merge dev branch #400

	name: Python Tests

	on:
	push:
	branches:
	- main
	pull_request:

	jobs:
	unit:
	env:
	AWS_ACCESS_KEY_ID: test
	AWS_SECRET_ACCESS_KEY: test
	REDCAP_API_TOKEN: test
	AZURE_BLOB_CONNECTION_STRING: test
	AZURE_OPENAI_API_KEY: test
	AZURE_OPENAI_LLM_DEPLOYMENT: test
	AZURE_OPENAI_ENDPOINT: test
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: Install uv
	run: pipx install uv
	- uses: actions/setup-python@v5
	with:
	python-version-file: pyproject.toml
	cache: pip
	- name: Install dependencies
	run: \|
	uv sync
	uv run python -m spacy download en_core_web_sm
	- name: Run tests
	id: run-tests
	run: >
	uv run pytest . \
	--junitxml=pytest.xml \
	--cov-report=term-missing:skip-covered \
	--cov-report=xml:coverage.xml \
	--cov=src tests \
	--log-level=DEBUG \
	--verbose
	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v5
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	verbose: true

	ruff:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: Install uv
	run: pipx install uv
	- uses: actions/setup-python@v5
	with:
	python-version-file: pyproject.toml
	cache: pip
	- name: Install dependencies
	run: \|
	uv sync
	uv run ruff check .

	mypy:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: Install uv
	run: pipx install uv
	- uses: actions/setup-python@v5
	with:
	python-version: '3.11'
	cache: pip
	- run: \|
	uv sync
	uv run mypy .

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