Metadata-Version: 2.5
Name: hca-anndata-mcp
Version: 0.8.0
Summary: MCP server for interactive exploration of AnnData h5ad files
Project-URL: Homepage, https://github.com/clevercanary/hca-validation-tools
Author-email: Clever Canary <dave@clevercanary.com>
License-Expression: MIT
Requires-Python: <4.0,>=3.10
Requires-Dist: fastmcp<3,>=2
Requires-Dist: hca-anndata-tools<0.8,>=0.6
Requires-Dist: hca-schema-validator<0.16,>=0.15
Description-Content-Type: text/markdown

# hca-anndata-mcp

MCP server for interactive exploration of AnnData h5ad files.

## Usage

```bash
# Run the MCP server
hca-anndata-mcp
```

Point an MCP client at the venv binary directly, not at a wrapper command:

```json
{
  "mcpServers": {
    "hca-anndata-mcp": {
      "command": "/abs/path/to/packages/hca-anndata-mcp/.venv/bin/hca-anndata-mcp"
    }
  }
}
```

`uv run hca-anndata-mcp` (like `poetry run` before it) does not work here. An MCP
client needs a stable executable to spawn, and a wrapper command that resolves
and syncs an environment first is not one.

## Tools

- **locate_files** — Find all .h5ad files in a directory
- **get_summary** — Structural overview: cell/gene counts, columns, embeddings, layers
- **get_storage_info** — HDF5 compression, chunking, sparse format details
- **get_descriptive_stats** — Descriptive statistics and value counts for obs/var columns
- **view_data** — View slices of any attribute (obs, var, X, obsm, uns, etc.)
- **plot_embedding** — UMAP/PCA scatter plots colored by obs column or gene
- **get_cap_annotations** — Inspect CAP cell annotation metadata, marker genes, rationale
