Hybkit

- 0.3.6 (2024-08) Changes include:
- Fix passing multiple error modes to --error_checks shell argument
- Change HybFoldIter error backend to non-recursive design
- Allow disabling of hyb / fold sequence mismatch checking by setting mismatches to "-1"
- Misc Bugfixes & Refinements

- 0.3.5 (2024-06) Changes include:
- Misc Bugfixes

* 0.3.4 (2023-11) Changes include:
* Misc Bugfixes and Refinements
* Switch code linting to Ruff
* Add hybkit.errors module and HybkitError classes
* Moved printing of warnings to python logging module
* Add option for direct passage of file-like object for construction of HybFile and ViennaFile
* Add HybRecord.to_csv_header(), HybRecord.to_fields(), and HybRecord.to_fields_header() methods
* Refine description of HybFile.open() constructor method
* Add typing_extensions dependency
* Add Python3.8-compatible type hints to API
* Documentation Updates

* 0.3.3 (2023-09) Changes include:
* Misc Bugfixes and Refinements
* Update integer bar-plot functions

* 0.3.2 (2023-08) Changes include:
* Misc Bugfixes and Refinements
* Add duplicate hybrid filtration (by HybRecord.id) options to hyb_filter
* Add duplicate hybrid filtration to example analyses

* 0.3.1 (2023-08) Changes include:
* Misc Bugfixes and Refinements
* Add --version flag to scripts
* Change move scripts output file description to argparse epilog
* Refine plot functions
* Change default plot colors to the Bang Wong scheme [Wong2011]_ for
colorblind accessibility
* Documentation corrections
* Spellcheck

* Simplifying HybRecord API
* Simplifying FoldRecord API
* Unifying settings information for argparse and modules
* Removing Support for ViennaD format
* Moving identifier-parsing code to module type_finder
* Moving target region analysis code to module region_finder
* Moving code for settings into a "settings" module
* Renamed HybRecord type_analysis and mirna_analysis to
eval_types and eval_mirna, respectively
to differentiate from analysis module functions
* Reimplemented analyses methods within a single Analysis class
* Added error checking / catching to HybFoldIter
* Removed Target-Region Analysis and associated files
due to lack of archival database information,
pending furure development
* Added "dynamic" seq_type to FoldRecord for non-identical fold/hybrid sequence handling
* Added shell implementation to all example pipelines
* Remove support for Python3.6, Python3.7
* Migrate to CircleCI for CI/CD
* Added Pytest unit testing integrated with CircleCI
* Other Misc. Improvements / Bugfixes