Lolipop

- Fixed a major bug when inferring the lineage of genotypes. The scoring method incorrectly incremented the score by the `derivative_cutoff` value rather than the actual calculated score.

- The scripts now attempt to convert `.csv` files that are encoded differently than expected. This mainly affected csv files generated on Macs.

- Changed some log messages.

- Increased the font size for the labels on some of the generated graphs.

- The scripts now attempt to load the first sheet by default when reading excel files rather than assuming the first sheet is named 'Sheet1'.

- Added additional trajectory filters
- Trajectories must now vary in frequency by 10% over the course of the experiment. This excludes trajectories which remain constant.
- Trajectories with a single data point are now excluded from the analysis
- Trajectories which are fixed at the initial timepoint (timepoint "0") are now removed.

- Added a `--include-single` flag to disable the filter which removes trajectories which are only detected once.

- Initial version available on pypi and install-able via pip.
- The trajectories which are rejected due to the trajectories_check method are now correctly reported in the output files.
- Updated the documentation to match pypi's intended usage.

- Added confidence intervals to the lineage diagram
- Added a table to the supplementary_files folder which reports the confidence scores between all tested pairs of nested genotypes.
- Added a progress bar for large datasets which may take a while to calculate the pairwise distances.
- The trajectories which are rejected are now reported in the output.

- Fixed a bug that disabled `--similarity-cutoff`

- Improved the speed of the scripts ~40% on large datasets.
- Added a `--no-outlines` option to disable the white outlines in the muller plots.

- Implemented a scoring system for detecting genotype lineage.
- Modified the colorscheme to highlight significant nodes when there are a large number of genotypes.
- Changed the available options controlling the nesting step.
- Adjusted the genotype clustering algorithm to account for genotypes that fix immediately.
- Changed how the lineage plots were implemented. They now use pygraphviz (rather than the mermaid language) and are now annotated with the mutations each genotype represents.
- Updated a large amount of the documentation. The markdown version was split into separate files. The latex version is a work in progress.
- Changed the example dataset to highlight the annotation feature.
- Fixed a large number of bugs.