Hictkpy

What's Changed

* hictk published in Bioinformatics! by robomics in https://github.com/paulsengroup/hictkpy/pull/61

New features and improvements

* Implement accessors for balancing weights by robomics in https://github.com/paulsengroup/hictkpy/pull/49
* Automatically infer the resolution when file is in .cool format by robomics in https://github.com/paulsengroup/hictkpy/pull/51
* Make the public API more Pythonic by robomics in https://github.com/paulsengroup/hictkpy/pull/85
* Support interfacing spdlog with Python's logging stdlib by robomics in https://github.com/paulsengroup/hictkpy/pull/88
* Expose the hictk::BinTable class by robomics in https://github.com/paulsengroup/hictkpy/pull/50

Bugfix

* Fix query mirroring when fetching pixels as dfs by robomics in https://github.com/paulsengroup/hictkpy/pull/54
* Fix bug when fetching whole-genome interactions as dense matrix by robomics in https://github.com/paulsengroup/hictkpy/pull/64
* Fix bug when fetching interactions as sparse matrix by robomics in https://github.com/paulsengroup/hictkpy/pull/65

Updates to CI

* Bump pypa/cibuildwheel from 2.17 to 2.21 by dependabot in https://github.com/paulsengroup/hictkpy/pull/52, https://github.com/paulsengroup/hictkpy/pull/55, https://github.com/paulsengroup/hictkpy/pull/58, and https://github.com/paulsengroup/hictkpy/pull/76
* Workaround macOS CI failure by robomics in https://github.com/paulsengroup/hictkpy/pull/63
* Update CI workflows by robomics in https://github.com/paulsengroup/hictkpy/pull/81
* Optimize CI by robomics in https://github.com/paulsengroup/hictkpy/pull/89
* Add jobs to publish releases/wheels to (Test) PyPI by robomics in https://github.com/paulsengroup/hictkpy/pull/100
* Fix CI by robomics in https://github.com/paulsengroup/hictkpy/pull/103

Updates to testing

* Implement fuzzer by robomics in https://github.com/paulsengroup/hictkpy/pull/74
* Test hictkpy against Python 3.13 by robomics in https://github.com/paulsengroup/hictkpy/pull/99
* Skip test_bin_table.py::TestClass::test_to_df when test deps are missing by robomics in https://github.com/paulsengroup/hictkpy/pull/102

Packaging and tooling

* Do not export header files in wheels by robomics in https://github.com/paulsengroup/hictkpy/pull/47
* Remove MANIFEST.in by robomics in https://github.com/paulsengroup/hictkpy/pull/70
* Bump nanobind and generate type stubs by robomics in https://github.com/paulsengroup/hictkpy/pull/57
* Update .pre-commit-config.yaml by robomics in https://github.com/paulsengroup/hictkpy/pull/66
* Update conan_provider.cmake to 8bf396b by robomics in https://github.com/paulsengroup/hictkpy/pull/59
* Make pandas and scipy optional deps by robomics in https://github.com/paulsengroup/hictkpy/pull/90
* Fix stubgen by robomics in https://github.com/paulsengroup/hictkpy/pull/96
* Pin pyarrow version and detect ABI incompatibilities at runtime by robomics in https://github.com/paulsengroup/hictkpy/pull/94
* Use the Arrow C and PyCapsule data interfaces to share data with Python by robomics in https://github.com/paulsengroup/hictkpy/pull/98
* Bump nanobind. Port to what will be hictk v2.0.0 in the near future by robomics in https://github.com/paulsengroup/hictkpy/pull/78
* Bump hictk to v2.0.1 by robomics in https://github.com/paulsengroup/hictkpy/pull/104

Various

* Update docs by robomics in https://github.com/paulsengroup/hictkpy/pull/60 and https://github.com/paulsengroup/hictkpy/pull/92
* Maintenance by robomics in https://github.com/paulsengroup/hictkpy/pull/80
* Explicitly link to std::filesystem by robomics in https://github.com/paulsengroup/hictkpy/pull/82
* Refactor by robomics in https://github.com/paulsengroup/hictkpy/pull/83
* Refuse to add pixels to files that have already been finalized by robomics in https://github.com/paulsengroup/hictkpy/pull/87
* Re-enable logging on Windows by robomics in https://github.com/paulsengroup/hictkpy/pull/93
* Undef SPDLOG_ACTIVE_LEVEL=SPDLOG_LEVEL_OFF when compiling on Windows by robomics in https://github.com/paulsengroup/hictkpy/pull/95
* Prepare for release by robomics in https://github.com/paulsengroup/hictkpy/pull/105

**Full Changelog**: https://github.com/paulsengroup/hictkpy/compare/v0.0.5...v1.0.0

What's Changed
* Bugfix: query mirroring by robomics in https://github.com/paulsengroup/hictkpy/pull/43
* Bump dependencies by robomics in https://github.com/paulsengroup/hictkpy/pull/44
* Cleanup fetch code by robomics in https://github.com/paulsengroup/hictkpy/pull/45
* Prepare for release by robomics in https://github.com/paulsengroup/hictkpy/pull/46


**Full Changelog**: https://github.com/paulsengroup/hictkpy/compare/v0.0.4...v0.0.5

What's Changed
* Bump actions/cache from 3 to 4 by dependabot in https://github.com/paulsengroup/hictkpy/pull/23
* Workaround import warning when running pytest by robomics in https://github.com/paulsengroup/hictkpy/pull/26
* Refactor CI by robomics in https://github.com/paulsengroup/hictkpy/pull/27
* Fix typos in attribute names. Properly handle missing attribute values by robomics in https://github.com/paulsengroup/hictkpy/pull/25
* Switch to nanobind by robomics in https://github.com/paulsengroup/hictkpy/pull/28
* Update the docs by robomics in https://github.com/paulsengroup/hictkpy/pull/33
* Add docstrings to class definitions by robomics in https://github.com/paulsengroup/hictkpy/pull/32
* Bump hictk to v0.0.9 by robomics in https://github.com/paulsengroup/hictkpy/pull/30
* Update nanobind to v1.9.2 by robomics in https://github.com/paulsengroup/hictkpy/pull/34
* Refactor MultiResFile by robomics in https://github.com/paulsengroup/hictkpy/pull/35
* Expose is_mcool() and is_scool() by robomics in https://github.com/paulsengroup/hictkpy/pull/37
* Support creating .hic and .cool files by robomics in https://github.com/paulsengroup/hictkpy/pull/31
* Update the docs by robomics in https://github.com/paulsengroup/hictkpy/pull/36
* Introduce the HICTKPY_PROJECT_TOP_LEVEL_INCLUDES build knob to disable conan by robomics in https://github.com/paulsengroup/hictkpy/pull/29
* Bump pypa/cibuildwheel from 2.16 to 2.17 by dependabot in https://github.com/paulsengroup/hictkpy/pull/38
* Support queries overlapping with the lower matrix triangle by robomics in https://github.com/paulsengroup/hictkpy/pull/39
* Support creating cooler files from float pixels by robomics in https://github.com/paulsengroup/hictkpy/pull/40
* Update docs by robomics in https://github.com/paulsengroup/hictkpy/pull/41
* Prepare for release by robomics in https://github.com/paulsengroup/hictkpy/pull/42


**Full Changelog**: https://github.com/paulsengroup/hictkpy/compare/v0.0.3...v0.0.4

What's Changed
* Bump docker/setup-qemu-action from 2 to 3 by dependabot in https://github.com/paulsengroup/hictkpy/pull/12
* Correct PixelSelector lifetime by robomics in https://github.com/paulsengroup/hictkpy/pull/15
* Add docs by robomics in https://github.com/paulsengroup/hictkpy/pull/16
* Expand API by robomics in https://github.com/paulsengroup/hictkpy/pull/17
* Bump actions/setup-python from 4 to 5 by dependabot in https://github.com/paulsengroup/hictkpy/pull/18
* Bump actions/upload-artifact from 3 to 4 by dependabot in https://github.com/paulsengroup/hictkpy/pull/19
* Bump actions/download-artifact from 3 to 4 by dependabot in https://github.com/paulsengroup/hictkpy/pull/20
* Bump pypa/cibuildwheel from 2.14 to 2.16 by dependabot in https://github.com/paulsengroup/hictkpy/pull/13
* Bump dependencies by robomics in https://github.com/paulsengroup/hictkpy/pull/21
* Prepare for release by robomics in https://github.com/paulsengroup/hictkpy/pull/22


**Full Changelog**: https://github.com/paulsengroup/hictkpy/compare/v0.0.2...v0.0.3

What's Changed
* Update conanfile.txt by robomics in https://github.com/paulsengroup/hictkpy/pull/9
* Bump actions/checkout from 3 to 4 by dependabot in https://github.com/paulsengroup/hictkpy/pull/10
* Bump hictk by robomics in https://github.com/paulsengroup/hictkpy/pull/11


**Full Changelog**: https://github.com/paulsengroup/hictkpy/compare/v0.0.1...v0.0.2