Highlights

Python 3.13 Support. ChimeraLM now supports Python 3.10, 3.11, 3.12, and 3.13. This fixes the Hugging Face Spaces demo which runs on Python 3.13.

Features

• Python 3.13 support: Extended requires-python to >=3.10,<3.14 and added Python 3.13 to the CI test matrix
• Lazy UI module loading: chimeralm -h and other CLI commands no longer trigger model loading at import time
• Lazy predictor initialization: The web UI defers model loading until the first prediction, improving startup time
• Suppressed third-party log noise: INFO-level logs from httpx, huggingface_hub, transformers, and urllib3 are now filtered in the web UI, keeping only ChimeraLM's own logs visible
  Dependency Updates
• torch: 2.5.1 -> 2.11.0
• GitHub Actions: actions/checkout v5->v6, actions/upload-artifact v5->v7, actions/download-artifact v4->v8, astral-sh/setup-uv v6->v7, release-drafter v6->v7, ghaction-github-labeler v5->v6
  Documentation
• Added Hugging Face Spaces demo link
• Enhanced Gradio web interface styling and documentation
• Various documentation fixes and formatting improvements
  Hugging Face Spaces
• Fixed build error caused by Python 3.13 incompatibility
• Updated Space dependencies to match package requirements
  Full Changelog: v1.0.4...v1.0.5

Changes

Fix

• missing dependencies lightning @cauliyang

Full Changelog: v1.0.3...v1.0.4

Changes

🧹 Maintenance

• chore(deps): bump release-drafter/release-drafter from 5 to 6 @dependabot[bot] (#26)
• chore(deps): bump actions/upload-artifact from 4 to 5 @dependabot[bot] (#27)
• chore(deps): bump actions/download-artifact from 4 to 6 @dependabot[bot] (#13)
• chore(deps): bump astral-sh/setup-uv from 3 to 7 @dependabot[bot] (#11)
• chore(deps): bump actions/setup-python from 5 to 6 @dependabot[bot] (#12)
• chore(deps): bump actions/checkout from 4 to 5 @dependabot[bot] (#14)
• chore(deps): bump peaceiris/actions-gh-pages from 3 to 4 @dependabot[bot] (#15)
• chore(deps): bump thiserror from 2.0.12 to 2.0.17 @dependabot[bot] (#19)
• chore(deps): bump log from 0.4.27 to 0.4.28 @dependabot[bot] (#20)

📝️ Documentation

• doc: build docs website @cauliyang (#10)

What's Changed

• Release First Version by @cauliyang in #8
• doc: build docs website by @cauliyang in #10
• chore(deps): bump log from 0.4.27 to 0.4.28 by @dependabot[bot] in #20
• chore(deps): bump thiserror from 2.0.12 to 2.0.17 by @dependabot[bot] in #19
• chore(deps): bump peaceiris/actions-gh-pages from 3 to 4 by @dependabot[bot] in #15
• chore(deps): bump actions/checkout from 4 to 5 by @dependabot[bot] in #14
• chore(deps): bump actions/setup-python from 5 to 6 by @dependabot[bot] in #12
• chore(deps): bump astral-sh/setup-uv from 3 to 7 by @dependabot[bot] in #11
• chore(deps): bump actions/download-artifact from 4 to 6 by @dependabot[bot] in #13
• chore(deps): bump actions/upload-artifact from 4 to 5 by @dependabot[bot] in #27
• chore(deps): bump release-drafter/release-drafter from 5 to 6 by @dependabot[bot] in #26

New Contributors

• @dependabot[bot] made their first contribution in #20

Full Changelog: v1.0.0...v1.0.1

ChimeraLM v1.0.0 (2025-10-06)

• Stable 1.0 release of chimeralm with Python package and CLI.
• End-to-end pipeline for detecting and filtering chimeric reads from BAM, with GPU support, Gradio UI.

Highlights

• New CLI: chimeralm predict and chimeralm filter for BAM inference with GPU, batching, and progress bar.
• Gradio UI chimeralm web for interactive inference and visualization.

Installation

pip install chimeralm
chimeralm -h

Requirements

• Python >= 3.10, < 3.12
• Optional: CUDA GPU for acceleration (recommend larger batch sizes with monitoring)