Let me know.

Otherwise, all suggestions are now integrated. Thanks.

labarba commented 1 year ago

Hmm. Try adding an extra white line below L52.

jwagemann 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:

jwagemann commented 1 year ago

@labarba An extra white line the trick. ;-)

labarba commented 1 year ago

@whedon accept deposit=true

whedon commented 1 year ago

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

whedon commented 1 year ago

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/jose-papers/pull/114
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/jose.00172
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

labarba commented 1 year ago

Congratulations, @jwagemann, your JOSE paper is published! 🚀

Big thanks to our Editor: @ashleefv, and the Reviewers: @djlampert, @BYL4746 — we depend on your kind contributions to provide this service to the community 🙏

whedon commented 1 year ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://jose.theoj.org/papers/10.21105/jose.00172/status.svg)](https://doi.org/10.21105/jose.00172)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/jose.00172">
  <img src="https://jose.theoj.org/papers/10.21105/jose.00172/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://jose.theoj.org/papers/10.21105/jose.00172/status.svg
   :target: https://doi.org/10.21105/jose.00172

This is how it will look in your documentation:

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