Rework library page (#114)

* Rework library page

* Update 404

* Add NormalizingFlows

Author: penelopeysm

404.qmd

@@ -4,4 +4,6 @@ title: Page Not Found
 
 The page you requested cannot be found (perhaps it was moved or renamed).
 
-You may want to visit [Get-Started Guide]({{< meta get-started >}}) or [Tutorials]({{< meta tutorials-intro >}}).
+You may want to return to the [home page](https://turinglang.org/).
+
+If you believe this is an error, please do report it by [opening an issue](https://github.com/TuringLang/turinglang.github.io/issues/new).

_quarto.yml

@@ -21,9 +21,9 @@ website:
     foreground: "#ffffff"
     left:
       - text: Get Started
-        href: https://turinglang.org/docs/tutorials/docs-00-getting-started/
+        href: https://turinglang.org/docs/getting-started/
       - text: Tutorials
-        href: https://turinglang.org/docs/tutorials/00-introduction/
+        href: https://turinglang.org/docs/tutorials/
       - text: Libraries
         href: library/
       - text: News
@@ -36,7 +36,7 @@ website:
         href: https://x.com/TuringLang
       - icon: github
         text: Turing GitHub
-        href: https://github.com/TuringLang/Turing.jl
+        href: https://github.com/TuringLang
 
   page-footer:
     background: "#073c44"
@@ -83,5 +83,5 @@ format:
 # Global Variables to use in any qmd files using:
 # {{< meta site-url >}}
 site-url: https://turinglang.org
-get-started: https://turinglang.org/docs/tutorials/docs-00-getting-started/
-tutorials-intro: https://turinglang.org/docs/tutorials/00-introduction/
+get-started: https://turinglang.org/docs/getting-started/
+tutorials-intro: https://turinglang.org/docs/tutorials/

assets/scripts/TuringNavbar.html

@@ -247,10 +247,10 @@
     <a style="color: white !important; font-size: 21.25px !important; margin-left: 10px;" href="https://turinglang.org/">Turing.jl</a>
     <ul class="ext-nav-links">
         <li>
-            <a class="ext-nav-link" href="https://turinglang.org/docs/tutorials/docs-00-getting-started/">Get Started</a>
+            <a class="ext-nav-link" href="https://turinglang.org/docs/getting-started/">Get Started</a>
         </li>
         <li>
-            <a class="ext-nav-link" href="https://turinglang.org/docs/tutorials/00-introduction/">Tutorials</a>
+            <a class="ext-nav-link" href="https://turinglang.org/docs/tutorials/">Tutorials</a>
         </li>
         <li>
             <p class="ext-nav-link" id="library-handler">Libraries</p>
@@ -304,7 +304,7 @@
                     </a>
                 </ul>
                 <ul>
-                    <li class="ext-dropdown-item-heading">Gaussion Processes</li>
+                    <li class="ext-dropdown-item-heading">Gaussian Processes</li>
                     <a href="https://juliagaussianprocesses.github.io/AbstractGPs.jl/">
                         <li>AbstractGPs</li>
                     </a>

library/index.qmd

@@ -1,61 +1,114 @@
 ---
 title: "Turing Libraries"
-page-layout: full
+search: false
+toc: false
 include-in-header:
     - text: |
         <style>a {text-decoration: none;}a:hover {text-decoration: underline;}</style>
+listing:
+  - id: libraries-main
+    template: table.ejs
+    contents: main.yml
+    field-required: [name, api, github, description, category]
+    include:
+      category: main
+  - id: libraries-modelling
+    template: table.ejs
+    contents: main.yml
+    field-required: [name, api, github, description, category]
+    include:
+      category: modelling
+  - id: libraries-mcmc
+    template: table.ejs
+    contents: main.yml
+    field-required: [name, api, github, description, category]
+    include:
+      category: mcmc
+  - id: libraries-vi
+    template: table.ejs
+    contents: main.yml
+    field-required: [name, api, github, description, category]
+    include:
+      category: vi
+  - id: libraries-utilities
+    template: table.ejs
+    contents: main.yml
+    field-required: [name, api, github, description, category]
+    include:
+      category: utilities
+  - id: libraries-diagnostics
+    template: table.ejs
+    contents: main.yml
+    field-required: [name, api, github, description, category]
+    include:
+      category: diagnostics
+  - id: libraries-distributions
+    template: table.ejs
+    contents: main.yml
+    field-required: [name, api, github, description, category]
+    include:
+      category: distributions
+  - id: libraries-infrastructure
+    template: table.ejs
+    contents: main.yml
+    field-required: [name, api, github, description, category]
+    include:
+      category: infrastructure
+  - id: libraries-gps
+    template: table.ejs
+    contents: main.yml
+    field-required: [name, api, github, description, category]
+    include:
+      category: gps
 ---
 
-This page lists all the packages that are part of the [The Turing Organization](https://github.com/TuringLang).
+This page lists all the packages that are part of the [The Turing Organisation](https://github.com/TuringLang), and provides links to their respective API documentation pages and GitHub repositories.
 
-## Modelling Languages
-
-- [DynamicPPL.jl](https://turinglang.org/DynamicPPL.jl/): A domain-specific language and backend for probabilistic programming languages used by Turing.jl.
+If you are looking for tutorials and usage guides, please visit [this page](https://turinglang.org/docs/).
 
-- [JuliaBUGS.jl](https://turinglang.org/JuliaBUGS.jl/): JuliaBUGS is a graph-based probabilistic programming language and a component of the Turing ecosystem.
+## Turing.jl itself
 
-- [TuringGLM.jl](https://turinglang.org/TuringGLM.jl/): A Julia package for Bayesian generalised linear models used for returning an instantiated Turing model using the formula syntax
+::: {#libraries-main}
+:::
 
-## Markov chain Monte Carlo (MCMC)
+## Modelling Languages
 
-- [AdvancedHMC.jl](https://turinglang.org/AdvancedHMC.jl/): It provides a robust, modular, and efficient implementation of advanced Hamiltonian Monte Carlo (HMC) algorithms.
+::: {#libraries-modelling}
+:::
 
-- [AbstractMCMC.jl](https://turinglang.org/AbstractMCMC.jl/): Abstract types and interfaces for Markov chain Monte Carlo methods. This defines an interface for sampling and combining Markov chains.
+## Markov Chain Monte Carlo (MCMC)
 
-- [ThermodynamicIntegration.jl](https://github.com/theogf/ThermodynamicIntegration.jl): A simple package to compute Thermodynamic Integration for computing the evidence in a Bayesian setting.
+::: {#libraries-mcmc}
+:::
 
-- [AdvancedPS.jl](https://turinglang.org/AdvancedPS.jl/): This is a lightweight package that implements particle-based Monte Carlo algorithms for the [Turing](https://turinglang.org/) ecosystem.
+## Variational Inference
 
-- [SliceSampling.jl](https://turinglang.org/SliceSampling.jl): This package is a collection of slice sampling algorithms including the univariate slice samplers by [Neal (2003)](https://arxiv.org/abs/physics/0009028).
+::: {#libraries-vi}
+:::
 
-- [EllipticalSliceSampling.jl](https://turinglang.org/EllipticalSliceSampling.jl/): This package implements elliptical slice sampling in the Julia language, as described in [Murray, Adams & MacKay (2010)](http://proceedings.mlr.press/v9/murray10a/murray10a.pdf).
+## Utilities
 
-- [NestedSamplers.jl](https://turinglang.org/NestedSamplers.jl/): A Julian implementation of single- and multi-ellipsoidal nested sampling algorithms using the [AbstractMCMC](https://github.com/turinglang/abstractmcmc.jl) interface.
+::: {#libraries-utilities}
+:::
 
 ## Diagnostics
 
-- [MCMCChains.jl](https://turinglang.org/MCMCChains.jl/): Implementation of Julia types for summarising MCMC simulations and utility functions for [diagnostics](https://turinglang.org/MCMCChains.jl/stable/diagnostics/#Diagnostics) and [visualisations](https://turinglang.org/MCMCChains.jl/stable/statsplots/#StatsPlots.jl).
-
-- [MCMCDiagnosticTools.jl](https://turinglang.org/MCMCDiagnosticTools.jl/): This package provides functionality for diagnosing samples generated using Markov Chain Monte Carlo.
+::: {#libraries-diagnostics}
+:::
 
-- [ParetoSmooth.jl](https://turinglang.org/ParetoSmooth.jl/): An implementation of Pareto smoothed importance sampling(PSIS) algorithms in Julia.
+## Distributions
 
-## Bijectors.jl
+::: {#libraries-distributions}
+:::
 
-- [Bijectors.jl](https://turinglang.org/Bijectors.jl/): A package for transforming distributions, used by [Turing.jl](https://github.com/TuringLang/Turing.jl).
+## Infrastructure
 
-## TuringCallbacks.jl
-
-- [TuringCallbacks.jl](https://turinglang.org/TuringCallbacks.jl/): A package containing some convenient callbacks to use when you sample in [`Turing.jl`](https://app.codecov.io/gh/TuringLang/Turing.jl).
-
-## TuringBenchmarking.jl
-
-- [TuringBenchmarking.jl](https://turinglang.org/TuringBenchmarking.jl/): A package for benchmarking and checking [`Turing.jl`](https://github.com/TuringLang/Turing.jl) models.
+::: {#libraries-infrastructure}
+:::
 
 ## Gaussian Processes
 
-- [AbstractGPs.jl](https://juliagaussianprocesses.github.io/AbstractGPs.jl): AbstractGPs.jl is a package that defines a low-level API for working with Gaussian processes (GPs), and basic functionality for working with them in the simplest cases.
-
-- [KernelFunctions.jl](https://juliagaussianprocesses.github.io/KernelFunctions.jl): Julia package for kernel functions for machine learning.
+The following packages come under the umbrella of the [JuliaGaussianProcesses organisation](https://github.com/JuliaGaussianProcesses).
 
-- [ApproximateGPs.jl](https://juliagaussianprocesses.github.io/ApproximateGPs.jl): This is a package that provides some approximate inference algorithms for Gaussian process models, built on top of [AbstractGPs.jl](https://github.com/JuliaGaussianProcesses/AbstractGPs.jl).
+::: {#libraries-gps}
+:::

library/main.yml

@@ -0,0 +1,153 @@
+- name: Turing
+  api: https://turinglang.org/Turing.jl/
+  github: https://github.com/TuringLang/Turing.jl
+  description: "The main entry point to the Turing ecosystem"
+  category: main
+
+- name: DynamicPPL
+  api: https://turinglang.org/DynamicPPL.jl/
+  github: https://github.com/TuringLang/DynamicPPL.jl
+  description: "Domain-specific language and backend for probabilistic programming; contains the core functionality of Turing.jl"
+  category: modelling
+- name: JuliaBUGS
+  api: https://turinglang.org/JuliaBUGS.jl/
+  github: https://github.com/TuringLang/JuliaBUGS.jl
+  description: "A graph-based probabilistic programming language"
+  category: modelling
+- name: TuringGLM
+  api: https://turinglang.org/TuringGLM.jl/
+  github: https://github.com/TuringLang/TuringGLM.jl
+  description: "Bayesian generalised linear models used for returning an instantiated Turing model using the formula syntax"
+  category: modelling
+- name: AbstractPPL
+  api: https://turinglang.org/AbstractPPL.jl/
+  github: https://github.com/TuringLang/AbstractPPL.jl
+  description: "An abstract interface for probabilistic programming languages"
+  category: modelling
+
+- name: AbstractMCMC
+  api: https://turinglang.org/AbstractMCMC.jl/
+  github: https://github.com/TuringLang/AbstractMCMC.jl
+  description: "Abstract types and interfaces for Markov chain Monte Carlo methods, featuring progress bars, parallel sampling, and user-defined callbacks"
+  category: mcmc
+- name: AdvancedHMC
+  api: https://turinglang.org/AdvancedHMC.jl/
+  github: https://github.com/TuringLang/AdvancedHMC.jl
+  description: "A robust, modular, and efficient implementation of advanced Hamiltonian Monte Carlo algorithms"
+  category: mcmc
+- name: AdvancedMH
+  api: https://turinglang.org/AdvancedMH.jl/
+  github: https://github.com/TuringLang/AdvancedMH.jl
+  description: "Random walk and adaptive Metropolis–Hastings algorithms"
+  category: mcmc
+- name: AdvancedPS
+  api: https://turinglang.org/AdvancedPS.jl/
+  github: https://github.com/TuringLang/AdvancedPS.jl
+  description: "Lightweight implementation of particle-based Monte Carlo algorithms"
+  category: mcmc
+- name: SliceSampling
+  api: https://turinglang.org/SliceSampling.jl/
+  github: https://github.com/TuringLang/SliceSampling.jl
+  description: "Univariate and multivariate slice sampling algorithms"
+  category: mcmc
+- name: EllipticalSliceSampling
+  api: https://turinglang.org/EllipticalSliceSampling.jl/
+  github: https://github.com/TuringLang/EllipticalSliceSampling.jl
+  description: "Elliptical slice sampling for inference in models with multivariate Gaussian priors"
+  category: mcmc
+- name: NestedSamplers
+  api: https://turinglang.org/NestedSamplers.jl/
+  github: https://github.com/TuringLang/NestedSamplers.jl
+  description: "Single- and multi-ellipsoidal nested sampling algorithms"
+  category: mcmc
+- name: ThermodynamicIntegration
+  api: https://theogf.github.io/ThermodynamicIntegration.jl/
+  github: https://github.com/theogf/ThermodynamicIntegration.jl
+  description: "Computing Bayesian evidence using thermodynamic integration"
+  category: mcmc
+
+- name: AdvancedVI
+  api: https://turinglang.org/AdvancedVI.jl/
+  github: https://github.com/TuringLang/AdvancedVI.jl
+  description: "Variational inference algorithms for Bayesian models"
+  category: vi
+- name: NormalizingFlows
+  api: https://turinglang.org/NormalizingFlows.jl/
+  github: https://github.com/TuringLang/NormalizingFlows.jl
+  description: "Variational inference and normalizing flows for Bayesian computation"
+  category: vi
+
+- name: TuringCallbacks
+  api: https://turinglang.org/TuringCallbacks.jl/
+  github: https://github.com/TuringLang/TuringCallbacks.jl
+  description: "Convenient callbacks for sampling in Turing.jl"
+  category: utilities
+- name: TuringBenchmarking
+  api: https://turinglang.org/TuringBenchmarking.jl/
+  github: https://github.com/TuringLang/TuringBenchmarking.jl
+  description: "Tools to benchmark and check Turing models"
+  category: utilities
+
+- name: MCMCChains
+  api: https://turinglang.org/MCMCChains.jl/
+  github: https://github.com/TuringLang/MCMCChains.jl
+  description: "Implementation of the Chains type returned by Turing sampling, with functions for diagnostics and visualisations"
+  category: diagnostics
+- name: MCMCDiagnosticTools
+  api: https://turinglang.org/MCMCDiagnosticTools.jl/
+  github: https://github.com/TuringLang/MCMCDiagnosticTools.jl
+  description: "Extra functionality for diagnosing samples generated with MCMC methods"
+  category: diagnostics
+- name: ParetoSmooth
+  api: https://turinglang.org/ParetoSmooth.jl/
+  github: https://github.com/TuringLang/ParetoSmooth.jl
+  description: "Leave-one-out cross-validation for fitted Bayesian models using Pareto smoothed importance sampling"
+  category: diagnostics
+
+- name: Bijectors
+  api: https://turinglang.org/Bijectors.jl/
+  github: https://github.com/TuringLang/Bijectors.jl
+  description: "Transformations for distributions"
+  category: distributions
+- name: DistributionsAD
+  api: https://turinglang.org/DistributionsAD.jl/
+  github: https://github.com/TuringLang/DistributionsAD.jl
+  description: "Automatic differentiation for calculating the log probability densities of distributions"
+  category: distributions
+
+- name: turinglang.github.io
+  api: ""
+  github: https://github.com/TuringLang/turinglang.github.io
+  description: "The code for this website itself"
+  category: infrastructure
+- name: docs
+  api: ""
+  github: https://github.com/TuringLang/docs
+  description: "The tutorials and usage guides; any page whose URL begins with  https://turinglang.org/docs is built here"
+  category: infrastructure
+- name: actions
+  api: ""
+  github: https://github.com/TuringLang/actions
+  description: "Shared GitHub Actions for the TuringLang organisation"
+  category: infrastructure
+
+- name: AbstractGPs
+  api: https://juliagaussianprocesses.github.io/AbstractGPs.jl
+  github: https://github.com/JuliaGaussianProcesses/AbstractGPs.jl
+  description: "Low-level API and basic functionality for working with Gaussian processes"
+  category: gps
+- name: KernelFunctions
+  api: https://juliagaussianprocesses.github.io/KernelFunctions.jl
+  github: https://github.com/JuliaGaussianProcesses/KernelFunctions.jl
+  description: "Kernel functions for machine learning"
+  category: gps
+- name: ApproximateGPs
+  api: https://juliagaussianprocesses.github.io/ApproximateGPs.jl
+  github: https://github.com/JuliaGaussianProcesses/ApproximateGPs.jl
+  description: "Approximate inference algorithms for Gaussian process models"
+  category: gps
+- name: GPLikelihoods
+  api: https://juliagaussianprocesses.github.io/GPLikelihoods.jl
+  github: https://github.com/JuliaGaussianProcesses/GPLikelihoods.jl
+  description: "Likelihoods used as building blocks in non-Gaussian problems"
+  category: gps

library/table.ejs

@@ -0,0 +1,14 @@
+<table width="100%">
+<tbody>
+<% for (const item of items) { %>
+<tr>
+<td style="padding: 5px 5px 5px 0"><span style="font-weight: bold"><%- item.name %></span></td>
+<% if (item.api !== "") { %>
+<td style="padding: 5px 5px"><a href="<%- item.api %>" target="_blank">API</a></td>
+<% } %>
+<td style="padding: 5px 5px"><a href="<%- item.github %>" target="_blank">GitHub</a></td>
+<td style="padding: 5px 0 5px 5px"><%- item.description %></td>
+</tr>
+<% } %>
+</tbody>
+</table>

team/index.qmd

@@ -18,4 +18,4 @@ listing:
 
 ::: {#team-data}
 
-:::
+:::