removing scgpt

Author: jkobject

src/methods/scgpt_finetuned/config.vsh.yaml

@@ -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
-        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
+        # 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
 
 runners:
   - type: executable

src/methods/scgpt_zeroshot/config.vsh.yaml

@@ -43,22 +43,15 @@ 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: |
-          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
-     # - 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
+          pip install --upgrade --no-deps --force-reinstall git+https://github.com/bowang-lab/scGPT.git
 
 runners:
   - type: executable