Releases: paulsengroup/hictk
Releases · paulsengroup/hictk
v2.0.1
The main motivation behind this release is to ensure that the up-to-date documentation is properly published on ReadTheDocs.
More details
hictk is relying on the linkcheck plugin to ensure that the documentation does not contain broken or invalid links.
However, when the documentation is being built by the ReadTheDocs CI, some of the links in the docs are not yet valid (but they will be once the up-to-date documentation is published).
linkcheck detected this issue and cancelled the CI job, which is why there is no documentation for hictk v2.0.0 on ReadTheDocs.
PR #299 updates linkcheck's ignore list such that the temporarily invalid links are not checked by linkcheck.
The up-to-date documentation for hictk v2.0.1 is available at: https://hictk.readthedocs.io/en/v2.0.1/
What's Changed
- Update linkcheck ignore list by @robomics in #299
- Remove unused workflow by @robomics in #300
- Implement bins_ptr() accessor for cooler::SingleCellFile() by @robomics in #298
- Prepare for release by @robomics in #301
- Fix typo in the README by @robomics in #303
Full Changelog: v2.0.0...v2.0.1
Contributors
robomics
Assets 2
v2.0.0
What's Changed
Changes to library code
- Fix bug when fetching whole-genome interactions as dense or sparse matrix by @robomics in #196, #197
- Expose bin_ptr() accessor wherever it makes sense by @robomics in #199
- Make hictk::common depend on the git-watcher target by @robomics in #233
- Various improvements and bug fixes to code related to fetching interactions as Eigen matrices by @robomics in #227
- Improve transformers::ToDataFrame() by @robomics in #234
- Support merging streams of pixels originating from files of different formats by @robomics in #243
- Fix division by zero when fetching pixels from coolers with bin tables with variable bin size by @robomics in #250
- Various improvements to balancing::Weights by @robomics in #251
- Fix bug when fetching normalized interactions as dense matrices by @robomics in #252
- Minor changes to iterators by @robomics in #253
- Improve support for "square" Cooler files by @robomics in #249
- Rewrite VectorOfAtomicDecimals by @robomics in #255
- Make constructors for To*Matrix transformers more flexible by @robomics in #266
- Improve performance of ToSparseMatrix by reducing memory allocations by @robomics in #277
- Refactor FileStream class by @robomics in #282
- Replace HICTK_UNREACHABLE_CODE macro with hictk::unreachable_code() by @robomics in #285
- Make sure cooler::File::close() does not attempt to finalize files twice by @robomics in #291
- Mark ~TmpDir() noexcept and log errors as warnings using spdlog by @robomics in #292
- Improve logging when failures occur from within class destructors by @robomics in #293
- Add option to exclude "ALL" chromosomes when calling nchroms() on .hic files by @robomics in #294
Changes to CLI tools
- Better handling of coolers with FP counts by @robomics in #201, #202
- Implement hictk metadata command by @robomics in #204, #222
- Improve error message when temporary folder cannot be safely determined by @robomics in #210
- Fix CLI exit code by @robomics in #215
- Add --no-create-weight-link CLI flag where appropriate by @robomics in #223
- Minor improvements to various hictk subcommands by @robomics in #229, #231, #232, #228, #238
- Add option to override count type used to convert .hic files to .[m]cool format by @robomics in #203
- hictk load: support ingesting interactions from pairs/pixel files with interactions overlapping with the lower-triangular matrix by @robomics in #264
- Tweak max active log level based on CMake build type by @robomics in #278
- Fix default log levels when compiling hictk in Debug mode by @robomics in #279
- Ensure no temporary files are written when balancing .hic files with --in-memory by @robomics in #280
- hictk load: support loading compressed interactions by @robomics in #244
- Fix temporary file name collisions in hictk convert *cool -> hic by @robomics in #274
Updates to CI
- Bump GH Actions by @dependabot in #61, #188
- Update .pre-commit-config.yaml by @robomics in #198, #270
- Use prettier to format MD and YAML files by @robomics in #221
- Reduce duration of fuzzy test CI when triggered by PRs by @robomics in #254
- Update cppstd.yml by @robomics in #259
- Disable ccache in fuzzy-testing.yml by @robomics in #260
- Optimize CI workflows by @robomics in #268
- Add workflows to lint project by @robomics in #269
- Use gersemi instead of cmake-format to format CMake files by @robomics in #283
- Bump clang-tidy used by CI by @robomics in #284
- Add macos-15 to CI test matrix by @robomics in #287
- Fix ccache cache eviction logic when using GHA job matrix by @robomics in #288
- Bump compiler used to build Dockerfile to clang-19 by @robomics in #256
Updates to testing
- Add automated tests covering hictk's packaging by @robomics in #246
- Rewrite hictk's fuzzer by @robomics in #226
- Test compatibility with newer C++ standards by @robomics in #258
- Overhaul of the integration test suite by @robomics in #257
- Improve coverage by @robomics in #263
- Increase integration test base timeout by @robomics in #281
- Fix to fuzzer suite by @robomics in #290
- Fix visibility warnings issued when compiling hictk_fuzzer using GCC by @robomics in #276
Various
- Allow dynamically linking to Arrow libs even when building with static linking by @robomics in #200
- Reduce size of hictk's Docker image by @robomics in #209
- Update docs by @robomics in #195, #208
- Refactor by @robomics in #245
- Add missing dep in conanfile.py by @robomics in #265
- Improve compilation times by @robomics in #262
- Fix SPDX headers by @robomics in #267
- Fix Release builds on GCC8 by @robomics in #273
- Bump dependencies by @robomics in #247
- Tweak spdlog by @robomics in #286
- Bump libarchive by @robomics in #289
- Prepare for release by @robomics in #296
Full Changelog: v1.0.0...v2.0.0
Contributors
dependabot and robomics
Assets 2
v1.0.0
What's Changed
- Fix incorrect overload being called when fetching pixels from cooler files by @robomics in #158
- Properly deal with .hic files with missing normalization vectors by @robomics in #162
- Fix fuzzy tests by @robomics in #165
- hictk balance: add --no-create-weight-link option by @robomics in #167
- hictk balance: honor --in-memory by @robomics in #166
- Add more benchmarks by @robomics in #164
- Throw an error when a non-existing folder is passed to --tmpdir by @robomics in #168
- Switch from conanfile.txt to conanfile.py by @robomics in #169
- Update Docker images used by CI by @robomics in #173
- Refactor code to return interactions as sparse/dense Eigen matrices by @robomics in #176
- Fix typo by @Phlya in #177
- Support fetching interactions as arrow::Table by @robomics in #170
- For the time being, refuse to build on big-endian architectures by @robomics in #181
- Support for fetching interactions from the lower triangle when it makes sense by @robomics in #179
- Drop unnecessary dependency from conanfile.py by @robomics in #184
- Ensure pixel transformers are well-behaved when given an empty range of pixels by @robomics in #182
- Support opening .hic files with only 1 bin per chromosome by @robomics in #180
- Fix typo in conanfile.py by @robomics in #186
- Update docs by @robomics in #183
- Various fixes to the build system by @robomics in #187
- Prepare for release by @robomics in #189
New Contributors
Full Changelog: v0.0.12...v1.0.0
Contributors
Phlya and robomics
Assets 2
v0.0.12
What's Changed
- Properly support aggregating .scool with float counts by @robomics in #145
- Install missing targets by @robomics in #146
- Fix segfault when computing the expected value vector by @robomics in #147
- Support chained calls to BinTable.subset() by @robomics in #148
- Drop macOS 11 from CI by @robomics in #149
- Minor updates to the build system by @robomics in #150
- Gracefully deal with files created on Win and read on *NIX by @robomics in #151
- Improve handling of temporary files by @robomics in #152
- Format project by @robomics in #153
- Bugfix: query mirroring by @robomics in #154
- Bump deps by @robomics in #155
- Prepare for release by @robomics in #156
Full Changelog: v0.0.11...v0.0.12
Contributors
robomics
Assets 2
V0.0.11
What's Changed
- Fix fuzzy tests by @robomics in #132
- Update docs by @robomics in #137
- Update CI by @robomics in #138
- Bump deps by @robomics in #136
- Address static-analysis warnings by @robomics in #139
- Improve performance of hictk zoomify when processing .hic files by @robomics in #133
- Implement hictk dump -t weights by @robomics in #140
- Add tutorials to the docs by @robomics in #141
- Implement SCALE and VC balancing by @robomics in #134
- Refactor by @robomics in #142
Full Changelog: v0.0.10...v0.0.11
Contributors
robomics
Assets 2
v0.0.10
Contributors
robomics
Assets 2
v0.0.9
What's Changed
- Remove xxhash leftovers by @robomics in #113
- Fix hictk dump -t bins for files in .scool format by @robomics in #114
- Expose .hic file attributes by @robomics in #115
- Add missing calls to find_dependency to Install.cmake by @robomics in #116
- Address compiler warnings when compiling with MSVC by @robomics in #117
- Bump dependencies by @robomics in #118
- Make hictk load honor the value passed through --assembly by @robomics in #119
- Initial implementation of a generic multi-res file handle by @robomics in #120
- Update CI by @robomics in #122
- Fix CI to build docker image by @robomics in #123
- Rename bin_size() to resolution() to make API more consistent by @robomics in #124
- Add links to hictk's publication by @robomics in #125
- Update docs by @robomics in #126, #127
- Prepare for release by @robomics in #128
Full Changelog: v0.0.8...v0.0.9
Contributors
robomics
Assets 2
v0.0.8
v0.0.7
What's Changed
- Bump actions/cache from 3 to 4 by @dependabot in #103
- Add native support to write .hic files by @robomics in #102
- Fix integer overflow that could occur when writing .cool files by @robomics in #104
- Update tests by @robomics in #105
- Bump dependencies by @robomics in #106
- Prepare for release by @robomics in #107
Full Changelog: v0.0.6...v0.0.7
Contributors
dependabot and robomics