Releases: paulsengroup/hictkpy
Releases · paulsengroup/hictkpy
v1.1.0
What's Changed
The highlights of this release are:
- Providing pre-built wheels for Python 3.13 #113
- Enable efficient computation of various descriptive statistics from streams of pixels #129
- Improved API ergonomics #123
The release also comes with a handful of bug fixes, minor performance improvements, and better documentation.
New features and improvements
- Support Python 3.13 by @robomics in #113
- Improve error message generated when invalid params are passed to hictkpy.File() by @robomics in #115
- Annotate functions with nb::rv_policy to avoid unnecessary copies by @robomics in #118
- Improve API of MultiResFile class by @robomics in #126
- Add accessors for BinTable objects to FileWriter classes by @robomics in #128
- Make API more ergonomic by @robomics in #123
- Implement several methods to efficiently compute various descriptive statistics given PixelSelector object by @robomics in #129
- Bring back compatibility with recent versions of MSVC by @robomics in #133
- Return balancing weights as numpy arrays by @robomics in #114
Bugfix
- Fix typo in cooler.FileWriter class by @robomics in #116
- Fix bug in BinTable::make_iterable() by @robomics in #121
- Fix PixelSelector::get_coord*() by @robomics in #122
- Ensure BinTable::to_df() does not fail when called on tables from .hic files by @robomics in #127
- Fix datarace in logging code by @robomics in #131
- Rename "bin_size" attribute from .hic files to "bin-size" by @robomics in #134
Updates to CI
- Use the latest manylinux_2_28 image available by @robomics in #119
- Pin manylinux image to avoid invalidating CI build cache too frequently by @robomics in #120
- Bump pypa/cibuildwheel from 2.21 to 2.22 by @dependabot in #130
- [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #101
Packaging and tooling
Documentation
- Fix typos in the README by @robomics in #109
- Update the docs by @robomics in #124
- Update the Quickstart section to showcase PixelSelector.describe() by @robomics in #136
Various
Full Changelog: v1.0.0...v1.1.0
Contributors
dependabot, pre-commit-ci, and robomics
Assets 2
v1.0.0
What's Changed
New features and improvements
- Implement accessors for balancing weights by @robomics in #49
- Automatically infer the resolution when file is in .cool format by @robomics in #51
- Make the public API more Pythonic by @robomics in #85
- Support interfacing spdlog with Python's logging stdlib by @robomics in #88
- Expose the hictk::BinTable class by @robomics in #50
Bugfix
- Fix query mirroring when fetching pixels as dfs by @robomics in #54
- Fix bug when fetching whole-genome interactions as dense matrix by @robomics in #64
- Fix bug when fetching interactions as sparse matrix by @robomics in #65
Updates to CI
- Bump pypa/cibuildwheel from 2.17 to 2.21 by @dependabot in #52, #55, #58, and #76
- Workaround macOS CI failure by @robomics in #63
- Update CI workflows by @robomics in #81
- Optimize CI by @robomics in #89
- Add jobs to publish releases/wheels to (Test) PyPI by @robomics in #100
- Fix CI by @robomics in #103
Updates to testing
- Implement fuzzer by @robomics in #74
- Test hictkpy against Python 3.13 by @robomics in #99
- Skip test_bin_table.py::TestClass::test_to_df when test deps are missing by @robomics in #102
Packaging and tooling
- Do not export header files in wheels by @robomics in #47
- Remove MANIFEST.in by @robomics in #70
- Bump nanobind and generate type stubs by @robomics in #57
- Update .pre-commit-config.yaml by @robomics in #66
- Update conan_provider.cmake to 8bf396b by @robomics in #59
- Make pandas and scipy optional deps by @robomics in #90
- Fix stubgen by @robomics in #96
- Pin pyarrow version and detect ABI incompatibilities at runtime by @robomics in #94
- Use the Arrow C and PyCapsule data interfaces to share data with Python by @robomics in #98
- Bump nanobind. Port to what will be hictk v2.0.0 in the near future by @robomics in #78
- Bump hictk to v2.0.1 by @robomics in #104
Various
- Update docs by @robomics in #60 and #92
- Maintenance by @robomics in #80
- Explicitly link to std::filesystem by @robomics in #82
- Refactor by @robomics in #83
- Refuse to add pixels to files that have already been finalized by @robomics in #87
- Re-enable logging on Windows by @robomics in #93
- Undef SPDLOG_ACTIVE_LEVEL=SPDLOG_LEVEL_OFF when compiling on Windows by @robomics in #95
- Prepare for release by @robomics in #105
Full Changelog: v0.0.5...v1.0.0
Contributors
dependabot and robomics
Assets 2
v0.0.5
v0.0.4
What's Changed
- Bump actions/cache from 3 to 4 by @dependabot in #23
- Workaround import warning when running pytest by @robomics in #26
- Refactor CI by @robomics in #27
- Fix typos in attribute names. Properly handle missing attribute values by @robomics in #25
- Switch to nanobind by @robomics in #28
- Update the docs by @robomics in #33
- Add docstrings to class definitions by @robomics in #32
- Bump hictk to v0.0.9 by @robomics in #30
- Update nanobind to v1.9.2 by @robomics in #34
- Refactor MultiResFile by @robomics in #35
- Expose is_mcool() and is_scool() by @robomics in #37
- Support creating .hic and .cool files by @robomics in #31
- Update the docs by @robomics in #36
- Introduce the HICTKPY_PROJECT_TOP_LEVEL_INCLUDES build knob to disable conan by @robomics in #29
- Bump pypa/cibuildwheel from 2.16 to 2.17 by @dependabot in #38
- Support queries overlapping with the lower matrix triangle by @robomics in #39
- Support creating cooler files from float pixels by @robomics in #40
- Update docs by @robomics in #41
- Prepare for release by @robomics in #42
Full Changelog: v0.0.3...v0.0.4
Contributors
dependabot and robomics
Assets 2
v0.0.3
What's Changed
- Bump docker/setup-qemu-action from 2 to 3 by @dependabot in #12
- Correct PixelSelector lifetime by @robomics in #15
- Add docs by @robomics in #16
- Expand API by @robomics in #17
- Bump actions/setup-python from 4 to 5 by @dependabot in #18
- Bump actions/upload-artifact from 3 to 4 by @dependabot in #19
- Bump actions/download-artifact from 3 to 4 by @dependabot in #20
- Bump pypa/cibuildwheel from 2.14 to 2.16 by @dependabot in #13
- Bump dependencies by @robomics in #21
- Prepare for release by @robomics in #22
Full Changelog: v0.0.2...v0.0.3
Contributors
dependabot and robomics