stack/pyproject.toml

[project]
name = "stack"
version = "0.1.0"
description = "Healthcare data platform — ACO analytics, CMS data, BCDA FHIR, PFS equations"
readme = "README.md"
requires-python = ">=3.12"
dependencies = [
    "pydantic>=2.0.0",
    # AGPL-3.0 — flag if shipping outside internal use. <2: pymupdf 2.x folds
    # in the former pymupdf_layout code (Polyform Noncommercial / Artifex
    # commercial) and pulls onnxruntime into every image — a licence call,
    # not a routine bump.
    "pymupdf>=1.27.2,<2",
    "python-docx>=1.1",
    "xlrd>=2.0.2",
]

[project.scripts]
stack = "cli:main"

[project.optional-dependencies]
conf = [
    "pydantic>=2.0.0",
    "httpx>=0.28.1",
    "duckdb>=1.5.4",
]
aco = [
    "stack[conf]",
    "narwhals>=2.17.0",
    "sqlglot>=26.0.0",
    "pyarrow>=23.0.1",
    "duckdb>=1.5.4",
]
api = [
    "stack[conf]",
    "fastapi>=0.139.0",
    "uvicorn>=0.41.0",
    "httpx>=0.28.1",
    "pyjwt>=2.15.1",
    "cryptography>=50.0.0",
]
bcda = [
    "stack[conf]",
    "httpx>=0.28.1",
    "fsspec>=2026.6.0",
    "narwhals>=2.17.0",
    "pyarrow>=23.0.1",
    "streamlit>=1.40",
    "polars>=1.0",
]
bib = [
    "stack[conf]",
    "pydantic>=2.0.0",
    "markdown-it-py>=4.0",
    "mdit-py-plugins>=0.4",
]
bls = []
llm = [
    "stack[conf]",
    "stack[bib]",
    "httpx>=0.28.1",
    "fastapi>=0.139.0",
    "uvicorn>=0.41.0",
    "langchain-core>=0.3.0",
    "langchain-ollama>=0.2.0",
    "langchain-postgres>=0.0.12",
    "psycopg[binary]>=3.2.0",
    "sqlalchemy>=2.0.0",
    "pyyaml>=6.0.0",  # dev/scripts/llm_golden.py (golden set YAML) runs inside the llm container
    "typer>=0.24.1",  # `stack llm index` runs inside the llm container (nightly comment pull)
]
ccw = [
    "pydantic>=2.0.0",
]
lead = [
    "stack[conf]",
    "narwhals>=2.17.0",
]
cli = [
    "stack[aco]",
    "stack[api]",
    "stack[bib]",
    "stack[llm]",
    "stack[mail]",
    "stack[nlm]",
    "typer>=0.24.1",
    "uvicorn>=0.41.0",
]
nlm = [
    "stack[conf]",
    "httpx>=0.28.1",
]
mail = [
    "httpx>=0.28.1",
    "pydo>=0.29.0",
    "resend>=2.0.0",
]
cms = [
    "narwhals>=2.17.0",
    "pydantic>=2.0.0",
]
opps = [
    "stack[conf]",
    "stack[rex]",
    "duckdb>=1.5.4",
    "narwhals>=2.17.0",
]
pfs = [
    "stack[conf]",
    "stack[rex]",
    "duckdb>=1.5.4",
    "narwhals>=2.17.0",
]
qpp = [
    "stack[conf]",
    "pydantic>=2.0.0",
]
rec = [
    "stack[conf]",
    "stack[pfs]",
    "duckdb>=1.5.4",
    "narwhals>=2.17.0",
    "typer>=0.24.1",
]
rex = [
    "stack[conf]",
    "narwhals>=2.17.0",
    "pyarrow>=23.0.1",
    "fsspec>=2026.6.0",
]
prisma = [
    "stack[conf]",
    "stack[bib]",
    "anthropic>=0.40.0",
    "httpx[socks]>=0.28.1",
    "pyyaml>=6.0.0",
    "pydo>=0.29.0",
    "pdfminer.six>=20221105",
    "resend>=2.0.0",
]
perf = [
    "stack[conf]",
    "opentelemetry-api>=1.45.1",
    "opentelemetry-sdk>=1.45.1",
    "opentelemetry-exporter-otlp-proto-grpc>=1.25.0",
    "opentelemetry-exporter-prometheus>=0.46b0",
    "opentelemetry-instrumentation-fastapi>=0.46b0",
    "opentelemetry-semantic-conventions>=0.46b0",
    "psutil>=5.9.0",
]
sem = [
    "coverage>=7.13.4",
]
lake = [
    "stack[aco]",
    "databricks-sdk>=0.85.0",
    "databricks-bundles>=0.295.0",
]
aws = [
    "boto3>=1.35.0",
    "s3fs>=2026.2.0",
]
gcp = [
    "google-cloud-storage>=2.18.0",
    "gcsfs>=2024.1.0",
]
azure = [
    "azure-storage-blob>=12.23.0",
    "adlfs>=2024.1.0",
]
# What notebooks/ reaches through src/. The notebooks container bind-mounts
# src/ and installs this extra (plus the base dependencies) — see
# infra/images/notebooks.Dockerfile — so a dependency a notebook-reachable
# module gains belongs in its own extra, and that extra belongs here.
notebooks = [
    "stack[conf]",
    "stack[aco]",
    "stack[bib]",
    "stack[cms]",
    "stack[nlm]",
    "stack[pfs]",
    # The image resolves without a lock, and every service shares the same
    # .duckdb files, so a new duckdb major must not land here first.
    "duckdb>=1.5.4,<2",
    "fsspec>=2026.6.0",  # bcda.store; the bcda extra itself drags in streamlit
    "openpyxl>=3.1.5",  # pfs.pipe reads CMS workbooks
    "fastexcel>=0.19.0",  # polars.read_excel's calamine engine
]
all = [
    "stack[aco]",
    "stack[api]",
    "stack[bcda]",
    "stack[bib]",
    "stack[bls]",
    "stack[ccw]",
    "stack[cli]",
    "stack[cms]",
    "stack[llm]",
    "stack[perf]",
    "stack[pfs]",
    "stack[qpp]",
    "stack[rec]",
    "stack[rex]",
    "stack[lake]",
    "stack[nlm]",
    "stack[lead]",
]

[dependency-groups]
dev = [
    "stack[all]",
    "coverage>=7.13.4",
    "dbt-core==1.12.6",
    "dbt-duckdb>=1.10,<1.11",
    "openpyxl>=3.1.5",
    "pdfplumber>=0.11.9",
    "polars>=1.38.1",
    "pytest>=9.0.2",
    "pytest-cov>=7.0.0",
    "pytest-xdist>=3.5.0",
    "marimo>=0.23.13",
    "ruff>=0.11.0",
    "altair>=6.0.0",
    "pandas>=3.0.1",
    "obstore>=0.9.2",
    "s3fs>=2026.2.0",
    "jinja2>=3.1.0",
    "fastexcel>=0.19.0",
]

[build-system]
requires = ["uv_build>=0.7,<1"]
build-backend = "uv_build"

[tool.ruff]
line-length = 88

[tool.ruff.lint]
select = ["E", "F", "I"]
ignore = ["E501", "E741"]

[tool.pytest.ini_options]
testpaths = ["tests"]
markers = [
    "stub: marks tests that report stub vs implemented status (deselect with '-m \"not stub\"')",
    "live: marks tests that need a live DuckDB replica on disk (skipped without one)",
]
filterwarnings = [
    "error::ResourceWarning",
    "ignore::ResourceWarning:coverage.*",
]

[tool.coverage.run]
# Required for reliable pytest-cov + pytest-xdist combining: each worker
# writes .coverage.<host>.<pid>, then pytest-cov auto-combines at exit.
# Without this, parallel test runs randomly drop coverage data.
parallel = true
source = ["src"]
concurrency = ["multiprocessing", "thread"]

[tool.uv]
# Supply-chain cooldown: resolve only releases at least a week old, so a
# hijacked or yanked-within-days upload never lands in the lock. Renovate's
# minimumReleaseAge matches. Exempt one package with
# `exclude-newer-package` when a CVE fix can't wait. Lives here, not in a
# uv.toml: images copy only pyproject.toml + uv.lock, and the lock records
# the span, so `uv sync --locked` fails wherever the setting isn't visible.
exclude-newer = "7 days"
# streamlit 1.66.1 (2026-10-21) is the first to allow pillow 13; 1.66.0
# caps pillow <13, and pillow 12.x carries 41 advisories (5 critical)
# fixed only in 13.0. Exempted from the cooldown for that CVE fix.
exclude-newer-package = { streamlit = "2026-10-22T00:00:00Z" }
# Never resolve back below the CVE fix, whatever pulls pillow in.
constraint-dependencies = ["pillow>=13.0.0"]
# Prevents broken .venv symlinks when uv runs under different users.
link-mode = "copy"
python-preference = "managed"

[tool.uv.build-backend]
module-name = ["aco", "api", "bcda", "bib", "bls", "ccw", "cli", "cms", "conf", "lead", "llm", "mail", "nlm", "opps", "perf", "pfs", "prisma", "qpp", "rec", "rex", "sem"]
namespace = true
source-exclude = ["compose.yml","infra/**","data/**","notebooks/**","tuva/**","assets/**","docs/**","dev/**","bundle/**","cloud/**"]