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1.3.0 (2019-11-23)

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)

1.2.4 (2019-09-19)

Added

  • 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)

Fixed

  • 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)

1.2.3 (2019-09-02)

Fixed

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

1.2.2 (2019-09-01)

Added

  • 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)

Fixed

  • 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)

1.2.1 (2019-07-20)

Added

  • 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)

Fixed

  • 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.

1.2.0 (2019-07-18)

Added

  • 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)

Fixed

  • 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)

1.1.7 (2019-06-23)

Added

  • 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)

Fixed

  • 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)

1.1.6 (2019-06-11)

Added

  • Jupytext now supports Javascript and Typescript, thanks to Hatem Hosny (#250)
  • Jupytext works with Python 3.8 as well

Fixed

  • Fix global auto pairing (#249)

1.1.5 (2019-06-06)

Fixed

  • Fixed implicit dependency on jupyter_client (#245)

1.1.4 (2019-06-05)

Added

  • New argument --set-kernel in Jupytext command line (#230)
  • Jupytext now accepts --to script or --to auto (#240)
  • Jupytext now has a real Sphinx documentation on readthedocs, thanks to Chris Holdgraf (#237)

Fixed

  • Invalid notebooks may cause a warning, but not a fatal error (#234)
  • Jupyter server extension leaves the contents manager unchanged if it is a sub-class of Jupytext's CM (#236)
  • Fixed format inference when metadata is present but not format information (#239)
  • Preserve executable and encoding information in scripts with metadata (#241)

1.1.3 (2019-05-22)

Added

  • Support for IDL notebooks and .pro scripts (#232)

1.1.2 (2019-05-16)

Added

  • Jupytext's content manager has a new notebook_extensions option (#224, #183)
  • Cells can be made inactive in scripts with the active-ipynb cell tag (#226)

Fixed

  • Directories ending in .jl (or .ipynb) are not notebooks (#228)
  • Empty notebooks have no language (#227)

1.1.1 (2019-04-16)

Added

  • Jupytext server extension leaves the contents manager unchanged when it is already a subclass of TextFileContentsManager (#218)
  • The base class for TextFileContentsManager defaults to FileContentsManager when LargeFileManager is not available (#217)

1.1.0 (2019-04-14)

Added

  • Markdown and R Markdown formats now support metadata (#66, #111, #188)
  • The light format for Scripts can use custom cell markers, e.g. Vim or VScode/PyCharm folding markers (#199)
  • Pandoc's Markdown format for Jupyter notebooks is available in Jupytext as md:pandoc (#208)

Fixed

  • Jupytext's contents manager is now based on LargeFileManager to allow large file uploads (#210)
  • YAML header parsed with yaml.safe_load rather than yaml.load (#215)
  • IPython line magic can be split across lines (#209)
  • jupytext --to py rather than --to python in the README (#216)

1.0.5 (2019-03-26)

Fixed

  • Fix the error 'notebook file has changed on disk' when saving large notebooks (#207)

1.0.4 (2019-03-20)

Added

  • Wildcard are now supported on Windows (#202)
  • Trusted notebooks remain trusted when inputs cells are modified (#203)

Fixed

  • Pre-commit mode adds the result of conversion to the commit (#200)

1.0.3 (2019-03-13)

Added

  • Matlab and Octave notebooks and scripts are now supported (#197)

Fixed

  • notebook_metadata_filter = "all" now works (#196)
  • Default pairing in subfolders fixed in Jupyter Lab (#180)

1.0.2 (2019-02-27)

Added

  • Rename notebooks in pairs in the tree view (#190)
  • Associate .scm file extension with Scheme scripts (#192)
  • Added support for Clojure, by bzinberg (#193)

Fixed

  • Allow spaces between ? or ! and python or bash command (#189)

1.0.1 (2019-02-23)

Fixed

  • Exclude tests in package deployment (#184)
  • Jupytext's serverextension only runs selected init steps (#185)
  • Added an additional test for magic arguments (#111)

1.0.0 (2019-02-19)

Added

  • Jupytext now includes a Jupyter Notebook extension and a JupyterLab extension (#86).
  • Jupytext command line has more arguments: --paired-paths to list the paths for the paired representations of the notebook, and --sync to synchronise the content of all paired paths based on the most recent file (#146). In addition, the --from argument is optional even when the notebook is read from stdin (#148).
  • The pairing information, and more generally the notebook metadata can be edited with the CLL, see the --set-formats and the --update-metadata arguments (#141).
  • Jupytext can --pipe the text representation of a notebook to external programs like black or flake8 (#154, #142)
  • The Python representation of notebooks containing PEP8 cells is now expected to be PEP8 compliant (#154).
  • Format specification allow prefix and suffix for path and file name (#138, #142). Use ipynb,prefix/suffix.py:percent to pair the current notebook named notebook.ipynb to a script named prefixnotebooksuffix.py. Suffix and prefix can also be configured on the ipynb file, with the same syntax.
  • Introducing a new hydrogen format for scripts, which derives from percent. In that format Jupyter magic commands are not commented (#59, #126, #132).
  • Introducing a new bare format for scripts, which derives from light. That format has no cell marker. Use a notebook metadata filter {"jupytext": {"notebook_metadata_filter":"-all"}} if you want no YAML header (#152).
  • The default format for R script is now light, as for the other languages.
  • Added support for q/kdb+ notebooks (#161).
  • Python scripts or Markdown documents that have no Jupyter metadata receive a metadata filter that ensures that metadata is not exported back to the text representation (#124).
  • Metadata filters are represented as strings rather than dictionaries to make YAML headers shorter. Previous syntax from #105 is still supported. They were also renamed to notebook_metadata_filter and cell_metadata_filter.
  • Markdown and RMarkdown formats have a new option split_at_heading to split Markdown cells at heading (#130)

Fixed

  • Main language of scripts is inferred from script extension. Fixes a round trip conversion issue for Python notebooks with a Javascript cell.
  • Non-Python scripts opened as notebooks in Jupyter are now correctly saved even when no matching kernel is found.
  • Jupyter magic commands like ls are commented in the light and R markdown format (#149).
  • Cell starting with %%html, %%latex are now commented out in the light, percent and Rmd formats (#179).

0.8.6 (2018-11-29)

Added

  • The language_info section is not part of the default header any more. Language information is now taken from metadata kernelspec.language. (#105).
  • When opening a paired notebook, the active file is now the file that was originally opened (#118). When saving a notebook, timestamps of all the alternative representations are tested to ensure that Jupyter's autosave does not override manual modifications.
  • Jupyter magic commands are now commented per default in the percent format (#126, #132). Version for the percent format increases from '1.1' to '1.2'. Set an option comment_magics to false either per notebook, or globally on Jupytext's contents manager, or on jupytext's command line, if you prefer not to comment Jupyter magics.
  • Jupytext command line has a pre-commit mode (#121).

0.8.5 (2018-11-13)

Added

  • bash scripts as notebooks (#127)
  • R scripts with .r extension are supported (#122)
  • Jupytext selects the first kernel that matches the language (#120)

0.8.4 (2018-10-29)

Added

  • Notebook metadata is filtered - only the most common metadata are stored in the text representation (#105)
  • New config option freeze_metadata on the content manager and on the command line interface (defaults to False). Use this option to avoid creating a YAML header or cell metadata if there was none initially. (#110)
  • Language magic arguments are preserved in R Markdown, and also supported in light and percent scripts (#111, #114, #115)
  • First markdown cell exported as a docstring when using the Sphinx format (#107)

0.8.3 (2018-10-19)

Added

  • Frozen cells are supported in R Markdown, light and percent scripts (#101)
  • Inactive cells extended to percent scripts (#108)
  • jupytext gains a --version argument (#103)
  • "ExecuteTime" cell metadata is not included in the text representation anymore (#106)

0.8.2 (2018-10-15)

Added

  • Round trip conversion testing with jupytext --test was improved (#99)
  • Round trip conversion tested on Jake Vanderplas' Python for Data Science Handbook.

Fixed

  • Nested lists and dictionaries are now supported in notebook metadata
  • Final empty code cell supported in Sphinx representation

0.8.1 (2018-10-11)

Fixed

  • Sphinx format tested on World population notebook (#97)
  • Mirror test made stronger on this occasion!
  • Markdown representation recognize Julia, Scheme and C++ code cells as such
  • Light representation of Scheme and C++ notebooks fixed (#61)

0.8.0 (2018-10-10)

Added

  • All jupytext related metadata goes to a jupytext section (#91). Please make sure your collaborators use the same version of Jupytext, as the new version can read previous metadata, but not the opposite.
  • Notebooks extensions can be prefixed with any prefix of at most three chars (#87).
  • Export of the same notebook to multiple formats is now supported. To export to all python formats, plus .ipynb and .md, use "jupytext": {"formats": "ipynb,pct.py:percent,lgt.py:light,spx.py:sphinx,md"},.
  • README includes a short section on how to extend light and percent formats to more languages (#61).
  • Jupytext's contents manager accepts the auto extension in default_jupytext_formats (#93).
  • All Jupyter magics are escaped in light scripts and R markdown documents. Escape magics in other formats with a comment_magics metadata (true or false), or with the contents manager comment_magics global flag (#94).

Fixed

  • Trusting notebooks made functional again.
  • Command line jupytext returns a meaningful error when no argument is given.
  • Fixed global pairing configuration (#95).

0.7.2 (2018-10-01)

Added

  • light and percent formats made available for scheme and cpp notebooks. Adding more formats is straightforward - just add a new entry to _SCRIPT_EXTENSIONS in languages.py, a sample notebook and a mirror test (#61)
  • Format name is automatically appended to extension in jupytext_formats when notebook is loaded/saved.

Fixed

  • Notebooks extensions can only be prefixed with .nb (#87)

0.7.1 (2018-09-24)

Fixed

  • Markdown cells header in sphinx gallery format may have a space between first # and following.

0.7.0 (2018-09-23)

Added

  • Header for cells in percent format is more robust: use [markdown] and [raw] to identify cell types. Cell type comes after the cell title. (#59)
  • Jupytext can read and write notebooks as Hydrogen/VScode/Spyder/PyCharm compatible scripts (cells starting with # %%) (#59)
  • Jupytext can read and write notebooks as Sphinx-gallery compatible scripts (#80)
  • Metadata are supported for all cell types in light python and percent formats (#66). Due to this, light python format version is now 1.3. Light python notebooks in versions 1.1 and 1.2 are still readable.
  • Command line jupytext has a from argument, and now accepts notebook from the standard input.

Fixed

  • Fix merging of input and output notebooks (#83)
  • Removed extra new line on stdout in command line jupytext (#84)

0.6.5 (2018-09-13)

Added

  • Code lines that start with a quotation mark in Jupyter are commented in the corresponding Python and Julia scripts (#73)
  • Update pypy, add flake8 tests on Travis CI (#74)

Fixed

  • Import notebook.transutils before notebook.services.contents.filemanager (#75)

0.6.4 (2018-09-12)

Added

  • Jupytext will not load paired notebook when text representation is out of date (#63)
  • Package tested against Python 3.7 (#68)

Fixed

  • Allow unicode characters in notebook path (#70)
  • Read README.md as unicode in setup.py (#71)

0.6.3 (2018-09-07)

Added

  • Lighter cell markers for Python and Julia scripts (#57). Corresponding file format version at 1.2. Scripts in previous version 1.1 can still be opened.
  • New screenshots for the README.

Fixed

  • Command line conversion tool jupytext fixed on Python 2.7 (#46)

0.6.2 (2018-09-05)

Added

  • Initial support for Jupyter notebooks as Julia scripts (#56)
  • Command line conversion tool jupytext has explicit to and output options (#46)
  • Round trip test with jupytext --test improved (#54)
  • Improved README (#51)

Fixed

  • testfixtures now in requirements (#55)
  • Empty code cells are now preserved (#53)

0.6.1 (2018-08-31)

Added

  • Package and conversion script renamed from nbrmd to jupytext.

0.6.0 (2018-08-31)

Added

  • Cell parsing and exporting done in two specialized classes. This is way easier to read. Pylint score at 9.9 !
  • Python file format updated to 1.1: default end of cell for python scripts is one blank space. Two blank spaces are allowed as well. Now you can reformat code in Python IDE without breaking notebook cells (#38).
  • Added support for plain markdown files (#40, #44).
  • Demonstration notebooks more user friendly (#45).
  • Command line tool simpler to use (#46).
  • Start code patterns present in Jupyter cells are escaped.
  • Default nbrmd_format is empty (mwouts/nbsrc/#5): no Jupyter notebook is created on disk when the user opens a Python or R file and saves it from Jupyter, unless the users asks for it by setting nbrmd_format.

Fixed

  • Fixed message in the nbsrc script (#43)
  • Technical metadata don't appear any more in scripts unless required (#42)
  • Code cells that are fully commented remain code cells after round trip (#41)

0.5.4 (2018-08-24)

Added

  • R to Rmd conversion compares well to knitr::spin (#26)
  • Increased coverage to 98%

0.5.3 (2018-08-22)

Fixed

  • Read and write version to the same metadata (#36)

0.5.2 (2018-08-22)

Added

  • Classical jupyter extensions (autoreload, rmagics) are also escaped (#35)
  • Explicit file format version, set at 1.0, to avoid overriding ipynb files by accident (#36)

0.5.1 (2018-08-21)

Fixed

  • Source only notebooks can be trusted.

0.5.0 (2018-08-21)

Added

  • Jupyter magic commands escaped when exported (#29)
  • 'endofcell' option for explicit (optional) end-of-cell marker (#31)
  • 'active' cell option now supported for .py and .R export (#30)
  • Raw cells now preserved when exported to .py or .R (#32)
  • Extensions can be prefixed, like .nb.py, (mwouts/nbsrc#5)
  • When a file with an extension not associated to 'ipynb' is opened and saved, no 'ipynb' file is created (mwouts/nbsrc#5)
  • Extensions can now be a sequence of groups. For instance, nbrmd_formats="ipynb,nb.py;script.ipynb,py" will create an ipynb file when a nb.py is opened (and conversely), and a script.ipynb file when a py file is opened (mwouts/nbsrc#5)
  • nbsrc script was moved to the nbrmd package. The nbsrc package now only contains the documentation (mwouts/nbsrc#3)

0.4.6 (2018-07-26)

  • Ping pypi - previous version still not available

0.4.5 (2018-07-26)

Fixed

  • Removed dependency of setup.py on yaml

0.4.4 (2018-07-26)

Fixed

  • Package republished with python setup.py sdist bdist_wheel to fix missing dependencies

0.4.3 (2018-07-26)

Added

  • Multiline comments now supported #25
  • Readme refactored, notebook demos available on binder #23

Fixed

  • ContentsManager can be imported even if notebook.transutils is not available, for compatibility with older python distributions.
  • Fixed missing cell metadata #27
  • Documentation tells how to avoid creating .ipynb files #16

0.4.2 (2018-07-23)

Added

  • Added test for R notebooks
  • Added pylint badge, imports now in correct order
  • New active cell metadata that allows cell activation only for desired extensions (currently available for Rmd and ipynb extensions only)

0.4.1 (2018-07-20)

Fixed

  • Indented python code will not start a new cell #20
  • Fixed parsing of Rmd cell metadata #21

0.4.0 (2018-07-18)

Added

  • .py format for notebooks is lighter and pep8 compliant

Fixed

  • Default nbrmd config not added to notebooks (#17)
  • nbrmd_formats becomes a configurable traits (#16)
  • Removed nbrmd_sourceonly_format metadata. Source notebook is current notebook when not .ipynb, otherwise the first notebook format in nbrmd_formats (not .ipynb) that is found on disk

0.3.0 (2018-07-17)

Added

  • Introducing support for notebooks as python .py or R scripts .R

0.2.6 (2018-07-13)

Added

  • Introduced nbrmd_sourceonly_format metadata
  • Inputs are loaded from .Rmd file when a matching .ipynb file is opened.

Fixed

  • Trusted notebooks remain trusted (#12)

0.2.5 (2018-07-11)

Added

  • Outputs of existing .ipynb versions are combined with matching inputs of R markdown version, as suggested by @grst (#12)

Fixed

  • Support for unicode text in python 2.7 (#11)

0.2.4 (2018-07-05)

Added

  • nbrmd will always open notebooks, even if header of code cells are not terminated. Merge conflicts can thus be solved in Jupyter directly.
  • New metadata 'main language' that preserves the notebook language.

Fixed

  • dependencies included in setup.py
  • pre_save_hook work with non-empty notebook_dir (#9)

0.2.3 (2018-06-28)

Added

  • Screenshots in README

Fixed

  • RMarkdown exporter for nbconvert fixed on non-recent python
  • Tests compatible with other revisions of nbformat >= 4.0
  • Tests compatible with older pytest versions

0.2.2 (2018-06-28)

Added

  • RMarkdown exporter for nbconvert
  • Parsing of R options robust to parenthesis
  • Jupyter cell tags are preserved

Fixed

  • requirements.txt now included in pypi packages

0.2.1 (2018-06-24)

Added

  • Support for editing markdown files in Jupyter
  • New pre-save hook update_selected_formats that saves to formats in metadata 'nbrmd_formats'
  • Rmd cell options directly mapped to cell metadata

Fixed

  • ContentManager compatible with Python 2.7

0.2.0 (2018-06-21)

Added

  • The package provides a RmdFileContentsManager for direct edit of R markdown files in Jupyter
  • Notebook metadata and cell options are preserved

0.1.1 (2018-06-19)

Added

  • nbrmd prints the result of conversion to stdout, unless flag -i is provided
  • Notebooks with R code chunks are supported

0.1 (2018-06-18)

  • Initial version with the nbrmd converter and Jupyter pre_save_hook