Update dependencies

[c0c0n3]

We need to update our dependencies to the latest versions to avoid bit rot.

Most of our Python libs are at least one major version number behind, which might make it difficult to fix security vulnerabilities especially if those vulnerabilities are found in libraries that our direct dependencies in turn depend on. Also, we're missing out on major improvements that recent releases bring in. This is also true of external components we use, e.g. Crate. So we should look into upgrading the whole stack since we haven't done it in a year.

As we do that, we should undo the changes implemented in #158---i.e. explicit dependencies on PyYAML and certifi. (Hopefully by the time we get to tackle this issue, PyYAML 4.2 will be out!)
We should also be able to get rid of the numpy dependency as it doesn't seem to be used anywhere at the moment.

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