pyiron inside pycharm: ValueError: Was not able to locate a periodic table about pyiron HOT 5 CLOSED

@niklassiemer Are you also using pyiron with WSL on windows? It sounds to me like and issue with the WSL interpreter not finding the environment variable ${CONDA_PREFIX} but I am not sure how to validate this: https://www.jetbrains.com/help/pycharm/using-wsl-as-a-remote-interpreter.html

@ahmedabdelkawy Can you try to print ${CONDA_PREFIX} on the command line? or in python using os.environ["CONDA_PREFIX"] ? If these are not set then pyiron can not find the resources and consequently cannot find the periodic table.

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Thanks, Jan, for the fast reply.

In Pycharm using python interpreter, os.environ["CONDA_PREFIX"] gives:
File ~/anaconda3/lib/python3.9/os.py:679, in _Environ.getitem(self, key)
676 value = self._data[self.encodekey(key)]
677 except KeyError:
678 # raise KeyError with the original key value
--> 679 raise KeyError(key) from None
680 return self.decodevalue(value)

KeyError: 'CONDA_PREFIX'

In WSL terminal using python, os.environ["CONDA_PREFIX"] gives: '/home/abdelkawy/anaconda3'

${CONDA_PREFIX} in WSL terminal Gives:
-bash: /home/abdelkawy/anaconda3: Is a directory

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I am using pycharm with the windows python.

Could you try import sys; print(sys.executable); print(sys.path) from the wsl python and the pycharm python?

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Pyiron installed in base
base is activated in WSL and base interpreter is selected in pycharm

WSL python:
print(sys.executable)
/home/abdelkawy/anaconda3/bin/python
print(sys.path)
['', '/home/abdelkawy/anaconda3/lib/python39.zip', '/home/abdelkawy/anaconda3/lib/python3.9', '/home/abdelkawy/anaconda3/lib/python3.9/lib-dynload', '/home/abdelkawy/anaconda3/lib/python3.9/site-packages']

pycharm python:
print(sys.executable)
/home/abdelkawy/anaconda3/bin/python3
print(sys.path)
['/mnt/c/Users/abdelkawy/Desktop/new_project_7', '/mnt/c/Users/abdelkawy/Desktop/new_project_7', '/mnt/c/Program Files/JetBrains/PyCharm 2022.2/plugins/python/helpers/pycharm_display', '/home/abdelkawy/anaconda3/lib/python39.zip', '/home/abdelkawy/anaconda3/lib/python3.9', '/home/abdelkawy/anaconda3/lib/python3.9/lib-dynload', '/home/abdelkawy/anaconda3/lib/python3.9/site-packages', '/mnt/c/Program Files/JetBrains/PyCharm 2022.2/plugins/python/helpers/pycharm_matplotlib_backend']

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Ok, both ways use the same executables (ans similar python paths), however, the pycharm interpreter does not know about the conda environment it runs in. This can be fixed by providing environment variables to be set for a given interpreter in pycharm. I would have to look up the exact location, however, pycharm offers a possibility to add environment variables to the interpreter. I just wonder why the conda environment is not setting these...

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