[build-system]

requires = ["hatchling"]

build-backend = "hatchling.build"

[project]

name = "hypermnesia-mcp"

version = "4.23.5"

description = "Scientifically-grounded memory system based on computational neuroscience research"

readme = "README.md"

license = "MIT"

requires-python = ">=3.10"

authors = [

{ name = "Clement Deust", email = "admin@ai-architect.tools" },

]

keywords = ["mcp", "codex", "gemini-cli", "claude-code", "memory", "cognitive-profiling"]

classifiers = [

"Development Status :: 4 - Beta",

"Intended Audience :: Developers",

"License :: OSI Approved :: MIT License",

"Programming Language :: Python :: 3",

"Topic :: Software Development :: Libraries",

]

dependencies = [

# source: ADR-1092

# macOS Intel wheels stop at cryptography 48.

# uvx resolves published metadata without the lock-shaping platform group.

"cryptography<49 ; sys_platform == 'darwin' and platform_machine == 'x86_64'",

# source: ADR-0874

#

#

#

#

#

#

#

#

#

"mcp>=2.0.0",

"anyio>=4.5",

"pydantic>=2.0.0",

"pydantic-settings>=2.0.0",

"numpy>=1.24.0",

# source: ADR-0874

#

#

#

#

#

#

#

"sentence-transformers>=3.0.0",

"flashrank>=0.2.0",

# source: ADR-0874

#

#

#

#

#

#

#

#

"python-dateutil>=2.8.2",

]

[project.urls]

Homepage = "https://github.com/cdeust/Cortex"

Repository = "https://github.com/cdeust/Cortex"

[project.scripts]

# source: ADR-0874

#

#

#

#

#

#

#

#

#

#

#

cortex-doctor = "mcp_server.doctor:run"

hypermnesia-mcp = "mcp_server.__main__:main"

# source: CHANGELOG.md Unreleased, ADR number 0874 uses this same interim

# form for the two scripts above until the console-entry-point ADR lands

hypermnesia-mcp-hook = "mcp_server.hooks.entry:main"

[project.optional-dependencies]

postgresql = [

"psycopg[binary]>=3.1",

"psycopg-pool>=3.2",

# source: ADR-0874

#

#

"pgvector>=0.4,<0.6",

]

sqlite = [

"sqlite-vec>=0.1.1",

]

codebase = [

"tree-sitter>=0.24.0,<0.27",

# source: ADR-0874

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

"tree-sitter-language-pack>=1.12.5,<1.22",

"networkx>=3.0",

# source: ADR-0874

#

#

"leidenalg>=0.10",

"igraph>=0.11",

]

# Optional CPU graph visualization endpoints: tiles, quadtree hit-testing, and layout recomputation.

# source: ADR-0874

viz-tile = [

"igraph>=0.11", # CPU layout (DrL / FR), MIT-licensed wheels

"datashader>=0.16.3", # tile rasterization, O(viewport pixels)

"pyarrow>=15.0", # Arrow IPC for the quadtree endpoint

"pandas>=2.2", # Datashader's native frame format

"cachetools>=5.0", # L1 in-memory tile LRU

"Pillow>=10.0", # PNG encode

]

benchmarks = [

"datasets>=2.14.0", # HuggingFace dataset loader (BEAM, LoCoMo, LongMemEval)

"sentence-transformers>=3.0.0", # all-MiniLM-L6-v2 embeddings

"flashrank>=0.2.0", # cross-encoder reranking (ms-marco-MiniLM-L-12-v2)

"psycopg[binary]>=3.1", # PostgreSQL driver

"psycopg-pool>=3.2", # pg_store.py imports ConnectionPool at module level

"pgvector>=0.4,<0.6", # vector similarity in PostgreSQL (bounds: see [postgresql])

"pymupdf>=1.24.0", # PDF parsing for some benchmark sources

]

# source: ADR-0874

#

#

#

#

#

otel = [

"opentelemetry-sdk>=1.24.0",

"opentelemetry-exporter-otlp-proto-http>=1.24.0",

]

dev = [

"pytest>=8.0.0",

"pytest-cov>=5.0.0",

"pytest-asyncio>=0.23.0",

# source: ADR-0874

#

#

#

#

"pytest-timeout>=2.3.0",

"sentence-transformers>=3.0.0",

"networkx>=3.0",

# source: ADR-0874

#

#

#

#

#

#

#

#

"exceptiongroup>=1.2.0",

]

[tool.hatch.build.targets.wheel]

packages = ["mcp_server"]

# source: ADR-0874

#

#

[tool.hatch.build.targets.sdist]

exclude = [

"/benchmarks/beam/variance/*.txt",

"/video/captures",

"/video/output",

"/docs/**/*.png",

"/docs/arxiv-*/**",

"/docs/campaigns/*.json",

]

# ── Resolver constraints ─────────────────────────────────────────────────

# source: ADR-0874

#

#

#

# source: ADR-0874

#

#

#

#

#

#

#

#

#

# source: ADR-0874

#

#

#

#

#

#

#

[tool.uv]

constraint-dependencies = [

"onnxruntime<1.24 ; python_full_version < '3.11'",

]

# source: ADR-0874

# source: ADR-0874

#

#

#

#

#

#

#

#

#

#

#

#

# source: ADR-0874

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

override-dependencies = [

"mpmath>=1.4.1,<1.5",

]

# ── CPU-only torch, resolved through the lock ────────────────────────────

# source: ADR-0874

#

#

#

#

# source: ADR-0874

#

#

#

# source: ADR-0874

#

#

#

#

#

#

# Use this explicit index only for packages mapped to it below.

# source: ADR-0874

# source: ADR-0874

#

#

#

#

#

#

[[tool.uv.index]]

name = "pytorch-cpu"

url = "https://download.pytorch.org/whl/cpu"

explicit = true

[tool.uv.sources]

torch = [{ index = "pytorch-cpu", marker = "sys_platform == 'linux'" }]

[tool.ruff]

# source: ADR-0874

#

#

#

extend-exclude = [".claude"]

[tool.ruff.lint]

# source: ADR-0874

#

#

#

select = [

"E4", # pycodestyle: import placement

"E7", # pycodestyle: statement/comparison errors

"E9", # pycodestyle: syntax/io errors

"F", # pyflakes

# source: ADR-0874

#

#

#

#

#

"S110",

# source: ADR-0874

#

#

#

#

#

#

"BLE001",

# source: ADR-0874

#

#

#

#

#

#

#

#

"PLR2004",

# source: ADR-0874

#

#

#

#

#

#

"E501",

# source: ADR-0874

#

#

#

#

#

#

#

#

#

#

"PLC0415",

# source: ADR-0874

#

#

#

#

#

#

"S608",

# source: ADR-0874

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

"B",

# source: ADR-0874

#

#

#

#

#

#

#

#

#

"RET",

# source: ADR-0874

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

"DTZ",

# source: ADR-0874

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

"N",

# source: ADR-0874

#

#

#

#

#

#

#

#

#

#

#

"ERA",

]

# source: ADR-0874

#

#

#

#

# source: ADR-0874

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

# source: ADR-0874

#

#

#

#

#

# source: ADR-0874

#

#

#

#

#

#

#

[tool.ruff.lint.per-file-ignores]

# source: ADR-0874

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

"tests_py/**" = ["S110", "BLE001", "PLR2004", "PLC0415", "S608"]

[tool.pytest.ini_options]

testpaths = ["tests_py"]

pythonpath = ["."]

# source: ADR-0874

#

#

#

timeout = 300

timeout_method = "thread"

# source: ADR-0874

#

#

#

#

#

#

required_plugins = ["pytest-timeout", "pytest-asyncio"]

# Narrow, message-anchored suppression of three DeprecationWarnings emitted by

# a SWIG-generated extension during import — never by mcp_server.

# source: ADR-0874

#

#

#

#

#

#

# source: ADR-0874

#

#

#

#

#

#

#

#

#

# source: ADR-0874

#

#

#

#

# Remove when: `sentencepiece` (or whichever SWIG-built package is installed)

# ships wheels built with SWIG >= 4.4.0 — verify with a full-suite run

# reporting 0 warnings after deleting this entry.

filterwarnings = [

"ignore:builtin type (SwigPyObject|SwigPyPacked|swigvarlink) has no __module__ attribute:DeprecationWarning",

# source: ADR-0874

#

#

#

#

#

#

#

#

"error:The default datetime adapter is deprecated as of Python 3.12.*:DeprecationWarning",

]

markers = [

"invariants: Phase 0.3+ testable invariant predicates (I1/I2/I3/I4 and parity tests)",

]

[tool.coverage.run]

source = ["mcp_server"]

[tool.coverage.report]

show_missing = true

[dependency-groups]

dev = [

"mutmut>=3.6.0",

]

# source: ADR-0874

#

#

# source: ADR-0874

# source: ADR-0874

#

#

#

lint = [

"ruff==0.16.10",

]

typecheck = [

"pyright==1.1.414",

]

packaging = [

"build>=1.2.0",

# source: ADR-0874

#

#

#

#

#

"hatchling>=1.24",

]

# source: ADR-0874

#

#

#

#

#

#

# source: ADR-0874

#

#

#

#

container = [

"torch",

]

# source: ADR-0874

#

#

#

# source: ADR-0874

#

#

#

#

#

#

#

#

fuzz = [

"atheris>=3.1.0; python_version >= '3.12' and sys_platform == 'linux' and platform_machine == 'x86_64'",

]

# What scripts/launcher.py installs lazily: the base set on every entry

# point, the ML set at SessionStart. Versions come from uv.lock only.

# source: ADR-1092

launcher-base = [

"mcp",

"pydantic",

"pydantic-settings",

"numpy",

"psycopg[binary]",

"psycopg-pool",

"pgvector",

"sqlite-vec",

]

launcher-ml = [

"sentence-transformers",

"flashrank",

"torch",

]

# Which torch / onnxruntime / numpy / transformers / cryptography each platform

# resolves to. uv keeps ONE version across platforms unless the specifiers of

# disjoint markers cannot overlap, so every bound below is paired with the

# opposite bound for the rest: otherwise the lock collapses to the oldest

# version everywhere on the next `uv lock --upgrade-package`. Not installed by

# any entry point; it only shapes the lock.

# - Intel macOS: PyTorch stops at 2.2.2 (CPython <= 3.12), built against the

# numpy 1 ABI, below transformers 5 (needs torch >= 2.4); onnxruntime stops

# at 1.23.2 and cryptography at 48 (no x86_64 wheel from 49).

# - Apple Silicon before macOS 14 (Darwin < 23): torch >= 2.12 and

# onnxruntime >= 1.24 publish macosx_14_0_arm64 wheels only. Its torch range

# must not overlap Intel's, or uv would give both the one version 2.2.2.

# - macOS 12 and older (Darwin < 22): onnxruntime 1.19.2 is the last release

# with macosx_11_0 wheels (cp310 to cp312), on either architecture.

# source: ADR-1092

platform-bounds = [

"torch==2.2.2 ; sys_platform == 'darwin' and platform_machine == 'x86_64' and python_full_version < '3.13'",

"torch>=2.4,<2.12 ; sys_platform == 'darwin' and platform_machine == 'arm64' and platform_release < '23'",

"torch>=2.12 ; sys_platform != 'darwin' or (platform_machine == 'arm64' and platform_release >= '23') or (platform_machine == 'x86_64' and python_full_version >= '3.13')",

"onnxruntime<1.20 ; sys_platform == 'darwin' and platform_release < '22'",

"onnxruntime>=1.20,<1.24 ; sys_platform == 'darwin' and platform_machine == 'x86_64' and platform_release >= '22'",

"onnxruntime>=1.20,<1.24 ; sys_platform == 'darwin' and platform_machine == 'arm64' and platform_release >= '22' and platform_release < '23'",

"onnxruntime>=1.24 ; python_full_version >= '3.11' and (sys_platform != 'darwin' or (platform_machine == 'arm64' and platform_release >= '23'))",

"numpy<2 ; sys_platform == 'darwin' and platform_machine == 'x86_64' and python_full_version < '3.13'",

"numpy>=2 ; sys_platform != 'darwin' or platform_machine != 'x86_64' or python_full_version >= '3.13'",

"transformers<5 ; sys_platform == 'darwin' and platform_machine == 'x86_64' and python_full_version < '3.13'",

"transformers>=5 ; sys_platform != 'darwin' or platform_machine != 'x86_64' or python_full_version >= '3.13'",

"cryptography<49 ; sys_platform == 'darwin' and platform_machine == 'x86_64'",

"cryptography>=49 ; sys_platform != 'darwin' or platform_machine != 'x86_64'",

]

[tool.mutmut]

# source: ADR-0874

#

#

#

#

# source: ADR-0874

#

#

#

#

#

#

#

#

source_paths = ["mcp_server"]

only_mutate = ["mcp_server/shared/json_native.py"]

# source: ADR-0874

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

#

also_copy = [

".github",

"tests_py",

"deps",

"docs",

"assets",

"scripts",

"README.md",

"CONTRIBUTING.md",

"SECURITY.md",

"CLAUDE.md",

"GOVERNANCE.md",

"manifest.json",

"server.json",

"package.json",

".bestpractices.json",

"uv.lock",

"requirements",

"pyproject.toml",

]

pytest_add_cli_args_test_selection = ["tests_py/shared/test_json_native.py"]

use_setproctitle = false