v0.11.0

This release fixes a backlog of bugs, adds a few small features, and modernizes the development setup. The cooler[test], cooler[dev] and cooler[docs] extras have been removed in favor of PEP735 dependency groups. Contributors should use uv sync for development instead.

Fixes

• Import cooler on AWS Lambda and other environments without process-shared semaphores (#329).
• Fixes to .scool appends: appending cells no longer adds a new copy of the bin table each time, and the ncells count stays correct.
• Appending cells with a different bin table to an existing .scool file now raises an error.
• Balancing with --ignore-diags 0 now counts the main diagonal once, so the resulting weights will differ from earlier versions.
• More robust inputs: blacklist BED files with a single line, no lines or header lines now work, and malformed chromsizes files give a clear error.
• Parallel runs wait for their worker processes to exit. Lingering workers can no longer hold file locks.
• No environment variables in -vv logs. The process info logged at exit is now a small, stable set of attributes.

API changes

• cooler show and cooler dump accept --weight-name to use a balancing weight column other than weight.

Documentation

• Genomic coordinates and range strings like chr1:10,000,000-11,000,000 are now documented as zero-based and half-open, not as 1-based coordinates.

New Contributors

• @dmalzl made their first contribution in #472
• @sapunyangkut made their first contribution in #483
• @jpaggi made their first contribution in #471
• @ShigrafS made their first contribution in #462
• @Snowman-cpu made their first contribution in #457

Thanks to everyone who contributed to this release: @jpaggi, @dmalzl, @ShigrafS, @Snowman-cpu, @a-detiste and @sapunyangkut.

Full Changelog: v0.10.4...v0.11.0