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Pull requests: NVIDIA/bionemo-framework

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Pull requests list

Add cursor rule to run pre-commit, update devcontainer for recipes to install cursor-agent
#1311 opened Nov 5, 2025 by pstjohn Loading…
log total tokens in esm2 recipe
#1309 opened Nov 5, 2025 by pstjohn Loading…
Yangzhang/codonfm 10b
#1305 opened Nov 4, 2025 by yzhang123 Loading…
3 of 9 tasks
8
Add BSHD inputs for llama3 model and ensure that inference works
#1303 opened Nov 3, 2025 by pstjohn • Draft
1
begin drafting yaml for fp8 thd jobs ciflow:skip Skip all CI tests for this PR
#1297 opened Oct 29, 2025 by jwilber Loading…
@jwilber
1
bump nemo ciflow:all Run all tests (unit tests, slow tests, and notebooks) for bionemo2 or enforce running all tests
#1296 opened Oct 29, 2025 by farhadrgh Loading…
9 tasks
7
Bump starlette from 0.48.0 to 0.49.1 in /bionemo-recipes/recipes/codonfm_ptl_te dependencies Pull requests that update a dependency file python Pull requests that update Python code
#1294 opened Oct 28, 2025 by dependabot bot Loading…
1
feat: benchmark annbatch in scspeedtest
#1290 opened Oct 28, 2025 by ilan-gold Loading…
1 of 9 tasks
7
Bump cryptography from 42.0.8 to 44.0.1 in /bionemo-recipes/recipes/codonfm_ptl_te dependencies Pull requests that update a dependency file python Pull requests that update Python code
#1287 opened Oct 28, 2025 by dependabot bot Loading…
1
Bump urllib3 from 1.26.20 to 2.5.0 in /bionemo-recipes/recipes/codonfm_ptl_te dependencies Pull requests that update a dependency file python Pull requests that update Python code
#1286 opened Oct 28, 2025 by dependabot bot Loading…
1
Fix to paginated loading in SCDL.
#1285 opened Oct 27, 2025 by polinabinder1 Loading…
1 of 5 tasks
35
Bump jupyterlab from 4.4.5 to 4.4.8 in /bionemo-recipes/recipes/codonfm_ptl_te dependencies Pull requests that update a dependency file python Pull requests that update Python code
#1280 opened Oct 27, 2025 by dependabot bot Loading…
1
Bump 3rdparty/Megatron-LM from f8d3e2e to f34fa11 dependencies Pull requests that update a dependency file submodules Pull requests that update Submodules code
#1277 opened Oct 27, 2025 by dependabot bot Loading…
1
Bump 3rdparty/NeMo from 8c6fd8b to b758aed dependencies Pull requests that update a dependency file submodules Pull requests that update Submodules code
#1276 opened Oct 27, 2025 by dependabot bot Loading…
1
Jwilber/debug tflops esm2
#1267 opened Oct 21, 2025 by jwilber Loading…
4
Add gradient accumulation to ESM-2.
#1254 opened Oct 14, 2025 by cspades Loading…
1 of 9 tasks
@cspades
7
Add new geneformer configs ciflow:skip Skip all CI tests for this PR
#1251 opened Oct 13, 2025 by jwilber Loading…
@jwilber
4
updates for jonathan
#1239 opened Oct 8, 2025 by pstjohn • Draft
2
LM Eval and llama support in prediction/optimizer removal
#1238 opened Oct 8, 2025 by jstjohn Loading…
6 of 9 tasks
28
add fp8 to distributed checkpointing tests
#1236 opened Oct 8, 2025 by pstjohn Loading…
19
CI tests on multi-GPU runners ciflow:all Run all tests (unit tests, slow tests, and notebooks) for bionemo2 or enforce running all tests
#1229 opened Oct 7, 2025 by gagank1 Loading…
7 of 9 tasks
@gagank1
44
LLAMA3 SQLite Baseline with ASCII Tokenizer
#1217 opened Oct 2, 2025 by savitha-eng • Draft
9 tasks
17
[WIP] LLAMA3 Integration with BioNeMo Recipes with ASCII Tokenization/EVO2-Style Dataloader
#1205 opened Sep 29, 2025 by savitha-eng • Draft
24
[WIP] Update base dependencies ciflow:all Run all tests (unit tests, slow tests, and notebooks) for bionemo2 or enforce running all tests
#1194 opened Sep 25, 2025 by trvachov Loading…
1 of 9 tasks
13
Fix checkpoint bug bad checkpoint hydra structure
#1185 opened Sep 24, 2025 by jomitchellnv Loading…
9 tasks
5
ProTip! Exclude everything labeled bug with -label:bug.