update sn template to 12/2023 and support csl or natbib

[cameronraysmith]

This PR

• updates the underlying latex template to 12/2023
  • this update separated sn-mathphys into sn-mathphys-ay and sn-mathphys-num
• clarifies the need to use natbib instead of the default citeproc cite-method if it is essential to respect the natbib bibliography styles from the upstream template
• 30d9b0f adds , after journal to support use of the classoption list now illustrated in 22281b4
• 8bb0150 vendors CSL files from zotero that approximately mirror the bst files provided in the upstream template to be maintained using the Makefile added in 43ae1f4
• ff74ecd sets the csl parameter in the template.qmd yaml header and enables html and docx output to illustrate that this approach allows for consistent citation styling among pdf, html, and docx artifacts
• 16461eb 2427327 b94de9a renames journal to natbibstyle 38b4098 migrates the contents of the journal field to journal.cite-style as discussed in update sn template to 12/2023 and support csl or natbib #2 (comment)
• d18b5ea mark vendored content in gitattributes

[christopherkenny]

Hi @cameronraysmith. Thanks for this, I'll review in the next few days!

[cameronraysmith]

Thanks for the template. Sounds good. Found one more issue with using classoption fixed in 30d9b0f. Line numbering is turned on by default in 22281b4 to illustrate the use of classoption.

[cameronraysmith]

After you review, it would be easier to follow-up with the atomic commit history if you wouldn't mind fastforward-merging from the command line rather than any of the options available from the github web ui. Apologies if this is obvious, but to be clear, for example:

fastforward merge update-122023

If you have the gh cli

gh pr checkout 2

git checkout main
git merge update-122023 --ff-only
git push origin main

or, if not, then something like

git fetch https://github.com/cameronraysmith/nature.git update-122023
git checkout -b update-122023 FETCH_HEAD

git checkout main
git merge update-122023 --ff-only
git push origin main

If this sounds like a crazy request, see https://github.com/orgs/community/discussions/4618 ;).
Incidentally, if interested, there's a nice relatively new tool for this: https://github.com/sequoia-pgp/fast-forward .

Thank you!

[cameronraysmith]

@VladimirAlexiev it'd be great to get your input on this PR regarding what you had planned in your fork or otherwise. Many thanks for your quarto-journals/article-format-template#5 (comment) in quarto-journals/article-format-template#5, which nicely summarized the current state of work on this template.

This PR does not directly address the points for this fork you mentioned in your comment

No examples of ORCID, colored links, colored text.

[VladimirAlexiev]

@cameronraysmith thanks a lot for this!! I haven't done anything with that fork, so there's nothing to carry over.
Regarding ORCID and colored text, maybe you can copy from https://github.com/sebdunnett/quarto-sn ?
Cheers!

[cameronraysmith]

Thank you @VladimirAlexiev!
I suppose simply ensuring consistency with https://github.com/quarto-journals/article-format-template, which I have not done here, will be useful for one additional PR to validate that this template should be relatively straightforward for anyone to use.

[cameronraysmith]

@christopherkenny no rush, but also wanted to point out I can also simply host this in my account if you don't want to accept and review broader contributions to your personal copy. I'll assume this is the case if you don't respond.

[christopherkenny]

Hi @cameronraysmith, thank you for the nudge. I lost track of how much time had passed here. Thank you for doing this, it looks mostly great to me. Can you help me understand a few specifics, detailed in the review?

Additionally, open to discussion on the journal -> natbibstyle point, but I'm not sure that name improves the understanding, absent another reason to rename it.

[cameronraysmith]

Many thanks for the review @christopherkenny. I'll respond within a week or so.

[cameronraysmith]

Thanks again for the review @christopherkenny! I won't ping you again unless I don't hear back for more than two weeks.

Regarding,

Additionally, open to discussion on the journal -> natbibstyle point, but I'm not sure that name improves the understanding, absent another reason to rename it.

let me know what you think after taking another look at sn-jnl.cls and #2 (comment). Just give me a definitive ruling in your next review ;) and I'm happy to update to your liking in what should be a final round.

Otherwise, let me know if there's anything else and please consider my comment about fast-forward merging. Happy to discuss further if the reason for requesting that isn't clear.

[christopherkenny]

Thanks for the updates. One just remaining question in the review. I think there's a good option for updating the name to align with other templates.

[christopherkenny]

Also, be sure to add your name to the _extension.yml file!

[cameronraysmith]

Many thanks for this second review @christopherkenny! Consistency with the upstream templates makes a lot of sense. This one just happens to be the first one I've ever taken a look at. I will update as you suggest within about twothree weeks. Feel free to ping me if it takes longer than that.

[cameronraysmith]

Also, be sure to add your name to the _extension.yml file!

Regarding f1a05ac, it looks like the _extension.yml author field doesn't support a list so I added this as a comma-separated string. Feel free to review if you think something else would be better.

[christopherkenny]

Hi @cameronraysmith. I've reviewed this and I'm happy to merge. Thank you for crafting such a helpful PR! I'll work through your preferred merge.

[christopherkenny]

Looks like that worked, please let me know if you disagree!

[cameronraysmith]

Hi @cameronraysmith. I've reviewed this and I'm happy to merge. Thank you for crafting such a helpful PR! I'll work through your preferred merge.

Perfect. Thank you!