jupytext

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)

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)

Added

• Jupytext has a pre-commit hook! Many thanks to John Paton and Aaron Gokaslan for making this happen (#698)
• Jupytext CLI will not rewrite files that don't change (#698).
• If you want to see the diff for changed files, use the new --diff option (#722)
• We have added isort and autoflake8 to the pre-commit configuration file used for developing the Jupytext project (#709)
• We made sure that py:percent scripts end with exactly one blank line (#682)
• We checked that Jupytext works well with symbolic links to folders (not files!) (#696)

Changed

• Jupytext does not work properly with the new cell ids of the version 4.5 of nbformat>=5.1.0 yet, so we added the requirement nbformat<=5.0.8 (#715)
• Jupytext will issue an informative error or warning on notebooks in a version of nbformat that is not known to be supported (#681, #715)

Fixed

• Code cells that contain triple backticks (or more) are now encapsulated with four backticks (or more) in the Markdown and MyST Markdown formats. The version number for the Markdown format was increased to 1.3, and the version number for the MyST Markdown format was increased to 0.13 (#712)
• Indented magic commands are supported (#694)

Fixed

• Include the lab extension that was missing in the conda package (#703).

Changed

• The Jupytext extension for JupyterLab is compatible with Jupyter Lab 3.0, thanks to Martin Renou's awesome contribution #683.

Changed

• Jupytext 1.8.2 depends on python>=3.6. The last version of Jupytext explicitly tested with Python 2.7 and 3.5 was Jupytext 1.7.1, cf. #697.

Changed

• The dependency on markdown-it-py is conditional on python>=3.6 (#697)

Changed

• Removed support for Python 2.7 and 3.5, a preliminary step towards a JupyterLab 3.0-compatible extension (#683)
• The MyST Markdown format uses markdown-it-py~=0.6.0 (#692)

1.7.1 (2020-11-16)

Fixed

• Text notebooks have the same format and mimetype as ipynb notebooks. This fixes the File Load Error - content.indexOf is not a function error on text notebooks (#659)

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, #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)
• 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, #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)
• 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)
• Jupytext's Contents Manager internal errors are logged on the console, and trigger an HTTP Error 500 (#638)
• The GitHub actions run on both push events and pull requests, and duplicate jobs are skipped (#605)
• Jupytext has a tox.ini file, thanks to Chris Sewell (#605)
• Jupytext is tested against Python 3.9
• The execution cell metadata is now filtered by default (#656)

Fixed

• Optional dependency on sphinx-gallery frozen to version ~=0.7.0 (#614)
• Codecov/patch reports should be OK now (#639)
• Jupytext tests work on non-English locales (#636)
• Cell metadata that are already present in text notebook can be filtered out using a config file (#656)
• Optional cell attributes like attachments are preserved (#671)

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, #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)
• 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, #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)
• 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)
• Jupytext's Contents Manager internal errors are logged on the console, and trigger an HTTP Error 500 (#638)
• The GitHub actions run on both push events and pull requests, and duplicate jobs are skipped (#605)
• Jupytext has a tox.ini file, thanks to Chris Sewell (#605)
• Jupytext is tested against Python 3.9
• The execution cell metadata is now filtered by default (#656)

Fixed

• Optional dependency on sphinx-gallery frozen to version ~=0.7.0 (#614)
• Codecov/patch reports should be OK now (#639)
• Jupytext tests work on non-English locales (#636)
• Cell metadata that are already present in text notebook can be filtered out using a config file (#656)
• Optional cell attributes like attachments are preserved (#671)

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, #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)
• 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, #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)
• 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)
• Jupytext's Contents Manager internal errors are logged on the console, and trigger an HTTP Error 500 (#638)
• The GitHub actions run on both push events and pull requests, and duplicate jobs are skipped (#605)
• Jupytext has a tox.ini file, thanks to Chris Sewell (#605)
• Jupytext is tested against Python 3.9
• The execution cell metadata is now filtered by default (#656)

Fixed

• Optional dependency on sphinx-gallery frozen to version ~=0.7.0 (#614)
• Codecov/patch reports should be OK now (#639)
• Jupytext tests work on non-English locales (#636)
• Cell metadata that are already present in text notebook can be filtered out using a config file (#656)
• Optional cell attributes like attachments are preserved (#671)

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, #635)
• Thanks to the above, Jupytext can work on top of contents manager that don't derive from FileContentsManager, and in particular with jupyterfs (#618)
• The documentation was reorganized. README.md was simplified and now includes many links to the documentation.

Added

• Configuration errors are reported in the console and/or in Jupyter (#613)
• Jupytext's Contents Manager internal errors are logged on the console, and trigger an HTTP Error 500 (#638)
• The GitHub actions run on both push events and pull requests, and duplicate jobs are skipped (#605)
• Jupytext has a tox.ini file, thanks to Chris Sewell (#605)

Fixed

• Optional dependency on sphinx-gallery frozen to version ~=0.7.0 (#614)
• Codecov/patch reports should be OK now (#639)
• Jupytext tests work on non-English locales (#636)

1.6.0 (2020-09-01)

Added

• New option hide_notebook_metadata to encapsulate the notebook metadata in an HTML comment (#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)
• New option doxygen_equation_markers to translate Markdown equations into Doxygen equations (#517)
• New option custom_cell_magics to comment out cells starting with user-specific cell magics (#513)
• Documented how to use isort on notebooks (#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)
• Warn if 'Include Metadata' is off when saving text files in Jupyter (#561)
• Test that notebooks paired through a configuration file are left unmodified (#598)
• Test that metadata filters in the configuration files are taken into account when using jupytext --to (#543)
• New argument --run-path to execute the notebooks at the desired location (#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)
• 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)
• The # %% cell marker has the same indentation as the first line in the cell (#562)
• Jupytext is now installed from source on MyBinder to avoid cache issues (#567)
• The tests that execute a notebook are now skipped on Windows to avoid timeout issues (#489)

Fixed

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

Added

• Activated GitHub code scanning alerts
• New option hide_notebook_metadata to encapsulate the notebook metadata in an HTML comment (#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)
• New option doxygen_equation_markers to translate Markdown equations into Doxygen equations (#517)
• New option custom_cell_magics to comment out cells starting with user-specific cell magics (#513)
• Tested isort on notebooks (#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)
• Warn if 'Include Metadata' is off when saving text files in Jupyter (#561)
• Test that notebooks paired through a configuration file are left unmodified (#598)
• Test that metadata filters in the configuration files are taken into account when using jupytext --to (#543)
• New argument --run-path to execute the notebooks at the desired location (#595)

Changed

• Install Jupytext from source on MyBinder to avoid cache issues (#567)
• Skip the tests that execute a notebook on Windows to avoid timeout issues (#489)
• The # %% cell marker has the same indentation as the first line in the cell (#562)
• 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)
• Jupytext now depends on markdown-it-py and always features the MyST-Markdown format (Python 3.6 and above, #591)

Fixed

• Configured coverage targets in codecov.yml
• Only scripts can have an encoding comment, not Markdown or R Markdown files (#576)
• Spaces in --pipe commands are supported (#562)
• Bash commands starting with special characters are now correctly detected, thanks to Aaron Gokaslan (#587)
• MyST Markdown files are recognized as such even if myst is missing (#556)
• Build JupyterLab with dev-build=False and minimize=False on mybinder to avoid build errors

1.5.2 (2020-07-21)

Changed

• The documentation uses the Alabaster theme

Fixed

• Preserve indentation when commenting out magic commands (#437)
• Fixed MyBinder - jupytext.py is not a configuration file (#559, #567)

1.5.1 (2020-07-05)

Fixed

• Added toml as a dependency (#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).

1.5.0 (2020-06-07)

Added

• Jupytext can use a local or global configuration file (#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)
• The extension for Jupyter Notebook has a New Text Notebook menu that creates text-only notebooks (#443)
• Groovy and Java are now supported, thanks to Przemek Wesołek (#500)
• The Coconut language is also supported, thanks to Thurston Sexton (#532)
• Resource files with .resource extension from the Robot Framework are supported, thanks to Hiski Valli (#535)
• Jupytext is tested in pip and conda environments, on Linux, Mac OS and Windows, using Github actions (#487)
• Jupytext uses pre-commit checks and automatic reformatting with pre-commit, black and flake8 (#483)
• Documentation improvements:
  • Mention that the YAML header can be created with either --set-kernel, --set-formats, or both (#485)
  • Mention that one should use double quotes, not single quotes, around jupytext --check commands like "pytest {}" on Windows (#475)
  • Improved error message when a file is in a version that can't be read by Jupytext (#531)

Fixed

• Skip the jupytext --execute tests when the warning Timeout waiting for IOPub output occurs, which is the case intermittently on Windows (#489)
• Fixed wrong paired paths when syncing with the --pre-commit flag (#506)

Added

• Jupytext can use a local or global configuration file (#508)
• Jupytext can pair notebooks in trees. Use e.g. notebooks///ipynb,scripts///py:percent if you want to replicate the arborescence of notebooks under notebooks in a folder named scripts (#424)
• The extension for Jupyter Notebook adds a New Text Notebook menu that creates text-only notebooks (#443)
• Jupytext is tested in pip and conda environments, on Linux, Mac OS and Windows, using Github actions (#487)
• Pre-commit checks and automatic reformatting of Jupytext's code with pre-commit, black and flake8 (#483)
• Groovy and Java are now supported, thanks to Przemek Wesołek's contribution (#500)
• Mention that the YAML header can be created with either --set-kernel, --set-formats, or both (#485)
• Mention that one should use double quotes, not single quotes, around jupytext --check commands like "pytest {}" on Windows (#475)

Fixed

• Skip the jupytext --execute tests when the warning Timeout waiting for IOPub output occurs, which is the case intermittently on Windows (#489)
• Fixed wrong paired paths when syncing with the --pre-commit flag (#506)

Added

• Jupytext can use a local or global configuration file (#508)
• Jupytext can pair notebooks in trees. Use e.g. notebooks///ipynb,scripts///py:percent if you want to replicate the arborescence of notebooks under notebooks in a folder named scripts (#424)
• The extension for Jupyter Notebook adds a New Text Notebook menu that creates text-only notebooks (#443)
• Jupytext is tested in pip and conda environments, on Linux, Mac OS and Windows, using Github actions (#487)
• Pre-commit checks and automatic reformatting of Jupytext's code with pre-commit, black and flake8 (#483)
• Groovy and Java are now supported, thanks to Przemek Wesołek's contribution (#500)
• Mention that the YAML header can be created with either --set-kernel, --set-formats, or both (#485)
• Mention that one should use double quotes, not single quotes, around jupytext --check commands like "pytest {}" on Windows (#475)

Fixed

• Skip the jupytext --execute tests when the warning Timeout waiting for IOPub output occurs, which is the case intermittently on Windows (#489)
• Fixed wrong paired paths when syncing with the --pre-commit flag (#506)