Issue adding site-packages directory to PYTHONPATH in Spyder

user_9921408 0
Viewed 1806

I am using Spyder and trying to add /usr/local/lib/python3.7/site-packages to the PYTHONPATH Manager. However, I receive an error informing me "This directory cannot be added to PATH. If you want to set a different Python interpreter, please go to Preferences > Main Interpreter".

However, I have already changed my interpreter to point to /usr/bin/python3

At the moment, I am using the rather annoying work around of putting the following at the top of all my code.

import sys
sys.path.append("/usr/local/lib/python3.7/site-packages")

Typing the following gives me the below. Is there a way which I can even ensure after running pip3 install XXX in the terminal, that the packages are downloaded somewhere such as the below?

for p in sys.path: print(p)

/Users/user
/usr/local/lib/python3.7
/Users/user/opt/anaconda3/lib/python37.zip
/Users/user/opt/anaconda3/lib/python3.7
/Users/user/opt/anaconda3/lib/python3.7/lib-dynload

/Users/user/opt/anaconda3/lib/python3.7/site-packages
/Users/user/opt/anaconda3/lib/python3.7/site-packages/aeosa
/Users/user/opt/anaconda3/lib/python3.7/site-packages/IPython/extensions
/Users/user/.ipython

Alternatively, and preferably, advice on how to add the above site-packages directory to my PATH? I feel I am missing something obvious.

spyder path python
2 Answers

(Spyder maintainer here) We forbid adding site-packages directories through our PYTHONPATH manager because it allows people to mix two different Python versions (which is what you're trying to do by adding your system site-packages to your Anaconda's Python).

And we do that because it usually generates odd errors and segfaults for binary packages such as Numpy, Pandas and Matplotlib, given that binary packages for one Python version are incompatible with packages for another one.

Finally, even though you found a workaround for that (by using sys.path), we strongly suggest you to stop doing that because it'll give you nothing by headaches in the future.

user_4383860

Doing what you are asking isn't the recommended path forward but you can solve the underlying problem in either of the following ways (A or B).

To "ensure pip installs packages to another location which Spyder can see" as the asker guessed in a comment on the accepted answer which got no answer (Method B below) is usually not a good idea. Keeping a clean environment for Spyder will ensure that you can determine requirements (including package version) for each of your projects reliably. Therefore, do the reverse of what you guessed: Ensure Spyder uses the Python interpreter in the environment where pip installed your project's required packages.

A. Change the Python interpreter

  1. Go to Tools, Preferences, and set Python interpreter to the python executable that was used to install the package (If using a virtual environment, it would be your_other_env/bin/python).
  2. Close and reopen Spyder (Spyder says to restart the IPython console, but it may not work in this case and show the error where Spyder cannot restart a kernel it didn't start).
  3. Open Spyder again and run any py file. You will get an error that says to install the spyder-kernels package (for some reason pip 22.0.4 will only install spyder_kernels: This issue is at "spyder-kernels should be spyder_kernels" :edit: but the issue is invalid, so upgrade pip first such as via pip install --upgrade pip in your virtual environment). Take note of the version in the error, since that is the version you need.
  4. If you are using conda or are on Windows the instructions will differ, so see Common Illnesses in the Spyder documentation instead of continuing this step.
source your_other_env/bin/activate
pip install --upgrade pip setuptools
pip install spyder-kernels=...
deactivate

but change ... to the version shown in your Spyder error from step 3. If you installed Spyder with conda as recommended, use the commands from the URL above instead.

I don't recommend Method B, as I've explained. However, it may be useful if you are manually installing Spyder plugins or test suites that apply to all projects but aren't in the requirements.txt or setup.py requirements for your project(s) (and therefore don't affect determining requirements for your users).

B. To "ensure pip installs packages to another location which Spyder can see" you would run "spyder_env/bin/python -m pip install ..." to install the package, where spyder_env is the virtualenv where Spyder is installed (but if Spyder is installed in the system using an installer or linux distro package, you may need to use your system's python such as via python3 -m pip install --user ... where ... is the package name. Always use --user instead of sudo or root to avoid mismatched files caused by mashing together the distro-packaged modules and your manually installed modules).

user_45411040
Related