updates ci caching

arfc · Nov 5, 2024 · cb5905d · cb5905d
1 parent c197f72
commit cb5905d
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -5,6 +5,11 @@ on:
     branches:
       - main
   pull_request:
+    branches:
+      - main
+
+env:
+  CACHE_NUMBER: 0 
 
 jobs:
   build:
@@ -35,24 +40,26 @@ jobs:
           environment-file: environment.yml
           use-mamba: true
           use-only-tar-bz2: true
+          cache-env: true
       - run: |
           conda config --env --set pip_interop_enabled True
 
       # Set up caching to speed up subsequent runs
-      - name: Set up cache
+      - name: Set up LaTeX cache
         uses: actions/cache@v3
+        id: latex-cache
         with:
           path: |
             ~/.texlive
-            ~/.miktex
             /usr/local/texlive
-            ${{ runner.temp }}/latex_cache
           key: ${{ runner.os }}-latex-${{ hashFiles('**/Snakefile') }}
           restore-keys: |
             ${{ runner.os }}-latex-
 
       # Install LaTeX on each OS
       - name: Install LaTeX
+        env: 
+          CACHE_HIT: ${{ steps.latex-cache.outputs.cache-hit }}
         run: |
           if [[ ${{ matrix.os }} == 'ubuntu-latest' ]]; then
             sudo apt-get update
@@ -77,5 +84,5 @@ jobs:
       - name: Upload PDF artifact
         uses: actions/upload-artifact@v3
         with:
-          name: thesis-pdf
-          path: docs/thesis.pdf
+          name: 2025-dotson-thesis
+          path: docs/2025-dotson-thesis.pdf
diff --git a/.gitignore b/.gitignore
@@ -34,3 +34,4 @@ __pycache__/
 data/benchmark/data/*
 docs/_minted-thesis
 pres/_minted-arfc-pres
+_minted-*
diff --git a/README.md b/README.md
@@ -3,40 +3,30 @@
 
 [![Build Dissertation](https://github.com/arfc/2025-dotson-dissertation/actions/workflows/CI.yml/badge.svg)](https://github.com/arfc/2025-dotson-dissertation/actions/workflows/CI.yml)
 
-This repository holds my preliminary exam document. The style guide comes from the University of Illinois Urbana-Champaign Graduate College. A link to the resources may be found [here](https://grad.illinois.edu/thesis/format).
+This repository holds my preliminary exam document. The style guide comes from
+the University of Illinois Urbana-Champaign Graduate College. A link to the
+resources may be found [here](https://grad.illinois.edu/thesis/format).
 
-# Compiling the prelim document
-
-## Windows
-The document style must be compiled using `biber`. Doing this from the command line is more reliable than modifying TeXworks or other editor (I have experienced issues with Windows blocking a biber.exe call from TeXworks). **Make sure your LaTeX installation is up-to-date.**
-
-```bash
-C:\Users\samgd\Research\2025-dotson-dissertation\docs>pdflatex -shell-escape 2025-dotson-thesis.tex
-C:\Users\samgd\Research\2025-dotson-dissertation\docs>biber 2025-dotson-thesis  # This is not a typo. Do not include a file extension.
-C:\Users\samgd\Research\2025-dotson-dissertation\docs>pdflatex -shell-escape 2025-dotson-thesis.tex
-C:\Users\samgd\Research\2025-dotson-dissertation\docs>pdflatex -shell-escape 2025-dotson-thesis.tex
-```
-
-## Linux
-
-```bash
-$ cd 2025-dotson-dissertation/docs
-$ make
-```
-
-## From the template repository
-### uiucthesis class
+# Reproducing the Analysis
 
-A LaTeX package for formatting theses in the format required by the University of Illinois at Urbana-Champaign.
+Many of the plots that were present in the original preliminary document were
+produced using a `juptyer notebook`. The analyses new to this thesis were
+developed using a `snakemake` workflow. This repository includes an
+`environment.yaml` file to facilitate reproducibility of this work.
 
+## Prerequisites
 
-# Reproducing the Analysis
+This workflow assumes users have a working installation of the following
 
-Many of the plots that were present in the original preliminary document were produced using a `juptyer notebook`. The analyses new to this thesis were developed using a `snakemake` workflow. This repository includes an `environment.yaml` file to facilitate reproducibility of this work.
+* `mamba`/`conda` (package dependency and environment management tools)
+* [LaTeX](https://www.latex-project.org/get/)
+* [biber](https://ctan.org/pkg/biber?lang=en) (per the recommendation from the
+  UIUC Graduate College)
 
 ## Setting up the environment
 
-To set up the `mamba` environment, run the following commands in either command prompt or terminal.
+To set up the `mamba` environment, run the following commands in either command
+prompt or terminal.
 
 ```bash
 cd 2025-dotson-dissertation
@@ -50,25 +40,60 @@ The `snakemake` workflow used here is shown by the DAG below.
 
 ![dag](analysis/dag.png)
 
-To run execute the `snakemake` workflow run the following commands in either command prompt or terminal.
+To run execute the `snakemake` workflow run the following commands in either
+command prompt or terminal.
 
 ```bash
 cd analysis
 snakemake --cores=1
 ```
 
+# Compiling the dissertation
+
+If you only want to reproduce the document itself without running any analysis,
+here are the following instructions.
+
+## Windows
+The document style must be compiled using `biber`. Doing this from the command
+line is more reliable than modifying TeXworks or other editor (I have
+experienced issues with Windows blocking a biber.exe call from TeXworks). **Make
+sure your LaTeX installation is up-to-date.**
+
+```bash
+C:\Users\samgd\Research\2025-dotson-dissertation\docs>pdflatex -shell-escape 2025-dotson-thesis.tex
+C:\Users\samgd\Research\2025-dotson-dissertation\docs>biber 2025-dotson-thesis  # This is not a typo. Do not include a file extension.
+C:\Users\samgd\Research\2025-dotson-dissertation\docs>pdflatex -shell-escape 2025-dotson-thesis.tex
+C:\Users\samgd\Research\2025-dotson-dissertation\docs>pdflatex -shell-escape 2025-dotson-thesis.tex
+```
+
+## Unix
+
+```bash
+$ cd 2025-dotson-dissertation/docs
+$ make
+```
+
+## From the template repository
+### uiucthesis class
+
+A LaTeX package for formatting theses in the format required by the University
+of Illinois at Urbana-Champaign.
+
 #### Update Notes
 
 - 3.1a (Samuel G Dotson)
   * Adds prelim macro
 - 3.1 (Zachary J Weiner)
-  * Format table of contents entries with titletoc, prepend "Chapter" and "Appendix"
-  * Place appendices after references, returning to `\mainmatter` so that appendices are still numbered
+  * Format table of contents entries with titletoc, prepend "Chapter" and
+    "Appendix"
+  * Place appendices after references, returning to `\mainmatter` so that
+    appendices are still numbered
   * Add copyright and licensing information
 - 3.0 (Zachary J Weiner)
   * Significant revision, obsolete options removed and source simplified
 - 2.25b (Stephen Mayhew)
   * Removed the Vita Section
   * Added a Makefile
   * Changed all dates from 2009 -> 2014
-  * Be careful when updating the date in the first line of uiucthesis2021.dtx! All numbers must be two digits, including month and day.
+  * Be careful when updating the date in the first line of uiucthesis2021.dtx!
+    All numbers must be two digits, including month and day.