Why does PyCharm give unresolved reference errors on some Numpy imports?

The following often helps to solve false-positive unresolved references

File | Invalidate Caches

The Python configuration is specified in (at least) two places: Run | Edit Configurations | Python | Python Interpreter, and File | Settings | Project | Project Interpreter. My mistake was I did not set the correct Python installation in the File | Settings .... Hence, it was referring to a Python configuration that did not have the import installed (e.g. NumPy).

After I set these two locations to point to the same, correct Python installation, I did a File | Invalidate Caches / Restart, then it was fine.

A third place to check is File | Default Settings... | Project Interpreter and make sure it matches the other settings.

You can disable inspections to specific libraries (such as numpy). I found this very helpful since my scrollbar was constantly lit up all over due to this issue. Go to Settings -> Editor -> Inspections -> Python -> Unresolved references (near the bottom) and go to the Ignore references section at the bottom right of the window.

Add an entry with “numpy.*” without the quotes and you won’t see these unresolved references in numpy lighting up your scrollbar any more!

I was able to resolve the issue simply using a virtualenv instead of the system interpreter. None of the other methods i found anywhere worked for me before.

I am using Windows 7, PyCharm Community Edition 2018.2.4, Python 3.6.7, Numpy 1.15.4

1. Create a new project named my_project and set it to use the system interpreter File -> Settings -> Project: my_project -> Project Interpreter -> Select your project -> Select the system interpreter

2. Create following test script script1.py inside the project:

   import numpy as np
   print(np.tan(8))
   

   Now running this script works fine and prints some number, but Pycharm throws an unresolved reference warning and Ctrl->Click on tan doesn’t go to the numpy code as it should.

3. Manually create the virtual environment

   $cd dir/to/my_project
   $virtualenv venv
   $venvScriptsactivate
   (venv) $pip install numpy
   (venv) $deactivate
   

   On Linux, replace the activate line with
   source venv/bin/activate

4. Tell PyCharm to use the virtual environment: File -> Settings -> Project: my_project -> Project Interpreter -> Select your project -> Select Python 3.6 (my_project) which should have the python.exe inside your project folder somewhere in the venv folder.
5. Now File -> Invalide Caches / Restart ... -> Invalidate and restart
6. Wait for all the indexing to be done and check whether you can Ctrl->Click on tan in your script1.py

This way I was able to fix the same problem for other packages like torch and opencv (simply creating a virtual environment with all the packages I need). No more unresolved references so far.

No idea why it would work this way but would not work with the system interpreter.

PyCharm developer posted a workaround for one possible cause of inspection failure:

https://youtrack.jetbrains.com/issue/PY-32029

Gist of it – inspection may fail if you have a venv folder in the project directory. Right click it, mark directory as excluded.

In PyCharm’s Project tool window, right-click on the directory and select Mark Directory As -> Sources Root.

What worked for me was
Settings > project > python interpreters > (cog wheel to the right of text bar) Show all >
(on python venv) enable associate this virtual environment with (project path)

You may have to install the package using pip install numpy

I run into a similar issue when refreshing my virtual env.
I’ve found that the following solves my issue:

1. Click on the python version in the bottom (right) bar to bring up the interpreter selection menu
2. Click on the the desired interpreter (might already be selected – but click it anyway)
3. Clicking it will update the skeletons