Python API

Refactor and optimize alignment and density map code #146

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Job	Run time
python_package (macos-15)	3m 26s
python_package (windows-2022)	7m 57s
python_package (ubuntu-24.04)	6m 26s
python_package (macos-14)	5m 47s
python_package (ubuntu-22.04)	4m 51s
	28m 27s