611a1d69c3
aiohttp 3.14.1→3.14.3 (CVE-2026-69244 client C-parser OOB heap read — the reachable one, client-only usage via s3fs/gcsfs/aiobotocore; CVE-2026-59881/-69243 are server-side WS paths, no aiohttp server here) pyasn1 0.6.3→0.6.4 (CVE-2026-59884/-59885/-59886 quadratic-decode DoS — no direct untrusted ASN.1 decoding; transitive via google-auth/rsa) cryptography 49.0.0→50.0.0 (CVE-2026-69247 PKCS7 decrypt padding oracle — no EnvelopedData decryption paths; direct dep, pyproject floor raised) Per-issue exploitability rationale in tracker issues #581-#587. Full suite green with bumped packages installed: 14023 passed (serial proof run 26m45s at ecc3bae-era tree; parallel hook run 13m58s). pkg-manifest regenerated.
218 lines
4.4 KiB
TOML
218 lines
4.4 KiB
TOML
[project]
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name = "stack"
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version = "0.1.0"
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description = "Healthcare data platform — ACO analytics, CMS data, BCDA FHIR, PFS equations"
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readme = "README.md"
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requires-python = ">=3.12"
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dependencies = [
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"pydantic>=2.0.0",
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"pymupdf>=1.24", # AGPL-3.0 — flag if shipping outside internal use
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"python-docx>=1.1",
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"xlrd>=2.0.2",
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]
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[project.scripts]
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stack = "cli:main"
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[project.optional-dependencies]
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conf = [
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"pydantic>=2.0.0",
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"httpx>=0.28.1",
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"duckdb>=1.0.0",
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]
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aco = [
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"stack[conf]",
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"narwhals>=2.17.0",
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"sqlglot>=26.0.0",
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"pyarrow>=23.0.1",
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"duckdb>=1.0.0",
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]
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api = [
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"stack[conf]",
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"fastapi>=0.139.0",
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"uvicorn>=0.41.0",
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"httpx>=0.28.1",
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"pyjwt>=2.13.0",
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"cryptography>=50.0.0",
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]
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bcda = [
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"stack[conf]",
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"httpx>=0.28.1",
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"fsspec>=2024.1.0",
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"narwhals>=2.17.0",
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"pyarrow>=23.0.1",
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]
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bib = [
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"stack[conf]",
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"pydantic>=2.0.0",
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"markdown-it-py>=4.0",
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"mdit-py-plugins>=0.4",
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]
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bls = []
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llm = [
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"stack[conf]",
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"stack[bib]",
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"httpx>=0.28.1",
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"fastapi>=0.139.0",
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"uvicorn>=0.41.0",
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"langchain-core>=0.3.0",
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"langchain-ollama>=0.2.0",
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"langchain-postgres>=0.0.12",
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"psycopg[binary]>=3.2.0",
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"sqlalchemy>=2.0.0",
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]
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ccw = [
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"pydantic>=2.0.0",
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]
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cli = [
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"stack[aco]",
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"stack[api]",
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"stack[bib]",
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"stack[llm]",
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"stack[mail]",
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"typer>=0.24.1",
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"uvicorn>=0.41.0",
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]
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mail = [
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"httpx>=0.28.1",
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"pydo>=0.29.0",
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"resend>=2.0.0",
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]
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cms = [
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"narwhals>=2.17.0",
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"pydantic>=2.0.0",
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]
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opps = [
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"stack[conf]",
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"stack[rex]",
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"duckdb>=1.0.0",
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"narwhals>=2.17.0",
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]
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pfs = [
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"stack[conf]",
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"stack[rex]",
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"duckdb>=1.0.0",
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"narwhals>=2.17.0",
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]
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rec = [
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"stack[conf]",
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"stack[pfs]",
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"duckdb>=1.0.0",
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"narwhals>=2.17.0",
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"typer>=0.24.1",
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]
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rex = [
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"stack[conf]",
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"narwhals>=2.17.0",
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"pyarrow>=23.0.1",
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"fsspec>=2024.1.0",
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]
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prisma = [
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"stack[conf]",
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"stack[bib]",
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"anthropic>=0.40.0",
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"httpx[socks]>=0.28.1",
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"pyyaml>=6.0.0",
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"pydo>=0.29.0",
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"pdfminer.six>=20221105",
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"resend>=2.0.0",
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]
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perf = [
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"stack[conf]",
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"opentelemetry-api>=1.25.0",
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"opentelemetry-sdk>=1.25.0",
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"opentelemetry-exporter-otlp-proto-grpc>=1.25.0",
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"opentelemetry-exporter-prometheus>=0.46b0",
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"opentelemetry-instrumentation-fastapi>=0.46b0",
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"opentelemetry-semantic-conventions>=0.46b0",
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"psutil>=5.9.0",
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]
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sem = [
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"coverage>=7.13.4",
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]
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lake = [
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"stack[aco]",
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"databricks-sdk>=0.85.0",
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"databricks-bundles>=0.295.0",
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]
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aws = [
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"boto3>=1.35.0",
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"s3fs>=2026.2.0",
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]
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gcp = [
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"google-cloud-storage>=2.18.0",
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"gcsfs>=2024.1.0",
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]
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azure = [
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"azure-storage-blob>=12.23.0",
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"adlfs>=2024.1.0",
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]
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all = [
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"stack[aco]",
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"stack[api]",
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"stack[bcda]",
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"stack[bib]",
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"stack[bls]",
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"stack[ccw]",
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"stack[cli]",
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"stack[cms]",
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"stack[llm]",
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"stack[perf]",
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"stack[pfs]",
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"stack[rec]",
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"stack[rex]",
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"stack[lake]",
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]
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[dependency-groups]
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dev = [
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"stack[all]",
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"coverage>=7.13.4",
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"dbt-core==1.10.15",
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"dbt-duckdb>=1.10,<1.11",
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"openpyxl>=3.1.5",
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"pdfplumber>=0.11.9",
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"polars>=1.38.1",
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"pytest>=9.0.2",
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"pytest-cov>=7.0.0",
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"pytest-xdist>=3.5.0",
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"marimo>=0.23.13",
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"ruff>=0.11.0",
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"altair>=6.0.0",
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"pandas>=3.0.1",
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"obstore>=0.9.2",
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"s3fs>=2026.2.0",
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"jinja2>=3.1.0",
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"fastexcel>=0.19.0",
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]
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[build-system]
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requires = ["uv_build>=0.7,<1"]
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build-backend = "uv_build"
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[tool.ruff]
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line-length = 88
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[tool.ruff.lint]
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select = ["E", "F", "I"]
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ignore = ["E501", "E741"]
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[tool.pytest.ini_options]
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testpaths = ["tests"]
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markers = [
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"stub: marks tests that report stub vs implemented status (deselect with '-m \"not stub\"')",
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]
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[tool.coverage.run]
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# Required for reliable pytest-cov + pytest-xdist combining: each worker
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# writes .coverage.<host>.<pid>, then pytest-cov auto-combines at exit.
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# Without this, parallel test runs randomly drop coverage data.
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parallel = true
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source = ["src"]
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concurrency = ["multiprocessing", "thread"]
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[tool.uv.build-backend]
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module-name = ["aco", "api", "bcda", "bib", "bls", "ccw", "cli", "cms", "conf", "llm", "mail", "opps", "perf", "pfs", "prisma", "rec", "rex", "sem"]
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namespace = true
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source-exclude = ["compose.yml","infra/**","data/**","notebooks/**","tuva/**","assets/**","docs/**","dev/**","bundle/**","cloud/**"]
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