Reorganise user guide section (#578)

* Don't let julia-actions delete cache

* Reorganise user guide

* Allow different workflows/PRs to share cached Julia environment

* Merge _quarto.yml and _metadata.yml

* Reorganise tutorials section

* Fix colon in title

* Fix aliases

* Fix more aliases

* Tidy up navigation bar

Author: penelopeysm

.github/workflows/preview.yml

@@ -10,7 +10,6 @@ concurrency:
   group: docs
 
 permissions:
-  actions: write
   contents: write
   pull-requests: write
 
@@ -31,6 +30,9 @@ jobs:
 
       - name: Load Julia packages from cache
         uses: julia-actions/cache@v2
+        with:
+          cache-name: julia-cache;${{ hashFiles('**/Manifest.toml') }}
+          delete-old-caches: false
 
       # Note: needs resolve() to fix #518
       - name: Instantiate Julia environment

_quarto.yml

@@ -20,9 +20,9 @@ website:
     background: "#073c44"
     foreground: "#ffffff"
     left:
-      - href: tutorials/docs-00-getting-started/
+      - href: getting-started/
         text: Get Started
-      - href: tutorials/00-introduction/
+      - href: tutorials/coin-flipping/
         text: Tutorials
       - href: https://turinglang.org/library/
         text: Libraries
@@ -50,52 +50,40 @@ website:
     - text: documentation
       collapse-level: 1
       contents:
-        - section: "Users"
-          # href: tutorials/index.qmd, This page will be added later so keep this line commented
-          contents:
-          - tutorials/docs-00-getting-started/index.qmd
-          - tutorials/docs-12-using-turing-guide/index.qmd
+        - getting-started/index.qmd
+        - core-functionality/index.qmd
 
-          - section: "Usage Tips"
-            collapse-level: 1
-            contents:
-              - tutorials/docs-10-using-turing-autodiff/index.qmd
-              - tutorials/usage-custom-distribution/index.qmd
-              - tutorials/usage-probability-interface/index.qmd
-              - tutorials/usage-modifying-logprob/index.qmd
-              - tutorials/usage-generated-quantities/index.qmd
-              - tutorials/docs-17-mode-estimation/index.qmd
-              - tutorials/docs-13-using-turing-performance-tips/index.qmd
-              - tutorials/docs-15-using-turing-sampler-viz/index.qmd
-              - tutorials/docs-11-using-turing-dynamichmc/index.qmd
-              - tutorials/docs-16-using-turing-external-samplers/index.qmd
-
-          - section: "Tutorials"
-            contents:
-              - tutorials/00-introduction/index.qmd
-              - text: Gaussian Mixture Models
-                href: tutorials/01-gaussian-mixture-model/index.qmd
-              - tutorials/02-logistic-regression/index.qmd
-              - tutorials/03-bayesian-neural-network/index.qmd
-              - text: Hidden Markov Models
-                href: tutorials/04-hidden-markov-model/index.qmd
-              - tutorials/05-linear-regression/index.qmd
-              - text: Infinite Mixture Model
-                href: tutorials/06-infinite-mixture-model/index.qmd
-              - tutorials/07-poisson-regression/index.qmd
-              - text: Multinomial Logistic Regression
-                href: tutorials/08-multinomial-logistic-regression/index.qmd
-              - text: Variational Inference
-                href: tutorials/09-variational-inference/index.qmd
-              - text: "Bayesian Differential Equations"
-                href: tutorials/10-bayesian-differential-equations/index.qmd
-              - text: "Probabilistic PCA"
-                href: tutorials/11-probabilistic-pca/index.qmd
-              - tutorials/13-seasonal-time-series/index.qmd
-              - text: "Introduction to Gaussian Processes"
-                href: tutorials/15-gaussian-processes/index.qmd
-              - text: "Gaussian Process Latent Variable Models"
-                href: tutorials/12-gplvm/index.qmd
+        - section: "Usage Tips"
+          collapse-level: 1
+          contents:
+            - usage/automatic-differentiation/index.qmd
+            - usage/custom-distribution/index.qmd
+            - usage/probability-interface/index.qmd
+            - usage/modifying-logprob/index.qmd
+            - usage/generated-quantities/index.qmd
+            - usage/mode-estimation/index.qmd
+            - usage/performance-tips/index.qmd
+            - usage/sampler-visualisation/index.qmd
+            - usage/dynamichmc/index.qmd
+            - usage/external-samplers/index.qmd
+
+        - section: "Tutorials"
+          contents:
+            - tutorials/coin-flipping/index.qmd
+            - tutorials/gaussian-mixture-models/index.qmd
+            - tutorials/bayesian-logistic-regression/index.qmd
+            - tutorials/bayesian-neural-networks/index.qmd
+            - tutorials/hidden-markov-models/index.qmd
+            - tutorials/bayesian-linear-regression/index.qmd
+            - tutorials/infinite-mixture-models/index.qmd
+            - tutorials/bayesian-poisson-regression/index.qmd
+            - tutorials/multinomial-logistic-regression/index.qmd
+            - tutorials/variational-inference/index.qmd
+            - tutorials/bayesian-differential-equations/index.qmd
+            - tutorials/probabilistic-pca/index.qmd
+            - tutorials/bayesian-time-series-analysis/index.qmd
+            - tutorials/gaussian-processes-introduction/index.qmd
+            - tutorials/gaussian-process-latent-variable-models/index.qmd
 
         - section: "Developers"
           contents:
@@ -144,13 +132,26 @@ format:
       light: cosmo
       dark: [cosmo, theming/theme-dark.scss]
     css: theming/styles.css
-    toc: true
     smooth-scroll: true
-    code-overflow: wrap
     output-block-background: true
-
+    toc: true
+    toc-title: "Table of Contents"
+    code-fold: false
+    code-overflow: scroll
 execute:
+  echo: true
+  output: true
   freeze: auto
+include-in-header:
+  - text: |
+      <style>
+        a {
+          text-decoration: none;
+        }
+        a:hover {
+          text-decoration: underline;
+        }
+      </style>
 
 # These variables can be used in any qmd files, e.g. for links:
 # the [Getting Started page]({{< meta get-started >}})

tutorials/docs-12-using-turing-guide/index.qmd renamed to core-functionality/index.qmd

@@ -1,6 +1,8 @@
 ---
 title: "Core Functionality"
 engine: julia
+aliases:
+  - ../tutorials/docs-12-using-turing-guide/index.html
 ---
 
 ```{julia}

tutorials/docs-00-getting-started/index.qmd renamed to getting-started/index.qmd

@@ -2,7 +2,8 @@
 title: Getting Started
 engine: julia
 aliases:
-   - ../../
+  - ../tutorials/docs-00-getting-started/index.html
+  - ../index.html
 ---
 
 ```{julia}

tutorials/_metadata.yml

@@ -1,6 +1,8 @@
 ---
-title: Bayesian Estimation of Differential Equations
+title: Bayesian Differential Equations
 engine: julia
+aliases:
+ - ../10-bayesian-differential-equations/index.html
 ---
 
 ```{julia}

tutorials/10-bayesian-differential-equations/index.qmd renamed to tutorials/bayesian-differential-equations/index.qmd

@@ -1,6 +1,8 @@
 ---
-title: Linear Regression
+title: Bayesian Linear Regression
 engine: julia
+aliases:
+ - ../05-linear-regression/index.html
 ---
 
 ```{julia}

tutorials/05-linear-regression/index.qmd renamed to tutorials/bayesian-linear-regression/index.qmd

@@ -1,6 +1,8 @@
 ---
 title: Bayesian Logistic Regression
 engine: julia
+aliases:
+ - ../02-logistic-regression/index.html
 ---
 
 ```{julia}
@@ -271,4 +273,4 @@ end
 
 The above shows that with a threshold of 0.07, we correctly predict a respectable portion of the defaults, and correctly identify most non-defaults. This is fairly sensitive to a choice of threshold, and you may wish to experiment with it.
 
-This tutorial has demonstrated how to use Turing to perform Bayesian logistic regression.
+This tutorial has demonstrated how to use Turing to perform Bayesian logistic regression.

tutorials/02-logistic-regression/index.qmd renamed to tutorials/bayesian-logistic-regression/index.qmd

@@ -1,6 +1,8 @@
 ---
 title: Bayesian Neural Networks
 engine: julia
+aliases:
+ - ../03-bayesian-neural-network/index.html
 ---
 
 ```{julia}

tutorials/03-bayesian-neural-network/index.qmd renamed to tutorials/bayesian-neural-networks/index.qmd

@@ -1,6 +1,8 @@
 ---
 title: Bayesian Poisson Regression
 engine: julia
+aliases:
+ - ../07-poisson-regression/index.html
 ---
 
 ```{julia}