Restructure tests into unit/ and integration/ directories

docs/test-isolation.md

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+# Test Isolation
+
+> Principle: Separate unit tests (fast, no dependencies) from integration/e2e tests.
+
+## Before
+
+All test files flat in `tests/`:
+```
+tests/
+  conftest.py                        # filename-based marker logic
+  test_cli.py
+  test_encoder_registry.py
+  test_kfp_constants.py
+  test_subset_selection_config.py
+  test_subset_selection_processor.py
+  test_notebook_parameters.py        # (in repo)
+  test_notebook_execution.py         # (in repo)
+```
+
+Isolation was marker-based only (`pytest -m unit`), enforced by maintaining a `UNIT_TEST_FILES` set in `conftest.py`. Fragile — adding a test file without updating the set meant it ran in neither category.
+
+## After
+
+Directory-based isolation with auto-applied markers:
+```
+tests/
+  conftest.py                        # shared fixtures (notebook discovery)
+  fixtures/                          # sample data for tests
+  unit/                              # fast tests, no external deps
+    __init__.py
+    conftest.py                      # auto-applies @pytest.mark.unit
+    test_cli.py
+    test_encoder_registry.py
+    test_kfp_constants.py
+    test_subset_selection_config.py
+    test_subset_selection_processor.py
+  integration/                       # slow tests, need GPU/network/Docker
+    __init__.py
+    conftest.py                      # auto-applies @pytest.mark.integration
+    test_notebook_parameters.py      # (existing, in repo)
+    test_notebook_execution.py       # (existing, in repo)
+```
+
+## How It Works
+
+Each subdirectory has a minimal `conftest.py` that auto-applies the marker:
+
+```python
+# tests/unit/conftest.py
+def pytest_collection_modifyitems(config, items):
+    for item in items:
+        item.add_marker(pytest.mark.unit)
+```
+
+**Adding a new test**: just place it in `tests/unit/` or `tests/integration/`. No need to annotate with `@pytest.mark.unit` or update any registry — the directory is the isolation boundary.
+
+## Three Ways to Run
+
+| Method | Unit tests | Integration tests | All tests |
+|---|---|---|---|
+| **Directory** (primary) | `pytest tests/unit/` | `pytest tests/integration/` | `pytest tests/` |
+| **Marker** (alternative) | `pytest -m unit` | `pytest -m integration` | `pytest` |
+| **Makefile** (recommended) | `make unittest` | `make integration-test` | `make test` |
+
+## Changes Made
+
+| File | Change |
+|---|---|
+| `tests/unit/` | **New directory** — moved 5 unit test files here |
+| `tests/unit/__init__.py` | **New** — makes it a package for pytest discovery |
+| `tests/unit/conftest.py` | **New** — auto-applies `@pytest.mark.unit` |
+| `tests/integration/` | **New directory** — integration test files go here |
+| `tests/integration/__init__.py` | **New** — makes it a package |
+| `tests/integration/conftest.py` | **New** — auto-applies `@pytest.mark.integration` |
+| `tests/conftest.py` | **Updated** — removed `UNIT_TEST_FILES`/`INTEGRATION_TEST_FILES` sets and filename-based marker logic; kept shared fixtures |
+| `pyproject.toml` | **Updated** — `testpaths = ["tests/unit", "tests/integration"]` |
+| `Makefile` | **Updated** — targets use directory paths (`tests/unit/`, `tests/integration/`) instead of `-m unit` |
+| `.github/workflows/ci.yml` | **Updated** — runs `pytest tests/unit/` instead of `pytest -m unit` |
+| `CLAUDE.md` | **Updated** — Key Directories, Test Commands, Test Isolation sections |
+
+## Migration Guide for Existing Tests
+
+The existing repo test files (`test_notebook_parameters.py`, `test_notebook_execution.py`) should be moved from `tests/` to `tests/integration/`:
+
+```bash
+mv tests/test_notebook_parameters.py tests/integration/
+mv tests/test_notebook_execution.py tests/integration/
+```
+
+The `from conftest import get_notebook_files` import in these files will continue to work — pytest makes the root `conftest.py` available to all subdirectories automatically.

tests/integration/conftest.py

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+"""Auto-apply 'integration' marker to all tests in this directory."""
+
+import pytest
+
+
+def pytest_collection_modifyitems(config, items):
+    for item in items:
+        item.add_marker(pytest.mark.integration)

tests/unit/conftest.py

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+"""Auto-apply 'unit' marker to all tests in this directory."""
+
+import pytest
+
+
+def pytest_collection_modifyitems(config, items):
+    for item in items:
+        item.add_marker(pytest.mark.unit)