Reworked logging to catch all logs and prints and be prettier

[mrvisscher]

Rework of the logging module making it log everything, from prints made by other modules to the StdOut and StdErr calls from C code.

• All StdOut and StdErr caught on different levels to create flexibility in logging information

• Console displays logging levels now

• Everything captured in log-file, now in .csv format for structured reading.

• Closes #1239

Checklist

• [x] Keep pull requests small so they can be easily reviewed.
• [x] Update the documentation, please follow the numpy style guide.
• [ ] Update tests.
• [x] Categorize the PR by setting a good title and adding one of the labels: bug, feature, ui, change, documentation, breaking, ci as they show up in the changelog.
• [x] Link this PR to related issues by using closing keywords.
• [x] Add a milestone to the PR for the intended release.
• [x] Request a review from another developer.