Update dev tools (#52)

Use ruff instead of pylint and isort.
Also, add pyupgrade.

Configure ruff starting from what is suggested at
https://learn.scientific-python.org/development/guides/style/

Update pre-commit hooks and dependency versions.

Update code base according to new dev tools.

Use `typing.Annotated` for all pydantic and FastAPI stuff.

Use lifespan in FastAPI.

.github/utils/docker_test.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python3
 """Run tests for the service."""
-# pylint: disable=import-error
+from __future__ import annotations
+
 import argparse
 import json
 import os
@@ -10,13 +11,14 @@
 
 import requests
 from dlite import Instance
+from fastapi import status
 from pymongo import MongoClient
 
 if TYPE_CHECKING:
     from typing import Any, Literal
 
 
-DLITE_TEST_ENTITIES: "list[dict[str, Any]]" = [
+DLITE_TEST_ENTITIES: list[dict[str, Any]] = [
     {
         "uri": "http://onto-ns.com/meta/0.1/Person",
         "meta": "http://onto-ns.com/meta/0.3/EntitySchema",
@@ -104,14 +106,15 @@
 
 def add_testdata() -> None:
     """Add MongoDB test data."""
-    mongodb_user = os.getenv("entity_service_mongo_user")
-    mongodb_pass = os.getenv("entity_service_mongo_password")
-    mongodb_uri = os.getenv("entity_service_mongo_uri")
+    mongodb_user = os.getenv("ENTITY_SERVICE_MONGO_USER")
+    mongodb_pass = os.getenv("ENTITY_SERVICE_MONGO_PASSWORD")
+    mongodb_uri = os.getenv("ENTITY_SERVICE_MONGO_URI")
     if any(_ is None for _ in (mongodb_user, mongodb_pass, mongodb_uri)):
-        raise ValueError(
-            "'entity_service_mongo_uri', 'entity_service_mongo_user', and "
-            "'entity_service_mongo_password' environment variables MUST be specified."
+        error_message = (
+            "ENTITY_SERVICE_MONGO_URI, ENTITY_SERVICE_MONGO_USER, and "
+            "ENTITY_SERVICE_MONGO_PASSWORD environment variables MUST be specified."
         )
+        raise ValueError(error_message)
 
     client = MongoClient(mongodb_uri, username=mongodb_user, password=mongodb_pass)
     collection = client.dlite.entities
@@ -124,34 +127,46 @@ def _get_version_name(uri: str) -> tuple[str, str]:
         r"^http://onto-ns\.com/meta/(?P<version>[^/]+)/(?P<name>[^/]+)$", uri
     )
     if match is None:
-        raise RuntimeError("Could not retrieve version and name from test entities.")
+        error_message = (
+            f"Could not retrieve version and name from {uri!r}. "
+            "URI must be of the form: "
+            "http://onto-ns.com/meta/{version}/{name}"
+        )
+        raise RuntimeError(error_message)
     return match.group("version") or "", match.group("name") or ""
 
 
-def _get_uri(entity: "dict[str, Any]") -> str:
+def _get_uri(entity: dict[str, Any]) -> str:
     """Return the uri for an entity."""
     namespace = entity.get("namespace")
     version = entity.get("version")
     name = entity.get("name")
     if any(_ is None for _ in (namespace, version, name)):
-        raise RuntimeError(
+        error_message = (
             "Could not retrieve namespace, version, and/or name from test entities."
         )
+        raise RuntimeError(error_message)
     return f"{namespace}/{version}/{name}"
 
 
 def run_tests() -> None:
     """Test the service."""
     host = os.getenv("DOCKER_TEST_HOST", "localhost")
     port = os.getenv("DOCKER_TEST_PORT", "8000")
+
     for test_entity in DLITE_TEST_ENTITIES:
         uri = test_entity.get("uri")
+
         if uri is None:
             uri = _get_uri(test_entity)
+
         if not isinstance(uri, str):
-            raise TypeError("uri must be a string")
+            error_message = f"uri must be a string. Got {type(uri)}."
+            raise TypeError(error_message)
+
         version, name = _get_version_name(uri)
         response = requests.get(f"http://{host}:{port}/{version}/{name}", timeout=5)
+
         assert response.ok, (
             f"Test data {uri!r} not found! (Or some other error).\n"
             f"Response:\n{json.dumps(response.json(), indent=2)}"
@@ -161,18 +176,23 @@ def run_tests() -> None:
         assert entity == test_entity
         Instance.from_dict(test_entity)
 
+    # Test that the service returns a Not Found (404) for non existant URIs
     version, name = _get_version_name("http://onto-ns.com/meta/0.3/EntitySchema")
     response = requests.get(f"http://{host}:{port}/{version}/{name}", timeout=5)
+
     assert not response.ok, "Non existant (valid) URI returned an OK response!"
     assert (
-        response.status_code == 404
+        response.status_code == status.HTTP_404_NOT_FOUND
     ), f"Response:\n\n{json.dumps(response.json(), indent=2)}"
 
+    # Test that the service raises a pydantic ValidationError and returns an "
+    # "Unprocessable Entity (422) for invalid URIs
     version, name = _get_version_name("http://onto-ns.com/meta/Entity/1.0")
     response = requests.get(f"http://{host}:{port}/{version}/{name}", timeout=5)
+
     assert not response.ok, "Invalid URI returned an OK response!"
     assert (
-        response.status_code != 404
+        response.status_code == status.HTTP_422_UNPROCESSABLE_ENTITY
     ), f"Response:\n\n{json.dumps(response.json(), indent=2)}"
 
 
@@ -189,14 +209,15 @@ def main(args: list[str] | None = None) -> None:
         default="run_tests",
     )
 
-    job: 'Literal["add-testdata","run-tests"]' = parser.parse_args(args).job
+    job: Literal["add-testdata", "run-tests"] = parser.parse_args(args).job
 
     if job == "add-testdata":
         add_testdata()
     elif job == "run-tests":
         run_tests()
     else:
-        raise ValueError(f"{job!r} isn't a valid input.")
+        error_message = f"Invalid job {job!r}."
+        raise ValueError(error_message)
 
 
 if __name__ == "__main__":

.github/workflows/ci_tests.yml

@@ -17,12 +17,10 @@ jobs:
 
       # pre-commit
       python_version_pre-commit: "3.10"
-      skip_pre-commit_hooks: pylint
 
       # pylint & safety
       python_version_pylint_safety: "3.10"
-      pylint_runs: |
-        --rcfile=pyproject.toml --extension-pkg-whitelist='pydantic' dlite_entities_service
+      run_pylint: false
 
       # Build dist
       python_version_package: "3.10"
@@ -51,9 +49,9 @@ jobs:
           MONGO_INITDB_ROOT_PASSWORD: root
 
     env:
-      entity_service_mongo_uri: mongodb://localhost:27017
-      entity_service_mongo_user: root
-      entity_service_mongo_password: root
+      ENTITY_SERVICE_MONGO_URI: mongodb://localhost:27017
+      ENTITY_SERVICE_MONGO_USER: root
+      ENTITY_SERVICE_MONGO_PASSWORD: root
       DOCKER_TEST_PORT: 8000
 
     steps:
@@ -71,9 +69,9 @@ jobs:
       - name: Run Docker container
         run: |
           docker run --rm -d \
-            --env entity_service_mongo_uri \
-            --env entity_service_mongo_user \
-            --env entity_service_mongo_password \
+            --env ENTITY_SERVICE_MONGO_URI \
+            --env ENTITY_SERVICE_MONGO_USER \
+            --env ENTITY_SERVICE_MONGO_PASSWORD \
             --env PORT=${DOCKER_TEST_PORT} \
             --name "entity-service" \
             --network "host" \

.github/workflows/ci_update_dependencies.yml

@@ -24,6 +24,5 @@ jobs:
       update_pre-commit: true
       python_version: "3.10"
       install_extras: "[dev]"
-      skip_pre-commit_hooks: "pylint"
     secrets:
       PAT: ${{ secrets.TEAM40_PAT }}

.pre-commit-config.yaml

@@ -18,21 +18,31 @@ repos:
     - id: trailing-whitespace
       args: [--markdown-linebreak-ext=md]
 
-  # isort is a tool to sort and group import statements in Python files
-  # It works on files in-place
-  - repo: https://github.com/timothycrosley/isort
-    rev: 5.12.0
-    hooks:
-    - id: isort
-      args: ["--profile", "black", "--filter-files", "--skip-gitignore"]
-
   # Black is a code style and formatter
   # It works on files in-place
   - repo: https://github.com/ambv/black
-    rev: 23.10.1
+    rev: 23.11.0
     hooks:
     - id: black
 
+  # Ruff is a code style and formatter
+  # It works on files in-place
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.6
+    hooks:
+    - id: ruff
+      args:
+        - --fix
+        - --show-fixes
+
+  # Pyupgrade is a code upgrade tool
+  # It works on files in-place
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.15.0
+    hooks:
+    - id: pyupgrade
+      args: [--py310-plus]
+
   # Bandit is a security linter
   # More information can be found in its documentation:
   # https://bandit.readthedocs.io/en/latest/
@@ -49,41 +59,10 @@ repos:
   # The project's documentation can be found at:
   # https://mypy.readthedocs.io/en/stable/index.html
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.6.1
+    rev: v1.7.0
     hooks:
     - id: mypy
       exclude: ^docs/example/.*$$
       additional_dependencies:
         - pydantic>=2
         - types-requests
-
-  - repo: local
-    hooks:
-    # pylint is a Python linter
-    # It is run through the local environment to ensure external packages can be
-    # imported without issue.
-    # For more information about pylint see its documentation at:
-    # https://pylint.pycqa.org/en/latest/
-    - id: pylint
-      name: pylint
-      entry: pylint
-      args: ["--rcfile=pyproject.toml"]
-      language: python
-      types: [python]
-      require_serial: true
-      exclude: ^(tests|docs/example)/.*$
-    # pylint is a Python linter
-    # It is run through the local environment to ensure external packages can be
-    # imported without issue.
-    # For more information about pylint see its documentation at:
-    # https://pylint.pycqa.org/en/latest/
-    # - id: pylint-tests
-    #   name: pylint - tests
-    #   entry: pylint
-    #   args:
-    #   - "--rcfile=pyproject.toml"
-    #   - "--disable=import-outside-toplevel,redefined-outer-name"
-    #   language: python
-    #   types: [python]
-    #   require_serial: true
-    #   files: ^tests/.*$

dlite_entities_service/__init__.py

@@ -1,4 +1,5 @@
 """DLite entities service."""
+from __future__ import annotations
 
 __version__ = "0.0.1"
 __author__ = "Casper Welzel Andersen"

dlite_entities_service/backend.py

@@ -1,4 +1,6 @@
 """Backend implementation."""
+from __future__ import annotations
+
 from pymongo import MongoClient
 
 from dlite_entities_service.config import CONFIG

dlite_entities_service/config.py

@@ -1,10 +1,11 @@
 """Service app configuration."""
-from typing import Any
+from __future__ import annotations
+
+from typing import Annotated, Any
 
 from pydantic import Field, SecretStr, field_validator
 from pydantic.networks import AnyHttpUrl, MultiHostUrl, UrlConstraints
 from pydantic_settings import BaseSettings, SettingsConfigDict
-from typing_extensions import Annotated
 
 MongoDsn = Annotated[
     MultiHostUrl, UrlConstraints(allowed_schemes=["mongodb", "mongodb+srv"])
@@ -15,20 +16,24 @@
 class ServiceSettings(BaseSettings):
     """Service app configuration."""
 
-    base_url: AnyHttpUrl = Field(
-        AnyHttpUrl("http://onto-ns.com/meta"),
-        description="Base URL, where the service is running.",
-    )
-    mongo_uri: MongoDsn = Field(
-        MongoDsn("mongodb://localhost:27017"),
-        description="URI for the MongoDB cluster/server.",
-    )
-    mongo_user: str | None = Field(
-        None, description="Username for connecting to the MongoDB."
-    )
-    mongo_password: SecretStr | None = Field(
-        None, description="Password for connecting to the MongoDB."
-    )
+    base_url: Annotated[
+        AnyHttpUrl,
+        Field(
+            description="Base URL, where the service is running.",
+        ),
+    ] = AnyHttpUrl("http://onto-ns.com/meta")
+    mongo_uri: Annotated[
+        MongoDsn,
+        Field(
+            description="URI for the MongoDB cluster/server.",
+        ),
+    ] = MongoDsn("mongodb://localhost:27017")
+    mongo_user: Annotated[
+        str | None, Field(description="Username for connecting to the MongoDB.")
+    ] = None
+    mongo_password: Annotated[
+        SecretStr | None, Field(description="Password for connecting to the MongoDB.")
+    ] = None
 
     @field_validator("base_url", mode="before")
     @classmethod

dlite_entities_service/logger.py

@@ -1,4 +1,6 @@
 """Logging to file."""
+from __future__ import annotations
+
 import logging
 import sys
 from contextlib import contextmanager
@@ -8,7 +10,6 @@
 from uvicorn.logging import DefaultFormatter
 
 if TYPE_CHECKING:  # pragma: no cover
-    # pylint: disable=ungrouped-imports
     import logging.handlers