executablebooks / MyST-NB

Parse and execute ipynb files in Sphinx
https://myst-nb.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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{eval}`thing` does not work with nb_execution_mode == 'off' #596

Open flying-sheep opened 6 months ago

flying-sheep commented 6 months ago

Describe the bug

context The {eval} role (user expressions) are not functional in a notebook rendered with nb_execution_mode == 'off'.

expectation I expected the renderer to simply fetch the existing execution results from the cell metadata.

bug I get WARNING: This document does not have a running kernel instead.

problem This is a problem for people using user expressions/the eval role/directive, because it makes them needlessly useless with nb_execution_mode == 'off'.

Reproduce the bug

  1. create a notebook with a code cell x = 1 and a Markdown cell containing {eval}`x`.

  2. Execute the notebook. This results in this output being stored in the cell metadata:

      {
       "cell_type": "markdown",
       "metadata": {
        "user_expressions": [
         {
          "expression": "x",
          "result": {
           "data": {
            "text/plain": "1'"
           },
           "metadata": {},
           "status": "ok"
          }
         }
        ]
       },
       "source": [
        "{eval}`x`"
       ]
      },
  3. Set nb_execution_mode = 'off' and build the documentation.

  4. You get the above warning and don’t see the output from the cell metad

List your environment

>>> hatch run docs:pip list
Package                       Version    Editable project location
----------------------------- ---------- ---------------------------------------------------
accessible-pygments           0.0.4
alabaster                     0.7.13
asttokens                     2.4.1
attrs                         23.1.0
Babel                         2.14.0
beautifulsoup4                4.12.2
certifi                       2023.11.17
charset-normalizer            3.3.2
click                         8.1.7
comm                          0.2.0
debugpy                       1.8.0
decorator                     5.1.1
docutils                      0.20.1
executing                     2.0.1
fastjsonschema                2.19.0
greenlet                      3.0.2
idna                          3.6
imagesize                     1.4.1
importlib-metadata            7.0.0
ipykernel                     6.27.1
ipython                       8.18.1
jedi                          0.19.1
Jinja2                        3.1.2
jsonschema                    4.20.0
jsonschema-specifications     2023.11.2
jupyter-cache                 1.0.0
jupyter_client                8.6.0
jupyter_core                  5.5.0
latexcodec                    2.0.1
markdown-it-py                3.0.0
MarkupSafe                    2.1.3
matplotlib-inline             0.1.6
mdit-py-plugins               0.4.0
mdurl                         0.1.2
myst-nb                       1.0.0
myst-parser                   2.0.0
nbclient                      0.9.0
nbformat                      5.9.2
nest-asyncio                  1.5.8
packaging                     23.2
parso                         0.8.3
pexpect                       4.9.0
pip                           23.3.1
platformdirs                  4.1.0
prompt-toolkit                3.0.43
psutil                        5.9.6
ptyprocess                    0.7.0
pure-eval                     0.2.2
pybtex                        0.24.0
pybtex-docutils               1.0.3
pydata-sphinx-theme           0.14.4
Pygments                      2.17.2
python-dateutil               2.8.2
PyYAML                        6.0.1
pyzmq                         25.1.2
referencing                   0.32.0
requests                      2.31.0
rpds-py                       0.13.2
scverse-tutorials             0.0.1      /home/phil/Dev/Python/Single Cell/scverse-tutorials
setuptools                    69.0.2
six                           1.16.0
snowballstemmer               2.2.0
soupsieve                     2.5
Sphinx                        7.2.6
sphinx-autodoc-typehints      1.25.2
sphinx-book-theme             1.1.2
sphinx-copybutton             0.5.2
sphinxcontrib-applehelp       1.0.7
sphinxcontrib-bibtex          2.6.1
sphinxcontrib-devhelp         1.0.5
sphinxcontrib-htmlhelp        2.0.4
sphinxcontrib-jsmath          1.0.1
sphinxcontrib-qthelp          1.0.6
sphinxcontrib-serializinghtml 1.1.9
sphinxext-opengraph           0.9.1
SQLAlchemy                    2.0.23
stack-data                    0.6.3
tabulate                      0.9.0
tornado                       6.4
traitlets                     5.14.0
typing_extensions             4.9.0
urllib3                       2.1.0
wcwidth                       0.2.12
wheel                         0.42.0
zipp                          3.17.0
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