BF,MNT: Fix bugs in loading of eddy acquisition parameters and volume indices; update code to use `pypdf`

The PyPDF2 library has been sunsetted, and replaced with pypdf; this requires a number of minor changes to the eddy_qc code.

There also seem to be some issue in the way that eddy_qc loads eddy acquisition parameter and volume index files (typically called acqparams.txt and index.txt). It was incapable of handling datasets with entries in acqparams.txt which were not referenced by index.txt. The relevant code has been re-written. Results should be the same, although order in which PE directions are reported in the eddy_qc output files may change.

The project has also been updated to use pyproject.toml instead of setup.py, which is necessary for modern Python build tooling.