Dissertation

PhD dissertation for UC Davis written with bookdown using a modified aggiedown and manubot.

A built PDF can be found by:

• Navigating to Actions
• Select most recent commit
• Scroll down to artifacts.

Local Build

Create the base conda environment:

mamba env create -f environment.yml
conda activate dissertation

Install the aggiedown in the R rule environment:

snakemake -j 1 --use-conda --conda-frontend mamba install_deps

Build:

snakemake -j 1 --use-conda --conda-frontend mamba

The resulting PDF will be in dissertation.pdf. The first run will take much longer than subsequent builds while the conda environment is created and manubot builds its reference cache.