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.github/actions/setup-uv-env/action.yml

@@ -0,0 +1,33 @@
+name: "setup-uv-env"
+description: "Composite action to setup the Python and uv environment."
+
+inputs:
+  python-version:
+    required: false
+    description: "The python version to use"
+    default: "3.11"
+
+runs:
+  using: "composite"
+  steps:
+    - name: Set up python
+      uses: actions/setup-python@v6
+      with:
+        python-version: ${{ inputs.python-version }}
+
+    - name: Install UV
+      run: curl -LsSf https://astral.sh/uv/install.sh | sh
+      shell: bash
+
+    - name: Load cached venv
+      id: cached-uv-dependencies
+      uses: actions/cache@v4
+      if: github.run_attempt == 1
+      with:
+        path: .venv
+        key: venv-${{ runner.os }}-${{ inputs.python-version }}-${{ hashFiles('uv.lock') }}
+
+    - name: Install dependencies
+      if: github.run_attempt > 1 || steps.cached-uv-dependencies.outputs.cache-hit != 'true'
+      run: uv sync --all-groups
+      shell: bash

.github/workflows/main.yml

@@ -20,7 +20,7 @@ jobs:
           key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}
 
       - name: Set up the environment
-        uses: ./.github/actions/setup-poetry-env
+        uses: ./.github/actions/setup-uv-env
 
       - name: Run checks
         run: make check
@@ -29,7 +29,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
       fail-fast: false
     defaults:
       run:
@@ -39,18 +39,21 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Set up the environment
-        uses: ./.github/actions/setup-poetry-env
+        uses: ./.github/actions/setup-uv-env
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Install xvfb
         run: sudo apt-get update && sudo apt-get install -y xvfb
 
+      - name: Sync uv project
+        run: uv sync --all-groups
+
       - name: Run tests
-        run: xvfb-run poetry run pytest tests --cov --cov-config=pyproject.toml --cov-report=xml
+        run: xvfb-run uv run pytest tests --cov --cov-config=pyproject.toml --cov-report=xml
 
       - name: Check typing
-        run: poetry run mypy
+        run: uv run mypy
 
       - name: Upload coverage reports to Codecov with GitHub Action on Python 3.11
         uses: codecov/codecov-action@v4
@@ -63,7 +66,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Set up the environment
-        uses: ./.github/actions/setup-poetry-env
+        uses: ./.github/actions/setup-uv-env
 
       - name: Check if documentation can be built
-        run: poetry run mkdocs build -s
+        run: uv run mkdocs build -s

.github/workflows/on-release-main.yml

@@ -13,7 +13,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Set up the environment
-        uses: ./.github/actions/setup-poetry-env
+        uses: ./.github/actions/setup-uv-env
 
       - name: Export tag
         id: vars
@@ -22,7 +22,7 @@ jobs:
       - name: Build and publish
         run: |
           source .venv/bin/activate
-          poetry version $RELEASE_VERSION
+          uv version $RELEASE_VERSION
           make build-and-publish
         env:
           PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
@@ -36,7 +36,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Set up the environment
-        uses: ./.github/actions/setup-poetry-env
+        uses: ./.github/actions/setup-uv-env
 
       - name: Deploy documentation
-        run: poetry run mkdocs gh-deploy --force
+        run: uv run mkdocs gh-deploy --force

Makefile

@@ -1,30 +1,29 @@
 .PHONY: install
-install: ## Install the poetry environment and install the pre-commit hooks
-	@echo "🚀 Creating virtual environment using pyenv and poetry"
-	@poetry install
-	@ poetry run pre-commit install
-	@poetry shell
+install: ## Install the uv environment and install the pre-commit hooks
+	@echo "🚀 Creating virtual environment using uv"
+	@uv sync
+	@uv run pre-commit install
 
 .PHONY: check
 check: ## Run code quality tools.
-	@echo "🚀 Checking Poetry lock file consistency with 'pyproject.toml': Running poetry check --lock"
-	@poetry check --lock
+	@echo "🚀 Checking UV lock file consistency with 'pyproject.toml': Running uv lock --check"
+	@uv lock --check
 	@echo "🚀 Linting code: Running pre-commit"
-	@poetry run pre-commit run -a
+	@uv run pre-commit run -a
 	@echo "🚀 Static type checking: Running mypy"
-	@poetry run mypy
+	@uv run mypy
 	@echo "🚀 Checking for obsolete dependencies: Running deptry"
-	@poetry run deptry --exclude=.venv --exclude=.venv_jupyter --exclude=examples --exclude=tests .
+	@uv run deptry --exclude=.venv --exclude=.venv_jupyter --exclude=examples --exclude=tests .
 
 .PHONY: test
 test: ## Test the code with pytest
 	@echo "🚀 Testing code: Running pytest"
-	@poetry run pytest --cov --cov-config=pyproject.toml --cov-report=xml
+	@uv run pytest --cov --cov-config=pyproject.toml --cov-report=xml
 
 .PHONY: build
-build: clean-build ## Build wheel file using poetry
+build: clean-build ## Build wheel file using uv
 	@echo "🚀 Creating wheel file"
-	@poetry build
+	@uv build
 
 .PHONY: clean-build
 clean-build: ## clean build artifacts
@@ -33,26 +32,25 @@ clean-build: ## clean build artifacts
 .PHONY: publish
 publish: ## publish a release to pypi.
 	@echo "🚀 Publishing: Dry run."
-	@poetry config pypi-token.pypi $(PYPI_TOKEN)
-	@poetry publish --dry-run
+	@uv publish --dry-run --token $(PYPI_TOKEN)
 	@echo "🚀 Publishing."
-	@poetry publish
+	@uv publish --token $(PYPI_TOKEN)
 
 .PHONY: build-and-publish
 build-and-publish: build publish ## Build and publish.
 
 .PHONY: docs-execute-notebooks
 docs-execute-notebooks: ## Execute guide notebooks and save outputs
 	@echo "🚀 Executing guide notebooks"
-	@poetry run jupyter nbconvert --to notebook --execute --inplace $(filter-out docs/guides/notebooks/remote-simulations.ipynb,$(wildcard docs/guides/notebooks/*.ipynb))
+	@uv run jupyter nbconvert --to notebook --execute --inplace $(filter-out docs/guides/notebooks/remote-simulations.ipynb,$(wildcard docs/guides/notebooks/*.ipynb))
 
 .PHONY: docs-test
 docs-test: ## Test if documentation can be built without warnings or errors
-	@poetry run mkdocs build -s
+	@uv run mkdocs build -s
 
 .PHONY: docs
 docs: ## Build and serve the documentation
-	@poetry run mkdocs serve
+	@uv run mkdocs serve
 
 .PHONY: help
 help:

examples/scripts/fielddata_from_image_workflow.py

@@ -19,7 +19,8 @@ def create_sinusoid(
     return sinusoid.astype(dtype=np.float64)
 
 
-with tempfile.TemporaryDirectory() as temp_dir_name, Path(temp_dir_name) as temp_dir:
+with tempfile.TemporaryDirectory() as temp_dir_name:
+    temp_dir = Path(temp_dir_name)
     print(f"temp_dir: {temp_dir}, exists={temp_dir.exists()}")
     # ----- make a workspace
     workspace_dir = temp_dir / "workspace"

examples/scripts/fielddata_from_sim_workflow.py

@@ -5,7 +5,8 @@
 
 import pyvcell.vcml as vc
 
-with tempfile.TemporaryDirectory() as temp_dir_name, Path(temp_dir_name) as temp_dir:
+with tempfile.TemporaryDirectory() as temp_dir_name:
+    temp_dir: Path = Path(temp_dir_name)
     # ----- make a workspace
     workspace_dir = temp_dir / "workspace"
     sim1_dir = workspace_dir / "sim1_dir"