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# Changelog
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- ## [ 0.3.0] - 2021-07-09
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+ ## [ 0.3.0] - 2021-07-12
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### Fixed
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- Refactor demultiplex.py for readability and faster execution
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- Logger is now compatible with snakemake logging module
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- Fixed small parsing bugs in gbk_convert.py
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### Changed
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- - Remove third party folder which contained ' bowtie' executables
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+ - Remove third- party folder which contained ` bowtie ` executables (now ` bowtie ` is installed via conda or manually)
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- file paths are now handled by pathlib
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- New settings class that is compatible with snakemake
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- The map_reads script is now a stand-alone script
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- Settings class which is used by snakemake and pyinseq
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- - Pyinseq and snakemake now use ` pathlib ` for handling filepaths
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- - Removed readthedocs website
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+ - Pyinseq and snakemake now use ` pathlib ` for handling file paths
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+ - Removed readthedocs website (documentation is now in the README.md; no longer using ReadTheDocs)
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- Removed docs/
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- Removed third-party/
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### Added
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- Snakemake can now execute workflows using Snakefile in pyinseq
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- - Additional Snakefiles for genomprep and demultiplex of pyinseq
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+ - Additional Snakefiles for genomeprep and demultiplex of pyinseq
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- Conda virtual environment files that allow conda to install ` bowtie ` software during runtime
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- - Parser.py script for parsing command line arguments
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+ - Parser.py script for parsing command- line arguments
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- Include '--test' option for running pytest on pyinseq
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- New pytests for testing workflows in pyinseq
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- Pyinseq will now summarize sample information and snakemake output
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