Attpc-spyral

Release candidate for shared memory in the pipeline

Fixed the analysis notebook to correctly evaluate the entire kinematic range of a state, including beam energy effects, as well as make it easier to plot multiple states at the same time.

Hi everyone! In this release of Spyral we focused on cleaning up some bugs in the Pipeline (thanks everyone for reporting them!) and cleaning up some parts that weren't really used any more.

Some highlights:

- Address a ton of issues: 119 120 121 122 123 125 126 127
- Update spyral-utils to 1.0.0
- Remove fractional_charge_threshold parameter and the charge analysis when joining clusters.
- clustering functions now return a list of labels for points in the parent point cloud

Thanks again to everyone who helped find these bugs! Note that the changes in here are breaking and that it also updates the version of some dependencies.

Fixes a bug where the default InterpSolverPhase saved it's data in the root of the workspace rather than the InterpSolver folder.

This is a big release and represents the biggest change to Spyral and it's usage so far! Spyral is now an installable package using
`pip install attpc_spyral` and focuses on a new analysis Pipeline. The default pipeline (v0.5.0 and earlier) still exists, but it is now much easier to inject new analysis by adding custom phases. There is a lot here, too much for just one release note, so we direct you to the updated [documentation](https://attpc.github.io/Spryal) for more complete details.

- Add Pipeline and Phase abstract concepts
- Re-implement original Phases as defaults
- Overhaul docs for new system
- Re-organize repo for better usage as a package
- Remove unused utilities and dependencies

This release is focused on the removal of Nearest-Neighbor Smoothing (NNS) from the clustering phase and accounting for all of the downstream effects. Some of the highlights are

- Removal of NNS! Finally! This was an old artifact from the Dalitz clustering method, which could have dramatic and often times unpredictable effects on the data, including the Particle ID.
- Removal of NNS revealed previously ignored artifact-ing in the point cloud data in the z-coordinate due to the improper handling of conversion from GET TimeBuckets to floating point values. Previously was a simple cast to float, which would result in "clumps" of data in z. Now cast to float and add a random smearing on the interval of [0.0, 1.0) in time buckets. This accurately represents the sampling behavior in the data.
- Removal of NNS as well as user reports revealed bug where point cloud data could sometimes become NaN or Inf if values outside the legal detector volume were attempted to be sent through the electric field correction. Illegal points are now pruned at the clustering phase.
- Removal of NNS necessitated a change to the clustering algorithm. No longer cluster on charge. Without NNS, charge is too diffuse to cluster on. This also allowed simplification of scales as all scales are in the same base units (mm). Only scaling applied is to scale the z-axis to match the x and y axis to avoid over emphasis of z separation in data. These changes affect the recommended default value for epsilon in HDBSCAN. Now recommend value of 10.0 for `cluster_selection_epsilon`.
- Smoothing factor in estimation phase also needs to be increased. New recommended value is 100.0 (verified with scipy).

Documentation is updated. Notebooks updated. Dependency versions have been bumped in this release, so please reinstall the requirements.txt.

This is a big change to the analysis, and can effect the data outcome. Please use caution when updating, and report any issues or unexpected behavior!