jupytext

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)
• 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

• Added an example with custom notebook metadata (#469)
• Added an example with custom cell tags (#478)

Changed

• The outputs from the .ipynb file are matched with the input cells from the text file with less strict rules. In this version, a search and replace on the text file will not remove the outputs any more (#464).
• Update parsing of myst notebooks to new (markdown-it based) parser (please upgrade to myst-parser to version ~0.8) (#473)
• Use os.path.samefile when searching for the kernel that corresponds to the current environment (--set-kernel -)

Fixed

• Fixed the CLI example for not commenting out magic commands: --opt comment_magics=false. In addition, most of the jupytext commands in using-cli.md are now tested! (#465)
• jupytext.read and jupytext.write now give more meaningful errors when the format information is incorrect (#462)
• Multiline comments starting or ending with quadruple quotes should not cause issues anymore (#460)
• Fixed active cells in the py:percent format (#477)

1.4.1 (2020-03-19)

Added

• Script of script (SoS) notebooks are now supported. Thanks to Thomas Pernet-coudrier for contributing the sample notebook (#453).
• New MyST Markdown format (md:myst), developed by the ExecutableBookProject team. Read more about the MyST Markdown format in the documentation. And many thanks to Chris Sewell for contributing the actual implementation! (#447 #456 #458)

Fixed

• When using jupytext --pipe cmd, the output of cmd should not appear in the terminal (#432)

Changed

• The new jupyterlab extension (in version 1.2.0) is compatible with JupyterLab 2.0. Many thanks to Jean Helie! (#449)
• It is not compatible with JupyterLab 1.x anymore. If you wish, you can install manually the previous version of the extension with jupyter labextension install [email protected].

Fixed

• Display the output/errors of command executed with jupytext --pipe or jupytext --check (#432)

Fixed

• Removed leading slash in notebook paths (#444)
• Fixed jupytext --set-formats when using formats with prefix and/or suffix (#450)

Added

• C# and F# Jupyter notebooks are now supported (#427, #429)

Fixed

• jupytext --to script *.ipynb now computes the script extension for each notebook (#428)
• Fix shebang handling for languages with non-# comments, by Jonas Bushart (#434)
• Indented bash commands are now commented out (#437)
• The main formats are documented in jupytext --help (#426, #433)

1.3.3 (2020-01-27)

Added

• Jupytext has a logo! Many thanks to Kyle Kelley for contributing the logo (#423), and to Chris Holdgraf for suggesting this (#260).
• Nested metadata filtering is now supported! You can use this to rid of jupytext_version if you wish (#416).

Fixed

• Code cells in the Markdown format can contain triple backticks inside multiline strings (#419).
• Changes in the YAML header when running jupytext --test on text files are ignored (#414).

Fixed

• The --pre-commit mode now ignores non-notebook files in the index (#338).
• nbformat_minor is taken from the notebook with outputs when inputs and outputs are merged.

Added

• New nomarker format in the Jupyter Notebook and JupyterLab extensions (#397)

Changed

• The normarker format replaces the one previously named bare.

Fixed

• Multiline strings are now accepted in the YAML header (#404). Fix contributed by ZHUO Qiang (#405).
• Fixed the instructions on how to use multiline comments for all Markdown cells in the py:percent format, by ZHUO Qiang (#403).
• Added cd to the list of magic commands.
• Do not read paired files when --set-formats is being used (fixes #399).

See also What's new in Jupytext 1.3?

Added

• Pairing a notebook to both .md and .py is now supported. Input cells are loaded from the most recent text representation (#290)
• Both the Jupyter Notebook and the Jupyter Lab extension for Jupytext were updated (#290)
• Raw cells are now encoded using HTML comments (<!-- #raw --> and <!-- #endraw -->) in Markdown files (#321)
• Markdown cells can be delimited with any of <!-- #region -->, <!-- #markdown --> or <!-- #md --> (#344)
• Code blocks from Markdown files, when they don't have an explicit language, appear in Markdown cells in Jupyter (#321)
• Code blocks with an explicit language and a .noeval attribute are inactive in Jupyter (#347)
• Markdown and raw cells can be quoted with triple quotes in the py:percent format. And Markdown cells can start with just # %% [md] (#305)
• The light format uses # + [markdown] rather than the previous cell_type metadata to identify markdown cells with metadata (#356)
• Explicit Markdown cells in the light format # + [markdown] can use triple quotes (#356)
• IPython magic help commands like float? are classified as magics, and thus commented in Python scripts (#297)
• Cell metadata can be encoded as either key=value (the new default) or in JSON. An automatic option cell_metadata_json should help minimize the impact on existing files (#344)
• R Markdown hidden inputs, outputs, or cells are now mapped to the corresponding Jupyter Book tags by default (#337)
• The notebook metadata filter is automatically updated when extra keys are added to the YAML header (#376)
• The Jupyter Notebook extension for Jupytext is compatible with Jupyter Notebook 6.0 (#346)
• jupytext notebook.py --to ipynb updates the timestamp of notebook.py so that the paired notebook still works in Jupyter (#335, #254)
• jupytext --check pytest notebook.ipynb can be used to run test functions in a notebook (#286)
• jupytext --check and jupytext --pipe can run commands that only operate on files: when {} is found in the text of the command, jupytext saves the text representation of the notebook in a temp file, and replaces {} with the name of that file before executing the command. (#286)
• Documented how to sync notebooks in a pre-commit hook (#338)
• Added support for Rust/Evxcr, by Jonas Bushart (#351)
• Added support for Robot Framework, by Asko Soukka (#378)
• Added support for PowerShell (#349)

Changed

• Use CHANGELOG.md rather than HISTORY.rst

Fixed

• Commands like cat = x are not magic commands, so they are not commented any more (#339)
• Fixed an inconsistent round trip (code cell with "cat" being converted to a markdown cell) in the py:light format (#339)
• jupytext --test textfile.ext now really compares the text file to its round trip (rather than the corresponding notebook) (#339)
• Markdown cells that contain code are now preserved in a round trip through the Markdown and R Markdown formats (#361)
• Code cells with a %%python3 cell magic are now preserved in a round trip through the Markdown format (#365)
• jupytext --execute runs the notebook in its folder (#382)
• Strings in the metadata of code cells are quoted in the Rmd representation. And we escape R code in chunk options with #R_CODE# (#383)

Read a more user friendly version here!

Added

• Pairing a notebook to both .md and .py is now supported. Input cells are loaded from the most recent text representation (#290)
• Both the Jupyter Notebook and the Jupyter Lab extension for Jupytext were updated (#290)
• Raw cells are now encoded using HTML comments (<!-- #raw --> and <!-- #endraw -->) in Markdown files (#321)
• Markdown cells can be delimited with any of <!-- #region -->, <!-- #markdown --> or <!-- #md --> (#344)
• Code blocks from Markdown files, when they don't have an explicit language, appear in Markdown cells in Jupyter (#321)
• Code blocks with an explicit language and a .noeval attribute are inactive in Jupyter (#347)
• Markdown and raw cells can be quoted with triple quotes in the py:percent format. And Markdown cells can start with just # %% [md] (#305)
• The light format uses # + [markdown] rather than the previous cell_type metadata to identify markdown cells with metadata (#356)
• Explicit Markdown cells in the light format # + [markdown] can use triple quotes (#356)
• IPython magic help commands like float? are classified as magics, and thus commented in Python scripts (#297)
• Cell metadata can be encoded as either key=value (the new default) or in JSON. An automatic option cell_metadata_json should help minimize the impact on existing files (#344)
• R Markdown hidden inputs, outputs, or cells are now mapped to the corresponding Jupyter Book tags by default (#337)
• The notebook metadata filter is automatically updated when extra keys are added to the YAML header (#376)
• The Jupyter Notebook extension for Jupytext is compatible with Jupyter Notebook 6.0 (#346)
• jupytext notebook.py --to ipynb updates the timestamp of notebook.py so that the paired notebook still works in Jupyter (#335, #254)
• jupytext --check pytest notebook.ipynb can be used to run test functions in a notebook (#286)
• jupytext --check and jupytext --pipe can run commands that only operate on files: when {} is found in the text of the command, jupytext saves the text representation of the notebook in a temp file, and replaces {} with the name of that file before executing the command. (#286)
• Documented how to sync notebooks in a pre-commit hook (#338)
• Added support for Rust/Evxcr, by Jonas Bushart (#351)
• Added support for Robot Framework, by Asko Soukka (#378)
• Added support for PowerShell (#349)

Changed

• Use CHANGELOG.md rather than HISTORY.rst

Fixed

• Commands like cat = x are not magic commands, so they are not commented any more (#339)
• Fixed an inconsistent round trip (code cell with "cat" being converted to a markdown cell) in the py:light format (#339)
• jupytext --test textfile.ext now really compares the text file to its round trip (rather than the corresponding notebook) (#339)
• Markdown cells that contain code are now preserved in a round trip through the Markdown and R Markdown formats (#361)
• Code cells with a %%python3 cell magic are now preserved in a round trip through the Markdown format (#365)
• jupytext --execute runs the notebook in its folder (#382)
• Strings in the metadata of code cells are quoted in the Rmd representation. And we escape R code in chunk options with #R_CODE# (#383)

Read a more user friendly version here!

Improvements

• Pairing a notebook to both .md and .py is now supported. Input cells are loaded from the most recent text representation (#290)
• Both the Jupyter Notebook and the Jupyter Lab extension for Jupytext were updated (#290)
• Raw cells are now encoded using HTML comments (<!-- #raw --> and <!-- #endraw -->) in Markdown files (#321)
• Markdown cells can be delimited with any of <!-- #region -->, <!-- #markdown --> or <!-- #md --> (#344)
• Code blocks from Markdown files, when they don't have an explicit language, appear in Markdown cells in Jupyter (#321)
• Code blocks with an explicit language and a .noeval attribute are inactive in Jupyter (#347)
• Markdown and raw cells can be quoted with triple quotes in the py:percent format. And Markdown cells can start with just # %% [md] (#305)
• The light format uses # + [markdown] rather than the previous cell_type metadata to identify markdown cells with metadata (#356)
• Explicit Markdown cells in the light format # + [markdown] can use triple quotes (#356)
• IPython magic help commands like float? are classified as magics, and thus commented in Python scripts (#297)
• Cell metadata can be encoded as either key=value (the new default) or in JSON. An automatic option cell_metadata_json should help minimize the impact on existing files (#344)
• R Markdown hidden inputs, outputs, or cells are now mapped to the corresponding Jupyter Book tags by default (#337)
• The Jupyter Notebook extension for Jupytext is compatible with Jupyter Notebook 6.0 (#346)
• jupytext notebook.py --to ipynb updates the timestamp of notebook.py so that the paired notebook still works in Jupyter (#335, #254)
• jupytext --check pytest notebook.ipynb can be used to run test functions in a notebook (#286)
• jupytext --check and jupytext --pipe can run commands that only operate on files: when {} is found in the text of the command, jupytext saves the text representation of the notebook in a temp file, and replaces {} with the name of that file before executing the command. (#286)
• Added support for Rust/Evxcr, by Jonas Bushart (#351)
• Added support for PowerShell (#349)

BugFixes

• Commands like cat = x are not magic commands, so they are not commented any more (#339)
• Fixed an inconsistent round trip (code cell with "cat" being converted to a markdown cell) in the py:light format (#339)
• jupytext --test textfile.ext now really compares the text file to its round trip (rather than the corresponding notebook) (#339)
• Markdown cells that contain code are now preserved in a round trip through the Markdown and R Markdown formats (#361)
• Code cells with a %%python3 cell magic are now preserved in a round trip through the Markdown format (#365)

Improvements

• Raw cells are now encoded using HTML comments (<!-- #raw --> and <!-- #endraw -->) in Markdown files. And code blocks from Markdown files, when they don't have an explicit language, are displayed as Markdown cells in Jupyter (#321)
• Markdown and raw cells can use multiline comments in the py:percent format (#305)
• jupytext notebook.py --to ipynb updates the timestamp of notebook.py so that the paired notebook still works in Jupyter (#335, #254)

BugFixes

• Fixed an inconsistent round trip (code cell with "cat" being converted to a markdown cell) in the py:light format (#339)
• Commands like cat = x are not magic commands {#339)
• jupytext --test now really compares the text (rather than the corresponding notebook) when run on text files (#339)

Improvements

• The documentation includes a mention on how to set metadata filters at the command line (#330)
• Jupytext will not catch any error when the flag --warn-only is not set (#327)

BugFixes

• Now the flag --warn-only catches every possible error (#263)
• .md and .markdown files are treated identically (#325)
• Fixed --set-kernel when using pipes (#326)
• Fixed utf-8 encoding on stdout on Python 2 (#331)

BugFixes

• Dependency on setuptools in pandoc.py made optional to fix the build of the conda package (#310, #323)

Improvements

• Documentation includes a section on how to use Jupytext as a Python library (#317)
• Mention of the server extension in the documentation (#304)
• Text notebooks can be tested with jupytext --execute notebook.md (#303)
• The default value of as_version in jupytext.read is nbformat.NO_CONVERT, as for nbformat.read
• Jupytext tests are now included in sdist (#310)

BugFixes

• Fixed the usability of the fmt argument in jupytext.read (#312)
• Fixed the download notebook error when c.notebook_extensions has a custom value (#318)
• String delimiters in commented text are now ignored (#307)

Improvements

• Added documentation on how to use Jupytext with JupyterLab 0.35 (#299)
• and on using Jupytext with the pre-commit package manager (#292)
• The read and write functions are easier to use (#292)

BugFixes

• Jupytext now ships the jupyterlab-jupytext extension in version 1.0.2. The version 1.0.1 erroneously introduces a target_formats metadata in the jupytext section, instead of formats, and works only after two clicks.

Improvements

• New --execute option in Jupytext CLI (#231)
• The --set-formats option in Jupytext CLI also triggers --sync, allowing shorter commands.
• jupytext's read and write functions can be used as drop-in replacements for nbformat's ones (#262).
• jupytext --sync will now skip unpaired notebooks (#281).
• The JupyterLab extension was updated. It now works on on text files (#213) and has a new option to include (or not) the metadata in the text representation of the notebook.
• Jupytext's contents manager class is derived dynamically from the default CM class for compatibility with
  jupyter_server (#270)
• Removed dependency on mock and testfixtures, thanks to Jean-Sebastien Dieu (#279)
• Added support for .markdown extension (#288)

BugFixes

• The jupyterlab-jupytext extension shipped with the python package is in version 1.0.1, and is compatible only with JupyterLab >= 1.0. If you use an earlier version of JupyterLab, please install the version 0.19 of the extension with jupyter labextension install [email protected] (#276, #278)
• Text files can be unpaired (#289)

Improvements

• New --execute option in Jupytext CLI (#231)
• The --set-formats option in Jupytext CLI also triggers --sync, allowing shorter commands.
• jupytext's read and write functions can be used as drop-in replacements for nbformat's ones (#262).
• jupytext --sync will now skip unpaired notebooks (#281).
• The JupyterLab extension was updated. It now works on on text files (#213) and has a new option to include (or not) the metadata in the text representation of the notebook.
• Jupytext's contents manager class is derived dynamically from the default CM class for compatibility with
  jupyter_server (#270)
• Removed dependency on mock and testfixtures, thanks to Jean-Sebastien Dieu (#279)

BugFixes

• The jupyterlab-jupytext extension shipped with the python package is in version 1.0, and is compatible only with JupyterLab >= 1.0. If you use an earlier version of JupyterLab, please install the version 0.19 of the extension with jupyter labextension install [email protected] (#276, #278)

Improvements

• Added support for Scala notebook, by Tobias Frischholz (#253)
• Added a getting started notebook for jupytext (and Binder), by Chris Holdgraf (#257)
• The Markdown and R Markdown representations are now tested for all the languages
• The Jupytext notebook extension also works when the notebook is a text file (#213)

BugFixes

• The Jupytext Menu in Jupyter Notebook is now compatible with jupyter_nbextensions_configurator (#178)
• Entries in the Jupytext menu are updated when the menu is hovered on (#248)
• Fixed link to .md files in the documentation (#255)