Merge pull request #80 from epifluidlab/develop

Develop

.gitignore

@@ -6,3 +6,5 @@ pip-wheel-metadata
 .vscode
 **/.DS_Store
 build/*
+tests/tmp/*
+.coverage*

CHANGELOG.md

@@ -5,6 +5,40 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.6.1] - 2024-05-26
+### Changed
+- add `__version` attribute
+- `finaletoolkit --version` displays package version
+- update PyPI page to include links
+
+## [0.6.0] - 2024-05-26
+
+### Fixed
+- Fixed intersect policy for `cleavage_profile`. Now it calls `frag_generator`
+with a policy of `any`.
+- Clean up some comments and docstrings
+- Fixed logging from coverage function
+
+### Added
+- Added numerous util functions
+- Added `left` and `right` options to `cleavage_profile` and CLI
+`cleavage-profile`.
+- Added tests for cleavage profile and WPS.
+
+### Changed
+- Minimum Python version 3.9
+- Changed `filter_bam` to have same filters as FinaleDB
+- `utils.frag_generator` raises `ValueError` if `start` or `stop`
+are specified without `contig`
+- Type hints changed to use literals when possible
+
+### Removed
+- Removed `utils.get_contig_lengths`
+- Removed `data`, `conda_envs`, and `figs` directories
+- Removed unused dependencies `click`, `pybedtools`, and `cython
+- Remove some unused imports from module files
+
+
 ## [0.5.2] - 2024-05-08
 
 ### Fixed

README.md

@@ -66,4 +66,4 @@ We encourage you to use our comprehensive database, FinaleDB, to access relevant
 - Yaping Liu: yaping@northwestern.edu
 
 ## License
-For academic research, please refer to MIT license. For commerical usage, please contact the authors.
+This project falls under an MIT license. See the included `LICENSE` file for details.