Implement parallel processing for partition discovery in load_folder.py and enhance column filtering in load_sas.py #9
@ -157,7 +157,6 @@ import threading
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from concurrent.futures import (
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from concurrent.futures import (
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CancelledError,
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CancelledError,
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ProcessPoolExecutor,
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ProcessPoolExecutor,
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ThreadPoolExecutor,
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as_completed,
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as_completed,
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)
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)
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from dataclasses import dataclass, field
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from dataclasses import dataclass, field
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@ -885,6 +884,94 @@ def discover_clusters(cfg: FolderConfig) -> List[ClusterSpec]:
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return clusters
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return clusters
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# ---------------------------------------------------------------------------
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# Top-level workers (must be importable for ProcessPoolExecutor pickling)
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# ---------------------------------------------------------------------------
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def _prescan_worker(
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path_str: str,
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delimiter: str,
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text_encoding: str,
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quotechar: str,
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) -> Tuple[
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str,
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Optional[int],
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Optional[Dict[str, Tuple[str, Optional[str]]]],
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Optional[str],
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]:
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"""Top-level prescan worker for ProcessPoolExecutor.
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Reads only metadata (pyreadstat ``metadataonly=True``) for one file and
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returns ``(path_str, number_rows, per_column_meta, error_message)``.
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Kept at module level so ``ProcessPoolExecutor`` can pickle it; the
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closure version we used to call from a ``ThreadPoolExecutor`` shared
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the parent's GIL and serialised the per-file Python work, which is
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why pre-scan felt slow even though the actual disk reads were fast.
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"""
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try:
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meta = read_sas_metadata(
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Path(path_str),
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delimiter=delimiter,
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text_encoding=text_encoding,
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quotechar=quotechar,
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)
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n = getattr(meta, "number_rows", None)
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col_meta = extract_union_metadata(meta)
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return (
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path_str,
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int(n) if n is not None else None,
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col_meta,
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None,
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)
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except Exception as e:
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return (path_str, None, None, f"{type(e).__name__}: {e}")
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def _partition_scan_worker(
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path_str: str,
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partition_by: List[str],
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delimiter: str,
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text_encoding: str,
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quotechar: str,
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) -> Tuple[str, Optional[dict], Optional[str]]:
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"""Top-level partition-discovery worker for ProcessPoolExecutor.
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Streams ``path_str`` with ``usecols=partition_by`` so pyreadstat only
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decodes the partition columns themselves - on a wide sas7bdat that's
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typically a 10x+ I/O reduction over reading every column. Returns
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``(path_str, partial_partition_tree, error_message)``.
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``columns`` is intentionally not passed: partition-value normalisation
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needs the cluster-wide schema, which is out of process. The merger in
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:func:`_discover_cluster_partitions` re-applies normalisation when it
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folds the per-file trees together.
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"""
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try:
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def _chunks() -> Any:
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for chunk_df, _meta in iter_sas_chunks(
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Path(path_str),
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delimiter=delimiter,
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text_encoding=text_encoding,
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quotechar=quotechar,
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usecols=list(partition_by),
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):
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yield chunk_df
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tree = discover_partition_values_chunked(
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_chunks(), list(partition_by),
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)
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return (path_str, tree, None)
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except Exception as e:
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import traceback as _traceback
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return (
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path_str,
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None,
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f"{type(e).__name__}: {e}\n{_traceback.format_exc()}",
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)
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# ---------------------------------------------------------------------------
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# ---------------------------------------------------------------------------
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# Per-cluster load
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# Per-cluster load
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# ---------------------------------------------------------------------------
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# ---------------------------------------------------------------------------
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@ -929,22 +1016,43 @@ def _infer_cluster_schema(
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def _discover_cluster_partitions(
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def _discover_cluster_partitions(
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cluster: ClusterSpec,
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cluster: ClusterSpec,
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columns: Dict,
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columns: Dict,
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*,
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workers: int = 1,
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) -> dict:
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) -> dict:
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"""Scan ALL files in ``cluster`` to discover partition values.
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"""Scan ALL files in ``cluster`` to discover partition values.
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Returns a nested partition-value tree suitable for passing to
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Returns a nested partition-value tree suitable for passing to
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:func:`load_sas.render_partition_ddl` and :func:`load_sas.create_table`.
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:func:`load_sas.render_partition_ddl` and :func:`load_sas.create_table`.
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Each file is scanned chunk-by-chunk so the full dataset is never
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materialized in memory.
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Each file is read with ``usecols=cluster.partition_by`` so pyreadstat
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only decodes the partition columns - on a wide sas7bdat that drops
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the bytes-touched-per-file by an order of magnitude vs the old
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full-row scan. With ``workers > 1`` the per-file scans run in a
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``ProcessPoolExecutor`` and the partial trees are merged as they
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complete (true parallelism, visible in ``htop`` as N python procs).
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``include`` / ``exclude`` are intentionally not honoured here:
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partition columns are validated against the inferred schema before
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we ever get called, which already enforces that they survived any
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explicit include/exclude filter. The old serial path applied the
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filter for symmetry, but it was a no-op once usecols pinned us to
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the partition set anyway.
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"""
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"""
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tkw = _build_text_kw(cluster)
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tkw = _build_text_kw(cluster)
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merged: dict = {}
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merged: dict = {}
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if not cluster.files:
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return merged
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n_workers = max(1, min(int(workers), len(cluster.files)))
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if n_workers <= 1 or len(cluster.files) == 1:
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for path in cluster.files:
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for path in cluster.files:
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def _filtered_chunks(p=path):
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def _filtered_chunks(p=path):
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for chunk_df, _chunk_meta in iter_sas_chunks(p, **tkw):
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for chunk_df, _meta in iter_sas_chunks(
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yield apply_column_filter(
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p, usecols=list(cluster.partition_by), **tkw,
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chunk_df, cluster.include, cluster.exclude
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):
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)
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yield chunk_df
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file_tree = discover_partition_values_chunked(
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file_tree = discover_partition_values_chunked(
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_filtered_chunks(), cluster.partition_by, columns,
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_filtered_chunks(), cluster.partition_by, columns,
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@ -952,6 +1060,41 @@ def _discover_cluster_partitions(
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_merge_partition_trees(merged, file_tree)
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_merge_partition_trees(merged, file_tree)
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return merged
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return merged
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with ProcessPoolExecutor(max_workers=n_workers) as ppool:
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futures = {
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ppool.submit(
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_partition_scan_worker,
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str(path),
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list(cluster.partition_by),
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tkw["delimiter"],
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tkw["text_encoding"],
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tkw["quotechar"],
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): path
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for path in cluster.files
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}
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bar = tqdm(
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total=len(futures),
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unit="file",
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desc=" discovering partitions",
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file=sys.stderr,
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dynamic_ncols=True,
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)
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try:
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for fut in as_completed(futures):
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path = futures[fut]
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_path_str, file_tree, err = fut.result()
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bar.update(1)
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if err is not None:
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raise RuntimeError(
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f"partition discovery failed for {path}: {err}"
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)
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if file_tree:
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_merge_partition_trees(merged, file_tree)
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finally:
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bar.close()
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return merged
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def load_cluster(
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def load_cluster(
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conn,
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conn,
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@ -1041,7 +1184,7 @@ def load_cluster(
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file=sys.stderr,
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file=sys.stderr,
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)
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)
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partition_values = _discover_cluster_partitions(
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partition_values = _discover_cluster_partitions(
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cluster, first_columns,
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cluster, first_columns, workers=workers,
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)
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)
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total_parts = _count_partitions(partition_values)
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total_parts = _count_partitions(partition_values)
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print(
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print(
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@ -1676,7 +1819,7 @@ def main(argv: Optional[List[str]] = None) -> int:
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file=sys.stderr,
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file=sys.stderr,
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)
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)
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partition_values = _discover_cluster_partitions(
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partition_values = _discover_cluster_partitions(
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c, columns,
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c, columns, workers=max(1, int(args.workers)),
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)
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)
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total_parts = _count_partitions(partition_values)
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total_parts = _count_partitions(partition_values)
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print(
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print(
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@ -1787,42 +1930,35 @@ def main(argv: Optional[List[str]] = None) -> int:
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file=sys.stderr,
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file=sys.stderr,
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)
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)
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else:
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else:
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prescan_workers = min(16, max(1, len(all_files)))
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# Cap at min(workers, file_count, 32). Pyreadstat metadata reads are
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# mostly C-side I/O + struct decoding, but the per-file Python work
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# (extract_union_metadata, dict construction) was being serialised
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# by the GIL in the old ThreadPool path - which is why the bar
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# crawled even though disk was idle. ProcessPool gives us actual
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# parallelism; you'll now see N python procs in htop.
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prescan_workers = min(
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32, max(1, max(workers, 16)), len(all_files),
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)
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print(
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print(
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f"pre-scanning row counts + per-column metadata for "
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f"pre-scanning row counts + per-column metadata for "
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f"{len(all_files)} file(s) across {prescan_workers} thread(s)...",
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f"{len(all_files)} file(s) across {prescan_workers} "
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f"process(es)...",
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file=sys.stderr,
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file=sys.stderr,
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)
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)
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def _scan_one(
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p: Path,
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) -> Tuple[
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Path,
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Optional[int],
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Optional[Dict[str, Tuple[str, Optional[str]]]],
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Optional[str],
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]:
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try:
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_prescan_tkw = dict(
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delimiter=cfg.delimiter,
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text_encoding=cfg.text_encoding,
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quotechar=cfg.quotechar,
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)
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meta = read_sas_metadata(p, **_prescan_tkw)
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n = getattr(meta, "number_rows", None)
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col_meta = extract_union_metadata(meta)
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return (
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p,
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int(n) if n is not None else None,
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col_meta,
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None,
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)
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except Exception as e:
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return (p, None, None, str(e))
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unknown_total_files: List[str] = []
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unknown_total_files: List[str] = []
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running_total = 0
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running_total = 0
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with ThreadPoolExecutor(max_workers=prescan_workers) as tpool:
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with ProcessPoolExecutor(max_workers=prescan_workers) as ppool:
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futures = {
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ppool.submit(
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_prescan_worker,
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str(p),
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|
cfg.delimiter,
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cfg.text_encoding,
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cfg.quotechar,
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): p
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for p in all_files
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}
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prescan_bar = tqdm(
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prescan_bar = tqdm(
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total=len(all_files),
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total=len(all_files),
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unit="file",
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unit="file",
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@ -1831,16 +1967,20 @@ def main(argv: Optional[List[str]] = None) -> int:
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dynamic_ncols=True,
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dynamic_ncols=True,
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)
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)
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try:
|
try:
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for p, n, col_meta, err in tpool.map(_scan_one, all_files):
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for fut in as_completed(futures):
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path_obj = futures[fut]
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path_str, n, col_meta, err = fut.result()
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prescan_bar.update(1)
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prescan_bar.update(1)
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if err is not None:
|
if err is not None:
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unknown_total_files.append(f"{p.name} ({err})")
|
unknown_total_files.append(
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|
f"{path_obj.name} ({err})"
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)
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elif n is None:
|
elif n is None:
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unknown_total_files.append(p.name)
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unknown_total_files.append(path_obj.name)
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else:
|
else:
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running_total += n
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running_total += n
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if col_meta is not None:
|
if col_meta is not None:
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file_meta_by_path[str(p)] = col_meta
|
file_meta_by_path[path_str] = col_meta
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finally:
|
finally:
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prescan_bar.close()
|
prescan_bar.close()
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|
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@ -811,6 +811,7 @@ def iter_text_chunks(
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encoding: str = "utf-8",
|
encoding: str = "utf-8",
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quotechar: str = '"',
|
quotechar: str = '"',
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chunksize: Optional[int] = None,
|
chunksize: Optional[int] = None,
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|
usecols: Optional[List[str]] = None,
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):
|
):
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"""Yield ``(df_chunk, meta)`` tuples for streaming text file loads.
|
"""Yield ``(df_chunk, meta)`` tuples for streaming text file loads.
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|
|
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@ -818,6 +819,10 @@ def iter_text_chunks(
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|||||||
iteration. The metadata object is rebuilt for each chunk with the
|
iteration. The metadata object is rebuilt for each chunk with the
|
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chunk's column names and ``number_rows`` set to the total file rows
|
chunk's column names and ``number_rows`` set to the total file rows
|
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(computed once up front).
|
(computed once up front).
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|
|
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|
When ``usecols`` is provided, only those columns are parsed - useful
|
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|
for cheap partition-value discovery scans where the rest of the row
|
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|
would be wasted I/O.
|
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"""
|
"""
|
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path = Path(path)
|
path = Path(path)
|
||||||
if chunksize is None:
|
if chunksize is None:
|
||||||
@ -832,8 +837,7 @@ def iter_text_chunks(
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|||||||
|
|
||||||
total = _count_text_lines(path, encoding)
|
total = _count_text_lines(path, encoding)
|
||||||
|
|
||||||
reader = pd.read_csv(
|
read_csv_kwargs: Dict[str, Any] = dict(
|
||||||
path,
|
|
||||||
delimiter=delimiter,
|
delimiter=delimiter,
|
||||||
encoding=encoding,
|
encoding=encoding,
|
||||||
quotechar=quotechar,
|
quotechar=quotechar,
|
||||||
@ -842,6 +846,10 @@ def iter_text_chunks(
|
|||||||
keep_default_na=True,
|
keep_default_na=True,
|
||||||
na_values=[""],
|
na_values=[""],
|
||||||
)
|
)
|
||||||
|
if usecols is not None:
|
||||||
|
read_csv_kwargs["usecols"] = list(usecols)
|
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|
|
||||||
|
reader = pd.read_csv(path, **read_csv_kwargs)
|
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for chunk_df in reader:
|
for chunk_df in reader:
|
||||||
meta = _build_text_metadata(list(chunk_df.columns), number_rows=total)
|
meta = _build_text_metadata(list(chunk_df.columns), number_rows=total)
|
||||||
yield chunk_df, meta
|
yield chunk_df, meta
|
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@ -941,6 +949,7 @@ def iter_sas_chunks(
|
|||||||
delimiter: str = ",",
|
delimiter: str = ",",
|
||||||
text_encoding: str = "utf-8",
|
text_encoding: str = "utf-8",
|
||||||
quotechar: str = '"',
|
quotechar: str = '"',
|
||||||
|
usecols: Optional[List[str]] = None,
|
||||||
):
|
):
|
||||||
"""Yield ``(df_chunk, meta)`` tuples for streaming loads.
|
"""Yield ``(df_chunk, meta)`` tuples for streaming loads.
|
||||||
|
|
||||||
@ -952,6 +961,13 @@ def iter_sas_chunks(
|
|||||||
parseable, otherwise from :data:`DEFAULT_CHUNK_ROWS`. An explicit int
|
parseable, otherwise from :data:`DEFAULT_CHUNK_ROWS`. An explicit int
|
||||||
always wins.
|
always wins.
|
||||||
|
|
||||||
|
When ``usecols`` is provided, pyreadstat only decodes the listed
|
||||||
|
columns. For wide sas7bdat files this is dramatically cheaper than
|
||||||
|
a full read - the C decoder skips unwanted columns instead of
|
||||||
|
materializing them. Used by partition-value discovery to avoid
|
||||||
|
re-reading every byte of every file just to extract a couple of
|
||||||
|
partition keys.
|
||||||
|
|
||||||
For text files, delegates to :func:`iter_text_chunks`.
|
For text files, delegates to :func:`iter_text_chunks`.
|
||||||
"""
|
"""
|
||||||
if _is_text_file(path):
|
if _is_text_file(path):
|
||||||
@ -961,6 +977,7 @@ def iter_sas_chunks(
|
|||||||
encoding=text_encoding,
|
encoding=text_encoding,
|
||||||
quotechar=quotechar,
|
quotechar=quotechar,
|
||||||
chunksize=chunksize,
|
chunksize=chunksize,
|
||||||
|
usecols=usecols,
|
||||||
)
|
)
|
||||||
return
|
return
|
||||||
if chunksize is None:
|
if chunksize is None:
|
||||||
@ -973,6 +990,9 @@ def iter_sas_chunks(
|
|||||||
else:
|
else:
|
||||||
chunksize = DEFAULT_CHUNK_ROWS
|
chunksize = DEFAULT_CHUNK_ROWS
|
||||||
reader, kwargs = _sas_reader(path)
|
reader, kwargs = _sas_reader(path)
|
||||||
|
if usecols is not None:
|
||||||
|
kwargs = dict(kwargs)
|
||||||
|
kwargs["usecols"] = list(usecols)
|
||||||
yield from pyreadstat.read_file_in_chunks(
|
yield from pyreadstat.read_file_in_chunks(
|
||||||
reader, str(Path(path)), chunksize=chunksize, **kwargs
|
reader, str(Path(path)), chunksize=chunksize, **kwargs
|
||||||
)
|
)
|
||||||
|
|||||||
Loading…
Reference in New Issue
Block a user