import pytest
from fastmcp import Client
import anndata
import numpy as np
from pathlib import Path
import nest_asyncio
# Apply nest_asyncio at module level
nest_asyncio.apply()
@pytest.mark.asyncio
async def test_subset_cells(mcp):
# Pass the server directly to the Client constructor
test_dir = Path(__file__).parent / "data/hg19"
async with Client(mcp) as client:
# First load the data
result = await client.call_tool("io_read", {"request":{"filename": test_dir}})
assert "AnnData" in result[0].text
# Test filtering with min_genes parameter
result = await client.call_tool("pp_subset_cells", {"request":{"min_genes": 200}})
assert "AnnData" in result[0].text
result = await client.call_tool("pp_calculate_qc_metrics", {"request":{}})
assert "total_counts" in result[0].text
result = await client.call_tool("pp_log1p", {"request":{}})
assert "log1p" in result[0].text
result = await client.call_tool("pp_normalize_total", {"request":{}})
assert "log1p" in result[0].text
result = await client.call_tool("pp_highly_variable_genes", {"request":{}})
assert "highly_variable" in result[0].text
result = await client.call_tool("tl_pca", {"request":{"n_comps": 50}})
assert "X_pca" in result[0].text
result = await client.call_tool("pp_neighbors", {"request":{}})
assert "neighbors" in result[0].text
