Migrate docs to MkDocs Material + GitHub Pages

.github/workflows/deploy.yml

@@ -0,0 +1,41 @@
+name: Deploy docs
+
+on:
+  push:
+    branches:
+      - master
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Build docs
+        run: |
+          pip install zensical
+          zensical build
+
+      - uses: actions/upload-pages-artifact@v3
+        with:
+          path: site/
+
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - id: deployment
+        uses: actions/deploy-pages@v4

.github/workflows/markdown-lint.yml

@@ -0,0 +1,18 @@
+name: Markdown Lint
+
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  lint:
+    name: Markdown Lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Run markdownlint
+        uses: DavidAnson/markdownlint-cli2-action@v19
+        with:
+          globs: "docs/**/*.md"

.github/workflows/spelling.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Spell Check
       uses: crate-ci/typos@master

.gitignore

@@ -1,15 +1,11 @@
-*tags
-tags
-
-*.DS_Store
+site/
 .DS_Store
-
-**.aux
-**.fls
-**.synctex.gz
-**.log
-**.fdb_latexmk
-**.bbl
-**.blg
-**.spl
-**.out
+*.aux
+*.fdb_latexmk
+*.fls
+*.log
+*.synctex.gz
+*.bbl
+*.blg
+*.out
+*.spl

.markdownlint.yaml

@@ -0,0 +1,7 @@
+default: false
+
+# Rules that affect rendering
+MD001: true   # heading increment
+MD032: true   # blank lines around lists
+MD012: true   # no multiple blank lines
+MD009: true   # no trailing spaces

docs/assets/extra.css

@@ -0,0 +1,65 @@
+:root {
+  --md-primary-fg-color: #292929;
+  --md-primary-fg-color--light: #3a3d3f;
+  --md-primary-fg-color--dark: #292929;
+  --md-accent-fg-color: #c0995e;
+  --md-accent-fg-color--transparent: #c0995e1a;
+}
+
+[data-md-color-scheme="slate"] {
+  --md-default-bg-color: #292929;
+  --md-default-bg-color--light: #2e3133;
+  --md-default-bg-color--lighter: #3a3d3f;
+  --md-default-bg-color--lightest: #454849;
+}
+
+.md-header {
+  background-color: #292929;
+  color: #fff;
+}
+
+.md-header a,
+.md-header__topic,
+.md-header__title {
+  color: #fff;
+}
+
+.md-header__topic {
+  font-weight: 700;
+}
+
+a {
+  color: #c0995e;
+}
+
+a:hover {
+  color: #d4b07a;
+}
+
+.md-nav__link--active,
+.md-nav__link:hover {
+  color: #c0995e;
+}
+
+.md-nav--secondary .md-nav__link--active {
+  color: #c0995e;
+  background-color: transparent;
+  border-left: 2px solid #c0995e;
+}
+
+.md-typeset a {
+  color: #c0995e;
+}
+
+.md-typeset a:hover {
+  color: #d4b07a;
+}
+
+.md-header__button.md-logo img {
+  height: 2.5rem;
+  width: auto;
+}
+
+.md-footer {
+  display: none;
+}

docs/assets/mathjax.js

@@ -0,0 +1,12 @@
+window.MathJax = {
+  tex: {
+    inlineMath: [["\\(", "\\)"], ["$", "$"]],
+    displayMath: [["\\[", "\\]"], ["$$", "$$"]],
+    processEscapes: true,
+    processEnvironments: true
+  },
+  options: {
+    ignoreHtmlClass: ".*|",
+    processHtmlClass: "arithmatex"
+  }
+};

group-syllabus/challenges.md → docs/group-syllabus/challenges.md

@@ -1,12 +1,5 @@
-<!-- START doctoc generated TOC please keep comment here to allow auto update -->
-<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
-## Table of Contents
 
-- [Challenges and Mental Health](#challenges-and-mental-health)
-
-<!-- END doctoc generated TOC please keep comment here to allow auto update -->
-
-## Challenges and Mental Health
+# Challenges and Mental Health
 
 The research or Ph.D. experience can be very challenging, sometimes in unexpected ways.
 It is common to experience mental health challenges during graduate school, or working on research and courses as an undergraduate.

group-syllabus/computers.md → docs/group-syllabus/computers.md

@@ -1,33 +1,22 @@
-## Computers
+# Computers
 
-<!-- START doctoc generated TOC please keep comment here to allow auto update -->
-<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
-## Table of Contents
-
-- [Georgia Tech](#georgia-tech)
-- [University Clusters](#university-clusters)
-- [DOE Labs](#doe-labs)
-- [DOD Labs](#dod-labs)
-
-<!-- END doctoc generated TOC please keep comment here to allow auto update -->
-
-### Georgia Tech
+## Georgia Tech
 
 * GT PACE Phoenix
     * User guide [here](https://docs.pace.gatech.edu/phoenix_cluster/gettingstarted_phnx/)
     * Login via `ssh <GTusername>@login-phoenix-rh9.pace.gatech.edu` to get the RHEL9 nodes
-    * Purpose: All-purpose campus resource of CPU and GPU jobs with a variety of hardware. 
+    * Purpose: All-purpose campus resource of CPU and GPU jobs with a variety of hardware.
     * "Rules": Use the `embers` queue type to use idle nodes at zero cost.
     * To get access, let Spencer know, and he will fill out [this form](https://gatech.service-now.com/home?id=sc_cat_item&sys_id=61bc5e351b37f994a8622f4b234bcbf0).
- 
+
 * GT ICE
   * [Resources/User guide](https://gatech.service-now.com/home?id=kb_article_view&sysparm_article=KB0042095) (click `Available Resources`, e.g.)
      * This looks like ~40 V100s, 8 A100s, 4 A40s, 20 RTX6000s, and 4 MI210s.
   * May need to contact Spencer for access.
   * __Most GPU nodes sit idle__
      * On those nodes: `MaxNodes=UNLIMITED MaxTime=18:00:00`
 
-* GT Rogues Gallery 
+* GT Rogues Gallery
     * User guide [here](https://gt-crnch-rg.readthedocs.io/en/main/)
     * Purpose: Use of brand-new, forward-looking, or weird hardware. At the time of writing, it includes an NV H100 server, GH200 nodes, AMD MI210 GPU server, Bluefield-2/3 SmartNICs, RISC-V and Arm CPUs, etc.
     * "Rules": There are few rules; just follow the guidelines in the documentation. There are no limitations on hardware access/node hours.
@@ -39,11 +28,11 @@
     * "Rules":  Be mindful of others' use of this machine as it does not have a scheduler.
     * Get access by emailing [Will Powell](mailto:will.powell@cc.gatech.edu), cc me.
 
-### University Clusters
+## University Clusters
 
 * ACCESS-CI computers
     * These are a set of university supercomputers listed [here](https://access-ci.org/resource-providers/). Each has its own user guide. At the time of writing, we have access to NCSA Delta (A100 GPUs), PSC Bridges2 (V100 GPUs), Purdue Anvil, and Texas A&M ACES (H100 GPUs), but we can change to others as needed. We primarily use NCSA Delta.
-    * Purpose: All-purpose resources for CPU and GPU simulation. 
+    * Purpose: All-purpose resources for CPU and GPU simulation.
     * "Rules": Be mindful of the available node hours. Queue times might be long.
     * Our account number:
        * `PHY240200` (ACCESS-CI Maximize, NCSA Delta only)
@@ -55,7 +44,7 @@
       * The account name is `bdiy-delta-gpu` (ACCESS-CI Maximize) or `bbsc-delta-gpu` (ACCESS-CI Accelerate) for GPU resources
       * Replace `-gpu` with `-cpu` for CPU resources
 
-### DOE Labs
+## DOE Labs
 
 * Oak Ridge National Lab OLCF: Frontier/Wombat/Andes/etc.
     * Purpose
@@ -83,7 +72,7 @@
                 * daas <- open this one
             * Can complete training and do other things here, like look at your WebCARS to get `WC_ID` (which you need to submit jobs)
         * Onto a computer remotely
-            * https://hpc.sandia.gov/access/ssh/
+            * https://hpc.sandia.gov/access/
             * Can do the below with DaaS (using my example username, `[usrname]`)
                 * `ssh [usrname]@srngate.sandia.gov`
                 * Passcode: `[PIN] + [yubikey one time pw]`
@@ -111,22 +100,20 @@
             * Can do the below with ssh (using my example username, `[usrname]`, for a specific LLNL machine, `[llnlmachine]`)
                 * `ssh [usrname]@[llnlmachine].llnl.gov`
                 * Passcode: `[PIN] + [rsa one time password]`
-             
-### DOD Labs
+
+## DOD Labs
 
 * Department of Defense
-    * Anyone working on a DOD project can use [DOD HPCMP](https://www.hpc.mil/) (non-restricted) resources 
+    * Anyone working on a DOD project can use [DOD HPCMP](https://www.hpc.mil/) (non-restricted) resources
     * The process of getting permissions to the non-restricted systems is a bit tedious but usually worth it
     * See [here](https://centers.hpc.mil/) for information on the available supercomputers
         * In particular, it's useful to keep an eye on [upcoming systems](https://centers.hpc.mil/systems/hardware.html#upcoming)
         * Current unclassified systems are [here](https://centers.hpc.mil/systems/unclassified.html)
     * Talk to Spencer about getting access to a DOD machine if you are working on a DOD project
     * Subproject: `ONRDC51242690`, Group: `5124D690`, Project: `5124`
        * Site: `NAVY`
-          * nautilus 
+          * nautilus
           * narwhal
        * Site: `ERDC`
           * carpenter
     * [Docs available here](https://centers.hpc.mil/users/docs/index.html#general)
-
-