Polyclonal

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- Change default positive colors.

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- Make ``Polyclonal.spatial_distances`` a public attribute.
- ``Polyclonal.fit`` allows epitopes with identical activities if they have different escape.
- Activity regularization penalizes both positive and negative values.
- Checks and int versus str dtype adjustment for ``spatial_distances`` in ``Polyclonal``.
- Adjust activity regularization based on concentration geometric mean so it is not sensitive to units of concentration.
- Renamed what was previously called the epitope similarity regularization to epitope uniqueness-squared, as it's a second uniqueness regularization but operates on square of escape values.
- Change default regularization strengths in ``Polyclonal.fit``.
- Rename ``reg_spatial_weight2`` to ``reg_spatial2_weight`` for ``Polyclonal.fit``.
- Update default values of regularization weights.
- Added antibody cocktail and HIV serum examples.
- Updated examples, for instance by adding spatial regularization to RBD example and slightly changing simulated data.

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- Flatten mutation-escape values for RBD simulation so most values are roughly zero. Previously many values were ~0.5 rather than 0. Also adjust activities for this simulation.
- Improve column spacing when ``Polyclonal.fit`` prints log.
- Added 'atom' as output column in ``pdb_utils.extract_atom_locations``
- Added ``pdb_utils.inter_residue_distances``
- Added ``Polyclonal.distance_matrix`` attribute, set via ``spatial_distances`` parameter.
- Added spatial regularization to ``Polyclonal.fit``
- Added uniqueness regularization to ``Polyclonal.fit`` as an alternative to similarity regularization that does not go with square of site-level values.

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- Add epitope similarity regularization that can be tuned by the parameter ``reg_similarity_weight``.
- Add ``real_mAb_cocktail.ipynb`` notebook that fits model to a real mAb cocktail dataset.

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- Fix bug introduced in version 2.3 that dropped wildtype sites if there were minimums set in ``slider_binding_range_kwargs`` to ``lineplot_and_heatmap``.

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- ``lineplot_and_heatmap`` computes the limit for the heatmap range **after** applying the minimum filters specified in the filters. This avoids having the range determined by mutations that are never plotted, and so is sort of a bug fix (prior behavior wasn't strictly a bug, but did not give sensible behavior).