v0.1.2

What's new

• Added Docker support: image available at ghcr.io/ethanfenton/seqseeker:0.1.2
  • Multi-stage build: C binary pre-compiled, runtime image requires no compiler
• Added GHCR publish workflow (builds and pushes on every release)
• Updated README with Docker installation and usage instructions

seqseeker v0.1.1

• Fix GitHub Actions versions (checkout@v6, setup-python@v6, upload-artifact@v7, download-artifact@v8)
• Add CI dev extras so pytest installs correctly
• Fix 8 ruff lint warnings (unused imports, bare f-strings)
• Add automated PyPI publish workflow (triggers on GitHub Release)

seqseeker v0.1.0

Initial release.

What's included

• C-backed k-mer scanner (~50M reads/min/core), compiles automatically at first use
• Search for any target sequence via raw string, FASTA file, or built-in name
• Built-in sequences: eGFP, Venus, mCherry, tdTomato
• Region selection (full / 5prime / 3prime) to index only part of the target
• Python package with CLI (seqseeker search/compile/list-sequences) and API
• R package with Seurat helpers (seqseeker_add_to_seurat)
• Bash wrapper for cluster environments
• Zero Python runtime dependencies
• GitHub Actions CI (Linux + macOS, Python 3.10–3.12)

Install

pip install git+https://github.com/ethanfenton/seqseeker.git