Use the bundled BioModEncoder, BioModLM and BioModLM_GO interfaces throughout. Remove obsolete CLI aliases and the external attention fallback. Centralize legacy configuration and state-dictionary translation in biomod_compat.py and document the shared asset. Model weights, paired configuration, datasets and unrelated files remain unchanged.
Unify downstream task layout and document dataset launch commands
Place each task notebook beside its README and train/evaluate entry point; organize helper code and shared module-source definitions. Add complete per-dataset launch commands and preserve declared zero-count cell annotation classes. Remove the unused environment template and stale ignore rules, and refresh project and data-directory README paths. Pretrained weights, paired configuration and raw data remain unchanged.
Rename project-owned entrypoints, resource directories, classes and helpers to BioMod/biomod, and update imports, notebooks, documentation and command examples. Preserve old CLI flags as aliases and keep serialized state/configuration keys, raw gene-set IDs, result schemas and third-party interfaces compatible. Move the existing checkpoint/configuration pair to weight/BioMod.pth and weight/BioMod.pkl using their unchanged objects. Remove only the eight approved duplicate files from the source module-data directory and nested attention package; retain the shared copies. Raw datasets, legacy reference data copies and all weight contents remain unchanged. Validation: 90 Python 3 files, 65 notebook cells, 12 utility tests, 7 synthetic backbone comparisons and 10 classifier comparisons passed. No real model weights or datasets were deserialized, and no real-data training was run.
Make project paths portable and standardize English code comments
Resolve bundled resource defaults from script locations, preserve caller-relative path overrides, and require missing external pretraining or legacy inputs explicitly. Translate comments and docstrings to English, update command examples and documentation, and add a path helper for legacy reference code. Validation: 97 Python 3 files and 65 notebook code cells compiled; 12 existing utility tests passed; parser, example-command, resource-path and local-link checks passed. Two historical DeepCDR entrypoints retain Python 2 syntax. No training or model inference was run. This commit updates 90 source/documentation files and adds one helper; pretrained weights, paired PKL, raw datasets and other files are unchanged.
18 days ago
Upload BioMod with datasets and the 0810 checkpoint
Publish the BioMod source tree, model dependencies, complete downstream datasets, and the unchanged 0810 weight/configuration pair. Include the updated model implementation, shared training utilities, CPU utility tests, and English documentation. Exclude download caches, local environments, and OS metadata.
