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Update mongo driver and fix deprecations

Andre Sterba requested to merge fix-deprecations into master

Description

Update mongo driver and fix deprecations. Also set version of installed tools in variables.

Checklist:

  • My code follows the code style of this project.
  • My change requires a change to the documentation.
  • I have updated the documentation accordingly.
  • I have read the CONTRIBUTING document.
  • I have added tests to cover my changes.
  • All new and existing tests passed.

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