From 79cdec9bb6e5622069e477dc5e337e69edba3580 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 14 Aug 2026 07:26:14 +0200 Subject: [PATCH] Upgrade pip before installing torch in scbutterfly --- CHANGELOG.md | 2 ++ src/methods/scbutterfly/scbutterfly_predict/config.vsh.yaml | 1 + src/methods/scbutterfly/scbutterfly_train/config.vsh.yaml | 1 + 3 files changed, 4 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4477e4f7..fad70d15 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/src/methods/scbutterfly/scbutterfly_predict/config.vsh.yaml b/src/methods/scbutterfly/scbutterfly_predict/config.vsh.yaml index ae9aac7b..fb4269d3 100644 --- a/src/methods/scbutterfly/scbutterfly_predict/config.vsh.yaml +++ b/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 diff --git a/src/methods/scbutterfly/scbutterfly_train/config.vsh.yaml b/src/methods/scbutterfly/scbutterfly_train/config.vsh.yaml index b68ca593..2bc93fc2 100644 --- a/src/methods/scbutterfly/scbutterfly_train/config.vsh.yaml +++ b/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