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So far, I think the best option is to ssh into the instance and do something like:
source /opt/python/run/venv/bin/activate && yes | pip uninstall package-to-uninstall
You can alternatively add the following as a container_command in your syspackages.config file in .ebextensions :
command: "source /opt/python/run/venv/bin/activate && yes | pip uninstall package-to-uninstall"
Please, let me know if you figured out a more elegant way to fix this.
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