Reorganoze tools module

[Sichao25]

No description provided.

[codecov-commenter]

Codecov Report

Attention: 1522 lines in your changes are missing coverage. Please review.

Comparison is base (389529e) 22.15% compared to head (960dff7) 22.56%.
Report is 10 commits behind head on master.

Files	Patch %	Lines
dynamo/tools/deprecated.py	15.65%	819 Missing ⚠️
dynamo/tools/Markov.py	19.23%	336 Missing ⚠️
dynamo/tools/DDRTree_graph.py	8.92%	51 Missing ⚠️
dynamo/tools/pseudotime.py	3.77%	51 Missing ⚠️
dynamo/tools/connectivity.py	31.42%	48 Missing ⚠️
dynamo/tools/recipes.py	10.25%	35 Missing ⚠️
dynamo/tools/pseudotime_velocity.py	8.82%	31 Missing ⚠️
dynamo/tools/moments.py	23.68%	29 Missing ⚠️
dynamo/tools/graph_calculus.py	32.25%	21 Missing ⚠️
dynamo/tools/DDRTree.py	21.73%	18 Missing ⚠️
... and 9 more

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Additional details and impacted files

@@            Coverage Diff             @@
##           master     #625      +/-   ##
==========================================
+ Coverage   22.15%   22.56%   +0.40%     
==========================================
  Files         166      160       -6     
  Lines       28058    28095      +37     
==========================================
+ Hits         6217     6340     +123     
+ Misses      21841    21755      -86     

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