Rich-style progress bars, some improvements to dimensionality reduction and plugin config

[jdrusso]

New features

haMSM building

• Progress bars have been swapped from tqdm to rich. In addition to looking better, these should spam logfile output less
• A new batch-PCA dimensionality reduction mode has been added, which does not do streaming

Plugins

The haMSM plugin now exposes:

• a boolean parameter for using weights in dimensionality reduction
• a ray_kwargs parameter, which is a dictionary of arbitrary arguments to pass to ray.init()
• a ray_address parameter, which is an address of a Ray cluster that can be passed to ray.init() (See https://docs.ray.io/en/latest/ray-core/package-ref.html#ray.init)
• a parameter for the number of validation groups. This can be set to 0 for rapid development of pipelines, to avoid costly recalculations involved in generating the validation models

Other

• Pre-commit hooks have been added for linting + black formatting

Bugfixes

• deeptime is now properly specified as a requirement
• The SynD progress coordinate update now uses the correct backmapper

[codecov[bot]]

Codecov Report

Merging #34 (24c3adc) into main (01855ca) will increase coverage by 2.37%. The diff coverage is 54.12%.

@@            Coverage Diff             @@
##             main      #34      +/-   ##
==========================================
+ Coverage   51.22%   53.60%   +2.37%     
==========================================
  Files          23       25       +2     
  Lines        3715     3871     +156     
==========================================
+ Hits         1903     2075     +172     
+ Misses       1812     1796      -16     

Impacted Files	Coverage Δ
msm_we/msm_we.py	42.26% <3.84%> (+2.43%)	:arrow_up:
msm_we/_hamsm/_dimensionality.py	41.86% <21.05%> (-2.21%)	:arrow_down:
msm_we/_hamsm/_fluxmatrix.py	18.21% <33.33%> (+0.23%)	:arrow_up:
msm_we/optimization.py	36.84% <75.00%> (ø)
msm_we/_hamsm/_clustering.py	53.37% <76.19%> (+5.40%)	:arrow_up:
msm_we/_hamsm/_data.py	44.57% <100.00%> (+5.08%)	:arrow_up:
tests/conftest.py	100.00% <100.00%> (ø)
tests/fixtures/hamsms.py	96.36% <100.00%> (+1.46%)	:arrow_up:
tests/test_optimization.py	100.00% <100.00%> (ø)
... and 6 more

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[jdrusso]

Yuck, I messed up history a little somewhere... I wanted to rebase this, but I'm just going to squash it.