scripts/profile_clusters_standardize_first.py

"""End-to-end TF-IDF pipeline on the **standardize-first** cache.

Shape-equivalent to ``scripts/profile_clusters.py`` (the filter-first
TF-IDF pipeline), but reads the standardize-first cache and writes
to ``output/standardize_first/tfidf/``. The two TF-IDF outputs are
first-class and never overwrite each other.

Run with:
    .venv/bin/python -m scripts.profile_clusters_standardize_first
"""
import time
from pathlib import Path

from src.core.features.cluster import cluster_tags
from src.core.features.cluster_memberships import save_cluster_memberships
from src.core.features.medoids import compute_cluster_medoids
from src.core.features.profile import profile_clusters_by_base_key
from src.core.features.reduce import reduce_dimensions
from src.core.features.render import render_profile_markdown
from src.core.features.tfidf import build_char_tfidf_matrix
from src.core.storage.cache import read_cache_df

CACHE = "/Volumes/Seagate M3/tag_features_standardize_first.sqlite"
OUTPUT = Path("output/standardize_first/tfidf/cluster_profile.md")
MEMBERSHIPS_OUTPUT = Path("output/standardize_first/tfidf/cluster_memberships.csv")
MIN_COUNT = 500


def main() -> None:
    t0 = time.time()
    df = read_cache_df(CACHE, min_count=MIN_COUNT)
    print(f"load: {time.time()-t0:.1f}s  rows: {len(df):,}")

    t0 = time.time()
    matrix, _ = build_char_tfidf_matrix(df["feature"].tolist())
    print(f"tfidf: {time.time()-t0:.1f}s  shape: {matrix.shape}")

    t0 = time.time()
    dense = reduce_dimensions(matrix, n_components=50)
    print(f"svd: {time.time()-t0:.1f}s  shape: {dense.shape}")

    t0 = time.time()
    labels = cluster_tags(dense, min_cluster_size=5, min_samples=2)
    n_clusters = len(set(labels) - {-1})
    n_noise = int((labels == -1).sum())
    print(
        f"hdbscan: {time.time()-t0:.1f}s  clusters: {n_clusters:,}  noise: {n_noise:,}"
    )

    t0 = time.time()
    medoids = compute_cluster_medoids(
        features=df["feature"].tolist(),
        dense=dense,
        labels=labels,
        counts=df["count_all"].tolist(),
    )
    print(f"medoids: {time.time()-t0:.1f}s  rows: {len(medoids):,}")

    t0 = time.time()
    profile = profile_clusters_by_base_key(medoids, top_n=5)
    print(f"profile: {time.time()-t0:.1f}s  base_keys: {len(profile)}")

    md = render_profile_markdown(profile)
    OUTPUT.parent.mkdir(parents=True, exist_ok=True)
    OUTPUT.write_text(md + "\n")
    print(f"wrote: {OUTPUT}")

    # Persist the per-cluster medoid DataFrame so downstream steps
    # (env/agri breakdown, blog post) can read real per-cluster counts
    # without re-running HDBSCAN.
    import pandas as pd
    medoids_path = OUTPUT.parent / "cluster_medoids.csv"
    medoids.to_csv(medoids_path, index=False)
    print(f"wrote: {medoids_path}  rows: {len(medoids):,}")

    # Per-tag membership CSV: one row per cache tag with its cluster
    # assignment. This is the raw, unfiltered output of HDBSCAN: no
    # LLM, no env/agri filter.
    t0 = time.time()
    memberships_path = save_cluster_memberships(labels, df, MEMBERSHIPS_OUTPUT)
    print(f"memberships: {time.time()-t0:.1f}s  wrote: {memberships_path}")

    print()
    print(profile.head(20).to_string(index=False))


if __name__ == "__main__":
    main()