+title: code-cells.el --- Lightweight notebooks in Emacs

+html:

+html:

+html:

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This package lets you efficiently navigate, edit and execute code split into cells according to certain magic comments. If you have [[https://github.com/mwouts/jupytext][Jupytext]] or [[https://pandoc.org/][Pandoc]] installed, you can also open ipynb notebook files directly in Emacs. They will be automatically converted to a script for editing, and converted back to notebook format when saving.

+caption: Working on a Jupyter notebook as a plain Python script

[[https://raw.githubusercontent.com/astoff/code-cells.el/images/screenshot.png]]

By default, three styles of comments are recognized as cell boundaries:

+begin_example

In[]:

%% Optional title

* Optional title

+end_example

The first is what you get by exporting a notebook to a script on Jupyter's web interface or with the command =jupyter nbconvert=. The second style is compatible with Jupytext, among several other tools. The third is in the spirit of Emacs's outline mode. Further percent signs or asterisks signify nested cells.

Note. As of version 0.3, the “outline mode” style heading requires /no space/ between the comment character and the asterisk. The previous behavior, which allowed spaces, led to many false positives.

** Minor mode The =code-cells-mode= minor mode provides the following things:

• Fontification of cell boundaries.
• Keybindings for the cell navigation and evaluation commands, under the =C-c %= prefix.
• Outline mode integration: cell headers have outline level determined by the number of percent signs or asterisks; within a cell, outline headings are as determined by the major mode, but they are demoted by an amount corresponding to the level of the containing cell. This provides code folding and hierarchical navigation, among other things, when =outline-minor-mode= is active.

=code-cells-mode= is automatically activated when opening an ipynb file, but of course you can activate it in any other buffer, either manually or through some hook. There is also the =code-cells-mode-maybe= function, which activates the minor mode if the current buffer seems to contain cell boundaries. It can be used like this, for instance:

+begin_src emacs-lisp

(add-hook 'python-mode-hook 'code-cells-mode-maybe)

+end_src

** Editing commands The following editing and navigation commands are provided. Their keybindings in =code-cells-mode-map= are also shown. Note, however, that these commands do not require the minor mode to be active.

• =C-c % e=: =code-cells-eval=
• =C-c % b=: =code-cells-backward-cell=
• =C-c % f=: =code-cells-forward-cell=
• =C-c % B=: =code-cells-move-cell-up=
• =C-c % F=: =code-cells-move-cell-down=
• =C-c % ;=: =code-cells-comment-or-uncomment=
• =C-c % @=: =code-cells-mark-cell=

The =code-cells-eval= command sends the current cell to a suitable REPL, chosen according to the current major and minor modes. The exact behavior is controlled by the =code-cells-eval-region-commands= variable, which can be customized to suit your needs.

You may prefer shorter keybindings for some of these commands. One sensible possibility is to use =C-c C-c= to evaluate and =M-p= resp. =M-n= to navigate cells. This can be achieved with the following configuration:

+begin_src emacs-lisp

(with-eval-after-load 'code-cells (let ((map code-cells-mode-map)) (define-key map (kbd "M-p") 'code-cells-backward-cell) (define-key map (kbd "M-n") 'code-cells-forward-cell) (define-key map (kbd "C-c C-c") 'code-cells-eval) ;; Overriding other minor mode bindings requires some insistence... (define-key map [remap jupyter-eval-line-or-region] 'code-cells-eval)))

+end_src

** Speed keys Similarly to org-mode's [[https://orgmode.org/manual/Speed-Keys.html][speed keys]], the =code-cells-speed-key= function returns a key definition that only acts when the point is at the beginning of a cell boundary. Since this is usually not an interesting place to insert text, you can assign short keybindings there.

No speed keys are set up by default. A sample configuration is as follows:

+begin_src emacs-lisp

(with-eval-after-load 'code-cells (let ((map code-cells-mode-map)) (define-key map "n" (code-cells-speed-key 'code-cells-forward-cell)) (define-key map "p" (code-cells-speed-key 'code-cells-backward-cell)) (define-key map "e" (code-cells-speed-key 'code-cells-eval)) (define-key map (kbd "TAB") (code-cells-speed-key 'outline-cycle))))

+end_src

For Evil users, the following can be used:

+begin_src emacs-lisp

(with-eval-after-load 'code-cells (let ((map code-cells-mode-map)) (define-key map [remap evil-search-next] (code-cells-speed-key 'code-cells-forward-cell)) ;; n (define-key map [remap evil-paste-after] (code-cells-speed-key 'code-cells-backward-cell)) ;; p (define-key map [remap evil-backward-word-begin] (code-cells-speed-key 'code-cells-eval-above)) ;; b (define-key map [remap evil-forward-word-end] (code-cells-speed-key 'code-cells-eval)) ;; e (define-key map [remap evil-jump-forward] (code-cells-speed-key 'outline-cycle)))) ;; TAB

+end_src

* Handling Jupyter notebook files With this package, you can edit Jupyter notebook (=.ipynb=) files as if they were normal plain-text scripts. Converting to and from the JSON-based ipynb format is done by an external tool, [[https://github.com/mwouts/jupytext][Jupytext]] by default, which needs to be installed separately.

Note that the result cells of ipynb files are not retained in the conversion to script format. This means that opening and then saving an ipynb file clears all cell outputs.

While editing a converted ipynb buffer, you can use the regular =write-file= command (=C-x C-w=) to save a copy in script format, as displayed on the screen. Moreover, from any script file with cell separators understood by Jupytext, you can call =code-cells-write-ipynb= to save a copy in notebook format.

*** Tweaking the ipynb conversion If relegating markdown cells to comment blocks offends your literate programmer sensibilities, try including the following in the YAML header of a converted notebook (and then save and revert it). It will cause text cells to be displayed as multiline comments.

+begin_example

jupyter: jupytext: cell_markers: '"""'

+end_example

It is also possible to convert notebooks to markdown or org format. For markdown, use the following:

+begin_src emacs-lisp

(setq code-cells-convert-ipynb-style '(("jupytext" "--to" "ipynb" "--from" "markdown") ("jupytext" "--to" "markdown" "--from" "ipynb") (lambda () #'markdown-mode)))

+end_src

To edit ipynb files as org documents, try using [[https://pandoc.org/][Pandoc]] with the configuration below. In combination with org-babel, this can provide a more notebook-like experience, with interspersed code and results.

+begin_src emacs-lisp

(setq code-cells-convert-ipynb-style '(("pandoc" "--to" "ipynb" "--from" "org") ("pandoc" "--to" "org" "--from" "ipynb") (lambda () #'org-mode)))

+end_src

A good reason to stick with Jupytext, though, is that it offers round-trip consistency: if you save a script and then revert the buffer, the buffer shouldn't change. With other tools, you may get some surprises.

** Alternatives [[https://github.com/thisch/python-cell.el][python-cell.el]] provides similar cell editing commands. It seems to be limited to Python code.

With Jupytext's [[https://jupytext.readthedocs.io/en/latest/paired-notebooks.html][paired notebook mode]] it is possible to keep a notebook open in JupyterLab and simultaneously edit a script version in an external text editor.

The [[https://github.com/dickmao/emacs-ipython-notebook][EIN]] package allows to open ipynb files directly in Emacs with an UI similar to Jupyter notebooks. Note that EIN also registers major modes for ipynb files; when installing both packages at the same time, you may need to adjust your =auto-mode-alist= manually.

** Contributing Discussions, suggestions and code contributions are welcome! Since this package is part of GNU ELPA, nontrivial contributions (above 15 lines of code) require a copyright assignment to the FSF.