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Dependency fixes

Anton Akhmerov requested to merge dependency-fixes into master

List of changes:

  • Update all dependencies in line with the "Debian stable/Ubuntu LTS from 6 months ago".
  • Remove legacy code that was there fore backwards compatibility
  • Fix a lot of deprecation warnings due to changes in python/scipy/numpy/mpl
  • Update all links to use https, resolve several permanent redirects, update or remove a few broken links
  • Remove unmaintained macports/homebrew installation instructions

Still TODO: squash/regroup commits.

Closes #386 (closed)

Edited by Anton Akhmerov

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