Create Zensical site

.github/workflows/website.yaml

@@ -0,0 +1,57 @@
+name: "Build and deploy website"
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches: ["main"]
+
+permissions:
+  pages: "write"
+  id-token: "write"
+
+jobs:
+  build-site:
+    runs-on: "ubuntu-latest"
+    steps:
+    - name: "Checkout repository"
+      uses: "actions/checkout@v4"
+
+    - name: "Install uv"
+      uses: "astral-sh/setup-uv@v6"
+      with:
+        enable-cache: true
+
+    - name: "Set up Python"
+      uses: "actions/setup-python@v5"
+
+    - name: "Install the project via uv"
+      run: "uv sync --locked --group docs"
+
+    - name: "Build site"
+      run: "uv run zensical build"
+
+    - name: "Upload site artifact"
+      uses: actions/upload-pages-artifact@v3
+      with:
+        name: "github-pages"
+        path: "site"
+        retention-days: "3"
+
+  deploy-site:
+    if: ${{ github.event_name == 'push' && github.ref_name == 'main' }} # test
+
+    runs-on: "ubuntu-latest"
+    needs: "build-site"
+
+    environment:
+      name: "github-pages"
+      url: "${{ steps.deployment.outputs.page_url }}"
+
+    steps:
+      - name: "Deploy site to GitHub Pages"
+        uses: actions/deploy-pages@v4
+        with:
+          artifact_name: "github-pages"
+          preview: false
+          token: "${{ secrets.GITHUB_TOKEN }}"

.gitignore

@@ -22,5 +22,7 @@ docs/source/generated
 demo/*
 demo/demo-data.tsv
 
+site/**
+
 # poetry lockfile
 poetry.lock

docs/api.md

@@ -0,0 +1,17 @@
+# API reference
+
+
+## Models
+::: pyter.models
+
+## Data
+::: pyter.data
+
+## Distributions
+::: pyter.distributions
+
+## Inference
+::: pyter.infer
+
+## Constraints
+::: pyter.constraints

docs/source/index.md → docs/index.md

@@ -1,8 +1,8 @@
-# About Pyter
+# Pyter
 
 Pyter is an open-source [Python](https://www.python.org/) package for analyzing virological data. It allows for flexible [Bayesian inference](https://xcelab.net/rm/statistical-rethinking/) of virus titers and virus environmental halflives from raw data on cell infection. Both endpoint titration and plaque assays are supported.
 
 
 Pyter is designed to be fairly plug-and-play for the scientist who has a relatively standard problem but is a novice coder, but the API also permits a more experienced user to build their own custom models without reinventing the wheel.
 
-PyTer uses [Numpyro](https://pyro.ai/numpyro/) to specify models and perform inference from them.
+Pyter uses [NumPyro](https://pyro.ai/numpyro/) to specify models and perform inference from them.

pyproject.toml

@@ -24,6 +24,11 @@ requires = ["hatchling"]
 build-backend = "hatchling.build"
 
 [dependency-groups]
+docs = [
+    "mkdocstrings>=1.0.4",
+    "mkdocstrings-python>=2.0.3",
+    "zensical>=0.0.43",
+]
 test = [
     "pytest>=8.4.1",
 ]