Hi all,
I have updated a number of packages (the whole jupyter/jupyterlab/matplotlib stack) and now I’m not able to get interactive plots with matplotlib in JupyterLab. Previously, I have used the magic %matplotlib notebook
to activate this interactive plot mode. Now, the notebook shows an error Javascript Error: IPython is not defined
.
Below is the environment.yml
file I am currently using where this fails as well as one where it works. I am installing via mamba using the conda-forge channel on linux.
Many thanks in advance!
-Andrew
name: wm01-rabbit
channels:
- conda-forge
- bioconda
dependencies:
- python=3.11
- pip=23.1.2
- snakemake-minimal=7.26.0
- numpy=1.24.3
- pandas=2.0.2
- matplotlib=3.7.1
- seaborn=0.12.2
- scipy=1.10.1
- scikit-image=0.20.0
- scikit-learn=1.2.2
- pytables=3.8.0
- imageio=2.28.1
- imageio-ffmpeg=0.4.8
- pymc=5.3.0
- python-graphviz=0.20.1
- nbgrader=0.8.2
- jupyterhub=4.0.1
- nbdev=2.2.10
- nbconvert=7.4.0
- jupyter_server=1.23.4
- requests=2.31.0
- biopython=1.81
- scanpy=1.9.3
- pip:
- adskalman==0.3.11
- dabest==2023.2.14
- figurefirst==0.0.6
And this was working:
name: pm21-tiger
channels:
- conda-forge
- bioconda
dependencies:
- python=3.10.4
- snakemake=7.8.2
- nbgrader=0.8.1
- sqlalchemy=1.4.37
- jinja2=3.1.2
- nbconvert=6.5.0
- jupyterhub=2.3.1
- jupyter_server=1.17.1
- numpy=1.22.4
- matplotlib=3.5.1
- pandas=1.4.2
- scipy=1.8.1
- seaborn=0.11.2
- imageio=2.9.0
- imageio-ffmpeg=0.4.7
- scikit-image=0.19.2
- scikit-learn=1.1.1
- python-graphviz=0.20
- nose=1.3.7
- pip=22.1.2
- biopython=1.79
- requests=2.28.0
- pyyaml=6.0
- sympy=1.10.1
- pytables=3.7.0
- panel=0.13.0
- hvplot=0.7.3
- napari=0.4.12
- pymc=4.2.2
- filterpy=1.4.5
- pip:
- adskalman==0.3.11
- dabest==0.3.1
- figurefirst==0.0.6