jupytext

Fixed

• Text-only notebooks are always trusted (as they don't include any output cells) (#941)
• We made sure that our tests also work in absence of a Python kernel (#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)

Added

• Added Tcl as a supported language (#930) - thanks to shishitao for this contribution
• Added Maxima as a supported language (#927) - thanks to Alberto Lusiani for contributing a sample Maxima notebook.

Changed

• The Jupytext contents manager is derived from the LargeFileManager imported from jupyter_server rathen than notebook (#933)
• Allow for markdown-it-py v2 (#924)
• We have updated the hooks used in the test pre-commits, to fix an issue on the CI (#940, #942)
• We updated the yarn.lock file for the jupyter lab extension (#904, #925, #935, #939)

Fixed

• The Jupytext CLI only suggest --update when the target is an .ipynb file (#905) - thanks to st-- for this contribution
• We made sure that commands like cat notebook.md | jupytext --execute work (#908)

Added

• Added Haskell as supported language (#909) - thanks to 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). 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)
• We have added pyupgrade to the pre-commit hooks used for developing Jupytext (#907)

Fixed

• The text_representation metadata of text notebooks is filtered from .ipynb files both in jupytext.write and in the contents manager for Jupyter (#900)

Changed

• Jupytext will not issue a warning when a format suffix starting with '.', '-' or '_' is passed to the --to option (#901)

Fixed

• Jupytext will not open a text notebook that is not UTF-8 (#896)
• Fixed typo in git tag (#899)

Fixed

• Jupytext will not open a text notebook that is not UTF-8 (#896)

Changed

• The test suite filters the warnings that don't belong to Jupytext (#823)

Fixed

• The parsing of notebooks that don't have a YAML header (like docs/formats.md) was improved.
• The test suite works with pytest-randomly (#838)

Changed

• The "Jupytext Notebook" factory that lets the user configure the Notebook viewer as the default for text notebooks accepts more filetypes: "myst", "r-markdown" and "quarto" (#803)
• Empty MyST Markdown files are valid notebooks (#883)
• Jupytext also works with markdown-it-py v2.0 (#885)

Changed

• The extension for Jupyter Lab benefited from a series of improvements contributed by Frédéric Collonval:
  • A new "Jupytext Notebook" factory offers the option to open text notebooks directly with the notebook view (#803). To use it, follow the instructions in the documentation.
  • The ICommandPalette is optional, for compatibility with RISE within JupyterLab RISE#605
  • Added support for translation
• Branch master was renamed to main (links update)

The version 1.13.1 did not get published to pip because of #866 - This is an attempt to publish that version.

• The magic commands in py:percent scripts with no explicit format information remain commented over a round trip (#848)

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)
• 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)
• The py:percent format will use raw strings when encoding Markdown cells as string, if they contain backslash characters (#836)

Fixed

• We have upgraded the jupyterlab extension dependencies and especially ansi-regex to fix a security vulnerability (#857)

Changed

• The Jupytext configuration file is reloaded only when a notebook is opened, saved, or when a different folder is explored (#797)

Added

• Jupytext supports Quarto notebooks (with .qmd extension) (#837)
• Jupytext can be configured through the pyproject.toml file. Thanks to Robin Brown for this contribution! (#828)
• Jupytext now supports OCaml files with .ml extension. Thanks to Quentin Fortier for getting this started (#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)

Fixed

• Fixed typos revealed by codespell - thanks to @hectormz for this contribution (#829)
• We updated the dependencies of the jupyterlab-jupytext extension to address several security issues (#842) (#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)

Changed

• The documentation illustrates how the cell_markers option (and the other ones) can be set directly in the jupytext.toml config file (#809).
• The dependency on mdit-py-plugins through markdown-it-py[plugins] was made explicit (#814)

Fixed

• System assigns of the form var = !cmd are commented out (#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)
• 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)
• 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)
• In the pre-commit mode, Jupytext now uses the commit timestamp to determine which file in the pair is the most recent (#780)

Fixed

• Dependencies of the JupyterLab extension have been upgraded to fix a security vulnerability (#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)
• Variables assigned from a magic command are commented out in py scripts (#781)
• Fixed a round-trip issue on notebooks that have None/null in their metadata (#792)

Changed

• Jupytext's dependency markdown-it-py is now in v1 (#769)
• The optional argument fmt in jupytext.reads now has the default value None - thanks to Yuvi Panda (#763)

Fixed

• All text files are opened with an explicit utf-8 encoding (#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)
• The timestamp of the source file is not updated any more when the destination file is not in the pair (#765, #767)

Added

• A new test documents when the ipython3 pygment lexer appears in MyST Markdown files (#759)

Fixed

• Format options stored in the notebook itself are now taken into account (Fixes #757)

Fixed

• The jupytext.toml config file can now be used together with the jupytext pre-commit hook (#752)
• The notebook_extensions option of the jupytext.toml file now works (#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)

Fixed

• We have updated marked, an indirect dependency of the jupyterlab-jupytext extension, to fix a moderate vulnerability (#750).
• We use non-random cell ids in the tests to avoid test failures due to duplicate cell ids (#747)

Fixed

• We have adjusted the MANIFEST.in file to exclude the node_modules but still include the JupyterLab extension that was missing in the .tar.gz (and conda) package in v1.10.1. Many thanks to Martin Renou for providing the fix at (#741)