v0.0.3

What's Changed

• Bump dependencies by @robomics in #34
• Refactor CI by @robomics in #35
• Bump project version in CMakeLists.txt as well by @robomics in #36
• Switch to C++23 by @robomics in #37
• Setup pre-commit by @robomics in #38
• Add integration tests by @robomics in #41
• Fix incorrect log ratio computation performed in NCHG::iterator by @robomics in #42
• Major refactor by @robomics in #39
• Remove redundant \n from critical log messages by @robomics in #44
• Initial implementation of NCHG cartesian-product by @robomics in #43
• Fix Docker build on linux/arm64 by @robomics in #45
• Restructure codebase by @robomics in #46
• Implement checks to identify partial and corrupted output files by @robomics in #48
• Workaround CI timeouts when building arm64 Docker images by @robomics in #51
• NCHG merge: do not attempt to open all input files at once by @robomics in #50
• [ci]: update dependabot.yml by @robomics in #54
• [ci]: refactor by @robomics in #55
• [dependencies]: bump by @robomics in #56
• Bump codecov/codecov-action from 4 to 5 by @dependabot in #47
• [pre-commit]: update config and add new hooks by @robomics in #53
• [docker]: simplify Dockerfile by @robomics in #58
• [ci]: update Ubuntu CI to respect -G Ninja by @robomics in #57
• [license]: fix SPDX headers by @robomics in #59
• [ci]: fix CodeQL warnings by @robomics in #60
• [ci]: rework build-dockerfile.yml to take advantage of the new ARM runners by @robomics in #62
• [fix]: ensure NCHG compute always creates its temporary directory by @robomics in #61
• [maintenance]: suppress compiler warnings due to third-party deps by @robomics in #63
• [refactor]: switch to Boost.Process v2 by @robomics in #64
• [fix]: Add a build knob to disable the use of pidfd_open() by @robomics in #66
• Add .editorconfig by @robomics in #68
• [feat]: support multiprocess logging by @robomics in #67
• [fix]: nchg compute: read the name of the log message queue from env variables by @robomics in #69
• [refactor]: optimize computing statistics over genomic domains by @robomics in #72
• [refactor]: various minor changes by @robomics in #71
• [feature]: embed version and license information using git and CMake by @robomics in #73
• [ci]: add tests for NCHG checksum by @robomics in #74
• [enhancement]: configure clang-tidy and run it as part of the CI by @robomics in #75
• [testing]: use lock files when fetching and extracting the test datasets by @robomics in #77
• [deps]: update hictk to v2.1.2 by @robomics in #76
• [ci]: simplify build-dockerfile.yml workflow by @robomics in #78
• Bump the github-actions group across 1 directory with 4 updates by @dependabot in #70
• Prepare for release by @robomics in #79

Full Changelog: v0.0.2...v0.0.3

v0.0.2

What's Changed

• Fix bug when processing trans-only interactions by @robomics in #33

Full Changelog: v0.0.1...v0.0.2

v0.0.1

What's Changed

• Fix windows builds by @robomics in #2
• Improve performance of CI by @robomics in #3
• Enable codecov CI by @robomics in #4
• Support computing statistical significance for interactions overlapping arbitrary 2D domains by @robomics in #1
• Make NCHG compute multithreaded by @robomics in #6
• Various bugfixes by @robomics in #7
• Expand integration test suite used by CI by @robomics in #8
• Add --expected-values option to NCHG compute by @robomics in #9
• Various minor improvements by @robomics in #10
• Implement NCHG filter --sorted by @robomics in #11
• Properly deal with non-finite values in NCHG filter by @robomics in #12
• Bump dependencies by @robomics in #13
• Maintenance by @robomics in #15
• Implement MAD-max filtering by @robomics in #14
• Do not bother testing domains with 0 observed interactions by @robomics in #17
• Use different cache scopes when building x86 and ARM docker images by @robomics in #18
• Add options --correct-pvals-chrom-by-chrom and --correct-pvals-cis-trans by @robomics in #16
• Improve estimation of the expected values profile by @robomics in #19
• Optimize IO by @robomics in #20
• Bump dependencies by @robomics in #21
• Performance optimization by @robomics in #22
• Fix bug in NCHG filter by @robomics in #23
• Support computing the expected values for cis/trans-only by @robomics in #24
• Support specifying custom bin masks by @robomics in #26
• Avoid needlessly computing cis expected values by @robomics in #25
• Bump docker/build-push-action from 5 to 6 by @dependabot in #27
• Fix bug in NCHG compute by @robomics in #29
• Improve error message when expected value file is lacking data for chrom pair by @robomics in #30
• Workaround spurious failures when spawning child processes by @robomics in #28
• Various minor bugfix by @robomics in #31
• Change how the log ratio is computed by @robomics in #32

New Contributors

• @robomics made their first contribution in #2
• @dependabot made their first contribution in #27

Full Changelog: https://github.com/paulsengroup/NCHG/commits/v0.0.1