fix(tooling): uvenv lock runner and deps

.github/PULL_REQUEST_TEMPLATE.md

@@ -9,7 +9,7 @@
 
 - [ ] Ran `tox` checks to avoid unnecessary CI fails:
     ```console
-    uvx tox -e all-checks,pytest
+    uvx tox
     ```
 - [ ] Considered adding appropriate tests for the changes.
 - [ ] Considered updating the online docs in the [./docs/](/leanEthereum/leanSpec/tree/main/docs/) directory.

.github/workflows/ci.yml

@@ -73,7 +73,7 @@ jobs:
           python-version: "3.14"
 
       - name: Sync dependencies
-        run: uv sync --all-packages --no-progress
+        run: uv sync --no-progress
 
       - name: Fill test fixtures
         run: uv run fill --fork=Devnet --clean

CLAUDE.md

@@ -17,7 +17,7 @@ subspecifications that the Lean Ethereum protocol relies on.
 
 ### Running Tests
 ```bash
-uv sync --all-packages            # Install dependencies
+uv sync                           # Install dependencies
 uv run pytest                     # Run unit tests
 uv run fill --fork=devnet --clean # Generate test vectors
 # Note: execution layer support is planned for future, infrastructure is ready

CONTRIBUTING.md

@@ -3,7 +3,7 @@
 ## Quick Start
 
 1. Fork and clone the repository
-2. Install dependencies: `uv sync --all-packages`
+2. Install dependencies: `uv sync`
 3. Make your changes
 4. Run checks: `uvx tox -e all-checks`
 5. Run tests: `uvx tox -e pytest`

README.md

@@ -175,19 +175,18 @@ def test_withdrawal_amount_above_uint64_max():
 
 ## Common Commands Reference
 
-| Task                                          | Command                                       |
-|-----------------------------------------------|-----------------------------------------------|
-| Install and sync project and dev dependencies | `uv sync --all-packages`                      |
-| Run tests                                     | `uv run pytest ...`                           |
-| Format code                                   | `uv run ruff format src tests packages`       |
-| Lint code                                     | `uv run ruff check src tests packages`        |
-| Fix lint errors                               | `uv run ruff check --fix src tests packages`  |
-| Type check                                    | `uv run mypy src tests packages`              |
-| Build docs                                    | `uv run mkdocs build`                         |
-| Serve docs                                    | `uv run mkdocs serve`                         |
-| Run everything (checks + tests + docs)        | `uvx tox`                                     |
-| Run all quality checks (no tests/docs)        | `uvx tox -e all-checks`                       |
-
+| Task                                          | Command                                      |
+|-----------------------------------------------|----------------------------------------------|
+| Install and sync project and dev dependencies | `uv sync`                                    |
+| Run tests                                     | `uv run pytest ...`                          |
+| Format code                                   | `uv run ruff format src tests packages`      |
+| Lint code                                     | `uv run ruff check src tests packages`       |
+| Fix lint errors                               | `uv run ruff check --fix src tests packages` |
+| Type check                                    | `uv run mypy src tests packages`             |
+| Build docs                                    | `uv run mkdocs build`                        |
+| Serve docs                                    | `uv run mkdocs serve`                        |
+| Run everything (checks + tests + docs)        | `uvx tox`                                    |
+| Run all quality checks (no tests/docs)        | `uvx tox -e all-checks`                      |
 
 ## Contributing
 

packages/testing/README.md

@@ -10,11 +10,11 @@ This package provides tools for generating consensus test fixtures, including:
 ## Installation
 
 This package is part of the lean-spec workspace and is automatically installed when you 
-sync the parent project with `--all-packages`.
+sync the parent project.
 
 ```bash
 # from `leanSpec/` (root of workspace)
-uv sync --all-packages
+uv sync
 ```
 
 ## Usage

packages/testing/pyproject.toml

@@ -28,10 +28,6 @@ dependencies = [
 
 license = {text = "MIT"}
 
-[project.optional-dependencies]
-test = ["pytest-cov>=6.0.0,<7"]
-lint = ["ruff>=0.11.8,<1", "mypy>=1.15.0,<1.16"]
-
 [project.urls]
 Homepage = "https://github.com/leanEthereum/lean-spec"
 Source = "https://github.com/leanEthereum/lean-spec"

packages/testing/src/framework/cli/fill.py

@@ -62,13 +62,22 @@ def fill(
         # Default layer is consensus
         fill tests/spec_tests/devnet --fork=Devnet --clean -v
     """
-    # Look for pytest-fill.ini in current directory (project root)
-    config_path = Path.cwd() / "pytest-fill.ini"
+    config_path = Path(__file__).parent / "pytest_ini_files" / "pytest-fill.ini"
+    # Find project root by looking for pyproject.toml with [tool.uv.workspace]
+    project_root = Path.cwd()
+    while project_root != project_root.parent:
+        if (project_root / "pyproject.toml").exists():
+            # Check if this is the workspace root
+            pyproject = project_root / "pyproject.toml"
+            if "[tool.uv.workspace]" in pyproject.read_text():
+                break
+        project_root = project_root.parent
 
     # Build pytest arguments
     args = [
         "-c",
         str(config_path),
+        f"--rootdir={project_root}",
         f"--output={output}",
         f"--fork={fork}",
         f"--layer={layer}",

pyproject.toml

@@ -117,31 +117,31 @@ members = ["packages/*"]
 lean-ethereum-testing = { workspace = true }
 
 [dependency-groups]
-dev = [
-    # debugging / convenience
-    "ipython>=8.31.0,<9",
-    "ipdb>=0.13",
-    "tomli-w>=1.0.0",
-    # packaging
-    "build>=1.2.0,<2",
-    "twine>=5.1.0,<6",
-    # test dependencies
+test = [
     "pytest>=8.3.3,<9",
     "pytest-cov>=6.0.0,<7",
     "pytest-xdist>=3.6.1,<4",
     "hypothesis>=6.138.14",
-    # docs
+    "lean-ethereum-testing",
+]
+lint = [
+    "mypy>=1.17.0,<2",
+    "ruff>=0.13.2,<1",
+    "codespell>=2.4.1,<3",
+]
+docs = [
     "mkdocs>=1.6.1,<2",
     "mkdocs-material>=9.5.45,<10",
     "mkdocstrings[python]>=0.27.0,<1",
-    "pyspelling>=2.8.2,<3",
-    "mdformat-gfm-alerts==2.0.0",
-    "mdformat-gfm==0.4.1",
-    "mdformat-ruff==0.1.3",
-    "mdformat-toc==0.3.0",
     "mdformat==0.7.22",
-    # dev
-    "ruff>=0.11.8,<1",
-    "mypy>=1.15.0,<1.16",
-    "codespell>=2.4.1,<3",
+]
+dev = [
+    {include-group = "test"},
+    {include-group = "lint"},
+    {include-group = "docs"},
+    "ipython>=8.31.0,<9",
+    "ipdb>=0.13",
+    "tomli-w>=1.0.0",
+    "build>=1.2.0,<2",
+    "twine>=5.1.0,<6",
 ]

tests/lean_spec/subspecs/ssz/test_hash.py

@@ -620,8 +620,8 @@ class Var(Container):
 
 
 # Set the ELEMENT_TYPE now that the classes are defined
-FixedVector4.ELEMENT_TYPE = Fixed  # type: ignore[has-type]
-VarVector2.ELEMENT_TYPE = Var  # type: ignore[has-type]
+FixedVector4.ELEMENT_TYPE = Fixed  # type: ignore[assignment]
+VarVector2.ELEMENT_TYPE = Var  # type: ignore[assignment]
 
 
 class Complex(Container):

tox.ini

@@ -4,17 +4,15 @@ requires =
     tox >=4.32.0,<5
     tox-uv >=1.29
 env_list =
+    # defines what runs when `uvx tox` is executed with no `-e` argument
     all-checks
     pytest
-    docs
-skip_missing_interpreters = true
-runner = uv-venv-lock-runner
+    docs-build
 
 [testenv]
-basepython = python3.14
 uv_python = >=3.12
-dependency_groups = dev
 package = editable
+runner = uv-venv-lock-runner
 
 [testenv:all-checks]
 description = Run all quality checks (lint, typecheck, spellcheck, mdformat)
@@ -57,10 +55,10 @@ commands = pytest {posargs} tests -n auto --maxprocesses=10 --durations=10 --dis
 description = Run tests with coverage (pytest)
 commands = pytest --cov --cov-report=html --cov-report=term {posargs}
 
-[testenv:docs]
-description = Serve documentation locally (mkdocs)
-commands = mkdocs serve {posargs}
-
 [testenv:docs-build]
 description = Build documentation (mkdocs)
 commands = mkdocs build {posargs}
+
+[testenv:docs-serve]
+description = Serve documentation locally (mkdocs)
+commands = mkdocs serve {posargs}