gviejo
commented
1 month ago Hi Ok it's a weird error. Does it happen if you call it outside spyder?
The function count is compiled with numba under the hood. It might be an issue with numba here but not sure. If you are comfortable with it, you can try to disable the compiling of the count function with the following steps:
git clone git@github.com:pynapple-org/pynapple.git
cd pynapple
Make sure you are in the right conda environment
pip install -e .
Open ~/pynapple/pynapple/core/_jitted_functions.py amd comment line 120.
Call again your scripts
If it works, there might be an incompatibility with numba with something else. If it doesn't work, you can paste the error here.
Hi, I'm running scripts that use pynapple through an IPython console in the Spyder IDE and I keep running into the following error:
Windows fatal exception: access violation
Thread 0x00005968 (most recent call first): File "C:\Users\Cam\miniconda3\envs\pynapple\lib\site-packages\zmq\utils\garbage.py", line 47 in run File "C:\Users\Cam\miniconda3\envs\pynapple\lib\threading.py", line 932 in _bootstrap_inner File "C:\Users\Cam\miniconda3\envs\pynapple\lib\threading.py", line 890 in _bootstrap
Main thread: Current thread 0x000037a0 (most recent call first): File "C:\Users\Cam\miniconda3\envs\pynapple\lib\site-packages\pynapple\core_core_functions.py", line 33 in _count File "C:\Users\Cam\miniconda3\envs\pynapple\lib\site-packages\pynapple\core\ts_group.py", line 704 in count File "c:\users\cam\documents\python scripts\ephys analysis\be05_behavior_spiking_analysis.py", line 1845 in
File "C:\Users\Cam\miniconda3\envs\pynapple\lib\site-packages\spyder_kernels\py3compat.py", line 356 in compat_exec
File "C:\Users\Cam\miniconda3\envs\pynapple\lib\site-packages\spyder_kernels\customize\spydercustomize.py", line 473 in exec_code
File "C:\Users\Cam\miniconda3\envs\pynapple\lib\site-packages\spyder_kernels\customize\spydercustomize.py", line 740 in _exec_cell
File "C:\Users\Cam\miniconda3\envs\pynapple\lib\site-packages\spyder_kernels\customize\spydercustomize.py", line 689 in runcell
File "C:\Users\Cam\AppData\Local\Temp\ipykernel_20848\4094378172.py", line 1 in
This results in the kernel crashing and restarting. The first section with the garbage collection thread is not always present, so I don't think that has anything to do with it. It looks to me like the issue happens when the count function is called? It doesn't happen every time I use count, but invariably occurs when I'm running loops that involve shuffling unit activity and running count hundreds of times. I tried deleting the pynapple environment and making it again from scratch but it didn't help. I'm using the latest version of pynapple. Any ideas?