Lolipop

- The `trajectories` table no includes the corresponding genotype as well as any additional information from the input trajectories table.
- The columns in the `edges` table were reordered so the table would be compatible with the `ggmuller` r package.
- Added r scripts to the `graphics` folder which can replicate the unannotated muller plots using the `ggmuller` package.

- Fixed a bug encountered when using very small datasets (ex. 5 trajectories) within the mullerformat object.
- Cleaned up imports.

- Removed a lot of code used for debugging
- Removed a lot of unused code
- Replaced the `fuzzywuzzy` library with `rapidfuzz` due to having a better licence.
- implemented the `lineageplot` utility
- Fixed the issue where the progress bar shown during the clustering process was twice as long as it should have been.
- Disabled the progressbars for small datasets since those are quick enough that a progress bar isn't necessary
- Improved the smoothness of the muller plots by using interpolation to generate cleaner curves.
- Added the genotype palettes to the output
- Added more clustering information to the output
- Fixed a number of misc. bugs.

This release presents an overhaul of the scoring system and adjusted the trajectory clustering workflow to improve genotype detection.

- Added multiprocessing support. The scripts can now use multiple processes to calculate the pairwise distances between mutations (by far the longest step, especially for large datasets). The number of processes can be configured using the `--threads` option.
- The output muller and timeseries plots now scale with dataset size.
- beta: added a `--filename-pairwise` option to allow users to provide the pairwise distance calculation results from a previous analysis. This is aimed at avoiding re-calculating large datasets which may take a while to compute.
- Switched to a pure python implementation of the `get_Muller_df` function from ggmuller and removed the dependancy on `r`. This also eliminated an issue which prevented the muller plots from being generated for large datasets.
- Added a `--highlight` and `--highlight-color` options to highlight specific series relevant to the user's interest. These options accept either a genotype name or a specific gene name and color in the corresponding series.
- Renamed the Muller.py script to lineage. This is more consistent with the purpose of the scripts.

- Added additional options to control how individual mutational trajectories are filtered:
- `--disable-filter-single`: Allows mutations detected at a single time point to pass the filters.
- `--disable-filter-startsfixed`: Allows mutations which start the experiment fixed to pass the filters
- `--filter-constant`: Sets the maximum delta a trajectory must obtain in order to pass the filters. Default is 0.10 (AKA 10%), set it to 0 to disable this filter.
- `--dissable-all-filters`: Renamed from `--no-filter`. Disables all filters.
- Modified how the graphics were generated. Each graphic is now saved as both a `.png` file and as a rendered `.svg` file. The render can be disabled using the `--no-render` flag.
- Genotypes can now be selected using extracted annotation data (ex. 'A134D') form the input dataset. This is currently implemented when manually setting the color of genotypes using the `--genotype-colors` flag, but will be extended to manually setting genotypes and lineage.] in a later update.