DRAFT: Deprecate old evo2 code in favor of mbridge#1491
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DRAFT: Deprecate old evo2 code in favor of mbridge#1491
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The new implementation at bionemo-recipes/recipes/evo2_megatron/ (Megatron-Bridge) has feature parity with the old sub-packages/bionemo-evo2 (NeMo2/PTL) for Hyena models. All matching tests pass in both containers. Known gaps (out of scope): LoRA/PEFT, Mamba, and Llama model support. Changes: - Remove bionemo-evo2 from meta-package dependencies and pyright/tach configs - Add deprecation notices to README, pyproject.toml, and __init__.py - Add DEPRECATED marker file and test results documentation Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…-packages These packages were only used by each other and the already-deprecated bionemo-evo2. No other active sub-packages import from them: - bionemo-llm: only used by bionemo-testing and bionemo-example_model - bionemo-testing: only used as test dependency by bionemo-llm and bionemo-example_model - bionemo-example_model: not imported by any other sub-package Also removes the stale bionemo.llm dependency from bionemo.webdatamodule in tach.toml (no actual imports exist). Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…sting, bionemo-example_model Hard-delete all four deprecated sub-packages and clean up all references throughout the repository: Deleted directories: - sub-packages/bionemo-evo2/ (replaced by bionemo-recipes/recipes/evo2_megatron/) - sub-packages/bionemo-llm/ (NeMo/Megatron LLM components, no longer maintained) - sub-packages/bionemo-testing/ (NeMo/Megatron test utilities, no longer maintained) - sub-packages/bionemo-example_model/ (NeMo/Megatron example model, no longer maintained) Deleted CI configs: - ci/benchmarks/partial-conv/evo2_pretrain.yaml - ci/benchmarks/partial-conv/evo2_finetuning.yaml - ci/benchmarks/perf/evo2_pretrain.yaml Cleaned up references in: - pyproject.toml (dependencies, uv.sources, pyright extraPaths) - tach.toml (source_roots, modules, stale webdatamodule->llm dep) - .devcontainer/framework/devcontainer.json (extraPaths) - CODEOWNERS (removed entries for deleted packages) - README.md (removed from sub-packages support matrix) - docs/ (SUMMARY files, getting-started, development, megatron_datasets, release notes, contributing, slurm guide) - sub-packages/bionemo-core/ (README, data README) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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/ok to test 12ceb5f |
The detect-secrets baseline needed a line number refresh after removing deprecated sub-packages shifted content in pyproject.toml. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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/ok to test 73a15e6 |
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #1491 +/- ##
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+ Coverage 76.45% 81.15% +4.69%
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Files 102 65 -37
Lines 7952 5110 -2842
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- Hits 6080 4147 -1933
+ Misses 1872 963 -909 |
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