Fix ci failures, mostly allow-listing pyrefly

Also:
- Add examples deps to root as optional to help check those.
- Upgrade pyrefly to 0.49

Author: posborne

.github/workflows/python-ci.yml

@@ -97,7 +97,7 @@ jobs:
         echo "CC=sccache clang" >> $GITHUB_ENV
         echo "CXX=sccache clang++" >> $GITHUB_ENV
     - name: Install dependencies
-      run: uv sync --extra dev --extra test
+      run: uv sync --extra dev --extra test --extra examples
     - name: Check formatting
       run: make format-check
     - name: Run linting

.gitignore

@@ -12,3 +12,4 @@ bin/
 # Rust
 target/
 *.so
+target/

Makefile

@@ -88,7 +88,7 @@ clean:
 lint: | $(STUBS_DIR)
 	@echo "Linting Python code..."
 	uv run --extra dev ruff check .
-	uv run --extra dev --extra test pyrefly check .
+	uv run --extra dev --extra test pyrefly check
 	@echo "Linting Rust code..."
 	cd crates/fastly-compute-py && cargo clippy -- -D warnings
 

pyproject.toml

@@ -16,7 +16,12 @@ test = [
 dev = [
     "componentize-py (>=0.19.3,<0.20)",
     "ruff (>=0.12.11,<0.13.0)",
-    "pyrefly (>=0.45.1,<0.46.0)",
+    "pyrefly (>=0.49.0,<0.50)",
+]
+# Example dependencies - needed for type-checking examples in CI
+examples = [
+    "flask (>=3.1.2,<4.0)",
+    "bottle (>=0.12.25)",
 ]
 
 [tool.pytest.ini_options]
@@ -88,3 +93,14 @@ py-modules = ["app"]
 [tool.pyrefly]
 python-version = "3.12"
 search-path = ["stubs"]
+use-ignore-files = true
+# Type-check source code, tests, and examples
+project-includes = [
+    "fastly_compute/**/*.py",
+    "tests/**/*.py",
+    "examples/**/*.py",
+]
+project-excludes = [
+    # CLI wrapper imports from native extension that doesn't exist until built
+    "fastly_compute/fastly_compute_py.py",
+]