Installation issues

In this section you find some known installation issues and how to fix them.

Setting up Python

Depending on how you have your Python set up on your machine, different preparation may be advisable. Here are some suggestions:

• Getting started with Python and Anaconda: If you have not yet installed Python or Anaconda on your computer at all, this explains how to set it up and create an environment that contain the most basic functionality (napari & Jupyterlab)

• Setting up a new environment: If you already have Python installed and want to create a new environment for napari-stress, follow these steps to create a new environment and install napari-stress into it.

conda create -n stress Python=3.9
conda acticate stress
conda install mamba -c conda-forge

mamba install napari pyqt devbio-napari
pip install napari-stress

If you want to make sure you are using the latest version, replace pip install napari-stress with pip install napari-stress==version.number (e.g., pip install napari-stress==0.1.0). You find the current version number on the pypi page and on top of the documentation frontpage.

Related packages

Some packages work well in conjunction with napari-stress, e.g., for better 3D interactivity, visualization of the results and/or data export. Here are some suggestions:

• Devbio-napari: Not strictly necessary but strongly recommended - this package brings many handy functionalities to an otherwise quite plain napari-viewer.

• Napari-threedee: Enhance rendering options in napari with a set of interesting tools for mesh lighting, plane rendering, etc.install type pip install napari-threedee.

• napari-process-points-and-surfaces: A plugin that allows you to process points and surfaces in 3D. To install, type pip install napari-process-points-and-surfaces.

Installation failing on Mac

When pip-installing napari-stress on M1 or M2 Macs, you may encounter the following error message (link to report):

ImportError: dlopen(/Users/manon/opt/anaconda3/envs/napari-stress/lib/python3.9/site-packages/open3d/cpu/pybind.cpython-39-darwin.so, 0x0002): Library not loaded: '/usr/local/opt/libomp/lib/libomp.dylib'
Referenced from: '/Users/xxxx/opt/anaconda3/envs/napari-stress/lib/python3.9/site-packages/open3d/cpu/pybind.cpython-39-darwin.so'
Reason: tried: '/usr/local/opt/libomp/lib/libomp.dylib' (no such file), '/usr/local/lib/libomp.dylib' (no such file), '/usr/lib/libomp.dylib' (no such file)

In order to fix this issue, please update the XCode tools on your Mac as described here.

Pygeodesic installation fail

On some Macs, the pygeodesic package fails to install with this error message:

building ‘pygeodesic.geodesic’ extension
creating build/temp.macosx-10.9-x86_64-cpython-39
creating build/temp.macosx-10.9-x86_64-cpython-39/pygeodesic
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/xxxx/opt/anaconda3/envs/mamba/envs/napari-stress-open3d/include -fPIC -O2 -isystem /Users/rachna.narayanan/opt/anaconda3/envs/mamba/envs/napari-stress-open3d/include -I/Users/xxxx/opt/anaconda3/envs/mamba/envs/napari-stress-open3d/include/python3.9 -I/Users/xxxx/opt/anaconda3/envs/mamba/envs/napari-stress-open3d/lib/python3.9/site-packages/numpy/core/include -Ipygeodesic\geodesic_kirsanov -c pygeodesic/geodesic.cpp -o build/temp.macosx-10.9-x86_64-cpython-39/pygeodesic/geodesic.o
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
error: command ‘/usr/bin/clang’ failed with exit code 1
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure

× Encountered error while trying to install package.
╰─> pygeodesic

note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.

Similar to this issue, this problem can be fixed by updating the XCode command line tools on your Mac as described above.

OSError (Windows) during installation

This describes how to fix the following error:

ERROR: Could not install packages due to an OSError: [WinError 5] Access is denied: 'C:\\Users\\xxx\\AppData\\Local\\Temp\\pip-uninstall-f7qla__t\\jupyter-trust.exe'
Consider using the `--user` option or check the permissions.

If this occurs, close all open Python instances (e.g., anaconda command line prompts, Jupyterlab instances, etc) and try again - this should fix the issue.