v0.3.1

v0.3.1 Release

Changed

• Documentation: Add bioconda installation guide
• Documentation: Update reference to publication

v0.3.0

v0.3.0 Release

Added

• Added latest R9.4.1 and R10.4.1 models
• Added Contributing Guide
• Advanced Parameters: Introduced a --show-advanced-options flag for experimental parameters in prediction mode.
• R9.4.1 Support: Added an R9.4.1 model and R9.4.1 profile for extended compatibility.
• Dwell Time Parameters: Added dwell-mean and dwell-std parameters for users preferring static distributions for dwell time generation.
• Model Download Simplification: Models can now be downloaded using the --profile argument, closes #7

Changed

• Noise Generation: Switched from NumPy to PyTorch for noise generation, ensuring consistent dependencies.
• Length Regulator: Fully transitioned to PyTorch, removing reliance on NumPy/Numba.
• Performance Boosts: Achieved small speedups by minimizing GPU-CPU data transfers and avoiding NumPy usage wherever possible.
• Preprocessing: Simplified preprocessing functions for improved maintainability.
• UUID Generation: Automatically generate a UUID4 in genome mode for unique identifiers and compability with dorado

v0.2.0

First PyPi release

Added

• function to automatically download the latest weights from GitHub
• __ version __ for version tracking
• version function to print the tool’s version
• Packaged the project with Poetry and prepared it for PyPI release

Changed

• Moved config.yaml to the src/ directory.
• Updated the README with the latest instructions and details
• Removed the wandb logger from the prediction process

Fixed

• Enabled prediction mode for CPU-only usage

Full Changelog: v0.1.0...v0.2.0

v0.1.0

v0.1.0 - 2024-08-13

Initial release