Unable to run higlass-python

[linxin1husky]

Happy New Year, Hi-Glass team!

I attempted to run the HiGlass Python package locally in a Conda environment and encountered some issues.

When I tried to execute the test script, hi-glass.py, I didn't receive any error messages, and no views of the .cool files appeared.

Here is the list of packages in my Conda environment:

Initially, I thought the problem might be related to my settings, so I continued to explore other options. I then tried running the Examples.ipynb file on Google Colab, but I still didn't see any results.

I am wondering how to get the package to work properly. Thank you so much!

[LiuJie1117]

I've got the same problem as you.

[LiuJie1117]

@linxin1husky Hi, I don't know how it worked but downgraded HiGlass to 1.3.3 can fix my problem. Hope that will help you.

[linxin1husky]

@LiuJie1117 Thanks for the suggestions. I've tried multiple combination of different versions of python3 with HiGlass 1.3.3. I still couldn't get anything to run... Do you mind to share the details of the environment?

[LiuJie1117]

@linxin1husky Here are some details of my conda environment & pip list. According to my earlier experience, the version of jupyter widget is important for higlass to display in jupyter-lab.

conda list: 
higlass-jupyter                  0.1.3            pypi_0                pypi
jupyter                          1.1.1            pypi_0                pypi
jupyter-client                   8.7.0            pypi_0                pypi
jupyter-console                  6.6.3            pypi_0                pypi
jupyter-core                     5.9.1            pypi_0                pypi
jupyter-events                   0.12.0           pypi_0                pypi
jupyter-lsp                      2.3.0            pypi_0                pypi
jupyter-server                   2.17.0           pypi_0                pypi
jupyter-server-terminals         0.5.3            pypi_0                pypi
jupyterlab                       4.5.1            pypi_0                pypi
jupyterlab-pygments              0.3.0            pypi_0                pypi
jupyterlab-server                2.28.0           pypi_0                pypi
jupyterlab-widgets               3.0.16           pypi_0                pypi
....
higlass-jupyter                  0.1.3            pypi_0                pypi
higlass-manage                   0.8.0            pypi_0                pypi
higlass-python                   1.3.3            pypi_0                pypi
higlass-schema                   0.2.1            pypi_0                pypi
higlass-widget                   0.1.2            pypi_0                pypi
.....
anywidget                        0.9.21           pypi_0                pypi
bwidget                          1.10.1           hce30654_1            conda-forge
higlass-widget                   0.1.2            pypi_0                pypi
ipywidgets                       8.1.8            pypi_0                pypi
jupyterlab-widgets               3.0.16           pypi_0                pypi
widgetsnbextension               4.0.15           pypi_0                pypi
---------------------------------
jupyter labextension list
JupyterLab v4.5.1
/Users/..../jupyter/labextensions
        anywidget v0.9.21 enabled OK
        jupyterlab_pygments v0.3.0 enabled OK (python, jupyterlab_pygments)
        jupyterlab-plotly v6.0.1 enabled OK (python, jupyterlab-plotly)
        @jupyter-notebook/lab-extension v7.5.1 enabled OK
        @jupyter-widgets/jupyterlab-manager v5.0.15 enabled OK (python, jupyterlab_widgets)