Update main to v0.6.5 of python-parakeet#54
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…ion. For plots created by cmd line, these pdb filenames and their index value are saved to csv along with plots. Also updating analysis tests to use files with updated orientations code
…ifact upload in github workflow
…ver plot_ctf.py needs updating still
…emove licensechecker
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Updates to make building roodmus easier
Have added instrucitons for how to install roodmus locally.
Readthedocs will be updated in future.