feat: use pydantic-settings for config and update FastAPI stuff

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}}/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 PackageNotFoundError, version
 
-
 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"

python/{{cookiecutter.project_slug}}/tests/data/service_info_openapi.yaml

@@ -0,0 +1,122 @@
+openapi: 3.0.2
+info:
+  title: 'GA4GH service-info API specification'
+  description: 'A way for a service to describe basic metadata concerning a service alongside a set of capabilities and/or limitations of the service. More information on [GitHub](https://github.com/ga4gh-discovery/ga4gh-service-info/).'
+  version: 1.0.0
+  license:
+    name: 'Apache 2.0'
+    url: 'https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-info/develop/LICENSE'
+  contact:
+    name: 'GA4GH Discovery Networks Team'
+    email: '[email protected]'
+security:
+  - bearerAuth: []
+paths:
+  /service-info:
+    get:
+      summary: 'Show information about this service. It is assumed that removing this endpoint from a URL will result in a valid URL to query against'
+      operationId: getServiceInfo
+      tags:
+        - service-info
+      responses:
+        '200':
+          description: 'A successful operation to request the service information about this running service.'
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/Service'
+components:
+  securitySchemes:
+    bearerAuth:
+      type: http
+      scheme: bearer
+      bearerFormat: JWT
+  schemas:
+    Service:
+      description: 'GA4GH service'
+      type: object
+      required:
+        - id
+        - name
+        - type
+        - organization
+        - version
+      properties:
+        id:
+          type: string
+          description: 'Unique ID of this service. Reverse domain name notation is recommended, though not required. The identifier should attempt to be globally unique so it can be used in downstream aggregator services e.g. Service Registry.'
+          example: 'org.ga4gh.myservice'
+        name:
+          type: string
+          description: 'Name of this service. Should be human readable.'
+          example: 'My project'
+        type:
+          $ref: '#/components/schemas/ServiceType'
+        description:
+          type: string
+          description: 'Description of the service. Should be human readable and provide information about the service.'
+          example: 'This service provides...'
+        organization:
+          type: object
+          description: 'Organization providing the service'
+          required:
+            - name
+            - url
+          properties:
+            name:
+              type: string
+              description: 'Name of the organization responsible for the service'
+              example: 'My organization'
+            url:
+              type: string
+              format: uri
+              description: 'URL of the website of the organization (RFC 3986 format)'
+              example: 'https://example.com'
+        contactUrl:
+          type: string
+          format: uri
+          description: 'URL of the contact for the provider of this service, e.g. a link to a contact form (RFC 3986 format), or an email (RFC 2368 format).'
+          example: 'mailto:[email protected]'
+        documentationUrl:
+          type: string
+          format: uri
+          description: 'URL of the documentation of this service (RFC 3986 format). This should help someone learn how to use your service, including any specifics required to access data, e.g. authentication.'
+          example: 'https://docs.myservice.example.com'
+        createdAt:
+          type: string
+          format: date-time
+          description: 'Timestamp describing when the service was first deployed and available (RFC 3339 format)'
+          example: '2019-06-04T12:58:19Z'
+        updatedAt:
+          type: string
+          format: date-time
+          description: 'Timestamp describing when the service was last updated (RFC 3339 format)'
+          example: '2019-06-04T12:58:19Z'
+        environment:
+          type: string
+          description: 'Environment the service is running in. Use this to distinguish between production, development and testing/staging deployments. Suggested values are prod, test, dev, staging. However this is advised and not enforced.'
+          example: 'test'
+        version:
+          type: string
+          description: 'Version of the service being described. Semantic versioning is recommended, but other identifiers, such as dates or commit hashes, are also allowed. The version should be changed whenever the service is updated.'
+          example: '1.0.0'
+    ServiceType:
+      description: 'Type of a GA4GH service'
+      type: object
+      required:
+        - group
+        - artifact
+        - version
+      properties:
+        group:
+          type: string
+          description: 'Namespace in reverse domain name format. Use `org.ga4gh` for implementations compliant with official GA4GH specifications. For services with custom APIs not standardized by GA4GH, or implementations diverging from official GA4GH specifications, use a different namespace (e.g. your organization''s reverse domain name).'
+          example: 'org.ga4gh'
+        artifact:
+          type: string
+          description: 'Name of the API or GA4GH specification implemented. Official GA4GH types should be assigned as part of standards approval process. Custom artifacts are supported.'
+          example: 'beacon'
+        version:
+          type: string
+          description: 'Version of the API or specification. GA4GH specifications use semantic versioning.'
+          example: '1.0.0'