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Update Scanpy Docker image to use a fixed requirements file #21
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dweemx
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All Scanpy packages are now locked in
requirements.txt. This fixes several bugs:--use-fast-tsnesegfaults #19), which appears to be resolved by upgrading numpy (it was previously locked at0.43.1).The virtualenv strategy is kept to try to keep the image size down.
The Scanpy package is installed in its own layer for quick image rebuilds (Scanpy is not present in
requirements.txt).Tested on the PBMC1k dataset with
-entry single_sample, and completes without errors.