Source Install CellProfiler on Windows - issues with pip

Hi @DStirling,

I am following the updated wiki:

I removed my previously installed python 3.7 and made a fresh install of python 3.8 in C:\Program Files (x86) (for all users)
I have installed all the other components and python is on my path variables

I opened command prompt and I cd into the directory where I have cell profiler C:\Users\debbi\Documents\GitHub\CellProfiler> but when I type pip install cython but i get "pip’ is not recognized as an internal or external command, operable program or batch file…

If I cd into the python 3.8 directory, i can install cython etc…
So should I install python in the cellprofiler directory instead of in the default location in appdata etc?



Note/ tried the conda install using

and get an error message: ResolvePackageNotFound: - wxpython=
(even after moving conda forge to the bottom of hte channels as recommended)

Is it the right version for CP4.0?

The Conda instructions are definitely outdated, and will be revised in the coming days.

Are you able to access Python 3.8 using python in the command line? If so, try python -m pip?

I used a workaround: using anaconda, i created a virtual environment for CellProfiler specifying Python 3.8 then git cloned cellprofiler from repo and followed the rest of the windows instructions ie cd into the CellProfiler folder and:

pip install cython
pip install numpy
pip install mysqlclient
pip install -e .

seems to have worked.

However, I wonder if to be able to follow the windows instructions you should not download python in the folder where you clone the repo?
will try tomorrow, now CP4 is running from source on my pipeline (and I will check if I still have the bug

There’s no need to download Python into the CellProfiler folder. You need Python 3.8 on your system, but not specifically tied to CellProfiler.

There have been a few fixes to the trackobjects module, so it’ll be interesting to find out if your issue was resolved.

We should have a Windows installer available on Github shortly, too.

1 Like