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Project goals

• Update from Python2.7 to Python3.6+
• Achieve full unit test coverage and CI testing
• Move away from the current monolithic structure and shift operations such as plotting and FASTQ/FASTA handling to sensible dependencies
• Future-proof by adopting high-performance data structures such as Dask DataFrames
• Add plugins for scoring functions and other core features such as input file handling
• Support R plugins for scoring functions (via rpy2)
• Develop a version for Bioconductor (via reticulate)
• Prioritize usability for non-computational researchers by updating the GUI and improving the deployment/installation process
• Retain cross-platform support for users on Linux, MacOS, and Windows

Coding guidelines

• The master branch should always be usable to run analyses
• Source files should be formatted using black
• Docstrings should be in numpy format
• Docstrings should include references and use intersphinx where possible
• Including workable examples in Jupyter notebooks is a useful style of documentation that we should do more of
• Type hinting is desirable but this will be an ongoing transition
• f-strings should be used throughout but this will be an ongoing transition

Code of conduct

This project is governed by the Contributor Covenant Code of Conduct.