From f79d4938bc8a069a8a9430dc257ac69dc7ebf636 Mon Sep 17 00:00:00 2001 From: belkassaby Date: Wed, 23 Sep 2026 12:21:25 -0400 Subject: [PATCH] chore: drop the unused geneweaver-testing dependency `geneweaver-testing` contributed nothing to this repository but constrained the whole workspace. It ships seven session-scoped pytest fixtures plus prebuilt test suites. Four conftests wildcard-imported the fixtures, but no test requested any of them, and the prebuilt suites were never imported at all -- so it added zero tests. The fixtures are not autouse, so nothing ever executed. Removing the imports leaves every suite byte-identical: core 48057, db 55886, client 6331, tools 76. It was also already broken here. `package_name_from_pyproject` reads `["tool"]["poetry"]["name"]`, and this workspace is PEP 621 + uv_build, so it would KeyError if requested. That is why the tools conftest hardcoded a `package_submodule_name` override -- a workaround for a fixture chain that cannot read this repo's pyproject. What it cost: it pinned `ruff>=0.2.2,<0.3`, which forced the `[tool.uv] override-dependencies` block (nothing else pins ruff); it capped `pytest<9` and `pytest-cov<5` workspace-wide; and it pulled in black, mypy, radon and tomli, none of which our code imports and none of which CI uses -- CI lints with ruff only. Removing it drops 8 packages and 233 lines of lockfile. Replaces the one assertion worth keeping, as `tests/test_namespace_integrity.py`. `geneweaver` is a PEP 420 namespace package shared by five distributions, and a stray `src/geneweaver/__init__.py` in any one of them shadows the rest: verified by adding one to packages/core, which left core importable while api, db, client and tools all raised ModuleNotFoundError. The upstream check covered a single package; this covers all five, globs for new ones, and anchors paths to the file rather than pytest's rootdir -- which shifts because CI runs the root suite from the repo root and each package suite from its own directory. Also deletes two conftests left with no content, and updates the AGENTS.md setup and lint commands, which still said `poetry install` and `black src tests` -- black is no longer installed after this change. --- AGENTS.md | 6 +- packages/client/tests/unit/conftest.py | 1 - packages/core/tests/unit/conftest.py | 1 - packages/db/tests/conftest.py | 6 - packages/tools/tests/unit/conftest.py | 10 -- pyproject.toml | 11 -- tests/test_namespace_integrity.py | 77 ++++++++ uv.lock | 233 ------------------------- 8 files changed, 80 insertions(+), 265 deletions(-) delete mode 100644 packages/db/tests/conftest.py delete mode 100644 packages/tools/tests/unit/conftest.py create mode 100644 tests/test_namespace_integrity.py diff --git a/AGENTS.md b/AGENTS.md index f824e7620..c759a4e86 100644 --- a/AGENTS.md +++ b/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 diff --git a/packages/client/tests/unit/conftest.py b/packages/client/tests/unit/conftest.py index ffcde4f23..ae0d65dde 100644 --- a/packages/client/tests/unit/conftest.py +++ b/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 diff --git a/packages/core/tests/unit/conftest.py b/packages/core/tests/unit/conftest.py index 0488b7932..b9b21c554 100644 --- a/packages/core/tests/unit/conftest.py +++ b/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") diff --git a/packages/db/tests/conftest.py b/packages/db/tests/conftest.py deleted file mode 100644 index 0f5b888a9..000000000 --- a/packages/db/tests/conftest.py +++ /dev/null @@ -1,6 +0,0 @@ -"""Pytest fixtures for unit tests. - -These fixtures are available to be used by all tests in the unit test suite. -""" - -from geneweaver.testing.fixtures import * # noqa: F403 diff --git a/packages/tools/tests/unit/conftest.py b/packages/tools/tests/unit/conftest.py deleted file mode 100644 index d923230ce..000000000 --- a/packages/tools/tests/unit/conftest.py +++ /dev/null @@ -1,10 +0,0 @@ -"""Fixtures available to all tests in the package.""" - -import pytest -from geneweaver.testing.fixtures import * # noqa: F403 - - -@pytest.fixture(scope="session") -def package_submodule_name() -> str: - """Return the name of the package submodule being tested.""" - return "framework" diff --git a/pyproject.toml b/pyproject.toml index 4c2bd6cb5..2988b582b 100644 --- a/pyproject.toml +++ b/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/*", diff --git a/tests/test_namespace_integrity.py b/tests/test_namespace_integrity.py new file mode 100644 index 000000000..f999dd53a --- /dev/null +++ b/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 diff --git a/uv.lock b/uv.lock index 897d1efd6..02abc28ab 100644 --- a/uv.lock +++ b/uv.lock @@ -18,7 +18,6 @@ members = [ "geneweaver-db", "geneweaver-tools", ] -overrides = [{ name = "ruff", specifier = "==0.15.11" }] [[package]] name = "aiohappyeyeballs" @@ -306,40 +305,6 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/88/c6/92fcd42f1ba33e1184263f25bfabf3d27c383410470f169e4b8163bf9c17/beautifulsoup4-4.15.0-py3-none-any.whl", hash = "sha256:d6f88de62e1d4e38ecb1077eb9724cd0eff29d2a08ca16a401e9b9e93f117cf9", size = 109924, upload-time = "2026-06-07T16:44:21.566Z" }, ] -[[package]] -name = "black" -version = "24.10.0" -source = { registry = "https://pypi.org/simple" } -dependencies = [ - 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