I am having a similar / identical issue to adding .egg files to the path , where in the PyCharm IDE it says:

However, from the console I have:
In[2]: from scipydirect import minimize
In[3]: import scipydirect
In[4]: scipydirect.__file__
Out[4]: '/home/user/Documents/InFoMM/bayesian_optimisation/venv2/local/lib/python2.7/site-packages/scipydirect-1.0-py2.7-linux-x86_64.egg/scipydirect/__init__.pyc'
How can I get PyCharm to resolve this issue and find the correct module, and add the .egg to my path?
I assume your PyCharm project using different python interpreter. You can check it in Settings -> Project -> Project Interpreter. If it's not using your virtual environment, just click on gear sign, select Add Local and choose /home/user/Documents/InFoMM/bayesian_optimisation/venv2/bin/python
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