updated packages and GHA

[Harika Bishai (HarikaBishai)]

This pull request includes a series of dependency updates, workflow improvements, and resource management fixes across the codebase. The most significant changes are grouped below by theme.

Dependency and Development Environment Updates:

• Updated multiple Python package dependencies to their latest versions in requirements-dev.txt to address security, compatibility, and feature improvements. Notable updates include aiohttp, anyio, attrs, black, certifi, locust, pytest, and many others. Removed pytest-asyncio and added new dependencies such as python-discovery and vcs-versioning. [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13]
• Updated pyproject.toml to use anyio_mode instead of asyncio_mode for pytest configuration, reflecting the shift away from pytest-asyncio.
• Removed pytest-asyncio from requirements-dev.in, aligning with the above configuration change.

CI/CD Workflow Improvements:

• Upgraded several GitHub Actions in .github/workflows/docker-publish.yml to their latest versions for improved security and reliability. Also standardized YAML formatting for consistency. [1] [2] [3]
• Minor cleanup in the workflow environment section.

Resource Management and Database Connection Handling:

• Modified MongoDB connection initialization in scripts (scripts/create_new_beamline.py, scripts/update_beamline.py) and the FastAPI app lifespan (src/nsls2api/infrastructure/app_setup.py) to return and explicitly close the MongoDB client, ensuring proper cleanup of resources. [1] [2] [3] [4] [5] [6] [7]

Model and Schema Adjustments:

• Updated the ApiUser model in src/nsls2api/models/apikeys.py to use json_schema_extra for the user_api_keys field, improving schema clarity. https://beanie-odm.dev/tutorial/relations/#back-links
• Updated the ProposalDisplay model in src/nsls2api/models/proposals.py to use the modern model_config approach with ConfigDict for extra field handling, replacing the deprecated Config class. [1] [2]

Minor Script and Typing Fixes:

• Minor fix to add a trailing comma in a function call for consistency in scripts/update_beamline.py.

These changes collectively improve dependency management, resource handling, and codebase maintainability.

Commands to Upgrade Dependencies:

uv pip compile requirements-dev.in --upgrade -o requirements-dev.txt
uv pip compile requirements.in --upgrade -o requirements.txt

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Test Cases Summary:

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JIRA: https://jira.nsls2.bnl.gov/browse/DT1-1431

[Padraic Shafer (padraic-shafer)]

All changes look good, though if we can continue to use any, let's use that instead of asyncio.

[Harika Bishai (HarikaBishai)]

All changes look good, though if we can continue to use any, let's use that instead of asyncio.

I have changed all the tests to use anyio, updated pyproject.toml to use anyio_mode

Had to add

@pytest.fixture
def anyio_backend():
    return "asyncio"

in confest.py to run all @pytest.mark.anyio tests using the asyncio backend only.