Jupytext

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

**Fixed**
- When the default contents manager is _async_ (i.e. `jupyter_server>=2.0.0`), the Jupyter server extension for Jupytext derives a contents manager from `LargeFileManager` instead, as async contents managers are not supported by Jupytext at the moment ([1020](https://github.com/mwouts/jupytext/issues/1020))
- We have made adjustments on the CI as flake8 was moved to GitHub, and Python 3.6 is not available anymore on `ubuntu-latest`

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

**Fixed**
- The sample notebooks have been normalized with `nbformat.validator.normalize` ([1002](https://github.com/mwouts/jupytext/issues/1002)).
- The warnings in the test suite that we cannot fix are filtered using a new `pytest.ini` file
- We updated the `yarn.lock` file for the jupyter lab extension to address security vulnerabilities ([984](https://github.com/mwouts/jupytext/issues/984), [#1005](https://github.com/mwouts/jupytext/issues/1005), [#1011](https://github.com/mwouts/jupytext/issues/1011))

**Changed**
- The CI uses Python 3.9 rather than 3.7 when testing conda environments

**Added**
- Gnuplot is now supported ([998](https://github.com/mwouts/jupytext/issues/998)) - thanks to [razimantv](https://github.com/razimantv) for this contribution
- We now test Jupytext against Python 3.6 to 3.11 on the CI
- We have added a test to document how to use the folder and prefix matching when pairing notebooks ([974](https://github.com/mwouts/jupytext/issues/974))

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

**Fixed**
- The timestamp of a paired notebook is the timestamp of the most recent paired file. This fixes the warning "File Changed"
after reloading the notebook in Jupyter ([978](https://github.com/mwouts/jupytext/issues/978)).

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

**Changed**
- The Jupytext configuration file has a new option `cm_config_log_level` that defaults to `info_if_changed`.
With that value, the contents manager will log a line regarding the configuration file used only when the
config file is not the same as the one previously used ([959](https://github.com/mwouts/jupytext/issues/959)) -
many thanks to R.C. Thomas for suggesting this and thoughtfully testing the patch.
- Hidden configuration files like `.jupytext.toml` or `.jupytext.py` are now ignored by Jupytext's contents manager
when `allow_hidden=False` (that option was introduced in `jupyter_server==2.0.0a1`) ([964](https://github.com/mwouts/jupytext/issues/964)).
- We have changed `jupytext --set-formats` to make it more similar to `jupytext --sync`. Now `--set-formats` will not
override existing paired files anymore ([969](https://github.com/mwouts/jupytext/issues/969)).

**Added**
- We have added a test `test_pre_commit_hook_sync_with_no_config` that documents how to use the pre-commit hook without
a configuration file ([967](https://github.com/mwouts/jupytext/issues/967))

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

**Fixed**
- Text-only notebooks are always trusted (as they don't include any output cells) ([941](https://github.com/mwouts/jupytext/issues/941))
- We made sure that our tests also work in absence of a Python kernel ([906](https://github.com/mwouts/jupytext/issues/906))
- The coverage of the `tests` folder has been restored at 100%
- Bash commands like `!{cmd}` are now correctly escaped in the `py:percent` format ([938](https://github.com/mwouts/jupytext/issues/938))

**Added**
- Added Tcl as a supported language ([930](https://github.com/mwouts/jupytext/issues/930)) - thanks to [shishitao](https://github.com/shishitao) for this contribution
- Added Maxima as a supported language ([927](https://github.com/mwouts/jupytext/issues/927)) - thanks to [Alberto Lusiani](https://github.com/alusiani) for contributing a sample Maxima notebook.

**Changed**
- The Jupytext contents manager is derived from the `LargeFileManager` imported from `jupyter_server` rathen than `notebook` ([933](https://github.com/mwouts/jupytext/issues/933))
- Allow for markdown-it-py v2 ([924](https://github.com/mwouts/jupytext/issues/924))
- We have updated the hooks used in the test pre-commits, to fix an issue on the CI ([940](https://github.com/mwouts/jupytext/issues/940), [#942](https://github.com/mwouts/jupytext/issues/942))
- We updated the `yarn.lock` file for the jupyter lab extension to address security vulnerabilities ([904](https://github.com/mwouts/jupytext/issues/904), [#925](https://github.com/mwouts/jupytext/issues/925), [#935](https://github.com/mwouts/jupytext/issues/935), [#939](https://github.com/mwouts/jupytext/issues/939))

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

**Fixed**
- The Jupytext CLI only suggest `--update` when the target is an .ipynb file ([905](https://github.com/mwouts/jupytext/issues/905)) - thanks to [st--](https://github.com/st--) for this contribution
- We made sure that commands like `cat notebook.md | jupytext --execute` work ([908](https://github.com/mwouts/jupytext/issues/908))

**Added**
- Added Haskell as supported language ([909](https://github.com/mwouts/jupytext/issues/909)) - thanks to [codeweber](https://github.com/codeweber) for this contribution

**Changed**
- We have updated the pre-commit hooks and in particular we switched to the first stable version of `black==22.1.0`.
- We require `pandoc==2.16.2` for testing. The representation for code cells changed from ` {.python}` to ` python` in that version of Pandoc ([906](https://github.com/mwouts/jupytext/issues/906)). We don't use `pandoc>=2.17` in tests at the moment because of the introduction of cell ids that cannot be filtered.
- Jupytext will not add anymore a UTF-8 encoding on Python scripts when the notebook contains non-ascii characters ([907](https://github.com/mwouts/jupytext/issues/907))
- We have added `pyupgrade` to the pre-commit hooks used for developing Jupytext ([907](https://github.com/mwouts/jupytext/issues/907))