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File structure reorganization #753

@dwhswenson

Description

@dwhswenson

Currently, we have a few modules that are extremely long and should be split into several modules in a subpackage. This would help new developers find their way to the relevant classes more easily.

The goals are:

  1. Do not change the API. Everything in the root openpathsampling namespace should stay there.
  2. Create shorter files. 1000 raw lines (including comments/docs/blanks) should be a rough maximum (this is a pylint suggestion, and one that I agree with).
  3. Create a clearer file structure for new devs.

Note that, at this point, I'm not proposing changing tests at all. I want all tests to pass with the only change being perhaps the way things are imported. Eventually, the tests should be also be reorganized so that there is one test module per code module, but I'm not planning to implement that now.

Tasks:

Others may also be added to this list later, but these are the ones where new devs are likely to be looking for models to implement their own things or to understand how the code works.

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