Commit History

  1. feat(eda): normalize dataset paths and deduplicate results in summary

    95969f7

  1. feat(eda): retrieve chunk size for each dataset in batch processing

    5e1e99a
  2. feat(eda): update large file processing to support parallel workers and enhance metadata caching

    75aa70e
  3. feat(config): fix some hard code config and docs

    685b361
  4. feat(eda): categorize datasets into small, dask-ready, and xlarge for improved processing

    f06cfcb
  5. feat(eda): adjust worker settings and add emergency mode for handling failed slices for extremly large

    db122fd
  6. feat(eda): enhance dataset processing for extra large

    2cdb847
  7. feat(eda): add adaptive scaling parameters and initial worker configuration for improved resource management

    d94a334
  8. feat(eda): enhance resource utilization by optimizing worker allocation and processing parameters

    32516b1
  9. feat(metadata): add handling for missing datasets in CELLxGENE metadata and update status reporting

    596560a
  10. feat(eda): add cache validation and retry mechanism for metadata build

    6eb2e4a
  11. fix(eda): optimize gene statistics calculation in distributed EDA⁠

    ac07329
  12. fix(eda): remove undefined 'info' variable reference causing crash⁠

    19a6596
  13. refactor(slurm): update resource allocation and remove deprecated script

    08c5297
  14. feat(eda): add resume capability and graceful error handling⁠

    34c9a87

  1. feat(eda): implement hybrid processing strategy for small and large datasets

    b8d98f3
  2. feat(eda): refactor distributed EDA script for improved performance and memory management⁠

    74e20c3
  3. fix(eda): optimize memory usage and ensure complete data computation⁠

    14cc169
  4. feat(eda): migrate to Dask distributed with adaptive scaling and memory limits

    450c8b2
  5. fix(eda): use recent throughput instead of cumulative average for adaptive scaling

    d25b7a0
  6. feat(eda): add adaptive worker reduction based on throughput monitoring

    e4396ec
  7. fix(config): remove mem_per_worker_gib from config files and calculate dynamically in resource_probe script

    0c8f912
  8. fix(config): clarify max_memory_gib allocation for staged processing

    2cae30c
  9. fix(retry): add size categorization after merge to prevent null categories

    05143cc
  10. fix(retry): include corrupted status in retry logic

    8822a1a
  11. fix(cache): categorize ok_retry and ok_h5py datasets by size

    cc36ee1
  12. fix(eda): include all successfully scanned datasets (ok_retry, ok_h5py)

    d2cd091
  13. feat(recovery): add corrupted file redownload script and documentation

    cee344c
  14. feat(retry_failed_cache): implement dataset retry mechanism and merging of results

    874e4c6
  15. fix(cache): implement two-phase scanning to handle large files serially and prevent OOM

    3ec846f
  16. fix(cache): use ProcessPoolExecutor for HDF5 thread-safety⁠

    655350f
  17. feat(pipeline): add YAML config, metadata-aware scheduling, and dataset slicing⁠

    856e1ba
  18. fix(eda): prevent BrokenProcessPool cascade failures

    790f422
  19. Initial commit: distributed EDA pipeline, max non-zero reporting, and notebook

    dddcc0f