ModuleNotFoundError: No module named 'nbformat'-CodePudding

I would like to run python in a Quarto document. I followed the docs about installing and using python in Quarto, but the error stays. Here is some reproducible code:

---
title: "matplotlib demo"
format:
  html:
    code-fold: true
jupyter: python3
---

For a demonstration of a line plot on a polar axis, see @fig-polar.

```{python}
#| label: fig-polar
#| fig-cap: "A line plot on a polar axis"

import numpy as np
import matplotlib.pyplot as plt

r = np.arange(0, 2, 0.01)
theta = 2 * np.pi * r
fig, ax = plt.subplots(
  subplot_kw = {'projection': 'polar'} 
)
ax.plot(theta, r)
ax.set_rticks([0.5, 1, 1.5, 2])
ax.grid(True)
plt.show()
```

Error output:

Starting python3 kernel...Traceback (most recent call last):
  File "/Applications/RStudio.app/Contents/Resources/app/quarto/share/jupyter/jupyter.py", line 21, in <module>
    from notebook import notebook_execute, RestartKernel
  File "/Applications/RStudio.app/Contents/Resources/app/quarto/share/jupyter/notebook.py", line 16, in <module>
    import nbformat
ModuleNotFoundError: No module named 'nbformat'

I also checked with Quarto if Jupyter is installed in the terminal like this:

quarto check jupyter

Output:

[✓] Checking Python 3 installation....OK
      Version: 3.7.11 (Conda)
      Path: /Users/quinten/Library/r-miniconda/envs/r-reticulate/bin/python
      Jupyter: 4.12.0
      Kernels: julia-1.8, python3

[✓] Checking Jupyter engine render....OK

Which seems to be OK. So I was wondering if anyone knows how to fix this error?

Edit: output conda info --envs

Output of conda info:

# conda environments:
#
                         /Users/quinten/.julia/conda/3
                         /Users/quinten/Library/r-miniconda
                         /Users/quinten/Library/r-miniconda/envs/r-reticulate
                         /Users/quinten/Library/rminiconda/general
                         /Users/quinten/opt/anaconda3
base                  *  /Users/quinten/opt/miniconda3

Edit: conda install Jupyter

The condo install Jupyter was installed (thanks to @shafee), now when I check with quarto if Jupyter exists, I get the following error:

quarto check jupyter

[✓] Checking Python 3 installation....OK
      Version: 3.7.11 (Conda)
      Path: /Users/quinten/Library/r-miniconda/envs/r-reticulate/bin/python
      Jupyter: 4.11.1
      Kernels: julia-1.8, python3

(/) Checking Jupyter engine render....Unable to load extension: pydevd_plugins.extensions.types.pydevd_plugin_pandas_types
Unable to load extension: pydevd_plugins.extensions.types.pydevd_plugin_pandas_types
[✓] Checking Jupyter engine render....OK

CodePudding user response：

The problem is that Quarto is referring to the r-reticulate environment and possibly jupyter is not installed in that environment. If thats the case, you simply need to install jupyter in the r-reticulate environment.

So first, activate the environment.

conda activate r-reticulate

and then install jupyter there,

conda install jupyter

Or, if conda could not find that environment, use the path to that environment to install jupyter in that environment,

/Users/quinten/Library/r-miniconda/envs/r-reticulate/bin/python -m pip install jupyter

Also, if you are wondering, why jupyter command runs even though it did not exist in the r-reticulate environment, its because you probably installed jupyter in the base environment and quarto is detecting that jupyter installation while checking.