Open DcShepherd opened 2 months ago
Hi @DcShepherd,
Thank you for reaching out. pytme comes with a set of c extensions that help performance but can be a bit tricky to build. I reproduce your error when installing like this
git clone https://github.com/KosinskiLab/pyTME.git
cd pyTME
python3 -mpip install .
Installing the library in editable mode fixed the issue for me python3 -mpip install -e .
. The other installation methods should also yield a working installation though (https://kosinskilab.github.io/pyTME/quickstart/installation.html).
Which installation method did you use? :)
Hi, Thanks for the quick reply, my installation process is shown below from this page: https://kosinskilab.github.io/pyTME/quickstart/installation.html
conda create \
--name pytme \
-c conda-forge \
python=3.11 \
pyfftw \
napari \
magicgui \
pyqt
conda activate pytme
pip install git+https://github.com/KosinskiLab/pyTME.git
pip install "pytme[cupy]"
pip install git+https://github.com/maurerv/napari-density-io.git
The good new is that the python3 -mpip install -e
command seems to have fixed the issue
Hi,
Thank you for sharing the installation process. I am glad to hear pytme is working now.
I was able to reproduce your error and have updated the installation instructions accordingly. Re-installing in editable mode did solve the issue, but it is a temporary solution at best. The editable mode can be avoided by modifying the file structure of the package. I plan to integrate this in the next 0.2.4 release.
Thanks again for reporting :)
Hello,
Thanks for the info! I also had to install Pytorch rather than CuPy to get all the test to pass. I'll have to check if it is a config problem with this machine.
Hello,
I have been following the tutorial for the installation of pyTME but I am running into this error when I run the pytest protocol.
Furthermore, check to see if the preprocess.py is working but then I get a similar error
I tried deleting and reinstalling multiple times but I get the same error. Would you be able to point out where I might have made of a mistake during the installation.