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Remove many unpinned python libraries

This MR cleans up upstream.yaml by removing a number of unpinned Python packages that nobody asked for. These were originally included as a dump of the first environment, but if required they should be brought in by their dependents. So, in practice this should have zero impact on the rendered environments.

upstream.yaml should contain only those thirdy-party packages that:

  • need to be constrained manually, OR
  • are not a direct dependency of any other packages but are required in some contexts (e.g. build/test tools)

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