Add lesson dependency instruction

[chartgerink]

This PR adds a suggested change for the guideline instruction, to highlight that you may need to install lesson specific packages manually.

This was discussed in #104 (comment) and I am making a suggested change. Feel free to take this suggestion, make it your own, or decline the PR. 😊

[github-actions]

Thank you!

Thank you for your pull request 😃

🤖 This automated message can help you check the rendered files in your submission for clarity. If you have any questions, please feel free to open an issue in {sandpaper}.

If you have files that automatically render output (e.g. R Markdown), then you should check for the following:

• 🎯 correct output
• 🖼️ correct figures
• ❓ new warnings
• ‼️ new errors

Rendered Changes

🔍 Inspect the changes: https://github.com/epiverse-trace/tutorials/compare/md-outputs..md-outputs-PR-110

The following changes were observed in the rendered markdown documents:

 config.yaml (new) |   82 +++
 renv.lock (new)   | 1984 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 2066 insertions(+)

What does this mean?

If you have source files that require output and figures to be generated (e.g. R Markdown), then it is important to make sure the generated figures and output are reproducible.

This output provides a way for you to inspect the output in a diff-friendly manner so that it's easy to see the changes that occur due to new software versions or randomisation.

⏱️ Updated at 2024-01-24 11:37:55 +0000

[Bisaloo]

It's probably a good addition for now but I want to highlight this is likely the local manifestation of carpentries/sandpaper#533, which we fix by installing a patched version of sandpaper in our GHA workflows:

tutorials/config.yaml

Lines 81 to 82 in 579799d

	# this is carpentries/sandpaper#533 in our fork so we can keep it up to date with main
	sandpaper: epiverse-trace/sandpaper@patch-renv-github-bug

If / once carpentries/sandpaper#533 is merged, we can remove this extra info from the instructions, alongside the custom install setting in config.yaml.

[joshwlambert]

I'm not sure if this is the best possible option (not enough experience with carpentries or {renv} to know), but I would be keen to discuss if there are other options for a more automatic installation of required dependencies (with user permission). I don't think it would be too much to put the burden of facilitating contribution and review on the repo maintainer rather than the contributor/reviewer.

[joshwlambert]

I don't think it would be too much to put the burden of facilitating contribution and review on the repo maintainer rather than the contributor/reviewer.

To be clear I think this should be a general policy for all Epiverse-TRACE repos, but happy to debate.

[avallecam]

It's probably a good addition for now but I want to highlight this is likely the local manifestation of carpentries/sandpaper#533

Oh, I didn't know this was likely a manifestation of that feature!

[avallecam]

I'm not sure if this is the best possible option

Possibly this PR may not directly tackle your current issue in #104 (comment) But, could it include it if we extend the suggestion to not only packages but OS-specific dependencies?

In the meantime, an intermediate solution to facilitate the review of #104 from online .md files instead of locally-rendered HTML files (similar to md-outputs-PR-110 for this PR) could come from solving #111

[avallecam]

thank you, @chartgerink, this is ready to merge 🚀