Migrate tooling to ruff, ty, and uv - #173
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Mirrors the migration done in ord-schema (#780, #783): replaces black /
isort / pylint / pytype with ruff + ty, switches dependency management
to uv, consolidates setup.py into pyproject.toml, and adds pre-commit.
Tooling
- pyproject.toml: full [project] block + [dependency-groups] dev;
[tool.uv] package = false; [tool.ruff] / [tool.ty.src] config matching
ord-schema. Drop [tool.black]/[tool.isort]/[tool.pytype]. Drop setup.py
and format.sh.
- Add .pre-commit-config.yaml (addlicense + ruff-check + ruff-format + ty).
- Generate uv.lock; bump numpy<2 -> numpy>=1.26.4 to enable cp313/cp314.
CI
- New checks.yml replaces cleanup.yml: ruff check + ruff format --check +
ty + addlicense + clang-format.
- run_tests.yml uses astral-sh/setup-uv@v5 + uv sync --frozen; matrix
bumped from 3.10-3.12 to 3.11-3.14 (matches ord-schema).
Source
- Strip 8 # pylint: disable and 1 # pytype: disable comments from
non-editor files.
- Exclude ord_interface/editor/ and ord_interface/interface.py from
ruff/ty (slated for removal in #N).
- Fix all 19 ty diagnostics:
* Type psycopg connection/cursor as dict[str, Any] rows (introduces
DictCursor alias in queries.py).
* Fix QueryResult.__eq__ Liskov violation (other: object + isinstance).
* Annotate kwargs: dict[str, Any] in queries_test.test_similarity_query.
* Generalize _pbtxt to accept any protobuf Message (callers pass both
Reaction and ProductCompound).
* cast(Chem.Mol, ...) around mol_from_compound (return type widens to
a tuple when return_identifier=True).
* Annotate yielding fixture as Iterator[Reaction].
* One # ty: ignore[invalid-await] on redis.asyncio client.ping()
(stub returns Awaitable[bool] | bool).
Dockerfile
- Replace setup.py egg_info + pip install dance with
uv sync --frozen --no-dev; drop the final pip install . (package=false).
Rename run_tests.yml to tests.yml, restrict push trigger to main, and drop the unused CACHE_TARGET env var. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
- Bump protobuf cap from <5 to <6 so resolution picks 5.29.6, which ships cp38-abi3 wheels and runs on Python 3.14. The 4.x series has no 3.14 wheels, so import fails with "Metaclasses with custom tp_new are not supported." Matches ord-schema's constraint. - test_app: invoke run_tests.sh via "uv run" so the venv's python and pytest are on PATH. The script's bare "python client/build_database.py" was hitting the system interpreter, which doesn't have ord_interface. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
The pyproject sets [tool.uv] package = false and has no [build-system], so uv sync only installs dependencies, not the ord_interface package itself. Pytest's rootdir handling masked this in test_ord_interface, but the test_app job runs build_test_database.sh which calls "python client/build_database.py" directly and hits ModuleNotFoundError. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
protobuf 5.x's MessageToBytes encodes the string form as ASCII by default and raises UnicodeEncodeError when the message contains non-ASCII content. as_utf8=True keeps non-ASCII bytes through to the output, matching the prior 4.x behavior in practice. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
skearnes
marked this pull request as ready for review
May 10, 2026 00:52
- Add [build-system] (setuptools+wheel) and [tool.setuptools.packages.find] scoped to ord_interface*; drop [tool.uv] package = false. uv sync now installs ord-interface as an editable wheel into the venv, so "import ord_interface" works from anywhere instead of requiring the repo root on sys.path. - tests.yml: drop the test_app PYTHONPATH workaround that compensated for the project not being installed. - tests.yml: add fail_ci_if_error to codecov-action so fork PRs and dependabot/* branches don't fail the job on tokenless uploads. Mirrors ord-schema's run_tests.yml. - Dockerfile: split uv sync into a deps-only pass before COPYing sources (--no-install-project) and a final sync after to install the project itself, preserving layer caching for deps. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Apply review feedback: - filters.py: cast(Chem.Mol | None, ...) instead of cast(Chem.Mol, ...) to preserve the meaning of the subsequent `if mol:` null-check. - search.py: replace `# ty: ignore[invalid-await]` on `redis.asyncio.Redis.ping()` with `cast(Awaitable[bool], ...)`, scoping the workaround to the actual problem (stub union return type). - pyproject.toml/uv.lock: move `testing-postgresql` from runtime dependencies to the `dev` group; lazy-import `Postgresql` in `api/main.py` inside the `ORD_INTERFACE_TESTING=TRUE` branch since that's the only path that instantiates it. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
bdeadman
approved these changes
May 11, 2026
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skearnes
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May 13, 2026
* Remove stale config and accidental commits - .pylintrc, .style.yapf: legacy linter/formatter configs replaced by ruff in #173. - copilot/: AWS Copilot CLI manifest, replaced by Pulumi/ECS in the ord-infrastructure repository. - dump.rdb: accidentally committed Redis snapshot. - README.md, CONTRIBUTING.md: setup.py / pip install instructions rewritten in terms of uv now that #173 has landed. - .gitignore: add .pytest_cache/, .ruff_cache/, .venv/, dump.rdb so these stop showing up in future working trees. Editor-tree `# pylint:` / `# pytype:` comments are intentionally left alone; the editor is excluded from ruff/ty and is being removed in #172. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * Refresh README - Drop the placeholder "How to Deploy" section. - Fix the project layout: api/ is the FastAPI server (not /client), and the description was missing it entirely. Mark editor/ as legacy (being removed in #172). - Tighten setup instructions and folder descriptions; trim filler. - Flag the host-port 5432 collision for `docker compose up`. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * Apply review feedback on cleanup PR - CONTRIBUTING.md: sweep remaining `ord-schema` references to `ord-interface` (title, issue-tracker URLs, fork instructions). The goals/non-goals readthedocs link is left as-is and rephrased to point at "the broader Open Reaction Database" so it's clear the reference is intentional. - README.md: add a brief Deployment section pointing at the ord-infrastructure repo (Pulumi/ECS) now that the old "How to Deploy" placeholder is gone. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * .gitignore: add trailing slashes to directory-only patterns Make the pre-existing directory patterns consistent with the new ones added in this branch (`.pytest_cache/`, `.ruff_cache/`, `.venv/`) and the already-slashed ones above (`.idea/`, `docs/_build/`, `.vscode/`). Trailing slash restricts a pattern to match directories only, which is what we actually want for `__pycache__`, `*.egg-info`, `.ipynb_checkpoints`, `build`, `dist`, `ketcher`, `standalone`, `node_modules`, and `coverage`. A future file accidentally named one of these wouldn't be silently ignored. `**/.pnp` is left as-is because Yarn 2+ uses `.pnp.cjs` files while Yarn 1 used a `.pnp` directory; the un-slashed form matches both. Verified `git check-ignore` still resolves the existing `.venv/`, `ord_interface.egg-info/`, `ord_interface/__pycache__/` directories through the new rules. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
Mirrors the tooling migration done in ord-schema (#780, #783):
[dependency-groups] dev)setup.pyintopyproject.toml; deletesetup.pyandformat.sh.pre-commit-config.yaml(addlicense + ruff-check + ruff-format + ty)numpy<2→numpy>=1.26.4for cp313/cp314 wheels; widenprotobuf==4.22.3→protobuf>=4.22,<6checks.yml(replacescleanup.yml);tests.ymlusesastral-sh/setup-uv@v5+uv sync --frozenDockerfileto useuv sync --frozen --no-devSource changes
# pylint: disable=...and 1# pytype: disable=...comments from non-editor filesdict[str, Any]rows (DictCursoralias)QueryResult.__eq__Liskov violationkwargs: dict[str, Any]in a test_pbtxtto accept any protobufMessagecast(Chem.Mol | None, ...)aroundmol_from_compound(preserves the subsequentif mol:null-check; return type widens withreturn_identifier=True)Iterator[Reaction]cast(Awaitable[bool], ...)aroundredis.asyncioclient.ping()(stub returnsAwaitable[bool] | bool)Packaging
testing-postgresqlfrom runtimedependenciesto thedevgroup; lazy-importPostgresqlinapi/main.pyinside theORD_INTERFACE_TESTING=TRUEbranch (the only place it's instantiated)Editor scope
The editor (and its entrypoint
ord_interface/interface.py) is slated for removal on a parallel branch. To avoid churning soon-to-be-deleted code and creating merge conflicts, those paths are excluded from ruff/ty here. They still ship and run as before.Test plan
Checksworkflow passes (ruff check + format, ty, addlicense, clang-format-js)Testsworkflow passes on 3.11, 3.12, 3.13, 3.14 (Linux + macOS)test_appworkflow (Docker / Vue) passes on 3.11–3.14uv run pytest ord_interface/visualizationpasses (verified)uv run pytest ord_interface/apipasses against a real postgres+rdkit cartridgedocker build -f ord_interface/Dockerfile -t openreactiondatabase/ord-interface .succeeds🤖 Generated with Claude Code