[REF] Move environment variable handling to Pydantic BaseSettings class

[alyssadai]

• Closes Refactor environment variable reading using pydantic-settings #316

Changes proposed in this pull request:

• Replace all global variables for environment variables with a single Settings class using pydantic-settings
• Use pytest-env to set a subset of environment vars to non-default values in the environment before any tests run, to allow basic test that environment variables are read in correctly
  • otherwise, since environment variables are read in on app startup (meaning the TestClient used by tests already has a settings instance), modifying settings values are done through simply monkeypatching attributes
• Change dummy test of invalid credentials to a meaningful integration test

Housekeeping:

• Update some leftover Pydantic v1 syntax
• Update README badges

Checklist

This section is for the PR reviewer

• PR has an interpretable title with a prefix ([ENH], [FIX], [REF], [TST], [CI], [MNT], [INF], [MODEL], [DOC]) (see our Contributing Guidelines for more info)
• PR has a label for the release changelog or skip-release (to be applied by maintainers only)
• PR links to GitHub issue with mention Closes #XXXX
• Tests pass
• Checks pass
• If the PR changes the SPARQL query template, the default Neurobagel query file has also been regenerated

For new features:

• Tests have been added

For bug fixes:

• There is at least one test that would fail under the original bug conditions.

Summary by Sourcery

This pull request refactors the application to use Pydantic's BaseSettings for managing environment variables. This change improves code maintainability and type safety by centralizing environment variable configuration and validation within a dedicated settings class. The application now uses a settings object to access environment variables, and tests have been updated to reflect this change.

Enhancements:

• Migrated environment variable handling to Pydantic BaseSettings class for improved type safety and validation.
• Replaced direct access to environment variables with the new settings object.

Tests:

• Updated tests to use the new settings object instead of directly patching environment variables.
• Added a new test module to verify that settings are read correctly from environment variables.

Summary by Sourcery

Refactors the application to use Pydantic's BaseSettings for managing environment variables, improving code maintainability and type safety. Tests have been updated to reflect this change.

Enhancements:

• Migrated environment variable handling to Pydantic BaseSettings class for improved type safety and validation.
• Replaced direct access to environment variables with a settings object.

Tests:

• Updated tests to use the new settings object instead of directly patching environment variables.
• Added a new test module to verify that settings are read correctly from environment variables.
• Added an integration test to verify that the app returns a 401 status code when given invalid credentials for the graph.

Chores:

• Updated some leftover Pydantic v1 syntax.

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request refactors the application to use Pydantic's BaseSettings for managing environment variables. This change improves code maintainability and type safety by centralizing environment variable configuration and validation within a dedicated settings class. The application now uses a settings object to access environment variables, and tests have been updated to reflect this change. Additionally, pytest-env was implemented to set environment variables for testing.

Sequence diagram for accessing graph database

sequenceDiagram
    participant App
    participant Settings
    participant httpx

    App->>Settings: Access settings.query_url, settings.graph_username, settings.graph_password
    Settings-->>App: Return values
    App->>httpx: Post query to graph database using httpx.post(url=settings.query_url, auth=(settings.graph_username, settings.graph_password))
    httpx-->>App: Return response

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Updated class diagram for Settings

classDiagram
    class Settings {
        +root_path: str
        +allowed_origins: str
        +graph_username: str | None
        +graph_password: str | None
        +graph_address: str
        +graph_db: str
        +graph_port: int
        +return_agg: bool
        +min_cell_size: int
        +auth_enabled: bool
        +client_id: str | None
        +query_url: str
    }
    note for Settings "Pydantic BaseSettings class for managing environment variables"

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File-Level Changes

Change	Details	Files
Replaced global variables for environment variables with a Settings class using pydantic-settings.	Created a Settings class to manage environment variables. Replaced direct access to environment variables with the new settings object. Updated code to use the settings object to access environment variables. Added a computed field for the query URL.	app/api/utility.py app/main.py app/api/crud.py app/api/security.py app/api/config.py tests/test_settings.py
Implemented pytest-env to set environment variables for testing.	Installed pytest-env. Configured pytest.ini to set environment variables for testing. Updated tests to use the new settings object instead of directly patching environment variables. Added a new test module to verify that settings are read correctly from environment variables.	tests/test_query.py tests/test_app_events.py tests/conftest.py pytest.ini tests/test_attribute_factory_routes.py tests/test_pipelines.py tests/test_attributes.py tests/test_security.py
Updated Pydantic v1 syntax to v2.	Updated leftover Pydantic v1 syntax to v2.	app/api/crud.py
Improved integration test for invalid credentials.	Changed dummy test of invalid credentials to a meaningful integration test.	tests/test_query.py tests/test_app_events.py

Assessment against linked issues

Issue	Objective	Addressed	Explanation
#316	Refactor the environment variable reading to allow for easier testing and dynamic replacement of variable values.	✅
#316	Use pydantic-settings to load environment variables.	✅
#316	Ensure that the environment variables are read at import time.	✅

Possibly linked issues

• Refactor environment variable reading using pydantic-settings #316: The PR addresses the issue by moving environment variable handling to a Pydantic BaseSettings class.
• Refactor environment variable reading using pydantic-settings #316: The PR uses pydantic-settings, which depends on Pydantic v2, to manage environment variables, addressing the dependency upgrade in the issue.

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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 97.30%. Comparing base (bc90678) to head (0659c2b).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #416      +/-   ##
==========================================
+ Coverage   97.24%   97.30%   +0.05%     
==========================================
  Files          24       26       +2     
  Lines         835      852      +17     
==========================================
+ Hits          812      829      +17     
  Misses         23       23              

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