[REVIEW]: Course Materials for an Introduction to Data-Driven Chemistry

whedon commented 1 year ago

Submitting author: @ppxasjsm (Antonia S J S Mey) Repository: https://github.com/Edinburgh-Chemistry-Teaching/Data-driven-chemistry Version: 1.1.0 Editor: @arm61 Reviewer: @lucydot, @ghutchis Archive: 10.5281/zenodo.7782433

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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

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

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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 @arm61 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 @lucydot

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: 1.1.0
[x] Authorship: Has the submitting author (@ppxasjsm) 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 @ghutchis

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: 1.1.0
[x] Authorship: Has the submitting author (@ppxasjsm) 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:

ppxasjsm commented 1 year ago

@whedon generate pdf

ppxasjsm 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:

arm61 commented 1 year ago

My only comment from proof reading (note some mild dyslexia means that proof reading probably isn't my best skill) is that on line 48 of the paper (https://github.com/Edinburgh-Chemistry-Teaching/Data-driven-chemistry/blob/9e37bde609c11a2df932c63cc3be07e08deb2a44/paper/paper.md?plain=1#L48) you should use the possessive form of "Software Carpentery" (i.e. "Software Carpentry's").

ppxasjsm commented 1 year ago

Ok cool thank you! I am equally useless with these things. I'll ask my co-authors to read through the pdf again to see if they spot anything else.

ppxasjsm 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:

ppxasjsm commented 1 year ago

I think I have now fixed the pandas reference. Can you let me know if you are happy with this? I'll send out the current version for final proof reading comments from my co-authors.

arm61 commented 1 year ago

For the pandas reference I think something like

  author       = {{The pandas development team}},

might remove the weird capital T (cause LaTeX thinks that "The" is someones first name.

ppxasjsm commented 1 year ago

I added a blank first name like this:

author       = {The pandas development team, {}},

arm61 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:

arm61 commented 1 year ago

Might be getting into a bit of a rabbit hole, but that now adds a full stop at the end of the author which shouldn't be there (the full stop in the other references is to indicate the abbreviation of the author's first names). I will have a look into the reference style that JOSE is using.

arm61 commented 1 year ago

According to this issue (https://github.com/openjournals/joss/issues/230, for JOSS but JOSE uses the same bot) the format is author-year (https://www.overleaf.com/learn/latex/Biblatex_bibliography_styles) so there shouldn't be a full stop between the author name and the bracketed year (unless the author first name is abbreviated). Can you try wrapping everything in curlys and see if that fixes it?

arm61 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:

arm61 commented 1 year ago

Looks like that didn't work. I will ask around the editorial team to see if someone has a fix. This should give your co-authors some time to proof read also.

ppxasjsm commented 1 year ago

Aren't there full stops after all the author names? To me it doesn't look different to other references, but happy to hear about an improved solution.

arm61 commented 1 year ago

There are, but those full stops indicate the abbreviation of the name i.e. Andrew -> A., however I have since found out that for “group authors” there is a full stop after (https://apastyle.apa.org/style-grammar-guidelines/references/examples/webpage-website-references). So I guess it is good as is! Sorry for the faff (I am still learning!).

arm61 commented 1 year ago

The next step is minting a DOI with Zenodo but we should wait until your coauthors have proof read before we go to that step.

ppxasjsm commented 1 year ago

Thank you! yes that makes sense. I should hear by Wednesday from everyone and will proceed then.

ppxasjsm 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:

ppxasjsm 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

- 10.26434/chemrxiv.13656665.v1 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1039/C8RP00105G is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1021/bk-2021-1387.ch009 is OK
- 10.21105/jose.00032 is OK
- 10.1021/acs.jchemed.1c00142 is OK
- 10.1021/acs.jchemed.9b01131 is OK
- 10.21105/jose.00148 is OK
- 10.1021/bk-2020-1365.ch001 is OK
- 10.1021/acsinfocus.7e5030 is OK
- 10.5281/zenodo.7344967 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.21105/jose.00139 is OK
- 10.1109/mcse.2006.122 is OK

MISSING DOIs

- None

INVALID DOIs

- None

ppxasjsm 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:

ppxasjsm commented 1 year ago

Hi @arm61, We have finalised the proofs.
I have bumped the version to 1.1.0 for the changes that have been made since the submission. The DOI from Zenodo is: 10.5281/zenodo.7782433

Is there anything else that is needed?

arm61 commented 1 year ago

@whedon set 10.5281/zenodo.7782433 as archive

whedon commented 1 year ago

OK. 10.5281/zenodo.7782433 is the archive.

arm61 commented 1 year ago

@whedon set 1.1.0 as version

whedon commented 1 year ago

OK. 1.1.0 is the version.

arm61 commented 1 year ago

@whedon recommend-accept

whedon commented 1 year ago

Attempting dry run of processing paper acceptance...

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/117

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/jose-papers/pull/117, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

whedon commented 1 year ago

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

OK DOIs

- 10.26434/chemrxiv.13656665.v1 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1039/C8RP00105G is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1021/bk-2021-1387.ch009 is OK
- 10.21105/jose.00032 is OK
- 10.1021/acs.jchemed.1c00142 is OK
- 10.1021/acs.jchemed.9b01131 is OK
- 10.21105/jose.00148 is OK
- 10.1021/bk-2020-1365.ch001 is OK
- 10.1021/acsinfocus.7e5030 is OK
- 10.5281/zenodo.7344967 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.21105/jose.00139 is OK
- 10.1109/mcse.2006.122 is OK

MISSING DOIs

- None

INVALID DOIs

- None

arm61 commented 1 year ago

Amazing @ppxasjsm, now we just wait for the editor-in-chief to make sure everything is okay!

ppxasjsm commented 1 year ago

Fantastic @arm61!

ppxasjsm commented 1 year ago

Dear @labarba I think the paper is ready for your final oversight.

arm61 commented 1 year ago

I messaged @labarba over Slack last week and she is aware that this is waiting but we very busy with grant applications. Hopefully, it will all be confirmed soon 🙂

ppxasjsm commented 1 year ago

No problem at all! I very much understand. I just wanted to check in! Thanks for letting me know.

ppxasjsm commented 1 year ago

Hi, I just wanted to check in on this again. Any rough idea when you may get a chance to look at this?

labarba commented 1 year ago

hi @ppxasjsm 👋 – I appreciate your patience with this. I'm on travel and have a huge backlog to deal with when I get back. Thank you.

labarba commented 1 year ago

Please merge my PR with minor edits to the paper: https://github.com/Edinburgh-Chemistry-Teaching/Data-driven-chemistry/pull/52 …and double check the figure caption, which isn't showing for me in the preview service, but should! (I'm not sure what is going on there.)

I checked everything else, and will publish as soon as you merge and fix the caption as needed.

ppxasjsm commented 1 year ago

Hi @labarba I have merged edits and have figured out the figure caption (it was a missing new line) and things are now displaying ok for me.

ppxasjsm 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:

ppxasjsm commented 1 year ago

I looked at the proof and it seems ok to me, or let me know if there is anything else I can fix.

labarba commented 1 year ago

One last thing! Can you check if adding curly brackets will fix the way "Project Jupyter" is appearing as an author in the nbgrader paper? It shows as "Jupyter, P." and that is not quite what we want...

openjournals / jose-reviews