mesengenic-hsc 0.1.0

Generative causal engine for perturbation manifold analysis and epistatic peak discovery.

Mesengenic

Generative causal engine for perturbation manifold analysis — CLI and Python SDK for computational biologists.

Install

Production (PyPI)

pip install --index-url https://pypi.org/simple mesengenic_hsc

Local development (pip install -e .)

Run from the repository root (where pyproject.toml lives):

cd mesengenic-v3
pip install -e .

Component	Resolves to
Python package	./mesengenic/ (live edits, no reinstall)
mesengenic command	mesengenic.cli:main via [project.scripts] in pyproject.toml
Checksum manifest	assets/weights/MANIFEST.json

Verify:

mesengenic info          # shows install path + entry module
python -m mesengenic     # same as `mesengenic`

Conda (secondary)

conda env create -f environment.yml
conda activate mesengenic

Required Assets

Not bundled in the PyPI wheel. Install after pip install mesengenic_hsc:

# Hosted URL (set by publisher)
export MESENGENIC_WEIGHTS_URL=https://your-host/vae_epoch_50_final.pth
mesengenic weights download
mesengenic weights verify

# Or from a file you received
mesengenic weights restore --from ~/Downloads/vae_epoch_50_final.pth

Publishers: ./scripts/package_weights_release.sh → share dist/mesengenic-weights-*.tar.gz

See PUBLISHING.md for PyPI build and partner handoff.

Asset	Default path	Env var
VAE weights	assets/weights/vae_epoch_50_final.pth	MESENGENIC_WEIGHTS_PATH
AnnData	data/norman19_processed.h5ad	MESENGENIC_DATA_PATH

Navigation

See docs/NAVIGATION.md for the full CLI guide, query rules, and PyPI migration notes.

CLI (quick start)

mesengenic                          # Novaflow-style landing + command catalog
mesengenic sweep --mode 1 -o peaks.csv
mesengenic query "KLF1" --json
mesengenic trajectory "CEBPA+CEBPE"
mesengenic validate
mesengenic shell --full

SDK

from mesengenic import MesengenicCausalEngine

engine = MesengenicCausalEngine()
edges, deltas, peaks = engine.execute_global_sweep()

Security

See SECURITY.md for publishing checklist, wheel contents, and supply-chain controls.