Refactor Python samples

[kaizu]

Most samples are moved into Jupyter Notebook. Some of the following Python scripts doesn't works with Python3. Refactor codes or remove if it's deprecated.
https://github.com/ecell/ecell4/tree/master/python/samples

[kaizu]

All the samples should be ported to https://github.com/ecell/ecell4-notebooks.

[kaizu]

The following commit accelerates the rule expansion 15 times faster: 5908525

egfr.py with max_itr=8:
Elapsed Time = 0:07:26.454877 -> 0:00:27.418062

[kaizu]

9 times faster now: Elapsed Time = 0:00:27.418062 -> 0:00:02.909375

It takes 14 seconds to generate all the 3749 reactions in egfr.py.