Migrate tooling to ruff, ty, and uv (#173)

* Migrate tooling to ruff, ty, and uv

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).

* Clean up tests workflow

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>

* Fix CI failures on modernize-tooling

- 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>

* test_app: set PYTHONPATH so bare python finds ord_interface

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>

* editor: pass as_utf8=True to text_format.MessageToBytes

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>

* Make ord-interface installable; align codecov with ord-schema

- 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>

* Tighten ty annotations; move testing-postgresql to dev group

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>

---------

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: skearnes

.github/workflows/cleanup.yml .github/workflows/checks.yml.github/workflows/cleanup.yml renamed to .github/workflows/checks.yml

@@ -1,4 +1,4 @@
-# Copyright 2020 Open Reaction Database Project Authors
+# Copyright 2026 Open Reaction Database Project Authors
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -12,52 +12,48 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-name: Lint
+name: Checks
 
-on: [ pull_request, push ]
+on:
+  pull_request:
+  push:
+    branches:
+      - main
 
 jobs:
   check_licenses:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-go@v3
+      - uses: actions/checkout@v4
+      - uses: actions/setup-go@v5
         with:
           go-version: '>=1.16'
-      - name: Install dependencies
+      - name: Install addlicense
         run: go install github.com/google/addlicense@latest
       - name: addlicense
         run: addlicense -check -c "Open Reaction Database Project Authors" -l apache .
 
   check_python:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
         with:
-          python-version: '3.10'
-      - name: Install ord-interface
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install wheel
-          python -m pip install .[tests]
-      - name: Run black
-        run: |
-          black --check .
-      - name: Run isort
-        run: |
-          isort --check .
-      - name: Run pylint
-        run: |
-          pylint ord_interface *.py
-      - name: Run pytype
-        run: |
-          pytype -j auto
+          enable-cache: true
+          python-version: "3.12"
+      - name: Install dependencies
+        run: uv sync --frozen
+      - name: ruff check
+        run: uv run ruff check ord_interface
+      - name: ruff format
+        run: uv run ruff format --check ord_interface
+      - name: ty
+        run: uv run ty check ord_interface
 
   check_javascript:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: clang-format
         run: |
           sudo apt update && sudo apt install clang-format --yes

.github/workflows/run_tests.yml .github/workflows/tests.yml.github/workflows/run_tests.yml renamed to .github/workflows/tests.yml

@@ -1,4 +1,4 @@
-# Copyright 2020 Open Reaction Database Project Authors
+# Copyright 2026 Open Reaction Database Project Authors
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -12,21 +12,20 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-name: CI
-
-on: [ pull_request, push ]
-
-env:
-  # See https://dev.to/dtinth/caching-docker-builds-in-github-actions-which-approach-is-the-fastest-a-research-18ei.
-  CACHE_TARGET: "docker.pkg.github.com/open-reaction-database/ord-interface/interface-cache"
+name: Tests
 
+on:
+  pull_request:
+  push:
+    branches:
+      - main
 
 jobs:
   test_ord_interface:
     strategy:
       matrix:
         os: ["ubuntu-latest", "macos-14"]
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
     runs-on: ${{ matrix.os }}
     env:
       PGDATA: $GITHUB_WORKSPACE/rdkit-postgres
@@ -41,51 +40,54 @@ jobs:
           # NOTE(skearnes): conda is only used for postgres (not python).
           conda install -c conda-forge rdkit-postgresql
           initdb
-      - uses: actions/setup-python@v4
+      - uses: astral-sh/setup-uv@v5
         with:
+          enable-cache: true
           python-version: ${{ matrix.python-version }}
       - name: actions-setup-redis
         uses: shogo82148/actions-setup-redis@v1.35.0
       - name: Install ord_interface
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install wheel
-          python -m pip install .[tests]
+        run: uv sync --frozen
       - name: Run tests
         shell: bash -l {0}
         run: |
-          coverage erase
-          pytest -vv --cov=ord_interface --durations=20 --ignore=ord_interface/editor
-          coverage xml
-      - uses: codecov/codecov-action@v1
+          uv run coverage erase
+          uv run pytest -vv --cov=ord_interface --durations=20 --ignore=ord_interface/editor
+          uv run coverage xml
+      # Codecov uses CODECOV_TOKEN when set. Do not fail the job when uploads cannot authenticate:
+      # fork PRs (tokenless), Dependabot PRs (no repo secrets + protected dependabot/* branches).
+      # Pushes to main and normal same-repo PRs stay strict.
+      - uses: codecov/codecov-action@v5
+        with:
+          files: coverage.xml
+          fail_ci_if_error: ${{ github.event_name == 'push' || (github.event_name == 'pull_request' && !github.event.pull_request.head.repo.fork && !startsWith(github.head_ref, 'dependabot/')) }}
+          token: ${{ secrets.CODECOV_TOKEN }}
 
   test_app:
     strategy:
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
     # NOTE(skearnes): Docker is not supported on macOS GitLab runners.
     # NOTE(skearnes): ubuntu-latest AppArmor doesn't play nicely with puppeteer.
     runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
+      - uses: astral-sh/setup-uv@v5
         with:
+          enable-cache: true
           python-version: ${{ matrix.python-version }}
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
       - name: actions-setup-redis
         uses: shogo82148/actions-setup-redis@v1.35.0
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
       - name: Install ord-interface
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install wheel
-          python -m pip install .[tests]
+        run: uv sync --frozen
       - name: Install non-python test dependencies
         run: |
           cd "${GITHUB_WORKSPACE}/ord_interface"
           npm install puppeteer
       - name: Run tests
         run: |
           cd "${GITHUB_WORKSPACE}/ord_interface"
-          ./run_tests.sh
+          uv run ./run_tests.sh

.pre-commit-config.yaml

@@ -0,0 +1,39 @@
+# Copyright 2026 Open Reaction Database Project Authors
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+repos:
+  - repo: https://github.com/google/addlicense
+    rev: v1.2.0
+    hooks:
+      - id: addlicense
+        args:
+          - -c
+          - Open Reaction Database Project Authors
+          - -l
+          - apache
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.10
+    hooks:
+      - id: ruff-check
+        args: [--fix]
+      - id: ruff-format
+
+  - repo: local
+    hooks:
+      - id: ty-check
+        name: ty check (ord_interface)
+        entry: uv run ty check ord_interface
+        language: system
+        pass_filenames: false

format.sh

@@ -61,13 +61,12 @@ RUN wget https://github.com/open-reaction-database/ord-schema/archive/refs/tags/
 
 # Install dependencies.
 WORKDIR /app/ord-interface
-COPY setup.py README.md ./
-RUN pip install --upgrade pip \
-   && pip install gunicorn wheel
-# https://stackoverflow.com/a/60511098.
-RUN python setup.py egg_info \
-   && pip install $(grep -v '^\[' *.egg-info/requires.txt) \
-   && rm -rf *.egg-info/
+RUN pip install --no-cache-dir uv
+ENV UV_PROJECT_ENVIRONMENT=/usr/local \
+    UV_COMPILE_BYTECODE=1 \
+    UV_LINK_MODE=copy
+COPY pyproject.toml uv.lock README.md ./
+RUN uv sync --frozen --no-dev --no-install-project
 
 # Copy the local state.
 COPY ord_interface/editor/js/ ord_interface/editor/js/
@@ -90,7 +89,7 @@ COPY ord_interface/about.html ord_interface/
 COPY ord_interface/interface.py ord_interface/
 COPY ord_interface/api/ ord_interface/api/
 COPY ord_interface/visualization/ ord_interface/visualization/
-RUN pip install .
+RUN uv sync --frozen --no-dev
 
 # Build and launch the interface.
 COPY ord_interface/start_app.sh .

ord_interface/Dockerfile

@@ -15,8 +15,9 @@
 """Pytest fixtures."""
 
 import os
+from collections.abc import AsyncIterator, Iterator
 from contextlib import ExitStack
-from typing import AsyncIterator, Iterator
+from typing import Any
 from unittest.mock import patch
 
 import psycopg
@@ -43,8 +44,8 @@ def test_postgres_fixture() -> Iterator[Postgresql]:
 
 
 @pytest_asyncio.fixture
-async def test_cursor(test_postgres) -> AsyncIterator[AsyncCursor]:
-    async with await psycopg.AsyncConnection.connect(
+async def test_cursor(test_postgres) -> AsyncIterator[AsyncCursor[dict[str, Any]]]:
+    async with await psycopg.AsyncConnection[dict[str, Any]].connect(
         test_postgres.url(), row_factory=dict_row, options="-c search_path=public,ord"
     ) as connection:
         await connection.set_read_only(True)
@@ -54,9 +55,12 @@ async def test_cursor(test_postgres) -> AsyncIterator[AsyncCursor]:
 
 @pytest.fixture(scope="session")
 def test_client(test_postgres) -> Iterator[TestClient]:
-    with TestClient(app) as client, RedisServer() as redis_server, patch.dict(
-        os.environ, {"REDIS_PORT": str(redis_server.dsn()["port"])}
-    ), ExitStack() as stack:
+    with (
+        TestClient(app) as client,
+        RedisServer() as redis_server,
+        patch.dict(os.environ, {"REDIS_PORT": str(redis_server.dsn()["port"])}),
+        ExitStack() as stack,
+    ):
         # NOTE(skearnes): Set ORD_INTERFACE_POSTGRES to use that database instead of a testing.postgresql instance.
         # To force the use of testing.postgresl, set ORD_INTERFACE_TESTING=TRUE.
         if os.environ.get("ORD_INTERFACE_TESTING", "FALSE") == "FALSE" and not os.environ.get("ORD_INTERFACE_POSTGRES"):

ord_interface/api/conftest.py

@@ -19,7 +19,6 @@
 from contextlib import asynccontextmanager
 
 from fastapi import FastAPI
-from testing.postgresql import Postgresql
 
 from ord_interface.api import search, view
 from ord_interface.api.testing import setup_test_postgres
@@ -30,6 +29,9 @@ async def lifespan(*args, **kwargs):
     """FastAPI lifespan setup; see https://fastapi.tiangolo.com/advanced/events/#lifespan."""
     del args, kwargs  # Unused.
     if os.getenv("ORD_INTERFACE_TESTING", "FALSE") == "TRUE":
+        # testing-postgresql is a dev dep; only required when ORD_INTERFACE_TESTING=TRUE.
+        from testing.postgresql import Postgresql
+
         with Postgresql() as postgres:
             url = re.sub("postgresql://", "postgresql+psycopg://", postgres.url())
             setup_test_postgres(url)