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Updating scgpt #29

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Merged
rcannood merged 18 commits into from
Oct 19, 2025
Merged

Updating scgpt #29

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ffba954
better loading of the model and new model
jkobject Mar 5, 2025
9c212cc
new solution to matching problem
jkobject Mar 10, 2025
50c20e2
removing gpu
jkobject Mar 10, 2025
ce28844
Merge branch 'main' into main
jkobject Mar 10, 2025
55f7528
proposing two versions
jkobject Mar 13, 2025
ae3626f
removing flag
jkobject Mar 14, 2025
d1372bc
default to linear sum
jkobject Mar 14, 2025
d55892e
Style and lint scPRINT script
lazappi Mar 18, 2025
af50d00
Update CHANGELOG
lazappi Mar 18, 2025
57758d0
Merge branch 'main' into main
jkobject Aug 12, 2025
4538bab
updating scprint version
jkobject Aug 12, 2025
6634908
Merge branch 'main' of https://github.com/jkobject/task_label_projection
jkobject Aug 12, 2025
f13b4a1
removing gpu device
jkobject Aug 12, 2025
62e72f4
better scgpt installation (now uses flash attention)
jkobject Sep 29, 2025
7c785a6
changing default parameters
jkobject Oct 13, 2025
f6adff5
removing scgpt
jkobject Oct 13, 2025
9987393
update
jkobject Oct 13, 2025
1119776
Merge remote-tracking branch 'upstream/main' into updating-scgpt
rcannood Oct 19, 2025
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12 changes: 6 additions & 6 deletions src/methods/scgpt_finetuned/config.vsh.yaml
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Expand Up @@ -37,13 +37,13 @@ engines:
- type: docker
image: openproblems/base_pytorch_nvidia:1
setup:
- type: python
pypi:
- gdown
- scgpt # Install from PyPI to get dependencies
- type: docker
# Force re-installing from GitHub to get bug fixes
run: pip install --upgrade --no-deps --force-reinstall git+https://github.com/bowang-lab/scGPT.git
run: |
git clone https://github.com/bowang-lab/scGPT && \
pip install torch==2.2.0 torchvision==0.17.0 torchaudio==2.2.0 --index-url https://download.pytorch.org/whl/cu121 && \
pip install "flash-attn<1.0.5" --no-build-isolation && \
pip install ipykernel pandas scanpy numba "numpy<1.24" torchtext==0.17.0 scib "scvi-tools<1.0" datasets==2.14.5 transformers==4.33.2 wandb "cell-gears<0.0.3" torch_geometric pyarrow==15.0.0 gdown && \
cd scGPT && pip install -e . --no-deps

runners:
- type: executable
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12 changes: 5 additions & 7 deletions src/methods/scgpt_zeroshot/config.vsh.yaml
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Expand Up @@ -43,15 +43,13 @@ engines:
- type: docker
image: openproblems/base_pytorch_nvidia:1
setup:
- type: python
pypi:
- gdown
- scgpt # Install from PyPI to get dependencies
- faiss-cpu # TODO: Try installing faiss-gpu
- type: docker
# Force re-installing from GitHub to get bug fixes
run: |
pip install --upgrade --no-deps --force-reinstall git+https://github.com/bowang-lab/scGPT.git
git clone https://github.com/bowang-lab/scGPT && \
pip install torch==2.2.0 torchvision==0.17.0 torchaudio==2.2.0 --index-url https://download.pytorch.org/whl/cu121 && \
pip install "flash-attn<1.0.5" --no-build-isolation && \
pip install ipykernel pandas scanpy numba "numpy<1.24" torchtext==0.17.0 scib "scvi-tools<1.0" datasets==2.14.5 transformers==4.33.2 wandb "cell-gears<0.0.3" torch_geometric pyarrow==15.0.0 gdown && \
cd scGPT && pip install -e . --no-deps
Comment on lines +48 to +52
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@rcannood rcannood Oct 19, 2025

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this aligns with how we install scgpt in the batch integration task and seems to work


runners:
- type: executable
Expand Down