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Modern path handling #89

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As described in #82

Fixes #81

Tests are passing on python3.12 locally.

Further review by someone who knows the model well is definitely needed.

Transform all path variables to the more modern `pathlib.Path` object.
This helps with cross-platform compatibility and makes the code more
readable.

Some type annotations were also passed.
Meant to be applied in conjunction with a move to Pydantic for configuration validation.

NOTE: If cherry-picked, needs to be revised carefully as the commit is
meant to be applied with a move to Pydantic.

Fixes cryotools#81
@benatouba benatouba force-pushed the modern_path_handling branch from 031ca9b to 897785b Compare November 29, 2024 16:20
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