Add nbformat to Optional Dependency Group (#43)

* [gha] fix `no module named 'nbformat'`

* [gha] shinx -> sphinx

* [pyproj] add more jupyter dependencies

* [readme] fix model constructor call

* [pyproj]  must depend on

* [gha] poetry -> sphinx-build

* [gha] actually install sphinx

* [gha] remove  invocation

* [gha] change bad doc path

.github/workflows/sphinx.yaml

@@ -1,79 +1,82 @@
-name: shinx
+name: sphinx
 
 on:
-    push:
-        branches: [main]
-    pull_request:
-        branches: [main]
-    release:
-        types: [published]
-    workflow_dispatch:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  release:
+    types: [published]
+  workflow_dispatch:
 
 # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
 permissions:
-    contents: read
-    pages: write
-    id-token: write
+  contents: read
+  pages: write
+  id-token: write
 
 jobs:
-    build:
-        runs-on: ubuntu-latest
-        permissions:
-            contents: write
-        steps:
-            - uses: actions/checkout@v4
-
-            # Setting up the environment
-            - name: Setup Pages
-              uses: actions/configure-pages@v5
-
-            - name: Set up Quarto
-              uses: quarto-dev/quarto-actions/setup@v2
-              with:
-                  version: 1.4.515
-
-            - name: Set up Python
-              uses: actions/setup-python@v5
-              with:
-                  python-version: "3.12"
-
-            # - name: Install Poetry
-            #   run: pip install poetry
-
-            - name: Install the package
-              run: pip install .
-
-            # Building
-            - name: Render Quarto File
-              run: quarto render README.qmd --to rst && mv README.rst docs/index.rst
-
-            - name: Build HTML using Poetry
-              run: poetry run -C docs sphinx-build -M html docs/source/ docs/build/
-
-            # Upload
-            - name: Upload artifacts
-              uses: actions/upload-pages-artifact@v3
-              with:
-                  name: github-pages
-                  path: docs/build/html/
-
-    deploy:
-        # Deploy to the github-pages environment
-        # but not on PRs
-        if: ${{ github.event_name != 'pull_request' }}
-        environment:
-            name: github-pages
-            url: ${{ steps.deployment.outputs.page_url }}
-
-        needs: build
-
-        # Specify runner + deployment step
-        runs-on: ubuntu-latest
-
-        steps:
-            - name: Deploy to GitHub Pages
-              id: deployment
-              uses: actions/deploy-pages@v4
-              with:
-                  artifact_name: github-pages
-                  preview: true # Not yet available to the public.
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      # Setting up the environment
+      - name: Setup Pages
+        uses: actions/configure-pages@v5
+
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+        with:
+          version: 1.4.515
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      # - name: Install Poetry
+      #   run: pip install poetry
+
+      - name: Install Sphinx
+        run: pip install sphinx
+
+      - name: Install the package
+        run: pip install ".[doc]"
+
+      # Building
+      - name: Render Quarto File
+        run: quarto render README.qmd --to rst && mv README.rst docs/index.rst
+
+      - name: Build HTML using Sphinx
+        run: sphinx-build -M html docs docs/build/
+
+      # Upload
+      - name: Upload artifacts
+        uses: actions/upload-pages-artifact@v3
+        with:
+          name: github-pages
+          path: docs/build/html/
+
+  deploy:
+    # Deploy to the github-pages environment
+    # but not on PRs
+    if: ${{ github.event_name != 'pull_request' }}
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    needs: build
+
+    # Specify runner + deployment step
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4
+        with:
+          artifact_name: github-pages
+          preview: true # Not yet available to the public.

README.qmd

@@ -29,7 +29,7 @@ Here we show how to create a `SEIR` object and add terms to it. We will use the
 import epiworldpy as epiworld
 
 # Create a SEIR model (susceptible, exposed, infectious, recovered), representing COVID-19.
-covid19 = epiworld.ModelSEIR(
+covid19 = epiworld.ModelSEIRCONN(
   name              = 'covid-19',
   n                 = 10000,
   prevalence        = .01,

pyproject.toml

@@ -28,6 +28,7 @@ classifiers = [
 
 [project.optional-dependencies]
 test = ["pytest"]
+doc = ["nbformat", "nbclient", "jupyter", "epiworldpy[viz]"]
 viz = ["ipympl>=0.8", "matplotlib>=3.5.0", "networkx>=3.0", "scipy>=1.0"]
 
 [tool.scikit-build]