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Add cli interface for esm2 checkpoint conversion#922

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pstjohn merged 2 commits into
NVIDIA-BioNeMo:mainfrom
pstjohn:pstjohn/esm-2-export-cli
Jun 5, 2025
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Add cli interface for esm2 checkpoint conversion#922
pstjohn merged 2 commits into
NVIDIA-BioNeMo:mainfrom
pstjohn:pstjohn/esm-2-export-cli

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@pstjohn pstjohn commented Jun 4, 2025

Follow-up to #918 with some minor improvements, additional testing, and the addition of a typer CLI command to initiate checkpoint conversions

You can now convert checkpoints to huggingface with

convert_esm2 convert-nemo-to-hf /path/to/existing/nemo/checkpoint /path/to/new/hf/checkpoint

Signed-off-by: Peter St. John <pstjohn@nvidia.com>
Signed-off-by: Peter St. John <pstjohn@nvidia.com>
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I like typer!

Comment thread sub-packages/bionemo-esm2/src/bionemo/esm2/model/convert.py
@pstjohn pstjohn enabled auto-merge June 4, 2025 18:55
@pstjohn pstjohn added this pull request to the merge queue Jun 4, 2025
@github-merge-queue github-merge-queue Bot removed this pull request from the merge queue due to failed status checks Jun 4, 2025
@pstjohn pstjohn added this pull request to the merge queue Jun 5, 2025
@github-merge-queue github-merge-queue Bot removed this pull request from the merge queue due to failed status checks Jun 5, 2025
@pstjohn pstjohn added this pull request to the merge queue Jun 5, 2025
Merged via the queue into NVIDIA-BioNeMo:main with commit e705df7 Jun 5, 2025
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@pstjohn pstjohn deleted the pstjohn/esm-2-export-cli branch June 5, 2025 20:38
camirr-nv pushed a commit that referenced this pull request Jun 26, 2025
Follow-up to #918 with some minor improvements, additional testing, and
the addition of a typer CLI command to initiate checkpoint conversions

You can now convert checkpoints to huggingface with
```
convert_esm2 convert-nemo-to-hf /path/to/existing/nemo/checkpoint /path/to/new/hf/checkpoint
```

---------

Signed-off-by: Peter St. John <pstjohn@nvidia.com>
Signed-off-by: Ubuntu <camirr@nvidia.com>
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3 participants