DeepChopper v1.2.6

What's Changed

• fix: Resolve multi-processing issues when predicting
• build(deps): bump crazy-max/ghaction-github-labeler from 5.0.0 to 5.1.0 by @dependabot in #27
• deps: update noodles requirement from 0.83.0 to 0.84.0 by @dependabot in #26

New Contributors

• @dependabot made their first contribution in #27

Full Changelog: py-cli-v1.2.5...py-cli-v1.2.6

DeepChopper v1.2.5

Changes

• add --version for cli

Full Changelog: py-cli-v1.2.4...py-cli-v1.2.5

DeepChopper v1.2.4

What's Changed

• feat: fix detection of mps backend by @cauliyang in #20

Full Changelog: py-cli-v1.2.2...py-cli-v1.2.4

DeepChopper v1.2.3

What's Changed

• refactor: Update CLI options in chop function by @cauliyang in #17

Full Changelog: py-cli-v1.2.1...py-cli-v1.2.3

DeepChopper v1.2.1

What's Changed

• docs: Polish the documentation by @cauliyang in #16

Full Changelog: py-cli-v1.2.0...py-cli-v1.2.1

First version V1.2.0

DeepChopper v1.2.0

We're excited to announce the release of DeepChopper v1.2.0! This version brings significant improvements and new features to our genomic language model for chimera artifact detection in Nanopore Direct RNA Sequencing.

🚀 New Features

• Improved encoding performance for large FASTQ files
• Enhanced prediction accuracy for chimera detection
• New web interface for easy interaction with the model
• Support for Python 3.12

🛠 Improvements

• Optimized Rust backend for faster processing
• Upgraded to PyTorch 2.1.0 and Lightning 2.1.2 for better performance
• Improved CLI with more intuitive commands and options
• Enhanced documentation and usage examples

🐛 Bug Fixes

• Fixed memory leak in long-running processes
• Resolved issues with multi-GPU support
• Corrected handling of edge cases in sequence chopping

📦 Installation

DeepChopper can now be installed via pip:

What's Changed

• use unzip files by @cauliyang in #2
• feat: Add functions to encode FASTQ files by @cauliyang in #3
• fix: Handle FileNotFoundError with logging instead of raising by @cauliyang in #4
• refactor the interface by @cauliyang in #5
• Model by @cauliyang in #6
• Deploy by @cauliyang in #8
• Deploy: publish to pypi by @cauliyang in #14
• docs: Add bumpversion configuration file by @cauliyang in #15

New Contributors

• @cauliyang made their first contribution in #2

Full Changelog: https://github.com/ylab-hi/DeepChopper/commits/py-cli-v1.2.0