chore: drop the unused geneweaver-testing dependency

AGENTS.md

@@ -6,12 +6,12 @@
 - Separate frontend app lives in `ui/`
 - Legacy code lives in `legacy/`; avoid changing it unless the task explicitly targets legacy behavior
 ## Setup
-- Install backend dependencies with `poetry install`
-- Run the backend with `poetry run uvicorn geneweaver.api.main:app --reload`
+- Install backend dependencies with `uv sync --all-packages --all-extras --all-groups`
+- Run the backend with `uv run uvicorn geneweaver.api.main:app --reload`
 - Install frontend dependencies with `cd ui && npm install`
 - Run the frontend with `cd ui && npm run dev`
 ## Validation
-- Lint backend changes with `ruff src tests --fix` and `black src tests`
+- Lint backend changes with `ruff check src tests --fix` and `ruff format src tests`
 - Run backend tests with `pytest tests --cov=geneweaver.api --cov-report term --cov-report html`
 - For UI tasks, run the smallest relevant test or build command from `ui/`
 - Prefer the smallest relevant test target first, then broaden only as needed

packages/client/tests/unit/conftest.py

@@ -17,7 +17,6 @@
     SourceType,
     StrainResult,
 )
-from geneweaver.testing.fixtures import *  # noqa: F403
 from numpy.random import Generator
 from pandas import DataFrame
 from requests.exceptions import HTTPError

packages/core/tests/unit/conftest.py

@@ -7,7 +7,6 @@
 
 import pytest
 from geneweaver.core.config_class import CoreSettings
-from geneweaver.testing.fixtures import *  # noqa: F403
 
 
 @pytest.fixture(scope="session")

pyproject.toml

@@ -34,8 +34,6 @@ Repository = "https://github.com/TheJacksonLaboratory/geneweaver"
 dev = [
     "pytest-asyncio>=0.21.0",
     "ruff==0.15.11",
-    # Shared pytest fixtures imported by packages/*/tests (geneweaver.testing.fixtures).
-    "geneweaver-testing>=0.1.2",
 ]
 # Documentation site (mkdocs.yml + docs/). Previously lived in the standalone
 # TheJacksonLaboratory/geneweaver-docs repo, which this replaces.
@@ -46,15 +44,6 @@ docs = [
     "mkdocs-jupyter>=0.24.2",
 ]
 
-[tool.uv]
-# geneweaver-testing pins ruff<0.3 for its own lint command, which is unsatisfiable
-# against this project's ruff==0.15.11. We only use its pytest fixtures, so override the
-# ruff pin. (Its pytest<9 / pytest-cov<5 caps are left to resolve naturally — pytest 9
-# requires Python 3.10+ while this project supports 3.9, so we must not force pytest>=9.)
-override-dependencies = [
-    "ruff==0.15.11",
-]
-
 [tool.uv.workspace]
 members = [
     "packages/*",

tests/test_namespace_integrity.py

@@ -0,0 +1,77 @@
+"""`geneweaver` must stay a PEP 420 namespace package.
+
+Five first-party distributions install into `geneweaver/`: the root `geneweaver-api`,
+plus `geneweaver-core`, `geneweaver-db`, `geneweaver-client` and `geneweaver-tools`
+from `packages/`. They can only coexist because `geneweaver` is a namespace package
+rather than a regular one.
+
+Adding an `__init__.py` to any single distribution's `src/geneweaver/` turns that
+portion into a regular package and shadows the rest: the offending distribution keeps
+importing fine, while the other four silently stop resolving. The symptom then appears
+far from its cause -- usually as an `ImportError` in an unrelated package's tests -- so
+it is worth asserting directly.
+
+This replaces the equivalent check that used to come from the archived
+`geneweaver-testing` package. Paths are derived from this file rather than from
+pytest's `rootdir`, because CI runs the root suite from the repository root and each
+package suite from inside that package's own directory, which moves `rootdir`.
+"""
+
+import importlib
+from pathlib import Path
+
+import pytest
+
+REPO_ROOT = Path(__file__).resolve().parents[1]
+
+#: Every distribution source root that contributes a portion to the namespace. Globbed
+#: rather than hard-coded so a newly added package is covered without editing this file.
+NAMESPACE_SOURCE_ROOTS = [
+    REPO_ROOT / "src",
+    *sorted((REPO_ROOT / "packages").glob("*/src")),
+]
+
+#: The subpackage each distribution provides under the `geneweaver` namespace.
+FIRST_PARTY_SUBPACKAGES = ["api", "core", "db", "client", "tools"]
+
+
+def _relative(path: Path) -> str:
+    """Render a path relative to the repository root, for readable test ids."""
+    return str(path.relative_to(REPO_ROOT))
+
+
+def test_namespace_source_roots_are_found() -> None:
+    """Guard the discovery itself, so the checks below cannot vacuously pass."""
+    assert len(NAMESPACE_SOURCE_ROOTS) >= len(FIRST_PARTY_SUBPACKAGES), (
+        f"Expected at least {len(FIRST_PARTY_SUBPACKAGES)} distribution source roots, "
+        f"found {[_relative(p) for p in NAMESPACE_SOURCE_ROOTS]}"
+    )
+
+
+@pytest.mark.parametrize("source_root", NAMESPACE_SOURCE_ROOTS, ids=_relative)
+def test_geneweaver_portion_is_not_a_regular_package(source_root: Path) -> None:
+    """No distribution may add an `__init__.py` to the shared namespace directory."""
+    init_file = source_root / "geneweaver" / "__init__.py"
+    assert not init_file.exists(), (
+        f"{_relative(init_file)} must not exist. It would make this distribution's "
+        "`geneweaver` portion a regular package and shadow every other distribution "
+        "sharing the namespace, breaking their imports."
+    )
+
+
+def test_geneweaver_is_a_namespace_package() -> None:
+    """The imported `geneweaver` package has no `__file__`, as namespace packages do."""
+    import geneweaver
+
+    assert getattr(geneweaver, "__file__", None) is None, (
+        "`geneweaver` resolved to a regular package "
+        f"({geneweaver.__file__}). Only one distribution's portion is now importable; "
+        "check for a stray `src/geneweaver/__init__.py`."
+    )
+
+
+@pytest.mark.parametrize("subpackage", FIRST_PARTY_SUBPACKAGES)
+def test_first_party_subpackage_is_importable(subpackage: str) -> None:
+    """Each distribution resolves through the shared namespace."""
+    module = importlib.import_module(f"geneweaver.{subpackage}")
+    assert module is not None