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pyproject.toml
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pyproject.toml
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[build-system]
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requires = ["setuptools>=68.0", "wheel"]
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build-backend = "setuptools.build_meta"
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[project]
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name = "pipeline-mco-pmsi-codage"
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version = "0.1.0"
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description = "Pipeline d'automatisation du codage médical PMSI avec architecture RAG"
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readme = "README.md"
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requires-python = ">=3.10"
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license = {text = "MIT"}
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authors = [
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{name = "DIM Team", email = "dim@hospital.fr"}
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]
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keywords = ["pmsi", "medical-coding", "rag", "llm", "healthcare"]
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classifiers = [
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"Development Status :: 3 - Alpha",
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"Intended Audience :: Healthcare Industry",
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"Topic :: Scientific/Engineering :: Medical Science Apps.",
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"Programming Language :: Python :: 3.10",
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"Programming Language :: Python :: 3.11",
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"Programming Language :: Python :: 3.12",
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]
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dependencies = [
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# Core dependencies
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"pydantic>=2.5.0",
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"pydantic-settings>=2.1.0",
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# Database
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"sqlalchemy>=2.0.0",
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"alembic>=1.13.0",
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"psycopg2-binary>=2.9.9", # PostgreSQL driver
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# Property-based testing
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"hypothesis>=6.92.0",
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# LLM and embeddings
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"langchain>=0.1.0",
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"langchain-community>=0.0.10",
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"sentence-transformers>=2.2.0",
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"transformers>=4.36.0",
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"torch>=2.1.0",
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# Vector store and search
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"faiss-cpu>=1.7.4", # or faiss-gpu for GPU support
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"qdrant-client>=1.7.0",
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# Text processing and NLP
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"spacy>=3.7.0",
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"nltk>=3.8.1",
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"regex>=2023.12.0",
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"edsnlp>=0.10.0", # EDS-NLP for French clinical text processing
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# Search and indexing
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"rank-bm25>=0.2.2",
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"whoosh>=2.7.4",
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# PDF processing
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"pypdf>=3.17.0",
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"pdfplumber>=0.10.0",
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# Excel processing
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"openpyxl>=3.1.0",
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"xlrd>=2.0.0",
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# Data validation and serialization
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"python-dateutil>=2.8.2",
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"pytz>=2023.3",
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# Cryptography for exports
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"cryptography>=41.0.0",
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# Configuration
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"pyyaml>=6.0.1",
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"python-dotenv>=1.0.0",
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# Logging and monitoring
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"structlog>=23.2.0",
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"python-json-logger>=2.0.7",
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# HTTP client for potential API calls
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"httpx>=0.25.0",
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# API framework
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"fastapi>=0.109.0",
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"uvicorn[standard]>=0.27.0",
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"python-multipart>=0.0.6",
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# CLI interface
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"click>=8.1.7",
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"rich>=13.7.0", # For beautiful CLI output
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# Utilities
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"tqdm>=4.66.0",
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"tenacity>=8.2.3", # Retry logic
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]
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[project.optional-dependencies]
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dev = [
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# Testing
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"pytest>=7.4.0",
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"pytest-cov>=4.1.0",
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"pytest-asyncio>=0.21.0",
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"pytest-mock>=3.12.0",
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"pytest-timeout>=2.2.0",
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# Code quality
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"black>=23.12.0",
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"isort>=5.13.0",
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"flake8>=7.0.0",
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"mypy>=1.8.0",
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"pylint>=3.0.0",
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# Documentation
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"sphinx>=7.2.0",
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"sphinx-rtd-theme>=2.0.0",
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# Development tools
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"ipython>=8.18.0",
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"ipdb>=0.13.13",
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]
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gpu = [
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"faiss-gpu>=1.7.4",
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]
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[project.scripts]
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pipeline-mco = "pipeline_mco_pmsi.cli:main"
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[tool.setuptools]
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packages = ["pipeline_mco_pmsi"]
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package-dir = {"" = "src"}
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[tool.pytest.ini_options]
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minversion = "7.0"
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testpaths = ["tests"]
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python_files = ["test_*.py", "*_test.py"]
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python_classes = ["Test*"]
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python_functions = ["test_*"]
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addopts = [
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"-v",
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"--strict-markers",
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"--tb=short",
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"--cov=pipeline_mco_pmsi",
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"--cov-report=term-missing",
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"--cov-report=html",
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"--cov-report=xml",
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]
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markers = [
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"unit: Unit tests",
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"integration: Integration tests",
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"property: Property-based tests",
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"slow: Slow tests",
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"gpu: Tests requiring GPU",
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]
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timeout = 300 # 5 minutes default timeout
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[tool.coverage.run]
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source = ["src"]
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omit = [
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"*/tests/*",
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"*/test_*.py",
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"*/__pycache__/*",
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"*/site-packages/*",
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]
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[tool.coverage.report]
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exclude_lines = [
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"pragma: no cover",
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"def __repr__",
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"raise AssertionError",
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"raise NotImplementedError",
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"if __name__ == .__main__.:",
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"if TYPE_CHECKING:",
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"@abstractmethod",
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]
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[tool.black]
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line-length = 100
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target-version = ['py310', 'py311', 'py312']
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include = '\.pyi?$'
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extend-exclude = '''
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/(
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# directories
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\.eggs
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| \.git
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| \.hg
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| \.mypy_cache
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| \.tox
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| \.venv
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| build
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| dist
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)/
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'''
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[tool.isort]
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profile = "black"
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line_length = 100
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multi_line_output = 3
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include_trailing_comma = true
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force_grid_wrap = 0
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use_parentheses = true
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ensure_newline_before_comments = true
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[tool.mypy]
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python_version = "3.10"
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warn_return_any = true
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warn_unused_configs = true
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disallow_untyped_defs = true
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disallow_incomplete_defs = true
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check_untyped_defs = true
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disallow_untyped_decorators = false
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no_implicit_optional = true
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warn_redundant_casts = true
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warn_unused_ignores = true
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warn_no_return = true
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follow_imports = "normal"
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ignore_missing_imports = true
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strict_equality = true
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[[tool.mypy.overrides]]
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module = "tests.*"
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disallow_untyped_defs = false
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[tool.pylint.messages_control]
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max-line-length = 100
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disable = [
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"C0111", # missing-docstring
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"C0103", # invalid-name
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"R0903", # too-few-public-methods
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"R0913", # too-many-arguments
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]
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[tool.hypothesis]
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# Configuration for Hypothesis property-based testing
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max_examples = 100
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deadline = 5000 # 5 seconds per test case
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derandomize = false
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print_blob = true
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