Jupytext

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**Added**
- The Jupytext CLI has a new `--diff` command to show the differences between two notebooks (and if you want to see the changes in a file being updated by Jupytext, use `--show-changes`) ([799](https://github.com/mwouts/jupytext/issues/799))
- Jupyter will show the diff between text and `ipynb` paired notebooks when it cannot open a paired notebook because the `ipynb` version is more recent. Also, if the inputs in the two files are identical then the notebook will open with no error ([799](https://github.com/mwouts/jupytext/issues/799))
- The `py:percent` format will use raw strings when encoding Markdown cells as string, if they contain backslash characters ([836](https://github.com/mwouts/jupytext/issues/836))

**Fixed**
- We have upgraded the jupyterlab extension dependencies and especially `ansi-regex` to fix a security vulnerability ([857](https://github.com/mwouts/jupytext/issues/857))

**Changed**
- The Jupytext configuration file is reloaded only when a notebook is opened, saved, or when a different folder is explored ([797](https://github.com/mwouts/jupytext/issues/797))

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**Added**
- Jupytext supports Quarto notebooks (with `.qmd` extension) ([837](https://github.com/mwouts/jupytext/issues/837))
- Jupytext can be configured through the `pyproject.toml` file. Thanks to Robin Brown for this contribution! ([828](https://github.com/mwouts/jupytext/issues/828))
- Jupytext now supports OCaml files with `.ml` extension. Thanks to Quentin Fortier for getting this started ([832](https://github.com/mwouts/jupytext/issues/832))

**Fixed**
- Added more test to make sure that notebooks can be trusted. In practice, notebooks could not be trusted in JupyterLab<3.0.13 because of the absence of cell ids ([826](https://github.com/mwouts/jupytext/issues/826))

-------------------

**Fixed**
- Fixed typos revealed by `codespell` - thanks to hectormz for this contribution ([829](https://github.com/mwouts/jupytext/issues/829))
- We updated the dependencies of the `jupyterlab-jupytext` extension to address several security issues ([842](https://github.com/mwouts/jupytext/issues/842)) ([#843](https://github.com/mwouts/jupytext/issues/843))
- The Jupytext dev environment (`requirements-dev.txt`) now uses `jupyterlab==3.0.17` rather than `3.0.0` because of another security issue ([839](https://github.com/mwouts/jupytext/issues/839))

-------------------

**Changed**
- The documentation illustrates how the `cell_markers` option (and the other ones) can be set directly in the `jupytext.toml` config file ([809](https://github.com/mwouts/jupytext/issues/809)).
- The dependency on `mdit-py-plugins` through `markdown-it-py[plugins]` was made explicit ([814](https://github.com/mwouts/jupytext/issues/814))

**Fixed**
- System assigns of the form `var = !cmd` are commented out ([816](https://github.com/mwouts/jupytext/issues/816))
- Fixed an `InconsistentPath` issue with notebooks paired with scripts in a folder. The prefix in the Jupytext formats always use /, while paths might use either / or \ ([806](https://github.com/mwouts/jupytext/issues/806))
- Tests that cannot succeed are skipped when either the Jupytext folder is not a git repository, when `sphinx-gallery` is too recent, or when `pandoc` is not up-to-date ([814](https://github.com/mwouts/jupytext/issues/814))
- Removed the mention of '--update' in 'jupytext --pipe' since outputs are preserved already

-------------------

**Changed**
- Jupytext CLI has a new option `--use-source-timestamp` that sets the last modification time of the output file equal to that of the source file (this avoids having to change the timestamp of the source file) ([784](https://github.com/mwouts/jupytext/issues/784))
- In the pre-commit mode, Jupytext now uses the commit timestamp to determine which file in the pair is the most recent ([780](https://github.com/mwouts/jupytext/issues/780))


**Fixed**
- Dependencies of the JupyterLab extension have been upgraded to fix a security vulnerability ([798](https://github.com/mwouts/jupytext/pull/798))
- The `--warn-only` option also applies to pipes. Use this if the pipe may fail, e.g. if you apply `black` on a possibly invalid script ([781](https://github.com/mwouts/jupytext/issues/781))
- Variables assigned from a magic command are commented out in `py` scripts ([781](https://github.com/mwouts/jupytext/issues/781))
- Fixed a round-trip issue on notebooks that have None/null in their metadata ([792](https://github.com/mwouts/jupytext/issues/792))

-------------------

**Changed**
- Jupytext's dependency markdown-it-py is now in v1 ([769](https://github.com/mwouts/jupytext/issues/769))
- The optional argument `fmt` in `jupytext.reads` now has the default value `None` - thanks to Yuvi Panda ([763](https://github.com/mwouts/jupytext/issues/763))

**Fixed**
- All text files are opened with an explicit `utf-8` encoding ([770](https://github.com/mwouts/jupytext/issues/770))
- Previously `--pipe black` was not always putting two blank lines between functions. To fix that we load the internal Jupytext
cell metadata like `lines_to_next_cell` from the text file rather than ipynb ([761](https://github.com/mwouts/jupytext/issues/761))
- The timestamp of the source file is not updated any more when the destination file is not in the pair ([765](https://github.com/mwouts/jupytext/issues/765), [#767](https://github.com/mwouts/jupytext/issues/767))

**Added**
- A new test documents when the `ipython3` pygment lexer appears in MyST Markdown files ([759](https://github.com/mwouts/jupytext/issues/759))