Version 0.3.4

Changes

• move package metadata to pyproject.toml
• only support Python 3.10
• improve documentation, both README.md and in docs/ folder
• change TensorFlow GPU support installation instructions in manual_install.md
• add deprecation warnings for unused parameters

v0.3.3

Version 0.3.3

Changes

• version parameter
• installation maintainability and versatility improvements
• issue templates
• simplifications in coverage handling

v0.3.2

release v0.3.2

Changes

• improve documentation, both README.md and in docs/ folder
• implement experimental transfer learning options from large generalizable models, to be
  able to tune a re-initalized final layer with the rest of the model frozen (with or without adding extrinsic information).
• improve flexibility in add_ngs_coverage.py script for extrinsic NGS information

version 0.3.1

CLI changes

• Helixer.py now sets reasonable default for --subsequence-length whenever --lineage is specified
• overlapping parameters can now be automatically derived from --subsequence-length

other changes

• check if output directory exists and is writable at start, instead of after data generation and prediction
• fetch_helixer_models.py is now a stand-alone script in the PATH (instead of having to call python fetch_helixer_models.py)
• user specified compression is now used for all steps in Helixer.py
• improvements to multi-threading performance during data generation
• improvements to clarity and accuracy of help function and error messages
• fixed corner-case bug causing overlapping to fail for very-small but still technically-possible batch-sizes (i.e. 5 w/ overlapping defaults).