Megalodon

Fix bug due to guppy 5.0.7 upgrade. Resolves 146

This patch release includes a number of bug fixes and two new features.
- New features
- Modified base validation from taiyaki mapped signal (basecaller training) file
- Allows easier validation of model performance and assessment of overfitting
- Command line access to minimap2 scoring parameters
- Bug fixes
- Live processing fixed
- `mapping.summary.txt` docs ( 145 )
- Better handling of corrupt FAST5 files

Fix bug where calibration files were not included in source release. (Resolves 128)

This minor release implements upgrades to the guppy interface.

* Guppy interface upgrades
- Convert from batching to streaming
- Default calibration files for guppy 4.5.2 modbase models
- Simplified Guppy logging
* Install upgrades
- Numpy no longer required before Megalodon install
- sklearn -> scikit-learn
* Faster HDF5 reading (via `driver="core"`)
* black formatting (https://black.readthedocs.io/en/stable/)
* Various bug fixes

This a point release including new features:
* Allow supplementary alignments with `--allow-supplementary-alignments` flag (resolves 71)
* Patch for guppy connection issues (full fix coming with future Guppy release)
* Better Guppy warnings and help pointers
* Add `megalodon_extras calibrate generate_modified_base_stats` command
* Lower aggregation batch size default (resolves 76)
Bug Fixes:
* describe_alphabet error (resolves 87)
* atomize_variants error (resolves 82)

Add calibration files for updated 5hmC model as well as `megalodon_extras` commands to assist in model training.