Cooler Versions Save

Bug fixes

• Fix estimation of mean bin size when using variable-sized bins #332.
• Fix regression bug to handle multiple convergence statuses in balance CLI #334.

Bug fixes

Several fixes from @robomics

• Improve handling of uint attributes
• Fix incorrect variance stored by _balance_cisonly
• cload.py: fix detection of pandas v2.. causing IOHandles error

Maintenance

• Export _IndexingMixin from cooler.core to keep private API used by cooltools.

New features

• New query engine implementation (no user-facing API changes).
• New logging context and verbosity system.

API changes

• cooler.balance_cooler now uses the same default argument values as the CLI.

Schema

• cooler balance now inserts divisive_weights: False metadata to balancing weights.

Maintenance

• Dropped Python 2 support.
• Removed deprecated io module.
• Deprecated tools module; renamed parallel.
• Various dependency maintenance upgrades.
• Modernized CI and dev tools.
• Migrated to pyproject.toml and modernized packaging infra.

Bug fixes

• Hotfix cooler cload pairs file header parsing to work with the latest version of pandas (>=1.2).
• Update CLI help for --balance-args to clarify usage. By @gfudenberg.

Bug fixes

• Fixed the new header parsing in cooler cload pairs to handle esoteric file stream implementations. Specifically GzipFile had stopped working. By @golobor

Enhancements

• Added single-cell cooler file flavor (.scool) (#201). Thanks @joachimwolff.

Date : 2020-06-23

Maintenance

• Improved code coverage
• Added missing autodoc for cooler balance
• Dropped pysam and biopython as hard dependencies
• Officially sunsetting Python 2.7 support

Enhancements

• Added zoom progressions (#203)

Bug fixes

• Allow hashes in read IDs in cload pairs (#193)

Maintenance

• Code styling with black
• Add coverage reporting

Bug fixes

• Replace json with simplejson to deal with attrs stored as bytes

Maintenance

• Added contributing guidelines

Bug fixes

• Fixed a related regression to the one fixed in v0.8.5 that affected selection of the chrom column in the bin selector.