[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[project]
name = "openmed"
dynamic = ["version"]
description = "Local-first SDK for clinical extraction and de-identification workflows on hardware you control."
readme = "README.md"
requires-python = ">=3.10"
classifiers = [
  "Programming Language :: Python :: 3 :: Only",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Programming Language :: Python :: 3.13",
  "Operating System :: POSIX :: Linux",
  "Operating System :: Microsoft :: Windows",
  "Operating System :: MacOS",
]
license = { text = "Apache-2.0" }
keywords = [
  "biomedical",
  "clinical",
  "NLP",
  "LLM",
  "healthcare",
  "medical",
  "natural language processing",
  "medical language models",
  "medical LLMs",
  "medical NLP",
  "medical NER",
  "medical de-identification",
  "medical extraction",
  "medical reasoning",
]
dependencies = [
  "pysbd>=0.3.4,<0.4",
  "faker>=22.0",
  "jieba>=0.42.1,<0.43",
  "pyyaml>=6.0",
  "jsonschema>=4.18,<5",
  "tomli>=2.0; python_version < '3.11'",
]

authors = [
  { name = "Maziyar Panahi" }
]

[project.optional-dependencies]
dev = [
  # 3.20.3 predates the affected lock code; patched 4.x requires Python 3.11+.
  "filelock==3.20.3; python_version < '3.11'",
  "filelock>=4.2.1; python_version >= '3.11'",
  "setuptools>=84.1.0",
  # Patched virtualenv, used by pre-commit, needs the newer filelock branch.
  "pre-commit>=4.0; python_version >= '3.11'",
  "cryptography>=50,<51",
  "rich>=13.0",
  "typer>=0.12",
  "pytest>=7.0",
  "pytest-cov>=4.0",
  "pytest-timeout>=2.3",
  "huggingface-hub>=0.30",
  "jinja2>=3.1.6",
  "mcp>=1.30,<2",
  "mypy==2.3.0",
  "opencc>=1.4.1,<2",
  # Pillow 13 fixes the image-parser advisories but requires Python 3.11+.
  "Pillow==13.0.0; python_version >= '3.11'",
  "duckdb>=1.0,<2",
  "numpy>=1.26",
  "openpyxl>=3.1,<4",
  "fastapi>=0.110",
  "httpx>=0.27",
  "dask[dataframe]>=2024.8",
  "opentelemetry-api>=1.45.1,<2",
  "opentelemetry-exporter-otlp-proto-http>=1.26,<2",
  "opentelemetry-sdk>=1.26,<2",
  "pandas>=2.0",
  "polars>=0.20",
  "python-dateutil>=2.8",
  "hypothesis>=6.100",
  "fsspec>=2026.6.0",
  "fonttools[woff]==4.61.1",
  "grpcio>=1.64",
  "grpcio-tools>=1.64",
  "protobuf>=5.26,<7",
  "ruff==0.15.22",
  "strawberry-graphql[fastapi]>=0.327.2,<1",
  "sqlalchemy>=2.0,<3",
  "tomli>=2.0; python_version < '3.11'",
  "nbclient>=0.8.0",
  "nbformat>=5.9.0",
  "ipykernel>=6.0",
]

cli = [
  "rich>=13.0",
  "typer>=0.12",
]

integrity = [
  "cryptography>=50,<51",
]

mcp = [
  "mcp>=1.30,<2",
]

lid = [
  "pycld2>=0.41,<1",
]

openmrs = [
  "httpx>=0.27",
]

fhir = [
  "httpx>=0.27",
]

presidio = [
  "filelock==3.20.3; python_version < '3.11'",
  "filelock>=4.2.1; python_version >= '3.11'",
  "setuptools>=84.1.0",
  "presidio-analyzer>=2.2.354,<3",
]

medspacy = [
  "setuptools>=84.1.0; python_version >= '3.12'",
  # Older Python versions require spaCy below the supported security floor.
  "medspacy>=1.3.1,<2; python_version >= '3.12'",
]

philter = [
  "philter-ucsf>=1.0.3,<2",
]

pydeid = [
  "pyDeid>=0.0.1",
]

scrubadub = [
  "scrubadub>=2.0,<3",
]

pandas = [
  "pandas>=2.0",
]

polars = [
  "polars>=0.20",
]

columnar = [
  "pyarrow>=16",
]

dask = [
  "fsspec>=2026.6.0",
  "jinja2>=3.1.6",
  "dask[dataframe]>=2024.8",
]

dagster = [
  "filelock==3.20.3; python_version < '3.11'",
  "filelock>=4.2.1; python_version >= '3.11'",
  "mako>=1.4.2",
  "fsspec>=2026.6.0",
  "jinja2>=3.1.6",
  "dagster>=1.8,<2",
]

sqlalchemy = [
  "sqlalchemy>=2.0,<3",
]

spacy = [
  "setuptools>=84.1.0",
  "click>=8.0",
  "spacy>=3.8.9",
]

zh = [
  "jieba>=0.42",
  "opencc>=1.4.1,<2",
  "pypinyin>=0.51",
]

indic = [
  "indic-nlp-library>=0.92",
]

scispacy = [
  "setuptools>=84.1.0",
  "scispacy>=0.5.4,<1",
]

quickumls = [
  "setuptools>=84.1.0",
  "quickumls>=1.4,<2",
]

# sdcMicro/R (GPL-2.0) and MedCAT/CogStack (Elastic License 2.0) are installed
# separately. This explicit extra opts into subprocess-only bridges without
# adding restricted code or dependencies.
interop-gpl = []

# The official HL7 FHIR validator is a user-fetched Java artifact invoked in a
# subprocess. This marker extra intentionally installs no validator code.
grounding-validate = []

# extract-msg is GPL-3.0 and is invoked only through OpenMed's isolated
# stdin/stdout subprocess bridge. This explicit extra keeps GPL code out of the
# base and general multimodal environments.
email-msg-gpl = [
  "extract-msg>=0.56,<0.57",
]

multimodal = [
  "filelock==3.20.3; python_version < '3.11'",
  "filelock>=4.2.1; python_version >= '3.11'",
  "setuptools>=84.1.0",
  "fsspec>=2026.6.0",
  "jinja2>=3.1.6",
  "torch>=2.13.0",
  "numpy>=1.26",
  "openpyxl>=3.1,<4",
  "onnx>=1.21",
  "pdfplumber>=0.11",
  "python-docx>=1.1",
  "python-pptx>=1.0",
  "Pillow>=13.0.0",
  "python-doctr>=1.0",
  "piexif>=1.1",
  "pikepdf>=9.0",
  "pydicom>=3.0",
  "pytesseract>=0.3.10",
  "markdown-it-py>=3.0,<5",
  "easyocr>=1.7",
]

notebook = [
  "nbformat>=5.9.0",
]

# PaddleOCR is a heavy, platform-sensitive backend (pulls in paddlepaddle), so
# it is opt-in rather than bundled into the general multimodal extra.
ocr-paddle = [
  "Pillow>=13.0.0",
  "paddleocr>=2.7",
]

zh-pkuseg = [
  "pkuseg>=0.0.25,<0.1",
]

zh-hanlp = [
  "filelock==3.20.3; python_version < '3.11'",
  "filelock>=4.2.1; python_version >= '3.11'",
  "setuptools>=84.1.0",
  "hanlp>=2.1,<3",
  "fsspec>=2026.6.0",
  "jinja2>=3.1.6",
  "torch>=2.13.0",
]

awq = [
  "filelock==3.20.3; python_version < '3.11' and sys_platform == 'linux'",
  "filelock>=4.2.1; python_version >= '3.11' and sys_platform == 'linux'",
  "setuptools>=84.1.0; sys_platform == 'linux'",
  "multidict>=6.9.1; sys_platform == 'linux'",
  "aiohttp>=3.14.4; sys_platform == 'linux'",
  "fsspec>=2026.6.0; sys_platform == 'linux'",
  "jinja2>=3.1.6; sys_platform == 'linux'",
  "autoawq==0.2.9; sys_platform == 'linux'",
  "datasets>=5.0.1; sys_platform == 'linux'",
  "torch>=2.13.0; sys_platform == 'linux'",
  "transformers==5.12.1; sys_platform == 'linux'",
]

gptq = [
  "filelock==3.20.3; python_version < '3.11'",
  "filelock>=4.2.1; python_version >= '3.11'",
  "setuptools>=84.1.0",
  "multidict>=6.9.1",
  "aiohttp>=3.14.4",
  "fsspec>=2026.6.0",
  "jinja2>=3.1.6",
  "auto-gptq>=0.7.1",
  "datasets>=5.0.1",
  "torch>=2.13.0",
]

grounding = [
  "rapidfuzz>=3.9,<4",
  "hnswlib>=0.8,<1",
  "numpy>=1.26",
]

langchain = [
  "langchain-core>=0.2,<2",
]

langgraph = [
  "langgraph>=0.2,<2",
  "langgraph-sdk>=0.4.4",
]

haystack = [
  "haystack-ai>=2,<3",
]

llamaindex = [
  "setuptools>=84.1.0",
  "Pillow>=13.0.0",
  "tinytag>=2.3.0",
  "multidict>=6.9.1",
  "aiohttp>=3.14.4",
  "fsspec>=2026.6.0",
  "jinja2>=3.1.6",
  "llama-index-core>=0.10,<1",
  "banks>=2.5.1",
]

agents = [
  "setuptools>=84.1.0",
  "Pillow>=13.0.0",
  "tinytag>=2.3.0",
  "multidict>=6.9.1",
  "aiohttp>=3.14.4",
  "fsspec>=2026.6.0",
  "jinja2>=3.1.6",
  "langchain-core>=0.2,<2",
  "langgraph>=0.2,<2",
  "langgraph-sdk>=0.4.4",
  "llama-index-core>=0.10,<1",
  "banks>=2.5.1",
]

beam = [
  "setuptools>=84.1.0",
  "Pillow>=13.0.0",
  "multidict>=6.9.1",
  "apache-beam>=2.73,<3",
  "pymongo>=4.18.2",
  "h2>=4.4.1",
]

airflow = [
  "mako>=1.4.2",
  "fsspec>=2026.6.0",
  "jinja2>=3.1.6",
  "apache-airflow>=3.2.2,<4",
]

duckdb = [
  "duckdb>=1.0,<2",
  "numpy>=1.26",
]

kafka = [
  "confluent-kafka>=2.3",
]

prefect = [
  "mako>=1.4.2",
  "fsspec>=2026.6.0",
  "jinja2>=3.1.6",
  "prefect>=3.7,<4",
  "h2>=4.4.1",
  "oauthlib>=4.0.0",
]

cloud = [
  "multidict>=6.9.1",
  "aiohttp>=3.14.4",
  "fsspec>=2026.6.0",
  "jinja2>=3.1.6",
  "s3fs>=2025.9.0",
  "gcsfs>=2025.9.0",
  "adlfs>=2025.8.0",
  "oauthlib>=4.0.0",
]

journey = [
  "fsspec>=2026.6.0",
  "jinja2>=3.1.6",
  "pg8000>=1.31.5,<2",
]

ray = [
  "filelock==3.20.3; python_version < '3.11'",
  "filelock>=4.2.1; python_version >= '3.11'",
  "fsspec>=2026.6.0",
  "jinja2>=3.1.6",
  "ray[data]>=2.30,<3",
]

spark = [
  "pyspark>=3.5,<4",
  "pandas>=2.0",
  "pyarrow>=16",
]

snowflake = [
  "filelock==3.20.3; python_version < '3.11'",
  "filelock>=4.2.1; python_version >= '3.11'",
  "setuptools>=84.1.0",
  "snowflake-snowpark-python>=1.0,<2",
]

hf = [
  "filelock==3.20.3; python_version < '3.11'",
  "filelock>=4.2.1; python_version >= '3.11'",
  "setuptools>=84.1.0",
  "fsspec>=2026.6.0",
  "jinja2>=3.1.6",
  "torch>=2.13.0",
  "transformers>=4.50",
  "huggingface-hub>=0.30",
  "accelerate>=0.29",
  "tokenizers>=0.15"
]

# Core pipeline observability. The SDK enables caller-owned in-process
# providers and test exporters; no network exporter is included or configured.
otel = [
  "opentelemetry-api>=1.45.1,<2",
  "opentelemetry-sdk>=1.26,<2",
]

service = [
  "cryptography>=50,<51",
  "fastapi>=0.110",
  "grpcio>=1.64",
  "httpx>=0.27",
  "opentelemetry-api>=1.45.1,<2",
  "opentelemetry-exporter-otlp-proto-http>=1.26,<2",
  "opentelemetry-sdk>=1.26,<2",
  "protobuf>=5.26,<7",
  "strawberry-graphql[fastapi]>=0.327.2,<1",
  "uvicorn[standard]>=0.29",
]

# Client libraries only. OpenMed never installs Triton or KServe servers.
triton = [
  "filelock==3.20.3; python_version < '3.11'",
  "filelock>=4.2.1; python_version >= '3.11'",
  "fsspec>=2026.6.0",
  "jinja2>=3.1.6",
  "grpcio>=1.64",
  "httpx>=0.27",
  "numpy>=1.26",
  "protobuf>=5.26,<7",
  "transformers>=4.50",
]

operator = [
  "multidict>=6.9.1",
  "aiohttp>=3.14.4",
  "kopf>=1.44.6,<2",
]

gliner = [
  "filelock==3.20.3; python_version < '3.11'",
  "filelock>=4.2.1; python_version >= '3.11'",
  "setuptools>=84.1.0",
  "fsspec>=2026.6.0",
  "jinja2>=3.1.6",
  "gliner[tokenizers]>=0.2.0",
  "torch>=2.13.0"
]

gliformer = [
  "filelock==3.20.3; python_version < '3.11'",
  "filelock>=4.2.1; python_version >= '3.11'",
  "setuptools>=84.1.0",
  "fsspec>=2026.6.0",
  "jinja2>=3.1.6",
  "gliformer>=0.1.3,<0.2",
  "Pillow>=13.0.0",
  # GLiFormer imports the current GLiNER packing API at module import time.
  "gliner>=0.2.29",
  "torch>=2.13.0",
]

gliner2 = [
  "filelock==3.20.3; python_version < '3.11'",
  "filelock>=4.2.1; python_version >= '3.11'",
  "setuptools>=84.1.0",
  "fsspec>=2026.6.0",
  "jinja2>=3.1.6",
  "gliner2[local]>=2.1.0,<3",
  "torch>=2.13.0",
]

mlx = [
  "filelock==3.20.3; python_version < '3.11'",
  "filelock>=4.2.1; python_version >= '3.11'",
  "fsspec>=2026.6.0",
  "jinja2>=3.1.6",
  "mlx>=0.22",
  "mlx-lm>=0.31",
  "huggingface-hub>=0.30",
  "Pillow>=13.0.0",
  "transformers>=4.50",
  "tokenizers>=0.15",
  "safetensors>=0.4",
  "tiktoken>=0.7",
]

coreml = [
  "filelock==3.20.3; python_version < '3.11'",
  "filelock>=4.2.1; python_version >= '3.11'",
  "setuptools>=84.1.0",
  "fsspec>=2026.6.0",
  "jinja2>=3.1.6",
  "coremltools>=8.0",
  "huggingface-hub>=0.30",
  "torch>=2.13.0",
  "transformers>=4.50",
]

onnx = [
  "filelock==3.20.3; python_version < '3.11'",
  "filelock>=4.2.1; python_version >= '3.11'",
  "setuptools>=84.1.0",
  "fsspec>=2026.6.0",
  "jinja2>=3.1.6",
  "onnx>=1.21",
  "onnxruntime>=1.16",
  "onnxscript>=0.1.0",
  "torch>=2.13.0",
  "transformers>=4.50",
]

onnx-runtime = [
  "filelock==3.20.3; python_version < '3.11'",
  "filelock>=4.2.1; python_version >= '3.11'",
  "fsspec>=2026.6.0",
  "jinja2>=3.1.6",
  "huggingface-hub>=0.30",
  "numpy>=1.26",
  "onnxruntime>=1.16",
  "tokenizers>=0.15",
]

# Minimal, local-artifact ONNX Runtime profile for aarch64 SBCs. It excludes
# graph-building, Torch, and Transformers dependencies; use onnx-runtime when
# the application also needs OpenMed's Hub download path.
edge-sbc = [
  "filelock==3.20.3; python_version < '3.11'",
  "filelock>=4.2.1; python_version >= '3.11'",
  "fsspec>=2026.6.0",
  "jinja2>=3.1.6",
  "numpy>=1.26",
  "onnxruntime>=1.16",
  "tokenizers>=0.15",
]

openvino = [
  "filelock==3.20.3; python_version < '3.11'",
  "filelock>=4.2.1; python_version >= '3.11'",
  "fsspec>=2026.6.0",
  "jinja2>=3.1.6",
  "openvino>=2024.0",
  "nncf>=2.10",
  "onnxruntime>=1.16",
  "transformers>=4.50",
]

docs = [
  "mkdocs>=1.6",
  "mkdocs-material>=9.5",
  "mkdocs-git-revision-date-localized-plugin>=1.2.6",
  "mkdocs-llmstxt>=0.5.0,<1",
  "mkdocs-minify-plugin>=0.8.0",
  "mkdocs-static-i18n>=1.3,<2",
  "pymdown-extensions>=11.0.1,<12",
  "gitpython>=3.2.1,<4",
  "mkdocstrings[python]",
  "griffe",
]

yasbd = [
  "yasbd-lib>=0.14.0,<0.15",
]

[project.scripts]
openmed = "openmed.cli:main"
openmed-sidecar = "openmed.service.sidecar:main"
openmed-executable-udf = "openmed.integrations.executable_udf:main"
openmed-mcp = "openmed.mcp.server:main"
openmed-journey = "openmed.deploy.journey:main"

[tool.uv]
constraint-dependencies = [
  "filelock==3.20.3; python_version < '3.11'",
  "filelock>=4.2.1; python_version >= '3.11'",
  "setuptools>=84.1.0",
  "certifi>=2026.10.19",
  "Pillow>=13.0.0; python_version >= '3.11'",
  "tinytag>=2.3.0",
  "mako>=1.4.2",
  "multidict>=6.9.1",
  "aiohttp>=3.14.4",
  "mcp>=1.30,<2",
  "fsspec>=2026.6.0",
  "jinja2>=3.1.6",
  "banks>=2.5.1",
  "langgraph-sdk>=0.4.4",
  "pymongo>=4.18.2",
  "datasets>=5.0.1",
  "h2>=4.4.1",
  "oauthlib>=4.0.0",
  # Keep transitive optional model backends above the checkpoint/native-op fixes.
  "torch>=2.13.0",
  "tornado>=6.5.9",
  "urllib3>=2.8.0",
  "virtualenv>=21.14.9",
  "brotli>=1.2.1",
  "brotlicffi>=1.2.1.0",
  "graphql-core>=3.2.12",
  "opentelemetry-api>=1.45.1",
  "gitpython>=3.2.1",
  "betterproto==2.0.0b6; python_version >= '3.11'",
  "pyjwt>=2.14.0",
]
override-dependencies = [
  # Snowflake 4.x caps filelock below its security fixes; validate cache locking.
  "filelock==3.20.3; python_version < '3.11'",
  "filelock>=4.2.1; python_version >= '3.11'",
  # Beam 2.75 caps these below their patched releases even though its
  # DirectRunner remains compatible with the secure versions.
  "cryptography>=50,<51",
  "httplib2>=0.32",
  # Beam also caps Pillow below the patched release on Python 3.11+.
  "Pillow>=13.0.0; python_version >= '3.11'",
  # Prefect 3.7 caps packaging below the release patched virtualenv needs, and
  # newer Prefect requires FastAPI releases that Airflow 3.3 excludes.
  "packaging>=26.3,<27",
]
conflicts = [
  [
    { extra = "airflow" },
    { extra = "ocr-paddle" },
  ],
  [
    { extra = "awq" },
    { extra = "gliner" },
  ],
  [
    { extra = "awq" },
    { extra = "gliformer" },
  ],
  [
    { extra = "onnx" },
    { extra = "scispacy" },
  ],
  [
    { extra = "multimodal" },
    { extra = "scispacy" },
  ],
]

[tool.hatch.build]
include = [
  "/openmed/**",
  "/openmed/py.typed",
  "/openmed/core/thresholds.json",
  "/openmed/core/policies/*.json",
  "/openmed/core/schemas/json/*.json",
  "/openmed/risk/data/*.json",
  "/eval/redteam/corpus/adversarial_phi.jsonl",
  "/gates/baseline.json",
  "/gates/registry_state.json",
  "/models.jsonl",
  "/models.jsonl.sigstore.json",
  "/LICENSE",
  "/NOTICE",
  "/README.md",
  "/pyproject.toml"
]

[tool.hatch.build.targets.sdist]
core-metadata-version = "2.4"

[tool.hatch.build.targets.wheel]
core-metadata-version = "2.4"

[tool.hatch.build.targets.wheel.force-include]
"eval/redteam/corpus/adversarial_phi.jsonl" = "openmed/eval/data/adversarial_phi.jsonl"

[tool.hatch.version]
path = "openmed/__about__.py"

[tool.hatch.publish.index]
disable = false

[tool.hatch.publish.index.repos]
pypi = { url = "https://upload.pypi.org/legacy/" }

[tool.pytest.ini_options]
markers = [
  "integration: marks end-to-end or external integration tests",
  "slow: marks tests that are expected to run slowly",
  "contract: marks property-based stage-boundary contract tests",
  "fuzz: marks property-based (Hypothesis) fuzz tests",
  "doctest_examples: runs doctest examples for targeted public modules"
]
python_files = [
  "test_*.py",
  "*_test.py",
]
testpaths = [
  "tests",
]

[tool.ruff]
target-version = "py310"
line-length = 88
extend-exclude = [
  "examples/notebooks",
  "openmed/service/proto/generated",
]

[tool.ruff.lint]
select = [
  "E9",
  "F63",
  "F7",
  "F82",
  "I",
]
fixable = ["I"]
unfixable = [
  "E9",
  "F63",
  "F7",
  "F82",
]

[tool.ruff.lint.isort]
known-first-party = ["openmed"]

[tool.ruff.format]
quote-style = "double"
indent-style = "space"
line-ending = "lf"

# Scoped type-checking configuration. This intentionally covers only the newer
# v1.6 public surfaces that already ship precise annotations and a py.typed
# marker; it is not a strict project-wide gate. The pinned development checker,
# local Make target, regression test, and CI lint job all use this same scope.
[tool.mypy]
python_version = "3.10"
files = [
  "openmed/core/audit.py",
  "openmed/core/pipeline.py",
  "openmed/clinical/context.py",
  "openmed/clinical/exporters/fhir/bundle.py",
]
ignore_missing_imports = true
follow_imports = "silent"
warn_unused_ignores = false