Jupytext

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**Changed**
- The documentation uses the Alabaster theme

**Fixed**
- Preserve indentation when commenting out magic commands ([437](https://github.com/mwouts/jupytext/issues/437))
- Fixed MyBinder - `jupytext.py` is not a configuration file ([559](https://github.com/mwouts/jupytext/issues/559), [#567](https://github.com/mwouts/jupytext/issues/567))

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**Fixed**
- Added `toml` as a dependency ([552](https://github.com/mwouts/jupytext/issues/552)).
- Filtered out `__pycache__` and `.pyc` files from the pip package.
- Fixed coverage upload by adding `coverage` as a dependency to the conda CI workflow.
- Fixed the conda CI / Python 2.7 job by explicitly installing `backports.functools_lru_cache` ([554](https://github.com/mwouts/jupytext/issues/554)).

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**Added**
- Jupytext can use a local or global [configuration file](https://github.com/mwouts/jupytext/blob/main/docs/config.md) ([#508](https://github.com/mwouts/jupytext/issues/508))
- Jupytext can pair notebooks in trees. Use e.g. `notebooks///ipynb,scripts///py:percent` if you want to replicate the tree of notebooks under `notebooks` in a folder named `scripts` ([424](https://github.com/mwouts/jupytext/issues/424))
- The extension for Jupyter Notebook has a _New Text Notebook_ menu that creates text-only notebooks ([443](https://github.com/mwouts/jupytext/issues/443))
- Groovy and Java are now supported, thanks to Przemek Wesołek ([500](https://github.com/mwouts/jupytext/issues/500))
- The Coconut language is also supported, thanks to Thurston Sexton ([532](https://github.com/mwouts/jupytext/issues/532))
- Resource files with `.resource` extension from the Robot Framework are supported, thanks to Hiski Valli ([535](https://github.com/mwouts/jupytext/issues/535))
- Jupytext is tested in `pip` and `conda` environments, on Linux, Mac OS and Windows, using Github actions ([487](https://github.com/mwouts/jupytext/issues/487))
- Jupytext uses pre-commit checks and automatic reformatting with `pre-commit`, `black` and `flake8` ([483](https://github.com/mwouts/jupytext/issues/483))
- Documentation improvements:
- Mention that the YAML header can be created with either `--set-kernel`, `--set-formats`, or both ([485](https://github.com/mwouts/jupytext/issues/485))
- Mention that one should use double quotes, not single quotes, around `jupytext --check` commands like `"pytest {}"` on Windows ([475](https://github.com/mwouts/jupytext/issues/475))
- Improved error message when a file is in a version that can't be read by Jupytext ([531](https://github.com/mwouts/jupytext/issues/531))

**Fixed**
- Skip the `jupytext --execute` tests when the warning _Timeout waiting for IOPub output_ occurs, which is the case intermittently on Windows ([489](https://github.com/mwouts/jupytext/issues/489))
- Fixed wrong paired paths when syncing with the --pre-commit flag ([506](https://github.com/mwouts/jupytext/issues/506))

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**Added**
- Added an example with custom notebook metadata ([469](https://github.com/mwouts/jupytext/issues/469))
- Added an example with custom cell tags ([478](https://github.com/mwouts/jupytext/issues/478))

**Changed**
- The outputs from the `.ipynb` file are matched with the input cells from the text file with less strict rules. In this version, a search and replace on the text file will not remove the outputs any more ([464](https://github.com/mwouts/jupytext/issues/464)).
- Update parsing of myst notebooks to new (markdown-it based) parser (please upgrade to `myst-parser` to version `~0.8`) ([473](https://github.com/mwouts/jupytext/issues/473))
- Use `os.path.samefile` when searching for the kernel that corresponds to the current environment (`--set-kernel -`)

**Fixed**
- Fixed the CLI example for not commenting out magic commands: `--opt comment_magics=false`. In addition, most of the `jupytext` commands in `using-cli.md` are now tested! ([465](https://github.com/mwouts/jupytext/issues/465))
- `jupytext.read` and `jupytext.write` now give more meaningful errors when the format information is incorrect ([462](https://github.com/mwouts/jupytext/issues/462))
- Multiline comments starting or ending with quadruple quotes should not cause issues anymore ([460](https://github.com/mwouts/jupytext/issues/460))
- Fixed active cells in the py:percent format ([477](https://github.com/mwouts/jupytext/issues/477))

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**Added**
- Script of script (SoS) notebooks are now supported. Thanks to Thomas Pernet-coudrier for contributing the sample notebook ([453](https://github.com/mwouts/jupytext/issues/453)).
- New MyST Markdown format (`md:myst`), developed by the [ExecutableBookProject](https://github.com/ExecutableBookProject) team. Read more about the MyST Markdown format in the [documentation](https://jupytext.readthedocs.io/en/latest/formats.html#myst-markdown). And many thanks to Chris Sewell for contributing the actual implementation! ([447](https://github.com/mwouts/jupytext/issues/447) [#456](https://github.com/mwouts/jupytext/issues/456) [#458](https://github.com/mwouts/jupytext/issues/458))

**Fixed**
- When using `jupytext --pipe cmd`, the output of `cmd` should not appear in the terminal ([432](https://github.com/mwouts/jupytext/issues/432))

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**Changed**
- The new jupyterlab extension (in version 1.2.0) is compatible with JupyterLab 2.0. Many thanks to Jean Helie! ([449](https://github.com/mwouts/jupytext/issues/449))
- It is not compatible with JupyterLab 1.x anymore. If you wish, you can install manually the previous version of the extension with `jupyter labextension install jupyterlab-jupytext1.1.1`.

**Fixed**
- Display the output/errors of command executed with `jupytext --pipe` or `jupytext --check` ([432](https://github.com/mwouts/jupytext/issues/432))