Jupyter Notebooks as Markdown Documents, Julia, Python or R scripts

Marc Wouts

Last update: Jan 4, 2023

Related tags

Documentation python markdown version-control rstudio jupyter-notebook rmarkdown knitr jupyterlab hydrogen notebooks jupyterlab-extension

Overview

Have you always wished Jupyter notebooks were plain text documents? Wished you could edit them in your favorite IDE? And get clear and meaningful diffs when doing version control? Then... Jupytext may well be the tool you're looking for!

Jupytext is a plugin for Jupyter that can save Jupyter notebooks as either

Markdown files (or MyST Markdown files, or R Markdown or Quarto text notebooks)
Scripts in many languages.

Use cases

Common use cases for Jupytext are:

Doing version control on Jupyter Notebooks
Editing, merging or refactoring notebooks in your favorite text editor
Applying Q&A checks on notebooks.

Install

You can install Jupytext with

pip install jupytext
or conda install jupytext -c conda-forge.

Please note that Jupytext includes an extension for Jupyter Lab. In the latest version of Jupytext, this extension is compatible with Jupyter Lab >= 3.0 only. If you use Jupyter Lab 2.x, please either stay with Jupytext 1.8.2, or install, on top of the latest pip or conda version of Jupytext, a version of the extension that is compatible with Jupyter Lab 2.x:

jupyter labextension install [email protected]  # For Jupyter Lab 2.x

Then, restart your Jupyter server (for more installation details, see the install section in the documentation).

When Jupytext is installed, .py and .md files have a notebook icon. And you can really open and run these files as notebooks

With a click on the text file in Jupyter Notebook

(click on the image above to try this on )

With a click on the text file in JupyterLab

To do that, you will need to change the default viewer for text notebooks by copy-pasting the following settings (or the subset that matches your use case) in the `Document Manager` section:

{
  "defaultViewers": {
    "markdown": "Jupytext Notebook",
    "myst": "Jupytext Notebook",
    "r-markdown": "Jupytext Notebook",
    "quarto": "Jupytext Notebook",
    "julia": "Jupytext Notebook",
    "python": "Jupytext Notebook",
    "r": "Jupytext Notebook"
  }
}

Here is a screencast of the steps to follow:

(click on the image above to try this on )

Another possibility is to activate this with a default_setting_overrides.json file in the .jupyter/labconfig folder with e.g.

wget https://raw.githubusercontent.com/mwouts/jupytext/main/binder/labconfig/default_setting_overrides.json -P  ~/.jupyter/labconfig/

Note: to open links to .md files in notebooks with the Notebook editor, use jupyterlab>=4.0.0a16.

With a right click and open with notebook in Jupyter Lab

(click on the image above to try this on )

Paired notebooks

The most convenient way to use Jupytext is probably through paired notebooks.

To pair a given .ipynb or text notebook to an additional notebook format, use either

the "pair notebook with..." commands in Jupyter Lab

the "pair notebook with..." menu entries in Jupyter Notebook

jupytext at the command line

with e.g.

jupytext --set-formats ipynb,py:percent notebook.ipynb

see the documentation.

or a local or global jupytext.toml configuration file.

with e.g. the following content:

formats = "ipynb,py:percent"

see the documentation.

When you save a paired notebook in Jupyter, both the .ipynb file and the text version are updated on disk.

When a paired notebook is opened or reloaded in Jupyter, the input cells are loaded from the text file, and combined with the output cells from the .ipynb file.

You can edit the text representation of the notebook in your favorite editor, and get the changes back in Jupyter by simply reloading the notebook (Ctrl+R in Jupyter Notebook, "reload notebook" in Jupyter Lab). And the changes are propagated to the .ipynb file when you save the notebook.

Alternatively, you can synchronise the two representations by running jupytext --sync notebook.ipynb at the command line.

Which text format?

Jupytext implements many text formats for Jupyter Notebooks. If your notebook is mostly made of code, you will probably prefer to save it as a script:

Use the percent format, a format with explicit cell delimiters (# %%), supported by many IDE (Spyder, Hydrogen, VS Code, PyCharm and PTVS)
Or use the light format, if you prefer to see fewer cell markers.

If your notebook contains more text than code, if you are writing a documentation or a book, you probably want to save your notebook as a Markdown document

Use the Jupytext Markdown format if you wish to render your notebook as a .md file (without its outputs) on GitHub
Use the MyST Markdown format, a markdown flavor that “implements the best parts of reStructuredText”, if you wish to render your notebooks using Sphinx or Jupyter Book.
Use the R Markdown format or the Quarto format if you want to open your Jupyter Notebooks in RStudio.

More resources?

If you're new to Jupytext, you may want to start with the FAQ or with the Tutorials, or with this short introduction to Jupytext: .

Comments

Maintain cell metadata for RISE

I wanted to use jupytext to have a paired md+ipynb notebook that I also use for presentation with the RISE plugin https://github.com/damianavila/RISE

Unfortunately, every time I reload the browser all the metadata information about whether a cell is a slide, fragment, or should be skipped, gets lost.

opened by boazbk 57
Pandoc format for Jupyter notebook

Pandoc allow users to create Jupyter notebook from Markdown files, cf. the documentation. We'll try to plug pandoc into Jupytext and see if that is usable.

opened by mwouts 40
How to build a documentation site with Jupytext?
The purpose of this issue is to document a few ways to build a documentation site. Our requirements are:

The source documents can be edited as Jupyter notebooks

Source files are text files (Markdown or others)

Documentation site can show the result of the code being executed, including plots.

We should explore at least

Jupyter Book (can we use it with Jupytext notebooks?)

Sphinx and Sphinx-gallery

documentation
opened by mwouts 38
Consider support for Quarto qmd format?
I wonder whether you would also consider supporting the new Quarto qmd format.

Why?

Because Quarto is looking like a very nice system for writing books and reports with excecutable documents, such as Jupyter and R notebooks. Qmd format is Quarto's cross-language text format for notebooks. It assumes .Rmd files are R notebooks, so Qmd format is the natural format for Jupyter notebooks in text form. We (@stefanv and I) are writing our new edition of a statistics book using Quarto. It would be a significant gain in usability if we could use the Jupytext / Notebook integration to edit and execute our documents in native Qmd format (although we are using Rmd at the moment).

What?

It's a slightly modified version of .Rmd format, where the cell metadata goes in comments at the top of the cell, as in:

```{python} #| warning: false #| echo: true ... ```
opened by matthew-brett 35
Enable integration with pre-commit
This is a first attempt at an implementation of the suggestion in #691 to enable "proper" integration with the pre-commit framework. The changes summarized:

A new .pre-commit-hooks.yaml file, which tells pre-commit how to install this package (pre-commit does this internally), which command to run, and what the default options are

A new cli argument, --add-untracked, which adds any output files that weren't previously tracked by git to the index. Two points to note here:

The reason we are tracking only new files is that pre-commit doesn't consider changes to them if they aren't in the index (pre-commit requires all files in the index be unchanged by all hooks before passing)

The command will return a non-zero status code in case any newly generated files are actually added. This is because by adding them "on the fly" during the hook, pre-commit doesn't pass them to any other configured hooks for further checks, so they could be wrongly accepted into the commit.

The net effect is a proper pre-commit hook, which will only allow a commit as long as the configured Jupytext command doesn't change any of the files in the index, or add any new ones. This is how pre-commit's hooks are expected to operate.

Questions:

This is a bit of an adjustment to how Jupytext's main command is operating - is it too much? How easy would it be to make this separate/not expose the --add-untracked option so publicly?

How to test this behaviour (will be investigating, this is a WIP)?
opened by JohnPaton 32
Metadata for hiding input/output or cells
Hi @mwouts,

I am currently working on a pipeline that chains together jupyter/jupytext notebooks into a reproducible workflow. I created two 'render engines', one based on papermill and one on knitr. Ideally, using jupytext, one could use them interchangeably on the same notebook.

I am currently struggling with the cell metadata to control the visibility of cell inputs/outputs. I have seen that you have been experimenting with both papermill and jupyterbook. I also observed that you implemented some conversion of cell metadata for Rmarkdown. Ideally, there would be common conventions between jupytext, jupyterbook, Rmarkdown etc.

First, my observations:

nbconvert supports contolling cell visibility when creating a html report by using nbconvert.preprocessors.TagRemovePreprocessor

Rmarkdown uses include=FALSE to hide an entire cell, results='hide' to hide output and echo=FALSE to hide input.

jupyter book supports hide_input and remove_input to hide the input, remove_cell for an entir cell, and to my knowledge no option to hide output only.

jupytext currently uses hide_output and hide_input when converting from Rmarkdown.

Now, my questions/suggestsions:

Are you aware of more/different tags from other projects?

Did you come up with current jupytext hide_output and hide_input, or are they supposed to be compatible with another project?

Rmarkdown include=FALSE translates currently into hide_output. I believe it should translate into remove_cell or equivalent.

Rmarkdown results='hide' is currently not converted. It should translate into hide_output.

Let me know what you think!

Best, Gregor
opened by grst 30
opening jupytext notebooks in jlab
Hiya

trying to migrate from classic to something more modern, I'm facing an issue that has to do with the awkward path that seems to be the only way to open a jupytext notebook under jlab

from the UI, clicking say foo.md in the file browser results in a markdown editor; I need to do right-click → open with → Notebook to get it to open as a notebook

from the outside, I'd need a way to do the same from a regular URL; opening lab/tree/path/foo.md has the same result as from the UI, so I can't seem to find any way to open it as a notebook from a URL

the first issue is an impediment but of course something I can live with; the second is more of a showstopper for me at this point

I'd love to find a way around this

ps for reference, I've be stirring this in a couple other threads already https://discourse.jupyter.org/c/jupyterlab/17 and more marginally in https://github.com/jupyterlab/retrolab/issues/162

in the latter @jtpio suggested that an extension could come in handy, but I must honestly admit that the whole jlab extension ecosystem has scared the hell out of me a bit, so I am unsure what this would actually involve..
opened by parmentelat 27
Extension not loading in jupyterlab 3
In Jupyterlab 3.0.4 with Jupytext 1.9.1 on Ubuntu 20.04.1 LTS the filemanager does not appear to be loading. Specifically the log line that says the jupytext file manager loads in not showing up. I can use the console commands to pair a notebook but no additional files are saved. The GUI also does not show previously paired files as notebooks either.

I can use the most recent version of jupytext with jupyter notebook just fine. I can also downgrade to lab 2.2 and the old plugin and it works fine as well.

I have tried all variations of enabling and configuration files listed in the install documentation and nothing has worked. I am fairly sure there is a bug here but there's no error message so it is a bit hard to say.

Let me know if there's any more information I can provide.

Here's a little bit of additional debug info:

g@g-ThinkPad-P51:~$ jupyter labextension list JupyterLab v3.0.4 /home/g/.local/share/jupyter/labextensions jupyterlab-jupytext v1.3.0 enabled OK (python, jupytext) @jupyter-widgets/jupyterlab-manager v3.0.0 enabled OK (python, jupyterlab_widgets) Other labextensions (built into JupyterLab) app dir: /home/g/.local/share/jupyter/lab

Contents of .jupyter/jupyter_notebook_config.json:

{ "NotebookApp": { "nbserver_extensions": { "jupytext": true } } }
documentation
opened by gstorer 27
Jupyter extension for Jupytext
An extension for Jupyter would make the configuration of paired notebooks easier. Rather than asking to edit the jupytext_formats metadata, we should offer the user an interface where the user can select the desired notebook extensions (among ipynb, py, jl, R, md, Rmd; the order matters), and the format for each extension (default, light, percent, sphinx...).

The documentation on how to distribute a notebook extension is here. Extensions have to be written in Javascript, which I have almost never practiced before - help is welcome!

Useful references are:

4 ways to extend jupyter notebook by @parente

the gist extension by @minrk

help wanted
opened by mwouts 27
Jupytext plugin for the pre-commit package, compatible with black and flake8
the pre-commit package (described in this blog) provides a framework for managing precommit hooks. It would be great if jupytext had an option that would allow it to be a pre-commit hook with that package -- essentially it would just need to suppress the stdout message and return 0, adding the translated file to the index. Specifically, this script is working for me now:

import sys import subprocess from pathlib import Path cmd = f"jupytext --to py:percent {sys.argv[1]}" notebook = Path(sys.argv[1]) pyfile = str(notebook.with_suffix(".py")) status1, output1 = subprocess.getstatusoutput(cmd) cmd = f"git add {pyfile}" status2, output2 = subprocess.getstatusoutput(cmd) with open("jupytext_logfile.txt", "w") as f: f.write( (f"{sys.argv}\n" f"{status1}\n" f"{output1}\n" f"{status2}\n" f"{output2}\n") ) sys.exit(0)

when I save it as pre_commit_jupytext.py and call it with a pre-commit config entry in .pre-commit-config.yaml that looks like this:

repos - repo: local hooks: - id: jupytext name: jupytext entry: python a301/scripts/pre_commit_jupytext.py language: system

but I think smoothing this a little with a command line option would be a nice addition.
opened by phaustin 23
Extend Jupytext to C# and F#
C#, F# and Powershell Jupyter notebooks were announced in this post from the .NET blog. A preview of Powershell notebooks was then provided by @TylerLeonhardt in this post.

In november 2019 (Jupytext 1.3) we extended Jupytext to Powershell. Now I'd be curious to extend Jupytext to C# and F#, and then experiment with a) turning documentation repositories like e.g. PowerShell-Docs or C#-Docs into live interactive Jupyter notebooks with MyBinder b) editing/running the .ipynb notebook through a paired script in Visual Studio Code.

The repository dotnet/interactive seems to be a great ressource to start with. There, one can find

an interactive binder service, see NotebooksOnBinder (followed by instructions on how to install the dotnet framework locally)

as well as example notebooks in the three languages.

This thread may also be of interest to @dfinke who authored PowerShellNotebook, a collection of scripts that can convert notebooks to scripts, and text to notebooks.
opened by mwouts 22

Windows sync different folders

I'm using:

jupytext --set-formats notebooks//ipynb,scripts//py:percent notebooks/*.ipynb

in Windows PowerShell

That command resulted in:

Paired paths 'notebooks/example.ipynb','scripts/example.py' do not include the current notebook path 'notebooks\example.ipynb'. Current format is 'notebooks//ipynb', and paired formats are 'notebooks//ipynb,scripts//py:percent'.

I think this is OS specific bug?

NOTE: already using the latest pypi package of jupytext and using VSCode power shell

opened by yasirroni 3

jupytext --execute is stalled and won't return

using the notebook here as a source, https://github.com/flotpython/exos/blob/main/ds-howtos/coronavirus-howto-nb.md

I try to execute it offline doing (from the repo root) jupytext --execute -v ./ds-howtos/coronavirus-howto-nb.md -o ./ds-howtos/coronavirus-howto-nb.md-trash.md and it hangs for as long as I have been to try - 10 minutes or something

while the same notebook under jupyter (classic) can be executed with 'run all cells' in a reasonable amount of time it's not fast, alright, but it does go through in a matter of 20-30 s or something

is there a way for me to troubleshoot this ? I was expecting some sort of --verbose or --debug option in an attempt to get a clue on what cell can be the problem, to no avail so far

thanks !

ps: I am using version 1.14.2; and then again with 1.14.4 but same behaviour

opened by parmentelat 0
1.14.4: Tags are not saved in MyST format
Add example tags to a MyST .md cell with a plain text editor as described here:

https://github.com/mwouts/jupytext/blob/main/docs/formats.md#myst-markdown

For example:

:tags: [hide-output, show-input]

When I then open the .md file with Jupytext, make changes, and save, the tags are removed. It seems like this is an obvious issue, but can anyone else reproduce? I'm having trouble guessing what I'm doing wrong.

Saving the tags to a cell within Jupyter to start also doesn't get them written (just ignored on save).
opened by davidvandebunte 0
Can't open the jupyter notebook after the jupytext installation

I followed the documentation and installed the jupytext into my environment. When I tried to open the jupyter notebook, it gave me an error as following: [C 17:38:32.393 NotebookApp] Bad config encountered during initialization: The 'contents_manager_class' trait of a NotebookApp instance expected a subclass of notebook.services.contents.manager.ContentsManager or jupyter_server.contents.services.managers.ContentsManage, not the JupytextContentsManager JupytextContentsManager.

opened by cacoto 17

Releases(v1.14.4)

v1.14.4(Dec 11, 2022)
Added

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

Source code(tar.gz)
Source code(zip)
v1.14.3(Dec 11, 2022)
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

Source code(tar.gz)
Source code(zip)
v1.14.2(Dec 5, 2022)
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)

Source code(tar.gz)
Source code(zip)
v1.14.1(Jul 29, 2022)
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).

Source code(tar.gz)
Source code(zip)
v1.14.0(Jul 3, 2022)
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)

Source code(tar.gz)
Source code(zip)
v1.13.8(Apr 4, 2022)
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)

Source code(tar.gz)
Source code(zip)
v1.13.7(Feb 9, 2022)
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)

Source code(tar.gz)
Source code(zip)
v1.13.6(Jan 11, 2022)
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)

Source code(tar.gz)
Source code(zip)
v1.13.5(Dec 28, 2021)
Fixed

Jupytext will not open a text notebook that is not UTF-8 (#896)

Fixed typo in git tag (#899)

Source code(tar.gz)
Source code(zip)
v.1.13.5(Dec 27, 2021)
Fixed

Jupytext will not open a text notebook that is not UTF-8 (#896)

Source code(tar.gz)
Source code(zip)
v1.13.4(Dec 12, 2021)
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)

Source code(tar.gz)
Source code(zip)
v1.13.3(Dec 4, 2021)
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)

Source code(tar.gz)
Source code(zip)
v1.13.2(Nov 30, 2021)
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)

Source code(tar.gz)
Source code(zip)
v1.13.1.2(Nov 8, 2021)

The version 1.13.1 did not get published to pip because of #866 - This is an attempt to publish that version.
Source code(tar.gz)
Source code(zip)
v1.13.1(Oct 7, 2021)
The magic commands in py:percent scripts with no explicit format information remain commented over a round trip (#848)

Source code(tar.gz)
Source code(zip)
v1.13.0(Sep 25, 2021)
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)

Source code(tar.gz)
Source code(zip)
v1.12.0(Sep 8, 2021)
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)

Source code(tar.gz)
Source code(zip)
v1.11.5(Aug 31, 2021)
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)

Source code(tar.gz)
Source code(zip)
v1.11.4(Jul 14, 2021)
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

Source code(tar.gz)
Source code(zip)
v1.11.3(Jun 10, 2021)
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)

Source code(tar.gz)
Source code(zip)
v1.11.2(May 2, 2021)
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)

Source code(tar.gz)
Source code(zip)
v1.11.1(Mar 25, 2021)
Fixed

Format options stored in the notebook itself are now taken into account (Fixes #757)

Source code(tar.gz)
Source code(zip)
v1.11.0(Mar 18, 2021)
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)

Source code(tar.gz)
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v1.10.3(Mar 7, 2021)
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)

Source code(tar.gz)
Source code(zip)
v1.10.2(Feb 16, 2021)
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)

Source code(tar.gz)
Source code(zip)
v1.10.1(Feb 10, 2021)
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)

Source code(tar.gz)
Source code(zip)
v1.10.1rc0(Feb 10, 2021)
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)

Source code(tar.gz)
Source code(zip)
v1.10.0(Feb 4, 2021)
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)

Source code(tar.gz)
Source code(zip)
v1.9.1(Jan 6, 2021)
Fixed

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

Source code(tar.gz)
Source code(zip)
v1.9.0(Jan 5, 2021)
Changed

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

Source code(tar.gz)
Source code(zip)