path: root/README.org

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

#+html: <p align="center">
#+html: <a href="http://elpa.gnu.org/packages/code-cells.html"><img alt="GNU ELPA" src="https://elpa.gnu.org/packages/code-cells.svg"/></a>
#+html: <a href="https://melpa.org/#/code-cells"><img alt="MELPA" src="https://melpa.org/packages/code-cells-badge.svg"/></a>
#+html: </p>

This package lets you efficiently navigate, edit and execute code
split into cells according to certain magic comments.  Moreover, 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, the following kinds of comment lines are recognized as
cell boundaries:

#+begin_example
  # In[<number>]:
  # %% 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.
More percent signs signify nested cells.  See section “Customization”
below to learn how to change the cell boundary pattern.

*Advertisement:* To complement this package, you may be interested in
[[http://elpa.gnu.org/packages/drepl.html][dREPL]], a fully featured shell for Python and other languages with
graphical capabilities.

** 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

This package provides a number of cell editing commands.  They are
listed below together with their bindings in =code-cells-mode-map=.
Note, however, that these commands do not require the minor mode to be
active; you can bind them to other keys or call them via =M-x=
anywhere you like.

- =code-cells-backward-cell= (=C-c % p=)
- =code-cells-forward-cell= (=C-c % n=)
- =code-cells-move-cell-up= (=C-c % P=)
- =code-cells-move-cell-down= (=C-c % N=)
- =code-cells-comment-or-uncomment= (=C-c % ;=)
- =code-cells-copy= (=C-c % w=)
- =code-cells-delete=
- =code-cells-duplicate= (=C-c % d=)
- =code-cells-eval= (=C-c % e=)
- =code-cells-eval-and-step= (=C-c % s=)
- =code-cells-eval-above= (=C-c % a=)
- =code-cells-eval-below=
- =code-cells-eval-whole-buffer=
- =code-cells-indent= (=C-c % \=)
- =code-cells-kill= (=C-c % C-w=)
- =code-cells-mark-cell= (=C-c % @=)

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))
      (keymap-set map "M-p" 'code-cells-backward-cell)
      (keymap-set map "M-n" 'code-cells-forward-cell)
      (keymap-set map "C-c C-c" 'code-cells-eval)
      ;; Overriding other minor mode bindings requires some insistence...
      (keymap-set map "<remap> <jupyter-eval-line-or-region>" 'code-cells-eval)))
#+end_src

Finally, a remark on prefix arguments.  For most commands, the logic
is that the absolute value of the numeric prefix stipulates the number
of cells around the current cell to act on, with the sign determining
whether to include cells above or below it.  The numeric prefixes 0
and -1 have a special meaning: they tell to act on the half of the
current cell below respective above the current line.

** Customization

Type =M-x customize-group RET code-cells RET= to see a listing of all
customization options.

The most important option is =code-cells-boundary-regexp=, which
determines which lines of a buffer should be regarded as a cell
boundary.  Some alternatives to the default value include:

- ="^#\\(#+\\)"=: This recognizes lines starting with 2 or more hash
  characters as cell boundaries, which is an interesting option, say,
  for Python:
  #+begin_src python
    ## Cell title (optional)
    # Some commentary, which normally starts with
    # a single hash character.
    print("hello")
  #+end_src
- ="^;;\\(;+\\) "=: This recognizes lines starting with 3 or more
  semicolons as cell boundaries, which is an interesting option, say,
  for Emacs Lisp code split into sections:
  #+begin_src emacs-lisp
    ;;; Section title
    ;; Some commentary, which by convention starts
    ;; with double semicolons.
    (message "hello")
  #+end_src
- ="^\\s<+\\(\\*+\\)"=: This regular expression recognizes lines of
  the following form as cell boundaries:
  #+begin_example python
    #*
    #**
    #***
  #+end_example
  This implements a kind of "reverse literate programming" where the
  prose part is behind comments and can have Org-like syntax (the
  number of asterisks determines the heading level).

As usual, you can customize =code-cells-boundary-regexp= globally, or
change it for a single major mode, for instance with

#+begin_src emacs-lisp
(add-hook 'emacs-lisp-mode-hook
          (lambda () (setq-local code-cells-boundary-regexp "^;;\\(;+\\)")))
#+end_src

or even modify it in a single project using [[https://www.gnu.org/software/emacs/manual/html_mono/elisp.html#Directory-Local-Variables][directory-local variables]],
e.g. by typing the following:

#+begin_example
  M-x add-dir-local-variable RET python-mode RET code-cells-boundary-regexp RET "^#\\(#+\\)" RET
#+end_example

*Note:* Until version 0.4, the third cell boundary style above was
included in the default settings.  Use the suggested customization to
recover the old behavior.

** 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_src yaml
  jupyter:
    jupytext:
      cell_markers: '"""'
#+end_src

It is also possible to convert notebooks to markdown or Org mode
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" "--extract-media" "./ipynb-images/")
                                         (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.