Remove src/src/data/taxonomy.py

src/src/data/taxonomy.py

@@ -1,150 +0,0 @@
-"""
-Taxonomic Hierarchy Engine for Western Australia Flora.
-Builds and maps Species -> Genus -> Family for hierarchical multi-task classification.
-"""
-import pandas as pd
-from pathlib import Path
-
-# Common WA Flora Genus -> Family mapping dictionary
-GENUS_TO_FAMILY = {
-    # Proteaceae
-    "Banksia": "Proteaceae", "Grevillea": "Proteaceae", "Hakea": "Proteaceae",
-    "Dryandra": "Proteaceae", "Adenanthos": "Proteaceae", "Isopogon": "Proteaceae",
-    "Petrophile": "Proteaceae", "Synaphea": "Proteaceae", "Conospermum": "Proteaceae",
-    "Lambertia": "Proteaceae", "Persoonia": "Proteaceae", "Xylomelum": "Proteaceae",
-    "Franklandia": "Proteaceae", "Stirlingia": "Proteaceae",
-    
-    # Myrtaceae
-    "Eucalyptus": "Myrtaceae", "Corymbia": "Myrtaceae", "Melaleuca": "Myrtaceae",
-    "Verticordia": "Myrtaceae", "Calothamnus": "Myrtaceae", "Darwinia": "Myrtaceae",
-    "Chamelaucium": "Myrtaceae", "Thryptomene": "Myrtaceae", "Beaufortia": "Myrtaceae",
-    "Baeckea": "Myrtaceae", "Regelia": "Myrtaceae", "Calytrix": "Myrtaceae",
-    "Eremaea": "Myrtaceae", "Kunzea": "Myrtaceae", "Micromyrtus": "Myrtaceae",
-    "Hypocalymma": "Myrtaceae", "Scholtzia": "Myrtaceae", "Phymatocarpus": "Myrtaceae",
-    "Leptospermum": "Myrtaceae", "Astartea": "Myrtaceae", "Taxandria": "Myrtaceae",
-
-    # Fabaceae (Legumes)
-    "Acacia": "Fabaceae", "Gastrolobium": "Fabaceae", "Daviesia": "Fabaceae",
-    "Jacksonia": "Fabaceae", "Bossiaea": "Fabaceae", "Hovea": "Fabaceae",
-    "Kennedia": "Fabaceae", "Hardenbergia": "Fabaceae", "Gompholobium": "Fabaceae",
-    "Mirbelia": "Fabaceae", "Chorizema": "Fabaceae", "Pultenaea": "Fabaceae",
-    "Isotropis": "Fabaceae", "Swainsona": "Fabaceae", "Senna": "Fabaceae",
-    "Indigofera": "Fabaceae", "Templetonia": "Fabaceae", "Latrobea": "Fabaceae",
-
-    # Orchidaceae (Orchids)
-    "Caladenia": "Orchidaceae", "Thelymitra": "Orchidaceae", "Diuris": "Orchidaceae",
-    "Pterostylis": "Orchidaceae", "Drakaea": "Orchidaceae", "Microtis": "Orchidaceae",
-    "Prasophyllum": "Orchidaceae", "Cyanicula": "Orchidaceae", "Ericksonella": "Orchidaceae",
-    "Leporella": "Orchidaceae", "Paracaleana": "Orchidaceae", "Pyrorchis": "Orchidaceae",
-    "Cryptostylis": "Orchidaceae", "Elythranthera": "Orchidaceae", "Spiculaea": "Orchidaceae",
-
-    # Haemodoraceae (Kangaroo Paws)
-    "Anigozanthos": "Haemodoraceae", "Macropidia": "Haemodoraceae", "Conostylis": "Haemodoraceae",
-    "Tribonanthes": "Haemodoraceae", "Haemodorum": "Haemodoraceae", "Phlebocarya": "Haemodoraceae",
-
-    # Ericaceae / Epacridaceae (Heaths)
-    "Leucopogon": "Ericaceae", "Astroloma": "Ericaceae", "Lysinema": "Ericaceae",
-    "Conostephium": "Ericaceae", "Andersonia": "Ericaceae", "Sphenotoma": "Ericaceae",
-    "Styphelia": "Ericaceae", "Cosmelia": "Ericaceae",
-
-    # Goodeniaceae
-    "Goodenia": "Goodeniaceae", "Dampiera": "Goodeniaceae", "Scaevola": "Goodeniaceae",
-    "Lechenaultia": "Goodeniaceae", "Velleia": "Goodeniaceae", "Anthotium": "Goodeniaceae",
-
-    # Stylidiaceae (Triggerplants)
-    "Stylidium": "Stylidiaceae", "Levenhookia": "Stylidiaceae",
-
-    # Droseraceae (Sundews / Carnivorous)
-    "Drosera": "Droseraceae",
-
-    # Asteraceae (Daisies)
-    "Rhodanthe": "Asteraceae", "Waitzia": "Asteraceae", "Schoenia": "Asteraceae",
-    "Podolepis": "Asteraceae", "Olearia": "Asteraceae", "Senecio": "Asteraceae",
-    "Brachyscome": "Asteraceae", "Lawrencella": "Asteraceae", "Xerochrysum": "Asteraceae",
-
-    # Xanthorrhoeaceae / Asphodelaceae
-    "Xanthorrhoea": "Asphodelaceae",
-
-    # Dasypogonaceae
-    "Kingia": "Dasypogonaceae", "Dasypogon": "Dasypogonaceae", "Calectasia": "Dasypogonaceae",
-
-    # Casuarinaceae (Sheoaks)
-    "Allocasuarina": "Casuarinaceae", "Casuarina": "Casuarinaceae",
-
-    # Pittosporaceae
-    "Marianthus": "Pittosporaceae", "Billardiera": "Pittosporaceae", "Pittosporum": "Pittosporaceae",
-    "Cheiranthera": "Pittosporaceae",
-
-    # Restionaceae (Rushes / Sedges)
-    "Desmocladus": "Restionaceae", "Alexgeorgea": "Restionaceae", "Loxocarya": "Restionaceae",
-    "Chordifex": "Restionaceae", "Lyginia": "Restionaceae",
-
-    # Chenopodiaceae / Amaranthaceae
-    "Atriplex": "Amaranthaceae", "Maireana": "Amaranthaceae", "Tecticornia": "Amaranthaceae",
-    "Ptilotus": "Amaranthaceae",
-
-    # Malvaceae
-    "Alyogyne": "Malvaceae", "Thomasia": "Malvaceae", "Guichenotia": "Malvaceae",
-    "Lasiopetalum": "Malvaceae", "Seringia": "Malvaceae", "Androcalva": "Malvaceae",
-
-    # Rutaceae (Boronias / Waxflowers)
-    "Boronia": "Rutaceae", "Philotheca": "Rutaceae", "Diplolaena": "Rutaceae",
-    "Correa": "Rutaceae", "Crowea": "Rutaceae", "Geleznowia": "Rutaceae",
-    "Asterolasia": "Rutaceae", "Eriostemon": "Rutaceae",
-
-    # Loranthaceae (Mistletoes / Christmas Tree)
-    "Nuytsia": "Loranthaceae", "Amyema": "Loranthaceae", "Lysiana": "Loranthaceae",
-}
-
-class TaxonomyHierarchy:
-    """Manages species -> genus -> family indices and mappings."""
-    def __init__(self, species_list: list[str]):
-        self.species_list = sorted(list(set(s for s in species_list if isinstance(s, str) and s.strip())))
-        
-        # 1. Species Index
-        self.species_to_idx = {s: i for i, s in enumerate(self.species_list)}
-        self.idx_to_species = {i: s for s, i in self.species_to_idx.items()}
-        self.n_species = len(self.species_list)
-
-        # 2. Genus Index
-        self.species_to_genus = {}
-        genera_set = set()
-        for s in self.species_list:
-            genus = s.split()[0] if s else "Unknown"
-            self.species_to_genus[s] = genus
-            genera_set.add(genus)
-        
-        self.genus_list = sorted(list(genera_set))
-        self.genus_to_idx = {g: i for i, g in enumerate(self.genus_list)}
-        self.idx_to_genus = {i: g for g, i in self.genus_to_idx.items()}
-        self.n_genera = len(self.genus_list)
-
-        # 3. Family Index
-        self.genus_to_family = {}
-        families_set = set()
-        for g in self.genus_list:
-            fam = GENUS_TO_FAMILY.get(g, f"{g}_Family")
-            self.genus_to_family[g] = fam
-            families_set.add(fam)
-
-        self.family_list = sorted(list(families_set))
-        self.family_to_idx = {f: i for i, f in enumerate(self.family_list)}
-        self.idx_to_family = {i: f for f, i in self.family_to_idx.items()}
-        self.n_families = len(self.family_list)
-
-        # Precompute lookup tables
-        self.species_idx_to_genus_idx = [
-            self.genus_to_idx[self.species_to_genus[self.idx_to_species[i]]]
-            for i in range(self.n_species)
-        ]
-        self.species_idx_to_family_idx = [
-            self.family_to_idx[self.genus_to_family[self.species_to_genus[self.idx_to_species[i]]]]
-            for i in range(self.n_species)
-        ]
-
-    def get_taxonomy_indices(self, species_name: str) -> tuple[int, int, int]:
-        """Returns (species_idx, genus_idx, family_idx)."""
-        s_idx = self.species_to_idx.get(species_name, -1)
-        if s_idx == -1:
-            return -1, -1, -1
-        return s_idx, self.species_idx_to_genus_idx[s_idx], self.species_idx_to_family_idx[s_idx]