Update workflows to use uv

.github/workflows/ci.yaml

@@ -36,10 +36,17 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          python-version: ${{ matrix.python-version }}
+          enable-cache: true
+          cache-suffix: ${{ runner.os }}-${{ matrix.python-version }}
+          activate-environment: true
+
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install -e .[dev,spatiotemporal]
+          uv pip install -e .[dev,spatiotemporal]
 
       - name: Test with pytest
         run: |

.github/workflows/docs.yaml

@@ -24,13 +24,16 @@ jobs:
             - uses: actions/setup-python@v5
               with:
                 python-version: 3.12
+            - name: Install uv
+              uses: astral-sh/setup-uv@v7
+              with:
+                python-version: 3.12
+                enable-cache: true
+                cache-suffix: docs
+                activate-environment: true
             - uses: nikeee/setup-pandoc@v1
-            - name: "Upgrade pip"
-              run: pip install --upgrade pip
-            - name: "Install jupyterbook"
-              run: pip install -r docs/requirements.txt
-            - name: "Install autoemulate"
-              run: pip install -e .
+            - name: "Install autoemulate with extras: dev, docs"
+              run: uv pip install -e .[dev,docs]
             - name: "Run jupyterbook"
               run: jupyter-book build docs --all 
             - name: "Deploy"

.github/workflows/precommit.yaml

@@ -30,13 +30,16 @@ jobs:
           - uses: actions/setup-python@v5
             with:
               python-version: "3.12"
+          - name: Install uv
+            uses: astral-sh/setup-uv@v7
+            with:
+              python-version: "3.12"
+              enable-cache: true
+              cache-suffix: precommit
+              activate-environment: true
           - name: Install dependencies
             run: |
-              python -m venv .venv
-              source .venv/bin/activate
-              python -m pip install --upgrade pip
-              pip install -e .[dev,spatiotemporal]
+              uv pip install -e .[dev,spatiotemporal]
 
-          - uses: pre-commit/[email protected]
-            with:
-              extra_args: --hook-stage manual --all-files
+          - name: Run pre-commit
+            run: uv run pre-commit run --hook-stage manual --all-files

.github/workflows/release.yaml

@@ -10,17 +10,24 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.10'
 
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          python-version: '3.10'
+          enable-cache: true
+          cache-suffix: release
+          activate-environment: true
+
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install build twine
+          uv pip install build twine
 
       - name: Build package
         run: python -m build

pyproject.toml

@@ -61,7 +61,7 @@ dev = [
     "sphinx-autodoc-typehints>=1.24.0",
     "black>=23.10.1",
     "pre-commit>=3.5.0",
-    "jupyter-book>=1.0.0",
+    "jupyter-book>=1.0.0,<2.0.0",
     "pytest-cov>=4.1.0",
     "coverage>=7.6.4",
     "plotnine>=0.13.6",