Dms-variants

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- Added ability to parse second upstream / downstream region in ``IlluminaBarcodeParser`` by adding ``upstream2`` and ``downstream2`` parameters. Also modified ``IlluminaBarcodeParser`` so that reads will only be parsed if they are long enough to fully cover the region containing the barcodes and specified upstream / downstream sequences. Based on docs, this is how it was supposed to function before but did not. Additionally, this adds another row ("reads too short") to the fates from the barcode parser, as well as the ``outer_flank_fates`` option to report just failing the additional upstream and downstream regions.
- Change default color of heatmaps made by ``CodonVariantTable`` due to current one being obsolete.
- Remove obsolete ``guide=False`` from some ``plotnine`` plots in examples / tests (this was removed in ``plotnine`` version 0.13).

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- Remove use of deprecated ``scipy`` functions like ``flip`` to use ``numpy`` alternatives instead (fixes [this issue](https://github.com/jbloomlab/dms_variants/issues/86)).
- Re-format code with latest version of ``black``.
- Lint with ``ruff`` rather than ``flake8``
- Add ``pyarrow`` as dependency as required by ``pandas``.
- Tweaks to work with new versions of ``pandas`` and ``plotnine``
- Test with GitHub Actions rather than Travis CI

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Added
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- Added ``primary_target_only`` option ``prob_escape``.

Changed
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- Use ``altair`` version 5.0.0rc1

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Added
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- Added ``**kwargs`` to ``fit_models`` to propagate arbitrary model fitting options.

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Fixed
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- Fixed test failures caused by deprecations and output changes.

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Added
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- Add ``CodonVariantTable.prob_escape`` to calculate escape probabilities from absolute standard, and notebook illustrating its use.