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rnabioco / molb-7950

MOLB 7950: Informatics and Statistics for Molecular Biology
https://rnabioco.github.io/molb-7950/
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molb-7950

quarto build

Course materials for "MOLB 7950: Informatics and Statistics for Molecular Biology".

Installing local packages

Posit Cloud

Create a new template project and manually install packages.

renv

While renv is a nice idea and is helpful for local development, in practice it doesn't seem robust enough on Posit Cloud.

If you wanted to try using renv, clone the direction and then run renv::activate() and renv::restore(), which will install project packages in a project-local library under renv/.

If you add new libraries to your content, run renv::snapshot(), follow instructions to renv::install() if needed, and then be sure to commit the renv.lock file.

You can also trying using pak for installation by setting RENV_CONFIG_PAK_ENABLED = TRUE in the user's .Renviron file (usethis::edit_r_environ()) to use pak installation, which is a lot faster (issue). In practice, pak with renv seems a bit flaky.

Previewing content

Use quarto render or quarto preview locally to inspect content prior to commit / push. A Github Action builds the site automatically unless you include [ci skip] in the commit message.

After a significant update (i.e., uploading a lot of class material), you should quarto render the entire site, and then commit & push the contents of the _freeze directory, which will enable rendering of only changed materials relative to that build.

File structure

Pages should be named based on the syllabus table, e.g., class-01.qmd.

The qmd files you want rendered as slides go in slides/, exercises/, problem-sets/, and problem-set-keys/

Each of these will be linked in the table on the front page.

If you want to suppress quarto rendering of a file, prefix the filename with an underscore like _class-01.qmd.

Syllabus updates

  1. Edit the "Syllabus" sheet on the Google Sheet. Contact Jay if you need access.
  2. Run data-raw/syllabus.R. You may be prompted to authenticate (one time). The writes a new data/syllabus.tsv file.
  3. Re-render the page (quarto render index.qmd) and check formatting.
  4. Commit and push to GitHub.

Acknowledgements

This work borrows fromand modifies: https://github.com/mine-cetinkaya-rundel/quarto-sdss