jupytext

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

• 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

• 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)