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williamgilpin / pypdb

A Python API for the RCSB Protein Data Bank (PDB)
MIT License
309 stars 77 forks source link

[Testing/Bugfix] - Fixed pathing issues to allow for testing of PyPDB #21

Closed lacoperon closed 3 years ago

lacoperon commented 3 years ago

I think I screwed up last commit with how I was importing various module components.

This commit fixes the imports such that pypdb should be usable again (I think my prior CL broke it due to a ModuleNotFoundError util).

I also added a pytest conda dependency. To run all tests against the project, just run pytest within the root project directory.

williamgilpin commented 3 years ago

Hey, thank you very much.

williamgilpin commented 3 years ago

@lacoperon Hey, whenever I try to import pypdb, I am running into this error:

ModuleNotFoundError: No module named 'pypdb.util'; 'pypdb' is not a package

I can fix it by adding an __init__.py file to the util directory, and then replacing the line from pypdb.util import http_requests with from util import http_requests. However, that causes the pytests to fail. What is the correct way to resolve this issue?

williamgilpin commented 3 years ago

@lacoperon sorry for the double-post. I managed to fix it by updating the path list in setup.py. I just pushed an update to master

As far as I can tell, both the tests and the imports are working now. The __init__.py files I added probably aren't necessary since we are using Python 3. Thanks again for all your help with this package

lacoperon commented 3 years ago

No worries! Yeah I ran into that trouble, sorry that my fixing the tests led to even worse breakages.

Totally no worries on my contributing, I use this package a lot with my thesis and I know it's helpful for folk, so glad to be useful.

I'm glad the setup.py fix worked. Thanks for the fyi.

On Wed, Nov 11, 2020, 7:19 PM William Gilpin notifications@github.com wrote:

@lacoperon https://github.com/lacoperon sorry for the double-post. I managed to fix it by updating the path list in setup.py. I just pushed an update to master

As far as I can tell, both the tests and the imports are working now. The init.py files I added probably aren't necessary since we are using Python 3. Thanks again for all your help with this package

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