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Error when loading Python .so (Linux) #29
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Sorry for the very late response. I have had some trouble myself getting the python plugin to work with the new version of open ephys. Your error is strange, I will ask around and see if there is any reason for it. Also it has been awhile since you posted, so let me know if you have made any progress! |
Hi. I suspect that PYTHON_PATH is not set correctly at some steps. Note that I do not use conda but virtualenv+pip but I have the exact problem with the same branch. Also note that you have to change the hidden file .config.py to be able to compile some python modules. |
@RoyVII : did you find a solution ? |
Does someone known why here https://github.com/NeuroNetMem/PythonPlugin/blob/master/PythonPlugin/PythonPlugin.cpp#L694 |
Sorry, I could not find a solution to this and I ran out of ideas... |
@Claybarn @fpbattaglia I am still fighting to install the pluguin with branch new_cmake_build branch. I am able to compile C++. Note that in the branch *new_cmake_build the .config.py have to be changed. Does anyone is able to compile some python and run it ? Any help from some dev would appreciated. |
Hey @samuelgarcia. I have been busy recently and have not been able to dedicate the time to get this new version of the plugin off the ground. I ran into the same problem you are experiencing. I too thought there was something wrong with the python path, I am not sure what happened. I can try to make some time in the near future. What have you tried thus far? As for cython 0.29, I do not remember what the issue was. That was awhile ago. Can give it a shot! But imagine you will run into the same problem. |
Hi @Claybarn I finally manage to run the python plugin. I am trying to run it with:
Here some important details:
It took me several hours to discover this. So I share it. Note that I have started a PR here to fix the cmake installation. I will also put some important details in the README if you are OK. Do you plan to merger th branch "new_cmake_build" into master soon ? |
Hey @samuelgarcia thank you for this! I will see if I can get it running with your instructions. Feel free to add to the README, and we certainly want to merge new_cmake_build into master soon. |
It seems like the file structure of OE has changed considerably, I am having to change a good amount of paths. @samuelgarcia did you also encounter this? Also, we will have to get the plugin working with GitHub workflows and should adopt the file structure of the plugins on open-ephys-plugins. |
No I did change path manually. With the cmake, all path have been set automagically for me. The branch new_cmake_build have already more or less the good folder structure no ? |
Hi everybody,
First of all, thank you very much for this plugin, is really useful!
I'm having some trouble when using the PythonPlugin to load a compiled Python code .so file. I get the following output
I'm using the code from the new_cmake_build branch and had no problem compiling the plugin. I'm also using an Anaconda environment with Python 3.6, Numpy 1.18.1 and Cython 0.28.2 and setting
export CONDA_HOME=/home/anaconda3/envs/oeEnv
. This is part of the CMake output:The Python module that I'm trying to load is just the template. I get the deprecated numpy warning when compiling but that's all.
I understand that the problem is related to the plugin not using the right environment so it does not find numpy, but I have oeEnv activated when launching Open Ephys and have even used
conda run -n oeEnv ./open-ephys
to be sure. If I add the following lines to thePythonPlugin::SetFile
functionthe output is
so I don't really get what is going on.
Do you have any idea of what might be causing this?
Thank you very much!
Rodrigo
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