mwouts / jupytext

Jupyter Notebooks as Markdown Documents, Julia, Python or R scripts
https://jupytext.readthedocs.io
MIT License
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Preserve the pygments_lexer of (unpaired) md:myst notebooks #789

Open mwouts opened 3 years ago

mwouts commented 3 years ago

This is a follow-up on #759 .

MyST Markdown notebooks normally use the pygments_lexer to anotate the code cells like e.g. ipython3 in this example:

```{code-cell} ipython3
1 + 1
```

This information comes from the language_info notebook metadata, which is taken either from the paired ipynb notebook, or recreated by Jupyter when the notebook is opened.

However when Jupytext CLI is used (e.g. jupytext --to md:myst on a MyST Markdown file), the language_info metadata might not be present, and the ipython3 marker disappears.

We should find a way to ensure the persistence of the lexer.

mforbes commented 1 month ago

A comment: jupytext --to md:myst sometimes makes other somewhat disturbing changes that preclude this being a good solution to issue #759. Let me know if I should open a new issue or a couple for each problem. Here are some examples:

Fenced code promoted to code-cells.

This could be bad in an environment where code cells are executed...

# Demo

You should be **very** careful about doing this:
```bash
#rm -rf *   # Commented out just in case!

After `jupytext --to md:myst *.md` this transmutes to

````markdown

# Demo

You should be **very** careful about doing this:

```{code-cell}
#rm -rf *   # Commented out just in case!

which might execute code... also there are whitespace changes (new lines) that break idempotence of the conversion.  After several runs of `jupytext --to md:myst *.md` I get

````markdown

+++

+++

# Demo

You should be **very** careful about doing this:

```{code-cell}
#rm -rf *   # Commented out just in case!

i.e. added blank notebook cells at the top.

Reference-link replacement.

Here is another example:

# Demo

This is a [reference-link to the issue][].

:::{note}
This note is key... not sure why.
:::

[reference-link to the issue]: <https://github.com/mwouts/jupytext/issues/789>

This gets transmuted to

---
jupytext:
  text_representation:
    extension: .md
    format_name: myst
    format_version: 0.13
    jupytext_version: 1.16.2
---

# Demo

This is a [reference-link to the issue](https://github.com/mwouts/jupytext/issues/789).

This note is key… not sure why.

after which it no longer changes (idempotent). Note that note admonition was removed, and the reference-link was converted to an absolute link.