Skip to content

Latest commit

 

History

History
109 lines (74 loc) · 3.13 KB

CHANGES.md

File metadata and controls

109 lines (74 loc) · 3.13 KB
Raw

Unreleased

New features

Enhancements

  • silent argument to query_* methods

Bug fixes

  • Fix MomicsDataset and generator.

v0.4.0

Date: 2024-10-25

API changes

  • MultiRangeQuery -> MomicsQuery.
  • manifest method to output the whole configuration of a Momics instance.
  • consolidate method to consolidate a Momics repository.
  • No submodules are imported in __init__.py anymore.
  • All export functions are now Momics methods.
  • All ingestion methods for Momics now start with ingest_*.

New features

  • aggregate submodule to merge dictionaries of partial coverage tracks (over pyranges) into genome-wide tracks.
  • Relatively basic ChromNN CNN TensorFlow model.
  • MomicsDataset class to pass data to TensorFlow models.
  • MomicsStreamer class to stream data from Momics repositories.
  • Momics can ingest pyranges objects to store genomic features.
  • Sequences, features and tracks can be extracted from a Momics repository.

Enhancements

  • CLI is now partially based on cloup to improve user experience.
  • seq(label = "...) now returns the sequence for an entire chromosome.
  • tracks(label = "...) now returns the genome-wide track.
  • MomicsQuery queries now rely on pyranges for range queries.
  • MomicsQuery queries can extract only a subset of the tracks.
  • add_track and remove methods for Momics class.
  • to_npz and to_json methods for MomicsQuery class.

Maintenance

  • Support jupyter notebooks in documentation.
  • Add changelog.
  • Improve docs.
  • Logging system updates.
  • CLI updates.
  • Add codecov support.

Bug fixes

  • Ensure that queries are done per chromosome, even if provided ranges are stranded.
  • All ranges are now 0-based half-open intervals, as in pyranges and BED files.
  • Parallelization for queries only relies on TileDB internal system.
  • Filters used in Momics tables.
  • Removal of Azure-hosted repositories.

v0.3.0

Date: 2024-09-26

New features

  • MultiRangeQuery relies on pybedtools for range queries.
  • Queries support both coordinates and multi-loci queries.
  • Added MultiRangeQuery class for queries.
  • New bins method for Momics.
  • Repositories can ingest fasta files.
  • Added export submodule.
  • Added MomicsConfig class to manage cloud configuration settings.
  • Added Click-based CLI commands.

Enhancements

  • Improve query filters.
  • CLI commands have mutli-threading options.

Maintenance

  • Added ruff support.
  • Changed doc theme.
  • Added support for autoapi in documentation.
  • Improved tests coverage.

Bug fixes

  • Fixed broken use of single-file temporary store in create_from_unordered.
  • Added heuristic in pairix cload to prevent excessively large chunks. #92
  • Added extra checks in cload pairix and cload tabix. #62, #75

v0.2.0

Date: 2024-07-31

Enhancements

  • Implement Momics class.

v0.1.0

Date: 2024-07-29

Enhancements

  • Initial prototype.