geniml

# Geniml Use Geniml for machine learning and statistical workflows over genomic interval sets. Treat coordinates, assemblies, token vocabularies, model artifacts, and sample grouping as explicit contracts. The bundled scripts validate or plan; they do not import Geniml, contact services, deserialize models, or execute training. `Bash` is declared only for explicit, user-approved `uv`, Python, Geniml, Gtars, Git, and native CLI commands shown in this guide; bundled Python helpers do not spawn subprocesses. Example paths under `data/`, `refs/`, `work/`, and `models/` are user-provided project placeholders, not missing bundled files. ## Verified release snapshot - Latest stable PyPI release on 2026-07-23: `geniml==0.8.4` (2026-01-14). - PyPI does not declare `Requires-Python`; its classifiers list Python 3.10-3.14. Prefer Python 3.11 or 3.12 where all native/ML wheels resolve. - `geniml==0.8.4` accepts `gtars>=0.2.5`; the verified base smoke used current `gtars==0.9.2` (2026-06-17, Python >=3.10). - Extras are `ml` and `test`. The base install omits Torch, Gensim, Scanpy, Hugging Face Hub, pyBigWig, and HMM dependencies. - Upstream documentation contains stale examples. Release source and installed `--help` output take precedence where they conflict. ## Install reproducibly Use a project environment and commit its generated lockfile: ```bash uv venv --python 3.12 uv pip install "geniml==0.8.4" "gtars==0.9.2" ``` For Region2Vec, scEmbed, evaluation, or universe me...