Bug fixes

• fix: Fix indexing in merge_breakpoints by @conradbzura in #468

Full Changelog: v0.10.3...v0.10.4

What's Changed

• Update to support numpy>=1.26 and numpy 2.x by @lrauschning in #446
• Dropped support for numpy < 1.26 and Python 3.8.
• Dropping pypairix dependency from cooler[all] until compilation issues are resolved.

New Contributors

• @lrauschning made their first contribution in #446

Full Changelog: v0.10.2...v0.10.3

Maintenance

• NumPy 2.0 was released. Pin numpy < 2 until we migrate.

Bug fixes

• fix: Pixel annotation with partial bin table by @nvictus and @Phlya in #426

New features

• Support custom contig separator characters in pairix index by @nvictus in #398

Performance improvements and bug fixes

• Make annotate faster by using indexing instead of merge by @Phlya in #353
• Fix input text file handling on certain pandas versions by @thomas-reimonn in #384
• Reduce memory consumption of very high-resolution merges by @nvictus in #408

Maintenance

• Add windows and macos platforms to CI by @nvictus in #383
• Add type annotations by @GarrettNg in #387
• docs: Replace ftp with OSN storage bucket for example data. by @nvictus in #399

New Contributors

• @a-detiste made their first contribution in #346
• @manzt made their first contribution in #363
• @thomas-reimonn made their first contribution in #380
• @GarrettNg made their first contribution in #387

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.