Update deps and theme

Author: Ben Jeffery

.github/workflows/build.yml

@@ -13,18 +13,19 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Cancel Previous Runs
-      uses: styfle/cancel-workflow-action@0.11.0
+      uses: styfle/cancel-workflow-action@0.12.0
       with:
         access_token: ${{ github.token }}
 
     - name: Checkout
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     # Install dependencies
-    - name: Set up Python 3.10
+    - name: Set up Python 3.11
       uses: actions/setup-python@v4
       with:
-        python-version: "3.10"
+        python-version: "3.11"
+        cache: "pip"
 
     - name: Install python dependencies
       run: |
@@ -52,7 +53,7 @@ jobs:
     # Push the book's HTML to github-pages
     - name: GitHub Pages action
       if: github.ref == 'refs/heads/main'
-      uses: peaceiris/actions-gh-pages@v3.5.9
+      uses: peaceiris/actions-gh-pages@v3.9.3
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         publish_dir: ./_build/html

_config.yml

@@ -33,8 +33,9 @@ sphinx:
     - sphinx.ext.intersphinx
     - IPython.sphinxext.ipython_console_highlighting
     config:
-      html_theme: tskit_book_theme
-      pygments_style: monokai
+      html_theme: sphinx_book_theme
+      html_theme_options:
+        pygment_dark_style: monokai
       todo_include_todos: true
       intersphinx_mapping:
         py: ["https://docs.python.org/3", null]

requirements-CI.txt

@@ -5,11 +5,10 @@ jupyter-book==0.15.1
 jupyter-cache==0.6.1
 msprime==1.2.0
 networkx==3.1
-pandas==2.0.3
-scikit-allel==1.3.6
+pandas==2.1.1
+scikit-allel==1.3.7
 stdpopsim==0.2.0
-tqdm==4.65.0
+tqdm==4.66.1
 tskit==0.5.5
-tskit-book-theme #Unpinned for easy updating
 tszip==0.2.2
 jsonschema==4.18.6 # Pinned due to 4.19 "AttributeError module jsonschema has no attribute _validators"

requirements.txt

@@ -10,5 +10,4 @@ scikit-allel
 stdpopsim
 tqdm
 tskit>=0.5.4
-tskit-book-theme
 tszip