theislab / ehrapy

Electronic Health Record Analysis with Python.
https://ehrapy.readthedocs.io/
Apache License 2.0
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Adding Scanpy's logging/settings & Scanpy functions #47

Closed Zethson closed 2 years ago

Zethson commented 3 years ago

Open discussion whether or not we should reimplement Scanpy algorithms or add it as a dependency.

Zethson commented 3 years ago

Regarding logging & settings:

  1. It would be easiest to solely use Scanpy's logging and settings & to integrate it into our code
  2. A nicer experience would be to write a new logger & settings based on Rich. In this case it likely would have to either monkeypatch Scanpy's logging & settings or the new custom logger would as a side effect also control Scanpy's equivalents.
  3. In any case, our own download & caching etc must respect the logging & settings

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