refactor(data): resolve names from master_enrichment, the one base table (#224)

app.py built its own name lookup from properties.parquet and then merged iupac_backfill.parquet
itself. build_enrichment.py had already done that work — and better — so the two diverged in three
ways, all silent:

  1. The enrichment build resolves a name curated-list-first, then PubChem common name, then IUPAC
     name, then a molecular-formula fallback, un-inverting CAS-style ordering along the way. None
     of that reached app.py's table.
  2. The merge read only `iupac_name` from the backfill and ignored the `common_name` column, so
     every PubChem Title the crawler recovered was thrown away on arrival.
  3. Nothing carried the formula fallback, so the molecules that only have one resolved to nothing.

Measured before the change: 754 molecules had a name in master_enrichment that app._NAME_TABLE did
not know — and not obscure ones. cedrol, fenchyl alcohol, hydroxycitronellal and musk ketone all
rendered by name in the grid and came back empty from the UI's own lookup. After: 0.

Sourcing the resolved name straight off the base table makes the grid and the lookup agree by
construction instead of by coincidence, and deletes a whole merge function rather than adding one.
That is what #224 is actually asking for, applied where the duplication genuinely was.

Note what is deliberately NOT folded in. profile_index.npz is an 8,850 x 183 matrix — that 183 is
the FLAVOUR-PROFILE vector (6 taste + 172 aroma + 5 mouthfeel), not the head count, which is 195.
The 12 Tox21 heads are excluded on purpose: safety is not a flavour-match dimension and must never
steer "what tastes similar". flavor_map.parquet is a UMAP embedding. Different shapes serving
different questions; forcing either into a row-oriented molecule table would be worse, not tidier.
odor_notes/taste_notes are documented-text SOURCES the enrichment build consumes — upstream of the
base table, not competitors to it.

Signed-off-by: Austin L. <86896075+rvnminers-A-and-N@users.noreply.github.com>

Author: rvnminers-A-and-N

training/app.py

@@ -215,40 +215,35 @@ def _svg(smi, w=320, h=220):
 
 
 def _load_name_table():
-    """inchikey-skeleton -> (common, IUPAC) from the precomputed enrichment table, so the
-    whole labeled set resolves instantly and offline. Empty until build_properties.py has
-    written name columns; live PubChem stays the fallback for anything not in the table."""
+    """skeleton -> (common, IUPAC), sourced from master_enrichment — the ONE base table (#224).
+
+    This used to read properties.parquet and then merge iupac_backfill.parquet itself, which
+    duplicated work build_enrichment.py had already done and silently diverged from it in three
+    ways. The enrichment build resolves a name by curated list first, then PubChem common name,
+    then IUPAC name, then a molecular-formula fallback — and it un-inverts CAS-style ordering
+    along the way. None of that reached this table, so 754 molecules the grid displayed by name
+    (cedrol, fenchyl alcohol, hydroxycitronellal, musk ketone...) resolved to nothing here. The
+    old merge also read only `iupac_name` from the backfill and ignored the `common_name` column,
+    so every PubChem Title the crawler recovered was thrown away.
+
+    Reading the resolved name straight off the base table makes the UI's lookup and the grid
+    agree by construction rather than by coincidence.
+    """
     try:
         import pandas as pd
-        df = pd.read_parquet(P.artifact("properties.parquet"))
-        if "common_name" not in df.columns:
-            return {}
-        out = {}
-        for ik, c, u in zip(df["inchikey"], df["common_name"], df["iupac_name"]):
-            if isinstance(ik, str) and (isinstance(c, str) or isinstance(u, str)):
-                out[ik.split("-")[0]] = (c if isinstance(c, str) else None,
-                                         u if isinstance(u, str) else None)
-        return out
-    except Exception:  # noqa: BLE001 — no table / no pandas; just fall back to live lookups
+        df = pd.read_parquet(P.artifact("master_enrichment.parquet"))
+    except Exception:  # noqa: BLE001 — no table / no pandas; live lookups still cover it
         return {}
+    out = {}
+    iupac = dict(zip(df.get("inchikey_skel", []), df.get("iupac_name", [])))  # optional column
+    for skel, name in zip(df["inchikey_skel"], df["name"]):
+        if isinstance(skel, str) and isinstance(name, str) and name.strip():
+            u = iupac.get(skel)
+            out[skel] = (name.strip(), u if isinstance(u, str) else None)
+    return out
 
 
-def _merge_iupac_backfill(table):
-    """Fold in IUPAC names that build_iupac_backfill.py recovered from PubChem for molecules
-    the main properties crawl missed (skeleton -> keep any common name, add the IUPAC)."""
-    try:
-        import pandas as pd
-        bf = pd.read_parquet(P.artifact("iupac_backfill.parquet"))
-    except Exception:  # noqa: BLE001 — backfill not built; nothing to merge
-        return table
-    for skel, u in zip(bf["inchikey_skel"], bf["iupac_name"]):
-        if isinstance(skel, str) and isinstance(u, str) and u:
-            common = table.get(skel, (None, None))[0]
-            table[skel] = (common, u)
-    return table
-
-
-_NAME_TABLE = _merge_iupac_backfill(_load_name_table())
+_NAME_TABLE = _load_name_table()
 
 
 @lru_cache(maxsize=8192)