feat: extend NetworkCommons toward perturbation biology with LEMBAS integration - #72

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Commits on Jun 17, 2026

Add LEMBAS data retrieval module to networkcommons

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5fe1821
Add LEMBAS perturbation-response pipeline with baselines and tests

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277a83c
Add per-condition evaluation axis, LEMBAS tutorial notebook, and torch optional dep

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9dd5377

Commits on Jun 22, 2026

chore: migrate to uv
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d422e5c
chore: simplify formatter w/ ruff
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7255b29
chore: complete migration from poetry to uv, modernise tooling

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e189579
fix: upgrade dependencies and fix pypath RaMP import crash

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ae3cc47
fix: adapt to corneto beta + decoupler 2.x API changes

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27cc9fb
docs: update installation guide for new dependencies and GPU setup

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578e24b
ci: migrate ReadTheDocs config to native uv integration

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93a28e0

Commits on Jun 26, 2026

chore: add flop/pertpy/torch-cu128 extras, rdata dep, and dev-cu128 env

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6d74147
fix: resolve issues surfaced by re-running notebooks after env modernisation

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a1bd6e3
feat: add get_hmdb_mapper to MOON data module

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3a1a3bd
feat: faithfully reimplement LEMBAS-RNN matching Nilsson et al. 2022

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f4bb2e7
fix: update tests broken by env modernisation and decoupler 2.x fix

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7616f06
ci: switch uv sync from --locked to --frozen in test workflow

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9150065

Commits on Jun 27, 2026

feat: add omnipath-client dependency, note workaround branch for get_hmdb_mapper

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a485f9b