Merge branch 'main' into fix-isort-errors

Author: jsstevenson

python/hooks/post_gen_project.py

@@ -15,9 +15,10 @@
 
 if not {{ cookiecutter.add_fastapi }}:
     Path("tests/test_api.py").unlink()
+    Path("tests/data/service_info_openapi.yaml").unlink()
     Path("src/{{ cookiecutter.project_slug }}/api.py").unlink()
     Path("src/{{ cookiecutter.project_slug }}/models.py").unlink()
-    Path("src/{{ cookiecutter.project_slug }}/config.py").unlink()
 
 if (not {{ cookiecutter.add_fastapi }}) and (not {{ cookiecutter.add_cli }}):
     Path("./src/{{ cookiecutter.project_slug }}/logging.py").unlink()
+    Path("src/{{ cookiecutter.project_slug }}/config.py").unlink()

python/{{cookiecutter.project_slug}}/.github/workflows/checks.yaml

@@ -15,12 +15,17 @@ jobs:
         with:
           python-version: {{ "${{ matrix.python-version }}" }}
 
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+
       - name: Install dependencies
         run: |
-          python3 -m pip install ".[tests]"
+        run: uv sync --extra tests
 
       - name: Run tests
-        run: python3 -m pytest
+        run: uv run pytest
 
   lint:
     name: lint
@@ -33,11 +38,16 @@ jobs:
         with:
           python-version: "3.11"
 
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+
       - name: Install dependencies
-        run: python3 -m pip install ".[dev]"
+        run: uv sync --extra dev
 
       - name: Check style
-        run: python3 -m ruff check . && python3 -m ruff format --check .
+        run: uv run ruff check && uv run ruff format --check
 
   precommit_hooks:
     runs-on: ubuntu-latest
@@ -72,12 +82,15 @@ jobs:
         with:
           python-version: 3.11
 
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+
       - name: Install dependencies
-        run: |
-          python3 -m pip install --upgrade pip
-          python3 -m pip install '.[docs]'
+        run: uv sync --extra docs
 
       - name: Attempt docs build
         working-directory: ./docs
-        run: make html
+        run: source ../.venv/bin/activate && make html
 {% endif %}

python/{{cookiecutter.project_slug}}/pyproject.toml

@@ -26,6 +26,9 @@ dependencies = [
     "fastapi",
     "pydantic~=2.1",
 {%- endif %}
+{%- if cookiecutter.add_fastapi or cookiecutter.add_cli %}
+    "pydantic-settings",
+{%- endif %}
 ]
 dynamic = ["version"]
 
@@ -35,6 +38,8 @@ tests = [
     "pytest-cov",
 {%- if cookiecutter.add_fastapi %}
     "httpx",
+    "jsonschema~=4.24",  # pin to avoid deprecation of ref resolver
+    "pyyaml",
 {%- endif %}
 ]
 dev = [

python/{{cookiecutter.project_slug}}/src/{{cookiecutter.project_slug}}/__init__.py

@@ -2,7 +2,6 @@
 
 from importlib.metadata import version, PackageNotFoundError
 
-
 try:
     __version__ = version("{{ cookiecutter.project_slug }}")
 except PackageNotFoundError:

python/{{cookiecutter.project_slug}}/src/{{cookiecutter.project_slug}}/api.py

@@ -1,13 +1,14 @@
 """Define API endpoints."""
 
+import logging
 from collections.abc import AsyncGenerator
 from contextlib import asynccontextmanager
 from enum import Enum
 
 from fastapi import FastAPI
 
 from {{ cookiecutter.project_slug }} import __version__
-from {{ cookiecutter.project_slug }}.config import config
+from {{ cookiecutter.project_slug }}.config import get_config
 from {{ cookiecutter.project_slug }}.logging import initialize_logs
 from {{ cookiecutter.project_slug }}.models import ServiceInfo, ServiceOrganization, ServiceType
 
@@ -20,7 +21,9 @@ async def lifespan(app: FastAPI) -> AsyncGenerator:  # noqa: ARG001
 
     :param app: FastAPI instance
     """
-    initialize_logs()
+    log_level = logging.DEBUG if get_config().debug else logging.INFO
+
+    initialize_logs(log_level=log_level)
     yield
 
 
@@ -46,20 +49,18 @@ class _Tag(str, Enum):
     docs_url="/docs",
     openapi_url="/openapi.json",
     swagger_ui_parameters={"tryItOutEnabled": True},
+    lifespan=lifespan
 )
 
 
 @app.get(
-    "/service_info",
+    "/service-info",
     summary="Get basic service information",
     description="Retrieve service metadata, such as versioning and contact info. Structured in conformance with the [GA4GH service info API specification](https://www.ga4gh.org/product/service-info/)",
     tags=[_Tag.META],
 )
 def service_info() -> ServiceInfo:
-    """Provide service info per GA4GH Service Info spec
-
-    :return: conformant service info description
-    """
+    """Provide service info per GA4GH Service Info spec"""
     return ServiceInfo(
-        organization=ServiceOrganization(), type=ServiceType(), environment=config.env
+        organization=ServiceOrganization(), type=ServiceType(), environment=get_config().env
     )

python/{{cookiecutter.project_slug}}/src/{{cookiecutter.project_slug}}/cli.py

@@ -1,8 +1,11 @@
 """Provide CLI for application."""
 
+import logging
+
 import click
 
 from {{ cookiecutter.project_slug }} import __version__
+from {{ cookiecutter.project_slug }}.config import get_config
 from {{ cookiecutter.project_slug }}.logging import initialize_logs
 
 
@@ -18,4 +21,5 @@ def cli() -> None:
 
     Conclude by summarizing additional commands
     """  # noqa: D301
-    initialize_logs()
+    log_level = logging.DEBUG if get_config().debug else logging.INFO
+    initialize_logs(log_level)

python/{{cookiecutter.project_slug}}/src/{{cookiecutter.project_slug}}/config.py

@@ -1,93 +1,37 @@
 """Read and provide runtime configuration."""
 
-import logging
-import os
+from functools import cache
 
-from pydantic import BaseModel
+from pydantic_settings import BaseSettings, SettingsConfigDict
 
 from {{ cookiecutter.project_slug }}.models import ServiceEnvironment
 
 
-_logger = logging.getLogger(__name__)
+class Settings(BaseSettings):
+    """Create app settings
 
-
-_ENV_VARNAME = "{{ cookiecutter.project_slug | upper }}_ENV"
-
-
-class Config(BaseModel):
-    """Define app configuration data object."""
-
-    env: ServiceEnvironment
-    debug: bool
-    test: bool
-
-
-def _dev_config() -> Config:
-    """Provide development environment configs
-
-    :return: dev env configs
-    """
-    return Config(env=ServiceEnvironment.DEV, debug=True, test=False)
-
-
-def _test_config() -> Config:
-    """Provide test env configs
-
-    :return: test configs
-    """
-    return Config(env=ServiceEnvironment.TEST, debug=False, test=True)
-
-
-def _staging_config() -> Config:
-    """Provide staging env configs
-
-    :return: staging configs
-    """
-    return Config(env=ServiceEnvironment.STAGING, debug=False, test=False)
-
-
-def _prod_config() -> Config:
-    """Provide production configs
-
-    :return: prod configs
+    This is not a singleton, so every new call to this class will re-compute
+    configuration settings, defaults, etc.
     """
-    return Config(env=ServiceEnvironment.PROD, debug=False, test=False)
-
-
-def _default_config() -> Config:
-    """Provide default configs. This function sets what they are.
 
-    :return: default configs
-    """
-    return _dev_config()
+    model_config = SettingsConfigDict(
+        env_prefix="{{ cookiecutter.project_slug }}_",
+        env_file=".env",
+        env_file_encoding="utf-8",
+        extra="ignore"
+    )
 
+    env: ServiceEnvironment = ServiceEnvironment.DEV
+    debug: bool = False
+    test: bool = False
 
-_CONFIG_MAP = {
-    ServiceEnvironment.DEV: _dev_config,
-    ServiceEnvironment.TEST: _test_config,
-    ServiceEnvironment.STAGING: _staging_config,
-    ServiceEnvironment.PROD: _prod_config,
-}
 
+@cache
+def get_config() -> Settings:
+    """Get runtime configuration.
 
-def _set_config() -> Config:
-    """Set configs based on environment variable `{{ cookiecutter.project_slug | upper }}_ENV`.
+    This function is cached, so the config object only gets created/calculated once.
 
-    :return: complete config object with environment-specific parameters
+    :return: Settings instance
     """
-    raw_env_value = os.environ.get(_ENV_VARNAME)
-    if not raw_env_value:
-        return _default_config()
-    try:
-        env_value = ServiceEnvironment(raw_env_value.lower())
-    except ValueError:
-        _logger.error(
-            "Unrecognized value for %s: '%s'. Using default configs",
-            _ENV_VARNAME,
-            raw_env_value
-        )
-        return _default_config()
-    return _CONFIG_MAP[env_value]()
-
-
-config = _set_config()
+    return Settings()

python/{{cookiecutter.project_slug}}/src/{{cookiecutter.project_slug}}/logging.py

@@ -3,7 +3,7 @@
 import logging
 
 
-def initialize_logs(log_level: int = logging.DEBUG) -> None:
+def initialize_logs(log_level: int = logging.INFO) -> None:
     """Configure logging.
 
     :param log_level: app log level to set

python/{{cookiecutter.project_slug}}/src/{{cookiecutter.project_slug}}/models.py

@@ -53,6 +53,6 @@ class ServiceInfo(BaseModel):
         "https://github.com/{{ cookiecutter.org }}/{{ cookiecutter.repo }}"
     )
     createdAt: Literal["{% now 'utc', '%Y-%m-%dT%H:%M:%S+00:00' %}"] = "{% now 'utc', '%Y-%m-%dT%H:%M:%S+00:00' %}"  # noqa: N815
-    updatedAt: str | None = None  # noqa: N815
+    updatedAt: Literal["{% now 'utc', '%Y-%m-%dT%H:%M:%S+00:00' %}"] = "{% now 'utc', '%Y-%m-%dT%H:%M:%S+00:00' %}"  # noqa: N815
     environment: ServiceEnvironment
     version: Literal[__version__] = __version__

python/{{cookiecutter.project_slug}}/tests/conftest.py

@@ -1,3 +1,9 @@
+
+from pathlib import Path
+
+import pytest
+
+
 def pytest_addoption(parser):
     """Add custom commands to pytest invocation.
 
@@ -20,3 +26,9 @@ def pytest_configure(config):
         # logging.getLogger("botocore").setLevel(logging.ERROR)
         # logging.getLogger("boto3").setLevel(logging.ERROR)
         # logging.getLogger("urllib3.connectionpool").setLevel(logging.ERROR)
+
+
+@pytest.fixture(scope="session")
+def test_data_dir() -> Path:
+    """Provide Path instance pointing to test data directory"""
+    return Path(__file__).parent / "data"