Update EVO2 tests according to Hyena arch changes#798

Merged

farhadrgh merged 41 commits into

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farhadr/evo2_cleanup

May 5, 2025

Commits on May 5, 2025

drop unused is_mlp
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update the in/out shapes
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bum NeMo
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change checkpoint name pattern (#786)
farhadrgh
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Revert commit 67a869b3c601096475b82c1da1d2339d860dbce1 (TE_VERSION=v1.13 fix) (#795)

dorotat-nv
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[cye/subpack-gpu-testing] Add GPU runner to testing job. (#776)

cspades
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Dockerfile improvements for ARM (#777)

trvachov
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Remove llama-index from container to fix CVEs (#800)

trvachov
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update
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Add local clone script (#787)

nvdreidenbach
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Fix ARM docker build (#801)

trvachov
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[cye/ml-subpackage-ci] Onboard bionemo-llm and bionemo-noodles to the sub-package CI. (#809)

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Update README.md link (#812)

nvdreidenbach
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Have dependabot update our docker base image (#813)

pstjohn
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Add .codecov.yml status checks (#618)

pstjohn
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Add AMPLIFY model documentation, minor type fixes (#788)

pstjohn
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Remove import guard in bionemo-llm (#804)

pstjohn
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Bump rust from 1.82.0 to 1.86.0 (#819)

dependabot[bot]
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Bump crossbeam-channel from 0.5.13 to 0.5.15 in /sub-packages/bionemo-noodles (#818)

dependabot[bot]
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Pbinder/geneformer partial conv (#802)

polinabinder1
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[cye/rapids-sc-install] Add rapids_singlecell import to BioNeMo FW container image. (#816)

cspades
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Biopharma mailing list docs addition. (#822)

trvachov
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unify the implementation of early training termination across BioNeMo subpackages and update benchmarks (#803)

dorotat-nv
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Fix bitsandbytes issue on ARM (#824)

trvachov
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Fixes for AMPLIFY QA scripts (#825)

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remove call to context_parallel loss
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updated configs for benchmarks (#833)

dorotat-nv
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temporary dependency fixes for upstream nemo changes

pstjohn
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pin ngcsdk

pstjohn
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Remove temporary pins in docs build (#828)

pstjohn
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Adding baseline metrics for benchmarking ESM2 model (#831)

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Updates docs for geneformer training, inference, and cellxclassification (#823)

jomitchellnv
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Add pre commit to verify test status (#841)

pstjohn
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fix geneformer image paths (#839)

jomitchellnv
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fix geneformer image links (#844)

jomitchellnv
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Pbinder/auto resume (#766)

polinabinder1
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Pbinder/esm2 document (#846)

polinabinder1
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h11 CRIT vuln fix (#847)

trvachov
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Docs fix (#826)

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Fix masked token loss refactor from NeMo bump. (#855)

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resolve conflicts
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