Move workshop to GitHub Pages

[fasterius]

Big PR here, with the overall changes required for moving to GitHub Pages using Roy's Specky template for Quarto. In summary:

• The website is now a Quarto-based website hosted at GitHub Pages, built and deployed using GitHub Actions.
• The website is accessed at https://nbisweden.github.io/workshop-reproducible-research/. It has important pages in a header (home, schedule, content, syllabus, pre-course and info), while lectures and pages can be found through links either in the schedule or content pages.
• The tutorials/ and lectures/ directories and unchanged, except that HTML lectures are no longer directly stored in the main Git repository, but are accessed from the website itself.
• The schedule can be changed by editing the schedule.xlsx Excel file in the repo root and will be formatted with cool code made by Roy.
• The website environment has been consolidated with the lecture environments into a single Docker image hosted in GHCR for this repository, and is automatically built using GHA whenever it is changed. It is used when building and deploying the website, but can also be used for local testing.
• The only thing left on Canvas will be the first page, which will be used as a landing page.

Some things still need to be done:

• [X] Go through lectures and check that they are formatted correctly for how they are rendered now.
• [X] Go through the entirety of the material and make sure that there is no odd formatting left from the conversion of the material from Markdown to Quarto. (Done, but needs other eyes as well.)
• [X] Check the other, already existing Actions and see which ones are not needed any more. (See comment below.)
• [ ] Make new images where required (e.g. the front page), Roy is helping out. (Not needed for a merge but before the course starts.)
• [X] Resolve devel conflicts

My proposal for this new system would be that we only keep the main branch and either remove/archive or ignore the dev branch, which was only used for testing changes on Canvas. This is no longer necessary as new changes/contributions can be tested by building the website locally before opening a PR from a feature branch. We can keep tagging course rounds as we have done previously, which can be re-build locally if somebody wants to check out them, although experience leads me to believe that this is unlikely to be the case.

This PR is against the devel branch to get a better diff against the latest changes, but as soon as this PR is approved we should also merge it directly into main.

[fasterius]

Regarding existing GitHub Actions:

• docker-run.yml / docker-build-and-run: This just tests that the Container tutorial image (Dockerfile not Dockerfile_slim) can be built and run. As this is the "final" image of the Container tutorial and not edited by the students it makes sense to keep this, but we might optimise it if we want.
• setup.yml / install: This attempts to install all Conda environments on both MacOS and Ubuntu. Good thing to test, but we should change the default fail-fast matrix option to false, as most jobs are currently being cancelled if a single job fails (which for this type of test we don't want). Some steps use outdated actions, which we should update. We should also filter for the relevant paths, so that the action doesn't run when none of its files have been changed.
• setup-slim.yml / docker-slim-install: This does the same as the above action, but inside the image created with the tutorials/containers/Dockerfile_slim Dockerfile. I'm not sure why we do this. I have tried searching through the tutorials and the pre-course setup and find where this image is mentioned, but it just seems that it's the image the students starts with in the tutorial and add changes to. Did we use this before as well for Windows or something, before we required WSL2 for Windows students? Or am I missing something? Currently it seems we could remove this action. (If there is good reason to keep it the same issues as for the above action applies.)

[johnne]

Did we use this before as well for Windows or something, before we required WSL2 for Windows students?

Yes that's exactly what it was for