Jupytext

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**Changed**
- Jupytext's contents manager uses the parent CM's `get` and `save` methods to read and save text files, and explicitly calls `jupytext.reads` and `jupytext.writes` to do the conversion. We don't use `mock` nor internal parent methods any more. Thanks to Max Klein for helping making this work! ([634](https://github.com/mwouts/jupytext/issues/634), [#635](https://github.com/mwouts/jupytext/issues/635))
- Thanks to the above, Jupytext can work on top of contents manager that don't derive from `FileContentsManager`, and in particular it works with `jupyterfs` ([618](https://github.com/mwouts/jupytext/issues/618))
- The documentation was reorganized. `README.md` was simplified and now includes many links to the documentation.
- The documentation now uses `myst_parser` rather than `recommonmark`. And we use `conda` on RTD ([650](https://github.com/mwouts/jupytext/issues/650), [#652](https://github.com/mwouts/jupytext/issues/652))
- The `readf` and `writef` functions were dropped (they had been deprecated in favor of `read` and `write` in June 2019, v1.2.0)
- The description & dependencies of the JupyterLab extension were updated ([654](https://github.com/mwouts/jupytext/issues/654))
- The `--set-kernel -` command, on a Python notebook, gives an explicit error when no kernel is not found that matches the current Python executable.
- All the GitHub workflow files were concatenated into a unique file, and we have added an `pypi-publish` step to automatically publish the package on PyPi when new releases are created.
- The `CHANGELOG.md` file was moved under `docs` to better expose the history of changes.

**Added**
- Configuration errors are reported in the console and/or in Jupyter ([613](https://github.com/mwouts/jupytext/issues/613))
- Jupytext's Contents Manager internal errors are logged on the console, and trigger an HTTP Error 500 ([638](https://github.com/mwouts/jupytext/issues/638))
- The GitHub actions run on both push events and pull requests, and duplicate jobs are skipped ([605](https://github.com/mwouts/jupytext/issues/605))
- Jupytext has a `tox.ini` file, thanks to Chris Sewell ([605](https://github.com/mwouts/jupytext/issues/605))
- Jupytext is tested against Python 3.9
- The `execution` cell metadata is now filtered by default ([656](https://github.com/mwouts/jupytext/issues/656))

**Fixed**
- Optional dependency on `sphinx-gallery` frozen to version `~=0.7.0` ([614](https://github.com/mwouts/jupytext/issues/614))
- Codecov/patch reports should be OK now ([639](https://github.com/mwouts/jupytext/issues/639))
- Jupytext tests work on non-English locales ([636](https://github.com/mwouts/jupytext/issues/636))
- Cell metadata that are already present in text notebook can be filtered out using a config file ([656](https://github.com/mwouts/jupytext/issues/656))
- Optional cell attributes like attachments are preserved ([671](https://github.com/mwouts/jupytext/issues/671))

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**Added**
- New option `hide_notebook_metadata` to encapsulate the notebook metadata in an HTML comment ([527](https://github.com/mwouts/jupytext/issues/527))
- New option `root_level_metadata_as_raw_cell`. Set it to `False` if you don't want to see root level metadata
of R Markdown notebooks as a raw cell in Jupyter ([415](https://github.com/mwouts/jupytext/issues/415))
- New option `doxygen_equation_markers` to translate Markdown equations into Doxygen equations ([517](https://github.com/mwouts/jupytext/issues/517))
- New option `custom_cell_magics` to comment out cells starting with user-specific cell magics ([513](https://github.com/mwouts/jupytext/issues/513))
- Documented how to use `isort` on notebooks ([553](https://github.com/mwouts/jupytext/issues/553))
- `jupytext notebook.ipynb --to filename.py` will warn that `--to` is used in place of `--output`.
- `jupytext --set-formats filename.py` will suggest to use `--sync` instead of `--set-formats` ([544](https://github.com/mwouts/jupytext/issues/544))
- Warn if 'Include Metadata' is off when saving text files in Jupyter ([561](https://github.com/mwouts/jupytext/issues/561))
- Test that notebooks paired through a configuration file are left unmodified ([598](https://github.com/mwouts/jupytext/issues/598))
- Test that metadata filters in the configuration files are taken into account when using `jupytext --to` ([543](https://github.com/mwouts/jupytext/issues/543))
- New argument `--run-path` to execute the notebooks at the desired location ([595](https://github.com/mwouts/jupytext/issues/595))
- Activated GitHub code scanning alerts

**Changed**
- Jupytext now depends on `markdown-it-py` (Python 3.6 and above) and always features the MyST-Markdown format,
thanks to Chris Sewell ([591](https://github.com/mwouts/jupytext/issues/591))
- The `md:myst` and `md:pandoc` are always included in the Jupytext formats, and an informative runtime
error will occur if the required dependencies, resp. `markdown-it-py` and `pandoc`, are not installed. ([556](https://github.com/mwouts/jupytext/issues/556))
- The ` %%` cell marker has the same indentation as the first line in the cell ([562](https://github.com/mwouts/jupytext/issues/562))
- Jupytext is now installed from source on MyBinder to avoid cache issues ([567](https://github.com/mwouts/jupytext/issues/567))
- The tests that execute a notebook are now skipped on Windows to avoid timeout issues ([489](https://github.com/mwouts/jupytext/issues/489))

**Fixed**
- Only scripts can have an encoding comment, not Markdown or R Markdown files ([576](https://github.com/mwouts/jupytext/issues/576))
- Spaces in `--pipe` commands are supported ([562](https://github.com/mwouts/jupytext/issues/562))
- Bash commands starting with special characters are now correctly detected, thanks to Aaron Gokaslan ([587](https://github.com/mwouts/jupytext/issues/587))
- MyST Markdown files are recognized as such even if MyST-Markdown is not available ([556](https://github.com/mwouts/jupytext/issues/556))
- Build JupyterLab with `dev-build=False` and `minimize=False` on mybinder to avoid build errors
- Configured coverage targets in `codecov.yml`

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

**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)).

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

**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))

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

**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))