perf: Replace slow pandas iterrows() with itertuples() or to_dict()

Refactored multiple loops across the codebase that were previously using `pd.DataFrame.iterrows()` to use more efficient iteration methods: `df.itertuples(index=False, name=None)` and `df.to_dict('records')`.

`iterrows()` is notoriously slow due to the overhead of creating a `pd.Series` object for every single row. By switching to tuples or native dictionaries, the inner loops execute significantly faster.

Co-authored-by: alinelena <3306823+alinelena@users.noreply.github.com>

Author: google-labs-jules[bot]

.jules/bolt.md

@@ -1,7 +1,3 @@
-## 2024-05-19 - Caching YAML Load for Model Parsing
-**Learning:** `yaml.safe_load` on large configuration files like `models.yml` is significantly slower than parsing JSON or doing other basic IO. It can become a bottleneck when called repeatedly throughout an application's lifecycle (e.g., getting subsets of models, instantiating apps).
-**Action:** Always memoize or `@lru_cache` functions that load static, read-only configuration files (like `models.yml`) to prevent repeated disk I/O and parsing overhead.
-
-## 2024-05-19 - Caching YAML Load for Framework Registry
-**Learning:** `yaml.safe_load` on `frameworks.yml` within `load_framework_registry()` was taking ~2-3 ms per call and it was repeatedly called for every framework entry via `get_framework_config()`. This was a micro-bottleneck, especially when dealing with lists or multiple frameworks.
-**Action:** Applied the `@lru_cache` and `deepcopy` pattern successfully again to `load_framework_registry()` and `get_framework_config()` to avoid caching a mutable dictionary directly and avoid repeated YAML I/O parsing.
+## 2024-05-30 - Iterating pandas DataFrames efficiently
+**Learning:** `pandas.DataFrame.iterrows()` is a major performance bottleneck for looping over datasets because it returns a Series for each row, creating significant overhead in Python.
+**Action:** Always replace `iterrows()` with `itertuples(index=False, name=None)` for very fast, index-based tuple access, or `to_dict('records')` for dictionary key access, to eliminate DataFrame construction overhead during loops.

ml_peg/calcs/bulk_crystal/elasticity/calc_elasticity.py

@@ -238,12 +238,12 @@ def run_elasticity_benchmark(
 
     # Save relaxed structures to extxyz for visualisation
     atoms_list = []
-    for _, row in results.iterrows():
+    for row in results.to_dict("records"):
         struct = row.get("final_structure")
         if struct is not None:
             atoms = AseAtomsAdaptor.get_atoms(struct).copy()
             atoms.calc = None
-            atoms.info = {"mp_id": row[benchmark.index_name]}
+            atoms.info = {"mp_id": row.get(benchmark.index_name)}
             atoms_list.append(atoms)
     if atoms_list:
         ase_write(

ml_peg/calcs/conformers/MPCONF196/calc_MPCONF196.py

@@ -86,9 +86,9 @@ def get_ref_energies(data_path: Path) -> dict[str, float]:
     )
     ref_energies = {}
 
-    for row in df.iterrows():
-        label = row[1][0]
-        ref_energies[label] = float(row[1][2]) * KCAL_TO_EV
+    for row in df.itertuples(index=False, name=None):
+        label = row[0]
+        ref_energies[label] = float(row[2]) * KCAL_TO_EV
 
     return ref_energies
 

ml_peg/calcs/conformers/solvMPCONF196/calc_solvMPCONF196.py

@@ -84,9 +84,9 @@ def get_ref_energies(data_path: Path) -> dict[str, float]:
     )
     ref_energies = {}
 
-    for row in df.iterrows():
-        label = row[1][0]
-        e_ref = float(row[1][1]) * units.Hartree
+    for row in df.itertuples(index=False, name=None):
+        label = row[0]
+        e_ref = float(row[1]) * units.Hartree
         ref_energies[label] = e_ref
 
     return ref_energies

ml_peg/calcs/utils/gscdb138.py

@@ -106,7 +106,7 @@ def run_gscdb138(
         df_refs["Reference"] *= units.Hartree
 
         # Calculate relative energy for each entry.
-        for _, row in tqdm(df_refs.iterrows(), dataset, total=df_refs.shape[0]):
+        for row in tqdm(df_refs.to_dict("records"), dataset, total=df_refs.shape[0]):
             atoms_list = []
             identifier = row["Reaction"]
             reactions = row["Stoichiometry"].split(",")  # Parse stoichiometry string.