Upgrade pip before installing torch in scbutterfly

CHANGELOG.md

@@ -98,6 +98,8 @@
 
 * `cellmapper_linear`, `cellmapper_scvi`: Require `cellmapper>=0.2.6,<0.3`. The package has twice renamed the `map_obsm` output key under a compatible-looking version bump, each time breaking these components on every dataset (PR #59).
 
+* `scbutterfly_train`, `scbutterfly_predict`: Upgrade pip before installing torch. The pip shipped in `python:3.9` rejects the `typing_extensions` wheel over the underscore in its metadata name, falls back to the sdist, and cannot build it because `flit_core` is not on the PyTorch index -- so the image stopped building the moment `typing_extensions` started requiring `flit_core>=3.11` (PR #64).
+
 # task_predict_modality 0.1.1
 
 ## NEW FUNCTIONALITY

src/methods/scbutterfly/scbutterfly_predict/config.vsh.yaml

@@ -22,6 +22,7 @@ engines:
     setup:
       - type: docker
         run:
+          - pip install --no-cache-dir --upgrade pip
           - pip install --no-cache-dir torch==1.13.1 torchvision==0.14.1 --index-url https://download.pytorch.org/whl/cu117
           - pip install --no-cache-dir --no-deps scButterfly
           - pip install --no-cache-dir "numpy==1.23.5" "scipy==1.9.3" "pandas<2" "scanpy==1.9.3" "anndata==0.8.0" "scikit-learn>=1.1" numba tqdm matplotlib adjustText bamnostic pysam legacy-api-wrap

src/methods/scbutterfly/scbutterfly_train/config.vsh.yaml

@@ -51,6 +51,7 @@ engines:
     setup:
       - type: docker
         run:
+          - pip install --no-cache-dir --upgrade pip
           - pip install --no-cache-dir torch==1.13.1 torchvision==0.14.1 --index-url https://download.pytorch.org/whl/cu117
           - pip install --no-cache-dir --no-deps scButterfly
           - pip install --no-cache-dir "numpy==1.23.5" "scipy==1.9.3" "pandas<2" "scanpy==1.9.3" "anndata==0.8.0" "scikit-learn>=1.1" numba tqdm matplotlib adjustText bamnostic pysam legacy-api-wrap