Update scGPT (#29)

* better loading of the model and new model

* new solution to matching problem

* removing gpu

* proposing two versions

* removing flag

* default to linear sum

* Style and lint scPRINT script

* Update CHANGELOG

* updating scprint version

* removing gpu device

* better scgpt installation (now uses flash attention)

* changing default parameters

* removing scgpt

* update

---------

Co-authored-by: Luke Zappia <luke@data-intuitive.com>
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

Author: 3 people

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
-        # 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

src/methods/scgpt_zeroshot/config.vsh.yaml

@@ -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
 
 runners:
   - type: executable