Polyclonal

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- Upgrade minimum ``altair`` to 5.0.0
- Use ``ruff`` as linter rather than ``flake8``
- Add ``Polyclonal.mut_icXX_df`` method
- Add ``Polyclonal.mut_icXX_plot`` method
- Add ``PolyclonalCollection.mut_icXX_df_replicates``, ``PolyclonalCollection.mut_icXX_df``, and ``PolyclonalCollection.mut_icXX_df_w_model_values`` methods.
- Add ``PolyclonalCollection.mut_icXX_plot`` method

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- Add *min_escape_magnitude* as an option for ``PolyclonalAverage`` escape averages and plots. This gives the value across models with the lowest magnitude (smallest absolute value).

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- In ``polyclonal.plot.lineplot_and_heatmap``, apply any hiding filter sliders before doing the max of the stat at the site slider. This avoids showing sites with all hidden values when trying to look at max.
- Pass ``nbval`` tests with ``pandas`` 2.0.

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- Update to using ``altair`` version 5.0.0rc1, which can be installed by `pip`. This also means for the first time ``polyclonal`` itself can be on PyPI, which changes installation instructions.

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- Increase default ``reg_activity_weight`` from 1.0 to 2.0, note that this will change results relative to models fit with earlier versions with the old default weight.
- Improvements to fitting of models:
- The optimization bounds to ``Polyclonal.fit`` can now be set as parameters (``activity_bounds``, etc) rather than hard-coded.
- Change regularization on Hill coefficient to a more quadratic form.
- Adjust regularization weight for Hill coefficient (decreasing to 25)
- Put upper bound on non-neutralizable fraction of 0.5.
- Add (and activate by default) ``fit_fixed_first`` to fit a model with a fixed Hill coefficient and non-neutralized fraction first, and the ``fit_fixed_first_reg_activity_weight`` option to fit it with a higher weight.
- Add ``check_concentration_scale`` to ``Polyclonal`` to keep concentrations in data to fit in reasonable range.

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- Added ``sites_to_show`` option to ``polyclonal.plot.lineplot_and_heatmap``.
- Remove `is_weighted_replicate` from ``curves_plot`` tooltip (it was an error this was ever shown).