Closed whedon closed 1 year ago
Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @lucydot, @ghutchis it looks like you're currently assigned to review this paper :tada:.
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Wordcount for paper.md
is 1764
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Software report (experimental):
github.com/AlDanial/cloc v 1.88 T=0.33 s (160.5 files/s, 82405.4 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
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Jupyter Notebook 26 0 23251 1547
SVG 5 128 2 1445
Markdown 15 81 0 260
TeX 1 14 0 221
YAML 3 12 19 81
Python 3 29 49 80
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SUM: 53 264 23321 3634
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Statistical information for the repository 'f0731c738416b805f4758c4a' was
gathered on 2023/01/17.
The following historical commit information, by author, was found:
Author Commits Insertions Deletions % of changes
DEGIACOMI 1 46 0 0.04
ppxasjsm 6 59543 59431 99.96
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
Matteo Degiacomi 46 100.0 0.0 23.91
ppxasjsm 112 0.2 0.6 26.79
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
MISSING DOIs
- None
INVALID DOIs
- None
Okay @lucydot and @ghutchis thanks for agreeing to review this interesting work! If you work through the checklist and if there is any problems/comments about the material, I would recommend opening an issue on the material repository and the authors can sort them out. More information about the review guidelines can be found on the Open Journals documentation pages: https://openjournals.readthedocs.io/en/jose/reviewer_guidelines.html
If anyone has any questions just ping me on here!
Hello @ppxasjsm -
Great first impressions scanning through the resource.
I'm working through the checklist, will start today and will continue through till next week.
First issue (small points regarding documentation) raised here: https://github.com/Edinburgh-Chemistry-Teaching/Data-driven-chemistry/issues/37
Thanks @lucydot! I will be on holidays next week, so I will be slow at responding. Just an FYI!
@ppxasjsm - thanks for letting me know and no problem, will give me nice chunk of time to do initial look through 👁️
Hi @ppxasjsm a quick heads up that I've raised two other issues on the repo. I'll add to the "Other small suggestions" as I work through the course.
Well this interaction has made my week!
:wave: @lucydot, please update us on how your review is going (this is an automated reminder).
:wave: @ghutchis, please update us on how your review is going (this is an automated reminder).
Sorry - fell to the bottom of the pile. I should be able to finish the review / comments this week.
@ppxasjsm I've updated https://github.com/Edinburgh-Chemistry-Teaching/Data-driven-chemistry/issues/38 with a few other bits.
I really like the problem solving introduction to the course and will use this for my own teaching. The Mentimetre integration is also great.
Note that I found it hard to judge the suitability of some of the questions for a UG chemistry curriculum as I studied physics, and am only familiar with a very particular part of chemistry (translation: I don't understand most of UG chemistry).
Some thoughts for the future (not acceptance blockers for this review):
- hosting this as an online book (using e.g. quarto) might improve readability. There is the option to integrate binder buttons so that it is not at the sake of user interaction.
Yes I've actually started looking into this, but then ran out of time to get an auto build for this for github actions...I can try and get this sorted for the review, but this will depend on when I have time to sort this out.
would you consider including the slides that are referenced?
Yes absolutely! I'll add them.
as a lecturer, one of the things I most struggle with is designing/writing summative assessment. It'd be great to understand a little more about how summative assessment fits in with this course.
Do you want this more generally or in the paper? We have two summative assessments after session 3 and 7 and then a mini workshop at the end that tests everything. I'd be happy to share one example of a summative assessment, but because we tend to reuse some of the material there are some restrictions around this.
I do see a bit of a disjoint between the parts of the course built from Software Carpentry resources (earlier chapters), and those that aren't (later chapters). The former have questions suitable for a more general audience, and explanations are split into smaller chunks (there are more headings). Exactly the same thing occured when I wrote a similar course for physicists, so I'm not really one to criticise. Ultimately, a course with domain-specific examples throughout, and perfectly consistent writing style / lesson structure would be ideal. But I'd say thats a hypothetical end point to aim for rather than a requirement for a complete and effective course, which this appears to be. Clearly a lot of work has already gone into it as it is.
Yes I totally agree with your point. I think the smaller headings kind of make sense early on and may be harder to keep up later on but this can be streamlined. For next year, I've started putting together some extra practice material that is geared towards the topics for the first 3 lessons for at home practice, but this isn't complete yet. I've also found it difficult to find 'truely' domain specific examples for teaching syntax etc...
Hi @ppxasjsm
Yes I've actually started looking into this, but then ran out of time to get an auto build for this for github actions...I can try and get this sorted for the review, but this will depend on when I have time to sort this out.
I don't think it's required for the review, as the course can be followed clear enough as is.
Do you want this more generally or in the paper? We have two summative assessments after session 3 and 7 and then a mini workshop at the end that tests everything. I'd be happy to share one example of a summative assessment, but because we tend to reuse some of the material there are some restrictions around this.
If you are able to share an example that would be great, but again not necessary for the review. Though it'd be great to have a chat with you about assessment sometime! That's outside the scope of this review though.
Hi @lucydot and @ghutchis, just a heads up that if you have any comments on the content of the course I have some capacity to make edits in the next couple of weeks to address any issues you might want to raise! Thanks :)
Hey @lucydot and @ghutchis, just checking in to see how things are going on the reviews. Looks like there is a lot of checkboxes filled, but just a couple still open. If you have particular comments/questions, ask them here or open an issue on the repository.
Hi @ppxasjsm, I'll update the tick boxes following outcome on the discussions at https://github.com/Edinburgh-Chemistry-Teaching/Data-driven-chemistry/issues/39 , https://github.com/Edinburgh-Chemistry-Teaching/Data-driven-chemistry/issues/38 and https://github.com/Edinburgh-Chemistry-Teaching/Data-driven-chemistry/issues/37 .
Thanks for the prompt - I'll come back and finish up my comments today.
I'll update the tick boxes following outcome on the discussions at https://github.com/Edinburgh-Chemistry-Teaching/Data-driven-chemistry/issues/39 , https://github.com/Edinburgh-Chemistry-Teaching/Data-driven-chemistry/issues/38 and https://github.com/Edinburgh-Chemistry-Teaching/Data-driven-chemistry/issues/37 .
Great! Will try and fix these this week.
@whedon generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@whedon generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
I decided to ditch binder. Updated paper to reflect only use of Colab.
@whedon generate pdf
@whedon generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
https://github.com/Edinburgh-Chemistry-Teaching/Data-driven-chemistry/issues/39
Fixed this. Now completely on colab. There is a bit of extra code for pulling data in, but should be useable.
@lucydot I think I have now addressed all comments in the issues you had opened. Please advise if you want me to make any further changes.
@ghutchis Please let me know if you have any other issues you would want to raise on the repository.
Thanks for all your useful comments so far everyone!
@ppxasjsm I've just read through the three issues, and I agree all have been addressed. I'm happy to recommend this work for publication - and I plan to adapt some of this for use in my own teaching :star:
Thank you @lucydot. Glad you think the material may also be useful to you!
That’s one review ticked off ✅. @ghutchis it looks like you are nearly done also?
Hi @ghutchis anything I can help with to finalise this review?
Yeah, sorry - slammed last week finishing a proposal and now getting caught up. I've set aside tomorrow afternoon (Pittsburgh time) to finish this off.
Amazing and thank you! I totally get the being very swamped with too many things problem!
Overall, I think you've fixed a lot of things I noted on my first assessment. I think my remaining issue would be: https://github.com/Edinburgh-Chemistry-Teaching/Data-driven-chemistry/issues/50
@ghutchis with commit 4f8bad5 I have now addressed https://github.com/Edinburgh-Chemistry-Teaching/Data-driven-chemistry/issues/50. I think this means I have addressed all open queries remaining for this review.
Thank you @lucydot and @ghutchis for all your useful comments and suggestions to improve the material. It looks like @ghutchis is happy with the above commit! @arm61 Please let me know how to proceed now and thank you for such a pleasant review process here on Github!
Nice work everyone. I will get started on the editorial stuff just now.
@whedon generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@whedon check references
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
MISSING DOIs
- 10.1109/mcse.2006.122 may be a valid DOI for title: Software Carpentry: Getting Scientists to Write Better Code by Making Them More Productive
INVALID DOIs
- None
@ppxasjsm two things in the references for resolve:
pandas
renders pretty weird at the moment (I think cause of the curlys) can you have a look.
I will get started on reading the paper now for typos and the like.
Thank you @arm61! I am working on the DOI/references stuff.
@whedon check references
@whedon generate pdf
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
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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@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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✨ 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
Code of Conduct
General checks
Documentation
Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)
JOSE paper
paper.md
file include a list of authors with their affiliations?Review checklist for @ghutchis
Conflict of interest
Code of Conduct
General checks
Documentation
Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)
JOSE paper
paper.md
file include a list of authors with their affiliations?