Fix: add control to skip empty ddf when time chunk is empty

scripts/sp2xr_pipeline.py

@@ -12,6 +12,7 @@ from sp2xr.helpers import (
     extract_partitioned_datetimes,
     get_time_chunks_from_range,
     delete_partition_if_exists,
+    partition_rowcount,
 )
 from sp2xr.apply_calib import calibrate_single_particle
 from sp2xr.resample_pbp_hk import (
@@ -80,12 +81,27 @@ def main():
             pbp_filters.append(("hour", "<", chunk_end.hour))
 
         # 2. HK processing --------------------------------------
-        ddf_hk = dd.read_parquet(
-            run_config["input_hk"],
-            engine="pyarrow",
-            filters=pbp_filters,
-            calculate_divisions=True,
-        )
+        try:
+            ddf_hk = dd.read_parquet(
+                run_config["input_hk"],
+                engine="pyarrow",
+                filters=pbp_filters,
+                calculate_divisions=True,
+            )
+        except (FileNotFoundError, OSError):
+            print(" → no HK files for this chunk; skipping.")
+            continue
+
+        if ddf_hk.npartitions == 0 or partition_rowcount(ddf_hk) == 0:
+            print(" → HK frame is empty; skipping.")
+            continue
+        ddf_hk = ddf_hk.map_partitions(lambda pdf: pdf.sort_index())
+        if not ddf_hk.known_divisions:
+            ddf_hk = (
+                ddf_hk.reset_index().set_index(  # 'calculated_time' becomes a column
+                    "calculated_time", sorted=False, shuffle="tasks"
+                )  # Dask now infers divisions
+            )
         ddf_hk = ddf_hk.repartition(freq="1h")
         meta = pd.DataFrame(
             {
@@ -103,12 +119,28 @@ def main():
         flow_dt = ddf_hk_dt["Sample Flow Controller Read (vccm)"].compute()
 
         # 3. PBP processing --------------------------------------
-        ddf_raw = dd.read_parquet(
-            run_config["input_pbp"],
-            engine="pyarrow",
-            filters=pbp_filters,
-            calculate_divisions=True,
-        )
+        try:
+            ddf_raw = dd.read_parquet(
+                run_config["input_pbp"],
+                engine="pyarrow",
+                filters=pbp_filters,
+                calculate_divisions=True,
+            )
+        except (FileNotFoundError, OSError):
+            print(" → no PbP files for this chunk; skipping.")
+            continue
+
+        if ddf_raw.npartitions == 0 or partition_rowcount(ddf_raw) == 0:
+            print(" → PbP frame is empty; skipping.")
+            continue
+
+        ddf_raw = ddf_raw.map_partitions(lambda pdf: pdf.sort_index())
+        if not ddf_raw.known_divisions:
+            ddf_raw = (
+                ddf_raw.reset_index().set_index(  # 'calculated_time' becomes a column
+                    "calculated_time", sorted=False, shuffle="tasks"
+                )  # Dask now infers divisions
+            )
         ddf_raw = ddf_raw.repartition(freq="1h")
 
         ddf_cal = calibrate_single_particle(ddf_raw, instr_config, run_config)

src/sp2xr/helpers.py

@@ -4,6 +4,7 @@ import re
 import yaml
 import argparse
 import pandas as pd
+import dask.dataframe as dd
 from pathlib import Path
 from dask_jobqueue import SLURMCluster
 import multiprocessing
@@ -427,6 +428,17 @@ def export_xr_ini_to_yaml(ini_path, yaml_path):
     )
 
 
+def partition_rowcount(ddf: dd.DataFrame) -> int:
+    """
+    Return total number of rows in a Dask DataFrame.
+    """
+    row_series = ddf.map_partitions(
+        lambda pdf: pd.Series([len(pdf)]),
+        meta=pd.Series(dtype="int64"),
+    )
+    return int(row_series.sum().compute())
+
+
 '''def normalize_dtypes(
     df: Union[pd.DataFrame, dd.DataFrame],
 ) -> Union[pd.DataFrame, dd.DataFrame]: