Closed leorrose closed 2 months ago
@leorrose Looking into this, but I can't seem to duplicate it on my end. Were any of the parameters in the notebook adjusted?
@srivarra thanks for looking into this. In the notebook itself I did not change any of the parameters.
I did the following steps:
git clone -b v0.7.0 https://github.com/angelolab/ark-analysis.git
.cd ark-analysis
.conda env create -f environment.yml
@leorrose if you have an old version of ark
installed you may need to explicitly install it. The pixel_pysom
argument is an addition to the pixel_som_clustering.pixel_pysom
function that is not backwards compatible with older versions. Even if you pulled the new version of ark
, caching can cause old installations to remain.
To do so, ensure you are in the root of the ark-analysis
directory and run pip install -e .
. This should ensure everything is up-to-date.
@alex-l-kong Thanks for the help!
I ended up solving it using what you suggested: pip install -e .
. But I did do some different steps from what is suggested in the readme and also added the --no-cache-dir flag:
https://github.com/angelolab/ark-analysis.git
.cd ark-analysis
.conda create -n ark_env python=3.10
.conda activate ark_env
.pip install -e . --no-cache-dir
.Now everything works 😊
Describe the bug Error when running the 2_Pixie_Cluster_Pixels.ipynb Assign pixel SOM clusters section.
Expected behavior Smooth running of the notebook without any errors.
To Reproduce Run cells in 2_Pixie_Cluster_Pixels.ipynb.
Full error (when running the