tools refactor

[colganwi]

No description provided.

[codecov]

Codecov Report

❌ Patch coverage is 94.53782% with 13 lines in your changes missing coverage. Please review.
✅ Project coverage is 87.56%. Comparing base (167881d) to head (d458f0e).
⚠️ Report is 1 commits behind head on 3.0.0.

Files with missing lines	Patch %	Lines
src/cassiopeia/tools/deprecated.py	83.72%	7 Missing ⚠️
src/cassiopeia/tools/ancestral_characters.py	92.00%	2 Missing ⚠️
src/cassiopeia/utils.py	75.00%	2 Missing ⚠️
src/cassiopeia/tools/parameter_estimators.py	98.00%	1 Missing ⚠️
src/cassiopeia/tools/tree_metrics.py	98.57%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##            3.0.0     #287      +/-   ##
==========================================
- Coverage   87.89%   87.56%   -0.33%     
==========================================
  Files          59       56       -3     
  Lines        5666     5485     -181     
==========================================
- Hits         4980     4803     -177     
+ Misses        686      682       -4     

Files with missing lines	Coverage Δ
src/cassiopeia/critique/compare.py	96.80% <100.00%> (+0.10%)	⬆️
src/cassiopeia/tools/__init__.py	100.00% <100.00%> (ø)
src/cassiopeia/tools/topology.py	100.00% <100.00%> (ø)
src/cassiopeia/tools/parameter_estimators.py	95.08% <98.00%> (-0.38%)	⬇️
src/cassiopeia/tools/tree_metrics.py	97.90% <98.57%> (+7.83%)	⬆️
src/cassiopeia/tools/ancestral_characters.py	89.28% <92.00%> (+1.05%)	⬆️
src/cassiopeia/utils.py	87.56% <75.00%> (-3.84%)	⬇️
src/cassiopeia/tools/deprecated.py	76.66% <83.72%> (+17.84%)	⬆️

... and 1 file with indirect coverage changes

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