jupytext

Changed

• Harden the github action (#1569). Thanks to Peyton Murray for this PR
• The JupyterLab extension is now built with jupyter-builder - Thanks to Mahendra Paipuri for this PR (#1590)
• zizmor and pre-commit are now required to pass before any other CI job runs, and the extension lint is now part of pre-commit (#1594)
• Enabled TypeScript strict null checks in the JupyterLab extension - Thanks to Michał Krassowski for this PR (#1586)

Fixed

• Detecting IPython help/shell commands no longer takes quadratic time on lines made of whitespace - Thanks to Naveed for this PR (#1582)
• Fixed unguarded access to the languageInfo.extensions array, which could still make Jupytext show notebook icons for Python files when the kernel metadata was incomplete - Thanks to Michał Krassowski for this PR (#1584)

Security

• marimo_py_to_notebook now reuses its secure (0600, mkstemp-backed) temporary files instead of closing and reopening them by name, which removed the safe permissions and left a window for a symlink attack on shared machines (#1568). Thanks to Naveed for reporting and fixing this!

Changed

• Jupytext's documentation is now at https://jupytext.org! (#1538)
• We have moved Jupytext to its own Jupytext organization (#1546)
• Updated the JupyterLab extension production dependencies (12 patch updates) (#1541)
• We require pandoc<3.10 on the CI as pandoc converts the "3.10" string to a float, which then causes issues in Jupytext (#1545)
• Fixed the CI so that tests also run on scheduled runs, and so that jupyterfs tests are skipped when their initialization fails (#1539)
• In the CI, the extension is build using a dedicated build pixi environment.

Fixed

• We now support unicode characters while dumping YAML (#1542)

Added

• A new custom_language_magics option is available (#1491). Thanks to steovd for making the PR!

Security

• Fixed GHSA-m22c-4q2m-m5wr: the update-playwright-snapshots workflow was triggerable by any user via an issue_comment event. It now checks that the comment author is an OWNER, MEMBER, or COLLABORATOR before running (#1535)
• Set persist-credentials: false on all workflow checkout steps as defense-in-depth, preventing a live GITHUB_TOKEN from being left in .git/config where attacker-controlled build hooks could read it. This is strictly required only for update-playwright-snapshots (fixed above), but applies to all workflows so they remain safe if their scope is later extended.

Fixed

• The Jupytext CLI issues a warning when a notebook is not trusted. Also, trust is preserved when empty outputs are added (follow-up on #1505)

Changed

• The dependabot config has been updated to correctly bump extension packages, now allowing only production updates and ignoring dev dependencies (#1532). Thanks to Mahendra Paipuri for this PR!
• Removed deprecated stylelint packages (stylelint-config-prettier and stylelint-prettier) from the JupyterLab extension dependencies (#1530)
• We have removed Python 3.9 testing from the CI (Python 3.9 reached EOL in October 2025)

Fixed

• Trusted notebooks remain trusted after jupytext --sync (#1505)
• We have fixed the homepage link in package.json. Thanks to Michał Krassowski for making this PR (#1494)
• Thanks to Brigitta Sipőcz for fixing a broken link in our CLI (#1428)
• The --quiet flag now suppresses the creating missing directory warning when writing to a path that includes a prefix (#1533)

Changed

• The CI workflow has been restructured to maximize parallelization. All test suites (pip, conda, UI) and the build step now run concurrently after pre-commit checks, instead of sequentially, reducing CI times (#1527)
• We have skipped the tests that involve jupyterfs on Python 3.12+ as they started failing on the CI with no obvious way to fix them (#1509)
• We have changed the configuration of Dependabot to get grouped dependency updates for our JupyterLab extension.
• We have merged a series of Dependabot security updates: #1516, #1517, #1519, #1520, #1522, #1524

Changed

• Jupytext does not change the file icons anymore! Thanks to Michał Krassowski for finally solving this long standing issue! (#398)
• We have bumped lodash from 4.17.21 to 4.17.23 in JupyterLab extension (#1483)
• We require marimo<=0.19.4 in tests following a change in the location of the marimo import (#1485)

1.19.0 (2026-01-18)

Changes

• The environment used to develop Jupytext is now maintained using Pixi (#1459)

Fixed

• We have restored the support for .qmd documents in Jupyter (#1435)
• We have fixed warnings about the cell ids like either Cell is missing an id field or Additional properties are not allowed ('id' was unexpected) when converting to some formats, including Pandoc (#1464)
• We have updated the dependencies of the Jupytext extension for JupyterLab. Many thanks to Mahendra Paipuri for his PR (#1477)!

Added

• We have added a new py:marimo format, which uses the marimo command line interface to convert notebooks to and from the Marimo format (#1431)

1.19.0.dev0 (2025-11-16)

Changes The environment used to develop Jupytext is now maintained using Pixi (#1459)

Fixed

• We have fixed the round trip tests and made them work with Quarto 1.8.25 (#1435)
• We have fixed warnings about the cell ids like either Cell is missing an id field or Additional properties are not allowed ('id' was unexpected) when converting to some formats, including Pandoc (#1464)

Added We have added a new py:marimo format, which uses the marimo command line interface to convert notebooks to and from the Marimo format (#1431)

Fixed

• Fixed test test_check_source_is_newer_when_using_jupytext_sync to work reliably on systems with low filesystem timestamp resolution (#1460)

Changed

• We now use pixi to maintain the local Python environments used for developing and testing Jupytext.

Added

• The documentation has a chapter on the Jupytext Sync extension for VS Code (#1395)
• We have added a new option --check-source-is-newer to the Jupytext CLI. Use this option if you want to make sure that the file passed as argument to Jupytext is the newest of all paired files, and/or newer than the destination file.
• We have added a section on Jupyter Collaboration which also provides a very useful autoreload functionality (#406, #1401)
• Pairing groups allow you to define different pairing configurations for specific subsets of notebooks. The formats configuration option now supports a list of format dictionaries for first-match pairing. Use [[formats]] sections in your TOML configuration to define multiple format specifications, where the first matching format is used. This allows applying different pairing rules to notebooks in different locations, such as generating documentation markdown files only for tutorial notebooks (#1383)
• We have added more tests to document the complex pairing formats, which also work on Windows (#1028)
• Pairing into nested folders was fixed on Windows (#1028)
• Jupytext is now tested with Python 3.14 (#1456)

Fixed

• The Jupytext CLI now detects if a file it has read or consulted has been modified while it was processing it. That can happen in the context of the Jupytext Sync extension for VS Code (#1411, vscode-jupytext-sync-#12). When such a synchronous modification is detected, Jupytext now raises an error. Many thanks to Anne Archibald for reporting the issue and preparing an inspiring PR (#1417).
• We don't import notebook when jupyter_server is available (#1436)
• Jupytext now supports more characters in the cell metadata keys, to improve compatibility with jupyterlab-slideshow (#1441). Thanks to Nicolas Thierry for this fix.
• The function find_jupytext_configuration_file now works with relative directories (#1440). This fix was contributed by Thierry Parmentelat.
• We have fixed a parsing error for R Markdown files (#1429)
• We have fixed a parsing error when the first cell of the notebook contains a YAML header that is not a dict (#1444)

Changed

• We have updated the pre-commit hooks. The code is now formatted using ruff format, and updated for Python 3.9+ using https://github.com/asottile/pyupgrade (#1423)

Added

• The documentation has a chapter on the Jupytext Sync extension for VS Code (#1395)
• We have added a new option --check-source-is-newer to the Jupytext CLI. Use this option if you want to make sure that the file passed as argument to Jupytext is the newest of all paired files, and/or newer than the destination file.
• We have added a section on Jupyter Collaboration which also provides a very useful autoreload functionality (#406, #1401)
• Pairing groups allow you to define different pairing configurations for specific subsets of notebooks. The formats configuration option now supports a list of format dictionaries for first-match pairing. Use [[formats]] sections in your TOML configuration to define multiple format specifications, where the first matching format is used. This allows applying different pairing rules to notebooks in different locations, such as generating documentation markdown files only for tutorial notebooks (#1383)
• We have added more tests do document the complex pairing formats, which also work on Windows (#1028)
• Pairing into nested folders was fixed on Windows (#1028)
• Jupytext is now tested with Python 3.14 (#1456)

Fixed

• The Jupytext CLI now detects if a file it has read or consulted has been modified while it was processing it. That can happen in the context of the Jupytext Sync extension for VS Code (#1411, vscode-jupytext-sync-#12). When such a synchronous modification is detected, Jupytext now raises an error. Many thanks to Anne Archibald for reporting the issue and preparing an inspiring PR (#1417).
• We don't import notebook when jupyter_server is available (#1436)
• Jupytext now support more characters in the cell metadata keys, to improve compatibility with jupyterlab-slideshow (#1441). Thanks to Nicolas Thierry for this fix.
• The function find_jupytext_configuration_file now works with relative directories (#1440). This fix was contributed by Thierry Parmentelat.
• We have fixed a parsing error for R Markdown files (#1429)

Changed

• We have updated the pre-commit hooks. The code is now formatted using ruff format, and updated for Python 3.9+ using https://github.com/asottile/pyupgrade (#1423)

Added

• All the extensions supported by Jupytext now appear in the --to paragraph of jupytext --help (#433)
• We have added a new function get_formats_from_notebook_path that returns the list of paired formats for a given notebook (#1419)

Fixed

• We have fixed jupytext --sync, and the contents manager, to make sure that a simple .py file (not in the percent format) will not be treated as a paired file when the Jupytext configuration file has formats="ipynb,py:percent" (#1418)
• A notebook can be moved in Jupyter even if that makes it unpaired (#1414)
• The test against jupyter-fs now installs its fs extra dependency (#1398)
• The jupytext --sync command now works correctly with symbolic links. Thanks to mccullerlp for reporting (#1407) and addressing (#1408) the problem!
• Jupytext will look for quarto.cmd on Windows. Thanks to mccullerlp for documenting the issue (#1406, #1409).
• We have corrected the jupytext --paired-paths command: it will now take the Jupytext configuration file, if any, into account (#1419)

Fixed

• The --set-formats argument takes precedence over pre-existing pairing information in the notebook (#1386)

Changed

• We have removed Python 3.8 from the list of supported Python version, and from the CI, as it has reached its EOL

Added

• ROOT-flavored C++ notebooks can be paired to .cpp files - thanks to Steven Gardiner for this contribution (#1384)

Fixed

• Renaming files other than notebooks will not load their content (#1376)

Added

• The MyST frontmatter found in MyST Markdown notebooks can be mapped to a YAML header at the top of the Jupyter notebook. This way MyST notebooks in either the md:myst or ipynb format can be used with MyST. Thanks to Ian Carroll for proposing and implementing this change (#1314)
• The context menu has a "New Text Notebook" entry. Thanks to Mahendra Paipuri for this PR (#1365)!

Changed

• Jupytext's default contents manager is now derived from the asynchronous AsyncLargeFileManager. Thanks to Darshan Poudel for making this finally happen (#1328)!
• The percent format is now the default format for scripts. If you run jupytext --to py notebook.ipynb you now get a py:percent script (use --to py:light for the light format) #1201
• The rst2md conversion now works with sphinx-gallery>=0.8. Thanks to Thomas J. Fan for fixing this! (#1334)
• We have updated the JupyterLab extension dependencies (#1300, #1355, #1360). Thanks to Mahendra Paipuri for these PRs!

Fixed

• We have added and fixed round trip tests on MyST Markdown notebooks (#759, #789, #1267, #1317)
• The --quiet option now works with the --pipe mode of Jupytext CLI (#1305)
• Jupytext is now compatible with the cell toolbar extension - thanks to Nicolas Brichet for the fix! (#1358)
• The project description on PyPI now uses absolute links (#1287)

Changed

• Jupytext's default contents manager is now derived from the asynchronous AsyncLargeFileManager. Thanks to Darshan Poudel for making this finally happen (#1328)!
• The MyST frontmatter found in MyST Markdown notebooks is now mapped to a YAML header at the top of the Jupyter notebook. This way MyST notebooks in either the md:myst or ipynb format can be used with MyST. Thanks to Ian Carroll for proposing and implementing this change (#1314)
• The percent format is now the default format for scripts. If you run jupytext --to py notebook.ipynb you now get a py:percent script (use --to py:light for the light format) #1201
• The rst2md conversion now works with sphinx-gallery>=0.8. Thanks to Thomas J. Fan for fixing this! (#1334)
• We have updated the JupyterLab extension dependencies (#1300, #1355, #1360). Thanks to Mahendra Paipuri for these PRs!

Added

• The context menu has a "New Text Notebook" entry. Thanks to Mahendra Paipuri for this PR (#1365)!

Fixed

• We have added and fixed round trip tests on MyST Markdown notebooks (#759, #789, #1267, #1317)
• The --quiet option now works with the --pipe mode of Jupytext CLI (#1305)
• Jupytext is now compatible with the cell toolbar extension - thanks to Nicolas Brichet for the fix! (#1358)
• The project description on PyPI now uses absolute links (#1287)

Changed

• Jupytext's default contents manager is now derived from the asynchronous AsyncLargeFileManager. Thanks to Darshan Poudel for making this finally happen (#1328)!
• The MyST frontmatter found in MyST Markdown notebooks is now mapped to a YAML header at the top of the Jupyter notebook. This way MyST notebooks in either the md:myst or ipynb format can be used with MyST. Thanks to Ian Carroll for proposing and implementing this change (#1314)
• The percent format is now the default format for scripts. If you run jupytext --to py notebook.ipynb you now get a py:percent script (use --to py:light for the light format) #1201
• The rst2md conversion now works with sphinx-gallery>=0.8. Thanks to Thomas J. Fan for fixing this! (#1334)
• We have updated the JupyterLab extension dependencies (#1300, #1355, #1360). Thanks to Mahendra Paipuri for these PRs!

Added

• The context menu has a "New Text Notebook" entry. Thanks to Mahendra Paipuri for this PR (#1365)!

Fixed

• We have added and fixed round trip tests on MyST Markdown notebooks (#759, #789, #1267, #1317)
• The --quiet option now works with the --pipe mode of Jupytext CLI (#1305)
• Jupytext is now compatible with the cell toolbar extension - thanks to Nicolas Brichet for the fix! (#1358)
• The project description on PyPI now uses absolute links (#1287)

Added

• Logtalk notebooks are now supported (#1308) - thanks to Paulo Moura for this contribution

Fixed

• We have updated the dependencies of the Jupyter Lab extension to address security issues.

Fixed

• We fixed a "File Changed" warning when saving notebooks (#1301)

Changed

• The original file name is easier to infer from the tmp file name in pre-commit hooks (#1289) - thanks to Lunin Leonid for making this change.

Fixed

• We have fixed a notebook corruption issue when using Jupytext with Jupyter-Collaboration (#1124, jupyter-collaboration 214).
• We have added the require_hash argument on the Jupytext contents manager. The hash of a paired file is the concatenation of the hash of the text file and the hash for the .ipynb file (#1165)
• The rst2md tests have been fixed by requiring sphinx<8 (#1266)
• Some dependencies of the JupyterLab extensions were updated (#1272, #1273, #1280, #1285, #1290)
• The pre-commit hook is now compatible with log.showsignature=True (#1281). Thanks to Justin Lecher for this fix.

Added

• Jupytext is now tested with Python 3.13 (#1242). Thanks to Jerry James for the suggested fixes!
• The extension of a notebook piped into stdin will be taken in the notebook metadata (#1282)

Fixed

• We use asyncio.iscoroutinefunction to determine whether the current contents manager is sync or async (#1260)

Fixed

• We use inspect to determine whether the current contents manager derives from AsyncContentsManager (which is not supported by Jupytext at the moment). This fixes a compatibility issue with jupyter-fs==1.0.0 (#1239). Thanks to Mahendra Paipuri for this PR!
• We have fixed a typo when build_jupytext_contents_manager_class can't be imported (#1162)
• A Python 3.13 deprecation warning was fixed #1241 - thanks to Jerry James
• We have fixed a typo when build_jupytext_contents_manager_class can't be imported (#1162)
• Some dependencies of the JupyterLab extensions were updated (#1243, #1245)

Added

• Lua notebooks are now supported (#1252) - thanks to erentar for this contribution
• Go notebooks are supported too (#1244)! Many thanks to Jan Pfeifer, author of GoNB, and to HaveF for their help on this topic.
• Empty prefixes are now allowed in Jupytext format when specified as a dictionary (#1144)

Changed

• We've had to deactivate the tests on the Quarto format in the CI as the Quarto round trip might now add a Markdown cell to the notebook (#1255)

Added

• Added support for Xonsh notebooks (#1213) - thanks to Jeffrey Odongo for this contribution

Changed

• By default, the JupyterLab extension for Jupytext is not included in the build (set HATCH_BUILD_HOOKS_ENABLE=true to include it). This simplifies the installation of Jupytext in pre-commit hooks (#1210)
• Temporary text notebooks for the --pipe or --check commands are now created in the notebook directory (#1206)
• Jupytext uses the standard library tomllib in Python 3.11, or tomli in Python 3.10 or older, to match JupyterLab's dependencies (#1195)
• The dependencies of the JupyterLab extension were updated (#1216, #1218, #1231)
• jupytext --sync will not update the timestamp of text notebooks if their content is unchanged (#1215)

Fixed

• Jupytext is now tested with pandoc>=3.0. Please note that switching to pandoc>=3.0 will add cell ids to your pandoc:md notebooks (#1006)

Changed

• The CI has been updated. Thanks to Christian Le for taking care of this! (#1190, #1204)

Fixed

• Fixed an issue about unpairing notebooks from the Jupytext Menu (#1197)
• JupyterLab's dependency follow-redirects was updated from 1.15.3 to 1.15.4 (#1203)

Added

• The Jupytext Menu is back! And text notebooks can be created directly from the launcher. This is an outstanding contribution by Mahendra Paipuri (#1154, #1163). This requires JupyterLab 4.x or Jupyter Notebook 7.x.

Changed

• Jupytext is now configured with pyproject.toml and built with hatch. The layout has been reorganised to follow src-layout (#1140). This is another outstanding contribution by Mahendra Paipuri.
• The tests are now part of the sdist. They have been reorganized into unit/functional/integration/external (#1167, #1173).
• The legacy extension for Jupyter Notebook <=6 (the Jupytext Menu) has been removed.

Fixed

• The bibliography section in Rmd files does not become a code cell anymore (#1161)
• Commented code in active-py cells is not uncommented anymore (#1131)
• The test coverage has been restored (#1167, #1173)
• We test Jupytext against the pre-release version of JupyterLab, and other dependencies (#1168)

Added

• The Jupytext Menu is back! And text notebooks can be created directly from the launcher. This is an outstanding contribution by Mahendra Paipuri (#1154, #1163). This requires JupyterLab 4.x or Jupyter Notebook 7.x.

Changed

• Jupytext is now configured with pyproject.toml and built with hatch. The layout has been reorganised to follow src-layout (#1140). This is another outstanding contribution by Mahendra Paipuri.
• The tests are now part of the sdist. They have been reorganized into unit/functional/integration/external (#1167, #1173).
• The legacy extension for Jupyter Notebook <=6 (the Jupytext Menu) has been removed.

Fixed

• The bibliography section in Rmd files does not become a code cell anymore (#1161)
• Commented code in active-py cells is not uncommented anymore (#1131)
• The test coverage has been restored (#1167, #1173)
• We test Jupytext against the pre-release version of JupyterLab, and other dependencies (#1168)

Added

• The Jupyter Lab extension is now compatible with the JupyterLab RISE extension. Many thanks to Frédéric Collonval for his PR (#1126)!

Added

• We have added a new command line interface jupytext-config that you can use to set Jupytext as the default viewer for text notebooks in Jupyter Lab and Jupyter Notebook 7. Thanks to Thierry Parmentelat for this contribution! (#1094)

Changed

• This version comes with a version of the JupyterLab extension that is compatible with JupyterLab 4.x. Many thanks to Thierry Parmentelat for his PRs! (#1092, #1109)
• Pandoc 3.0 is now supported, thanks to Raniere Silva for his PR (#1099)
• We have reorganized the documentation and the README.md (#1031, #1073)
• Invalid pyproject.toml files will be ignored by Jupytext in Jupyter (#1103)
• We have updated the pre-commit tools

Changed

• This version comes with a version of the JupyterLab extension that is compatible with JupyterLab 4.x. Many thanks to Thierry Parmentelat for his PRs! (#1092, #1107)
• We have reorganized the documentation and the README.md (#1031, #1073)

Changed

• This version comes with a version of the JupyterLab extension that is compatible with JupyterLab 4.x. Many thanks to Thierry Parmentelat for this PR! (#1092)
• We have reorganized the documentation and the README.md (#1031, #1073)

Changed

• We have updated the GitHub workflows - thanks to Matthew Feickert and to Cristian Le for their help on this subject (#1037)
• We have removed the upper bound on markdown-it-py<3. Now we test Jupytext with markdown-it-py in versions 2.x and 3.x on the CI (#1075)

Fixed

• Notebooks with an empty YAML header work (#1070)
• Double quote strings in R Markdown options can contain single quotes (#1079)
• The necessary directories are created when paired notebooks are moved to a sub-folder (#1059)
• Commented quotes are recognized as such (#1060)
• Jupytext can use either pkg_resources or packaging to parse version numbers (#1085)

Changed

• This version comes with a build requirement jupyterlab>=3,<4, as the Jupyterlab extension for Jupytext is not compatible with JupyterLab 4 yet (#1054)
• The JupyterLab extension was released to npm in version 1.3.9.

Added

• Added Stata as a supported language (#1027) - thanks to Raffaele Mancuso for this contribution
• Added SAS as a supported language (#1047) - thanks to lawrencet149 for this contribution
• We have added a series of test to make sure that the main formats support cell tags (#1024)

Fixed

• When a metadata key is not a valid identifier, a warning is emitted and the metadata is not saved to the text representation (#1042)
• The CI was fixed by Matthew Feickert (#1035)
• We now use concurrency to cancel previous runs on the same branch/PR (#1037)
• We use both codecov.notify.after_n_builds and comment.after_n_builds to get only the final codecov comment

Changed

• Empty tags are not exported to the text notebook anymore (#960)
• We updated the yarn.lock file for the jupyter lab extension to address security vulnerabilities (#1030, #1036)
• In the pre-commit tests we now use main for the main branch

Added

• Added Wolfram Language as a supported language (#1014) - thanks to Etienne Dechamps for this contribution

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)
• 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).
• 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, #1005, #1011)

Changed

• The CI uses Python 3.9 rather than 3.7 when testing conda environments

Added

• Gnuplot is now supported (#998) - thanks to 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)

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).

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) - 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).
• 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).

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)

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)

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 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)

Added

• The recursive glob pattern **/*.ipynb is now supported by Jupytext - Thanks to Banst for this contribution (#731)
• Sage notebooks are supported. They can be converted to .sage and .md files and back. Thanks to Lars Franke for suggesting this! (#727)
• Jupytext is also accessible with python -m jupytext. Thanks to Matthew Brett for his PR! (#739)

Changed

• We have tested Jupytext with the new cell ids introduced in nbformat>=5.1.0. Cell ids are preserved by the --sync and --update command. So we removed the constraint on the version of nbformat (#735).

Fixed

• We filtered out the node_modules folder from the .tar.gz package for Jupytext (#730)