fix: 修复预处理流水线 4 个致命问题

- pipeline: 单条数据异常不再崩溃整条流水线, 改 log warning 后跳过
- pipeline: _align_bucket 统一用 len(ids) 填充, 修复多输出模式下长度错配
- writer: BinWriter/H5Writer 写入失败自动清理残留文件并记录详细错误
- packing: BFDPacking 真正将序列打包进 bin 而非仅重排, 减少碎片

astrai/preprocessing/packing.py

@@ -6,8 +6,7 @@ pipeline later flattens the result into contiguous tensors.
 """
 
 from abc import ABC, abstractmethod
-from collections import defaultdict
-from typing import Dict, List, Tuple
+from typing import Dict, List
 
 from astrai.factory import BaseFactory
 
@@ -53,6 +52,15 @@ class SimplePacking(PackingStrategy):
 
 @PackingStrategyFactory.register("bfd")
 class BFDPacking(PackingStrategy):
+    """Best-Fit Decreasing bin packing.
+
+    Assigns sequences to bins using a best-fit heuristic (sorted by
+    decreasing length) and concatenates sequences within each bin into
+    a single packed sequence.  Packed sequences are truncated to
+    *max_packed_len* so that each packed bin fits within one context
+    window during training.
+    """
+
     def apply(
         self,
         keys: Dict[str, List[List[int]]],
@@ -62,24 +70,40 @@ class BFDPacking(PackingStrategy):
         sequences = keys.get("sequence", [])
         if not sequences:
             return keys
-        plan = self._plan(sequences, max_packed_len)
-        reordered: dict = defaultdict(list)
-        for orig_idx, _ in plan:
+        bins = self._plan(sequences, max_packed_len, truncation_mode)
+
+        packed: Dict[str, List[List[int]]] = {}
         for k, vals in keys.items():
-                reordered[k].append(
-                    _truncate(vals[orig_idx], max_packed_len, truncation_mode)
+            packed[k] = [
+                _truncate(
+                    self._concat_bin(vals, bin_indices),
+                    max_packed_len,
+                    truncation_mode,
                 )
-        return dict(reordered)
+                for bin_indices in bins
+            ]
+        return packed
 
     @staticmethod
-    def _plan(sequences: List[List[int]], max_packed_len: int) -> List[Tuple[int, int]]:
+    def _concat_bin(vals: List[List[int]], indices: List[int]) -> List[int]:
+        result: List[int] = []
+        for i in indices:
+            result.extend(vals[i])
+        return result
+
+    @staticmethod
+    def _plan(
+        sequences: List[List[int]], max_packed_len: int, truncation_mode: str
+    ) -> List[List[int]]:
         n = len(sequences)
         order = sorted(range(n), key=lambda i: len(sequences[i]), reverse=True)
         bins: List[List[int]] = []
         bin_lengths: List[int] = []
 
         for orig_idx in order:
-            seq_len = min(len(sequences[orig_idx]), max_packed_len)
+            seq_len = len(
+                _truncate(sequences[orig_idx], max_packed_len, truncation_mode)
+            )
             best_bin = None
             best_remain = max_packed_len + 1
             for i, bl in enumerate(bin_lengths):
@@ -94,8 +118,4 @@ class BFDPacking(PackingStrategy):
                 bins.append([orig_idx])
                 bin_lengths.append(seq_len)
 
-        plan: List[Tuple[int, int]] = []
-        for bin_indices in bins:
-            for orig_idx in bin_indices:
-                plan.append((orig_idx, min(len(sequences[orig_idx]), max_packed_len)))
-        return plan
+        return bins

astrai/preprocessing/pipeline.py

@@ -7,6 +7,7 @@ dispatched by configuration keys.
 """
 
 import json
+import logging
 import os
 from collections import defaultdict
 from itertools import chain
@@ -22,6 +23,8 @@ from astrai.preprocessing.position_id import PositionIdStrategyFactory
 from astrai.preprocessing.writer import StoreWriterFactory
 from astrai.tokenize import AutoTokenizer
 
+logger = logging.getLogger(__name__)
+
 _STR_TO_DTYPE: dict[str, torch.dtype] = {
     "bool": torch.bool,
     "uint8": torch.uint8,
@@ -88,7 +91,13 @@ class Pipeline:
             if pp.max_items and count >= pp.max_items:
                 break
 
+            try:
                 result = self.transform(item)
+            except Exception:
+                logger.warning(
+                    "Failed to process item #%d, skipping", count + 1, exc_info=True
+                )
+                continue
             if result is None:
                 continue
 
@@ -105,7 +114,7 @@ class Pipeline:
                 continue
 
             bucket = domains[domain]
-            self._align_bucket(bucket, result, ids, is_multi)
+            self._align_bucket(bucket, result, ids)
             for key, val in result.items():
                 bucket[key].append(val)
 
@@ -130,15 +139,11 @@ class Pipeline:
         return []
 
     @staticmethod
-    def _align_bucket(bucket: dict, result: dict, ids: list, is_multi: bool):
+    def _align_bucket(bucket: dict, result: dict, ids: list):
         """Pad previously-accumulated keys that are missing from *result*."""
         for key in list(bucket.keys()):
             if key in result:
                 continue
-            if is_multi:
-                pad = bucket[key][-1] if bucket[key] else [1] * len(ids)
-                bucket[key].append(pad)
-            else:
             bucket[key].append([1] * len(ids))
 
     def _iter_items(self):

astrai/preprocessing/writer.py

@@ -6,7 +6,9 @@ List[Tensor]}`` dict and delegates the write to the writer selected
 by ``output.storage_format``.
 """
 
+import logging
 import os
+import shutil
 from abc import ABC, abstractmethod
 from typing import Dict, List
 
@@ -15,6 +17,8 @@ import torch
 from astrai.dataset.storage import save_bin, save_h5
 from astrai.factory import BaseFactory
 
+logger = logging.getLogger(__name__)
+
 
 class StoreWriter(ABC):
     """Write pre-tokenized tensors to disk in a format-specific way."""
@@ -37,11 +41,35 @@ class StoreWriterFactory(BaseFactory["StoreWriter"]):
 class BinWriter(StoreWriter):
     def save(self, output_dir, domain, shard_idx, tensors):
         shard_path = os.path.join(output_dir, domain, f"shard_{shard_idx:04d}")
+        try:
             save_bin(shard_path, tensors)
+        except Exception:
+            if os.path.exists(shard_path):
+                shutil.rmtree(shard_path, ignore_errors=True)
+            logger.error(
+                "Failed to write shard %s/%s_%04d, cleaned up partial output",
+                domain,
+                "shard",
+                shard_idx,
+                exc_info=True,
+            )
+            raise
 
 
 @StoreWriterFactory.register("h5")
 class H5Writer(StoreWriter):
     def save(self, output_dir, domain, shard_idx, tensors):
         chunk_dir = os.path.join(output_dir, domain)
+        file_path = os.path.join(chunk_dir, f"data_{shard_idx:04d}.h5")
+        try:
             save_h5(chunk_dir, f"data_{shard_idx:04d}", tensors)
+        except Exception:
+            if os.path.exists(file_path):
+                os.remove(file_path)
+            logger.error(
+                "Failed to write shard %s/data_%04d.h5, cleaned up partial output",
+                domain,
+                shard_idx,
+                exc_info=True,
+            )
+            raise