PathManager refactoring

IMSY-DKFZ / simpa

The Simulation and Image Processing for Photonics and Acoustics (SIMPA) toolkit.

https://simpa.readthedocs.io/en/main/

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PathManager refactoring #296

Closed leoyala closed 3 months ago

leoyala commented 3 months ago

PathManager now accepts environment variables being defined by the user and not through a .env file.

In summary:

Removed FileNotFound raise from PathManager and replaced with KeyError only when querying the variables through get_...
Removed tests that checked for FileNotFound being raised
Added Tags for the variable names that simpa expects
Added short instructions to CONTRIBUTING guidelines

Fixes #294

jgroehl commented 3 months ago

I am wondering why the target branch for this pull request is main even though it seems to be based off the develop branch? Can we change the target to develop, or first integrate the current develop into main? @kdreher what do you think?

leoyala commented 3 months ago

I updated the target to develop, I think that is a cleaner solution. We can configure which branch is the default target for merge requests, currently it seems to be main, but I believe that we should probably make it develop instead.

jnoelke commented 3 months ago

Since we also have docs/source in the repository we should update it with the changes made in the readme.md. Especially the file docs/source/introduction.md should be updated by building the documentation and then committing the file.