pyproject.toml

[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "pyrite"
version = "0.25.5"
description = "Knowledge-as-Code for you and your agents"
readme = "README.md"
license = {text = "MIT"}
requires-python = ">=3.11"
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Developers",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Topic :: Scientific/Engineering :: Information Analysis",
]
keywords = ["knowledge-base", "knowledge-management", "mcp", "ai", "knowledge-graph", "agent-memory", "zettelkasten"]

dependencies = [
    "pydantic>=2.11.0",
    "python-dotenv>=1.0.1",
    "PyYAML>=6.0.1",
    "ruamel.yaml>=0.18.0",
    "SQLAlchemy>=2.0.0",
    # pyrite/server/mcp_server.py's build_sdk_server() uses the mcp SDK's
    # 1.x low-level Server API (e.g. Server.list_tools() as a decorator),
    # which the SDK's 2.0.0 release removed/renamed. An unbounded install
    # picks up 2.0.0 and every MCP request 500s with
    # AttributeError: 'Server' object has no attribute 'list_tools'.
    #
    # The floor is 1.3.0, not 1.0.0: build_sdk_server()'s read_resource
    # adapter (#217) imports mcp.server.lowlevel.helper_types.ReadResourceContents
    # and returns an Iterable of it, which is the shape
    # Server.read_resource()'s decorator has expected since 1.3.0 (verified
    # against PyPI's published wheels for 1.0.0 through 1.3.0rc1 -- the
    # module and the class do not exist before 1.3.0rc1). An install pinned
    # below that has no such module to import and resources/read fails at
    # import time instead of at the call.
    "mcp>=1.27.2,<2.0.0",  # 1.27.2: SSE same-owner check (mcp_routes._session_owner)
]

[project.optional-dependencies]
server = [
    # 0.132.0: strict_content_type (default on) -- a body without a JSON
    # Content-Type is not parsed as JSON for a handler.
    "fastapi>=0.132.0",
    "uvicorn[standard]>=0.30.1",
    "slowapi>=0.1.9",
    # Used directly by pyrite/server/auth_rate_limit.py (slowapi depends on it too).
    "limits>=3.1",
    "httpx>=0.27.0",
    "jinja2>=3.1.4",
    "watchdog>=4.0.1",
    "alembic>=1.13.0",
    "markdownify>=0.14.1",
    "bcrypt>=4.0.0",
]
cli = [
    "typer[all]>=0.12.3",
    "rich>=13.7.1",
]
ai = [
    "openai>=1.30.0",
    "anthropic>=0.30.0",
]
semantic = [
    "sentence-transformers>=2.3.0",  # trust_remote_code (embedding_service._load_model)
    "sqlite-vec>=0.1.0",
]
postgres = [
    "psycopg2-binary>=2.9.0",
    "pgvector>=0.3.0",
]
dev = [
    # Pinned exactly (#128): CI resolved pytest 9.1.1 on 3.12 and 9.0.2 on
    # 3.13 from an unbounded `>=8.0.0` -- every worktree venv got 9.1.1, the
    # main checkout 9.0.2. #81's `@classmethod` fixtures passed the
    # one-interpreter PR gate under whichever version resolved there and
    # broke `dev` twice on 3.13 (fixed in #129). All three are pure-Python
    # wheels with no interpreter-specific build, so one version installs
    # identically on 3.11/3.12/3.13; `tests/test_dev_process_config.py`
    # (TestPinnedTestRunner) asserts the pin stays exact.
    "pytest==9.1.1",
    "pytest-cov==7.1.0",
    "pytest-xdist==3.8.0",
    # Diff coverage on the PR's 3.12 leg (advisory; see ci.yml's test job).
    "diff-cover==10.6.0",
    # Pinned exactly: tests/test_storage_invariants.py runs derandomized, and
    # its strict xfails depend on the sequences this version generates.
    "hypothesis==6.168.1",
    "mypy>=1.9.0",
    "ruff>=0.15.0,<0.16",
    "build>=1.0.0",
    "pre-commit>=3.6.0",
]
all = [
    "pyrite[server,cli,ai,semantic,dev]",
]

[project.scripts]
pyrite = "pyrite.cli:main"
pyrite-read = "pyrite.read_cli:main"
pyrite-admin = "pyrite.admin_cli:main"
pyrite-server = "pyrite.server.api:main"

[project.urls]
Homepage = "https://github.com/pyrite-wiki/pyrite"
Documentation = "https://github.com/pyrite-wiki/pyrite#readme"
Repository = "https://github.com/pyrite-wiki/pyrite"

[tool.setuptools.packages.find]
where = ["."]
include = ["pyrite", "pyrite.*"]

[tool.pytest.ini_options]
testpaths = ["tests", "extensions"]
python_files = ["test_*.py"]
addopts = "-v --tb=short -m 'not slow and not e2e'"
markers = [
    "integration: tests requiring full environment setup (DB, indexing, network)",
    "api: REST API endpoint tests",
    "mcp: MCP server protocol tests",
    "cli: CLI command tests",
    "slow: long-running performance tests (1000+ entries)",
    # Smoke layer (ADR-0032 §3a "breadth"): starts a real `pyrite-server`
    # subprocess or a real `pyrite mcp` stdio process and drives it as a
    # client. Minutes, not seconds -- excluded from the default run (and so
    # from the pre-push hook and the PR matrix) and gated on the push to dev
    # in CI. Run it deliberately with `pytest tests/e2e -m e2e`.
    "e2e: live-process smoke tests (real server subprocess, real client)",
    "embeddings: needs write-time embedding on (loads the sentence-transformers model)",
    # The local smoke set scripts/test-affected always runs (#356): storage,
    # the KB service, read scoping, the REST app factory, MCP dispatch and the
    # CLI entry point. Keep it under a minute at -n 4.
    "core: always run by scripts/test-affected, whatever the branch changed",
    # verify-red (scripts/verify_red_ci.py): a test the PR adds on purpose to
    # pass without the fix too (a "still works" guard), so it is not warned about.
    # It must say why: reason=... or the test's docstring; a bare marker is rejected.
    "control(reason): a deliberate negative control; verify-red expects it to pass without the fix",
]

[tool.mypy]
python_version = "3.11"
warn_return_any = true
warn_unused_configs = true
ignore_missing_imports = true

# ci-make-green-and-load-bearing item 6: ratchet mypy strict on the storage
# layer specifically -- 280-error field-bug history samples concentrate
# there (dual-registry drift, silent index desync). Not repo-wide --scope
# is deliberately narrow so this is achievable incrementally.
#
# Baseline as of 2026-07-03 (`mypy pyrite/storage/ --ignore-missing-imports
# --follow-imports=silent --disallow-untyped-defs`): 281 errors in 15
# files. This override does NOT fail CI yet -- mypy stays
# continue-on-error in ci.yml until the count is burned down (tracked in
# mypy-strict-ratchet-burn-down-storage-layer-errors). Turning this on
# is step 1: enforce no NEW untyped defs in storage/ going forward,
# without yet requiring the existing 281 to be fixed.
[[tool.mypy.overrides]]
module = "pyrite.storage.*"
disallow_untyped_defs = true

# ci-make-green-and-load-bearing item 5: ratchet coverage instead of just
# measuring it. Baseline as of 2026-07-04 (full suite, disk-space-healthy
# run): 71% (`pytest --cov=pyrite --cov-report=term`, 3952 passed). Set a
# few points below to tolerate normal fluctuation while still catching a
# real regression; ratchet up over time rather than setting it at the
# ceiling immediately.
[tool.coverage.report]
fail_under = 68

[tool.ruff]
line-length = 100
target-version = "py311"

[tool.ruff.lint]
# PT (flake8-pytest-style, #128) is enabled here in `select` but effectively
# scoped to tests/: ruff has no per-file *select*, only per-file *ignore*, so
# it is turned back off for every non-test path below. It is also a no-op in
# practice for the rest of the repo -- no pyrite/, extensions/*/pyrite_*/ or
# scripts/ file uses a pytest construct (fixture/parametrize/raises) that PT
# matches -- but the per-file-ignore makes "PT applies to tests/ only" true
# by construction, not by accident of what the code happens to contain.
select = ["E", "F", "W", "I", "N", "UP", "B", "C4", "PT"]
ignore = [
    "E501",  # Line too long (handled by formatter)
    "B008",  # Function call in argument defaults (standard Typer pattern)
    "B904",  # raise-without-from in except (typer.Exit doesn't chain)
    "E741",  # Ambiguous variable name (l for link is clear in context)
    "N802",  # Function name should be lowercase (do_GET is HTTP convention)
]

[tool.ruff.lint.per-file-ignores]
# Test files: unused imports (fixtures, side effects), unused assignments,
# import order, and module-level imports not at top (importorskip pattern).
# Four PT (#128) rules ignored here, each judgment-required rather than
# mechanical (14 mechanical PT001/PT006/PT022 findings were fixed instead,
# not ignored):
#   PT011 -- pytest.raises(ValueError) needs a match= chosen per call site
#   PT012 -- raises-block-is-one-statement needs restructuring per call site
#   PT018 -- splitting a compound assert changes its failure message; needs
#            a human picking the message, not a mechanical split
#   PT019 -- converting `_fixture` params to @pytest.mark.usefixtures touches
#            every call site's signature; no autofix exists even unsafely
"tests/*" = ["F401", "F841", "E402", "I001", "PT011", "PT012", "PT018", "PT019"]
# PT is pytest-only style; turn it off everywhere that isn't a test file.
"!tests/**" = ["PT"]