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Pull requests: NVIDIA/bionemo-framework

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Pull requests list

fix esm2 downstream task finetune config saving issue
#832 opened Apr 15, 2025 by zmsunnyday Loading…
2 of 9 tasks
1
Adding baseline metrics for benchmarking … SKIP_CI Completely skips the CI pipeline
#831 opened Apr 15, 2025 by ShevaNguyen Loading…
4 of 8 tasks
1
Draft: outline push-to-gitlab-registry step
#830 opened Apr 14, 2025 by jwilber Loading…
2
Fixes how num_layers relates to pipeline_model_parallel_size in ESM2 bug Something isn't working ESM2
#829 opened Apr 14, 2025 by gagank1 Loading…
3 of 9 tasks
1
@gagank1
1
Remove temporary pins in docs build
#828 opened Apr 14, 2025 by pstjohn Loading…
1
Bump 3rdparty/Megatron-LM from 62529f1 to f70b5b8 dependencies Pull requests that update a dependency file submodules Pull requests that update Submodules code
#827 opened Apr 14, 2025 by dependabot bot Loading…
1
Docs fix
#826 opened Apr 11, 2025 by trvachov Loading…
1 of 9 tasks
2
Updates docs for geneformer training (it's a draft)
#823 opened Apr 10, 2025 by jomitchellnv Loading…
2 of 9 tasks
1
added duration info to the pytest INCLUDE_NOTEBOOKS_TESTS Add Jupyter notebook validation to the CI pipeline INCLUDE_SLOW_TESTS Add unit tests marked as slow to CI pipeline
#817 opened Apr 10, 2025 by dorotat-nv Loading…
1 of 9 tasks
6
automated benchmarks: add partial conv config for AMPLIFY
#811 opened Apr 8, 2025 by dorotat-nv Loading…
1 of 9 tasks
1
Geneformer gene embeddings calculation. Now limits the changes to bionemo.geneformer only
#808 opened Apr 7, 2025 by jyin-bst Loading…
1 of 8 tasks
10
Bump 3rdparty/NeMo from b685967 to 7d7a10c dependencies Pull requests that update a dependency file submodules Pull requests that update Submodules code
#807 opened Apr 7, 2025 by dependabot bot Loading…
3
Add second test for amplify infer batch mode
#805 opened Apr 7, 2025 by pstjohn • Draft
1
Upgrade base image to pytorch 25.03
#799 opened Apr 2, 2025 by trvachov Loading…
9 tasks
4
Update EVO2 tests according to Hyena arch changes
#798 opened Apr 2, 2025 by farhadrgh Loading…
9 tasks
16
Bump pyo3 from 0.18.3 to 0.24.1 in /sub-packages/bionemo-noodles dependencies Pull requests that update a dependency file rust Pull requests that update rust code
#797 opened Apr 2, 2025 by dependabot bot Loading…
1
fix Evo2 training crash - TE commit INCLUDE_NOTEBOOKS_TESTS Add Jupyter notebook validation to the CI pipeline INCLUDE_SLOW_TESTS Add unit tests marked as slow to CI pipeline
#796 opened Apr 1, 2025 by dorotat-nv Loading…
9 tasks
@dorotat-nv
11
added fastadatamodule
#790 opened Mar 27, 2025 by Geraldene Loading…
9 tasks
1
[fix] Fixes geneformer notebook INCLUDE_NOTEBOOKS_TESTS Add Jupyter notebook validation to the CI pipeline
#782 opened Mar 24, 2025 by jomitchellnv Loading…
1 of 8 tasks
11
PR labels checked for modified slow tests and notebooks
#780 opened Mar 24, 2025 by dorotat-nv Loading…
1 of 9 tasks
@dorotat-nv
10
Speed up Geneformer pydantic recipe and training tests INCLUDE_SLOW_TESTS Add unit tests marked as slow to CI pipeline
#774 opened Mar 21, 2025 by skothenhill-nv Loading…
6 of 9 tasks
11
PoC: organising Github CI labels and markers ciflow:notebooks Run Jupyter notebooks execution tests ciflow:slow Run slow single GPU integration tests marked as @pytest.mark.slow
#771 opened Mar 20, 2025 by dorotat-nv Loading…
1 of 9 tasks
@dorotat-nv
4
Pbinder/auto resume
#766 opened Mar 19, 2025 by polinabinder1 • Draft
4
Jwilber/cleanup docs examples dir documentation Improvements or additions to documentation INCLUDE_NOTEBOOKS_TESTS Add Jupyter notebook validation to the CI pipeline SKIP_CI Completely skips the CI pipeline
#765 opened Mar 17, 2025 by jwilber Loading…
2
[do not merge]inference with protein string on single gpu
#714 opened Mar 3, 2025 by yzhang123 • Draft
9 tasks
2
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