usage updates (toward removing the submodule)

[AgnieszkaZaba]

• PySDM:
  • badges & header cells new logic for tests - bad and good example; hook checking nb outputs; #61
  • notebooks executed and without warn, err new logic for tests - bad and good example; hook checking nb outputs; #61
  • todos (should address this issue convert todo-checks into a precommit hook #54)
  • run_notebooks
  • check show plot and anim
  • ...
  • remove submodule
• PyMPDATA:
  • ...
  • remove submodule
• PyPartMC
  • ...
  • remove submodule