Reorganise tutorials section

penelopeysm · penelopeysm · commit 18437a0d2833 · 2025-01-17T18:06:04.000Z
diff --git a/_quarto.yml b/_quarto.yml
@@ -56,43 +56,34 @@ website:
         - 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
+            - 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/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
+            - 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:
@@ -142,7 +133,6 @@ format:
       dark: [cosmo, theming/theme-dark.scss]
     css: theming/styles.css
     smooth-scroll: true
-    code-overflow: wrap
     output-block-background: true
     toc: true
     toc-title: "Table of Contents"
diff --git a/tutorials/bayesian-differential-equations/index.qmd b/tutorials/bayesian-differential-equations/index.qmd
@@ -1,6 +1,8 @@
 ---
-title: Bayesian Estimation of Differential Equations
+title: Bayesian Differential Equations
 engine: julia
+aliases:
+ - ../10-bayesian-differential-equations/index.html
 ---
 
 ```{julia}
diff --git a/tutorials/bayesian-linear-regression/index.qmd b/tutorials/bayesian-linear-regression/index.qmd
@@ -1,6 +1,8 @@
 ---
-title: Linear Regression
+title: Bayesian Linear Regression
 engine: julia
+aliases:
+ - ../05-linear-regression/index.html
 ---
 
 ```{julia}
diff --git a/tutorials/bayesian-logistic-regression/index.qmd b/tutorials/bayesian-logistic-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.
diff --git a/tutorials/bayesian-neural-networks/index.qmd b/tutorials/bayesian-neural-networks/index.qmd
@@ -1,6 +1,8 @@
 ---
 title: Bayesian Neural Networks
 engine: julia
+aliases:
+ - ../03-bayesian-neural-network/index.html
 ---
 
 ```{julia}
diff --git a/tutorials/bayesian-poisson-regression/index.qmd b/tutorials/bayesian-poisson-regression/index.qmd
@@ -1,6 +1,8 @@
 ---
 title: Bayesian Poisson Regression
 engine: julia
+aliases:
+ - ../07-poisson-regression/index.html
 ---
 
 ```{julia}
diff --git a/tutorials/bayesian-time-series-analysis/index.qmd b/tutorials/bayesian-time-series-analysis/index.qmd
@@ -1,6 +1,8 @@
 ---
 title: Bayesian Time Series Analysis
 engine: julia
+aliases:
+ - ../13-seasonal-time-series/index.html
 ---
 
 ```{julia}
diff --git a/tutorials/coin-flipping/index.qmd b/tutorials/coin-flipping/index.qmd
@@ -2,7 +2,7 @@
 title: "Introduction: Coin Flipping"
 engine: julia
 aliases: 
-  - ../
+  - ../00-introduction/index.html
 ---
 
 ```{julia}
diff --git a/tutorials/docs-08-using-turing/index.qmd b/tutorials/docs-08-using-turing/index.qmd
diff --git a/tutorials/docs-09-using-turing-advanced/index.qmd b/tutorials/docs-09-using-turing-advanced/index.qmd
diff --git a/tutorials/gaussian-mixture-models/index.qmd b/tutorials/gaussian-mixture-models/index.qmd
@@ -1,6 +1,8 @@
 ---
-title: Unsupervised Learning using Bayesian Mixture Models
+title: Gaussian Mixture Models
 engine: julia
+aliases:
+ - ../01-gaussian-mixture-model/index.html
 ---
 
 ```{julia}
@@ -10,7 +12,7 @@ using Pkg;
 Pkg.instantiate();
 ```
 
-The following tutorial illustrates the use of Turing for clustering data using a Bayesian mixture model.
+The following tutorial illustrates the use of Turing for an unsupervised task, namely, clustering data using a Bayesian mixture model.
 The aim of this task is to infer a latent grouping (hidden structure) from unlabelled data.
 
 ## Synthetic Data
diff --git a/tutorials/gaussian-process-latent-variable-models/index.qmd b/tutorials/gaussian-process-latent-variable-models/index.qmd
@@ -1,6 +1,8 @@
 ---
-title: Gaussian Process Latent Variable Model
+title: Gaussian Process Latent Variable Models
 engine: julia
+aliases:
+ - ../12-gplvm/index.html
 ---
 
 ```{julia}
@@ -231,4 +233,4 @@ let
 end
 ```
 
-Now, the split between the two groups is visible again.
+Now, the split between the two groups is visible again.
diff --git a/tutorials/gaussian-processes-introduction/index.qmd b/tutorials/gaussian-processes-introduction/index.qmd
@@ -1,6 +1,8 @@
 ---
-title: Gaussian Processes
+title: Gaussian Processes: Introduction
 engine: julia
+aliases:
+ - ../15-gaussian-processes/index.html
 ---
 
 ```{julia}
diff --git a/tutorials/hidden-markov-models/index.qmd b/tutorials/hidden-markov-models/index.qmd
@@ -1,6 +1,8 @@
 ---
-title: Bayesian Hidden Markov Models
+title: Hidden Markov Models
 engine: julia
+aliases:
+ - ../04-hidden-markov-model/index.qmd
 ---
 
 ```{julia}
diff --git a/tutorials/infinite-mixture-models/index.qmd b/tutorials/infinite-mixture-models/index.qmd
@@ -1,6 +1,8 @@
 ---
-title: Probabilistic Modelling using the Infinite Mixture Model
+title: Infinite Mixture Models
 engine: julia
+aliases:
+ - ../06-infinite-mixture-model/index.html
 ---
 
 ```{julia}
diff --git a/tutorials/multinomial-logistic-regression/index.qmd b/tutorials/multinomial-logistic-regression/index.qmd
@@ -1,6 +1,8 @@
 ---
-title: Bayesian Multinomial Logistic Regression
+title: Multinomial Logistic Regression
 engine: julia
+aliases:
+ - ../08-multinomial-logistic-regression/index.html
 ---
 
 ```{julia}
diff --git a/tutorials/probabilistic-pca/index.qmd b/tutorials/probabilistic-pca/index.qmd
@@ -1,6 +1,8 @@
 ---
-title: Probabilistic Principal Component Analysis (p-PCA)
+title: Probabilistic PCA
 engine: julia
+aliases:
+ - ../11-probabilistic-pca/index.html
 ---
 
 ```{julia}
diff --git a/tutorials/variational-inference/index.qmd b/tutorials/variational-inference/index.qmd
@@ -1,6 +1,8 @@
 ---
-title: Variational inference (VI) in Turing.jl
+title: Variational Inference
 engine: julia
+aliases:
+ - ../tutorials/09-variational-inference/index.qmd
 ---
 
 ```{julia}
diff --git a/usage/automatic-differentiation/index.qmd b/usage/automatic-differentiation/index.qmd
@@ -1,6 +1,8 @@
 ---
 title: Automatic Differentiation
 engine: julia
+aliases:
+  - ../../tutorials/docs-10-using-turing-autodiff/index.html
 ---
 
 ```{julia}
diff --git a/usage/custom-distribution/index.qmd b/usage/custom-distribution/index.qmd
@@ -1,6 +1,9 @@
 ---
 title: Custom Distributions
 engine: julia
+aliases:
+  - ../../tutorials/usage-custom-distribution/index.html
+  - ../../tutorials/docs-09-using-turing-advanced/index.html
 ---
 
 ```{julia}
diff --git a/usage/dynamichmc/index.qmd b/usage/dynamichmc/index.qmd
@@ -1,6 +1,8 @@
 ---
 title: Using DynamicHMC
 engine: julia
+aliases:
+ - ../../tutorials/docs-11-using-turing-dynamichmc/index.html
 ---
 
 ```{julia}
@@ -33,4 +35,4 @@ end
 # Pull 2,000 samples using DynamicNUTS.
 dynamic_nuts = externalsampler(DynamicHMC.NUTS())
 chn = sample(gdemo(1.5, 2.0), dynamic_nuts, 2000, progress=false)
-```
+```
diff --git a/usage/external-samplers/index.qmd b/usage/external-samplers/index.qmd
@@ -1,6 +1,8 @@
 ---
 title: Using External Samplers
 engine: julia
+aliases:
+ - ../../tutorials/docs-16-using-turing-external-samplers/index.html
 ---
 
 ```{julia}
diff --git a/usage/generated-quantities/index.qmd b/usage/generated-quantities/index.qmd
@@ -1,6 +1,8 @@
 ---
 title: Generated Quantities
 engine: julia
+aliases:
+  - ../../tutorials/usage-generated-quantities/index.html
 ---
 
 ```{julia}
diff --git a/usage/mode-estimation/index.qmd b/usage/mode-estimation/index.qmd
@@ -1,6 +1,8 @@
 ---
 title: Mode Estimation
 engine: julia
+aliases:
+ - ../../tutorials/docs-17-mode-estimation/index.html
 ---
 
 ```{julia}
diff --git a/usage/modifying-logprob/index.qmd b/usage/modifying-logprob/index.qmd
@@ -1,6 +1,8 @@
 ---
 title: Modifying the Log Probability
 engine: julia
+aliases:
+ - ../../tutorials/usage-modifying-logprob/index.html
 ---
 
 ```{julia}
diff --git a/usage/performance-tips/index.qmd b/usage/performance-tips/index.qmd
@@ -1,6 +1,8 @@
 ---
 title: Performance Tips
 engine: julia
+aliases:
+ - ../../tutorials/docs-13-using-turing-performance-tips/index.html
 ---
 
 ```{julia}
diff --git a/usage/probability-interface/index.qmd b/usage/probability-interface/index.qmd
@@ -1,6 +1,8 @@
 ---
 title: Querying Model Probabilities
 engine: julia
+aliases:
+  - ../../tutorials/usage-probability-interface/index.html
 ---
 
 ```{julia}
diff --git a/usage/sampler-visualisation/index.qmd b/usage/sampler-visualisation/index.qmd
@@ -1,6 +1,8 @@
 ---
 title: Sampler Visualization
 engine: julia
+aliases:
+ - ../../tutorials/docs-15-using-turing-sampler-viz/index.html
 ---
 
 ```{julia}
