Quarto运行Python代码遇nbformat缺失错误，求解决方案

问题描述 #

在Quarto文档中运行Python代码时，反复出现ModuleNotFoundError: No module named 'nbformat'错误，但终端执行quarto check jupyter显示环境正常，尝试安装Jupyter后仍未解决。相关代码、报错及环境信息如下：

可复现Quarto代码：

---
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()

**报错信息**：

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

**环境检查结果**：

[✓] 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

### 解决方案

#### 1. 确认Quarto实际调用的Python环境
先检查Quarto默认使用的Python路径是否与预期一致：
```bash
quarto config get tools.python

如果输出不是/Users/quinten/Library/r-miniconda/envs/r-reticulate/bin/python，手动指定环境：

• 临时方案：在Quarto文档的YAML头部添加python字段：

  ---
  title: "matplotlib demo"
  format:
    html:
      code-fold: true
  jupyter: python3
  python: /Users/quinten/Library/r-miniconda/envs/r-reticulate/bin/python
  ---
  

• 全局方案：在终端执行命令设置全局默认Python：

  quarto config set tools.python /Users/quinten/Library/r-miniconda/envs/r-reticulate/bin/python
  

2. 给目标环境安装nbformat

激活r-reticulate conda环境，安装nbformat：

conda activate r-reticulate
pip install nbformat
# 或用conda安装：conda install nbformat -c conda-forge

3. 排查RStudio集成的环境冲突

如果在RStudio中运行Quarto，可能存在环境不一致问题：

• 在RStudio控制台执行，强制使用r-reticulate环境：

  reticulate::use_condaenv("r-reticulate", required = TRUE)
  

• 重启RStudio后重新渲染文档
• 也可直接在终端渲染文档，排除RStudio干扰：

  quarto render your-document.qmd
  

4. 重置Jupyter Kernel（可选）

若上述步骤无效，检查并重置Jupyter Kernel：

1. 查看当前Kernel列表：

   jupyter kernelspec list
   

2. 若python3 Kernel未指向r-reticulate环境，重新安装Kernel：

   conda activate r-reticulate
   python -m ipykernel install --user --name python3 --display-name "Python (r-reticulate)"
   

内容的提问来源于stack exchange，提问作者Quinten