Improve comments and variable names

[jf514]

Some improvements to comments, etc.

1. Explain why mjx data (comment about creating on GPU): https://github.com/talmolab/stac-mjx/blob/main/stac_mjx/controller.py#L201
2. Change _lb and _ub to _joint_lower_bound and _joint_upper_bounds https://github.com/talmolab/stac-mjx/blob/main/stac_mjx/controller.py#L79
3. Fix comment (quaternion 4): https://github.com/talmolab/stac-mjx/blob/main/stac_mjx/controller.py#L27
4. Change n to more descriptive variable name: https://github.com/talmolab/stac-mjx/blob/main/stac_mjx/controller.py#L62C8-L64C10
5. Doc string out of date: https://github.com/talmolab/stac-mjx/blob/main/stac_mjx/controller.py#L111-L118
6. Remove commented field #phyisics: https://github.com/talmolab/stac-mjx/blob/main/stac_mjx/controller.py#L159
7. Comment as to why regulariation is here or move to it's own function: https://github.com/talmolab/stac-mjx/blob/main/stac_mjx/controller.py#L151-L156
8. Comment or more descriptive names or both: https://github.com/talmolab/stac-mjx/blob/main/stac_mjx/controller.py#L71-L72
9. Clarify or enumerate "and such": https://github.com/talmolab/stac-mjx/blob/main/stac_mjx/controller.py#L210
10. What do we mean by 'optimize`: https://github.com/talmolab/stac-mjx/blob/main/stac_mjx/compute_stac.py#L25
11. Change to "returns an mjx_data updated such that..."
12. Explain magic number 7: https://github.com/talmolab/stac-mjx/blob/main/stac_mjx/compute_stac.py#L54
13. Change this function to just take a single frame: https://github.com/talmolab/stac-mjx/blob/main/stac_mjx/compute_stac.py#L16
14. Change 'res' to residual: https://github.com/talmolab/stac-mjx/blob/main/stac_mjx/compute_stac.py#L57
15. Change 'update' to 'run inverse kinematics', and add argument parameters: https://github.com/talmolab/stac-mjx/blob/main/stac_mjx/stac_base.py#L86C8-L86C15
16. Change output to say 'q_opt 2 finished in ...' https://github.com/talmolab/stac-mjx/blob/main/stac_mjx/compute_stac.py#L95
17. Change to run_kinematics: https://github.com/talmolab/stac-mjx/blob/main/stac_mjx/operations.py#L12
18. Set default frame parameter to make it clear this only happening on first frame: https://github.com/talmolab/stac-mjx/blob/main/stac_mjx/controller.py#L222
19. Change to 'Optimize marker offsets such that...': https://github.com/talmolab/stac-mjx/blob/main/stac_mjx/compute_stac.py#L117
20. Change to 'updated such that...': https://github.com/talmolab/stac-mjx/blob/main/stac_mjx/compute_stac.py#L131
21. Change m_opt to marker_optimization: https://github.com/talmolab/stac-mjx/blob/main/stac_mjx/stac_base.py#L186
22. Clarify 'phase optimization': https://github.com/talmolab/stac-mjx/blob/main/stac_mjx/stac_base.py#L197
23. Fill out these values: https://github.com/talmolab/stac-mjx/blob/main/stac_mjx/stac_base.py#L200-L207
24. Change name to sample_frame_indices: https://github.com/talmolab/stac-mjx/blob/main/stac_mjx/compute_stac.py#L138
25. Add site_idxs arg to doc string:

    stac-mjx/stac_mjx/operations.py

    Line 43 in f022418

    mjx_data (mjx.Data):

26. Same here:

    stac-mjx/stac_mjx/stac_base.py

    Line 37 in f022418

    site_idxs: jp.ndarray,

27. Comment this line to explain that these are the new params, and possibly change variable name:

    stac-mjx/stac_mjx/compute_stac.py

    Line 161 in f022418

    offset_opt_param = res.params

[charles-zhng]

Thanks for enumerating these. Some comments on some of these:
7. This is just for defining the is_regularized mask, which is there because it uses site_index_map. Can move to new function.
12. Wrong link?
13. This can be done after we set up the workflow for testing each optimization step individually to find if the second optimization step is helpful or not.
14. res -> result. Can change to that instead
22. I think I meant to say "m_phase" here. Def need to write a real docstring for that one