Jupytext

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**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))

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

**Fixed**
- Format options stored in the notebook itself are now taken into account (Fixes [757](https://github.com/mwouts/jupytext/issues/757))

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

**Fixed**
- The `jupytext.toml` config file can now be used together with the `jupytext` pre-commit hook ([752](https://github.com/mwouts/jupytext/issues/752))
- The `notebook_extensions` option of the `jupytext.toml` file now works ([746](https://github.com/mwouts/jupytext/issues/746))

**Changed**
- The options in `jupytext.toml` where renamed to match the `jupytext` metadata in the text notebooks. One should now use `formats` rather than `default_jupytext_formats` and `notebook_metadata_filter` rather than `default_notebook_metadata_filter` ([753](https://github.com/mwouts/jupytext/issues/753))

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

**Fixed**
- We have updated `marked`, an indirect dependency of the `jupyterlab-jupytext` extension, to fix a moderate vulnerability ([750](https://github.com/mwouts/jupytext/issues/750)).
- We use non-random cell ids in the tests to avoid test failures due to duplicate cell ids ([747](https://github.com/mwouts/jupytext/issues/747))