Improving Pose.cache dictionary getter and setter performance

[klimaj]

This PR aims to improve the performance of Pose.cache dictionary data accessors. Several code pathways run with O(N^2) (quadratic time complexity) behavior, and new functionally equivalent fast data accessor methods are introduced to run with O(N) (linear time complexity) behavior:

• Pose.cache.fast_items()
• Pose.cache.fast_values()
• Pose.cache.metrics.fast_items()
• Pose.cache.metrics.fast_values()
• Pose.cache.metrics.real.fast_items()
• Pose.cache.metrics.string.fast_values()
• Pose.cache.metrics.composite_real.fast_items()
• Pose.cache.metrics.composite_real.fast_values()
• Pose.cache.metrics.composite_string.fast_items()
• Pose.cache.metrics.composite_string.fast_values()
• Pose.cache.metrics.per_residue_real.fast_items()
• Pose.cache.metrics.per_residue_real.fast_values()
• Pose.cache.metrics.per_residue_string.fast_items()
• Pose.cache.metrics.per_residue_string.fast_values()
• Pose.cache.metrics.per_residue_probabilities.fast_items()
• Pose.cache.metrics.per_residue_probabilities.fast_values()
• Pose.cache.extra.fast_items()
• Pose.cache.extra.fast_values()
• Pose.cache.extra.real.fast_items()
• Pose.cache.extra.real.fast_values()
• Pose.cache.extra.string.fast_items()
• Pose.cache.extra.string.fast_values()
• Pose.cache.energies.fast_items()
• Pose.cache.energies.fast_values()

Users must update their API calls to take advantage of these upgrades: dict(pose.cache) -> dict(pose.cache.fast_items()), etc. These improvements are only really noticable when there are hundreds to thousands of scores cached in the Pose.cache dictionary. The basis for the performance improvement is the following:

• dict(pose.cache) relies on __iter__ (returns pose.cache.all) + __getitem__(key) (returns maybe_decode(pose.cache.all[key])), where it materializes the full scores dictionary for each key (O(N^2)).
• Instead, dict(pose.cache.fast_items()) relies on simply for k, v in pose.cache.all.items(); yield k, maybe_decode(v), so the full scores dictionary is materialized once for all keys (O(N)).
• It's also worth noting that the deprecated Pose.scores dictionary (note scores not cache) has always performed with quadratic time complexity (O(N^2)), and does not contain Pose.scores.fast_items() or Pose.scores.fast_values() methods.

This PR also makes the Pose.cache.all_scores property run with O(N) behavior, and removes an unnecessary argument from a private method: self._has_sm_data(pose) -> self._has_sm_data().

Additionally, this PR provides two new fast setter methods for mappables (avoiding the relatively slow Pose.cache.metrics cleanup after each item is set with __setitem__, and instead only performing one cleanup at the end):

• Pose.cache.metrics.real.set_mappable()
• Pose.cache.metrics.string.set_mappable()

Micro-updates to the PyRosettaCluster interface are made to take advantage of these performance improvements.

[ajasja]

LGTM :)