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Update environment.yml

Marco Clemencic requested to merge update-conda-environment into master

For the runtime environment of the nightly builds, use as much as possible from conda leaving to pip only the packages that do not exist in conda-forge.

I also made a few other minor changes:

  • update the version of Python used in the tests
  • add a test to validate the content of environment.yml
  • add/updated a few pre-commit checks
  • fixed an issue with a test

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