Pipfile refresh for v0.9.0

[weiji14]

PyGMT VCS dependency causing problems with dependabot updating Pipfile packages (see #137, #139, #140, #142, #143, #144...). This branch/PR is used to temporarily remove pygmt from the Pipfile so that the other dependencies can be updated properly one-by-one with dependabot's documented changes manually!

TODO:

• [x] Remove pygmt from Pipfile and disable pygmt required tests (ea40d50661bd57c3a182b9cd901681728e455b45)
• Have dependabot upgrade various data science dependencies
• [x] Manually update dependencies in blocks:
  • Machine Learning/Deep Learning packages (eede354f10ce4fd9fb8f64268e0c21896a754189)
  • PyData/Data Science packages (8d7ea0ef55be5953e240e9fcf601006d04898ab3)
  • Development related packages (299a0323ac1c7df55b8c3ee2c32e6d803d137760)
• [x] Restore pygmt into the Pipfile and re-enable pygmt tests (b3917243c9b0596046902153d1cc57b57211762a)

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