Cognee mcp docker fix (#1195)
<!-- .github/pull_request_template.md --> ## Description Resolve issues with Cognee MCP docker use ## DCO Affirmation I affirm that all code in every commit of this pull request conforms to the terms of the Topoteretes Developer Certificate of Origin.
This commit is contained in:
Igor Ilic
GitHub
parent
c686e396f3
commit
f4a37edc3f
5 changed files with 47 additions and 131 deletions
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@ -51,7 +51,7 @@ RUN apt-get update && apt-get install -y \
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WORKDIR /app
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COPY --from=uv /root/.local /root/.local
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COPY --from=uv /usr/local /usr/local
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COPY --from=uv /app /app
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RUN chmod +x /app/entrypoint.sh
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@ -48,27 +48,27 @@ if [ "$ENVIRONMENT" = "dev" ] || [ "$ENVIRONMENT" = "local" ]; then
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if [ "$DEBUG" = "true" ]; then
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echo "Waiting for the debugger to attach..."
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if [ "$TRANSPORT_MODE" = "sse" ]; then
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exec python -m debugpy --wait-for-client --listen 0.0.0.0:$DEBUG_PORT -m cognee --transport sse
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exec python -m debugpy --wait-for-client --listen 0.0.0.0:$DEBUG_PORT -m cognee --transport sse --no-migration
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elif [ "$TRANSPORT_MODE" = "http" ]; then
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exec python -m debugpy --wait-for-client --listen 0.0.0.0:$DEBUG_PORT -m cognee --transport http --host 0.0.0.0 --port $HTTP_PORT
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exec python -m debugpy --wait-for-client --listen 0.0.0.0:$DEBUG_PORT -m cognee --transport http --host 0.0.0.0 --port $HTTP_PORT --no-migration
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else
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exec python -m debugpy --wait-for-client --listen 0.0.0.0:$DEBUG_PORT -m cognee --transport stdio
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exec python -m debugpy --wait-for-client --listen 0.0.0.0:$DEBUG_PORT -m cognee --transport stdio --no-migration
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fi
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else
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if [ "$TRANSPORT_MODE" = "sse" ]; then
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exec cognee --transport sse
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exec cognee --transport sse --no-migration
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elif [ "$TRANSPORT_MODE" = "http" ]; then
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exec cognee --transport http --host 0.0.0.0 --port $HTTP_PORT
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exec cognee --transport http --host 0.0.0.0 --port $HTTP_PORT --no-migration
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else
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exec cognee --transport stdio
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exec cognee --transport stdio --no-migration
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fi
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fi
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else
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if [ "$TRANSPORT_MODE" = "sse" ]; then
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exec cognee --transport sse
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exec cognee --transport sse --no-migration
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elif [ "$TRANSPORT_MODE" = "http" ]; then
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exec cognee --transport http --host 0.0.0.0 --port $HTTP_PORT
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exec cognee --transport http --host 0.0.0.0 --port $HTTP_PORT --no-migration
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else
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exec cognee --transport stdio
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exec cognee --transport stdio --no-migration
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fi
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fi
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@ -8,7 +8,7 @@ requires-python = ">=3.10"
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dependencies = [
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# For local cognee repo usage remove comment bellow and add absolute path to cognee. Then run `uv sync --reinstall` in the mcp folder on local cognee changes.
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# "cognee[postgres,codegraph,gemini,huggingface,docs,neo4j] @ file:/Users/vasilije/Projects/tiktok/cognee",
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"cognee[postgres,codegraph,gemini,huggingface,docs,neo4j]>=0.2.0,<1.0.0",
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"cognee[postgres,codegraph,gemini,huggingface,docs,neo4j]==0.2.1",
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"fastmcp>=2.10.0,<3.0.0",
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"mcp>=1.12.0,<2.0.0",
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"uv>=0.6.3,<1.0.0",
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@ -938,30 +938,38 @@ async def main():
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help="Log level for the HTTP server (default: info)",
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)
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args = parser.parse_args()
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# Run Alembic migrations from the main cognee directory where alembic.ini is located
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print("Running database migrations...")
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migration_result = subprocess.run(
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["python", "-m", "alembic", "upgrade", "head"],
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capture_output=True,
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text=True,
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cwd=Path(__file__).resolve().parent.parent.parent,
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parser.add_argument(
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"--no-migration",
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default=False,
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action="store_true",
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help="Argument stops database migration from being attempted",
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)
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if migration_result.returncode != 0:
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migration_output = migration_result.stderr + migration_result.stdout
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# Check for the expected UserAlreadyExists error (which is not critical)
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if (
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"UserAlreadyExists" in migration_output
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or "User default_user@example.com already exists" in migration_output
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):
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print("Warning: Default user already exists, continuing startup...")
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else:
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print(f"Migration failed with unexpected error: {migration_output}")
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sys.exit(1)
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args = parser.parse_args()
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print("Database migrations done.")
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if not args.no_migration:
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# Run Alembic migrations from the main cognee directory where alembic.ini is located
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logger.info("Running database migrations...")
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migration_result = subprocess.run(
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["python", "-m", "alembic", "upgrade", "head"],
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capture_output=True,
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text=True,
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cwd=Path(__file__).resolve().parent.parent.parent,
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)
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if migration_result.returncode != 0:
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migration_output = migration_result.stderr + migration_result.stdout
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# Check for the expected UserAlreadyExists error (which is not critical)
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if (
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"UserAlreadyExists" in migration_output
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or "User default_user@example.com already exists" in migration_output
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):
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logger.warning("Warning: Default user already exists, continuing startup...")
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else:
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logger.error(f"Migration failed with unexpected error: {migration_output}")
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sys.exit(1)
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logger.info("Database migrations done.")
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logger.info(f"Starting MCP server with transport: {args.transport}")
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if args.transport == "stdio":
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106
cognee-mcp/uv.lock
generated
106
cognee-mcp/uv.lock
generated
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@ -621,8 +621,8 @@ wheels = [
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[[package]]
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name = "cognee"
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version = "0.2.1.dev7"
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source = { directory = "../" }
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version = "0.2.1"
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source = { registry = "https://pypi.org/simple" }
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dependencies = [
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{ name = "aiofiles" },
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{ name = "aiohttp" },
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@ -664,6 +664,10 @@ dependencies = [
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{ name = "tiktoken" },
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{ name = "typing-extensions" },
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]
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sdist = { url = "https://files.pythonhosted.org/packages/41/46/e7df1faebc92fa31ef8e33faf81feb435782727a789de5532d178e047224/cognee-0.2.1.tar.gz", hash = "sha256:bf5208383fc841981641c040e5b6588e58111af4d771f9eab6552f441e6a8e6c", size = 15497626, upload-time = "2025-07-25T15:53:57.009Z" }
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wheels = [
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{ url = "https://files.pythonhosted.org/packages/b3/0e/b705c6eeb538dcdd8fbbb331be25fe8e0bbc1af7d76e61566ec9845b29d3/cognee-0.2.1-py3-none-any.whl", hash = "sha256:6e9d437e0c58a16233841ebf19b1a3d8b67da069460a4f08d0c0e00301b1d36d", size = 1019851, upload-time = "2025-07-25T15:53:53.488Z" },
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]
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[package.optional-dependencies]
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codegraph = [
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@ -690,102 +694,6 @@ postgres = [
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{ name = "psycopg2" },
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]
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[package.metadata]
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requires-dist = [
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{ name = "aiofiles", specifier = ">=23.2.1,<24.0.0" },
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{ name = "aiohttp", specifier = ">=3.11.14,<4.0.0" },
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{ name = "aiosqlite", specifier = ">=0.20.0,<1.0.0" },
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{ name = "alembic", specifier = ">=1.13.3,<2" },
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{ name = "anthropic", marker = "extra == 'anthropic'", specifier = ">=0.26.1,<0.27" },
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{ name = "asyncpg", marker = "extra == 'postgres'", specifier = ">=0.30.0,<1.0.0" },
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{ name = "asyncpg", marker = "extra == 'postgres-binary'", specifier = ">=0.30.0,<1.0.0" },
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{ name = "chromadb", marker = "extra == 'chromadb'", specifier = ">=0.3.0,<0.7" },
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{ name = "coverage", marker = "extra == 'dev'", specifier = ">=7.3.2,<8" },
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{ name = "debugpy", marker = "extra == 'debug'", specifier = ">=1.8.9,<2.0.0" },
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{ name = "deepeval", marker = "extra == 'deepeval'", specifier = ">=2.0.1,<3" },
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{ name = "deptry", marker = "extra == 'dev'", specifier = ">=0.20.0,<0.21" },
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{ name = "dlt", extras = ["sqlalchemy"], specifier = ">=1.9.0,<2" },
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{ name = "falkordb", marker = "extra == 'falkordb'", specifier = ">=1.0.9,<2.0.0" },
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{ name = "fastapi", specifier = ">=0.115.7,<1.0.0" },
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{ name = "fastapi-users", extras = ["sqlalchemy"], specifier = ">=14.0.1,<15.0.0" },
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{ name = "fastembed", marker = "python_full_version < '3.13' and extra == 'codegraph'", specifier = "<=0.6.0" },
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{ name = "filetype", specifier = ">=1.2.0,<2.0.0" },
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{ name = "gdown", marker = "extra == 'evals'", specifier = ">=5.2.0,<6" },
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{ name = "gitpython", marker = "extra == 'dev'", specifier = ">=3.1.43,<4" },
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{ name = "google-generativeai", marker = "extra == 'gemini'", specifier = ">=0.8.4,<0.9" },
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{ name = "graphiti-core", marker = "extra == 'graphiti'", specifier = ">=0.7.0,<0.8" },
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{ name = "groq", marker = "extra == 'groq'", specifier = ">=0.8.0,<1.0.0" },
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{ name = "gunicorn", marker = "extra == 'api'", specifier = ">=20.1.0,<24" },
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{ name = "instructor", specifier = ">=1.9.1,<2.0.0" },
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{ name = "jinja2", specifier = ">=3.1.3,<4" },
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{ name = "kuzu", specifier = "==0.11.0" },
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{ name = "lancedb", specifier = ">=0.24.0,<1.0.0" },
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{ name = "langchain-text-splitters", marker = "extra == 'langchain'", specifier = ">=0.3.2,<1.0.0" },
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{ name = "langfuse", specifier = ">=2.32.0,<3" },
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{ name = "langsmith", marker = "extra == 'langchain'", specifier = ">=0.2.3,<1.0.0" },
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{ name = "limits", specifier = ">=4.4.1,<5" },
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{ name = "litellm", specifier = ">=1.57.4,<1.71.0" },
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{ name = "llama-index-core", marker = "extra == 'llama-index'", specifier = ">=0.12.11,<0.13" },
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{ name = "matplotlib", specifier = ">=3.8.3,<4" },
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{ name = "mistral-common", marker = "extra == 'mistral'", specifier = ">=1.5.2,<2" },
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{ name = "mkdocs-material", marker = "extra == 'dev'", specifier = ">=9.5.42,<10" },
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{ name = "mkdocs-minify-plugin", marker = "extra == 'dev'", specifier = ">=0.8.0,<0.9" },
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{ name = "mkdocstrings", extras = ["python"], marker = "extra == 'dev'", specifier = ">=0.26.2,<0.27" },
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{ name = "modal", marker = "extra == 'distributed'", specifier = ">=1.0.5,<2.0.0" },
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{ name = "mypy", marker = "extra == 'dev'", specifier = ">=1.7.1,<2" },
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{ name = "neo4j", marker = "extra == 'neo4j'", specifier = ">=5.28.0,<6" },
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{ name = "networkx", specifier = ">=3.4.2,<4" },
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{ name = "nltk", specifier = ">=3.9.1,<4.0.0" },
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{ name = "notebook", marker = "extra == 'dev'", specifier = ">=7.1.0,<8" },
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{ name = "notebook", marker = "extra == 'notebook'", specifier = ">=7.1.0,<8" },
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{ name = "numpy", specifier = ">=1.26.4,<=4.0.0" },
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{ name = "onnxruntime", specifier = ">=1.0.0,<2.0.0" },
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{ name = "openai", specifier = ">=1.80.1,<2" },
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{ name = "pandas", specifier = ">=2.2.2,<3.0.0" },
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{ name = "pgvector", marker = "extra == 'postgres'", specifier = ">=0.3.5,<0.4" },
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{ name = "pgvector", marker = "extra == 'postgres-binary'", specifier = ">=0.3.5,<0.4" },
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{ name = "plotly", marker = "extra == 'evals'", specifier = ">=6.0.0,<7" },
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{ name = "posthog", marker = "extra == 'posthog'", specifier = ">=3.5.0,<4" },
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{ name = "pre-commit", specifier = ">=4.0.1,<5" },
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{ name = "psycopg2", marker = "extra == 'postgres'", specifier = ">=2.9.10,<3" },
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{ name = "psycopg2-binary", marker = "extra == 'postgres-binary'", specifier = ">=2.9.10,<3.0.0" },
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{ name = "pydantic", specifier = ">=2.10.5,<3.0.0" },
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{ name = "pydantic-settings", specifier = ">=2.2.1,<3" },
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{ name = "pylance", specifier = ">=0.22.0,<1.0.0" },
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{ name = "pylint", marker = "extra == 'dev'", specifier = ">=3.0.3,<4" },
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{ name = "pympler", specifier = ">=1.1,<2.0.0" },
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{ name = "pypdf", specifier = ">=4.1.0,<6.0.0" },
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{ name = "pypika", marker = "extra == 'chromadb'", specifier = "==0.48.8" },
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{ name = "pyside6", marker = "extra == 'gui'", specifier = ">=6.8.3,<7" },
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{ name = "pytest", marker = "extra == 'dev'", specifier = ">=7.4.0,<8" },
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{ name = "pytest-asyncio", marker = "extra == 'dev'", specifier = ">=0.21.1,<0.22" },
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{ name = "pytest-cov", marker = "extra == 'dev'", specifier = ">=6.1.1,<7.0.0" },
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{ name = "python-dotenv", specifier = ">=1.0.1,<2.0.0" },
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{ name = "python-multipart", specifier = ">=0.0.20,<1.0.0" },
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{ name = "qasync", marker = "extra == 'gui'", specifier = ">=0.27.1,<0.28" },
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{ name = "qdrant-client", marker = "extra == 'qdrant'", specifier = ">=1.14.2,<2" },
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{ name = "rdflib", specifier = ">=7.1.4,<7.2.0" },
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{ name = "ruff", marker = "extra == 'dev'", specifier = ">=0.9.2,<1.0.0" },
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{ name = "s3fs", extras = ["boto3"], specifier = "==2025.3.2" },
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{ name = "s3fs", extras = ["boto3"], marker = "extra == 'aws'", specifier = "==2025.3.2" },
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{ name = "scikit-learn", specifier = ">=1.6.1,<2" },
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{ name = "sentry-sdk", extras = ["fastapi"], specifier = ">=2.9.0,<3" },
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{ name = "sqlalchemy", specifier = ">=2.0.39,<3.0.0" },
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{ name = "structlog", specifier = ">=25.2.0,<26" },
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{ name = "tiktoken", specifier = ">=0.8.0,<1.0.0" },
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{ name = "transformers", marker = "extra == 'codegraph'", specifier = ">=4.46.3,<5" },
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{ name = "transformers", marker = "extra == 'huggingface'", specifier = ">=4.46.3,<5" },
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{ name = "transformers", marker = "extra == 'ollama'", specifier = ">=4.46.3,<5" },
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{ name = "tree-sitter", marker = "extra == 'codegraph'", specifier = ">=0.24.0,<0.25" },
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{ name = "tree-sitter-python", marker = "extra == 'codegraph'", specifier = ">=0.23.6,<0.24" },
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{ name = "tweepy", marker = "extra == 'dev'", specifier = ">=4.14.0,<5.0.0" },
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{ name = "typing-extensions", specifier = ">=4.12.2,<5.0.0" },
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{ name = "unstructured", extras = ["csv", "doc", "docx", "epub", "md", "odt", "org", "ppt", "pptx", "rst", "rtf", "tsv", "xlsx"], marker = "extra == 'docs'", specifier = ">=0.18.1,<19" },
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{ name = "uvicorn", marker = "extra == 'api'", specifier = ">=0.34.0,<1.0.0" },
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{ name = "websockets", marker = "extra == 'api'", specifier = ">=15.0.1,<16.0.0" },
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]
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provides-extras = ["api", "distributed", "qdrant", "neo4j", "postgres", "postgres-binary", "notebook", "langchain", "llama-index", "gemini", "huggingface", "ollama", "mistral", "anthropic", "deepeval", "posthog", "falkordb", "groq", "chromadb", "docs", "codegraph", "evals", "gui", "graphiti", "aws", "dev", "debug"]
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[[package]]
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name = "cognee-mcp"
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version = "0.4.0"
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@ -804,7 +712,7 @@ dev = [
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[package.metadata]
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requires-dist = [
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{ name = "cognee", extras = ["postgres", "codegraph", "gemini", "huggingface", "docs", "neo4j"], directory = "../" },
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{ name = "cognee", extras = ["postgres", "codegraph", "gemini", "huggingface", "docs", "neo4j"], specifier = "==0.2.1" },
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{ name = "fastmcp", specifier = ">=2.10.0,<3.0.0" },
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{ name = "mcp", specifier = ">=1.12.0,<2.0.0" },
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{ name = "uv", specifier = ">=0.6.3,<1.0.0" },
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