Metadata-Version: 2.4
Name: hca-anndata-mcp
Version: 0.5.0
Summary: MCP server for interactive exploration of AnnData h5ad files
License: MIT
Author: Clever Canary
Author-email: dave@clevercanary.com
Requires-Python: >=3.10,<4.0
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Requires-Dist: fastmcp (>=2,<3)
Requires-Dist: hca-anndata-tools (>=0.1.0,<1)
Requires-Dist: hca-schema-validator (>=0.10.0,<1)
Project-URL: Homepage, https://github.com/clevercanary/hca-validation-tools
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

# Or via poetry
poetry run hca-anndata-mcp
```

## 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

