stripepy-hic - v1.1.1

What's Changed

StripePy published in Bioinformatics 🎉 Read the paper here!

This is a small release introducing a few small features and addressing minor bugs.

New CLI options

We introduce options --license and --cite, which can be used to print StripePy's license and reference on the terminal.

Improved documentation

We restructured and expanded StripePy's documentation, which is now hosted on ReadTheDocs at stripepy.readthedocs.io.

Telemetry

This release introduces initial support to collect application telemetry from StripePy, refer to the Telemetry section in the documentation for more details.

Changelog

New features

• Add CLI options to display Stripepy's license and bibtex entry by @robomics in https://github.com/paulsengroup/StripePy/pull/162
• Initial support for telemetry collection by @robomics in https://github.com/paulsengroup/StripePy/pull/168

Documentation

• Add documentation by @robomics and @rea1991 in https://github.com/paulsengroup/StripePy/pull/60
• Setup ReadTheDocs by @robomics in https://github.com/paulsengroup/StripePy/pull/164
• Restructure README by @rea1991 in https://github.com/paulsengroup/StripePy/pull/165
• Improve API docs by @robomics in https://github.com/paulsengroup/StripePy/pull/171

Bugfix

• Fix help strings by @robomics in https://github.com/paulsengroup/StripePy/pull/163
• Correct parsing of CLI options by @robomics in https://github.com/paulsengroup/StripePy/pull/169

Dependencies

• Update pyproject.toml by @robomics in https://github.com/paulsengroup/StripePy/pull/167
• Bump the github-actions group across 1 directory with 3 updates by @dependabot in https://github.com/paulsengroup/StripePy/pull/161
• Pre-commit autoupdate by @pre-commit-ci in https://github.com/paulsengroup/StripePy/pull/77
• Update pyproject.toml to include a [doc] option group by @robomics in https://github.com/paulsengroup/StripePy/pull/170

Full Changelog: https://github.com/paulsengroup/StripePy/compare/v1.1.0...v1.1.1

- Python
Published by rea1991 11 months ago

stripepy-hic - v1.1.0

This release exposes a new CLI argument --k-neighbour on the stripepy call subcommand to allow users to customize the number of bins considered to calculate the bio-descriptors.

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

- Python
Published by rea1991 about 1 year ago

stripepy-hic - v1.0.0

What's Changed

This release comes with several new features, bug fixes, and performance optimization.

We updated how stripe biodescriptors are calculated to better deal with stripes located close to the beginning or the end of the chromosome. Among other things, this required us to update the schema of the HDF5 file produced by stripepy call.

We also addressed a bug that could cause slightly different results when running stripepy call on different platforms. This was due to how different CPU architectures and operating systems handle floating-point operations.

Regarding computational performance, we introduced several optimizations that resulted in the halving of memory requirements as well as significantly better multithreaded performance (we observed a 4x performance improvement when running stripepy call with default parameters on ENCFF993FGR.mcool on a MacBook Pro M1 (2020) using 8 CPU cores).

Finally, we re-architectured the logging code to support writing detailed log messages to a dedicated file and to make the messages printed to the terminal more user-friendly.

New features

• Setup application logging by @robomics in https://github.com/paulsengroup/StripePy/pull/27
• Improve error messages issued upon failure of CLI argument type validation by @robomics in https://github.com/paulsengroup/StripePy/pull/83
• Add dynamic progress bar by @robomics in https://github.com/paulsengroup/StripePy/pull/86
• Update HDF5 schema by @robomics in https://github.com/paulsengroup/StripePy/pull/85
• Improve parameter validation in Stripe class by @robomics in https://github.com/paulsengroup/StripePy/pull/107
• Re-introduce progress bars by @robomics in https://github.com/paulsengroup/StripePy/pull/120
• Show default values when calling stripepy ... --help by @robomics in https://github.com/paulsengroup/StripePy/pull/118
• Update stripepy view to support showing stripes with their biodescriptors by @robomics in https://github.com/paulsengroup/StripePy/pull/154

Bugfix

• Ensure private datasets are downloaded only when selected explicitly by @robomics in https://github.com/paulsengroup/StripePy/pull/89
• Correct bug in file name inside plotstripes_helper by @rea1991 in https://github.com/paulsengroup/StripePy/pull/93
• Fix bug when running stripepy-call --unit-test by @robomics in https://github.com/paulsengroup/StripePy/pull/94
• Fix inconsistent results produced on different platforms by @robomics in https://github.com/paulsengroup/StripePy/pull/92
• Fix off-by-one error in code computing stripe biodescriptors by @robomics in https://github.com/paulsengroup/StripePy/pull/116
• Correct bound checking in stripe plotting code by @robomics in https://github.com/paulsengroup/StripePy/pull/125
• Fix handling of chromosomes without stripes by @rea1991 in https://github.com/paulsengroup/StripePy/pull/127
• Fix k-neighborhood definition in compute_biodescriptors by @rea1991 in https://github.com/paulsengroup/StripePy/pull/123
• stripepy download: ignore errors occurring while updating the progress bar by @robomics in https://github.com/paulsengroup/StripePy/pull/142
• stripepy view: bring back compatibilty with v1 result files by @robomics in https://github.com/paulsengroup/StripePy/pull/145
• Disable colored logging when stderr is not a TTY by @robomics in https://github.com/paulsengroup/StripePy/pull/152

CI and testing

• Simplify CI by adding the "minimal_install" param to the job matrix by @robomics in https://github.com/paulsengroup/StripePy/pull/95
• Address CodeQL warnings by @robomics in https://github.com/paulsengroup/StripePy/pull/96
• Bump github-actions by @dependabot and @robomics https://github.com/paulsengroup/StripePy/pull/100, https://github.com/paulsengroup/StripePy/pull/108, https://github.com/paulsengroup/StripePy/pull/109, https://github.com/paulsengroup/StripePy/pull/114, https://github.com/paulsengroup/StripePy/pull/124, https://github.com/paulsengroup/StripePy/pull/148, https://github.com/paulsengroup/StripePy/pull/149, and https://github.com/paulsengroup/StripePy/pull/151
• pre-commit: update config and add new hooks by @robomics in https://github.com/paulsengroup/StripePy/pull/147

Performance optimization

• Optimize find_HIoIs() by @robomics in https://github.com/paulsengroup/StripePy/pull/91
• Various optimizations for stripepy call by @robomics in https://github.com/paulsengroup/StripePy/pull/106
• Take advantage of the new hictkpy.File.fetch() capabilities by @robomics in https://github.com/paulsengroup/StripePy/pull/143
• Optimize performance when processing very tall stripes by @robomics in https://github.com/paulsengroup/StripePy/pull/153

Various

• [documentation]: update README and CITATION.cff by @robomics and @rea1991 in https://github.com/paulsengroup/StripePy/pull/82, https://github.com/paulsengroup/StripePy/pull/99, https://github.com/paulsengroup/StripePy/pull/115, https://github.com/paulsengroup/StripePy/pull/146, and https://github.com/paulsengroup/StripePy/pull/155
• [refactor]: rewrite stripepy call to use the new plotting functions by @robomics in https://github.com/paulsengroup/StripePy/pull/84
• [refactor]: update stripepy plot to use the new plot API by @robomics in https://github.com/paulsengroup/StripePy/pull/87
• [refactor]: restructure stripepy call outputs by @robomics in https://github.com/paulsengroup/StripePy/pull/97
• [refactor]: remove unused code by @robomics in https://github.com/paulsengroup/StripePy/pull/98
• [refactor]: rework project layout by @robomics in https://github.com/paulsengroup/StripePy/pull/132
• [refactor]: simplify assertion for neighborhood size by @rea1991 in https://github.com/paulsengroup/StripePy/pull/102
• [dependencies]: bump dependencies and remove unused by @robomics and @dependabot in https://github.com/paulsengroup/StripePy/pull/88, https://github.com/paulsengroup/StripePy/pull/131, https://github.com/paulsengroup/StripePy/pull/140, and https://github.com/paulsengroup/StripePy/pull/150
• [benchmark]: update benchmark/run-over-StripeBench.py by @rea1991 in https://github.com/paulsengroup/StripePy/pull/128, https://github.com/paulsengroup/StripePy/pull/156, and https://github.com/paulsengroup/StripePy/pull/126

Full Changelog: https://github.com/paulsengroup/StripePy/compare/v0.0.2...v1.0.0

- Python
Published by rea1991 about 1 year ago

stripepy-hic - v0.0.2

What's Changed

• Rework StripePy IO by @robomics in https://github.com/paulsengroup/StripePy/pull/71
• Add script to run StripePy over the StripeBench benchmark by @rea1991 in https://github.com/paulsengroup/StripePy/pull/70
• Initial implementation of stripepy plot by @robomics in https://github.com/paulsengroup/StripePy/pull/76
• Rename package from stripepy to stripepy-hic by @robomics in https://github.com/paulsengroup/StripePy/pull/80
• Update the README by @robomics in https://github.com/paulsengroup/StripePy/pull/81
• Updates to CI @dependabot, @pre-commit-ci https://github.com/paulsengroup/StripePy/pull/68, https://github.com/paulsengroup/StripePy/pull/65, https://github.com/paulsengroup/StripePy/pull/75

New Contributors

• @dependabot made their first contribution in https://github.com/paulsengroup/StripePy/pull/68
• @pre-commit-ci made their first contribution in https://github.com/paulsengroup/StripePy/pull/65

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

- Python
Published by rea1991 over 1 year ago

stripepy-hic - v0.0.1

Initial release

Contributors

• @robomics made their first contribution in https://github.com/paulsengroup/StripePy/pull/1
• @obikenobi23 made their first contribution in https://github.com/paulsengroup/StripePy/pull/2
• @rea1991 made their first contribution in https://github.com/paulsengroup/StripePy/pull/5

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

- Python
Published by rea1991 over 1 year ago