#!/usr/bin/env python3
"""
Inspect an AnnData / single-cell file and print a structured summary.

Reports shape, obs/var columns (with dtypes and category counts), layers,
obsm/varm/uns keys, X dtype and value range, and whether the data looks like
raw counts or normalized values. Use this before analysis to understand an
unfamiliar dataset and decide which pipeline steps still need to run.

Examples:
    python inspect_data.py data.h5ad
    python inspect_data.py 10x_dir/
"""

import argparse

import numpy as np

from _common import configure_scanpy, info, load_anndata


def _is_integer_matrix(X, n=10000):
    sub = X[:50] if X.shape[0] > 50 else X
    arr = sub.toarray() if hasattr(sub, "toarray") else np.asarray(sub)
    arr = arr.ravel()[:n]
    if arr.size == 0:
        return False
    return bool(np.all(np.equal(np.mod(arr, 1), 0)))


def main():
    p = argparse.ArgumentParser(description=__doc__,
                                formatter_class=argparse.RawDescriptionHelpFormatter)
    p.add_argument("input", help="Input file (.h5ad, .h5, .csv, .loom, or 10x mtx dir)")
    p.add_argument("--max-cols", type=int, default=40, help="Max obs/var columns to list")
    args = p.parse_args()

    configure_scanpy()
    adata = load_anndata(args.input)

    print("=" * 70)
    print(f"AnnData: {adata.n_obs} cells x {adata.n_vars} genes")
    print("=" * 70)

    X = adata.X
    looks_int = _is_integer_matrix(X)
    xmax = X.max() if not hasattr(X, "toarray") else X.max()
    print(f"\nX dtype={X.dtype}  max={float(xmax):.2f}  "
          f"=> {'raw counts (likely)' if looks_int else 'normalized/log (likely)'}")

    print(f"\nobs columns ({len(adata.obs.columns)}):")
    for c in adata.obs.columns[:args.max_cols]:
        col = adata.obs[c]
        if str(col.dtype) in ("category", "object"):
            nuniq = col.nunique()
            extra = f"  {nuniq} categories" + (f": {list(col.unique()[:8])}" if nuniq <= 8 else "")
        else:
            extra = f"  range=[{col.min():.2f}, {col.max():.2f}]"
        print(f"  - {c} ({col.dtype}){extra}")

    print(f"\nvar columns ({len(adata.var.columns)}): {list(adata.var.columns[:args.max_cols])}")
    print(f"\nlayers: {list(adata.layers.keys())}")
    print(f"obsm: {list(adata.obsm.keys())}")
    print(f"varm: {list(adata.varm.keys())}")
    print(f"uns:  {list(adata.uns.keys())}")
    print(f"raw:  {'present' if adata.raw is not None else 'none'}")

    done = []
    if any(k in adata.obsm for k in ("X_pca",)):
        done.append("PCA")
    if "neighbors" in adata.uns:
        done.append("neighbors")
    if "X_umap" in adata.obsm:
        done.append("UMAP")
    if any(k in adata.obs.columns for k in ("leiden", "louvain")):
        done.append("clustering")
    print("\nPipeline steps already present: " + (", ".join(done) if done else "none"))


if __name__ == "__main__":
    main()