Fix/editable install cython build

• Changes the directory structure of the cal_tools module to a more standard one (removing the separate cython directory)
• Uses src layout now since that was the easiest way to get the tests working correctly and importing the modules from the right location for the installation type
• Minor adjustment to setup.py to account for the directory change
• Expanded CI and tests to check that compiled modules can be imported both in standard installations and editable ones
• Updated imports of the agipdalgs module in some notebooks

Description

• Fixes editable installations as they were previously missing the compiled modules, making local development and testing easier
• Brings the package more in-line with 'standard' python package layouts
• Makes running tools like codecoverage/autodocs easier (as the module name and source location now match)
• Tests can now run both from relative imports (with pip install -e) for development or from absolute (pip install .) for production

How Has This Been Tested?

• Tested locally by running editable and standard install commands and seeing that relevant modules can be imported
• Expanded CI to test that compiled modules are available in both modes

Relevant Documents (optional)

N/A

Types of changes

• Bug fix (non-breaking change which fixes an issue)

Checklist:

• My code follows the code style of this project.
• My change requires a change to the documentation.
• I have updated the documentation accordingly.

Reviewers

@calibration

I did a basic find and replace to change from cal_tools.cython import agipdalgs as calgs to from cal_tools import agipdalgs as calgs, far as I could find that was the only line that referenced the module but I'm not sure if I actually got everything.