hictkpy - v1.3.0

What's Changed

The main change introduced with this release is the update to hictk v2.1.2, which comes with a fix for a bug that could lead to incorrect results being returned when fetching interactions from cis regions with unusual shapes as DataFrames of pixels with query_span="full".

See https://github.com/paulsengroup/hictk/pull/406 for more details.

Another change is that the count_type argument of the fetch() method on hictkpy.PixelSelector objects now accepts numeric type objects (e.g., int, np.int64, etc.).

Changelog

Improvements

• [refactor]: streamline Pixel class by @robomics in https://github.com/paulsengroup/hictkpy/pull/173
• [feature]: support using type objects when calling fetch() on PixelSelectors by @robomics in https://github.com/paulsengroup/hictkpy/pull/174

Documentation

• [docs]: add recommendation to use clang when building wheels by @robomics in https://github.com/paulsengroup/hictkpy/pull/168
• [docs]: update the documentation by @robomics in https://github.com/paulsengroup/hictkpy/pull/177

Various

• [deps]: bump dependencies by @dependabot, @pre-commit-ci, and @robomics in https://github.com/paulsengroup/hictkpy/pull/137, https://github.com/paulsengroup/hictkpy/pull/169, and https://github.com/paulsengroup/hictkpy/pull/172
• [ci]: various updates by @robomics in https://github.com/paulsengroup/hictkpy/pull/175 and https://github.com/paulsengroup/hictkpy/pull/176

Full Changelog: https://github.com/paulsengroup/hictkpy/compare/v1.2.0...v1.3.0

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Published by robomics 9 months ago

hictkpy - v1.2.0

What's Changed

This release comes with a few new features and performance improvements.

Changelog

Features

• [feature]: support creating .cool files with no interactions by @robomics in https://github.com/paulsengroup/hictkpy/pull/159
• [feature]: support efficient computation of statistics including pixels wo/ interactions by @robomics in https://github.com/paulsengroup/hictkpy/pull/154 and https://github.com/paulsengroup/hictkpy/pull/158
• [feature]: improve pixel validation when creating .cool/hic files by @robomics in https://github.com/paulsengroup/hictkpy/pull/160
• [feature]: support fetching interactions overlapping with a band around the matrix diagonal by @robomics in https://github.com/paulsengroup/hictkpy/pull/165

Updates to CI

• [ci]: refactor by @robomics in https://github.com/paulsengroup/hictkpy/pull/142
• [ci]: Address CodeQL warnings by @robomics in https://github.com/paulsengroup/hictkpy/pull/143
• [pre-commit]: update config and add new hooks by @robomics in https://github.com/paulsengroup/hictkpy/pull/152
• [ci]: dependabot: reduce update frequency by @robomics in https://github.com/paulsengroup/hictkpy/pull/153
• [ci]: setup dependabot for updating Python deps by @robomics in https://github.com/paulsengroup/hictkpy/pull/162
• [ci]: fix undefined variable error by @robomics in https://github.com/paulsengroup/hictkpy/pull/166
• Bump the github-actions group across 1 directory with 3 updates by @dependabot in https://github.com/paulsengroup/hictkpy/pull/155

Various

• [docs]: speed up documentation builds on RTD by @robomics in https://github.com/paulsengroup/hictkpy/pull/146
• Update pyproject.toml to comply with PEP 639 by @robomics in https://github.com/paulsengroup/hictkpy/pull/147
• pyproject.toml: make BUILDSHAREDLIBS and CMAKEOSXDEPLOYMENT_TARGET tunable by @robomics in https://github.com/paulsengroup/hictkpy/pull/148
• [testing]: exclude chrY and chrM from fuzzy-testing.yml when --format=describe by @robomics in https://github.com/paulsengroup/hictkpy/pull/149
• [docs]: fix RTD builds by @robomics in https://github.com/paulsengroup/hictkpy/pull/150
• [deps]: bump hictk and other deps by @robomics in https://github.com/paulsengroup/hictkpy/pull/161
• [fix]: suppress warnings about leaked refs to nanobind objects by @robomics in https://github.com/paulsengroup/hictkpy/pull/163
• [deps]: bump hictk to v2.1.1 by @robomics in https://github.com/paulsengroup/hictkpy/pull/164

Full Changelog: https://github.com/paulsengroup/hictkpy/compare/v1.1.0...v1.2.0

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Published by robomics 11 months ago

hictkpy - v1.1.0

What's Changed

The highlights of this release are: - Providing pre-built wheels for Python 3.13 https://github.com/paulsengroup/hictkpy/pull/113 - Enable efficient computation of various descriptive statistics from streams of pixels https://github.com/paulsengroup/hictkpy/pull/129 - Improved API ergonomics https://github.com/paulsengroup/hictkpy/pull/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 https://github.com/paulsengroup/hictkpy/pull/113
• Improve error message generated when invalid params are passed to hictkpy.File() by @robomics in https://github.com/paulsengroup/hictkpy/pull/115
• Annotate functions with nb::rv_policy to avoid unnecessary copies by @robomics in https://github.com/paulsengroup/hictkpy/pull/118
• Improve API of MultiResFile class by @robomics in https://github.com/paulsengroup/hictkpy/pull/126
• Add accessors for BinTable objects to FileWriter classes by @robomics in https://github.com/paulsengroup/hictkpy/pull/128
• Make API more ergonomic by @robomics in https://github.com/paulsengroup/hictkpy/pull/123
• Implement several methods to efficiently compute various descriptive statistics given PixelSelector object by @robomics in https://github.com/paulsengroup/hictkpy/pull/129
• Bring back compatibility with recent versions of MSVC by @robomics in https://github.com/paulsengroup/hictkpy/pull/133
• Return balancing weights as numpy arrays by @robomics in https://github.com/paulsengroup/hictkpy/pull/114

Bugfix

• Fix typo in cooler.FileWriter class by @robomics in https://github.com/paulsengroup/hictkpy/pull/116
• Fix bug in BinTable::make_iterable() by @robomics in https://github.com/paulsengroup/hictkpy/pull/121
• Fix PixelSelector::get_coord*() by @robomics in https://github.com/paulsengroup/hictkpy/pull/122
• Ensure BinTable::to_df() does not fail when called on tables from .hic files by @robomics in https://github.com/paulsengroup/hictkpy/pull/127
• Fix datarace in logging code by @robomics in https://github.com/paulsengroup/hictkpy/pull/131
• Rename "bin_size" attribute from .hic files to "bin-size" by @robomics in https://github.com/paulsengroup/hictkpy/pull/134

Updates to CI

• Use the latest manylinux228 image available by @robomics in https://github.com/paulsengroup/hictkpy/pull/119
• Pin manylinux image to avoid invalidating CI build cache too frequently by @robomics in https://github.com/paulsengroup/hictkpy/pull/120
• Bump pypa/cibuildwheel from 2.21 to 2.22 by @dependabot in https://github.com/paulsengroup/hictkpy/pull/130
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/paulsengroup/hictkpy/pull/101

Packaging and tooling

• Bump deps in conanfile.py by @robomics in https://github.com/paulsengroup/hictkpy/pull/132
• Prepare for release by @robomics in https://github.com/paulsengroup/hictkpy/pull/135

Documentation

• Fix typos in the README by @robomics in https://github.com/paulsengroup/hictkpy/pull/109
• Update the docs by @robomics in https://github.com/paulsengroup/hictkpy/pull/124
• Update the Quickstart section to showcase PixelSelector.describe() by @robomics in https://github.com/paulsengroup/hictkpy/pull/136

Various

• Remove dead code by @robomics in https://github.com/paulsengroup/hictkpy/pull/117
• Improve tests by @robomics in https://github.com/paulsengroup/hictkpy/pull/125

Full Changelog: https://github.com/paulsengroup/hictkpy/compare/v1.0.0...v1.1.0

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Published by robomics about 1 year ago

hictkpy - v1.0.0

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 testbintable.py::TestClass::testtodf 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 SPDLOGACTIVELEVEL=SPDLOGLEVELOFF 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

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Published by robomics over 1 year ago

hictkpy - v0.0.5

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

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Published by robomics almost 2 years ago

hictkpy - v0.0.4

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 ismcool() and isscool() 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 HICTKPYPROJECTTOPLEVELINCLUDES 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

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Published by robomics almost 2 years ago

hictkpy - v0.0.3

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

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Published by robomics about 2 years ago

hictkpy - v0.0.2

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

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Published by robomics over 2 years ago

hictkpy - v0.0.1

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Published by robomics over 2 years ago